Hasil untuk "gr-qc"

Ravi K. Patel, Mukesh Jain

Next generation sequencing (NGS) technologies provide a high-throughput means to generate large amount of sequence data. However, quality control (QC) of sequence data generated from these technologies is extremely important for meaningful downstream analysis. Further, highly efficient and fast processing tools are required to handle the large volume of datasets. Here, we have developed an application, NGS QC Toolkit, for quality check and filtering of high-quality data. This toolkit is a standalone and open source application freely available at http://www.nipgr.res.in/ngsqctoolkit.html. All the tools in the application have been implemented in Perl programming language. The toolkit is comprised of user-friendly tools for QC of sequencing data generated using Roche 454 and Illumina platforms, and additional tools to aid QC (sequence format converter and trimming tools) and analysis (statistics tools). A variety of options have been provided to facilitate the QC at user-defined parameters. The toolkit is expected to be very useful for the QC of NGS data to facilitate better downstream analysis.

Chi-Lam Cheang, Guangzeng Chen, Ya Jing et al.

We present GR-2, a state-of-the-art generalist robot agent for versatile and generalizable robot manipulation. GR-2 is first pre-trained on a vast number of Internet videos to capture the dynamics of the world. This large-scale pre-training, involving 38 million video clips and over 50 billion tokens, equips GR-2 with the ability to generalize across a wide range of robotic tasks and environments during subsequent policy learning. Following this, GR-2 is fine-tuned for both video generation and action prediction using robot trajectories. It exhibits impressive multi-task learning capabilities, achieving an average success rate of 97.7% across more than 100 tasks. Moreover, GR-2 demonstrates exceptional generalization to new, previously unseen scenarios, including novel backgrounds, environments, objects, and tasks. Notably, GR-2 scales effectively with model size, underscoring its potential for continued growth and application. Project page: \url{https://gr2-manipulation.github.io}.

T. G. McWilliams, A. Prescott, G. Allen et al.

Whether mitophagy occurs within specific cellular subtypes in vivo is unclear. McWilliams et al. present “mito-QC,” a transgenic mouse containing a pH-sensitive fluorescent mitochondrial signal, allowing in vivo detection of mitophagy and mitochondrial morphology at single-cell resolution.

Ian Linsmeier, Jordon Johnson, A. Chaturvedula et al.

R. Wang, C. Noddings, Elaine Kirschke et al.

C. Cook, Yanwei Wu, H. Odeh et al.

G4C2 repeat–derived poly(GR) plays a key role in mediating TDP-43 mislocalization and aggregation in vitro and in vivo. Unraveling protein clumping Repeat expansion in the C9orf72 gene causes amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), two neurodegenerative disorders with common features. A proportion of patients with ALS/FTD present cytoplasmic TDP-43 aggregates in the brain. The mechanisms mediating the formation of TDP-43 aggregates are unclear. Now, Cook et al. show that a poly glycine-arginine protein [poly(GR)] produced by the repeat expansion enhanced the formation of TDP-43 aggregates in vitro and in vivo in mice by altering nucleocytoplasmic transport. Targeting the repeat expansion with a specific antisense oligonucleotide reduced the formation of TDP-43 aggregates. The results shine the light on the mechanisms mediating the formation of toxic aggregates in neurodegenerative diseases. TAR DNA-binding protein 43 (TDP-43) inclusions are a pathological hallmark of frontotemporal dementia (FTD) and amyotrophic lateral sclerosis (ALS), including cases caused by G4C2 repeat expansions in the C9orf72 gene (c9FTD/ALS). Providing mechanistic insight into the link between C9orf72 mutations and TDP-43 pathology, we demonstrated that a glycine-arginine repeat protein [poly(GR)] translated from expanded G4C2 repeats was sufficient to promote aggregation of endogenous TDP-43. In particular, toxic poly(GR) proteins mediated sequestration of full-length TDP-43 in an RNA-independent manner to induce cytoplasmic TDP-43 inclusion formation. Moreover, in GFP-(GR)200 mice, poly(GR) caused the mislocalization of nucleocytoplasmic transport factors and nuclear pore complex proteins. These mislocalization events resulted in the aberrant accumulation of endogenous TDP-43 in the cytoplasm where it co-aggregated with poly(GR). Last, we demonstrated that treating G4C2 repeat–expressing mice with repeat-targeting antisense oligonucleotides lowered poly(GR) burden, which was accompanied by reduced TDP-43 pathology and neurodegeneration, including lowering of plasma neurofilament light (NFL) concentration. These results contribute to clarification of the mechanism by which poly(GR) drives TDP-43 proteinopathy, confirm that G4C2-targeted therapeutics reduce TDP-43 pathology in vivo, and demonstrate that alterations in plasma NFL provide insight into the therapeutic efficacy of disease-modifying treatments.

