bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metrological aspects of the safety and quality of meat products
Authors: Oganyan N G , Semenova A A , Dobrovolskiy V I 
Published: March 2022

Abstract
The meat industry is one of the most important sectors of the economy closely related to animal husbandry. In the human diet, meat is the main source of animal protein. Therefore, quality of a final product is extremely important and depends on many factors at all stages of the production. Requirements for parameters of food safety and quality are established in the most countries and are revised permanently depending on the new scientific data.
In the Russian Federation and the Customs Union, the controlled parameters are normalized on the basis of scientific data and approved for use in the relevant Technical Regulations. In order to avoid actions misleading consumers, special requirements for product labeling have been developed. In particular, the labeling of slaughter products and meat products must be conformed in accordance to the Technical Regulation of the Customs Union "Food products in terms of their labeling " - TR CU 022/2011, as well as to the some clauses of the Technical Regulation TR CU 034/2013 On the Safety of Meat and Meat Products.
According to the working regulation, the manufacturers must indicate nutritional parameters (protein, fat, carbohydrates) of meat products on the product label as the parameter true values. At the same time, each standard for analytical methods includes a permissible relative error of the measured value at the confidence level of 0.95, which had not to be exceeded under the conditions described in the standard. In that way target measurement uncertainty is established.
This paper shows the possible risks of false decisions when assessing meat products for its compliance with the labeling, depending on the measurement uncertainty, as well as methods for minimizing these risks.
Metrological problems of measurements of environmental objects in terms of spectrometry and radiometry of alpha, beta, gamma-emitting radionuclides
Authors: Berlyand T P , Tonkikh N G 
Published: March 2022

Abstract
This article deals with methods for measuring the characteristics of ionizing radiation in solving problems of radiation monitoring of the environment, industrial premises, sanitary protection zones, human pollution control using measurement techniques certified in the prescribed manner. The types of measuring instruments involved in the measurement of various quantities are listed. The main objects of measurements used in radiation monitoring of the environment, control of surface contamination and human contamination are named. The metrological characteristics (measured quantities) of measuring instruments are compared with the metrological characteristics of real measurement objects. A number of necessary established metrological characteristics for radiometric and spectrometric measuring instruments for the successful use of a measuring instrument in solving one or another problem of radiation measurements is indicated. An example from a real work is considered, in which the method of mathematical modeling when calculating additional metrological characteristics showed a significant discrepancy with the real data obtained during the experiment.
Development of a lunar soil simulator for Earth-based experiments
Authors: Alexandrov P A , Vasiliev A L , Kalechits V I , Kapustin Yu V , Klyuev V V , Makaveev P Yu , Patsaev T D , Shakhov M N 
Published: March 2022

Abstract
A simulator of lunar soil and lunar dust has been developed, designed for modeling various engineering processes in terrestrial conditions. The elemental and granulometric compositions of the simulator were studied using X-ray fluorescence analysis, scanning electron microscopy and laser light scattering. The resulting material will be used in the future to simulate thermophysical processes when creating lunar power generating plants. The finely dispersed component of the simulator based on basalt wool will be used to study the filtration of lunar dust.
A moving platform photometric observation based attitude and angular velocity estimation method for space target
Authors: Chen Shengyi , Fan Chaoran , Zhang Feng , Shi Liu 
Published: March 2022

Abstract
Based on the photometric information, a method is proposed for estimating space target attitude and angular velocity under the condition of moving observation platform. Firstly, according to the dynamically changing relative pose relationship among the target, the observation platform and the sun, photometric measurement model is established. Then, in the framework of Unscented Kalman Filter, the joint estimation of target attitude and angular velocity is realized by combining use of quaternion and Modified Rodriguez Parameters. Finally, the feasibility and estimation accuracy of the method are verified by numerical simulation experiments. The results show that the proposed method achieves high accuracy and has certain value in practical application.
Molecular mechanism study of Astragalus adsurgens Pall synergistically induced by plasma and plasma-activated water
Authors: LI Yibing , ZHANG Tao , SONG Zhiqing , DING Changjiang , CHEN Hao 
Published: March 2022

