bluuebunny/crossref_metadata_2025_split huggingface dataset:
Inferring dark matter substructure with astrometric lensing beyond the power spectrum
Authors: Mishra-Sharma Siddharth 
Published: January 2022

Abstract
Astrometry—the precise measurement of positions and motions of celestial objects—has emerged as a promising avenue for characterizing the dark matter population in our Galaxy. By leveraging recent advances in simulation-based inference and neural network architectures, we introduce a novel method to search for global dark matter-induced gravitational lensing signatures in astrometric datasets. Our method based on neural likelihood-ratio estimation shows significantly enhanced sensitivity to a cold dark matter population and more favorable scaling with measurement noise compared to existing approaches based on two-point correlation statistics. We demonstrate the real-world viability of our method by showing it to be robust to non-trivial modeled as well as unmodeled noise features expected in astrometric measurements. This establishes machine learning as a powerful tool for characterizing dark matter using astrometric data.
StainedGlass: interactive visualization of massive tandem repeat structures with identity heatmaps
Authors: Vollger Mitchell R , Kerpedjiev Peter , Phillippy Adam M , Eichler Evan E 
Published: January 2022

Abstract

Summary
The visualization and analysis of genomic repeats is typically accomplished using dot plots; however, the emergence of telomere-to-telomere assemblies with multi-megabase repeats requires new visualization strategies. Here, we introduce StainedGlass, which can generate publication-quality figures and interactive visualizations that depict the identity and orientation of multi-megabase tandem repeat structures at a genome-wide scale. The tool can rapidly reveal higher-order structures and improve the inference of evolutionary history for some of the most complex regions of genomes.

Availability and implementation
StainedGlass is implemented using Snakemake and available open source under the MIT license at https://mrvollger.github.io/StainedGlass/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Milk and hygiene in Eastern France: the ‘goutte de lait’ at Besançon and the ‘œuvre du bon lait’ at Bar-le-Duc (late nineteenth to early twentieth centuries)
Authors: Knittel Fabien 
Published: January 2022

Abstract—
Food security held a central place in the hygienist project to improve the quality of milk. While it may be difficult to grasp the question of milk and dairy products globally in hygienist discourse, this article proposes a focused study of two specific ‘œuvres de la goutte de lait’ (‘drop of milk’—the name given to specific social projects for milk quality) at Besançon and Bar-le-Duc in Eastern France. The ‘œuvre de la goutte de lait’ was an institution that sought to supply healthy milk to mothers who were unable to suckle their babies. This preoccupation with infant hygiene was allied to the development of pediatrics and childcare. Milk as a foodstuff was at the heart of the hygienist project of the turn of the twentieth century: on the one hand, it could carry tuberculosis, and was thus suspect; on the other, it provided an alternative to the problems of maternal breastfeeding. These projects helped contribute more broadly to the development of a municipal hygienics that was an essential characteristic of the emerging modern state in France.
The thermal structure of subduction zones predicted by plate cooling models with variable thermal properties
Authors: Morishige M 
Published: January 2022

SUMMARY
Previous modelling studies have investigated the effects of experimentally constrained thermal properties (i.e. thermal conductivity, specific heat and the thermal expansion coefficient) on the thermal structure of subduction zones. However, these studies have not carefully considered whether the assumed thermal structure of the slab before subduction is consistent with geophysical observations. This study investigates the effects of thermal properties on the thermal structure of the Tohoku subduction zone, northeast Japan, by using the slab temperature at the trench determined from plate cooling models. Three types of thermal properties were tested: constant, temperature-dependent and temperature- and lithology-dependent types. For each case, the parameters for the plate cooling models were inferred based on the observed surface heat flow and seafloor depth using Bayes’ theorem. It was found that the predicted temperature and location of phase boundaries in the slab, which are possibly related to intermediate-depth earthquakes, are similar for the three cases. This suggests that, in the Tohoku subduction zone, constant thermal properties can be used in modelling to examine phenomena related to slab dehydration. The depth uncertainties for isotherms in the oceanic plate and slab increase with temperature, and are about ±10 and ±20 km for the 600 and 1200 °C isotherms, respectively. When this uncertainty is considered, the location of the serpentinite-out boundary matches that of the lower plane of double seismic zone, suggesting that dehydration may be important in triggering intermediate-depth seismicity. However, the large uncertainty makes it difficult to discuss in detail the origins of intraplate earthquakes, the lithosphere–asthenosphere boundary, and the lower boundary of the slab in terms of temperature.
The anti-inflammatory mechanism of SAHA in acute pancreatitis through HDAC5/SLIT2/Akt/β-catenin axis
Authors: Tong Jinxue , Zhou Jiandang , Fang Min , Wang Gang , Fu Songbin , Sun Bei , Lv Jiachen 
Published: January 2022

