bluuebunny/crossref_metadata_2025_split huggingface dataset:
Autoantibodies Against Trisulfated Heparin Disaccharide and Fibroblast Growth Factor Receptor-3 May Play a Role in the Pathogenesis of Neuropathic Corneal Pain
Authors: Bayraktutar Betul N. , Atocha Vanessa , Farhad Khosro , Soto Oscar , Hamrah Pedram 
Published: October 2022

Purpose:
The aim of this study was to describe cases of patients with presumable dysimmune small-fiber neuropathy (SFN)-related neuropathic corneal pain (NCP), presenting with autoantibodies against trisulfated heparin disaccharide (TS-HDS) or fibroblast growth factor receptor-3 (FGFR-3).

Methods:
This study was a case series of 3 patients with NCP with positive anti-TS-HDS and/or anti-FGFR-3 autoantibodies and systemic SFN as confirmed by positive skin biopsy results.

Results:
All 3 patients were women with a mean age of 34.3± 6.1 years. They suffered from moderate to severe persistent chronic ocular discomfort (10/10, 10/10, and 9/10 on a visual analogue scale, respectively). Although 1 patient suffered from ocular pain and photophobia alone, the other 2 patients experienced additional non-ocular pain. One of the patients had pain on her face and head, and 1 patient reported neck and lower back pain. Two patients had high anti-TS-HDS IgM titers, whereas 1 patient had both high anti-TS-HDS IgM and anti-FGFR-3 IgG titers. Skin biopsy confirmed the presence of SFN in all patients by demonstrating decreased intraepidermal nerve fiber density.

Conclusions:
The presence of anti-TS-HDS and anti-FGFR-3 autoantibodies in patients with NCP with positive skin biopsy findings for SFN highlights the potential role of dysimmune SFN in the pathogenesis of this disease.
Promoting understanding of medical decision-making coding for nurse practitioner students
Authors: Shanahan Tonya D. , Gurley Lisa E. , Chatman Sherri H. , Cunningham Jill L. 
Published: October 2022

ABSTRACT
Nurse practitioners (NPs) are often responsible for coding patient encounters for reimbursement. Students should learn the basics of this skill during their educational preparation. On January 1, 2021, the American Medical Association and the Centers for Medicare & Medicaid Services implemented new guidelines to the evaluation and management office appointment documentation and coding. The new medical decision-making (MDM) guidelines created a learning curve for NP students, faculty, and preceptors. An additional obstacle was encountered when on-campus preclinical intensives, which included a coding practice session, were canceled due to the COVID-19 pandemic. The faculty of an NP program identified MDM coding as a difficult concept to teach in an asynchronous learning environment. In response, the faculty developed and implemented synchronous online case study sessions that incorporated active student participation and real-time feedback, thus increasing engagement with peers, faculty, and the MDM concepts. The purpose of this article was to present a synchronous method for teaching MDM coding to NP students, and the outcomes, lessons learned, and implications for nursing education and practice.
Coronavirus disease 2019 vaccine effectiveness among a population-based cohort of people living with HIV
Authors: Chambers Catharine , Samji Hasina , Cooper Curtis L. , Costiniuk Cecilia T. , Janjua Naveed Z. , Kroch Abigail E. , Arbess Gordon , Benoit Anita C. , Buchan Sarah A. , Chung Hannah , Kendall Claire E. , Kwong Jeffrey C. , Langlois Marc-André , Lee Samantha M. , Mbuagbaw Lawrence , McCullagh John , Moineddin Rahim , Nambiar Devan , Walmsley Sharon , Anis Aslam H. , Burchell Ann N. 
Published: October 2022

Objective:
People with HIV were underrepresented in coronavirus disease 2019 (COVID-19) vaccine clinical trials. We estimated vaccine effectiveness (VE) against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection for the BNT162b2, mRNA-1273, and ChAdOx1 vaccines among a population-based cohort of people with HIV in Ontario, Canada.

Design:
Test-negative design

Methods:
We identified people with HIV aged ≥19 years who were tested for SARS-CoV-2 by RT-PCR between December 14, 2020 (first availability of COVID-19 vaccines) and November 21, 2021 (pre-Omicron circulation). Outcomes included any infection, symptomatic infection, and COVID-19-related hospitalization/death. We compared the odds of vaccination between test-positive cases and test-negative controls using multivariable logistic regression with adjustment for age, sex, region, calendar time, SARS-CoV-2 test histories, influenza vaccination, comorbidities, and neighborhood-level socio-economic status. VE was derived as (1 – adjusted odds ratio) × 100%.

