Sequence variation observed in populations of pathogens can be used for important public health and evolutionary genomic analyses, especially outbreak analysis and transmission reconstruction. Identifying this variation is typically achieved by aligning sequence reads to a reference genome, but this approach is susceptible to reference biases and requires careful filtering of called genotypes. There is a need for tools that can process this growing volume of bacterial genome data, providing rapid results, but that remain simple so they can be used without highly trained bioinformaticians, expensive data analysis, and long-term storage and processing of large files. Here we describe split k-mer analysis (SKA2), a method that supports both reference-free and reference-based mapping to quickly and accurately genotype populations of bacteria using sequencing reads or genome assemblies. SKA2 is highly accurate for closely related samples, and in outbreak simulations, we show superior variant recall compared with reference-based methods, with no false positives. SKA2 can also accurately map variants to a reference and be used with recombination detection methods to rapidly reconstruct vertical evolutionary history. SKA2 is many times faster than comparable methods and can be used to add new genomes to an existing call set, allowing sequential use without the need to reanalyze entire collections. With an inherent absence of reference bias, high accuracy, and a robust implementation, SKA2 has the potential to become the tool of choice for genotyping bacteria. SKA2 is implemented in Rust and is freely available as open-source software.

You can purchase Steven Camley's cartoons by calling 0141 302 7000 or visiting thepicturedesk.co.uk.

Manufacturing efficiency has always been a priority. As competition grows, optimizing every aspect of production becomes critical. Manufacturers turn to experts to make the right improvements and introduce systems that boost overall performance. One key area where many businesses seek help is through Manufacturing Execution Systems (MES). MES consultants play a pivotal role in achieving […]

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Last week, Gameloft announced the next major and free Disney Dreamlight Valley update for PC and consoles alongside Disney Dreamlight …

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Recent research has demonstrated that a widely prescribed hypertension medication, medlinkamlodipine/medlink, is safe for patients. This finding contradicts

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Artificial intelligence (AI) service software provider Freshworks has announced a workforce reduction of 13 per cent to streamline its operations, affecting at least 660 employees worldwide.

To further ensure high-speed and ultra-low latency services required in 5G, the Department of Telecommunications (DoT) on Saturday said it has signed an agreement with Linearized Amplifier Technology Services and Vedang Radio Tech.

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1. This is an appeal challenging the judgment and order of the Additional Sessions Judge, Nagpur in Sessions Trial No.39/2018 (State Vs. Kamlesh Dube and Others) thereby questioning the legality of judgment and order of convicting both the appellants under Section 235(2) of the Code of Criminal Procedure for the offence punishable under Section 302 2 cr.appeal.128.2022-JF.odt read with Section 34 of the Indian Penal Code, and sentencing both of them for life imprisonment alongwith fine of Rs.5000/- in default to suffer 3 months imprisonment.

2. The facts in short are as under :

On 19.09.2017, one Sumit Kamble died at about 1.46 p.m. It is alleged that appellant Kamlesh Dube and Shekhar Dube committed his murder. It is the prosecution case that both accused and the deceased were working as a driver on garbage vehicle at Kanak Resources Company. On the day of incident i.e. on 19.09.2017 at about 1.46 p.m. Sumit along with his friend Rahul and Yogiraj went to the Bhandewadi Dumping Yard by riding on the motorcycle of Sumit. At said place, the sister of informant Rahul and other women were picking the garbage. Kamlesh and Shekhar both accused also went there to unload the garbage by their garbage vehicle. Kamlesh was on driving seat whilst Shekhar was sitting beside him. Kamlesh has married with the sister of deceased Sumit. Kamlesh and sister of Sumit namely Tanu were having love affair, which was not liked by Sumit. Both of them ran away and performed marriage before 15 days. On their return, sister of Sumit was staying with Kamlesh. Because of said marriage, there was dispute between Kamlesh and Sumit. They used to quarrel with each other. On the date of occurrence, when Sumit saw Kamlesh, he went to him and there was hot exchange of words between them. At that time, Shekhar alighted from truck and assaulted Sumit with

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1. This writ petition is filed by the petitioner seeking to impugn the show cause notice dated 15.09.2014, the demolition order dated 29.04.2015, the order of the ATMCD dated 10.08.2016 and the order of the Appellate Authority dated 10.08.2018.

2. The case of the petitioner is that the property bearing No. 8770/14B, Shidi Pura, Karol Bagh, Delhi (measuring 85 sq. yards) was purchased by Late Sh.Prem Nath Shrama, husband of the petitioner on 20.09.1982. Prior to the said property, he had also purchased the adjacent property bearing No. 8771/14 B (measuring 160 sq. yards) on 28.10.1972. Sh. Prem Nath Sharma died on 11.05.1996. Pursuant to a Will, the petitioner became the absolute owner of the two properties.

PRESENT: MS. GURSHARAN K. MANN, ADVOCATE FOR THE PETITIONER.

MR. GAURAV DHURIWALA, SR.DAG, PUNJAB.

