bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optimizing combat readiness for military surgeons without trauma fellowship training: Engaging the “voluntary faculty” model
Authors: Yonge John , Schaetzel Shaina , Paull Jessie , Jensen Guy , Wallace James , O'Brien Brendan , Pak Grace , Schreiber Martin , Glaser Jacob 
Published: May 2023

BACKGROUND
Appropriate operative volume remains a critical component in mitigating surgical atrophy and maintaining clinical competency. The initiation of military-civilian surgical partnerships (MCPs) has been proposed for addressing knowledge, skills, and abilities (KSA) metrics to address concerns over operational readiness and the low acuity experienced by military surgeons. This study investigates the first partnership for Navy surgical staff at a nonacademic Military Treatment Facility (MTF) with a regional academic Army Military Treatment Facility (AMTF) and a civilian, nonacademic level II trauma center devised to improve operational readiness for attending surgeons. We hypothesize that a skill sustainment MCP will allow military surgeons to meet combat readiness standards as measured by the KSA metric.

METHODS
A memorandum of understanding was initiated between the Navy Military Treatment Facility (NMTF), the AMTF, and the level II civilian trauma center (CTC). The single military surgeon in this study was classified as “voluntary faculty” at the CTC. Total case volume and acuity were recorded over an 11-month period. Knowledge, skills, and abilities metrics were calculated using the standard national provider identifier number and the novel case-log based method.

RESULTS
A total of 156 cases were completed by a single surgeon over the study period, averaging 52 cases per institution. Significantly more KSAs were obtained at the CTC compared with NMTF (5,954 vs. 2,707; p < 0.001). Significantly more emergent cases were observed at the CTC compared with the MTFs (χ2 = 7.1, n = 96, p < 0.05). At a single site, AMTF, a significant difference in the calculated KSA score, was observed between the national provider identifier and case-log methods (5,278 vs. 3,297; p = 0.04).

CONCLUSION
The skill sustainment MCP between NMTF and CTC increased surgical readiness and exposed surgeons to increased operative acuity. The voluntary faculty model reduces direct litigation exposure and encourages clinical competency for military surgeons while remaining a deployable asset to the global military effort.

LEVEL OF EVIDENCE
Therapeutic/Care Management; Level IV.
Craniodental anatomy in Permian–Jurassic Cynodontia and Mammaliaformes (Synapsida, Therapsida) as a gateway to defining mammalian soft tissue and behavioural traits
Authors: Norton Luke A. , Abdala Fernando , Benoit Julien 
Published: May 2023

Mammals are diagnosed by more than 30 osteological characters (e.g. squamosal-dentary jaw joint, three inner ear ossicles, etc.) that are readily preserved in the fossil record. However, it is the suite of physiological, soft tissue and behavioural characters (e.g. endothermy, hair, lactation, isocortex and parental care), the evolutionary origins of which have eluded scholars for decades, that most prominently distinguishes living mammals from other amniotes. Here, we review recent works that illustrate how evolutionary changes concentrated in the cranial and dental morphology of mammalian ancestors, the Permian–Jurassic Cynodontia and Mammaliaformes, can potentially be used to document the origin of some of the most crucial defining features of mammals. We discuss how these soft tissue and behavioural traits are highly integrated, and how their evolution is intermingled with that of craniodental traits, thus enabling the tracing of their previously out-of-reach phylogenetic history. Most of these osteological and dental proxies, such as the maxillary canal, bony labyrinth and dental replacement only recently became more easily accessible—thanks, in large part, to the widespread use of X-ray microtomography scanning in palaeontology—because they are linked to internal cranial characters.This article is part of the theme issue ‘The mammalian skull: development, structure and function’.
<xhtml:span xmlns:xhtml="http://www.w3.org/1999/xhtml" xml:lang="en">Purpura fulminans secondary to <em>Capnocytophaga canimorsus</em>&#160;bacteraemia following a dog bite: A case report and review of literature.
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Authors: Killington Kieran , Lee Nathaniel , Asher Radha , Farrant Olivia , Stone Neil 
Published: May 2023