Saikat Das, M. Cox, Patricia N. Tynan et al.

Setting casing as close as possible to the top of the reservoir is critical in deep water carbonate exploration drilling strategy in Malaysia for several reasons, such as the pressure difference from the overburden and mud loss related to vugs, fractures, and karsts. Missing accurately setting this critical casing point may lead to severe rig NPT and related additional operational costs and, in extreme cases, may lead to abandoning the well. This challenge requires a novel and fail-safe strategy to ensure the identification of the Top of Carbonate (TOC) precisely during drilling. An expected pressure ramp at the top part of the carbonate reservoir in the subject exploration well located in deep water off Malaysia was a critical drilling challenge. Hence, accurately establishing the TOC depth, followed by placing a casing shoe close to it, and thus isolating the overburden shale was necessary before drilling the reservoir section. The seismic uncertainty of the TOC at the pre-drilling phase was large. Hence a comprehensive solution involving seismic while drilling, near-bit gamma ray, and resistivity measurement was deployed to progressively reduce the depth uncertainty while drilling. This solution allowed the client to accurately identify the TOC depth and eventually decide on the section TD to set the casing. Borehole Seismic (VSP) while drilling look-ahead technology was selected as the ideal solution to reduce the depth uncertainty of the TOC. To acquire VSP data a downhole receiver was deployed in the drilling Bottom Hole Assembly (BHA) and surface sources were used to provide the acoustic source as for normal wireline VSP. During drilling, the BHA was stopped when required; the surface sources were fired and the signal was recorded downhole by the receiver. In seismic while drilling technology, the shooting sequence triggers the tool to stack live data shots and create a data extract. Once drilling resumes this extract is transmitted to the surface by the mud pulse system for QC on the rig and further VSP processing. Subsequently, the data extract was processed to create a zero-phase multiple-free Corridor Stack. The result was available within 20 minutes allowing the team to decide on a further drilling strategy A Comparison of the VSP corridor stack and the Surface Seismic allowed the correlation of the TOC event wavelet. The wavelet picked from the Surface Seismic was used to identify the corresponding wavelet on the VSP data. As the time/depth of the VSP downhole receiver was a known point we could then calculate the time that the TOC wavelet was ahead of the current VSP receiver depth, creating an estimate of the depth of the top carbonate (Figure 1). As the VSP downhole receiver was much closer to the target than the surface seismic sources and receivers, the look-ahead estimate was more accurate, and as more VSP data was recorded the depth estimate was refined. The Near Bit GR and Resistivity services were also deployed to acquire those data as early as possible. The GR of the carbonate was substantially lower, and the resistivity was much higher than the overburden shale. The sudden deflection of those measurements indicated the TOC as soon as the drill bit penetrated the reservoir. These complementary measurements were planned as a backup to the seismic- based solution and eventually helped to identify the TOC with confidence. The lookahead TOC depth was predicted when the deepest VSP level was approximately 120 m above the Carbonate with uncertainty as low as 2m with the precise depth being confirmed by Near-bit measurement. This accurate while drilling novel approach saved rig time and money by eliminating the need for conventional wireline look ahead VSP and enabled drilling of the reservoir section safely by placing the casing shoe exactly at TOC

S. Choi, R. López-González, G. Krishnan et al.

C. Noddings, R. Wang, Jill L. Johnson et al.

Carleton Coffrin, H. Hijazi, P. Van Hentenryck

André Märtens, Johannes Holle, B. Mollenhauer et al.

