bluuebunny/crossref_metadata_2025_split huggingface dataset:
Appendiceal neurofibroma in a patient with neurofibromatosis 1 and recurrent abdominal infections from ventriculoperitoneal shunt: a case report
Authors: Greenberg Anya L , Choi Won-Tak , Shaked Oren , Lee Anthony T , Berrahou Iman K , Jacques Line G , Lebares Carter C 
Published: March 2021

Abstract
Appendiceal neurofibromas are exceedingly rare, with neither experimental nor observational data to support evidence-based diagnosis or treatment. We describe the case of a 52-year-old woman with neurofibromatosis 1 (NF1) complicated by aqueductal stenosis and resultant hydrocephalus needing a ventriculoperitoneal shunt (VPS). She presented to the emergency department with abdominal pain and was found to have abnormalities in the right hemiabdomen on cross-section imaging, also a Staphylococcus epidermidis growth at the distal portion of the VPS. She was initially treated with two rounds of intravenous antibiotics and VPS removal without improvement. She ultimately underwent an appendectomy, which revealed pathologic evidence of NF. The appendectomy was key to ruling out malignancy, addressing further symptoms and preventing future malignant transformation. This case highlights the importance of including appendiceal neurofibromas in the differential diagnoses of abdominal pain in patients with NF1.
Understanding IIIF image usage based on server log analysis
Authors: Nishioka Chifumi , Nagasaki Kiyonori 
Published: March 2021

Abstract
Numerous libraries and museums have adopted the International Image Interoperability Framework (IIIF) that promotes mutual use of images among different institutions. In a IIIF-compatible digital collection, images are retrieved via IIIF Image API (Application Programming Interface), wherein regions of images can be specified. Thus, it is possible to investigate image usage in detail by examining the image regions that have been requested. In this article, we propose a log analysis method to measure the image usage and to visualize the analysis outcomes. Specifically, we employ the number of accesses to each pixel and visualize the results using heat maps. Given that a pixel is the smallest image unit, we apply herein a fine-grained analysis. The analysis method can be used in different applications including research tools in which researchers examine images and heat maps that show which regions of the images have already been examined by collaborators.
Epidemiology and Outcomes of Patients With Healthcare Facility–Onset Clostridioides difficile Infection
Authors: Eberly Matthew D , Susi Apryl , Adams Daniel J , Love Christopher S , Nylund Cade M 
Published: March 2021

ABSTRACT

Background
Clostridioides difficile infection (CDI) has become a rising public health threat. Our study aims to characterize the epidemiology and measure the attributable cost, length of stay, and in-hospital mortality of healthcare facility–onset Clostridioides difficile infection (HO-CDI) among patients in the U.S. Military Health System (MHS).

Methods
We performed a case–control and cross-sectional inpatient study of HO-CDI using MHS database billing records. Cases included those who were at least 18 years of age admitted to a military treatment facility with a stool sample positive for C. difficile obtained &gt;3 days after admission. Risk factors in the preceding year were identified. Patient case-mix adjusted outcomes including in-hospital mortality, length of stay, and hospitalization cost were evaluated by high-dimensional propensity score adjusted logistic regression.

Results
Among 474,518 admissions within the MHS from 2008 to 2015, we identified 591 (0.12%) patients with HO-CDI and found a significant increase in the trend of HO-CDI over the 7-year study period (P &lt; .001). Patients with HO-CDI had significantly higher hospitalization cost (attributable difference $66,044, P &lt; .001), prolonged hospital stay (attributable difference 12.4 days, P &lt; 0.001), and increased odds of in-hospital mortality (case-mix adjusted odds ratio 1.98; 95% CI, 1.43-2.74).