MANOJ BAJAJ, J.(ORAL) Kamlesh Verma @ Kiran Mummy has filed this petition for grant of regular bail in case FIR No.56 dated 9.5.2019 under Sections 376- D/120-B IPC, Police Station E-Division, District Amritsar. The petitioner is in custody since her arrest on 18.2.2020. The above FIR in question was initially registered at Police Station Padampur, District Sri Ganganagar as Zero FIR and was later on forwarded to District Amritsar where the above FIR was recorded.

As per the allegations, the victims had voluntarily left their house on 31.7.2018 and reached at Amritsar, where they came in contact with two persons, namely, Gagan and Vicky. They both promised a job for them and took them to the house of Vicky, where they raped the victims repeatedly. Later on, the victims were sent to other persons as well and accused Simmi facilitated the illegal sexual activities at her residence. Gagan used to send one of the victims outside the town as well. One of the 1 of 3 ::: Downloaded on - 08-05-2020 21:07:10 ::: CRM-M-12077-2020 (O&M) -2-

Nanoparticles are essential electrocatalysts in chemical production, water treatment and energy conversion, but engineering efficient and specific catalysts requires understanding complex structure–reactivity relations. Recent experiments have shown that Bragg coherent diffraction imaging might be a powerful tool in this regard. The technique provides three-dimensional lattice strain fields from which surface reactivity maps can be inferred. However, all experiments published so far have investigated particles an order of magnitude larger than those used in practical applications. Studying smaller particles quickly becomes demanding as the diffracted intensity falls. Here, in situ nanodiffraction data from 60 nm Au nanoparticles under electrochemical control collected at the hard X-ray nanoprobe beamline of MAX IV, NanoMAX, are presented. Two-dimensional image reconstructions of these particles are produced, and it is estimated that NanoMAX, which is now open for general users, has the requisites for three-dimensional imaging of particles of a size relevant for catalytic applications. This represents the first demonstration of coherent X-ray diffraction experiments performed at a diffraction-limited storage ring, and illustrates the importance of these new sources for experiments where coherence properties become crucial.

The transmission of the optical components of the Bernina branch of the Aramis beamline at SwissFEL has been measured with an X-ray gas monitor from DESY and compared with a PSI gas detector upstream of the optical components. The transmission efficiencies of the Mo, Si and SiC mirror coatings of the Aramis beamline and the various other in-beam components were evaluated and compared with theoretical calculations, showing an agreement of 6% or better in all cases. The experiment has also shown the efficacy of the high-harmonic rejection mirrors at the Bernina branch of the Aramis beamline at SwissFEL, and characterized the transmission efficiency of the on-line spectrometer in the Aramis beamline. The theoretical transmission of the mirror coatings match the experimental data to within 7%. The accuracy of these measurements was checked against a radiative bolometer from a Japanese collaboration and found to agree to a level of 4% or better. Further comparisons with a diamond detector from a US-based inter-institute collaboration demonstrated a good agreement for the attenuator settings of the beamline.

The design and performance of the high-resolution wavelength-dispersive multi-crystal von Hamos-type spectrometer at PETRA III beamline P64 are described. Extended analyzer crystal collection available at the beamline allows coverage of a broad energy range from 5 keV to 20 keV with an energy resolution of 0.35–1 eV. Particular attention was paid to enabling two-color measurements by a combination of two types of analyzer crystals and two two-dimensional detectors. The performance of the spectrometer is demonstrated by elastic-line and emission-line measurements on various compounds.

A new Rococo 2 X-ray fluorescence detector was implemented into the cryogenic sample environment at the Hard X-ray Micro/Nano-Probe beamline P06 at PETRA III, DESY, Hamburg, Germany. A four sensor-field cloverleaf design is optimized for the investigation of planar samples and operates in a backscattering geometry resulting in a large solid angle of up to 1.1 steradian. The detector, coupled with the Xspress 3 pulse processor, enables measurements at high count rates of up to 106 counts per second per sensor. The measured energy resolution of ∼129 eV (Mn Kα at 10000 counts s−1) is only minimally impaired at the highest count rates. The resulting high detection sensitivity allows for an accurate determination of trace element distributions such as in thin frozen hydrated biological specimens. First proof-of-principle measurements using continuous-movement 2D scans of frozen hydrated HeLa cells as a model system are reported to demonstrate the potential of the new detection system.

A new setup for picosecond pump–probe X-ray scattering at the Austrian SAXS beamline at Elettra-Sincrotrone Trieste is presented. A high-power/high-repetion-rate laser has been installed on-site, delivering UV/VIS/IR femto­second-pulses in-sync with the storage ring. Data acquisition is achieved by gating a multi-panel detector, capable of discriminating the single X-ray pulse in the dark-gap of the Elettra hybrid filling mode. Specific aspects of laser- and detection-synchronization, on-line beam steering as well protocols for spatial and temporal overlap of laser and X-ray beam are also described. The capabilities of the setup are demonstrated by studying transient heat-transfer in an In/Al/GaAs superlattice structure and results are confirmed by theoretical calculations.

