bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validation of fetal microchimerism after pregnancy in the ovine using qPCR
Authors: Brown J Alison , Niland Erika S , Pierce Natalie L , Taylor J Bret 
Published: June 2021

Abstract
Fetal microchimerism has been detected in maternal tissues of humans and rodents during and after pregnancy. Studies focusing on fetal DNA transfer to maternal tissues in domestic animals are limited, especially in sheep. Fetal ram DNA was observed in the maternal circulation during pregnancy, but it is not known if this chimerism persists in soft tissues after parturition. The objectives of this exploratory study were to: 1) determine if male fetal DNA is detectable in soft tissues of mature ewes after parturition and if so, determine if detection repeatability differed with lifetime offspring sex ratio and 2) determine if male fetal DNA was present in soft tissues of yearling (primiparous) ewes shortly after parturition. Eight mature (open, non-lactating) and 8 yearling (primiparous, periparturient) Rambouillet ewes were used. Mature ewes (5- to 7-yr old) had given birth to primarily 82% males (n = 4) or 71% female (n = 4) over a lifetime. Yearling ewes had birthed either a singleton male (n = 4) or female (n = 4) lambs. DNA was extracted from 10 and 11 different soft tissues from the mature and yearling ewes, respectively. Real-time PCR (qPCR) was used to identify the presence of the SRY gene in each tissue sample. Male DNA was detected in the brain and liver from one mature open ewe that had given birth to two males and six females during her lifetime. In younger ewes that gave birth to a ram lamb, male DNA was observed in the thyroid of one ewe and the pancreas and brain of a second ewe. Male DNA was detected in the ovary of one ewe that had given birth to a female lamb. Based on these data, we suggest fetal microchimerism in soft maternal tissues is possible in sheep and may remain after pregnancy has ended. The detection repeatability of male fetal DNA was not associated with sex ratio of lifetime offspring. Male DNA was observed in maternal soft tissues collected shortly after parturition. The greater detection of fetal male DNA found in younger ewes shortly after parturition may be due to not having enough time for fetal DNA clearance to occur. Future studies are warranted to further study XY chimerism in maternal tissues of the ewe and its potential role in ovine physiology.
OsRAM2 Function in Lipid Biosynthesis Is Required for Arbuscular Mycorrhizal Symbiosis in Rice
Authors: Liu Ying-Na , Liu Cheng-Chen , Zhu An-Qi , Niu Ke-Xin , Guo Rui , Tian Li , Wu Ya-Nan , Sun Bo , Wang Bin 
Published: June 2021

Arbuscular mycorrhiza (AM) is a mutualistic symbiosis formed between most land plants and Glomeromycotina fungi. During symbiosis, plants provide organic carbon to fungi in exchange for mineral nutrients. Previous legume studies showed that the required for arbuscular mycorrhization2 (RAM2) gene is necessary for transferring lipids from plants to AM fungi (AMF) and is also likely to play a “signaling” role at the root surface. To further explore RAM2 functions in other plant lineages, in this study, two rice (Oryza sativa) genes, OsRAM2 and OsRAM2L, were identified as orthologs of legume RAM2. Examining their expression patterns during symbiosis revealed that only OsRAM2 was strongly upregulated upon AMF inoculation. CRISPR/Cas9 mutagenesis was then performed to obtain three Osram2 mutant lines (-1, -2, and -3). After inoculation by AMF Rhizophagus irregularis or Funneliformis mosseae, all of the mutant lines showed extremely low colonization rates and the rarely observed arbuscules were all defective, thus supporting a conserved “nutritional” role of RAM2 between monocot and dicot lineages. As for the signaling role, although the hyphopodia numbers formed by both AMF on Osram2 mutants were indeed reduced, their morphology showed no abnormality, with fungal hyphae invading roots successfully. Promoter activities further indicated that OsRAM2 was not expressed in epidermal cells below hyphopodia or outer cortical cells enclosing fungal hyphae but instead expressed exclusively in cortical cells containing arbuscules. Therefore, this suggested an indirect role of RAM2 rather than a direct involvement in determining the symbiosis signals at the root surface. [Formula: see text] The author(s) have dedicated the work to the public domain under the Creative Commons CC0 “No Rights Reserved” license by waiving all of his or her rights to the work worldwide under copyright law, including all related and neighboring rights, to the extent allowed by law, 2022.
Ligamentum-preserved/Temporary Preserved Minimally Invasive Transforaminal Lumbar Interbody Fusion for Lumbar Spondylolisthesis: Technical Note and 2-year Follow-up
Authors: Wang Lianlei , Li Hao , Zhao Yiwei , Yuan Suomao , Tian Yonghao , Liu Xinyu 
Published: June 2021

Study Design.
Prospective study.