Conclusions
Healthcare facility–onset Clostridioides difficile infection is rising in patients within the MHS and is associated with increased length of stay, hospital costs, and in-hospital mortality. We identified a significantly increased burden of hospitalization among patients admitted with HO-CDI, highlighting the importance of infection control and antimicrobial stewardship initiatives aimed at decreasing the spread of this pathogen.
Clustering and halo abundances in early dark energy cosmological models
Authors: Klypin Anatoly , Poulin Vivian , Prada Francisco , Primack Joel , Kamionkowski Marc , Avila-Reese Vladimir , Rodriguez-Puebla Aldo , Behroozi Peter , Hellinger Doug , Smith Tristan L 
Published: March 2021

ABSTRACT
Cold Dark Matter with cosmological constant (ΛCDM) cosmological models with early dark energy (EDE) have been proposed to resolve tensions between the Hubble constant $H_0=100\, h$ km ṡ−1Ṁpc−1 measured locally, giving h ≈ 0.73, and H0 deduced from Planck cosmic microwave background (CMB) and other early-Universe measurements plus ΛCDM, giving h ≈ 0.67. EDE models do this by adding a scalar field that temporarily adds dark energy equal to about 10 per cent of the cosmological energy density at the end of the radiation-dominated era at redshift z ∼ 3500. Here, we compare linear and non-linear predictions of a Planck-normalized ΛCDM model including EDE giving h = 0.728 with those of standard Planck-normalized ΛCDM with h = 0.678. We find that non-linear evolution reduces the differences between power spectra of fluctuations at low redshifts. As a result, at z = 0 the halo mass functions on galactic scales are nearly the same, with differences only 1–2 per cent. However, the differences dramatically increase at high redshifts. The EDE model predicts 50 per cent more massive clusters at z = 1 and twice more galaxy-mass haloes at z = 4. Even greater increases in abundances of galaxy-mass haloes at higher redshifts may make it easier to reionize the universe with EDE. Predicted galaxy abundances and clustering will soon be tested by the James Webb Space Telescope (JWST) observations. Positions of baryonic acoustic oscillations (BAOs) and correlation functions differ by about 2 per cent between the models – an effect that is not washed out by non-linearities. Both standard ΛCDM and the EDE model studied here agree well with presently available acoustic-scale observations, but the Dark Energy Spectroscopic Instrument and Euclid measurements will provide stringent new tests.
Discovery of tidal debris stars from G1/Mayall II in M31
Authors: Gregg Michael D , West Michael J , Lemaux Brian C , Küpper Andreas H W 
Published: March 2021

ABSTRACT
The object Mayall II or G1 is the brightest globular cluster belonging to M31. Because of its extreme properties for a globular cluster, it has been speculated that G1 is the remnant nucleus of a dwarf galaxy that has been stripped by the tidal field of M31. Using the Keck DEIMOS spectrograph, we have conducted a survey for tidally stripped stars from G1, obtaining a sample of 351 stellar velocities over ∼320 sq. arcmin of sky centred on G1. 13 are within $25~{\, \rm km\, s^{-1}\, }$ of the systemic velocity of G1, and exhibit spatial and velocity correlations consistent with being dynamically associated with G1, and all 13 are well outside the tidal radius of the cluster. These 13 stars could be either (i) the remnants of an almost completely evaporated stellar envelope or (ii) G1 member stars lost through tidal interaction with M31. Estimates of the implied mass-loss rate based on our data suggest a short dissolution time-scale for G1, thus favouring the stellar envelope hypothesis for the origin of the tidal tail stars, or, at the very least, an advanced stage of cluster dissolution. In either case, G1 and by extension compact stellar systems in general have likely played a significant role in building the halo of M31.
Photometric observations of NGC 281: detection of 228 variable stars
Authors: Lata Sneh , Pandey A K , Pandey J C , Panwar Neelam , Paul Paulomi 
Published: March 2021

ABSTRACT
We identify 228 periodic variables in the region of young open cluster NGC 281 using time series photometry carried out from 1 m class ARIES telescopes, Nainital. The cluster membership of these identified variables is determined on the basis of colour–magnitude, two colour diagrams, and kinematic data. A total of 81 variable stars are found to be members of the cluster NGC 281. Of 81 variables, 30 and 51 are probable main-sequence and pre-main-sequence members, respectively. This study classifies main-sequence variable stars into different variability types according to their periods of variability, shape of light curves, and location in the Hertzsprung–Russell diagram. These identified main-sequence variables could be β Cep, δ Scuti, slowly pulsating B type, and new class variables. Among 51 pre-main-sequence variables, majority of them are weak line T Tauri stars. The remaining 147 variables could belong to the field population. The variability characteristics of the field population indicate that these variables could be RR Lyrae, δ Scuti, and binaries-type variables.
emerge: constraining merging probabilities and time-scales of close galaxy pairs
Authors: O’Leary Joseph A , Moster Benjamin P , Krämer Eva 
Published: March 2021