Results:
Among 21 023 adults living with HIV, there were 801 (8.3%) test-positive cases and 8,879 (91.7%) test-negative controls. 20.1% cases and 47.8% of controls received ≥1 COVID-19 vaccine dose; among two-dose recipients, 93.4% received ≥1 mRNA dose. Two-dose VE ≥7 days before specimen collection was 82% (95% confidence interval [CI] = 74–87%) against any infection, 94% (95% CI = 82–98%) against symptomatic infection, and 97% (95% CI = 85–100%) against hospitalization/death. Against any infection, VE declined from 86% (95% CI = 77–92%) within 7–59 days after the second dose to 66% (95% CI = −15–90%) after ≥180 days; we did not observe evidence of waning protection for other outcomes.

Conclusion:
Two doses of COVID-19 vaccine offered substantial protection against symptomatic illness and hospitalization/death in people with HIV prior to the emergence of the Omicron variant. Our findings do not support a broad conclusion that COVID-19 VE is lower among people with HIV in populations that, for the most part, are attending HIV care, taking antiretroviral medication, and are virally suppressed.
A “Leopard Man” Aspect on 18F-FDG PET/CT Revealing a VEXAS Syndrome
Authors: Fagart Alexandre , Quemeneur Thomas , Collet Guillaume , Demailly Franck , Rousselin Clementine 
Published: October 2022

Abstract
VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome is an adult-onset autoinflammatory disease caused by somatic UBA1 mutations first described in 2020. Most of these patients met clinical criteria for an inflammatory syndrome (relapsing polychondritis, Sweet syndrome, polyarteritis nodosa, or giant-cell arteritis) or a hematologic condition (myelodysplastic syndrome or multiple myeloma) or both. We described here an FDG PET/CT “leopard man” appearance, with abnormal marrow recruitment the findings, in a 70-year-old man diagnosed with a VEXAS syndrome.
Isolated Liver Metastasis Detected by 68Ga-PSMA PET/CT in Newly Diagnosed Prostate Cancer
Authors: Önner Hasan , Özer Halil , Çelik Ahmet Volkan , Yilmaz Farise , Kara Gedik Gonca 
Published: October 2022

Abstract
Lymph nodes, bones, and liver are the most typical metastatic sites for prostate cancer. However, isolated liver metastasis from prostate cancer is extremely rare. Here, we report a 75-year-old man with newly diagnosed prostate adenocarcinoma, with isolated liver metastasis detected by 68Ga-PSMA (68Ga–prostate-specific membrane antigen) PET/CT. There was no sign of regional or distant metastases elsewhere. This case highlights the value of 68Ga-PSMA PET/CT in detecting a very uncommon solitary liver metastasis from prostate cancer.
POSTINJURY FECAL MICROBIOME TRANSPLANT DECREASES LESION SIZE AND NEUROINFLAMMATION IN TRAUMATIC BRAIN INJURY
Authors: Davis Booker T , Chen Zhangying , Islam Mecca B.A.R. , Timken Madeline E. , Procissi Daniele , Schwulst Steven J. 
Published: October 2022