Abstract
The mutagenic effects of discharge plasma and plasma+PAW (plasma and its activated water combined) on Astragalus adsurgens Pall seeds were explored. Needle array-plate dielectric-barrier discharge plasma was used to treat A. adsurgens Pall seeds and PAW was prepared at the same time. The deionized water and the obtained PAW were used to cultivate plasma-treated seeds in groups and the survival rate of each group was counted. Results showed that the survival rate of the treated seeds of A. adsurgens Pall when cultured with deionized water was not significantly different from that of the control check (CK). The culture with PAW had an obvious lethal effect and each group reached the half-lethal dose. Reactive oxygen species (ROS) and RNA-Seq analysis of seedlings in the 3 h treatment group showed that the content of ROS in the 3 d post-treatment group was significantly higher than that of the CK. Because expression of the gene with the function of scavenging superoxide free radicals was upregulated, the ROS content of seedlings on the sixth day was significantly lower than that on the third day. Plasma and plasma+PAW treatments changed a large number of gene expressions; particularly, the plasma+PAW group caused plant-growth genes to be significantly upregulated. After treatment, the seedlings of A. adsurgens Pall may grow faster and have higher nutritional value. This research is of great significance to the wider application of isoelectronic bodies and their activated water physicochemical mutagens in biological effects and breeding research.
Effect of short carbon fiber/SiC on tribological properties of aluminium matrix hybrid composites
Authors: Joshi Tanmay Vivek , Mohanty Akash 
Published: March 2022

Abstract
This research study was carried out to combine the benefits of Silicon Carbide (SiC) and short carbon fiber (CF) as reinforcements in the aluminum matrix to develop the composites for automotive applications. The powder metallurgy (PM) technique was used to fabricate five samples with different compositions. Linear wear, coefficient of friction, density, and Vickers hardness of the samples were determined and compared. The sample with 6 wt.% CF and 10 wt.% SiC was found to have the optimal properties. It was observed that the linear wear was 52.32% less and the hardness was 14.58% more than the base metal.
Statin Medications and Amyotrophic Lateral Sclerosis Incidence and Mortality
Authors: Weisskopf Marc G , Levy Joseph , Dickerson Aisha S , Paganoni Sabrina , Leventer-Roberts Maya 
Published: March 2022

Abstract
Studies of statins and amyotrophic lateral sclerosis (ALS) incidence and survival have had conflicting findings possibly related to difficulties with confounding by indication. We considered potency of statins used and duration of use to explore confounding by indication. Within the Clalit Health Services in Israel, we identified 948 ALS case patients from 2004 through 2017 and matched them with 1,000 control subjects each. Any statin use up to 3 years before ALS onset was not associated with ALS incidence but was associated with a reduced hazard ratio (HR) for death. Odds of ALS did not vary by statin potency, but use of only lower-potency statins was associated with longer survival (HR = 0.82, 95% CI: 0.68, 0.98), whereas the association with higher-potency statins was null compared with those case patients who did not use statins. However, duration of statin use appeared to account for these findings. Those who used statins only up to 3 years had longer survival (HR = 0.77, 95% CI: 0.61, 0.96) than did case patients who did not use statins, but those who used statins for &gt;3 years did not. Although other explanations are possible, these findings could suggest a protective effect of statins on ALS survival that is partially masked by a worse prognosis from underlying reasons for taking statins that deserves further exploration.
LIQUORICE: detection of epigenetic signatures in liquid biopsies based on whole-genome sequencing data
Authors: Peneder Peter , Bock Christoph , Tomazou Eleni M 
Published: March 2022

Abstract

Summary
Fragmentation patterns of cell-free DNA reflect the chromatin structure of the cells from which these fragments are derived. Nucleosomes protect the DNA from fragmentation, resulting in decreased sequencing coverage in regions of open chromatin. LIQUORICE is a user-friendly software tool that takes aligned whole-genome sequencing data as input and calculates bias-corrected coverage signatures for predefined, application-specific sets of genomic regions. The tool thereby enables a blood-based analysis of cell death in the body, and it provides a minimally invasive assessment of tumor chromatin states and cell-of-origin. With user-defined sets of regions that exhibit tissue-specific or disease-specific open chromatin, LIQUORICE can be applied to a wide range of detection, classification and quantification tasks in the analysis of liquid biopsies.

