bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multiphase magnetic fields in the galaxy NGC 3627
Authors: Liu Mingrui , Hu Yue , Lazarian A , Xu Siyao , Soida Marian 
Published: December 2022

ABSTRACT
Magnetic fields play an important role in the formation and evolution of a galaxy, but it is challenging to measure them by observation. Here, we study the Seyfert galaxy NGC 3627’s magnetic field orientations measured from the synchrotron polarization observed with the Very Large Array and from the Velocity Gradient Technique (VGT) using spectroscopic data. The latter employs the magnetohydrodynamical turbulence’s anisotropy to probe the magnetic fields. Being applied to the CO (2–1) and H α emission lines obtained from the PHANGS-ALMA and PHANGS-MUSE surveys, it reveals the magnetic field orientation globally consistent with the polarization. The agreement of the VGT-CO and polarization suggests that the magnetic fields associated with synchrotron emission also percolate through star-forming regions. The VGT-H α measurement reveals the magnetic fields in the warm ionized medium that permeates the disc and disc’s vicinity so that it exhibits less agreement with polarization. We find prominent radial fields measured by synchrotron polarization appear in the transition regions from the spiral arms to the galactic bar, while such morphology is less apparent in the VGT-CO and VGT-H α measured magnetic fields. The radial fields suggest that the magnetic torque is important in removing orbiting gas’ angular momentum. We notice that magnetic fields inferred from the dust polarization, VGT-CO, and synchrotron polarization are different in the east arm. We interpret this difference as arising from the fact that the three measurements are tracing the magnetic fields associated with pre-collision, the mixture of pre-collision and post-collision, and post-collision flows, respectively.
Endemism and Reemergence Potential of the Ipomovirus Sweet Potato Mild Mottle Virus (FamilyPotyviridae) in Eastern Africa: Half a Century of Mystery
Authors: Tugume Arthur K. , Mbanzibwa Deusdedith R. , Alicai Titus , Omongo Christopher A. , Maruthi M. N. 
Published: December 2022

Viruses have the ability to frequently colonize new hosts and ecological niches because of their inherently high genetic and evolutionary plasticity. However, a virus may emerge and remain of no or less economic importance until changes in viral or environmental factors dictate its epidemiological status. An example is sweet potato mild mottle virus (SPMMV), which was first reported in the 1970s on sweetpotato in eastern Africa. SPMMV has remained endemic in the region and poorly understood, yet accounting for 60 to 95% of losses, especially in mixed infections. Unlike other sweetpotato viruses which have global incidences, SPMMV has never been confirmed outside eastern Africa. This implicates the region as its center of origin but does not fully account for SPMMV's exclusive geographic delimitation to eastern Africa. Despite its importance, several mysteries and research gaps surround SPMMV, which decelerate efforts for effective virus disease management in sweetpotato. The aim of this review is to articulate research gaps, propose pivotal scientific directions, and stimulate knowledge generation for better management of virus diseases in sweetpotato. Vector-mediated transmission of SPMMV remains enigmatic. Here, we postulate testable hypotheses to explain SPMMV transmission. Comparisons between SPMMV and cassava brown streak ipomoviruses demonstrate epidemiological “hallmarks” for monitoring SPMMV. Evolutionary forces on SPMMV coupled with the virus' broad host range imply a “silent build up” of more fit variants in a changing climate, and this could explode into a worse disease conundrum. These information gaps need urgent filling to ease future management of virus disease emergences in sweetpotato.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .
Ligneous Conjunctivitis Secondary to Viral Conjunctivitis
Authors: Quintero-Estades Jose A. , Iacob Codrin E. , Donnenfeld Eric D. , Perry Henry D. 
Published: December 2022

Abstract
Ligneous conjunctivitis is a rare cause of chronic conjunctivitis that may be triggered by ocular insults such as trauma or infections. We present an interesting case of ligneous conjunctivitis caused by a viral infection that responded well to conservative management. Topical cyclosporine and heparin are a good treatment regimen that caused resolution of lesions and prevented recurrences.
Outbreak of KPC-producing Klebsiella pneumoniae at a Portuguese university hospital: Epidemiological characterization and containment measures
Authors: Peres David , Figueiredo Paulo , Andrade Paulo , Rocha-Pereira Nuno , Carvalho Cláudia , Ferraz Rita , Duro Raquel , Dias Arnaldo , Gomes Abel , Pereira Cláudia , Braga Gisélia , Pereira Virginia , Azevedo Lino , Moniz Edgar , Ribeiro Manuela , Ferreira Eugénia , Manageiro Vera , Teixeira José , Guimarães Tiago , Caniça Manuela , Alves Carlos 
Published: December 2022

Abstract

Background:
KPC-producing K pneumoniae (KPC-Kp) is a public health problem with important clinical and epidemiological implications. We describe an outbreak of KPC-Kp at vascular surgery and neurosurgery wards in a central hospital in Porto, Portugal.