ABSTRACT

Background: Traumatic brain injury (TBI) is an underrecognized public health threat. The constitutive activation of microglia after TBI has been linked to long-term neurocognitive deficits and the progression of neurodegenerative disease. Evolving evidence indicates a critical role for the gut-brain axis in this process. Specifically, TBI has been shown to induce the depletion of commensal gut bacteria. The resulting gut dysbiosis is associated with neuroinflammation and disease. Hypothesis: We hypothesized that fecal microbiota transplantation would attenuate microglial activation and improve neuropathology after TBI. Methods: C57Bl/6 mice were subjected to severe TBI (n = 10) or sham injury (n = 10) via an open-head controlled cortical impact. The mice underwent fecal microbiota transplantation (FMT) or vehicle alone via oral gavage once weekly for 4 weeks after injury. At 59 days after TBI, mice underwent three-dimensional, contrast-enhanced magnetic resonance imaging. Following imaging, mice were killed, brains harvested at 60 DPI, and CD45+ cells isolated via florescence-activated cell sorting. cDNA libraries were prepared using the 10x Genomics Chromium Single Cell 3′ Reagent kit followed by sequencing on a HiSeq4000 instrument, and computational analysis was performed. Results: Fecal microbiota transplantation resulted in a >marked reduction of ventriculomegaly (P < 0.002) and preservation of white matter connectivity at 59 days after TBI (P < 0.0001). In addition, microglia from FMT-treated mice significantly reduced inflammatory gene expression and enriched pathways involving the heat-shock response compared with mice treated with vehicle alone. Conclusions: We hypothesized that restoring gut microbial community structure via FMT would attenuate microglial activation and reduce neuropathology after TBI. Our data demonstrated significant preservation of cortical volume and white matter connectivity after an injury compared with mice treated with vehicle alone. This preservation of neuroanatomy after TBI was associated with a marked reduction in inflammatory gene expression within the microglia of FMT-treated mice. Microglia from FMT-treated mice enriched pathways in the heat-shock response, which is known to play a neuroprotective role in TBI and other neurodegenerative disease processes.
No Stone Left Unturned: Utilization of an Organ Procurement Organization Donor Surgeon at Procurement Reduces Discards of Marginal Liver Allografts
Authors: Shubin Andrew D. , MacConmara Malcolm P. , Patel Madhukar S. , Wang Benjamin K. , Feizpour Cyrus A. , Reese Jeffrey , Niles Patricia A. , Shah Jigesh A. , Desai Dev M. , De Gregorio Lucia , Hanish Steven I. , Vagefi Parsia A. , Hwang Christine S. 
Published: October 2022

Background.
The recent trend of organ procurement organizations (OPOs) employing independent surgeons for organ procurement has been developed with the goal of improving the supply of suitable organs for transplantation. We investigated the effects that the addition of an OPO-employed, organ-procurement specialist has on liver allograft discard rate, marginal organ utilization, and graft survival.

Methods.
Organ Procurement and Transplant Network and OPO data were retrospectively studied between April 1, 2014‚ and July 31, 2019‚ within the Southwest Transplant Alliance donor service area. Liver procurements with an OPO-surgeon present (OPO-Present) were compared to those without the involvement of an OPO surgeon (OPO-Absent). Donor and recipient characteristics as well as outcomes were analyzed across groups using propensity score matching.

Results.
In total 869 OPO-Present liver allografts had similar rates of discard (5.2%) compared to 771 OPO-Absent livers (5.8%). However, after adjusting for donor risk, OPO-Present livers had a lower propensity of discard compared to OPO-Absent (3.4% versus 7.6%, P < 0.05). OPO-Present livers were more likely to be shared nationally (11.0% versus 4.8%, P < 0.001). Outcome analysis showed allograft survival of OPO-Present livers at 5 y was comparable to OPO-Absent livers (79.5% versus 80%, P = 0.34).

Conclusions.
The presence of an OPO surgeon was associated with decreased liver allograft discard and increased utilization of marginal donor organs. The OPO surgeon’s presence represents a potential strategy to increase organ utilization nationally.
Image-based quantification of histological features as a function of spatial location using the Tissue Positioning System
Authors: Wang Yunguan , Rong Ruichen , Wei Yonglong , Wang Tao , Xiao Guanghua , Zhu Hao 
Published: October 2022

ABSTRACTTissues such as the liver lobule, kidney nephron, and intestinal gland exhibit intricate patterns of zonated gene expression corresponding to distinct cell types and functions. To quantitatively understand zonation, it would be important to measure cellular or genetic features as a function of position along a zonal axis. While it is possible to manually count, characterize, and locate features in relation to the zonal axis, it is very difficult to do this for more than a few hundred instances. We addressed this challenge by developing a deep-learning-based quantification method called the “Tissue Positioning System” (TPS), which can automatically analyze zonation in the liver lobule as a model system. By using algorithms that identified vessels, classified vessels, and segmented zones based on the relative position along the portal vein to central vein axis, TPS was able to spatially quantify gene expression in mice with zone specific reporters. TPS could discern expression differences between zonal reporter strains, ages, and disease states. TPS could also reveal the zonal distribution of cells previously thought to be randomly distributed. The design principles of TPS could be generalized to other tissues to explore the biology of zonation.The software is available athttps://github.com/yunguan-wang/Tissue_positioning_system.
Improved breeding forFusarium pseudograminarium(Fusarium crown rot) using qPCR measurement of infection in multi-species winter cereal experiments
Authors: Milgate Andrew , Baxter Brad , Simpfendorfer Steven , Yang Nannan , Orchard Beverly , Ovenden Ben 
Published: October 2022