ABSTRACT
Theoretical models are vital for exploring the galaxy merger process, which plays a crucial role in the evolution of galaxies. Recent advances in modelling have placed tight constraints on the build-up of stellar material in galaxies across cosmic time. Despite these successes, extracting the merger rates from observable data remains a challenge. Differences in modelling techniques, combined with limited observational data, drive conflicting conclusions on the merging time-scales of close pairs. We employ an empirical model for galaxy formation that links galaxy properties to the growth of simulated dark matter haloes, along with mock light-cone galaxy catalogues, to probe the dependences of pair merging probabilities and merging time-scales. In this work, we demonstrate that the pair merging probabilities are best described by a logistic function and that mean merging time-scales can be well approximated by a linear relation in the projected separation and line of sight velocity difference in observed pairs. Together, our fitting formulas can accurately predict merger rates from galaxy pairs to at least z ∼ 4 under a wide variety of pair selection criteria. Additionally, we show that some commonly used pair selection criteria may not represent a suitable sample of galaxies to reproduce underlying merger rates. Finally, we conclude from our analysis that observation time-scales are primarily driven by dynamics and are not strongly impacted by the star formation properties of the component galaxies.
Understanding the Origins of Loss of Protein Function by Analyzing the Effects of Thousands of Variants on Activity and Abundance
Authors: Cagiada Matteo , Johansson Kristoffer E , Valanciute Audrone , Nielsen Sofie V , Hartmann-Petersen Rasmus , Yang Jun J , Fowler Douglas M , Stein Amelie , Lindorff-Larsen Kresten 
Published: March 2021

Abstract
Understanding and predicting how amino acid substitutions affect proteins are keys to our basic understanding of protein function and evolution. Amino acid changes may affect protein function in a number of ways including direct perturbations of activity or indirect effects on protein folding and stability. We have analyzed 6,749 experimentally determined variant effects from multiplexed assays on abundance and activity in two proteins (NUDT15 and PTEN) to quantify these effects and find that a third of the variants cause loss of function, and about half of loss-of-function variants also have low cellular abundance. We analyze the structural and mechanistic origins of loss of function and use the experimental data to find residues important for enzymatic activity. We performed computational analyses of protein stability and evolutionary conservation and show how we may predict positions where variants cause loss of activity or abundance. In this way, our results link thermodynamic stability and evolutionary conservation to experimental studies of different properties of protein fitness landscapes.
Exons and introns exhibit transcriptional strand asymmetry of dinucleotide distribution, damage formation and DNA repair
Authors: Heilbrun Elisheva E , Merav May , Adar Sheera 
Published: March 2021

Abstract
Recent cancer sequencing efforts have uncovered asymmetry in DNA damage induced mutagenesis between the transcribed and non-transcribed strands of genes. Here, we investigate the major type of damage induced by ultraviolet (UV) radiation, the cyclobutane pyrimidine dimers (CPDs), which are formed primarily in TT dinucleotides. We reveal that a transcriptional asymmetry already exists at the level of TT dinucleotide frequency and therefore also in CPD damage formation. This asymmetry is conserved in vertebrates and invertebrates and is completely reversed between introns and exons. We show the asymmetry in introns is linked to the transcription process itself, and is also found in enhancer elements. In contrast, the asymmetry in exons is not correlated to transcription, and is associated with codon usage preferences. Reanalysis of nucleotide excision repair, normalizing repair to the underlying TT frequencies, we show repair of CPDs is more efficient in exons compared to introns, contributing to the maintenance and integrity of coding regions. Our results highlight the importance of considering the primary sequence of the DNA in determining DNA damage sensitivity and mutagenic potential.
Maize decrease in DNA methylation 1 targets RNA-directed DNA methylation on active chromatin
Authors: Long Jincheng , Liu Jinghan , Xia Aiai , Springer Nathan M. , He Yan 
Published: March 2021

