bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pooled testing of sputum with Xpert MTB/RIF and Xpert Ultra during tuberculosis active case finding campaigns in Lao People’s Democratic Republic
Authors: Iem Vibol , Chittamany Phonenaly , Suthepmany Sakhone , Siphanthong Souvimone , Siphanthong Phitsada , Somphavong Silaphet , Kontogianni Konstantina , Dodd James , Khan Jahangir AM , Dominguez Jose , Wingfield Tom , Creswell Jacob , Cuevas Luis E 
Published: February 2022

IntroductionActive case finding (ACF) of individuals with tuberculosis (TB) is a key intervention to find the 30% of people missed every year. However, ACF requires screening large numbers of individuals who have a low probability of positive results, typically <5%, which makes using the recommended molecular tests expensive.MethodsWe conducted two ACF surveys (in 2020 and 2021) in high TB burden areas of Lao PDR. Participants were screened for TB symptoms and received a chest X-ray. Sputum samples of four consecutive individuals were pooled and tested with Xpert Mycobacterium tuberculosis (MTB)/rifampicin (RIF) (Xpert-MTB/RIF) (2020) or Xpert-Ultra (2021). The agreement of the individual and pooled samples was compared and the reasons for discrepant results and potential cartridge savings were assessed.ResultsEach survey included 436 participants, which were tested in 109 pools. In the Xpert-MTB/RIF survey, 25 (sensitivity 89%, 95% CI 72.8% to 96.3%) of 28 pools containing MTB-positive samples tested positive and 81 pools containing only MTB-negative samples tested negative (specificity 100%, 95% CI 95.5% to 100%). In the Xpert-Ultra survey, all 32 (sensitivity 100%, 95% CI 89.3% to 100%) pools containing MTB-positive samples tested positive and all 77 (specificity 100%, 95% CI 95.3% to 100%) containing only MTB-negative samples tested negative. Pooling with Xpert-MTB/RIF and Xpert-Ultra saved 52% and 46% (227/436 and 199/436, respectively) of cartridge costs alone.ConclusionTesting single and pooled specimens had a high level of agreement, with complete concordance when using Xpert-Ultra. Pooling samples could generate significant cartridge savings during ACF campaigns.
Prevalence of suspected child abuse in children with constipation: a case–control study
Authors: Vriesman Mana H , Vrolijk- Bosschaart Thekla F , Lindauer Ramón J L , van der Lee Johanna H , Brilleslijper-Kater Sonja , Teeuw Arianne H , Benninga Marc A 
Published: February 2022

BackgroundA possible association between child abuse and neglect (CAN) and functional constipation (FC) has been described in adults, however, limited data are available in children. Our objective was to determine the prevalence of suspected CAN in children with FC as compared with their healthy peers.MethodsA case–control study was carried out in children aged 3–10 years. Children with FC were recruited at a tertiary outpatient clinic, and healthy controls were recruited at schools. Parents were asked to fill out questionnaires about the history and behaviour of their child, children were inquired using a semistructured interview about experienced traumatic events and sexual knowledge. The interview was scored by two independent observers. The prevalence of suspected CAN was determined according to the questionnaires and interview.ResultsIn total, 228 children with FC and 153 healthy controls were included. Both groups were age and gender comparable (50% females, median age 6 years (not significant)). No significant difference in the prevalence of suspected CAN was found between children with FC and healthy controls (23.3% vs 30.1%, 95% CI 0.44 to 1.12, p=0.14), including a suspicion of sexual, emotional and physical abuse.ConclusionSuspected CAN was detected in both children with FC as in healthy controls. The possible association between CAN and FC in children could not be confirmed.
Temperature exposure in cod driven by changes in abundance
Authors: von Leesen Gotje , Bogstad Bjarte , Hjörleifsson Einar , Ninnemann Ulysses S. , Campana Steven E. 
Published: February 2022