Objective.
The aim of this study was to prospectively assess the clinical outcomes of modified minimally invasive transforaminal lumbar interbody fusion (MIS-TLIF) for the treatment of singlesegment lumbar spondylolisthesis.

Summary of Background Data.
MIS-TLIF is a safe and effective procedure in the treatment of lumbar degenerative disease. To avoid durotomy and nerve root injury, we modified the surgical order of MIS-TLIF such that the interbody fusion procedure was performed before the decompression procedure.

Methods.
One hundred thirty-nine patients with single-segment lumbar spondylolisthesis were separated into two groups. Sixty-seven patients underwent modified MIS-TLIF (group A). In group B, 72 patients underwent routine MIS-TLIF. The Japanese Orthopedic Association (JOA) score and the visual analogue scale (VAS) scores for lower back pain (LBP) and leg pain were assessed during the postoperative follow-up, and the lumbar interbody fusion rate was evaluated by CT scanning.

Results.
The mean operative time, incision length, average blood loss, and incision pain level were not significantly different (P
> 0.05) between the two groups. No nerve root or dural injuries were observed in group A. In group B, there were two cases of dural injury and three cases of nerve root injury. One patient experienced temporary numbness and weakness on dorsiflexion of the foot, which recovered in 3 months. No differences were identified between the two groups when postoperative JOA scores, back pain, leg pain VAS scores, or the lumbar interbody fusion rate.

Conclusion.
Both methods are effective in the treatment of lumbar degenerative disease. Modified MIS-TLIF is a safe and effective procedure that can significantly reduce the occurrence of injury to the dura and nerve root during decompression and the interbody fusion procedure.

Level of Evidence: 3
Ambulatory blood pressure changes with lung ultrasound-guided dry-weight reduction in hypertensive hemodialysis patients: 12-month results of a randomized controlled trial
Authors: Loutradis Charalampos , Sarafidis Pantelis A. , Ekart Robert , Tsouchnikas Ioannis , Papadopoulos Christodoulos , Kamperidis Vasileios , Alexandrou Maria Eleni , Ferro Charles J. , Papagianni Aikaterini , London Gerard , Mallamaci Francesca , Zoccali Carmine 
Published: June 2021

Objectives:
Hypertension is highly prevalent and independently associated with adverse outcomes in patients undergoing hemodialysis. Volume overload is the main mechanism of increased blood pressure (BP) in these individuals. This study examines the long-term effects of dry-weight reduction with a standardized lung-ultrasound (US)-guided strategy on ambulatory BP in hypertensive hemodialysis patients.

Methods:
This is the report of the 12-month follow-up of a randomized controlled trial in 71 clinically euvolemic, hemodialysis patients with hypertension. Patients were randomized to dry-weight reduction guided by prehemodialysis lung ultrasound and to standard care. A 48-h ambulatory BP monitoring (ABPM) was performed in all study participants at baseline and after 12 months.

Results:
During follow-up, a greater proportion of patients in the active group underwent dry-weight reduction compared with the control group (71.4% vs. 22.2%; P < 0.001). The number of lung US-B lines (a metric of lung water) reduced in the active (−4.83 ± 13.73) and increased in the control arm (+5.53 ± 16.01; P = 0.005) paralleling dry-weight changes (−1.68 ± 2.38 vs. 0.54 ± 2.32 kg; P < 0.001). At 12 months, 48-h systolic BP (136.19 ± 14.78 vs. 130.31 ± 13.57 mmHg; P = 0.034) and diastolic BP (80.72 ± 9.83 vs. 76.82 ± 8.97 mmHg; P = 0.008) were lower compared to baseline in the active but similar in the control group. Changes in 48-h systolic BP (−7.78 ± 13.29 vs. −0.10 ± 14.75 mmHg; P = 0.021) were significantly greater in the active compared to the control group. The proportion of patients experiencing ≥1 episode of intradialytic hypotension was nominally lower in the active group (71.4% vs. 88.9%, P = 0.065).

