etho Case Study: How to adapt multiple input methods on Intel based hybrid devices By feedproxy.google.com Published On :: 2014-10-09T12:22:00+05:30 Trine* 2 from Frozenbyte, Inc. struggled with optimal playability on Intel® processor-based touchscreens and 2 in 1s running Windows* 8. Supporting varied play styles and local multiplayer require... Full Article
etho Free LCI Webinar on 'High Conflict Mediation feat. Scientific Methods!' By www.lawyersclubindia.com Published On :: Pascal Comvalius is going to discuss with the participants on how to deal with hostile parties on a negotiation table. How to mould the brick into a shape that you are comfortable in! Date & Timing: 28th April, 2020 @4.30 PM Meeting Link: Click Here Full Article
etho [Women's Basketball] Women's Basketball Falls to Central Methodist University By www.haskellathletics.com Published On :: Wed, 18 Dec 2019 11:05:00 -0600 Full Article
etho Verifying Power Intent in Analog and Mixed-Signal Designs Using Formal Methods By feedproxy.google.com Published On :: Thu, 21 Feb 2019 22:15:00 GMT Analog and Mixed-signal (AMS) designs are increasingly using active power management to minimize power consumption. Typical mixed-signal design uses several power domains and operate in a dozen or more power modes including multiple functional, standby and test modes. To save power, parts of design not active in a mode are shut down or may operate at reduced supply voltage when high performance is not required. These and other low power techniques are applied on both analog and digital parts of the design. Digital designers capture power intent in standard formats like Common Power Format (CPF), IEEE1801 (aka Unified Power Format or UPF) or Liberty and apply it top-down throughout design, verification and implementation flows. Analog parts are often designed bottom-up in schematic without upfront defined power intent. Verifying that low power intent is implemented correctly in mixed-signal design is very challenging. If not discovered early, errors like wrongly connected power nets, missing level shifters or isolations cells can cause costly rework or even silicon re-spin. Mixed-signal designers rely on simulation for functional verification. Although still necessary for electrical and performance verification, running simulation on so many power modes is not an effective verification method to discover low power errors. It would be nice to augment simulation with formal low power verification but a specification of power intent for analog/mixed-signal blocs is missing. So how do we obtain it? Can we “extract” it from already built analog circuit? Fortunately, yes we can, and we will describe an automated way to do so! Virtuoso Power Manager is new tool released in the Virtuoso IC6.1.8 platform which is capable of managing power intent in an Analog/MS design which is captured in Virtuoso Schematic Editor. In setup phase, the user identifies power and ground nets and registers special devices like level shifters and isolation cells. The user has the option to import power intent into IEEE1801 format, applicable for top level or any of the blocks in design. Virtuoso Power Manager uses this information to traverse the schematic and extract complete power intent for the entire design. In the final stage, Virtuoso Power Manager exports the power intent in IEEE1801 format as an input to the formal verification tool (Cadence Conformal-LP) for static verification of power intent. Cadence and Infineon have been collaborating on the requirements and validation of the Virtuoso Power Manager tool and Low Power verification solution on real designs. A summary of collaboration results were presented at the DVCon conference in Munich, in October of 2018. Please look for the paper in the conference proceedings for more details. Alternately, can view our Cadence webinar on Verifying Low-Power Intent in Mixed-Signal Design Using Formal Method for more information. Full Article AMS Virtuoso Schematic Editor Low Power virtuoso power manager Virtuoso-AMS mixed signal design mixed signal solution Virtuoso low-power design mixed signal mixed-signal verification
etho Dynamic MessageBoxA||W PEB And Import Table Method Shellcode By packetstormsecurity.com Published On :: Wed, 18 Mar 2020 15:10:48 GMT 232 bytes small Dynamic MessageBoxA||W PEB and Import Table Method shellcode. Full Article
etho Microsoft Mocks Google For Failed Security Fix Deployment Methodology By packetstormsecurity.com Published On :: Thu, 19 Oct 2017 14:17:08 GMT Full Article headline microsoft flaw google chrome
etho NTR ActiveX Control Check() Method Buffer Overflow By packetstormsecurity.com Published On :: Sat, 22 Sep 2012 06:44:12 GMT This Metasploit module exploits a vulnerability found in NTR ActiveX 1.1.8. The vulnerability exists in the Check() method, due to the insecure usage of strcat to build a URL using the bstrParams parameter contents, which leads to code execution under the context of the user visiting a malicious web page. In order to bypass DEP and ASLR on Windows Vista and Windows 7 JRE 6 is needed. Full Article
etho Meterpreter Swaparoo Windows Backdoor Method By packetstormsecurity.com Published On :: Mon, 20 May 2013 20:50:36 GMT Swaparoo - Windows backdoor method for Windows Vista/7/8. This code sneaks a backdoor command shell in place of Sticky Keys prompt or Utilman assistant at login screen. Full Article
etho Back to Black but not quite yet: Revised methodology agreed but no new EU blacklist before 2020 By www.eversheds.com Published On :: 2019-10-11 As the European Council met today to discuss a revised methodology to be used in the creation of a new EU blacklist of ‘high-risk third countries’ with strategic AML and CTF deficiencies, Zia Ullah and Ruth Paley of Eversheds Sutherland ... Full Article
etho Amendments to food labelling regulations: More information requirements for labels and new methods of presentation By www.eversheds.com Published On :: 2014-12-02 Starting 13 December 2014, businesses will be required to comply with the great majority of the rules set forth in the EU’s Food Information Regulation (1169/2011). The Regulation went into force on 12 December 2011 but provided for a long, 3-... Full Article
etho Competition Tribunal adopts structured methodological approach to penalties By www.eversheds.com Published On :: 2020-05-06 Introducing Hong Kong’s four-step fining framework… On 29 April 2020, Justice Godfrey Lam, President of the Competition Tribunal, handed down judgment in relation to the fines to be imposed on the parties in the W. Hing and Others case.... Full Article