Animals actively select the most suitable habitat in terms of fitness, much of which is mediated by temperature. We reconstructed population abundance, oxygen isotope and temperature chronologies for the Icelandic and the Northeast Arctic (NEA) cod (Gadus morhua) populations to determine if their temperature selectivity over the last 100 years was driven by rising water temperatures and (or) changes in abundance. Individual annual growth increments from immature and mature life history stages of cod collected in southern Iceland and the Lofoten area (Norway) were micromilled from adult otoliths and then assayed for stable oxygen isotopes (δ18Ootolith). Linear mixed effect models were used to identify and quantify the density-dependent temperature exposure of both cod populations. The results indicated that Icelandic cod migrated into warmer waters with increasing abundance (p < 0.05), whereas NEA cod moved into colder waters (p < 0.001). Our results suggest that thermal preferences and density-dependent effects can be used to forecast potential redistribution scenarios of fish as oceans warm.
A simple game and its dynamical richness for modeling synchronization in firefly-like oscillators
Authors: Ramírez-Ávila G. M. , Depickère S. , Deneubourg J. L. , Kurths J. 
Published: February 2022

AbstractSynchronization in pulse-coupled oscillators has been broadly studied under different perspectives. We present a game with simple rules to describe synchronization in such kinds of oscillators. This game, intended to describe easily how fireflies synchronize, constitutes a discrete model different from those based on maps, ordinary differential equations, or multi-agent systems. Our results on complete synchronization depend strongly on the used rules that we compare statistically. We also calculate the basins of attraction to quantify the importance of the initial conditions in reaching or not synchronization and the time intervals required for that.
Evaluation of Antioxidant, Cytotoxic, Anti-Inflammatory, Antiarthritic, Thrombolytic, and Anthelmintic Activity of Methanol Extract of Lepidagathis hyalina Nees Root
Authors: Islam Shafiqul , Fahad Fowzul Islam , Sultana Arifa , Sayem Syed Al Jawad , Roy Shawon Baran , Islam Mohammad Nazmul , Roy Arpita , Sayeed Mohammed Abu 
Published: February 2022

Lepidagathis hyalina Nees is an ethnomedicinally potential Asian herb, locally used to treat cardiovascular diseases and coughs. The study was intended to evaluate qualitative and quantitative investigation to ensure numerous pharmacological properties of methanol extracts of L. hyalina Ness root (MELHR). MELHR manifested strong radical scavenging activity in the reducing power and DPPH (1, 1-diphenyl-2-picrylhydrazyl) assays, and phenol and flavonoid in the quantitative assays. In the study of the thrombolytic assay, MELHR showed moderate explicit percentage of clot lysis (29.39 ± 1.40%) with moderate (135.35 µg/mL) toxic properties. The in vitro anti-inflammatory activity was evaluated by the inhibition of hypotonicity-induced RBC hemolysis, whereas the plant extract exhibited a significant (p

p

˂ 0.005) dose-dependent inhibition and the highest inhibition was found 55.01 ± 3.22% at 1000 µg/mL concentration. Moreover, the MELHR also showed significant (

p

< 0.005) dose-dependent potentiality on protein denaturation which is considered as antiarthritic activity, and the peak inhibition was found significant (71.97 ± 2.71%) at 1000 µg/mL concentration. MELHR also exhibited the dose-dependent and statistically significant anthelmintic potential on aquarium worm (Tubifex tubifex). So, the present investigation suggests that L. hyalina could be the best choice for the management of cardiovascular, inflammation, arthritis, and anthelmintic diseases. Further investigation should be necessary to determine behind the mechanism of bioactivity and therapeutic potential of this plant.
Effect of Different Dietary Selenium Sources on Growth Performance, Antioxidant Capacity, Gut Microbiota, and Molecular Responses in Pacific White Shrimp Litopenaeus vannamei
Authors: Yu Qiuran , Xia Chuyan , Han Fenglu , Xu Chang , Rombenso Artur , Qin Jian G. , Chen Liqiao , Li Erchao 
Published: February 2022

This study investigated the effect of different dietary selenium (Se) sources on the growth performance, antioxidant capacity, gut microbiota, and molecular responses of the Pacific white shrimp Litopenaeus vannamei. Four Se sources (sodium selenite, L-selenomethionine, selenium yeast, or Se nanoparticles) were added to purified diets to 0.4 mg Se/kg diet for shrimp (