Introduction. Infection due to Capnocytophaga canimorsus may result in a wide variety of clinical presentations. We present a case of life-threatening Capnocytophaga canimorsus infection with evolution of ecchymosis to purpura fulminans.
Case description. We present a case of a 43-year-old male with a significant history of alcohol use who presented with features of sepsis following a dog bite. This was associated with a striking, widespread purpuric rash. A causative pathogen, C. canimorsus was identified through blood culture and 16S RNA sequencing. His initially purpuric rash underwent bullous change and was diagnosed clinically as purpura fulminans, confirmed on skin biopsy. He made a full recovery with prompt antimicrobial therapy, initially with amoxiclav/clavulanic acid but escalated to clindamycin and meropenem due to clinical deterioration and concerns of beta-lactamase resistance.
Discussion . b-lactamase producing Capnocytophaga strains are of increasing concern. This particular concern is reflected in our case as five days into treatment with b-lactamase inhibitor combination therapy the patients clinical condition deteriorated but demonstrably improved on switching to a carbapenem.
The development of biopsy proven purpura fulminans in this immunocompetent case is a rare severe manifestation of the previously reported manifestation of DIC in Capnocytophaga septicaemia. The case reported describes characteristics common with other DIC presentations such as the presence of clinical risk factors (history of alcohol excess) and symmetrical involvement. However, an unusual feature in that initial purpuric lesions were followed by the development of a bullous appearance and peripheral necrotic features concerning for purpura fulminans and confirmed with skin biopsy.
Shimia ponticola sp. nov., an aerobic anoxygenic photoheterotrophic bacterium, isolated from surface seawater in the South China Sea
Authors: Chen Qi , He Bowen , Lin Ta-Hui , Jiao Nianzhi , Zheng Qiang 
Published: May 2023

A Gram-stain-negative marine bacterium, designated as WX04T, was isolated from the South China Sea. The genome of strain WX04T contained a complete photosynthetic gene cluster and is the first identified photoheterotroph of the genus

Shimia

with high photochemical efficiency (Fv/Fm=0.705±0.010), indicating its diverse metabolic and growth strategies, and unique evolution in the genus

Shimia

. The genome size of strain WX04T is 3.78 Mbp, and the G+C content is 58.8 %. Its isolate formed pink colonies and the cells were non-flagellated and rod-shaped. Growth was observed at 15–35 °C (optimum, 30 °C), at pH 5.0–11.0 (optimum, pH 7.0) and in the presence of 3–5 % (w/v) NaCl (optimum, 3 %). Both catalase activity and oxidase activity were found to be negative. The 16S rRNA gene sequence analyses revealed that this isolate represents a novel species within the genus

Shimia

, sharing 96.8 and 95.6% sequence identities with

Shimia aestuarii

DSM 15283T and

Shimia marina

DSM 26895T, respectively. The respiratory quinone was ubiquinone-10 (100 %). The primary cellular fatty acids (>5 %) were summed feature 8 (C18 : 1
ω7c and/or C18 : 1
ω6c), C18 : 0,C18 : 1
ω7c 11-methyl and C10 : 0 3-OH. The dominant polar lipids of strain WX04T comprised phosphatidylcholine, phosphatidylethanolamine and phosphatidylglycerol. The combined polyphasic data shows that strain WX04T is a novel species within the genus

Shimia

, which is proposed as Shimia ponticola sp. nov., and the type strain is WX04T (=KCTC 62628T=MCCC 1K02295T).
Delineating the effect of sex hormone intake on immunity in cis and trans women with HIV
Authors: Pasin Chloé , Nuñez David Garcia , Kusejko Katharina , Hachfeld Anna , Buvelot Hélène , Cavassini Matthias , Damonti Lauro , Fux Christoph , Martinez de Tejada Begoña , Notter Julia , Trkola Alexandra , Günthard Huldrych F. , Aebi-Popp Karoline , Kouyos Roger D. , Abela Irene A. ,   the Swiss HIV Cohort Study
Published: May 2023