Abstract
DNA methylation plays vital roles in repressing transposable element activity and regulating gene expression. The chromatin-remodeling factor Decrease in DNA methylation 1 (DDM1) is crucial for maintaining DNA methylation across diverse plant species, and is required for RNA-directed DNA methylation (RdDM) to maintain mCHH islands in maize (Zea mays). However, the mechanisms by which DDM1 is involved in RdDM are not well understood. In this work, we used chromatin immunoprecipitation coupled with high-throughput sequencing to ascertain the genome-wide occupancy of ZmDDM1 in the maize genome. The results revealed that ZmDDM1 recognized an 8-bp-long GC-rich degenerate DNA sequence motif, which is enriched in transcription start sites and other euchromatic regions. Meanwhile, 24-nucleotide siRNAs and CHH methylation were delineated at the edge of ZmDDM1-occupied sites. ZmDDM1 co-purified with Argonaute 4 (ZmAGO4) proteins, providing further evidence that ZmDDM1 is a component of RdDM complexes in planta. Consistent with this, the vast majority of ZmDDM1-targeted regions co-localized with ZmAGO4-bound genomic sites. Overall, our results suggest a model that ZmDDM1 may be recruited to euchromatic regions via recognition of a GC-rich motif, thereby remodeling chromatin to provide access for RdDM activities in maize.
Patterns of Childcare Use for Young Children within Women’s Work/Family Pathways: A Group-Based Multi-Trajectory Modeling Approach
Authors: Shattuck Rachel M 
Published: March 2021

Abstract
Approximately 65 percent of US mothers with children aged six and under are employed. Although their ability to maintain employment generally depends on nonparental childcare, childcare has been relatively little-studied as it relates to mothers’ employment in the United States. With the NLSY97 (N = 2,108), I track childcare use, employment, second births, and coresidential partnership among women who are initially employed following a first birth. I use Group-Based Multi-Trajectory Modeling to identify the five most common pathways by which women combine and sequence these behaviors. I investigate the sociodemographic characteristics predicting each pathway. Three groups of women maintain high or moderate employment and make high use of childcare while their children are young: highly employed, partnered mothers who have a second birth (closely aligned with the privileged “having it all” norm); highly employed mothers of one child, about half of whom are single; and moderately employed (some full-time, some part-time) primarily single mothers who have a second birth. Two groups of women make less use of childcare when initially employed: partnered mothers who have a second birth and largely exit the labor force (closely aligned with the privileged “stay-at-home-mom” norm), and primarily single mothers with some part-time employment and one child. White and Hispanic women, and those with Bachelor’s degrees, are most likely to mirror the “having it all” norm. White women and those with Bachelor’s degrees are most likely to mirror the “stay-at-home mom” norm. I argue that improved access to adequate, affordable childcare could help to offset gender, socioeconomic, and race/ethnic employment disparities in the United States.
The Mental Health Consequences of Vicarious Adolescent Police Exposure
Authors: Turney Kristin 
Published: March 2021

AbstractPolice stops are a pervasive form of criminal justice contact among adolescents, particularly adolescents of color, that have adverse repercussions for mental health. Yet, the mental health consequences of adolescent police stops likely proliferate to parents of adolescents exposed to this form of criminal justice contact. In this article, I conceptualize adolescent police stops as a stressor, drawing on the stress process perspective to examine how and under what conditions this form of criminal justice contact damages the mental health of adolescents’ mothers. The results, based on data from the Fragile Families and Child Wellbeing Study, suggest three conclusions. First, the mental health consequences of adolescent police stops proliferate, increasing the likelihood of depression and anxiety among adolescents’ mothers. These relationships persist across modeling strategies that adjust for observed confounders, including adolescent characteristics such as delinquency and substance use. Second, the relationship between adolescent police stops and mothers’ mental health is contingent, concentrated among mothers with prior exposure to the criminal justice system (either via themselves or their adolescents’ fathers). Third, mothers’ emotional support buffers the relationship between adolescent police stops and mothers’ mental health. Taken together, this research highlights the role of police exposure as a stressor that is experienced vicariously and that has contingent consequences and, accordingly, documents the expansive and proliferating repercussions of police contact. Given the concentration of police contact among marginalized adolescents, including adolescents of color, these findings highlight another way the criminal justice system exacerbates structural inequalities.
Brain reactivity to humorous films is affected by insomnia
Authors: Sanz-Arigita Ernesto , Daviaux Yannick , Joliot Marc , Dilharreguy Bixente , Micoulaud-Franchi Jean-Arthur , Bioulac Stéphanie , Taillard Jacques , Philip Pierre , Altena Ellemarije 
Published: March 2021