Untargeted metabolomics is an important tool in studying health and disease and is employed in fields such as biomarker discovery and drug development, as well as precision medicine. Although significant technical advances were made in the field of mass-spectrometry driven metabolomics, instrumental drifts, such as fluctuations in retention time and signal intensity, remain a challenge, particularly in large untargeted metabolomics studies. Therefore, it is crucial to consider these variations during data processing to ensure high-quality data. Here, we will provide recommendations for an optimal data processing workflow using intrastudy quality control (QC) samples that identifies errors resulting from instrumental drifts, such as shifts in retention time and metabolite intensities. Furthermore, we provide an in-depth comparison of the performance of three popular batch-effect correction methods of different complexity. By using different evaluation metrics based on QC samples and a machine learning approach based on biological samples, the performance of the batch-effect correction methods were evaluated. Here, the method TIGER demonstrated the overall best performance by reducing the relative standard deviation of the QCs and dispersion-ratio the most, as well as demonstrating the highest area under the receiver operating characteristic with three different probabilistic classifiers (Logistic regression, Random Forest, and Support Vector Machine). In summary, our recommendations will help to generate high-quality data that are suitable for further downstream processing, leading to more accurate and meaningful insights into the underlying biological processes.

S. Verma, A. Bhatnagar, V. Shukla et al.

Abstract The present investigation reports the effect of TiH2 templated over graphene (TiH2@Gr) on the hydrogen sorption characteristics of MgH2/Mg. The as synthesized TiH2@Gr leads to significant effect on sorption in MgH2 by the following effects: the first is dehydrogenation of MgH2–TiH2@Gr, which leads to the conversion of some part of TiH2 into TiH1.924. TiH2 together with TiH1.924 works as a better catalyst than TiH2 alone. The second is ball-milling of TiH2@Gr, which produces defective graphene, which also works as co-catalyst. The third is anchoring of TiH2 on graphene, which does not allow the catalyst to agglomerate. The catalytic effect of TiH2@Gr on MgH2 is found to be better than Ti@Gr and TiO2@Gr. The onset desorption temperature for MgH2–TiH2@Gr is ~204 °C, which is 31 °C and 36 °C lower than MgH2–Ti@Gr, MgH2–TiO2@Gr respectively. The better catalytic behavior of TiH2@Gr also persists during de/re-hydrogenation kinetics and cycling study of MgH2. The feasible mechanism for superior catalytic for TiH2@Gr on MgH2 has been put forward.

Shima Ziajahromi, F. Leusch

Although a growing number of studies have reported microplastics (MPs) in biosolids and soils, there are significant differences in the concentrations found across different regions worldwide. This has raised questions about the quality of studies due to a lack of standardized sampling and analysis methods for detecting MPs in such complex samples. In this study, we applied a systematic quantitative literature review (SQLR) methodology to analyze studies reporting MPs in sludge/biosolids and agricultural soils. We also assessed the quality of individual studies on MPs in sludge/biosolids and soils based on the inclusion of quality assurance/quality control (QA/QC) procedures. There is limited understanding about MPs in soils with a history of biosolid application with only 9% of publications reporting MPs in biosolid-amended soil. There was almost eight orders of magnitude difference (3.4×10-5 to 9.4×103 particles/g) between the highest concentrations of MPs in sludge/biosolid samples compared to the lowest virgin soil samples. The literature shows a consistency in the polymer types (polyester, PP and PE) and morphotypes (fibres and fragments) of MPs most frequently detected in biosolids and soils, suggesting a potential role of biosolids in soils MP pollution. Despite the large variations in the sizes of MPs, there was a negative correlation between the lowest size detected and concentrations reported. This indicates that current concentrations of MPs are influenced by the detection size. Our assessment shows that the majority of studies to-date lack critical QA/QC measures, particularly field blank, positive control and method validation. This highlights an urgent need for quality improvement of future research in this field to produce reliable data, ultimately crucial to assess the risk of MPs and derive suitable environmental guidelines. It is recommended that MPs studies methodically include QA/QC protocols at every step of the process to ensure the integrity of the data that is published.

Yi-Ting Liu, Danielle A. Sliter, Mario K. Shammas et al.