Beamline 8A (BL 8A) is an undulator-based soft X-ray beamline at Pohang Accelerator Laboratory. This beamline is aimed at high-resolution ambient-pressure X-ray photoelectron spectroscopy (AP-XPS), soft X-ray absorption spectroscopy (soft-XAS) and scanning photoemission microscopy (SPEM) experiments. BL 8A has two branches, 8A1 SPEM and 8A2 AP-XPS, that share a plane undulator, the first mirror (M1) and the monochromator. The photon beam is switched between the two branches by changing the refocusing mirrors after the monochromator. The acceptance angle of M1 is kept glancing at 1.2°, and Pt is coated onto the mirrors to achieve high reflectance, which ensures a wide photon energy range (100–2000 eV) with high resolution at a photon flux of ∼1013 photons s−1. In this article, the main properties and performance of the beamline are reported, together with selected experiments performed on the new beamline and experimental system.

With the introduction of the multi-bend achromats in the new fourth-generation storage rings the emittance has decreased by an order of magnitude resulting in increased brightness. However, the higher brightness comes with smaller beam sizes and narrower radiation cones. As a consequence, the requirements on mechanical stability regarding the beamline components increases. Here an innovative five-axis parallel kinematic mirror unit for use with soft X-ray beamlines using off-axis grazing-incidence optics is presented. Using simulations and measurements from the HIPPIE beamline at the MAX IV Laboratory it is shown that it has no Eigen frequencies below 90 Hz. Its positioning accuracy is better than 25 nm linearly and 17–35 µrad angularly depending on the mirror chamber dimensions.

Reducing the sample-exchange time is a crucial issue in maximizing the throughput of macromolecular crystallography (MX) beamlines because the diffraction data collection itself is completed within a minute in the era of pixel-array detectors. To this end, an upgraded sample changer, SPACE-II, has been developed on the basis of the previous model, SPACE (SPring-8 Precise Automatic Cryo-sample Exchanger), at the BL41XU beamline at SPring-8. SPACE-II achieves one sample-exchange step within 16 s, of which its action accounts for only 11 s, because of three features: (i) the implementation of twin arms that enable samples to be exchanged in one cycle of mount-arm action, (ii) the implementation of long-stroke mount arms that allow samples to be exchanged without withdrawal of the detector and (iii) the use of a fast-moving translation and rotation stage for the mount arms. By pre-holding the next sample prior to the sample-exchange sequence, the time was further decreased to 11 s in the case of automatic data collection, of which the action of SPACE-II accounted for 8 s. Moreover, the sample capacity was expanded from four to eight Uni-Pucks. The performance of SPACE-II has been demonstrated in over two years of operation at BL41XU; the average number of samples mounted on the diffractometer in one day was increased from 132 to 185, with an error rate of 0.089%, which counted incidents in which users could not continue with an experiment without recovery work by entering the experimental hutch. On the basis of these results, SPACE-II has been installed at three other MX beamlines at SPring-8 as of July 2019. The fast and highly reliable SPACE-II is now one of the most important pieces of infrastructure for the MX beamlines at SPring-8, providing users with the opportunity to fully make use of limited beamtime with brilliant X-rays.

ID30A-3 (or MASSIF-3) is a mini-focus (beam size 18 µm × 14 µm) highly intense (2.0 × 1013 photons s−1), fixed-energy (12.81 keV) beamline for macromolecular crystallography (MX) experiments at the European Synchrotron Radiation Facility (ESRF). MASSIF-3 is one of two fixed-energy beamlines sited on the first branch of the canted undulator setup on the ESRF ID30 port and is equipped with a MD2 micro-diffractometer, a Flex HCD sample changer, and an Eiger X 4M fast hybrid photon-counting detector. MASSIF-3 is recommended for collecting diffraction data from single small crystals (≤15 µm in one dimension) or for experiments using serial methods. The end-station has been in full user operation since December 2014, and here its current characteristics and capabilities are described.

In recent years, there have been numerous efforts worldwide to develop the synchrotron X-ray scanning tunneling microscopy (SX-STM) technique. Here, the inauguration of XTIP, the world's first beamline fully dedicated to SX-STM, is reported. The XTIP beamline is located at Sector 4 of the Advanced Photon Source at Argonne National Laboratory. It features an insertion device that can provide left- or right-circular as well as horizontal- and vertical-linear polarization. XTIP delivers monochromatic soft X-rays of between 400 and 1900 eV focused into an environmental enclosure that houses the endstation instrument. This article discusses the beamline system design and its performance.

Inelastic X-ray scattering is a powerful and versatile technique for studying lattice dynamics in materials of scientific and technological importance. In this article, the design and capabilities of the momentum-resolved high-energy-resolution inelastic X-ray spectrometer (HERIX) at beamline 30-ID of the Advanced Photon Source are reported. The instrument operates at 23.724 keV and has an energy resolution of 1.3–1.7 meV. It can accommodate momentum transfers of up to 72  nm−1, at a typical X-ray flux of 4.5 × 109 photons s−1 meV−1 at the sample. A suite of in situ sample environments are provided, including high pressure, static magnetic fields and uniaxial strains, all at high or cryogenic temperatures.