Methods:
A case of KPC-Kp was considered to be a patient positive for KPC-Kp with strong epidemiological plausibility of having acquired this microorganism in the affected wards and/or with genetic relationship ≥92% between KPC-Kp isolates. Active surveillance cultures (ASCs) and real-time polymerase chain reaction were used for the detection of carbapenemase genes through rectal swab in a selected population. Molecular analysis was performed using pulsed-field gel electrophoresis at the National Reference Laboratory. Patient risk factors were collected from the electronic medical record system. Information regarding outbreak containment strategy was collected from the Infection Control Unit records.

Results:
Of the 16 cases, 11 (69%) were identified through active screening, representing 1.4% of the total 766 ASCs collected. The most frequent risk factors identified were previous admission (63%), antibiotic exposure in the past 6 months (50%), and immunodepression (44%). The length of stay until KPC-Kp detection was high (0–121 days, mean 35.6), as was the total length of stay (5–173 days, mean 56.6). Three patients (19%) were infected by KPC-Kp, 2 of whom died. One previously colonized patient died later because of KPC-Kp infection.

Conclusions:
Multifactorial strategy based on contact precautions (with patient and healthcare professional cohorts) and ASC, as well as Antibiotic Stewardship Program reinforcement, allowed to contain this KPC-Kp outbreak.
Capturing the distribution as it shifts: chile pepper (Capsicum annuumL.) domestication gradient meets geography
Authors: Martínez-Ainsworth NE , Scheppler H , Moreno-Letelier A , Bernau V , Kantar MB , Mercer KL , Jardón-Barbolla L 
Published: December 2022

AbstractAimDomestication is an ongoing well-described process. However, while many have studied the changes domestication causes in the genetic landscape, few have explored the way domestication changes the geographic landscape in which the plants exist. Therefore, the goal of this study was to understand how the domestication status changed the suitable geographic space of chile pepper in its center of origin.MethodsCapsicum annuumis a major crop species globally whose domestication center, Mexico, has been well studied. This provides a unique opportunity to explore the degree to which ranges of different domestication classes diverged and how these ranges might be altered by climate change. To this end, we created ecological niche models for four domestication classes (wild, semiwild, landrace, modern cultivar) based on present climate and future climate scenarios for 2050, 2070, and 2090.ResultsConsidering present environment, we found substantial overlap in the geographic niches of all the domestication gradient categories. Yet, there were also clear unique environmental and geographic aspects to the current ranges. Wild and commercial varieties were at ease in desert conditions as opposed to landraces. With projections into the future, habitat was lost asymmetrically, with wild, semiwild and landraces at far greater risk than modern cultivars. Further, we identified areas where future suitability overlap between landraces and wilds is expected to decouple.Main conclusionsWhile range expansion is widely associated with domestication, there is little support of a constant niche expansion (either in environmental or geographical space) throughout the domestication gradient. However, a shift to higher altitudes with cooler climate was identified for landraces. The clear differences in environmental adaptation, such as higher mean diurnal range and precipitation seasonality along the domestication gradient classes and their future potential range shifts show the need to increase conservation efforts, particularly to preserve landraces and semiwild genotypes.
Administration of amniotic fluid stem cell extracellular vesicles promotes development of fetal hypoplastic lungs by immunomodulating lung macrophages
Authors: Antounians Lina , Figueira Rebeca Lopes , Kukreja Bharti , Zani-Ruttenstock Elke , Khalaj Kasra , Montalva Louise , Doktor Fabian , Obed Mikal , Blundell Matisse , Wu Taiyi , Chan Cadia , Wagner Richard , Lacher Martin , Wilson Michael D. , Kalish Brian T. , Zani Augusto 
Published: December 2022

