bluuebunny/crossref_metadata_2025_split huggingface dataset:
Epidemiology of Trauma History and Body Pain: A Retrospective Study of Community-Based Australian Women
Authors: Flehr Alison , Coles Jan , Dixon John B , Gibson Stephen J , Brilleman Samuel L , Harris Melissa L , Loxton Deborah 
Published: January 2021

Abstract

Objective
To assess whether body pain was associated with different trauma histories (physical injury vs. interpersonal injury [IPI]) within Australian women, along with body pain and trauma history associations with biological and psychological (biopsycho) confounders.

Methods
A retrospective cross-sectional analysis was conducted on the Australian Longitudinal Study on Women’s Health (ALSWH) 1973–1978 birth cohort wave 6 data. Relevant life events were categorized into two types of traumatic experience and included as exposure variables in a multinomial regression model for body pain subgroups. Also, subgroup analyses considered trauma and pain effects and interactions on biopsycho burden.

Results
The unadjusted multinomial regression model revealed that a history of physical injury was found to be significantly associated with body pain severity, as was a history of IPI trauma. After the model was adjusted to include biopsycho confounders, the association between IPI and body pain was no longer significant, and post hoc analysis revealed the relationship was instead mediated by biopsycho confounders. Women with a history of IPI and body pain were also found to have the greatest biopsycho (physical functioning, stress, anxiety, and depression) burden.

Discussion
The relationship between IPI and body pain was found to be mediated by biopsycho burden, whereas the relationship between physical injury and body pain was not. Also, a history of IPI was associated with a greater biopsycho burden than was a history of physical injury. These results suggest there is clinical value in considering the comprehensive trauma history of patients with pain when developing their biopsychosocial model of care.
TNF-α Inhibitors for the Management of Intractable Corneal Melt: Report of Three Cases and Review of the Literature
Authors: Utine Canan Asli , Birlik Merih , Özizmirliler Denizcan , Karakaş Ali , Akbulut Betül , Durak Ismet 
Published: January 2021

Objective:
To report three consecutive cases with noninfectious corneal melting, whose disease progression could only be halted with tumor necrosis-α (TNF-α) inhibitor infusion, with a review of the relevant literature.

Materials and methods:
Patients with toxic epidermal necrolysis, severe alkaline burn, and Sjögren syndrome had experienced severe corneal melting following penetrating keratoplasty, Boston type 1 keratoprosthesis implantation or spontaneously, respectively. Topical autologous serum eye-drops, medroxyprogesterone, and acetylcysteine formulations; frequent nonpreserved lubrication; systemic tetracyclines and vitamin-C supplements; topical and systemic steroids and steroid-sparing agents; surgical approaches including amniotic membrane transplantation, tectonic graft surgery; and tarsorraphy failed to alter the disease courses.

Results:
Upon consultation with the rheumatology clinic, TNF-α inhibitor infliximab (Remicade; Centocor Ortho Biotech Inc, Horsham, PA) 5 mg/kg infusion was planned for each patient. After 0-, 2-, and 6-week doses, monthly infusion at the same dose was maintained for 12 months because of severe and intractable course of their diseases. Each case showed dramatic improvements in corneal melts; and sterile vitritis in the eye with Boston keratoprosthesis responded, as well.

Conclusions:
Inhibiting TNF-α-mediated expression of matrix metalloproteinases responsible for collagen breakdown should be considered in refractory cases, as a means of globe salvage.
Anterior Segment Ischemia After Peripheral Annular Lamellar Sclerokeratoplasty for Advanced Terrien Marginal Degeneration
Authors: Mudgil Tanvi , Fernandes Merle 
Published: January 2021