1.60
±
0.14

g

). Each treatment was randomly assigned to 3 replicated tanks and 30 shrimp in each tank (500 L). After 8 weeks of breeding, L-selenomethionine and selenium yeast significantly increased weight gain compared with sodium selenite treatment, while sodium selenite significantly decreased the shrimp hepatosomatic index compared with the other groups. The L-selenomethionine significantly increased the superoxide dismutase and glutathione peroxidase activities in the hepatopancreas compared with the shrimp fed sodium selenite and decreased catalase activity and malondialdehyde content compared with other groups. The composition and β-diversity of gut microbiota were markedly changed in each group. The abundances of Rubrobacter and Rubritalea, Winogradskyella and Motilimonas, and Photobacterium in the gut microbiota were specially altered by L-selenomethionine, Se yeast, and Se nanoparticles, respectively. The sodium selenite group showed lower complexity of gut interspecies interactions. RNA-seq analysis showed that “arachidonic acid metabolism”-related genes were significantly enriched in the L-selenomethionine and Se yeast groups; “peroxisome” and “drug metabolism–other enzymes”-related genes were enriched in the Se nanoparticle group. Vibrio, Motilimonas, and Photobacterium were associated with amino acid and lipid metabolism. Pseudoalteromonas, Silicimonas, Roseovarius, and Halomonas inhibited the expression of glutathione peroxidase genes. These results suggested that organic Se, especially selenomethionine, is an effective feed supplement to promote growth and antioxidant capacity, maintain the health of gut microbiota, and promote the utilization of fatty acid and glutathione peroxidase genes in shrimp fed a 0.4 mg Se/kg diet.
Damaris (Acts 17:34) and an Aristocratic Family from Sparta
Authors: den Heijer Arco 
Published: February 2022

Abstract
This article surveys epigraphic evidence for Damaris, Damares and Damari(o)n to show that these are distinctively Spartan or Laconian names. It rejects the hypothesis that Damaris is a Lukan construction from Homeric δάµαρ (wife) or a typical name for a courtesan. Positively, it suggests that the woman named Damaris in Acts 17:34 could be imagined as a member of the Voluseni family, a prominent Spartan family connected with the Athenian elite. Finally, it examines the rhetorical force that a recognizably Spartan name could have in the narrative of Acts.
Gathered into One
Authors: Yoder Keith L. 
Published: February 2022

Abstract
This article reconsiders the two enigmatic scenes of Mary at Jesus’ feet in John 11 and 12. Previous scholarship has recognized ordered connections between John 11–12, and between John 12–13. Examination of John’s distinctive linkage between Mary and Judas uncovers an artistic network of figural cantilevers and triads that connect, or gather into one, scenes from all three chapters: Jesus’ Raising of Lazarus, Mary’s Anointing of Jesus, and the Foot Washing. This network architecture enables information transfer and implicit commentary between the three contexts, which in turn illuminates Jesus’ emotional anagnorisis with Mary on his way to Lazarus’ tomb, as well as Mary’s unconventional wiping of the ointment from his feet with her hair. Her opposition to Judas points up her alignment with Jesus, wherein he shares her tears and she shares his anointing. Finally, this network model provides an intelligible platform for the migration of key Synoptic elements away from John’s Anointing into his Lazarus story.
The Imperative Transformation beyond the Capitalism Pandemic
Authors: Liodakis George 
Published: February 2022

Abstract
This article starts with a brief exploration of the multiple crises currently facing global capitalism, encompassing over-accumulation crisis, an exacerbated environmental and ecological crisis, the evolving epidemiological crisis associated with the COVID-19 pandemic, and a dramatic cultural and ideological crisis. This manifold crisis is considered as a specific “capitalism pandemic.” The most important implications of this generalized crisis are subsequently analyzed, focusing in particular on globalization and its ecological implications associated more specifically with the COVID-19 pandemic. This general crisis raises the need of an imperative transformation beyond capitalism and towards socialism/communism. Finally, we briefly outline the main characteristics of communism as a specific form of social organization, and analyze the main aspects of a prolonged transformation period between capitalism and communism.
Encampment of Refugees in Kenya and the Failure of Economic Integration
Authors: Ngendakurio John Bosco 
Published: February 2022

Abstract
This article demonstrates how Kenya’s refugee encampment practice undermines refugees’ potential and fails local, regional, and global economy. It limits refugees’ integration and access to opportunities outside the refugee camps, rendering the benefits of globalization irrelevant. This article specifically looks at the impacts of the refugee encampment on participation, health, wellbeing, skills, and education. It also outlines the missed opportunities as a direct result of this practice. Highlighting these adverse impacts is a good start to advocate for more socially cohesive practices to help millions of refugees regain their freedom and achieve their potential – financially, socially, and politically.
Keepers of the Vineyard and the Fence around the Torah: The Vineyard Metaphor in Rabbinic Literature
Authors: Teugels Lieve M. 
Published: February 2022