AbstractCongenital diaphragmatic hernia (CDH) is a devastating condition characterized by incomplete closure of the diaphragm and herniation of abdominal organs into the chest. As a result, fetuses have pulmonary hypoplasia, whose severity is the main determinant of poor outcome. The pathogenesis of pulmonary hypoplasia secondary to CDH is at least in part explained by lack or dysregulation of miRNAs that are known to regulate lung developmental processes. Herein, we report that intra-amniotic administration of extracellular vesicles derived from amniotic fluid stem cells (AFSC-EVs) rescues lung growth and maturation in a fetal rat model of CDH. To understand which fetal lung cells and biological pathways are affected by AFSC-EVs, we conducted whole lung single nucleus RNA-sequencing. We discovered that CDH lungs have a multilineage inflammatory signature with macrophage enrichment, and confirmed these findings in autopsy samples of lungs from human fetuses with CDH. Transcriptomic analysis of CDH fetal rat lungs also showed that AFSC-EV treatment reduced macrophage density and inflammation to normal levels. Analyzing the miRNAs contained in the AFSC-EV cargo with validated mRNA targets, we found that the downregulated genes in AFSC-EV treated CDH lungs were involved in inflammatory response and immune system processes. This study reports a single cell atlas of normal and hypoplastic CDH fetal rat lungs and provides evidence that AFSC-EVs restore lung development by addressing multiple pathophysiological aspects of CDH.One Sentence SummaryAmniotic fluid stem cell extracellular vesicle treatment for fetal lung macrophage modulation
DEFECTIVE KERNEL1 (DEK1) regulates cellulose synthesis and affects primary cell wall mechanics
Authors: Novaković Lazar , Yakubov Gleb E. , Ma Yingxuan , Bacic Antony , Blank Kerstin G. , Sampathkumar Arun , Johnson Kim L. 
Published: December 2022

ABSTRACTThe cell wall is one of the defining features of plants, controlling cell shape, regulating growth dynamics and hydraulic conductivity, as well as mediating plants interactions with both the external and internal environments. Here we report that a putative mechanosensitive Cys-protease DEFECTIVE KERNEL1 (DEK1) interacts with cell wall integrity (CWI) pathways and regulation of cellulose synthesis. Our results indicate that DEK1 is an important regulator of cellulose synthesis in epidermal tissue ofArabidopsis thalianacotyledons during early post-embryonic development. DEK1 is involved in regulation of cellulose synthase complexes (CSCs) by modifying their biosynthetic properties, possibly through interactions with various cellulose synthase regulatory proteins. Mechanical properties of the primary cell wall are altered inDEK1modulated lines supporting a role in maintenance of CWI. DEK1 affects stiffness of the cell wall and thickness of the cellulose microfibrils bundles in epidermal cell walls of cotyledons.
ACR TI-RADS®SCORE ULTRASOUND – PICTORIAL ESSAY OF ULTRASOUND / ELASTOSONOGRAPHY / ANATOMY / CYTOLOGY and HISTOLOGY
Authors: Andrade Luís Jesuíno De Oliveira , De Oliveira Luis Matos , Vinhaes Bittencourt Alcina Maria , De Carvalho Lourenço Letícia Góes , Matos De Oliveira Gabriela Correia 
Published: December 2022

ABSTRACTIntroductionThyroid Imaging Reporting and Data System (TI-RADS®) is a system for classifying thyroid nodules detected at ultrasonography, aiming at a descriptive standardization as well as to classify their risk of malignancy based on sonographic findings.AiumTo present a pictorial essay by composing anatomical, histological, ultrasound and elastography images of the TI-RADS®score.MethodUsing software for image composition, based on the ultrasound image of the various types of thyroid nodules, we adapt to the anatomical image, the elastosonography, and histological corresponding TI-RADS®and present a pictorial essay.ResultsThe correlation between the sonographic, elastography, anatomical, cytology and histological images corresponding to the TI-RADS®score are demonstrated.ConclusionUltrasonographic features, elastosonography, anatomical, and histological in evaluation of thyroid nodules can correlate with features TI-RADS® score.
Massively parallel characterization of insulator activity across the genome
Authors: Hong Clarice KY , Erickson Alyssa A , Li Jie , Federico Arnold J , Cohen Barak A 
Published: December 2022