Abstract
Acute pancreatitis (AP) is widely recognized to be an inflammation-related disease, in which HDAC was upregulated. The anti-inflammatory role of suberoylanilide hydroxamic acid (SAHA), a HDAC inhibitor, has been documented. In this context, this research was implemented to figure out whether SAHA manipulated inflammation in AP. Subsequent to induction of AP mouse model, HDAC5 expression was detected. The binding of HDAC5 and SLIT2 was detected by Co-Immunoprecipitation and Chromatin immunoprecipitation assays. SAHA treatment and gain- and loss-of-function approaches were used in AP mice and lipopolysaccharide (LPS)-induced pancreatic acinar cells. In mice, biochemical methods were implemented to measure activities of pancreatic lipase, trypsin, myeloperoxidase (MPO) and pancreatic edema, TUNEL staining to determine pancreatic cell apoptosis, and flow cytometry to assess the total number of leukocytes and neutrophils in pancreas. In pancreatic acinar cells, CCK-8 was performed to evaluate cell viability. HDAC5 exhibited overexpression in AP mice. Mechanical analysis showed that HDAC5 facilitated SLIT2 deacetylation to downregulate SLIT2, thus activating Akt/β-catenin pathway in pancreatic acinar cells. SAHA treatment, HDAC5 silencing or SLIT2 overexpression diminished inflammation in AP in vivo and in vitro. SAHA treatment, HDAC5 silencing or SLIT2 overexpression reduced activities of pancreatic lipase, trypsin, MPO, pancreatic edema and cell apoptosis in AP mice as well as elevated viability of LPS-induced pancreatic acinar cells. SAHA might exert anti-inflammatory effects in AP mice via HDAC5/SLIT2/Akt/β-catenin axis.
Conjoined twins after single blastocyst transfer: a case report including detailed time-lapse recording of the earliest embryogenesis, from zygote to expanded blastocyst
Authors: Grøndahl Marie Louise , Tharin Julie Elisabeth , Maroun Lisa Leth , Stener Jørgensen Finn 
Published: January 2022

ABSTRACT
Conjoined twins are estimated to occur in 1:50 000 pregnancies. Eighteen cases of pregnancies achieved by ART have been published of which three were achieved after single embryo transfer, allowing discussion of embryo characteristics. We report, to the best of our knowledge, the first case of parapagus conjoined twins after ART. Furthermore, this is the first report of conjoined twins with detailed morphokinetics of the earliest embryogenesis from zygote to expanded and hatched blastocyst stage. The case zygote had three refractile bodies, which were all allocated to one blastomere at first cleavage following an asynchronous pronuclei fading. Within 2 h, this blastomere cleaved to four and fragmented. The remaining blastomere cleaved symmetrically and regularly and a blastocyst (score: 4AB) was vitrified 120 h after IVF. Pregnancy was achieved following a frozen-thawed single blastocyst transfer. The etiopathogenetic mechanism of the origin of conjoined twins is unknown and several hypotheses exist. The morphokinetics in the present case and morphology of other reported cases will be discussed in this context.
Monophosphoryl Lipid A Tolerance Against Chronic Stress-Induced Depression-Like Behaviors in Mice
Authors: Li Fu , Lu Xu , Ma Yaoying , Gu Yue , Ye Ting , Huang Chao 
Published: January 2022

Abstract

Backgrounds
Our recent studies reported that a single injection with lipopolysaccharide (LPS) before stress exposure prevents depression-like behaviors in stressed mice. Monophosphoryl lipid A (MPL) is a derivative of LPS that lacks the undesirable properties of LPS. We hypothesize that MPL can exert a prophylactic effect on depression.

Methods
The experimental mice were pre-injected with MPL before stress exposure. Depression in mice was induced through chronic social defeat stress (CSDS). Behavioral tests were conducted to identify depression-like behaviors. Real-time polymerase chain reaction and biochemical assays were performed to examine the gene and protein expression levels of pro-inflammatory cytokines.