Availability and implementation
LIQUORICE is freely and openly available as a Python package and command-line tool for UNIX-based systems from bioconda. Documentation, examples and usage instructions are provided at http://liquorice.computational-epigenetics.org.

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
A comprehensive evaluation of regression-based drug responsiveness prediction models, using cell viability inhibitory concentrations (IC50 values)
Authors: Park Aron , Joo Minjae , Kim Kyungdoc , Son Won-Joon , Lim GyuTae , Lee Jinhyuk , Kim Jung Ho , Lee Dae Ho , Nam Seungyoon 
Published: March 2022

AbstractMotivationPredicting drug response is critical for precision medicine. Diverse methods have predicted drug responsiveness, as measured by the half-maximal drug inhibitory concentration (IC50), in cultured cells. Although IC50s are continuous, traditional prediction models have dealt mainly with binary classification of responsiveness. However, since there are few regression-based IC50 predictions, comprehensive evaluations of regression-based IC50 prediction models, including machine learning (ML) and deep learning (DL), for diverse data types and dataset sizes, have not been addressed.ResultsHere, we constructed 11 input data settings, including multi-omics settings, with varying dataset sizes, then evaluated the performance of regression-based ML and DL models to predict IC50s. DL models considered two convolutional neural network architectures: CDRScan and residual neural network (ResNet). ResNet was introduced in regression-based DL models for predicting drug response for the first time. As a result, DL models performed better than ML models in all the settings. Also, ResNet performed better than or comparable to CDRScan and ML models in all settings.Availability and implementationThe data underlying this article are available in GitHub at https://github.com/labnams/IC50evaluation.Supplementary informationSupplementary data are available at Bioinformatics online.
Fast and accurate inference of gene regulatory networks through robust precision matrix estimation
Authors: Passemiers Antoine , Moreau Yves , Raimondi Daniele 
Published: March 2022

AbstractMotivationTranscriptional regulation mechanisms allow cells to adapt and respond to external stimuli by altering gene expression. The possible cell transcriptional states are determined by the underlying gene regulatory network (GRN), and reliably inferring such network would be invaluable to understand biological processes and disease progression.ResultsIn this article, we present a novel method for the inference of GRNs, called PORTIA, which is based on robust precision matrix estimation, and we show that it positively compares with state-of-the-art methods while being orders of magnitude faster. We extensively validated PORTIA using the DREAM and MERLIN+P datasets as benchmarks. In addition, we propose a novel scoring metric that builds on graph-theoretical concepts.Availability and implementationThe code and instructions for data acquisition and full reproduction of our results are available at https://github.com/AntoinePassemiers/PORTIA-Manuscript. PORTIA is available on PyPI as a Python package (portia-grn).Supplementary informationSupplementary data are available at Bioinformatics online.
Extending prediction models for use in a new target population with failure time outcomes
Authors: Steingrimsson Jon A 
Published: March 2022

Summary
Prediction models are often built and evaluated using data from a population that differs from the target population where model-derived predictions are intended to be used in. In this article, we present methods for evaluating model performance in the target population when some observations are right censored. The methods assume that outcome and covariate data are available from a source population used for model development and covariates, but no outcome data, are available from the target population. We evaluate the finite sample performance of the proposed estimators using simulations and apply the methods to transport a prediction model built using data from a lung cancer screening trial to a nationally representative population of participants eligible for lung cancer screening.
Cumulative Antibiotic Exposure in the First 5 Years of Life: Estimates for 45 Low- and Middle-Income Countries From Demographic and Health Survey Data
Authors: Levine Gillian A , Bielicki Julia , Fink Günther 
Published: March 2022

Abstract

Background
Estimates of the total cumulative exposure to antibiotics of children in low-resource settings, and the source of these treatments, are limited.