Conclusions:
Lung-US-guided dry-weight reduction can effectively and safely decrease ambulatory BP levels in the long-term.
Associations of serum apolipoprotein A1, B levels and their ratio with blood pressure in Chinese adults with coronary artery disease
Authors: Dong Hongli , Yang Xuemei , Zhang Yaju , Hu Ping , Liu Yang , Liang Shuxia 
Published: June 2021

Objective
We examined the relationships of apolipoprotein A1 (ApoA1), ApoB levels and ApoB/A1 ratio with blood pressure (BP) in Chinese adults with coronary artery disease (CAD).

Methods
This cross-sectional study included 4921 adults with CAD. SBP, DBP, serum ApoA1 and ApoB levels were measured. The associations between Apo and BP were assessed by analyses of covariance.

Results
Serum ApoA1 was inversely associated with BP, whereas ApoB and the ApoB/A1 ratio exhibited positive associations with BP. For all subjects, a higher ApoA1 level was associated with lower SBP. Subjects in the fourth quartile for ApoA1 exhibited − 2.85 and − 2.63% lower DBP and mean arterial pressure (MAP), respectively than those in the third quartile. In contrast, higher ApoB and ApoB/A1 ratios were associated with higher SBP, DBP and MAP. The mean differences between ApoB quartiles 4 and 1 were 1.54% for SBP, 2.92% for DBP and 2.29% for MAP. The mean differences between the ApoB/A1 ratio quartiles 4 and 1 were 1.94% for SBP, 3.53% for DBP and 2.80% for MAP. In analyses stratified by gender, graded and inverse associations of ApoA1 with SBP, DBP and MAP were observed in both men and women, but positive associations were observed for ApoB and the ApoB/A1 ratio. Path analysis showed that BMI mediated the associations between ApoB and the ApoB/A1 ratio and SBP.

Conclusions
In general, serum ApoA1 was inversely associated with BP in persons with CAD. In contrast, serum ApoB and the ApoB/A1 ratio were positively associated with BP, and these associations were mediated by BMI.
GRP78 binds SARS-CoV-2 Spike protein and ACE2 and GRP78 depleting antibody
blocks viral entry and infection in vitro
Authors: Carlos Anthony J. , Ha Dat P. , Yeh Da-Wei , Van Krieken Richard , Gill Parkash , Machida Keigo , Lee Amy S. 
Published: June 2021

Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the
causative agent of the current COVID-19 global pandemic, utilizes the host
receptor angiotensin-converting enzyme 2 (ACE2) for viral entry. However, other
host factors may also play major roles in viral infection. Here we report that
the stress-inducible molecular chaperone GRP78 can form a complex with the
SARS-CoV-2 Spike protein and ACE2 intracellularly and on the cell surface, and
that the substrate binding domain of GRP78 is critical for this function.
Knock-down of GRP78 by siRNA dramatically reduced cell surface ACE2 expression.
Treatment of lung epithelial cells with a humanized monoclonal antibody
(hMAb159), selected for its ability to cause GRP78 endocytosis and its safe
clinical profile in preclinical models, reduces cell surface ACE2 expression,
SARS-CoV-2 Spike-driven viral entry, and significantly inhibits SARS-CoV-2
infection in vitro. Our data suggest that GRP78 is an
important host auxiliary factor for SARS-CoV-2 entry and infection and a
potential target to combat this novel pathogen and other viruses that utilize
GRP78.
Genomic epidemiology and associated clinical outcomes of a SARS-CoV-2 outbreak in a general adult hospital in Quebec
Authors: Paré Bastien , Rozendaal Marieke , Morin Sacha , Poujol Raphaël , Mostefai Fatima , Grenier Jean-Christophe , Kaufmann Léa , Xing Henry , Sanchez Miguelle , Yechouron Ariane , Racette Ronald , Hussin Julie , Wolf Guy , Pavlov Ivan , Smith Martin A. 
Published: June 2021