Abstract
Rabbinic texts apply the metaphor of the vineyard to the Torah as well as to Israel. Conceptual Metaphor Theory allows us to explain the parallel use of the vineyard metaphor for the two target domains, Israel and the Torah. The conceptual metaphor of the vineyard includes such aspects as the fence, the vines and the wine. The generic metaphor something precious is a cultivated piece of land enables us to include related conceptual fields, such as a field of wheat, or another cultivated piece of land. By means of the principle of the “creation of similarity,” the Torah and Israel are linked in the rabbinic cultural world, using the notion of preciousness, segulah. The metaphor of the vineyard not only reflects, but also induces the similarity: conceived as vineyards, Israel and the Torah become precious in the minds of the people using and hearing or reading the metaphorical texts.
Still Allies? The Women Spinners’ Strike in Arzignano and Italian/British Tensions in Italy During the Immediate Post-First World War Period
Authors: Pozzato Paolo , Samuels Martin 
Published: February 2022

Abstract
Social, political and industrial upheavals swept across Europe after November 1918. These affected the victors too, with some social groups seeking to consolidate gains made during the war, while others attempted to restore pre-war norms. In Italy, industrial unrest in Vincenza added a distinctive gendered character. An overlooked factor is the role of British troops, who became involved with local women factory workers, and hence drawn into direct conflict with the Italian authorities as these attempted to suppress strikes. This confrontation, part of the wider falling out between the wartime allies, was only resolved through the hasty removal of British forces.
Cross-Tropopause Transport of Surface Pollutants during the Beijing 21 July Deep Convection Event
Authors: Chen Xi , Wu Luolin , Chen Xiaoyang , Zhang Yan , Guo Jianping , Safieddine Sarah , Huang Fuxiang , Wang Xuemei 
Published: February 2022

Abstract
Air transport from the troposphere to the stratosphere plays an important role in altering the vertical distribution of pollutants in the upper troposphere and lower stratosphere (UTLS). On 21 July 2012, Beijing was hit by an unprecedented extreme rainfall event. In the present study, the Community Multiscale Air Quality Modeling System (CMAQ) is used to simulate the change in vertical profiles of pollutants during this event. The integrated process rate (IPR) method was applied to quantify the relative contributions from different atmospheric processes to the changes in the vertical profile of pollutants and to estimate the vertical transport flux across the tropopause. The results revealed that, in the tropopause layer, during the torrential rainfall event, the values of O3 decreased by 35% and that of CO increased by 98%, while those of SO2, NO2, and PM2.5 increased slightly. Atmospheric transport was the main cause for the change in O3 values, contributing 32% of the net increase and 99% of the net decrease of O3. The calculations showed that the transport masses of CO, O3, PM2.5, NO2, and SO2 to the stratosphere by this deep convection in 25 h were 6.0 × 107, 2.4 × 107, 7.9 × 105, 2.2 × 105, and 2.7 × 103 kg, respectively, within the ∼300 km × 300 km domain. In the midlatitudes of the Northern Hemisphere, penetrating deep convective activities can transport boundary layer pollutants into the UTLS layer, which will have a significant impact on the climate of this layer.
Interictal plasma endothelin-1 levels do not change in individuals with episodic and chronic migraine
Authors: Kim Jiyoung , Park Chae Gyu , Chu Min Kyung 
Published: February 2022

Background Individuals with migraine present ictal elevation of endothelin-1 levels. Migraine can be subclassified into episodic migraine and chronic migraine. Apart from the inconsistent reports on interictal endothelin-1 levels, most studies did not distinguish between episodic migraine and chronic migraine. Methods We measured plasma endothelin-1 levels in participants with episodic migraine (n = 87), with chronic migraine (n = 88), and controls (n = 50). Results Interictal endothelin-1 levels were not significantly different among participants with episodic migraine, those with chronic migraine, and controls (pg/ml, median and interquartile range, 10.19 [7.76–13.69] vs. 9.25 [6.91–10.73] vs. 9.46 [7.00–14.19], p = 0.131). After excluding participants with fibromyalgia (n = 50) and medication-overuse headache (n = 21), endothelin-1 levels were still similar among groups (10.51 [7.96–14.10] vs. 9.24 [6.96–10.81] vs. 9.46 [7.00–14.19], p = 0.230). Endothelin-1 levels did not significantly differ among participants with migraine with aura, those with migraine without aura, and controls (9.36 [4.26–13.35] vs. 9.50 [7.23–13.02] vs. 9.46 [7.00–14.19], p = 0.975). There was no significant association of endothelin-1 with headache intensity (mild, 8.99 [8.99–8.99] vs. moderate, 8.71 [6.85–12.15] vs. severe, 9.55 [7.23–13.13], p = 0.517) or headache frequency per month (exponential and 95% confidence interval, 0.709 [0.296–1.698], p = 0.440) in participants with episodic migraine and chronic migraine. Conclusions Interictal plasma endothelin-1 level is an unlikely marker for episodic migraine and chronic migraine.
MutationalPatterns: the one stop shop for the analysis of mutational processes
Authors: Manders Freek , Brandsma Arianne M. , de Kanter Jurrian , Verheul Mark , Oka Rurika , van Roosmalen Markus J. , van der Roest Bastiaan , van Hoeck Arne , Cuppen Edwin , van Boxtel Ruben 
Published: February 2022