Methods
We estimated the average number of antibiotic treatments children received in the first 5 years of life in 45 low- and middle-income countries (LMICs) using Demographic and Health Survey data. The 2-week point prevalence of fever, diarrhea, or cough and antibiotic treatment for these illnesses were estimated for ages 0–59 months and aggregated to estimate cumulative illness and antibiotic treatment for each country. We estimated treatment rates and contribution to total antibiotic use attributable to medical care, informal care, and self-medication.

Results
Forty-five countries contributed 438 140 child-observations. The proportion of illness episodes treated with antibiotics ranged from 10% (95% confidence interval [CI], 9%–12%]) in Niger to 72% (95% CI, 69%–75%) in Jordan. A mean of 42.7% (95% CI, 42.1%–43.3%) of febrile and 32.9% of nonfebrile (95% CI, 32.4%–33.5%) illness episodes received antibiotics. In their first 5 years, we estimate children received 18.5 antibiotic treatments on average (interquartile range [IQR], 11.6–24.6) in LMICs. Cumulative antibiotic exposure ranged from 3.7 treatments in Niger (95% CI, 2.8%–4.6%) to 38.6 treatments in the Democratic Republic of Congo (95% CI, 34.7%–42.4%). A median of 9.0% of antibiotic treatments was attributable to informal care (IQR, 5.9%–21.2%), and 16.9% to self-medication (IQR, 9.5%–26.2%).

Conclusions
Childhood antibiotic exposure is high in some LMICs, with considerable variability. While access to antibiotics for children is still not universal, important opportunities for reducing excess use also exist, particularly with respect to the informal care sector and self-medication.
Impact of the COVID-19 pandemic on contact tracing of patients with pulmonary tuberculosis
Authors: Godoy Pere , Parrón Ignasi , Barrabeig Irene , Caylà Joan A , Clotet Laura , Follia Núria , Carol Monica , Orcau Angels , Alsedà Miquel , Ferrús Gloria , Plans Pere , Jane Mireia , Millet Joan-Pau , Domínguez Angela ,   the Transmission of Tuberculosis in Catalonia (Spain) Working Group, Alsedà Miquel , Barrabeig Irene , Carol Monica , Caylà Joan , Clotet Laura , Domínguez Angela , Ferrús Gloria , Follia Núria , Godoy Pere , Jané Mireia , Minguell Sofia , Millet Joan Pau , Orcau Angels , Parrón Ignasi , Plans Pere , Ros Miriam , Sabater Maria , Sala Maria-Rosa , Toledo Diana 
Published: March 2022

Abstract

Background
The COVID-19 pandemic could have negative effects on tuberculosis (TB) control. The objective was to assess the impact of the pandemic in contact tracing, TB and latent tuberculosis infection (LTBI) in contacts of patients with pulmonary TB in Catalonia (Spain).

Methods
Contact tracing was carried out in cases of pulmonary TB detected during 14 months in the pre-pandemic period (1 January 2019 to 28 February 2020) and 14 months in the pandemic period (1 March 2020 to 30 April 2021). Contacts received the tuberculin skin test and/or interferon gamma release assay and it was determined whether they had TB or LTBI. Variables associated with TB or LTBI in contacts (study period and sociodemographic variables) were analyzed using adjusted odds ratio (aOR) and the 95% confidence intervals (95% CI).

Results
The pre-pandemic and pandemic periods showed, respectively: 503 and 255 pulmonary TB reported cases (reduction of 50.7%); and 4676 and 1687 contacts studied (reduction of 36.1%). In these periods, the proportion of TB cases among the contacts was 1.9% (84/4307) and 2.2% (30/1381) (P = 0.608); and the proportion of LTBI was 25.3% (1090/4307) and 29.2% (403/1381) (P &lt; 0.001). The pandemic period was associated to higher LTBI proportion (aOR = 1.3; 95% CI 1.1–1.5), taking into account the effect on LTBI of the other variables studied as sex, age, household contact and migrant status.

