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2022 ◽  
Author(s):  
Agustin Carbajal ◽  
Irma Gryniuk ◽  
Rodrigo de Castro ◽  
Roberto Pezza

Chromatin-based mechanisms regulating developmental transitions during meiosis are fundamental but understudied aspects of male gametogenesis. Indeed, chromatin undergoes extensive remodeling dur-ing meiosis, leading to specific patterns of gene expression and chromosome organization, which ulti-mately controls fundamental meiotic processes such as recombination and homologous chromosome associations. Recent game-changing advances have been made by analysis of chromatin binding sites of meiotic specific proteins genome-wide in mouse spermatocytes. However, further progress is still highly dependent on the reliable isolation of sufficient quantities of spermatocytes at specific stages of prophase I. Here, we describe a combination of methodologies adapted for rapid and reliable isolation of synchronized fixed mouse spermatocytes. We show that chromatin isolated from these cells can be used to study chromatin binding sites by ChIP-seq. High quality data we obtained from INO80 ChIP-seq in zygotene cells was used for functional analysis of chromatin binding sites.


2022 ◽  
Vol 43 (3) ◽  
Author(s):  
Marcin Buchowiecki

AbstractThis study is aimed to determine collision integrals for atoms interacting according to the m-6-8 and Hulburt–Hirschfelder potentials and analyze the differences between potentials. The precision of four significant digits was reached at all tested temperatures, and for high-temperature applications, six digits were calculated. The proposed method was tested on the Lennard-Jones potential and found to excellently agree with the recent high-quality data. In addition, the Hulburt–Hirschfelder potential was used for determining the collision integrals of the interaction of nitrogen atoms in the ground electronic state and compared with other known values. The calculations were performed using Mathematica computation system which can deal with singularities (so-called orbiting).


2021 ◽  
Author(s):  
Andressa de Zawadzki ◽  
Maja Thiele ◽  
Tommi Suvitaival ◽  
Asger Wretlind ◽  
Min Kim ◽  
...  

(1) Background: Feces are the product of our diets and have been linked to diseases of the gut, including Crohn's disease and metabolic diseases such as diabetes. For screening metabolites in heterogeneous samples such as feces, it is necessary to use fast and reproducible analytical methods that maximize metabolite detection. (2) Methods: As sample preparation is crucial to obtain high quality data in MS-based clinical metabolomics, we developed a novel, efficient and robust method for preparing fecal samples for analysis with a focus in reducing aliquoting and detecting both polar and non-polar metabolites. Fecal samples (n= 475) from patients with alcohol-related liver disease and healthy controls were prepared according to the proposed method and analyzed in an UHPLC-QQQ targeted platform in order to obtain a quantitative profile of compounds that impact liver-gut axis metabolism. (3) Results: MS analyses of the prepared fecal samples have shown reproducibility and coverage of n=28 metabolites, mostly comprising bile acids and amino acids. We report metabolite-wise relative standard deviation (RSD) in quality control samples, inter-day repeatability, LOD, LOQ and range of linearity. The average concentrations for 135 healthy participants are reported here for clinical applications. (4) Conclusions: our high-throughput method provides an efficient tool for investigating gut-liver axis metabolism in liver-related diseases using a noninvasive collected sample.


Author(s):  
Sethu Arun Kumar ◽  
Thirumoorthy Durai Ananda Kumar ◽  
Narasimha M Beeraka ◽  
Gurubasavaraj Veeranna Pujar ◽  
Manisha Singh ◽  
...  

Predicting novel small molecule bioactivities for the target deconvolution, hit-to-lead optimization in drug discovery research, requires molecular representation. Previous reports have demonstrated that machine learning (ML) and deep learning (DL) have substantial implications in virtual screening, peptide synthesis, drug ADMET screening and biomarker discovery. These strategies can increase the positive outcomes in the drug discovery process without false-positive rates and can be achieved in a cost-effective way with a minimum duration of time by high-quality data acquisition. This review substantially discusses the recent updates in AI tools as cheminformatics application in medicinal chemistry for the data-driven decision making of drug discovery and challenges in high-quality data acquisition in the pharmaceutical industry while improving small-molecule bioactivities and properties.


2021 ◽  
Author(s):  
Christina Bohk-Ewald ◽  
Enrique Acosta ◽  
Tim Riffe ◽  
Christian Dudel ◽  
Mikko Myrskyla

How deadly is an infection with SARS-CoV-2 worldwide over time? This information is critical for developing and assessing public health responses on the country and global levels. However, imperfect data have been the most limiting factor for estimating the COVID-19 infection fatality burden during the first year of the pandemic. Here we leverage recently emerged compelling data sources and broadly applicable modeling strategies to estimate the crude infection fatality rate (cIFR) in 77 countries from 28 March 2020 to 31 March 2021, using 2.4 million reported deaths and estimated 435 million infections by age, sex, country, and date. The global average of all cIFR estimates is 1.2% (10th to 90th percentile: 0.2% to 2.4%). The cIFR varies strongly across countries, but little within countries over time, and it is often lower for women than men. Cross-country differences in cIFR are largely driven by the age structures of both the general and the truly infected population. While the broad trends and patterns of the cIFR estimates are more robust, we show that their levels are uncertain and sensitive to input data and modeling choices. In consequence, increased efforts at collecting high-quality data are essential for accurately estimating the cIFR, which is a key indicator for better understanding the health and mortality consequences of this pandemic.