etho It’s time we rethought our idea of monogamy By www.nation.co.ke Published On :: 2020-05-09T07:30:00Z Some people are just built differently. Some people are poor at compromising. Full Article
etho Residents Perspectives on and Application of Dental Public Health Competencies Using Case-Based Methods By www.jdentaled.org Published On :: 2019-12-01T06:00:19-08:00 The aims of this study were to qualitatively assess dental public health (DPH) residents’ perspectives on teaching methods for DPH competencies and to develop and implement a case-based simulation to address those competencies, constructed on the basis of the qualitative assessment. Focus group discussions were conducted with 18 DPH residents enrolled in two university-based DPH programs. Topic areas discussed in the two focus groups were perceived value of DPH competencies, ways to acquire new DPH skills/abilities, and additional skills/abilities needed by DPH residents. The focus groups’ responses showed that the residents felt competent in the analytical thinking competencies such as research methodology and critiquing literature. They emphasized the importance of learning leadership skills and reported feeling somewhat uncertain about their mastery of the policy and advocacy and system evaluation competencies. Of the two distinct categories of DPH skills and competencies— analytical/critical thinking and practical competencies—these residents reported that a greater proportion of time needed to be devoted to integrating the practical competencies into their education. Based on the residents’ feedback, the authors developed a structured seminar series taking a case-based approach to simulate real-world DPH problems, using real and semi-hypothetical planning projects to meet the residents’ perceived needs and covering gaps between didactic learning and practice. Full Article
etho Tracking a Global Threat: a New Genotyping Method for Candida auris By mbio.asm.org Published On :: 2020-03-10T01:30:41-07:00 ABSTRACT Over the past decade, Candida auris has emerged as an urgent threat to public health. Initially reported from cases of ear infections in Japan and Korea, C. auris has since been detected around the world. While whole-genome sequencing has been extensively used to trace the genetic relationships of the global emergence and local outbreaks, a recent report in mBio describes a targeted genotyping method as a rapid and inexpensive method for classifying C. auris isolates (T. de Groot, Y. Puts, I. Berrio, A. Chowdhary, and J. F. Meis, mBio 11:e02971-19, https://doi.org/10.1128/mBio.02971-19, 2020). Full Article
etho A Solution to Antifolate Resistance in Group B Streptococcus: Untargeted Metabolomics Identifies Human Milk Oligosaccharide-Induced Perturbations That Result in Potentiation of Trimethoprim By mbio.asm.org Published On :: 2020-03-17T01:30:14-07:00 ABSTRACT Adjuvants can be used to potentiate the function of antibiotics whose efficacy has been reduced by acquired or intrinsic resistance. In the present study, we discovered that human milk oligosaccharides (HMOs) sensitize strains of group B Streptococcus (GBS) to trimethoprim (TMP), an antibiotic to which GBS is intrinsically resistant. Reductions in the MIC of TMP reached as high as 512-fold across a diverse panel of isolates. To better understand HMOs’ mechanism of action, we characterized the metabolic response of GBS to HMO treatment using ultrahigh-performance liquid chromatography–high-resolution tandem mass spectrometry (UPLC-HRMS/MS) analysis. These data showed that when challenged by HMOs, GBS undergoes significant perturbations in metabolic pathways related to the biosynthesis and incorporation of macromolecules involved in membrane construction. This study represents reports the metabolic characterization of a cell that is perturbed by HMOs. IMPORTANCE Group B Streptococcus is an important human pathogen that causes serious infections during pregnancy which can lead to chorioamnionitis, funisitis, premature rupture of gestational membranes, preterm birth, neonatal sepsis, and death. GBS is evolving antimicrobial resistance mechanisms, and the work presented in this paper provides evidence that prebiotics such as human milk oligosaccharides can act as adjuvants to restore the utility of antibiotics. Full Article
etho A Simple, Cost-Effective, and Robust Method for rRNA Depletion in RNA-Sequencing Studies By mbio.asm.org Published On :: 2020-04-21T01:31:26-07:00 ABSTRACT The profiling of gene expression by RNA sequencing (RNA-seq) has enabled powerful studies of global transcriptional patterns in all organisms, including bacteria. Because the vast majority of RNA in bacteria is rRNA, it is standard practice to deplete the rRNA from a total RNA sample such that the reads in an RNA-seq experiment derive predominantly from mRNA. One of the most commonly used commercial kits for rRNA depletion, the Ribo-Zero kit from Illumina, was recently discontinued abruptly and for an extended period of time. Here, we report the development of a simple, cost-effective, and robust method for depleting rRNA that can be easily implemented by any lab or facility. We first developed an algorithm for designing biotinylated oligonucleotides that will hybridize tightly and specifically to the 23S, 16S, and 5S rRNAs from any species of interest. Precipitation of these oligonucleotides bound to rRNA by magnetic streptavidin-coated beads then depletes rRNA from a complex, total RNA sample such that ~75 to 80% of reads in a typical RNA-seq experiment derive from mRNA. Importantly, we demonstrate a high correlation of RNA abundance or fold change measurements in RNA-seq experiments between our method and the Ribo-Zero kit. Complete details on the methodology are provided, including open-source software for designing oligonucleotides optimized for any bacterial species or community of interest. IMPORTANCE The ability to examine global patterns of gene expression in microbes through RNA sequencing has fundamentally transformed microbiology. However, RNA-seq depends critically on the removal of rRNA from total RNA samples. Otherwise, rRNA would comprise upward of 90% of the reads in a typical RNA-seq experiment, limiting the reads coming from mRNA or requiring high total read depth. A commonly used kit for rRNA subtraction from Illumina was recently unavailable for an extended period of time, disrupting routine rRNA depletion. Here, we report the development of a "do-it-yourself" kit for rapid, cost-effective, and robust depletion of rRNA from total RNA. We present an algorithm for designing biotinylated oligonucleotides that will hybridize to the rRNAs from a target set of species. We then demonstrate that the designed oligonucleotides enable sufficient rRNA depletion to produce RNA-seq data with 75 to 80% of reads coming from mRNA. The methodology presented should enable RNA-seq studies on any species or metagenomic sample of interest. Full Article