AbstractInsulators arecis-regulatory sequences (CRSs) that can block enhancers from activating target promoters or act as barriers to block the spread of heterochromatin. Their name derives from their ability to ‘insulate’ transgenes from genomic position effects, an important function in gene therapy and biotechnology applications that require high levels of sustained transgene expression. In theory, flanking transgenes with insulators protects them from position effects, but in practice, efforts to insulate transgenes meet with mixed success because the contextual requirements for insulator function in the genome are not well understood. A key question is whether insulators are modular elements that can function anywhere in the genome or whether they are adapted to function only in certain genomic locations. To distinguish between these two possibilities we developed MPIRE (MassivelyParallel IntegratedRegulatoryElements) and used it to measure the effects of three insulators (A2, cHS4, ALOXE3) and their mutants at thousands of locations across the genome. Our results show that each insulator functions in only a small number of genomic locations, and that insulator function depends on the sequence motifs that comprise each insulator. All three insulators can block enhancers in the genome, but specificity arises because each insulator blocks enhancers that are bound by different sets of transcription factors. All three insulators can block enhancers in the genome, but only ALOXE3 can act as a heterochromatin barrier. We conclude that insulator function is highly context dependent and that MPIRE is a robust and systematic method for revealing the context dependencies of insulators and othercis-regulatory elements across the genome.
High SARS-CoV-2 seroprevalence in Lagos, Nigeria with robust antibody and cellular responses
Authors: Akanmu Sulaimon , Herrera Bobby Brooke , Chaplin Beth , Ogunsola Sade , Osibogun Akin , Onawoga Fatima , John-Olabode Sarah , Akase Iorhen E. , Nwosu Augustina , Hamel Donald J , Chang Charlotte A , Kanki Phyllis J 
Published: December 2022

AbstractBackgroundEarly evidence suggested that the impact of the COVID-19 pandemic was less severe in Africa compared to other parts of the world. However, more recent studies indicate higher SARS-CoV-2 infection and COVID-19 mortality rates on the continent than previously documented. Research is needed to better understand SARS-CoV-2 seroprevalence and immunity in Africa.MethodsOur collaboration with the Lagos State COVID-19 Taskforce, enabled secondary analyses of immune responses in healthcare workers (HCWs) and Oxford/AstraZeneca COVID-19 vaccine recipients from the general population across 5 local government areas (LGAs) in Lagos State, Nigeria. Western blots were used to simultaneously detect SARS-CoV-2 spike and nucleocapsid (N) antibodies and stimulation of peripheral blood mononuclear cells with N followed by an IFN-γ ELISA was used to examine T cell responses.FindingsAntibody data demonstrated high SARS-CoV-2 seroprevalence of 71.6% (96/134) in HCWs and 54.8% (63/115) in the general population. Antibodies directed to only SARS-CoV-2 N, suggesting pre-existing coronavirus immunity, were seen in 10.4% (14/134) of HCWs and 20.0% (23/115) of the general population. T cell data showed that IFN-γ responses against SARS-CoV-2 N were robust in detecting exposure to the virus, demonstrating 87.5% sensitivity and 92.3% specificity.InterpretationThese results have important implications for understanding the paradoxical high SARS-CoV-2 infection with low mortality rate in Africa as compared to other parts of the world, as well as for the development of T cell-based diagnostics and vaccines.FundingHarvard University, Motsepe Presidential Research Accelerator Fund for Africa
Development and validation of AI-based pre-screening of large bowel biopsies
Authors: Bilal Mohsin , Tsang Yee Wah , Ali Mahmoud , Graham Simon , Hero Emily , Wahab Noorul , Dodd Katherine , Sahota Harvir , Wu Shaobin , Lu Wenqi , Jahanifar Mostafa , Robinson Andrew , Azam Ayesha , Benes Ksenija , Nimir Mohammed , Hewitt Katherine , Bhalerao Abhir , Eldaly Hesham , Ahmed Raza Shan E , Gopalakrishnan Kishore , Minhas Fayyaz , Snead David , Rajpoot Nasir 
Published: December 2022