AbstractThe first confirmed case of COVID-19 in Quebec, Canada, occurred at Verdun Hospital on February 25, 2020. A month later, a localized outbreak was observed at this hospital. We performed tiled amplicon whole genome nanopore sequencing on nasopharyngeal swabs from all SARS-CoV-2 positive samples from 31 March to 17 April 2020 in 2 local hospitals to assess the viral diversity of the outbreak. We report 264 viral genomes from 242 individuals (both staff and patients) with associated clinical features and outcomes, as well as longitudinal samples, technical replicates and the first publicly disseminated SARS-CoV-2 genomes in Quebec. Viral lineage assessment identified multiple subclades in both hospitals, with a predominant subclade in the Verdun outbreak, indicative of hospital-acquired transmission. Dimensionality reduction identified two subclades that evaded supervised lineage assignment methods, including Pangolin, and identified certain symptoms (headache, myalgia and sore throat) that are significantly associated with favorable patient outcomes. We also address certain limitations of standard SARS-CoV-2 bioinformatics procedures, notably when presented with multiple viral haplotypes.
Epidemiological profile study of COVID-19 in West African countries: Nigeria, Senegal, Mauritania, Cape Verde and Mali
Authors: Ba Mouhamadou Faly , Diop Boly , Bassoum Oumar , Sougou Ndèye Marème , Niang Khadim , Bonnet Emmanuel , Ridde Valéry , Faye Adama 
Published: June 2021

ABSTRACTIntroductionThe COVID-19 pandemic was first reported in West Africa on 27 February 2020 in Nigeria. It subsequently spread to other countries in the region. The objective of this study is to analyze the epidemiological profile of COVID-19 in West Africa from the first reported case to 31 January 2021.MethodWe publicly used available data from reliable sources and from the “COVID-19R” package. We used epidemic curves to describe the trends in the daily evolution of confirmed cases and deaths of COVID-19 in West Africa and specifically in the five countries. The reproduction rate and evolution rates were calculated from these trends.ResultsAs of 31 January 2021, West Africa had 342,938 confirmed cases of COVID-19 with 4,496 deaths. Nigeria had 131,242 cases with 1,586 deaths. Senegal had 26,523 cases with 628 deaths. The case-fatality rate in Mali was 4.08% and the attack rate in Cape Verde was 2587 cases per 100,000 inhabitants. In Nigeria, Senegal, Mauritania and Mali, the epidemic curves supported by the evolution rates showed an increase in confirmed cases and deaths of COVID-19 during December 2020 and January 2021 compared to the last two months. The effective reproduction rates (Re) inferred a slowdown in virus transmission (Re < 1) in these countries except for Senegal.ConclusionThe results showed that COVID-19 was still circulating in some West African countries in late 2020 and early 2021. By improving the health system and with context-specific public health interventions and vaccination, these countries should effectively control COVID-19.
TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them
Authors: Brezovsky Jan , Thirunavukarasu Aravind Selvaram , Surpeta Bartlomiej , Sequeiros-Borja Carlos Eduardo , Mandal Nishita , Sarkar Dheeraj Kumar , Dongmo Foumthuim Cedrix J. , Agrawal Nikhil 
Published: June 2021

AbstractInformation regarding pathways through voids in biomolecules and their roles in ligand transport is critical to our understanding of the function of many biomolecules. Recently, the advent of high-throughput molecular dynamics simulations has enabled the study of these pathways, and of rare transport events. However, the scale and intricacy of the data produced requires dedicated tools in order to conduct analyses efficiently and without excessive demand on users. To fill this gap, we developed the TransportTools, which allows the investigation of pathways and their utilization across large, simulated datasets. TransportTools also facilitates the development of custom-made analyses. TransportTools is implemented in Python3 and distributed as pip and conda packages. The source code is available at https://github.com/labbit-eu/transport_tools.
Experimental Urolithiasis Model to assess Phyto-fractions as Anti-lithiatic Contributors: A Herbaceutical Approach
Authors: Devi Aishwarya Tripurasundari , Yashaswini N , Zameer Farhan , Nagendra Prasad MN 
Published: June 2021

AbstractLife-style disorders have bought a serious burden on the maintenance of health in animals and humans. Lithiasis specifically nephro- and urolithiasis is no exception and needs urgent attention. Currently, only semi-invasive and surgical methods are widely employed which leads to trauma and reoccurrence of kidney stones. Hence complementary and alternative herbal medicine could pave newer ways in exploring anti-lithiatic contributors. The current study attempts to screen twenty herbal hot aqueous leaf extracts for assessing their antioxidant potency (anti-stress) and efficiency against urolithiasis in an experimental calcium oxalate-inducedin vitro(chicken egg membrane) model. The study was further validated byIn silicomolecular docking studies using the Molegro software package on enzymatic biomarkers involved in scavenging oxidants in the host and regulating oxalate metabolism at a cellular level. Among the screened botanicalsKalanchoe pinnataexhibited promising results compared to the standard chemical (potassium-magnesium citrate) and phyto-formulation drug (cystone) currently used by clinicians for treating urolithiasis. The phytochemical profiling (qualitative and quantitative) and virtual studies indicated rutin fromKalanchoe pinnataas a potential candidate for preventing kidney stones. The results of the current study provide better insights into the design and development of newer, smart, and cost-effective herbal therapeutics making food as medicine.Graphical Abstract
Genomic Abelian Finite Groups
Authors: Sanchez Robersy , Barreto Jesús 
Published: June 2021