etho Machine Learning Techniques for Classifying the Mutagenic Origins of Point Mutations [Methods, Technology, [amp ] Resources] By www.genetics.org Published On :: 2020-05-05T06:43:41-07:00 There is increasing interest in developing diagnostics that discriminate individual mutagenic mechanisms in a range of applications that include identifying population-specific mutagenesis and resolving distinct mutation signatures in cancer samples. Analyses for these applications assume that mutagenic mechanisms have a distinct relationship with neighboring bases that allows them to be distinguished. Direct support for this assumption is limited to a small number of simple cases, e.g., CpG hypermutability. We have evaluated whether the mechanistic origin of a point mutation can be resolved using only sequence context for a more complicated case. We contrasted single nucleotide variants originating from the multitude of mutagenic processes that normally operate in the mouse germline with those induced by the potent mutagen N-ethyl-N-nitrosourea (ENU). The considerable overlap in the mutation spectra of these two samples make this a challenging problem. Employing a new, robust log-linear modeling method, we demonstrate that neighboring bases contain information regarding point mutation direction that differs between the ENU-induced and spontaneous mutation variant classes. A logistic regression classifier exhibited strong performance at discriminating between the different mutation classes. Concordance between the feature set of the best classifier and information content analyses suggest our results can be generalized to other mutation classification problems. We conclude that machine learning can be used to build a practical classification tool to identify the mutation mechanism for individual genetic variants. Software implementing our approach is freely available under an open-source license. Full Article
etho Phosphoflow Protocol for Signaling Studies in Human and Murine B Cell Subpopulations [NOVEL IMMUNOLOGICAL METHODS] By www.jimmunol.org Published On :: 2020-05-04T13:00:28-07:00 Key Points Method for highly sensitive detection of phosphorylation in B cell subpopulations. B cell subpopulations show different phosphorylation levels upon BCR stimulation. Full Article
etho In vitro-virtual-reality: an anatomically explicit musculoskeletal simulation powered by in vitro muscle using closed loop tissue-software interaction [METHODS [amp ] TECHNIQUES] By jeb.biologists.org Published On :: 2020-04-06T07:24:08-07:00 Christopher T. Richards and Enrico A. EberhardMuscle force-length dynamics are governed by intrinsic contractile properties, motor stimulation and mechanical load. Although intrinsic properties are well-characterised, physiologists lack in vitro instrumentation accounting for combined effects of limb inertia, musculoskeletal architecture and contractile dynamics. We introduce in vitro virtual-reality (in vitro-VR) which enables in vitro muscle tissue to drive a musculoskeletal jumping simulation. In hardware, muscle force from a frog plantaris was transmitted to a software model where joint torques, inertia and ground reaction forces were computed to advance the simulation at 1 kHz. To close the loop, simulated muscle strain was returned to update in vitro length. We manipulated 1) stimulation timing and, 2) the virtual muscle's anatomical origin. This influenced interactions among muscular, inertial, gravitational and contact forces dictating limb kinematics and jump performance. We propose that in vitro-VR can be used to illustrate how neuromuscular control and musculoskeletal anatomy influence muscle dynamics and biomechanical performance. Full Article
etho A fast and effective method for dissecting parasitic spores: myxozoans as an example [METHODS [amp ] TECHNIQUES] By jeb.biologists.org Published On :: 2020-04-06T07:24:08-07:00 Qingxiang Guo, Yang Liu, Yanhua Zhai, and Zemao GuDisassembling the parasitic spores and acquiring the main subunits is a prerequisite for deep understanding of the basic biology of parasites. Herein we present a fast and efficient method to dissect the myxospores in a few steps, which mainly involved sonication, sucrose density gradient and Percoll density gradient. We tested our method on three myxozoans species and demonstrated this method allows the dismembering of myxospores, isolation of intact and clean nematocysts and shell valves within 2h by low-cost. This new tool will facilitate subsequent analyses and enable a better understanding of the ecological and evolutionary significance of parasitic spores. Full Article
etho The aerodynamic force platform as an ergometer [METHODS [amp ] TECHNIQUES] By jeb.biologists.org Published On :: 2020-04-06T07:24:08-07:00 Marc E. Deetjen, Diana D. Chin, and David LentinkAnimal flight requires aerodynamic power, which is challenging to determine accurately in vivo. Existing methods rely on approximate calculations based on wake flow field measurements, inverse dynamics approaches, or invasive muscle physiological recordings. In contrast, the external mechanical work required for terrestrial locomotion can be determined more directly by using a force platform as an ergometer. Based on an extension of the recent invention of the aerodynamic force platform, we now present a more direct method to determine the in vivo aerodynamic power by taking the dot product of the aerodynamic force vector on the wing with the representative wing velocity vector based on kinematics and morphology. We demonstrate this new method by studying a slowly flying dove, but it can be applied more generally across flying and swimming animals as well as animals that locomote over water surfaces. Finally, our mathematical framework also works for power analyses based on flow field measurements. Full Article