Abstract

Study objectives
Emotional reactivity to negative stimuli has been investigated in insomnia, but little is known about emotional reactivity to positive stimuli and its neural representation.

Methods
We used 3 Tesla functional magnetic resonance imaging (fMRI) to determine neural reactivity during the presentation of standardized short, 10- to 40-seconds, humorous films in patients with insomnia (n = 20, 18 females, aged 27.7 +/− 8.6 years) and age-matched individuals without insomnia (n = 20, 19 females, aged 26.7 +/− 7.0 years) and assessed humor ratings through a visual analog scale. Seed-based functional connectivity was analyzed for the left and right amygdalas (lAMYG and rAMYG, respectively) networks: group-level mixed-effects analysis (FLAME; FMRIB Software Library [FSL]) was used to compare amygdala connectivity maps between groups.

Results
fMRI seed-based analysis of the amygdala revealed stronger neural reactivity in patients with insomnia than in controls in several brain network clusters within the reward brain network, without humor rating differences between groups (p = 0.6). For lAMYG connectivity, cluster maxima were in the left caudate (Z = 3.88), left putamen (Z = 3.79), and left anterior cingulate gyrus (Z = 4.11), whereas for rAMYG connectivity, cluster maxima were in the left caudate (Z = 4.05), right insula (Z = 3.83), and left anterior cingulate gyrus (Z = 4.29). Cluster maxima of the rAMYG network were correlated with hyperarousal scores in patients with insomnia only.

Conclusions
The presentation of humorous films leads to increased brain activity in the neural reward network for patients with insomnia compared with controls, related to hyperarousal features in patients with insomnia, in the absence of humor rating group differences. These novel findings may benefit insomnia treatment interventions.

Clinical trial
The Sleepless Brain: Neuroimaging Support for a Differential Diagnosis of Insomnia (SOMNET). ClinicalTrials.gov identifier: NCT02821234; https://clinicaltrials.gov/ct2/show/NCT02821234.
Cyclic di‐GMP sensing histidine kinase PdtaS controls mycobacterial adaptation to carbon sources
Authors: Hariharan Vignesh Narayan , Yadav Rahul , Thakur Chandrani , Singh Albel , Gopinathan Renu , Singh Devendra Pratap , Sankhe Gaurav , Malhotra Vandana , Chandra Nagasuma , Bhatt Apoorva , Saini Deepak Kumar 
Published: March 2021

AbstractCell signaling relies on second messengers to transduce signals from the sensory apparatus to downstream signaling pathway components. In bacteria, one of the most important and ubiquitous second messenger is the small molecule cyclic diguanosine monophosphate (c‐di‐GMP). While the biosynthesis, degradation, and regulatory pathways controlled by c‐di‐GMP are well characterized, the mechanisms through which c‐di‐GMP controls these processes are not entirely understood. Herein we present the report of a c‐di‐GMP sensing sensor histidine kinase PdtaS (Rv3220c), which binds to c‐di‐GMP at submicromolar concentrations, subsequently perturbing signaling of the PdtaS‐PdtaR (Rv1626) two‐component system. Aided by biochemical analysis, genetics, molecular docking, FRET microscopy, and structural modelling, we have characterized the binding of c‐di‐GMP in the GAF domain of PdtaS. We show that a pdtaS knockout in Mycobacterium smegmatis is severely compromised in growth on amino acid deficient media and exhibits global transcriptional dysregulation. The perturbation of the c‐di‐GMP‐PdtaS‐PdtaR axis results in a cascade of cellular changes recorded by a multiparametric systems’ approach of transcriptomics, unbiased metabolomics, and lipid analyses.