Abstract:
A man with 360° bilateral peripheral thinning, peripheral vascularization, and lipid deposition diagnosed with Terrien marginal degeneration, underwent a 360° peripheral annular lamellar sclerokeratoplasty (PALK) (tuck-in) in the right eye for 90% peripheral thinning and high astigmatism. One-week postoperatively, a sudden drop in vision to counting fingers 1 m from 20/50 with circumciliary congestion, diffuse corneal edema, intense anterior chamber inflammation, keratic precipitates with fixed dilated pupil, and hypotony led to a diagnosis of suspected anterior segment ischemia. Anterior segment fluorescein angiography was suggestive of ischemia. After intensive topical and systemic steroids tapered over 6 months, his symptoms and signs improved. At the last follow-up 4 years later, his best contact lens-corrected visual acuity was 20/30. Anterior segment ischemia has not been reported after a PALK for advanced corneal ectatic disorders. Prompt diagnosis and commencement of intensive steroids was helpful in reversing this condition.
Good Visual Outcomes After Pituitary Tumor Surgery Are Associated With Increased Visual Cortex Functional Connectivity
Authors: Lang Stefan T. , Ryu Won Hyung A. , Starreveld Yves P. , Costello Fiona E. ,   the PITNET Study Group
Published: January 2021

Background:
Patients presenting with visual impairment secondary to pituitary macroadenomas often experience variable recovery after surgery. Several factors may impact visual outcomes including the extent of neuroaxonal damage in the afferent visual pathway and cortical plasticity. Optical coherence tomography (OCT) measures of retinal structure and resting-state functional MRI (rsfMRI) can be used to evaluate the impact of neuroaxonal injury and cortical adaptive processes, respectively. The purpose of this study was to determine whether rsfMRI patterns of functional connectivity (FC) distinguish patients with good vs poor visual outcomes after surgical decompression of pituitary adenomas.

Methods:
In this retrospective cohort study, we compared FC patterns between patients who manifested good (GO) vs poor (PO) visual outcomes after pituitary tumor surgery. Patients (n = 21) underwent postoperative rsfMRI a minimum of 1 year after tumor surgery. Seed-based connectivity of the visual cortex (primary [V1], prestriate [V2], and extrastriate [V5]) was compared between GO and PO patients and between patients and healthy controls (HCs) (n = 19). Demographics, visual function, and OCT data were compared preoperatively and postoperatively between patient groups. The threshold for GO was visual field mean deviation equal or less than −5.00 dB and/or visual acuity equal to or better than 20/40.

Results:
Increased postoperative FC of the visual system was noted for GO relative to PO patients. Specifically, good visual outcomes were associated with increased connectivity of right V5 to the bilateral frontal cortices. Compared with HCs, GO patients showed increased connectivity of V1 and left V2 to sensorimotor cortex, increased connectivity of right and left V2 to medial prefrontal cortex, and increased connectivity of right V5 the right temporal and frontal cortices.

Conclusions:
Increased visual cortex connectivity is associated with good visual outcomes in patients with pituitary tumor, at late phase of recovery. Our findings suggest that rsfMRI does distinguish GO and PO patients after pituitary tumor surgery. This imaging modality may have a future role in characterizing the impact of cortical adaptation on visual recovery.
Novosphingobium olei sp. nov., with the ability to degrade diesel oil, isolated from oil-contaminated soil and proposal to reclassify Novosphingobium stygium as a later heterotypic synonym of Novosphingobium aromaticivorans
Authors: Chaudhary Dhiraj Kumar , Dahal Ram Hari , Kim Dong-Uk , Kim Jaisoo 
Published: January 2021

Two yellow-pigmented, non-motile, Gram-stain-negative, and rod-shaped bacteria, designated TW-4T and TNP-2 were obtained from oil-contaminated soil. Both strains degrade diesel oil, hydrolyse aesculin, DNA, Tween 40 and Tween 60. A phylogenetic analysis based on its 16S rRNA gene sequence revealed that strain TW-4T formed a lineage within the family