etho Tracking isotopically labeled oxidants using boronate-based redox probes [Methods and Resources] By www.jbc.org Published On :: 2020-05-08T03:41:14-07:00 Reactive oxygen and nitrogen species have been implicated in many biological processes and diseases, including immune responses, cardiovascular dysfunction, neurodegeneration, and cancer. These chemical species are short-lived in biological settings, and detecting them in these conditions and diseases requires the use of molecular probes that form stable, easily detectable, products. The chemical mechanisms and limitations of many of the currently used probes are not well-understood, hampering their effective applications. Boronates have emerged as a class of probes for the detection of nucleophilic two-electron oxidants. Here, we report the results of an oxygen-18–labeling MS study to identify the origin of oxygen atoms in the oxidation products of phenylboronate targeted to mitochondria. We demonstrate that boronate oxidation by hydrogen peroxide, peroxymonocarbonate, hypochlorite, or peroxynitrite involves the incorporation of oxygen atoms from these oxidants. We therefore conclude that boronates can be used as probes to track isotopically labeled oxidants. This suggests that the detection of specific products formed from these redox probes could enable precise identification of oxidants formed in biological systems. We discuss the implications of these results for understanding the mechanism of conversion of the boronate-based redox probes to oxidant-specific products. Full Article
etho Genetic lineage tracing with multiple DNA recombinases: A user's guide for conducting more precise cell fate mapping studies [Methods and Resources] By www.jbc.org Published On :: 2020-05-08T03:41:14-07:00 Site-specific recombinases, such as Cre, are a widely used tool for genetic lineage tracing in the fields of developmental biology, neural science, stem cell biology, and regenerative medicine. However, nonspecific cell labeling by some genetic Cre tools remains a technical limitation of this recombination system, which has resulted in data misinterpretation and led to many controversies in the scientific community. In the past decade, to enhance the specificity and precision of genetic targeting, researchers have used two or more orthogonal recombinases simultaneously for labeling cell lineages. Here, we review the history of cell-tracing strategies and then elaborate on the working principle and application of a recently developed dual genetic lineage-tracing approach for cell fate studies. We place an emphasis on discussing the technical strengths and caveats of different methods, with the goal to develop more specific and efficient tracing technologies for cell fate mapping. Our review also provides several examples for how to use different types of DNA recombinase–mediated lineage-tracing strategies to improve the resolution of the cell fate mapping in order to probe and explore cell fate–related biological phenomena in the life sciences. Full Article
etho Geospatial assessment methods for geotechnical asset management of legacy railway embankments By qjegh.lyellcollection.org Published On :: 2020-05-01T00:46:18-07:00 Most British railway embankments were constructed between 120 and 180 years ago without the benefit of modern design and construction methods. This can result in undesirable load-deformation characteristics and consequent disruption to present-day railway operations, for which there is unprecedented demand. Annual rail passenger kilometres have approximately doubled in the last 20 years and freight has increased by 60% over the same period. Whereas elements such as rails or bridges can be refurbished or replaced to meet increasing demand, the same is not usually feasible for embankments. Development of techniques to assess embankment performance risks posed by operational capacity enhancements is therefore of increasing significance to railway geotechnical asset management. The two case studies presented in this paper demonstrate how geospatial analysis and data management techniques may be applied to this challenge at both strategic (regional or national) and tactical (site-specific) scales for embankments incorporating plastic clay fill. The case studies also demonstrate, in a world of ever more abundant data, the growing need for engineering geologists and geotechnical engineers to augment their traditional knowledge with comprehensive data management and geospatial analysis skills, these being essential for modern infrastructure asset management. Thematic collection: This article is part of the ‘Ground-related risk to transportation infrastructure’ collection available at: https://www.lyellcollection.org/cc/Ground-related-risk-to-transportation-infrastructure Full Article
etho Transcriptome reconstruction and functional analysis of eukaryotic marine plankton communities via high-throughput metagenomics and metatranscriptomics [METHOD] By genome.cshlp.org Published On :: 2020-04-27T12:09:24-07:00 Large-scale metagenomic and metatranscriptomic data analyses are often restricted by their gene-centric approach, limiting the ability to understand organismal and community biology. De novo assembly of large and mosaic eukaryotic genomes from complex meta-omics data remains a challenging task, especially in comparison with more straightforward bacterial and archaeal systems. Here, we use a transcriptome reconstruction method based on clustering co-abundant genes across a series of metagenomic samples. We investigated the co-abundance patterns of ~37 million eukaryotic unigenes across 365 metagenomic samples collected during the Tara Oceans expeditions to assess the diversity and functional profiles of marine plankton. We identified ~12,000 co-abundant gene groups (CAGs), encompassing ~7 million unigenes, including 924 metagenomics-based transcriptomes (MGTs, CAGs larger than 500 unigenes). We demonstrated the biological validity of the MGT collection by comparing individual MGTs with available references. We identified several key eukaryotic organisms involved in dimethylsulfoniopropionate (DMSP) biosynthesis and catabolism in different oceanic provinces, thus demonstrating the potential of the MGT collection to provide functional insights on eukaryotic plankton. We established the ability of the MGT approach to capture interspecies associations through the analysis of a nitrogen-fixing haptophyte-cyanobacterial symbiotic association. This MGT collection provides a valuable resource for analyses of eukaryotic plankton in the open ocean by giving access to the genomic content and functional potential of many ecologically relevant eukaryotic species. Full Article