AbstractFusarium crown rot (FCR) causes significant grain yield loss in winter cereals around the world. Breeding for resistance and/or tolerance to FCR has been slow with relatively limited success. In this study, multi-species experiments were used to demonstrate an improved method to quantify FCR infection levels at plant maturity using qPCR, as well as the genotype yield retention using residual regression deviation. Using qPCR to measure FCR infection allowed a higher degree of resolution between genotypes than traditional visual stem basal browning assessments. The results were consistent across three environments with different levels of disease expression. The improved measure of FCR infection along with genotype yield retention allows for partitioning of both tolerance and partial resistance. Together these methods offer new insights to FCR partial resistance and its relative importance to tolerance in bread wheat and barley. This new approach offers a more robust, cost-effective way to select for both FCR traits within breeding programs.Key messageGenetic gain for tolerance and partial resistance against Fusarium crown rot (FCR) in winter cereals has been impeded by laborious and variable visual measures of infection severity. This paper presents results of an improved method to quantify FCR infection that are strongly correlated to yield loss and reveal previously unrecognised partial resistance in barley and wheat varieties.
Refphase: Multi-sample reference phasing reveals haplotype-specific copy number heterogeneity
Authors: Watkins Thomas BK , Colliver Emma C , Huska Mathew R , Kaufmann Tom L , Lim Emilia L , Haase Kerstin , Van Loo Peter , Swanton Charles , McGranahan Nicholas , Schwarz Roland F 
Published: October 2022

AbstractMost computational methods that infer somatic copy number alterations (SCNAs) from bulk sequencing of DNA analyse tumour samples individually. However, the sequencing of multiple tumour samples from a patient’s disease is an increasingly common practice. We introduce Refphase, an algorithm that leverages this multi-sampling approach to infer haplotype-specific copy numbers through multi-sample reference phasing. We demonstrate Refphase’s ability to infer haplotype-specific SCNAs and characterise their intra-tumour heterogeneity, to uncover previously undetected allelic imbalance in low purity samples, and to identify parallel evolution in the context of whole genome doubling in a pan-cancer cohort of 336 samples from 99 tumours.
Quartile coefficient of variation is more robust than CV for traits calculated as a ratio1
Authors: Botta-Dukát Zoltán 
Published: October 2022

SummaryComparing within-species variations of traits can be used in testing ecological theories. In these comparisons, it is useful to remove the effect of the difference in mean trait values, therefore measures of relative variation, most often the coefficient of variation (CV), are used. The studied traits are often calculated as the ratio of the size or mass of two organs: e.g. SLA is the ratio of leaf size and leaf mass. Often the inverse of these ratios is also meaningful; for example, the inverse of SLA is often referred to as LMA (leaf mass per area). Relative variation of a trait and its inverse should not considerably differ. However, it is illustrated that using the coefficient of variation may result in differences that could influence the interpretation, especially if there are outlier trait values. The alternative way for estimating CV from the standard deviation of log-transformed data assuming log-normal distribution and Kirkwood’s geometric coefficient of variation free from this problem, but they proved to be sensitive to outlier values. Quartile coefficient of variation performed best in the tests: it gives the same value for a trait and its inverse and it is not sensitive to outliers.
A chromosome-scale assembly ofBrassica carinata(BBCC) accession HC20 containing resistance to multiple pathogens and an early generation assessment of introgressions intoB. juncea(AABB)
Authors: Paritosh Kumar , Rajarammohan Sivasubramanian , Yadava Satish Kumar , Sharma Sarita , Verma Rashmi , Mathur Shikha , Mukhopadhyay Arundhati , Gupta Vibha , Pradhan Akshay K , Kaur Jagreet , Pental Deepak 
Published: October 2022