Erythrobacteraceae

and clustered as members of the genus

Novosphingobium

. The closest members of strain TW-4T were

Novosphingobium subterraneum

DSM 12447T (97.9 %, sequence similarity),

Novosphingobium lubricantis

KSS165-70T (97.8 %),

Novosphingobium taihuense

T3-B9T (97.8 %),

Novosphingobium aromaticivorans

DSM 12444T (97.7 %),

Novosphingobium flavum

UCT-28T (97.7 %), and

Novosphingobium bradum

STM-24T (97.6 %). The sequence similarity for other members was ≤97.6 %. The genome of strain TW-4T was 4 683 467 bp long with 44 scaffolds and 4280 protein-coding genes. The sole respiratory quinone was Q-10. The major cellular fatty acids were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), summed feature 3 (C16 : 1
ω7c and/or C16 : 1
ω6c), C16 : 0 and C14 : 0 2-OH. The major polar lipids were phosphatidylethanolamine (PE), phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylcholine (PC), phosphatidyl-n-methylethanolamine (PME) and sphingoglycolipid (SGL). The DNA G+C content of the type strain was 65.0 %. The average nucleotide identity (ANIu) and in silico DNA–DNA hybridization (dDDH) relatedness values between strain TW-4T and closest members were below the threshold value for species delineation. Based on polyphasic taxonomic analyses, strain TW-4T represents novel species in the genus

Novosphingobium

, for which the name Novosphingobium olei sp. nov. is proposed. The type strain is TW-4T (=KACC 21628T=NBRC 114364T) and strain TNP-2 (=KACC 21629=NBRC 114365) represents an additional strain. Based on new data obtained in this study, it is also proposed to reclassify

Novosphingobium stygium

as a later heterotypic synonym of

Novosphingobium aromaticivorans

.
Protein scaffold-based multimerization of soluble ACE2 efficiently blocks SARS-CoV-2 infectionin vitroandin vivo
Authors: Kayabolen Alisan , Akcan Ugur , Ozturan Dogancan , Ulbegi-Polat Hivda , Sahin Gizem Nur , Degirmenci Nareg Pinarbasi , Bayraktar Canan , Soyler Gizem , Sarayloo Ehsan , Nurtop Elif , Ozer Berna , Guney-Esken Gulen , Barlas Tayfun , Yildirim Ismail Selim , Dogan Ozlem , Karahuseyinoglu Sercin , Lack Nathan A. , Kaya Mehmet , Albayrak Cem , Can Fusun , Solaroglu Ihsan , Bagci-Onder Tugba 
Published: January 2021

AbstractSoluble ACE2 (sACE2) decoy receptors are promising agents to inhibit SARS-CoV-2, as their efficiency is less likely to be affected by common escape mutations in viral proteins. However, their success may be limited by their relatively poor potency. To address this challenge, we developed a large decoy library of sACE2 fusion proteins, generated with several protease inhibitors or multimerization tags. Among these decoys, multimeric sACE2 consisting of SunTag or MoonTag systems, which were originally utilized for signal amplification or gene activation systems, were extremely effective in neutralizing SARS-CoV-2 in pseudoviral systems and in clinical isolates. These novel sACE2 fusion proteins exhibited greater than 100-fold SARS-CoV-2 neutralization efficiency, compared to monomeric sACE2. SunTag or MoonTag in combination with a more potent version of sACE2, which has multiple point mutations for greater binding (v1), achieved near complete neutralization at a sub-nanomolar range, comparable with clinical monoclonal antibodies. Pseudoviruses bearing mutant versions of Spike, alpha, beta, gamma or delta variants, were also neutralized efficiently with SunTag or MoonTag fused sACE2(v1). Finally, therapeutic treatment of sACE2(v1)-MoonTag provided protection against SARS-CoV-2 infection in anin vivomouse model. Overall, we suggest that the superior activity of the sACE2-SunTag or sACE2-MoonTag fusions is due to the greater occupancy of the multimeric sACE2 receptors on Spike protein as compared to monomeric sACE2. Therefore, these highly potent multimeric sACE2 decoy receptors may offer a promising treatment approach against SARS-CoV-2 infections.One Sentence SummaryMultimerization of sACE2 markedly enhanced the neutralization of SARS-CoV-2 by blocking multiple viral spike proteins simultaneously.
Natural variation inCaenorhabditis elegansresponses to the anthelmintic emodepside
Authors: Wit Janneke , Rodriguez Briana C. , Andersen Erik. C. 
Published: January 2021