etho Inhibition of transcription leads to rewiring of locus-specific chromatin proteomes [METHOD] By genome.cshlp.org Published On :: 2020-04-27T12:09:24-07:00 Transcription of a chromatin template involves the concerted interaction of many different proteins and protein complexes. Analyses of specific factors showed that these interactions change during stress and upon developmental switches. However, how the binding of multiple factors at any given locus is coordinated has been technically challenging to investigate. Here we used Epi-Decoder in yeast to systematically decode, at one transcribed locus, the chromatin binding changes of hundreds of proteins in parallel upon perturbation of transcription. By taking advantage of improved Epi-Decoder libraries, we observed broad rewiring of local chromatin proteomes following chemical inhibition of RNA polymerase. Rapid reduction of RNA polymerase II binding was accompanied by reduced binding of many other core transcription proteins and gain of chromatin remodelers. In quiescent cells, where strong transcriptional repression is induced by physiological signals, eviction of the core transcriptional machinery was accompanied by the appearance of quiescent cell–specific repressors and rewiring of the interactions of protein-folding factors and metabolic enzymes. These results show that Epi-Decoder provides a powerful strategy for capturing the temporal binding dynamics of multiple chromatin proteins under varying conditions and cell states. The systematic and comprehensive delineation of dynamic local chromatin proteomes will greatly aid in uncovering protein–protein relationships and protein functions at the chromatin template. Full Article
etho Time course regulatory analysis based on paired expression and chromatin accessibility data [METHOD] By genome.cshlp.org Published On :: 2020-04-27T12:09:24-07:00 A time course experiment is a widely used design in the study of cellular processes such as differentiation or response to stimuli. In this paper, we propose time course regulatory analysis (TimeReg) as a method for the analysis of gene regulatory networks based on paired gene expression and chromatin accessibility data from a time course. TimeReg can be used to prioritize regulatory elements, to extract core regulatory modules at each time point, to identify key regulators driving changes of the cellular state, and to causally connect the modules across different time points. We applied the method to analyze paired chromatin accessibility and gene expression data from a retinoic acid (RA)–induced mouse embryonic stem cells (mESCs) differentiation experiment. The analysis identified 57,048 novel regulatory elements regulating cerebellar development, synapse assembly, and hindbrain morphogenesis, which substantially extended our knowledge of cis-regulatory elements during differentiation. Using single-cell RNA-seq data, we showed that the core regulatory modules can reflect the properties of different subpopulations of cells. Finally, the driver regulators are shown to be important in clarifying the relations between modules across adjacent time points. As a second example, our method on Ascl1-induced direct reprogramming from fibroblast to neuron time course data identified Id1/2 as driver regulators of early stage of reprogramming. Full Article
etho Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis [METHOD] By genome.cshlp.org Published On :: 2020-04-27T12:09:24-07:00 Cellular heterogeneity in gene expression is driven by cellular processes, such as cell cycle and cell-type identity, and cellular environment such as spatial location. The cell cycle, in particular, is thought to be a key driver of cell-to-cell heterogeneity in gene expression, even in otherwise homogeneous cell populations. Recent advances in single-cell RNA-sequencing (scRNA-seq) facilitate detailed characterization of gene expression heterogeneity and can thus shed new light on the processes driving heterogeneity. Here, we combined fluorescence imaging with scRNA-seq to measure cell cycle phase and gene expression levels in human induced pluripotent stem cells (iPSCs). By using these data, we developed a novel approach to characterize cell cycle progression. Although standard methods assign cells to discrete cell cycle stages, our method goes beyond this and quantifies cell cycle progression on a continuum. We found that, on average, scRNA-seq data from only five genes predicted a cell's position on the cell cycle continuum to within 14% of the entire cycle and that using more genes did not improve this accuracy. Our data and predictor of cell cycle phase can directly help future studies to account for cell cycle–related heterogeneity in iPSCs. Our results and methods also provide a foundation for future work to characterize the effects of the cell cycle on expression heterogeneity in other cell types. Full Article
etho RETrace: simultaneous retrospective lineage tracing and methylation profiling of single cells [METHOD] By genome.cshlp.org Published On :: 2020-04-27T12:09:24-07:00 Retrospective lineage tracing harnesses naturally occurring mutations in cells to elucidate single cell development. Common single-cell phylogenetic fate mapping methods have utilized highly mutable microsatellite loci found within the human genome. Such methods were limited by the introduction of in vitro noise through polymerase slippage inherent in DNA amplification, which we characterized to be approximately 10–100x higher than the in vivo replication mutation rate. Here, we present RETrace, a method for simultaneously capturing both microsatellites and methylation-informative cytosines to characterize both lineage and cell type, respectively, from the same single cell. An important unique feature of RETrace was the introduction of linear amplification of microsatellites in order to reduce in vitro amplification noise. We further coupled microsatellite capture with single-cell reduced representation bisulfite sequencing (scRRBS), to measure the CpG methylation status on the same cell for cell type inference. When compared to existing retrospective lineage tracing methods, RETrace achieved higher accuracy (88% triplet accuracy from an ex vivo HCT116 tree) at a higher cell division resolution (lowering the required number of cell division difference between single cells by approximately 100 divisions). Simultaneously, RETrace demonstrated the ability to capture on average 150,000 unique CpGs per single cell in order to accurately determine cell type. We further formulated additional developments that would allow high-resolution mapping on microsatellite-stable cells or tissues with RETrace. Overall, we present RETrace as a foundation for multi-omics lineage mapping and cell typing of single cells. Full Article