AbstractBackgroundAlthough sex hormones are recognized to induce immune variations, little is known on the effect of exogenous sex hormone intake on immune responses in cis and trans women. Here, we aimed at quantifying how sex hormone intake affects HIV-1 immune markers in cis women (CW) and trans women (TW) with HIV.MethodsWe considered measurements of key HIV-1 immune markers (CD4, CD8, lymphocyte counts, and CD4:CD8 ratio) from cis men (CM), CW, and TW enrolled in the Swiss HIV Cohort Study. We modeled immune markers using linear mixed-effects models with an interaction between the variables “group” (CW, TW) and “with sex hormone intake” (yes/no). We conducted serum proteomics measurements of 92 inflammation markers on samples from 31 TW before and after sex hormone intake to assess the inflammation environment.ResultsWe included 54’141 measurements from 3’092 CW and 83 TW sampled between 2015 and 2022, and 147’298 from 8’611 CM. Sex hormone intake was associated with significant distinct effects on CD4 and CD4:CD8 ratio between the different groups of women (p=0.0025 and 0.015). TW with sex hormone intake had significantly higher CD4 counts (median = 772 (1Q-3Q=520-1’006)) than without (median = 617 (1Q-3Q=426-892)). This increase was similar in magnitude to the difference in CD4 counts between CW and CM. None of the serum inflammation proteins showed significant concentration difference before and after sex hormone intake in TW.ConclusionThis study highlights the need to consider the potential role of sex hormone intake in modulating the immune system among other biological and social factors, especially in TW in HIV.
NGLY1 Deficiency: A Prospective Natural History Study (NHS)
Authors: Tong Sandra , Ventola Pamela , Frater Christina H. , Klotz Jenna , Phillips Jennifer M. , Muppidi Srikanth , Dwight Selina S. , Mueller William F. , Beahm Brendan J. , Wilsey Matt , Lee Kevin J. 
Published: May 2023

AbstractN-glycanase 1 (NGLY1) Deficiency is a debilitating, ultra-rare autosomal recessive disorder caused by loss of function of NGLY1, a cytosolic enzyme that deglycosylates other proteins. It is characterized by severe global developmental delay and/or intellectual disability, hyperkinetic movement disorder, transient elevation of transaminases, (hypo)alacrima, and progressive, diffuse, length-dependent sensorimotor polyneuropathy. A prospective natural history study (NHS) was conducted to elucidate clinical features and disease course. Twenty-nine participants were enrolled (15 onsite, 14 remotely) and followed for up to 32 months, representing ∼29% of the ∼100 patients identified worldwide. Participants exhibited profound developmental delays, with almost all developmental quotients below 20 on the Mullen Scales of Early Learning, well below the normative score of 100. Increased difficulties with sitting and standing suggested decline in motor function over time. Most patients presented with (hypo)alacrima and reduced sweat response. Pediatric quality of life was poor except for emotional function. Language/communication and motor skill problems including hand use were reported by caregivers as the most bothersome symptoms. Levels of the substrate biomarker, GlcNAc-Asn (aspartylglucosamine; GNA), were consistently elevated in all participants over time, independent of age. Liver enzymes were elevated for some participants but improved especially in younger patients and did not reach levels indicating severe liver disease. Three participants died during the study period. Data from this NHS informs selection of endpoints and assessments for future clinical trials for NGLY1 Deficiency interventions. Potential endpoints include GNA biomarker levels, neurocognitive assessments, autonomic and motor function (particularly hand use), (hypo)alacrima, and quality of life.
Aggregatibacter actinomycetemcomitans(Aa) cytolethal distending toxin (Cdt) modulates host phagocytic function
Authors: Kim Taewan J. , Shenker Bruce J. , Macelroy Andrew , Pankoski Lisa , Boesze-Battaglia Kathleen 
Published: May 2023

ABSTRACTCytolethal distending toxins (Cdt) are a family of toxins produced by several human pathogens which infect mucocutaneous tissue and induce inflammatory disease. Human macrophages exposed toAggregatibacter actinomycetemcomitans(Aa) Cdt respond through canonical and non-canonical inflammasome activation to stimulate cytokine release. The inflammatory response is dependent on PI3K signaling blockade via the toxin’s phosphatidylinositol-3,4,5-triphosphate (PIP3) phosphatase activity; converting PIP3 to phosphatidylinsoitol-3,4-diphosphate (PI3,4P2) thereby depleting PIP3 pools. Phosphoinositides, also play a critical role in phagosome trafficking, serving as binding domains for effector proteins during phagosome maturation and subsequent fusion with lysosomes. We now demonstrate thatAaCdt manipulates the phosphoinositide (PI) pools of phagosome membranes and alters Rab5 association. Exposure of macrophages toAaCdt slowed phagosome maturation and decreased phago-lysosome formation, thereby compromising macrophage phagocytic function. Moreover, macrophages exposed to Cdt showed decreased bactericidal capacity leading to increase inAggregatibacter actinomycetemcomitanssurvival. Thus, Cdt may contribute to increased susceptibility to bacterial infection. These studies uncover an underexplored aspect of Cdt function and provide new insight into the virulence potential of Cdt in mediating the pathogenesis of disease caused by Cdt-producing organisms such asAa.
Historical biogeography supports Point Conception as the site of turnover between temperate East Pacific ichthyofaunas
Authors: Miller Elizabeth Christina 
Published: May 2023