AbstractTreatment of parasitic nematode infections depends primarily on the use of anthelmintics. However, this drug arsenal is limited, and resistance against most anthelmintics is widespread. Emodepside is a new anthelmintic drug effective against gastrointestinal and filarial nematodes. Nematodes that are resistant to other anthelmintic drug classes are susceptible to emodepside, indicating that the emodepside mode of action is distinct from previous anthelmintics. The laboratory-adaptedCaenorhabditis elegansstrain N2 is sensitive to emodepside, and genetic selection andin vitroexperiments implicatedslo-1, a BK potassium channel gene, in emodepside mode of action. In an effort to understand how natural populations will respond to emodepside, we measured brood sizes and developmental rates of wildC. elegansstrains after exposure to the drug and found natural variation across the species. Some of the observed variation inC. elegansemodepside responses correlates with amino acid substitutions inslo-1, but genetic mechanisms other thanslo-1coding variants likely underlie emodepside resistance in wildC. elegansstrains. Additionally, the assayed strains have higher offspring production in low concentrations of emodepside (a hormetic effect), which could impact treatment strategies when parasites are underdosed. We find that natural variation affects emodepside sensitivity, supporting the suitability ofC. elegansas a model system to study emodepside responses across natural nematode populations.Graphical abstractHighlightsEmodepside responses vary across theC. elegansspecies.Wild strains ofC. elegansmodel natural differences in parasite emodepside responses.Variation in the emodepside targetslo-1and other loci correlate with resistance.Low doses of emodepside cause a hormetic effect on offspring production.
Adipocyte-specific deletion of the oxygen-sensor PHD2 sustains elevated energy expenditure at thermoneutrality
Authors: Salazar Mario Gomez , Cervera Iris Pruñonosa , Wang Rongling , French Karen , García-Martín Ruben , Blüher Matthias , Schofield Christopher J , Stimson Roland H , Chavakis Triantafyllos , Gudmundsson Elias F , Jennings Lori L , Gudnason Vilmundur G , Morton Nicholas M , Emilsson Valur , Michailidou Zoi 
Published: January 2021

AbstractEnhancing brown adipose tissue (BAT) function to combat metabolic disease is a promising therapeutic strategy. A major obstacle to this strategy is that a thermoneutral environment, relevant to most modern human living conditions, deactivates functional BAT. We showed that we can overcome the dormancy of BAT at thermoneutrality by inhibiting the main oxygen sensor HIF-prolyl hydroxylase, PHD2, specifically in adipocytes. Mice lacking adipocyte PHD2 (P2KOad) and housed at thermoneutrality maintained greater BAT mass, had detectable UCP1 protein expression in BAT and higher energy expenditure. Mouse brown adipocytes treated with the pan-PHD inhibitor, FG2216, exhibited higherUcp1mRNA and protein levels, effects that were abolished by antagonising the canonical PHD2 substrate, HIF-2a. Induction ofUCP1mRNA expression by FG2216, was also confirmed in human adipocytes isolated from obese individuals. Human serum proteomics analysis of 5457 participants in the deeply phenotyped Age, Gene and Environment Study revealed that serum PHD2 (aka EGLN1) associates with increased risk of metabolic disease. Our data suggest adipose–selective PHD2 inhibition as a novel therapeutic strategy for metabolic disease and identify serum PHD2 as a potential biomarker.
Cellular feedback to organotelluranes displays modulation of antioxidant proteins gene expression
Authors: Pessoto Felipe S. , Yokomizo César H. , Cunha Rodrigo L. O. R. , Nantes-Cardoso Iseli L. 
Published: January 2021