Conclusions
COVID-19 is affecting TB control due to less exhaustive TB and LTBI case detection. An increase in LTBI was observed during the pandemic period. Efforts should be made to improve detection of TB and LTBI among contacts of TB cases.
Response to leucine in Schizosaccharomyces pombe (fission yeast)
Authors: Ohtsuka Hokuto , Shimasaki Takafumi , Aiba Hirofumi 
Published: March 2022

Abstract
Leucine (Leu) is a branched-chain, essential amino acid in animals, including humans. Fungi, including the fission yeast Schizosaccharomyces pombe, can biosynthesize Leu, but deletion of any of the genes in this biosynthesis leads to Leu auxotrophy. In this yeast, although a mutation in the Leu biosynthetic pathway, leu1-32, is clearly inconvenient for this species, it has increased its usefulness as a model organism in laboratories worldwide. Leu auxotrophy produces intracellular responses and phenotypes different from those of the prototrophic strains, depending on the growing environment, which necessitates a certain degree of caution in the analysis and interpretation of the experimental results. Under amino acid starvation, the amino acid-auxotrophic yeast induces cellular responses, which are conserved in higher organisms without the ability of synthesizing amino acids. This mini-review focuses on the roles of Leu in S. pombe and discusses biosynthetic pathways, contribution to experimental convenience using a plasmid specific for Leu auxotrophic yeast, signaling pathways, and phenotypes caused by Leu starvation. An accurate understanding of the intracellular responses brought about by Leu auxotrophy can contribute to research in various fields using this model organism and to the understanding of intracellular responses in higher organisms that cannot synthesize Leu.
Patent protection and foreign R&D investment location choices: inventor mobility and policy convergence
Authors: Park Jinhyuck (Joseph) , Belderbos René 
Published: March 2022

Abstract
We suggest two boundary conditions for the positive role of patent protection in attracting inward foreign R&D investments. Patent protection is less effective in limiting the leakage of nonpatented knowledge through interfirm mobility of employees, and a gradual strengthening of patent protection worldwide diminishes its effect as countries get closer to the intellectual property rights (IPR) frontier. We provide evidence in an empirical analysis of 3393 multinational firms’ R&D location choices for 8015 greenfield R&D investments in 105 (potential) host countries, during 2003–2014. The relationship between R&D investment location choices and IPR protection is subject to declining marginal effects and negatively moderated by inventor mobility.
Adaptive regularization minimization algorithms with nonsmooth norms
Authors: Gratton S , Toint Ph L 
Published: March 2022

AbstractAn adaptive regularization algorithm (AR$1p$GN) for unconstrained nonlinear minimization is considered, which uses a model consisting of a Taylor expansion of arbitrary degree and regularization term involving a possibly nonsmooth norm. It is shown that the nonsmoothness of the norm does not affect the ${\mathcal {O}}(\epsilon _1^{-(p+1)/p})$ upper bound on evaluation complexity for finding first-order $\epsilon _1$-approximate minimizers using $p$ derivatives, and that this result does not hinge on the equivalence of norms in $\mathbb {R}^n$. It is also shown that, if $p=2$, the bound of ${\mathcal {O}}(\epsilon _2^{-3})$ evaluations for finding second-order $\epsilon _2$-approximate minimizers still holds for a variant of AR$1p$GN named AR2GN, despite the possibly nonsmooth nature of the regularization term. Moreover, the adaptation of the existing theory for handling the nonsmoothness results is an interesting modification of the subproblem termination rules, leading to an even more compact complexity analysis. In particular, it is shown when the Newton’s step is acceptable for an adaptive regularization method. The approximate minimization of quadratic polynomials regularized with nonsmooth norms is then discussed, and a new approximate second-order necessary optimality condition is derived for this case. A specialized algorithm is then proposed to enforce first- and second-order conditions that are strong enough to ensure the existence of a suitable step in AR$1p$GN (when $p=2$) and in AR2GN, and its iteration complexity is analyzed. A final section discusses how practical approximate curvature measures may lead to weaker second-order optimality guarantees.