2021 ◽  
Vol 2 ◽  
Author(s):  
Julia Adelöf ◽  
Jaime M. Ross ◽  
Madeleine Zetterberg ◽  
Malin Hernebring

Lifespan analyses are important for advancing our understanding of the aging process. There are two major issues in performing lifespan studies: 1) late-stage animal lifespan analysis may include animals with non-terminal, yet advanced illnesses, which can pronounce indirect processes of aging rather than the aging process per se and 2) they often involves challenging welfare considerations. Herein, we present an option to the traditional way of performing lifespan studies by using a novel method that generates high-quality data and allows for the inclusion of excluded animals, even animals removed at early signs of disease. This Survival-span method is designed to be feasibly done with simple means by any researcher and strives to improve the quality of aging studies and increase animal welfare.


2021 ◽  
Vol 73 (1) ◽  
Author(s):  
J. Michael Grappone ◽  
James M. Russell ◽  
Andrew J. Biggin

AbstractHigh-quality data are vital to the research field of paleointensity, which has long suffered from poor-quality and/or sparse data. Previous paleointensity work has established that repeatedly heating specimens increases the opportunity for thermochemical alteration to decrease the reliability of paleointensity data. In addition, recent work has shown that repeatedly heating specimens in paleointensity experiments can also exaggerate the effects of non-ideal, non-single domain grains. Arai plots resulting from paleointensity experiments containing such grains are often curvilinear (two-slope) across most of the specimen’s unblocking temperature spectrum, except in the temperature range nearest to the grains’ Curie temperature. This study tests the following strategy to mitigate these effects: that of performing a Thellier paleointensity experiment using fewer temperature steps that are also concentrated at higher temperatures. For this purpose, we use natural specimens with well-constrained rock magnetic data from the Hawaiian Scientific Observation Hole 1 (SOH1) drill core in paleointensity experiments with starting temperatures ranging from 200 °C to 500+ °C. Those experiments that focused in on the portion of the unblocking temperature spectrum nearest the Curie temperature of the specimen (HiTeCT) had an exceptionally low success rate, whereas those with initial temperatures at comparatively moderate temperatures (200–400 °C) had high success rates (~ 70%). Thermochemical alteration was minimized with a start temperature of 400 °C, but the curvature of the Arai plots had no clear dependance on start temperature. We conclude herein that increasing the start temperature can help avoid the effects of low-temperature alterations. Additionally, we found that the approach of focusing in on the highest temperature range is not a feasible one to apply in paleointensity experiments, in general, and consider this likely to be a result of a lack of intermediate-temperature checks for alteration and insufficient independence of temperature steps. Graphical abstract


2021 ◽  
pp. 004051752110608
Author(s):  
Abdel Salam Malek ◽  
Ashraf Elnahrawy ◽  
Hamed Anwar ◽  
Mohamed Naeem

Wearable electrocardiogram (ECG) systems should be comfortable, non-stigmatizing, and capable of producing high-quality data. Many different designs of wearable textile ECG systems have recently emerged. Some of them are not considered to be smart garments, whereas most of the others present only the electronic side of the system. Our research work introduces a comprehensive study for an improved single-lead ECG smart shirt to identify automatically premature ventricular contraction as a common form of arrhythmia. For artifact-free results, Marvelous Designer is implemented to design our optimized relaxed slim fit shirt. In addition, a weft-knitted fabric of 80% nylon–20% spandex is used to manufacture the outer part of the shirt. Moreover, lightweight and small size electronic components are integrated to the outer part via low-resistance dry textile electrodes and 100% cotton fabric as an inner layer for easy transmission of weak ECG signals.


2021 ◽  
Author(s):  
Aimie L Peek ◽  
Trudy J Rebbeck ◽  
Andrew M Leaver ◽  
Nicolaas Puts ◽  
Sheryl Foster ◽  
...  

Background: The aim of this guideline is to provide a series of evidence-based recommendations that allow those new to the field of MEGA-PRESS to produce high-quality data for the measurement of GABA levels using edited magnetic resonance spectroscopy with the MEGA-PRESS sequence at 3T. GABA is the main inhibitory neurotransmitter of the central nervous system and has been increasingly studied due to its relevance in many clinical disorders of the central nervous system. MEGA-PRESS is the most widely used method for quantification of GABA at 3T, but is technically challenging and operates at a low signal-to-noise ratio. Therefore, the acquisition of high-quality MRS data relies on avoiding numerous pitfalls and observing important caveats. Methods: The guideline was developed by a working party that consisted of experts in MRS and experts in guideline development and implementation, together with key stakeholders. Strictly following a translational framework, we first identified evidence using a systematically conducted scoping literature review, then synthesised and graded the quality of evidence that formed recommendations. These recommendations were then sent to a panel of 21 world leaders in MRS for feedback and approval using a modified-Delphi process across two rounds. Results: The final guideline consists of 23 recommendations across six domains essential for GABA MRS acquisition (Parameters, Practicalities, Data acquisition, Confounders, Quality/reporting, Post-processing). Overall, 78% of recommendations were formed from high-quality evidence, and 91% received agreement from over 80% of the expert panel. Conclusion: These 23 expert-reviewed recommendations and accompanying extended documentation form a readily usable guideline to allow those new to the field of MEGA-PRESS to design appropriate MEGA-PRESS study protocols and generate high-quality data.


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