AbstractBackgroundHistopathological examination is a pivotal step in the diagnosis and treatment planning of many major diseases. With the aims of facilitating diagnostic decision-making and improving the use of pathologists’ time, we developed an AI-based pre-screening tool that analyses whole slide images (WSIs) of large bowel biopsies to identify normal, inflammatory, and neoplastic biopsies.MethodsTo learn the differential histological patterns from digitised WSIs of large bowel biopsy slides stained with Haematoxylin and Eosin (H&E), our proposed weakly supervised deep learning method uses only slide-level diagnostic labels and no detailed cell or region-level annotations. The proposed method was developed on an internal cohort of biopsy slides (n=5054) from a single laboratory labelled with corresponding diagnostic categories assigned by pathologists. Performance of the tool was evaluated on the internal development cohort (n=5054) in a cross-validation setting, and three external unseen cohorts (n=1536) for independent validation.FindingsThe proposed tool demonstrates high degree of accuracy to assist with the pre-screening of large bowel biopsies, being able to identify neoplastic biopsies (AUROC = 0·993), inflammatory biopsies (AUROC = 0·966) and all abnormal biopsies (AUROC = 0·979). On the three independent validation cohorts, it achieves AUROC values of 0·943, 0·958 and 0·964 for the detection of abnormal biopsies. Analysis of saliency maps confirms the representation of disease heterogeneity in model predictions and their association with relevant histological features. Interestingly, after examining diagnostic discrepancies between the proposed AI tool and original diagnostic labels, a panel of pathologists found that the proposed tool correctly identified a number of abnormal slides that had been initially reported as normal.InterpretationsThe proposed tool with its high sensitivity of detecting abnormal colorectal biopsies promises significant improvements in clinical workflow efficiency and assistance in diagnostic decision-making through pre-screening of normal biopsies.FundingInnovate UK on behalf of UK Research and Innovation.
Integrated fragmentomic profile and 5-Hydroxymethylcytosine of capture-based low-pass sequencing data enables pan-cancer detection via cfDNA
Authors: Zhang Zhidong , Pi Xuenan , Gao Chang , Zhang Jun , Xia Lin , Yan Xiaoqin , Hu Xinlei , Yan Ziyue , Zhang Shuxin , Wei Ailin , Guo Yuer , Liu Jingfeng , Li Ang , Liu Xiaolong , Zhang Wei , Liu Yanhui , Xie Dan 
Published: December 2022

AbstractUsing epigenetic markers and fragmentomics of cell-free DNA for cancer detection has been proven applicable. We further combine the two features and explore the diagnostic potential of the features on pan-cancer detection. We extracted cfDNA fragmentomic features from 191 whole-genome sequencing data and investigated them in 396 low-pass 5hmC sequencing data from four common cancer types and controls. We identified aberrant ultra-long fragments (220-500bp) of cancer samples in 5hmC sequencing data, both in size and coverage profile, and showed its dominant role in cancer prediction. Since cfDNA hydroxymethylation and fragmentomic markers can be detected simultaneously in low-pass 5hmC sequencing data, we built an integrated model including 63 features of both fragmentomic features and hydroxymethylation signatures for pan-cancer detection with high sensitivity and specificity (88.52% and 82.35%, respectively). We showed that fragmentomic information in 5hmC sequencing data is an ideal marker for cancer detection and that it shows high performance in low-pass sequencing data.
Unraveling the viral dark matter of the rumen microbiome with a new global virome database
Authors: Yan Ming , Pratama Akbar Adjie , Li Zongjun , Jiang Yu , Sullivan Matthew B. , Yu Zhongtang 
Published: December 2022

AbstractLike in the human gut and other environments, viruses are probably also diverse and modulate the microbiome (both population and function) in the rumen of ruminants, but it remains largely unknown. Here we mined 975 published rumen metagenomes for viral sequences, created the first rumen virome database (RVD), and perform ecogenomic meta-analyses of these data. This identified 397,180 species-level viral operational taxonomic units (vOTUs) and allowed for a 10-fold increase in classification rate of rumen viral sequences compared with other databases. Most of the classified vOTUs belong to the orderCaudovirales, but distinct from those in the human gut. Rumen viruses likely have ecosystem impacts as they were predicted to infect dominant fiber degraders and methane producers, and they carry diverse auxiliary metabolic genes and antibiotic resistance genes. Together, the RVD database and these findings provide a baseline framework for future research on how viruses may impact the rumen ecosystem.