Results
A single MPL injection 1 day before stress exposure at the dosages of 400, 800, and 1600 μg/kg but not 200 μg/kg prevented CSDS-induced depression-like behaviors in mice. This effect of MPL, however, vanished with the extension of the interval time between drug injection and stress exposure from 1 day or 5 days to 10 days, which was rescued by a second MPL injection 10 days after the first MPL injection or by a 4× MPL injection 10 days before stress exposure. A single MPL injection (800 μg/kg) before stress exposure prevented CSDS-induced increases in the gene expression levels of pro-inflammatory cytokines in the hippocampus and prefrontal cortex. Pre-inhibiting the innate immune stimulation by minocycline pretreatment (40 mg/kg) abrogated the preventive effect of MPL on CSDS-induced depression-like behaviors and neuroinflammatory responses in animal brains.

Conclusions
MPL, through innate immune stimulation, prevents stress-induced depression-like behaviors in mice by preventing neuroinflammatory responses.
Coordination in practice or performance? The political economy of refugee aid coordination in Jordan
Authors: Dhingra Reva 
Published: January 2022

Abstract
Political economy literature on the incentives of international actors during humanitarian crises has cast international aid coordination inefficiencies during humanitarian crises as a product of vertical principal–agent problems with informational asymmetries, divergent interests, and inter-agent competition. However, horizontal coordination between international actors represents an important and understudied dimension of the political economy of international aid during refugee responses. Horizontal coordination structures, while offering a potential solution to the principal–agent problem of humanitarian responses, can either result in coordination in practice or coordination in performance. I argue that the incentives of coordinating actors, the level of donor monitoring, and the risk of elimination of some organizations or material opportunities as a result of effective coordination all factor into international organization and international non-governmental organization coordination behaviour. I examine the relationships between stakeholders during the Syrian refugee response in Jordan and the differential take-up of coordination technologies to test my theory with policy implications.
Characterization of Long-range Aeromedical Transport and Its Relationship to the Development of Traumatic Extremity Compartment Syndrome: A 7-year, Retrospective Study
Authors: Maddry Joseph K , Mora Alejandra G , Perez Crystal A , Reeves Lauren K , Paciocco Joni A , Clemons Melissa A , Sheean Andrew , Kester Nurani M , Bebarta Vikhyat S 
Published: January 2022

ABSTRACT

Background
Military aeromedical transport evacuates critically injured patients are for definitive care, including patients with or at risk for developing traumatic compartment syndrome of the extremities (tCSoE). Compartment pressure changes of the extremities have not been determined to be associated with factors inherent to aeromedical transport in animal models, but the influence of aeromedical evacuation (AE) transport on the timing of tCSoE development has not been studied in humans. Using a registry-based methodology, this study sought to characterize the temporal features of lower extremity compartment syndrome relative to the timing of transcontinental AE. With this approach, this study aims to inform practice in guidelines relating to the timing and possible effects of long-distance AE and the development of lower extremity compartment syndrome. Using patient care records, we sought to characterize the temporal features of tCSoE diagnosis relative to long-range aeromedical transport. In doing so, we aim to inform practice in guidelines relating to the timing and risks of long-range AE and postulate whether there is an ideal time to transport patients who are at risk for or with tCSoE.

Methods
We performed a retrospective record review of patients with a diagnosis of tCSoE who were evacuated out of theater from January 2007 to May 2014 via aeromedical transport. Data abstractors collected flight information, laboratory values, vital signs, procedures, in-flight assessments, and outcomes. We used the duration of time from injury to arrival at Landstuhl Regional Medical Center (LRMC) to represent time to transport. We compared groups based on time of tCSoE (inclusive of upper and lower extremity) diagnosis relative to injury day and time of transport (preflight versus postflight). We used descriptive statistics and multivariable regression models to determine the associations between time to transport, time to tCSoE diagnosis, and outcomes.

Results
Within our study window, 238 patients had documentation of tCSoE. We found that 47% of patients with tCSoE were diagnosed preflight and 53% were diagnosed postflight. Over 90% in both groups developed tCSoE within 48 hours of injury; the time to diagnosis was similar for casualties diagnosed pre- and postflight (P = .65). There was no association between time to arrival at LRMC and day of tCSoE diagnosis (risk ratio, 1.06; 95% CI, 0.96-1.16).