ABSTRACTOrganotelluranes RT3 and RT4 are thiol reagents that induce mitochondrial transition pore (MTP) opening in a sensitive and insensitive manner to cyclosporin A. Although RT3 and RT4 promote glutathione depletion, paradoxically, they are also an efficient antioxidant for membrane lipids. These compounds’ antagonistic effects elicited the challenging question of how the gene expression of antioxidant enzymes would respond to treatment with these compounds. The influence of RT3 and RT4 on antioxidant enzyme expression was investigated in cultured aortic smooth muscle cells (ASMC). RT3 and RT4 promoted disruption of ionic calcium homeostasis, mitochondrial transmembrane potential (ΔΨ), and cell death in a dose-dependent manner. The cell death mechanisms responded qualitatively to the increase of the organotellurane concentration and changed from apoptosis to necrosis. RT3 and RT4 increased the expression of thioredoxin significantly. RT3 also increased the expression of glutaredoxin and glutathione peroxidase, slightly the catalase expression without significant effects on SOD expression. The results are consistent with GSH and protein thiol depletion and discussed based on the cell toxicity mechanism exhibited by these compounds.Abstract Figure
Chromosomal Characteristics of Salt Stress Heritable Gene Expression in the Rice Genome
Authors: McGowan Matthew T. , Zhang Zhiwu , Ficklin Stephen P. 
Published: January 2021

AbstractBackgroundGene expression is potentially an important heritable quantitative trait that mediates between genetic variation and higher-level complex phenotypes through time and condition-dependent regulatory interactions. Increasing quantities of high-throughput DNA and RNA sequencing and standardization of research populations has resulted in the accumulation of overlapping -omics data allowing for deeper investigation into the genomic structure and conditional stability of gene expression traits. Therefore, we sought to explore both the genomic and condition-specific characteristics of gene expression heritability within the context of chromosomal structure, using a diverse, 84-line,Oryza sativa(rice) population under optimal and salt-stressed conditions.ResultsHeritability was estimated for the 84 genotypes with common tools and an approach using biological gene expression replicates similar to a twin study in humans. Overall, 5,936 genes were found to have heritable expression regardless of condition and 1,377 genes were found to have heritable expression only during salt stress. These genes with salt-specific heritable expression are enriched for functional terms associated with response to stimulus and transcription factor activity. Additionally, we discovered that highly and lowly expressed genes, and genes with heritable expression are distributed differently along the chromosomes in patterns that follow previously identified chromosomal conformation capture (Hi-C) A/B chromatin compartments. Furthermore, multiple genomic hot-spots enriched for genes with salt-specific heritability were identified on chromosomes 1, 4, 6, and 8. These hotspots were found to contain genes functionally enriched for transcriptional regulation and overlaps with a previously identified major QTL for salt-tolerance in rice.ConclusionsInvestigating the heritability of traits, and in-particular gene expression traits, is important towards a basic understanding of how regulatory networks behave across a population. Additionally, heritable gene expression architecture can be used for further exploration of gene-trait relationships, assist in interpretation and analysis of eQTLs, used as priors for approaches seeking to identification of potential biomarkers, or used in genomic selection modules with potential applications in plant breeding. This work provides insights into patterns of expression and spatial patterns at the chromosomal level.
Genomic signatures of UV resistance evolution inEscherichia colidepend on the growth phase during exposure
Authors: Selveshwari S , Lele Kasturi , Dey Sutirth 
Published: January 2021

AbstractPhysiological states can determine the ability of organisms to handle stress. Does this mean that the same selection pressure will lead to different evolutionary outcomes, depending on the organisms’ physiological state? If yes, what will be the genomic signatures of such adaptation(s)? We used experimental evolution inEscherichia colifollowed by whole-genome whole-population sequencing to investigate these questions. The sensitivity ofEscherichia colito ultraviolet (UV) radiation depends on the growth phase during which it experiences the radiation. We evolved replicateE. colipopulations under two different conditions of UV exposures, namely exposure during the lag and the exponential growth phases. Initially, the UV sensitivity of the ancestor was greater during the exponential phase than the lag phase. However, at the end of 100 cycles of exposure, UV resistance evolved to similar extents in both treatments. Genome analysis showed that mutations in genes involved in DNA repair, cell membrane structure and RNA polymerase were common in both treatments. However, different functional groups were found mutated in populations experiencing lag and exponential UV treatment. In the former, genes involved in transcriptional and translational regulations and cellular transport were mutated, whereas the latter treatment showed mutations in genes involved in signal transduction and cell adhesion. Interestingly, the treatments showed no phenotypic differences in a number of novel environments. Taken together, these results suggest that selection pressures at different physiological stages can lead to differences in the genomic signatures of adaptation, which need not necessarily translate into observable phenotypic differences.