AbstractExperimental studies reveal that genome architecture splits into DNA sequence domains suggesting a well-structured genomic architecture, where, for each species, genome populations are integrated by individual mutational variants. Herein, we show that, consistent with the fundamental theorem of Abelian finite groups, the architecture of population genomes from the same or closed related species can be quantitatively represented in terms of the direct sum of homocyclic Abelian groups of prime-power order defined on the genetic code and on the set of DNA bases, where populations can be stratified into subpopulations with the same canonical decomposition intop-groups. Through concrete examples we show that the architectures of current annotated genomic regions including (but not limited to) transcription factors binding-motif, promoter regulatory boxes, exon and intron arrangement associated to gene splicing are subjects for feasible modeling as decomposable Abelianp-groups. Moreover, we show that the epigenomic variations induced by diseases or environmental changes also can be represented as an Abelian group decomposable into homocyclic Abelianp-groups. The nexus between the direct sum of homocycle Abelianp-groups and the endomorphism ring paved the ways to unveil unsuspected stochastic-deterministic logical propositions ruling the ensemble of genomic regions. Our study aims to set the basis for concrete applications of the theory in computational biology and bioinformatics. Consistently with this goal, a computational tool designed for the analysis of fixed mutational events in gene/genome populations represented as endomorphisms and automorphisms is provided. Results suggest that complex local architectures and evolutionary features no evident through the direct experimentation can be unveiled through the analysis of the endomorphism ring and the subsequent application of machine learning approaches for the identification of stochastic-deterministic logical rules (reflecting the evolutionary pressure on the region) constraining the set of possible mutational events (represented as homomorphisms) and the evolutionary paths.
Imprecise recombinant viruses evolve via a fitness-driven, iterative process of polymerase template-switching events
Authors: Bentley Kirsten , Alnaji Fadi G. , Woodford Luke , Jones Siân , Woodman Andrew , Evans David 
Published: June 2021

AbstractRecombination is a common feature of many positive-strand RNA viruses, playing an important role in virus evolution. However, to date, there is limited understanding of the mechanisms behind the process. Utilising in vitro assays, we have previously shown that the template-switching event of recombination is a random and ubiquitous process that often leads to recombinant viruses with imprecise genomes containing sequence duplications. Subsequently, a process termed resolution, that has yet to be mechanistically studied, removes these duplicated sequences resulting in a virus population of wild type length genomes. Using defined imprecise recombinant viruses together with Oxford Nanopore and Illumina high throughput next generation sequencing technologies we have investigated the process of resolution. We show that genome resolution involves subsequent rounds of template-switching recombination with viral fitness resulting in the survival of a small subset of recombinant genomes. This alters our previously held understanding that recombination and resolution are independent steps of the process, and instead demonstrates that viruses undergo frequent and continuous recombination events over a prolonged period until the fittest viruses, predominantly those with wild type length genomes, dominate the population.Author SummaryViruses with positive-sense RNA genomes, such as poliovirus, have several mechanisms by which they evolve. One of these is the process of recombination involving the large-scale exchange of genetic information. Recombination occurs during replication when the viral polymerase switches from copying one genome to another. However, the polymerase does not always accurately switch between the two, resulting in sequence duplications or deletions, and genomes that are referred to as imprecise. Over multiple rounds of replication sequence duplications are lost and genomes are resolved to wild type length, but it is unclear how this occurs. Here we used synthetic polioviruses containing defined sequence duplications to determine that the genome population undergoes repeated rounds of recombination until sequence duplications are lost and viruses with precise, wild type length genomes are selected for. This selection is based on the overall fitness of the virus population, with less fit imprecise viruses evolving more quickly. Our study suggests that recombination is a continual process where virus fitness drives the selection of a small subset of recombinant variants. These data are important for understanding how novel viruses evolve via recombination and how this process can be blocked to prevent novel and dangerous pathogens from arising.