etho Complete characterization of the human immune cell transcriptome using accurate full-length cDNA sequencing [METHOD] By genome.cshlp.org Published On :: 2020-04-27T12:09:24-07:00 The human immune system relies on highly complex and diverse transcripts and the proteins they encode. These include transcripts encoding human leukocyte antigen (HLA) receptors as well as B cell and T cell receptors (BCR and TCR). Determining which alleles an individual possesses for each HLA gene (high-resolution HLA typing) is essential to establish donor–recipient compatibility in organ and bone marrow transplantations. In turn, the repertoires of millions of unique BCR and TCR transcripts in each individual carry a vast amount of health-relevant information. Both short-read RNA-seq-based HLA typing and BCR/TCR repertoire sequencing (AIRR-seq) currently rely on our incomplete knowledge of the genetic diversity at HLA and BCR/TCR loci. Here, we generated over 10,000,000 full-length cDNA sequences at a median accuracy of 97.9% using our nanopore sequencing-based Rolling Circle Amplification to Concatemeric Consensus (R2C2) protocol. We used this data set to (1) show that deep and accurate full-length cDNA sequencing can be used to provide isoform-level transcriptome analysis for more than 9000 loci, (2) generate accurate sequences of HLA alleles, and (3) extract detailed AIRR data for the analysis of the adaptive immune system. The HLA and AIRR analysis approaches we introduce here are untargeted and therefore do not require prior knowledge of the composition or genetic diversity of HLA and BCR/TCR loci. Full Article
etho Implementation and Scale-Up of the Standard Days Method of Family Planning: A Landscape Analysis By ghspjournal.org Published On :: 2020-03-31T15:28:55-07:00 ABSTRACTThe Standard Days Method (SDM), a modern fertility awareness-based family planning method, has been introduced in 30 countries since its development in 2001. It is still unclear to what extent the SDM was mainstreamed within the family planning method mix, particularly in low- and middle-income country (LMIC) settings, where the SDM had been introduced by donors and implementing partners. This review of implementation science publications on the SDM in LMICs first looked at community pilot studies of the SDM to determine the acceptability of the method; correct use and efficacy rates; demographics of users; and changes to contraceptive prevalence rates and family planning behaviors, especially among men and couples. Then, we examined the status of the SDM in the 16 countries that had attempted to scale up the method within national family planning protocols, training, and service delivery. At the community level, evidence demonstrated a high level of acceptability of the method; efficacy rates comparable to the initial clinical trials; diversity in demographic characteristics of users, including first-time or recently discontinued users of family planning; increased male engagement in family planning; and improved couple's communication. Nationally, few countries had scaled up the SDM due to uneven stakeholder engagement, lackluster political will, and competing resource priorities. Results of this review could help policy makers determine the added value of the SDM in the contraceptive method mix and identify potential barriers to its implementation moving forward. Full Article
etho Women’s experiences of diagnosis and management of polycystic ovary syndrome: a mixed-methods study in general practice By bjgp.org Published On :: 2020-04-30T16:04:41-07:00 BackgroundPolycystic ovary syndrome (PCOS) is a common lifelong metabolic condition with serious associated comorbidities. Evidence points to a delay in diagnosis and inconsistency in the information provided to women with PCOS.AimTo capture women’s experiences of how PCOS is diagnosed and managed in UK general practice.Design and settingThis was a mixed-methods study with an online questionnaire survey and semi-structured telephone interviews with a subset of responders.MethodAn online survey to elicit women’s experiences of general practice PCOS care was promoted by charities and BBC Radio Leicester. The survey was accessible online between January 2018 and November 2018. A subset of responders undertook a semi-structured telephone interview to provide more in-depth data.ResultsA total of 323 women completed the survey (average age 35.4 years) and semi-structured interviews were conducted with 11 women. There were five key themes identified through the survey responses. Participants described a variable lag time from presentation to PCOS diagnosis, with a median of 6–12 months. Many had experienced mental health problems associated with their PCOS symptoms, but had not discussed these with the GP. Many were unable to recall any discussion about associated comorbidities with the GP. Some differences were identified between the experiences of women from white British backgrounds and those from other ethnic backgrounds.ConclusionFrom the experiences of the women in this study, it appears that PCOS in general practice is not viewed as a long-term condition with an increased risk of comorbidities including mental health problems. Further research should explore GPs’ awareness of comorbidities and the differences in PCOS care experienced by women from different ethnic backgrounds. Full Article
etho Association between media attention and presentation of vaccination information on Canadian chiropractors websites: a prospective mixed-methods cohort study By www.cmajopen.ca Published On :: 2020-05-05T05:00:14-07:00 Background: Historically, some chiropractors have been critical of vaccination, and this has been the subject of recent media attention in Canada. We explored the association between media attention and public dissemination of vaccination information on Canadian chiropractors’ websites. Methods: In 2016, we identified all Canadian chiropractors’ websites that provided information on vaccination by extracting details from the regulatory college website for each province using the search engine on their "find a chiropractor" page. We assessed the quality of information using the Web Resource Rating Tool (scores range from 0% [worst] to 100% [best]), determined whether vaccination was portrayed in a positive, neutral or negative manner, and conducted thematic analysis of vaccination content. We revisited