ABSTRACT PINK1 and PRKN, which cause Parkinson disease when mutated, form a quality control mitophagy pathway that is well-characterized in cultured cells. The extent to which the PINK1-PRKN pathway contributes to mitophagy in vivo, however, is controversial. This is due in large part to conflicting results from studies using one of two mitophagy reporters: mt-Keima or mito-QC. Studies using mt-Keima have generally detected PINK1-PRKN mitophagy in vivo, whereas those using mito-QC generally have not. Here, we directly compared the performance of mito-QC and mt-Keima in cell culture and in mice subjected to a PINK1-PRKN activating stress. We found that mito-QC was less sensitive than mt-Keima for mitophagy, and that this difference was more pronounced for PINK1-PRKN mitophagy. These findings suggest that mito-QC’s poor sensitivity may account for conflicting reports of PINK1-PRKN mitophagy in vivo and caution against using mito-QC as a reporter for PINK1-PRKN mitophagy. Abbreviations: DFP: deferiprone; EE: exhaustive exercise; FBS: fetal bovine serum; OAQ: oligomycin, antimycin, and Q-VD-OPH; OMM: outer mitochondrial membrane; PBS: phosphate-buffered saline; PD: Parkinson disease; UPS: ubiquitin-proteasome system.

Vladimir L. Petrović, Milos M. Markovic, Dragomir M. El Mezeni et al.

Modern communication standards, such as 5G new radio (5G NR), require a high speed decoder for highly irregular quasi-cyclic low density parity check (QC-LDPC) codes. A widely used approach in QC-LDPC decoders is a layered decoding schedule which processes the parity check matrix in parts, thus providing faster convergence. However, pipelined layered decoding architecture suffers from data hazards that reduce the throughput. This paper presents a novel architecture, which can facilitate any QC-LDPC decoding without stall cycles caused by pipeline hazards. The decoder conveniently incorporates both the layered and the flooding schedules in cases when hazards occur. The paper also presents the genetic algorithm based optimization of the decoding schedule for better signal-to-noise ratio (SNR) performance. The proposed architecture enables insertion of a large number of pipeline stages, thus providing high operating frequency. As a case study, the FPGA implementation for WiMAX, DVB-S2X, and 5G NR provided coded throughput of up to 1.77 Gbps, 4.32 Gbps, and 4.92 Gbps at 10 iterations, respectively. The results show a strong throughput increase of 30%–109% compared with the conventional layered decoder for 5G NR for the same SNR performance. The decoder provides highly efficient utilization of resources when compared with the state-of-the-art solutions.

Nir Drucker, S. Gueron, Dusan Kostic

M. Midha, D. Campbell, C. Kapil et al.

Data-independent acquisition (DIA) mass spectrometry, also known as Sequential Window Acquisition of all Theoretical Mass Spectra (SWATH), is a popular label-free proteomics strategy to comprehensively quantify peptides/proteins utilizing mass spectral libraries to decipher inherently multiplexed spectra collected linearly across a mass range. Although there are many spectral libraries produced worldwide, the quality control of these libraries is lacking. We present the DIALib-QC (DIA library quality control) software tool for the systematic evaluation of a library’s characteristics, completeness and correctness across 62 parameters of compliance, and further provide the option to improve its quality. We demonstrate its utility in assessing and repairing spectral libraries for correctness, accuracy and sensitivity. Most data-independent acquisition (DIA) methods depend on mass spectral libraries for peptide identification but tools to assess library quality are lacking. Here, the authors develop DIALib- QC for the systematic evaluation and correction of spectral libraries.

T. Nguyen, Tuy Nguyen Tan, Hanho Lee

This paper presents a novel efficient encoding method and a high-throughput low-complexity encoder architecture for quasi-cyclic low-density parity-check (QC-LDPC) codes for the 5th-generation (5G) New Radio (NR) standard. By storing the quantized value of the permutation information for each submatrix instead of the whole parity check matrix, the required memory storage size is considerably reduced. In addition, sharing techniques are employed to reduce the hardware complexity. The encoding complexity of the proposed method was analyzed, and indicated a substantial reduction in the required area as well as memory storage when compared with existing state-of-the-art encoding approaches. The proposed method requires only 61% gate area, and 11% ROM storage when compared with a similar LDPC encoder using the Richardson–Urbanke method. Synthesis results on TSMC 65-nm complementary metal-oxide semiconductor (CMOS) technology with different submatrix sizes were carried out, which confirmed that the design methodology is flexible and can be adapted for multiple submatrix sizes. For all the considered submatrix sizes, the throughput ranged from 22.1–202.4 Gbps, which sufficiently meets the throughput requirement for the 5G NR standard.

Elise Meyer, P. Grussenmeyer, T. Tidafi et al.

X. C. D. Lega