Conclusion
The timing of tCSoE diagnosis is not associated with the timing of transport; therefore, AE likely does not influence the development of tCSoE.
Different modes of spacer acquisition by the Staphylococcus epidermidis type III-A CRISPR-Cas system
Authors: Aviram Naama , Thornal Ashley N , Zeevi David , Marraffini Luciano A 
Published: January 2022

Abstract
CRISPR-Cas systems provide prokaryotic organisms with an adaptive defense mechanism that acquires immunological memories of infections. This is accomplished by integration of short fragments from the genome of invaders such as phages and plasmids, called ‘spacers’, into the CRISPR locus of the host. Depending on their genetic composition, CRISPR-Cas systems can be classified into six types, I-VI, however spacer acquisition has been extensively studied only in type I and II systems. Here, we used an inducible spacer acquisition assay to study this process in the type III-A CRISPR-Cas system of Staphylococcus epidermidis, in the absence of phage selection. Similarly to type I and II spacer acquisition, this type III system uses Cas1 and Cas2 to preferentially integrate spacers from the chromosomal terminus and free dsDNA ends produced after DNA breaks, in a manner that is enhanced by the AddAB DNA repair complex. Surprisingly, a different mode of spacer acquisition from rRNA and tRNA loci, which spans only the transcribed sequences of these genes and is not enhanced by AddAB, was also detected. Therefore, our findings reveal both common mechanistic principles that may be conserved in all CRISPR-Cas systems, as well as unique and intriguing features of type III spacer acquisition.
Elongation factor TFIIS is essential for heat stress adaptation in plants
Authors: Szádeczky-Kardoss István , Szaker Henrik Mihály , Verma Radhika , Darkó Éva , Pettkó-Szandtner Aladár , Silhavy Dániel , Csorba Tibor 
Published: January 2022

Abstract
Elongation factor TFIIS (transcription factor IIS) is structurally and biochemically probably the best characterized elongation cofactor of RNA polymerase II. However, little is known about TFIIS regulation or its roles during stress responses. Here, we show that, although TFIIS seems unnecessary under optimal conditions in Arabidopsis, its absence renders plants supersensitive to heat; tfIIs mutants die even when exposed to sublethal high temperature. TFIIS activity is required for thermal adaptation throughout the whole life cycle of plants, ensuring both survival and reproductive success. By employing a transcriptome analysis, we unravel that the absence of TFIIS makes transcriptional reprogramming sluggish, and affects expression and alternative splicing pattern of hundreds of heat-regulated transcripts. Transcriptome changes indirectly cause proteotoxic stress and deterioration of cellular pathways, including photosynthesis, which finally leads to lethality. Contrary to expectations of being constantly present to support transcription, we show that TFIIS is dynamically regulated. TFIIS accumulation during heat occurs in evolutionary distant species, including the unicellular alga Chlamydomonas reinhardtii, dicot Brassica napus and monocot Hordeum vulgare, suggesting that the vital role of TFIIS in stress adaptation of plants is conserved.
Differentiating perinatal Insomnia Disorder and sleep disruption: a longitudinal study from pregnancy to 2 years postpartum
Authors: Quin Nina , Lee Jin Joo , Pinnington Donna M , Newman Louise , Manber Rachel , Bei Bei 
Published: January 2022