all identified websites in 2019 to explore for changes to posted vaccination material. Results: In July 2016, of 3733 chiropractic websites identified, 94 unique websites provided information on vaccination: 59 (63%) gave negative messaging, 19 (20%) were neutral and 16 (17%) were positive. The quality of vaccination content on the websites was generally poor, with a median Web Resource Rating Tool score of 19%. We identified 4 main themes: there are alternatives to vaccination, vaccines are harmful, evidence regarding vaccination and health policy regarding vaccination. From 2012 to 2016, there was 1 Canadian newspaper story concerning antivaccination statements by chiropractors, whereas 51 news articles were published on this topic between 2017 and 2019. In April 2019, 45 (48%) of the 94 websites we had identified in 2016 had removed all vaccination content or had been discontinued. Interpretation: In 2016, a minority of Canadian chiropractors provided vaccination information on their websites, the majority of which portrayed vaccination negatively. After substantial national media attention, about half of all vaccination material on chiropractors’ websites was removed within several years. Full Article
etho Method Enables Nanoscale Mapping of Protein Interactions on Live Cells [Techniques] By cancerdiscovery.aacrjournals.org Published On :: 2020-05-01T00:05:26-07:00 A new method called MicroMapping can identify nanoscale protein–protein interactions on live cells. Full Article
etho Harnessing Population Pedigree Data and Machine Learning Methods to Identify Patterns of Familial Bladder Cancer Risk By cebp.aacrjournals.org Published On :: 2020-05-01T00:05:36-07:00 Background: Relatives of patients with bladder cancer have been shown to be at increased risk for kidney, lung, thyroid, and cervical cancer after correcting for smoking-related behaviors that may concentrate in some families. We demonstrate a novel approach to simultaneously assess risks for multiple cancers to identify distinct multicancer configurations (multiple different cancer types that cluster in relatives) surrounding patients with familial bladder cancer. Methods: This study takes advantage of a unique population-level data resource, the Utah Population Database (UPDB), containing vast genealogy and statewide cancer data. Familial risk is measured using standardized incidence risk (SIR) ratios that account for sex, age, birth cohort, and person-years of the pedigree members. Results: We identify 1,023 families with a significantly higher bladder cancer rate than population controls (familial bladder cancer). Familial SIRs are then calculated across 25 cancer types, and a weighted Gower distance with K-medoids clustering is used to identify familial multicancer configurations (FMC). We found five FMCs, each exhibiting a different pattern of cancer aggregation. Of the 25 cancer types studied, kidney and prostate cancers were most commonly enriched in the familial bladder cancer clusters. Laryngeal, lung, stomach, acute lymphocytic leukemia, Hodgkin disease, soft-tissue carcinoma, esophageal, breast, lung, uterine, thyroid, and melanoma cancers were the other cancer types with increased incidence in familial bladder cancer families. Conclusions: This study identified five familial bladder cancer FMCs showing unique risk patterns for cancers of other organs, suggesting phenotypic heterogeneity familial bladder cancer. Impact: FMC configurations could permit better definitions of cancer phenotypes (subtypes or multicancer) for gene discovery and environmental risk factor studies. Full Article
etho Genomics Methods for Xenopus Embryos and Tissues By cshprotocols.cshlp.org Published On :: 2020-05-01T06:29:31-07:00 High-throughput sequencing methods have created exciting opportunities to explore the regulatory landscape of the entire genome. Here we introduce methods to characterize the genomic locations of bound proteins, open chromatin, and sites of DNA–DNA contact in Xenopus embryos. These methods include chromatin immunoprecipitation followed by sequencing (ChIP-seq), a combination of DNase I digestion and sequencing (DNase-seq), the assay for transposase-accessible chromatin and sequencing (ATAC-seq), and the use of proximity-based DNA ligation followed by sequencing (Hi-C). Full Article
etho New computational method unravels single-cell data from multiple people By www.sciencedaily.com Published On :: Wed, 06 May 2020 12:37:48 EDT A new computational method for assigning the donor in single cell RNA sequencing experiments provides an accurate way to unravel data from a mixture of people. The Souporcell method could help study how genetic variants in different people affect which genes are expressed during infection or response to drugs, and help research into transplants, personalized medicine and malaria. Full Article
etho Wiley believes coronavirus is a method of 'depopulation' By www.music-news.com Published On :: Thu, 07 May 2020 06:11:00 +0100 The grime star is convinced the highly-contagious disease was deliberately introduced in China as a “control method” and a way to kill huge numbers within society. Full Article
etho New simple method for measuring the state of lithium-ion batteries By www.sciencedaily.com Published On :: Thu, 07 May 2020 13:13:16 EDT Scientists have presented a non-contact method for detecting the state of charge and any defects in lithium-ion batteries. Full Article
etho 'Superfast' new manufacturing method could mean breakthrough in battery technology, scientists say By www.independent.co.uk Published On :: 2020-05-01T13:29:00Z 'Reinvention' of ceramics firing process could be used by artificial intelligence to create new materials with wide range of possible applications Full Article
etho The Big Night In review – telethon triumphs over the lockdown By www.theguardian.com Published On :: 2020-04-23T22:30:22Z BBC One’s star-filled charity appeal needed imagination and technical skill to get round distancing rulesSee all our coronavirus coverageSocially distanced presenters, a skeleton crew, no live audience and automated phonelines only – this is national telethonning, lockdown-style. Comic Relief and Children in Need have joined forces to create The Big Night In on BBC One and raise money for the charities and projects who need more support than ever as Covid-19 strains resources everywhere.First shift is taken, as is traditional, by Lenny Henry and Davina McCall – joined, not too closely of course, by Matt Baker this time – whose recreation of normality for the viewer in what must, in the studio, be an absolutely bizarre set-up is unimpeachable proof of their professional talents. Continue reading... Full Article Television Culture Television & radio UK news Comic Relief BBC Entertainment TV Media Lenny Henry Davina McCall Matt Lucas Prince William Rishi Sunak Coronavirus outbreak