AbstractBackgroundThe collective of somatic mutations in a genome represents a record of mutational processes that have been operative in a cell. These processes can be investigated by extracting relevant mutational patterns from sequencing data.ResultsHere, we present the next version of MutationalPatterns, an R/Bioconductor package, which allows in-depth mutational analysis of catalogues of single and double base substitutions as well as small insertions and deletions. Major features of the package include the possibility to perform regional mutation spectra analyses and the possibility to detect strand asymmetry phenomena, such as lesion segregation. On top of this, the package also contains functions to determine how likely it is that a signature can cause damaging mutations (i.e., mutations that affect protein function). This updated package supports stricter signature refitting on known signatures in order to prevent overfitting. Using simulated mutation matrices containing varied signature contributions, we showed that reliable refitting can be achieved even when only 50 mutations are present per signature. Additionally, we incorporated bootstrapped signature refitting to assess the robustness of the signature analyses. Finally, we applied the package on genome mutation data of cell lines in which we deleted specific DNA repair processes and on large cancer datasets, to show how the package can be used to generate novel biological insights.ConclusionsThis novel version of MutationalPatterns allows for more comprehensive analyses and visualization of mutational patterns in order to study the underlying processes. Ultimately, in-depth mutational analyses may contribute to improved biological insights in mechanisms of mutation accumulation as well as aid cancer diagnostics. MutationalPatterns is freely available athttp://bioconductor.org/packages/MutationalPatterns.
Large-scale association study on daily weight gain in pigs reveals overlap of genetic factors for growth in humans
Authors: Cai Zexi , Christensen Ole Fredslund , Lund Mogens Sandø , Ostersen Tage , Sahana Goutam 
Published: February 2022

AbstractBackgroundImputation from genotyping array to whole-genome sequence variants using resequencing of representative reference populations enhances our ability to map genetic factors affecting complex phenotypes in livestock species. The accumulation of knowledge about gene function in human and laboratory animals can provide substantial advantage for genomic research in livestock species.ResultsIn this study, 201,388 pigs from three commercial Danish breeds genotyped with low to medium (8.5k to 70k) SNP arrays were imputed to whole genome sequence variants using a two-step approach. Both imputation steps achieved high accuracies, and in total this yielded 26,447,434 markers on 18 autosomes. The average estimated imputation accuracy of markers with minor allele frequency ≥ 0.05 was 0.94. To overcome the memory consumption of running genome-wide association study (GWAS) for each breed, we performed within-breed subpopulation GWAS then within-breed meta-analysis for average daily weight gain (ADG), followed by a multi-breed meta-analysis of GWAS summary statistics. We identified 15 quantitative trait loci (QTL). Our post-GWAS analysis strategy to prioritize of candidate genes including information like gene ontology, mammalian phenotype database, differential expression gene analysis of high and low feed efficiency pig and human GWAS catalog for height, obesity, and body mass index, we proposedMRAP2,LEPROT, PMAIP1,ENSSSCG00000036234, BMP2, ELFN1, LIG4andFAM155Aas the candidate genes with biological support for ADG in pigs.ConclusionOur post-GWAS analysis strategy helped to identify candidate genes not just by distance to the lead SNP but also by multiple sources of biological evidence. Besides, the identified QTL overlap with genes which are known for their association with human growth-related traits. The GWAS with this large data set showed the power to map the genetic factors associated with ADG in pigs and have added to our understanding of the genetics of growth across mammalian species.