AbstractStudy ObjectivesInsomnia Disorder diagnoses require persistent sleep complaints despite “adequate sleep opportunity.” Significant Perinatal Sleep Disruption makes this diagnosis challenging. This longitudinal study distinguished between Insomnia Disorder and Perinatal Sleep Disruption and their sleep and mental health correlates.MethodsOne hundred sixty-three nulliparous females (age M ± SD = 33.35 ± 3.42) participating in a randomized controlled trial repeated the Insomnia Disorder module of the Duke Structured Interview for Sleep Disorders and Patient-Reported Outcome Measurement Information System measures for sleep and mental health at 30- and 35-weeks’ gestation, and 1.5, 3, 6, 12, and 24 months postpartum (944 interviews, 1009 questionnaires completed). We compared clinical features when Diagnostic and Statistical Manual of Mental Disorders (DSM-5) Insomnia Disorder criteria (without the Duration criterion) were: (1) met (Insomnia Disorder), (2) not met only because of the sleep opportunity criteria (Perinatal Sleep Disruption), and (3) not met due to other criteria (Low Complaint).ResultsProportions of Insomnia Disorder were 16.0% and 19.8% during early and late third trimester, and ranged 5.3%–11.7% postpartum. If the sleep opportunity criteria were not considered, rates of Insomnia would be 2–4 times higher (21.4%–40.4%) across time-points. Mixed-effects models adjusting for covariates showed that compared to Low Complaint, both Insomnia Disorder and Perinatal Sleep Disruption scored significantly higher on insomnia and sleep disturbance scales, sleep effort, and sleep-related impairments (p values &lt; .01), but depression and anxiety were comparable (p values &gt; .12).ConclusionAssessing sleep complaints without considering sleep opportunities can result in over-diagnosis of Insomnia Disorder in the perinatal periods. Insomnia Disorder and Perinatal Sleep Disruption were both associated with adverse sleep and mood outcomes, and need to be carefully differentiated and appropriately addressed.Clinical Trial Registration: The SEED Project (Sleep, Eat, Emotions, and Development): A randomized controlled pilot study of a perinatal sleep intervention on sleep and wellbeing in mothers and infants. https://www.anzctr.org.au/Trial/Registration/TrialReview.aspx?id=371634, Australian New Zealand Clinical Trials Registry: ACTRN12616001462471.
Social Disharmony and Racial Injustice: W. E. B. Du Bois’s Theories on Crime
Authors: Werth S Rose 
Published: January 2022

Abstract
Although W. E. B. Du Bois addresses crime in Black communities in many of his writings, he is rarely recognized as having a cohesive theory on crime, and his work is often conflated with Shaw and McKay’s social disorganization theory. While both social disorganization and Du Bois’s theories pushed sociology and criminology away from pseudo-biological explanations of crime to the social environment, the Chicago School analyzed how social control broke down within neighborhoods, while Du Bois analyzed how racist social and economic exclusion of Black communities led to crime. Du Bois’s criminological theories of social disharmony and racial injustice also consider the social construction of crime and the criminalization of Blackness where social disorganization does not. Focusing on the relations of racial exclusion led Du Bois to propose solutions to crime that focus on mechanisms of oppression and economic injustice across various levels of society. This approach differs widely from community-level interventions driven by social disorganization theory, which focus on improving informal social control within neighborhoods. Du Bois's theories on crime and the social environment provide an analytic lens for sociologists to link the social organization within communities to the social organization across communities.
Clinical Profile and Short-Term Outcome of SARS-CoV-2-Infected Neonates from a Government Medical College in West Bengal, India
Authors: Banerjee Mukut , Pal Jonaki , Mondal Tanushree , Ghosh Taraknath , Nayek Kaustav 
Published: January 2022

Abstract

Introduction
Severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has led to a terrifying global pandemic. The presentations in neonates are varied with less case severity compared to adults.

Aim
To describe the clinical and laboratory features and outcomes of neonates admitted with SARS-CoV-2 infection during the second surge of COVID-19 pandemic in a Government Medical College, West Bengal, India.

Materials and Methods
It is a hospital-based observational cross-sectional study conducted in the newborn unit of Burdwan Medical College and Hospital between 1 April 2021 and 31 July 2021 including all SARS-CoV-2 Real time RT-PCR (Reverse transcriptase polymerase chain reaction) positive neonates. The demographic, clinical and laboratory characteristics of all the neonates and their outcomes were documented and analysed.

Results
Twenty-two neonates were found to be SARS-CoV-2 RT-PCR positive out of which 9 (40.9%) were found to be asymptomatic and 6 (27.27%) required neonatal intensive care unit admissions. Among the symptomatic neonates, most common presentations were respiratory distress (40.9%) and gastrointestinal manifestations (40.9%). Eight (36.36%) neonates required respiratory support. Three (13.6%) neonates had pneumonia of which one had right middle lobe collapse. Laboratory parameters were nonspecific except for the two (9%) cases of multisystem inflammatory syndrome in neonates. High-resolution computed tomography findings in two cases were suggestive of SARS-CoV-2 infection-induced changes. Two (9%) neonates died of which one was likely due to SARS-CoV-2 infection.

Conclusion
Neonates with SARS-CoV-2 infection are mostly asymptomatic. However, clinicians must be vigilant as atypical presentations such as consolidation, collapse, meningitis or multisystem inflammatory syndrome may occur.