etho Can today’s hottest sustainable building method actually slow climate change? By grist.org Published On :: Sat, 09 May 2020 07:50:21 +0000 Cross-laminated timber draws praise -- and skeptics. Full Article Business & Technology Climate Climate & Energy New Economy Climate Desk
etho Pallone and Neal Demand Transparency into Methodology and Distribution of COVID-19 Health Care Provider Relief Funds By energycommerce.house.gov Published On :: Thu, 07 May 2020 17:28:14 -0400 Energy and Commerce Chairman Frank Pallone, Jr. (D-NJ) and Ways and Means Chairman Richard E. Neal (D-MA) sent a letter to Health and Human Services (HHS) Secretary Alex Azar and Centers for Medicare & Medicaid Services (CMS) Administrator Seema Verma today raising a series of concerns over the methodology used to distribute and the lack of transparency into how COVID-19 relief funds and loans for health care providers are being spent. “We write to raise serious concerns about the Provider Relief Fund and the Accelerated and Advance Payment Programs,” Pallone and Neal wrote. “With respect to each, we are concerned about the lack of transparency with Congress and the American people about how funds are being spent or loans are being made. We also have grave concerns regarding the methodology being used to distribute $175 billion Congress appropriated for the Provider Relief Fund.” The Chairmen’s letter documents concerns with how the programs are being run, in particular the Administration’s methodologies for distributing funding that has shortchanged a number of critical providers and makes clear that more transparency is needed for Congress to accurately assess the ongoing needs of health care providers as the COVID-19 crisis unfolds. “The Administration’s efforts to establish the Provider Relief Fund to date has been at best, a series of missteps, and at worst, a disregard of Congress’ intent for the program,” Pallone and Neal continued in their letter. Pallone and Neal wrote that when Congress passed the CARES Act, it was clear that the funding provided to HHS for the Provider Relief Fund was for the express purpose, “to prevent, prepare for, and respond to coronavirus.” The two Chairs voiced concern that some of the funding formulas adopted to date fail to target funding based on the statutory framework relating to COVID-19 driven costs. In fact, the Chairs write that the level of funding appears to be, “completely disconnected from need.” The Chairmen requested an immediate response from HHS regarding documents and information pertaining to the Provider Relief Fund and the Accelerated and Advanced Payment Program. Pallone and Neal also wrote that if HHS is unable to immediately provide the information, it should provide a timeline of when the Committees would receive the requested information. While recognizing the incredible demands on the Department at this difficult time, the Chairmen emphasized that, “This crisis demands that we work swiftly and based on the best data available. Currently, despite repeated requests, this Administration has prevented Congress from obtaining the data that the Department has available on funding for our health care system, data that is necessary to inform near future legislation. We look forward to receiving this information so that we can conduct the business the American people expect of us. We look forward to having you join us at the earliest possible date in each of our Committees to discuss these and other COVID-related issues.” To read the full letter, click HERE. ### Full Article
etho Houstons Methodist Hospital to Pay U.S. More Than $9 Million to Resolve Allegations of Overcharging Medicare By www.justice.gov Published On :: Thu, 26 Mar 2009 11:43:10 EDT Methodist Hospital in Houston has agreed to pay the United States $9.99 million to settle allegations that it defrauded the federal Medicare program. The settlement resolves allegations that Methodist improperly increased charges to Medicare patients in order to obtain enhanced reimbursement from Medicare. Full Article OPA Press Releases
etho Justice Department Files Lawsuit in Alaska Against Air Methods Corporation and LifeMed Alaska LLC to Enforce Employment Rights of Army National Guard Member By www.justice.gov Published On :: Thu, 7 Apr 2011 18:48:58 EDT The Justice Department today announced that it has filed a lawsuit alleging that Air Methods Corp. and LifeMed Alaska LLC willfully violated the Uniformed Services Employment and Reemployment Rights Act of 1994 (USERRA) by discriminating against and failing to reemploy Chief Warrant Officer Third Class Jonathon L. Goodwin of Wasilla, Alaska. Full Article OPA Press Releases
etho Justice Department Settles with Air Methods Corporation and Lifemed Alaska Llc to Enforce the Employment Rights to Army National Guard Member in Alaska By www.justice.gov Published On :: Fri, 13 Apr 2012 17:29:14 EDT The Justice Department today announced that it has resolved a lawsuit alleging that Air Methods Corp. and LifeMed Alaska, LLC willfully violated the Uniformed Services Employment and Reemployment Rights Act of 1994 (USERRA) by discriminating against and failing to reemploy Chief Warrant Officer Third Class Jonathon L. Goodwin of Wasilla, Alaska. The suit was filed in federal district court in Alaska. Full Article OPA Press Releases
etho Joint Statement by Attorney General Eric Holder and Director of National Intelligence James Clapper on New Reporting Methods for National Security Orders By www.justice.gov Published On :: Mon, 27 Jan 2014 13:07:39 EST Attorney General Eric Holder and Director of National Intelligence James Clapper released the following joint statement Monday. Full Article OPA Press Releases
etho A metabolic labeling method detects m<sup>6</sup>A transcriptome-wide at single base resolution By feeds.nature.com Published On :: 2020-04-27 Full Article
etho Effects of acute and repeated treatment with methocinnamox, a mu opioid receptor antagonist, on fentanyl self-administration in rhesus monkeys By feeds.nature.com Published On :: 2020-05-06 Full Article
etho SHMT inhibition is effective and synergizes with methotrexate in T-cell acute lymphoblastic leukemia By feeds.nature.com Published On :: 2020-05-07 Full Article