SummaryBrassica carinata(BBCC) commonly referred to as Ethiopian mustard is a natural allotetraploid containing the genomes ofBrassica nigra(BB) andBrassica oleracea(CC). It is an oilseed crop endemic to the Northeastern regions of Africa. Although it is grown in a limited manner,B. carinatais of value as it is resistant/highly tolerant to most of the pathogens affecting cultivated Brassica species of the U’s triangle that are grown worldwide as oilseed and vegetable crops. We report a chromosome-scale genome assembly ofB. carinataaccession HC20 using long-read Oxford Nanopore and Illumina sequencing and BioNano optical maps. The assembly has a scaffold N50 of ~39.8 Mb and covers ~1.11 Gb of the genome. We compared the available long-read genome assemblies of the six species of the U’s triangle and found a highly conserved gene number and collinearity suggesting thatB. juncea(AABB),B. napus(AACC), andB. carinataare strict allopolyploids. We cataloged the nucleotide-binding and leucine-rich repeat immune receptor (NLR) repertoire ofB. carinataresulting in the identification of 465 NLRs. We investigated the extent and nature of early generation genomic interactions between the subgenomes ofB. carinataandB. junceain interspecific crosses between the two species. We found that C chromosome additions are well tolerated, with homoeologous exchanges occurring between the A and C genomes. Based on the genomic interactions, we propose strategies to utilize the interspecific crosses for transferring disease resistance fromB. carinatatoB. junceaand other Brassica species.
Environmental drivers of earthworm communities along an altitudinal gradient in the French Alps
Authors: Gabriac Quentin , Ganault Pierre , Barois Isabelle , Aranda-Delgado Eduardo , Cimetière Elisa , Cortet Jérôme , Gautier Montan , Hedde Mickaël , Marchán Daniel F. , Pimentel Reyes José Carlos , Stokes Alexia , Decaëns Thibaud 
Published: October 2022

AbstractThe study of elevational diversity gradients is a central topic in biodiversity research. In this study, we tested for the effect of climate, resource quality and habitat heterogeneity on earthworm communities along an altitudinal gradient and around the treeline in the French Alps. Earthworm communities and environmental properties (i.e. climate, soil properties and vegetation structure and composition) were sampled in six altitudinal stages from 1400 to 2400 m. Results were analysed through multi-table factorial analyses and structural equation modelling. We found average density, biomass and species richness in the range of what is usually reported in comparable ecosystems. We found no monotonic decrease in species richness along the altitudinal gradient, which we explain by the species pool being dominated by taxa with high environmental tolerance and dispersal capacities. Instead, we highlighted the ecotone associated with the treeline as the primary driving factor of earthworm communities: at 1800-2000m altitude, communities were more abundant and diverse, and had a greater variability in body mass. This result was largely explained by the structure and composition of the vegetation, whereas soil and climate appeared to have only indirect effects. Therefore, the treeline effect on earthworm communities can be explained both by the effect of environmental heterogeneity and of trophic resource quality which increases at the ecotone level.
Single-cell transcriptomics of the immune system in ME/CFS at baseline and following symptom provocation
Authors: Ahmed Faraz , Vu Luyen Tien , Zhu Hongya , Iu David Shing Huk , Fogarty Elizabeth A. , Kwak Yeonui , Chen Weizhong , Franconi Carl J. , Munn Paul R. , Levine Susan M. , Stevens Jared , Mao Xiangling , Shungu Dikoma C. , Moore Geoffrey E. , Keller Betsy A. , Hanson Maureen R. , Grenier Jennifer K. , Grimson Andrew 
Published: October 2022

SUMMARYME/CFS is a serious and poorly understood disease. To understand immune dysregulation in ME/CFS, we used single-cell RNA-seq (scRNA-seq) to examine immune cells in cohorts of patients and controls. Post-exertional malaise (PEM), an exacerbation of symptoms following strenuous exercise, is a characteristic symptom of ME/CFS. Thus, to detect changes coincident with PEM, we also performed scRNA-seq on the same cohorts following exercise. At baseline, ME/CFS patients displayed dysregulation of classical monocytes suggestive of inappropriate differentiation and migration to tissue. We were able to identify both diseased and more normal monocytes within patients, and the fraction of diseased cells correlated with metrics of disease severity. Comparing the transcriptome at baseline and post-exercise challenge, we discovered patterns indicative of improper platelet activation in patients, with minimal changes elsewhere in the immune system. Taken together, these data identify immunological defects present at baseline in patients and an additional layer of dysregulation following exercise.HighlightsME/CFS is a debilitating disease with unknown causes. Here, we provide, for the first time, an extensive single cell resolution dataset detailing the gene expression programs of circulating immune cells of ME/CFS cases at baseline and after symptom provocation. We were able to detect robust dysregulation in certain immune cells from patients, with dysregulation of classical monocytes manifesting the strongest signal. Indeed, the fraction of aberrant monocytes in ME/CFS patients correlated with the degree of disease severity. Surprisingly, platelet transcriptomes were also altered in ME/CFS, and they were the only component of the immune system that showed large-scale changes following symptom provocation.