ABSTRACTThe northern and southern marine faunas of the temperate Northeastern Pacific meet within California as part of one of the few eastern boundary upwelling ecosystems of the world. Traditionally, it is believed that Point Conception is the precise site of turnover between these two faunas due to sharp changes in oceanographic conditions. However, evidence from intraspecific phylogeography and species range terminals do not support this view, finding stronger biogeographic breaks elsewhere along the coast. Here I develop a new application of historical biogeographic approaches to uncover sites of transition between faunas without needing ana priorihypothesis of where these occur. I used this approach to determine whether the point of transition between northern and southern temperate faunas occurs at Point Conception or elsewhere within California. I also take advantage of expert-vetted latitudinal range data of California fish species from the 1970s and the 2020s to assess how biogeography could change with the backdrop of climate change. The site of turnover was found to occur near Point Conception, in concordance with the traditional view. I suggest that recent species- and population-level processes such as dispersal and speciation could be expected to give signals of different events from historical biogeography, possibly explaining the discrepancy across studies. Species richness of California has increased since the 1970s, mostly due to new species from Baja California. Range shifts under warming conditions will have the consequence of increasing the disparity between northern and southern faunas of California, creating a more divergent biogeography.
Facile determination of the Poisson’s ratio and Young’s modulus of polyacrylamide gels and polydimethylsiloxane
Authors: Smith Ariell M. , Inocencio Dominique Gabriele , Pardi Brandon M. , Gopinath Arvind , Eguiluz Roberto Andresen 
Published: May 2023

ABSTRACTPolyacrylamide hydrogels (PAH) and polydimethylsiloxane (PDMS) are two soft materials often used in cell mechanics and mechanobiology, in manufacturing lab-on-a chip applications, among others. This is partly due to the ability to tune their elasticity with ease, in addition to various chemical modifications. For affine polymeric networks, two (of three) elastic constants – the Young’s modulus (E), the shear modulus (G), and the Poisson’s ratio (ν) – describe the purely elastic response to external forces. However, the literature addressing the experimental determination of ν for PAH (also sometimes referred to as PAA gels in the literature) and PDMS is surprisingly limited when compared to the literature reporting values ofEandG. Here, we present a facile method to obtain the Poison’s ratio and Young’s modulus for PAH and PDMS based on static tensile tests, and cross-correlate these values with those obtained via a second independent method, shear rheology. We show that: i) the Poisson’s ratio may vary significantly from the value for incompressible materials (ν = 0.5), and ii) find a high degree of agreement between shear rheology and macroscopic static tension tests for PAH but not PDMS.Abstract Figure
MIM-CyCIF: Masked Imaging Modeling for Enhancing Cyclic Immunofluorescence (CyCIF) with Panel Reduction and Imputation
Authors: Sims Zachary , Mills Gordon B. , Chang Young Hwan 
Published: May 2023

ABSTRACTCyCIF quantifies multiple biomarkers, but panel capacity is compromised by technical challenges including tissue loss. We propose a computational panel reduction, inferring surrogate CyCIF data from a subset of biomarkers. Our model reconstructs the information content from 25 markers using only 9 markers, learning co-expression and morphological patterns. We demonstrate strong correlations in predictions and generalizability across breast and colorectal cancer tissue microarrays, illustrating broader applicability to diverse tissue types.
Mendelian Randomization analyses identify causal associations of human gut microbiome composition on intelligence
Authors: Yao Shi , Han Ji-Zhou , Wang Xin , Wang Jia-Hao , Qian Long , Wu Hao , Guo Jing , Dong Shan-Shan , Guo Yan , Yang Tie-Lin 
Published: May 2023

AbstractBackgroundGrowing evidence indicates that dynamic changes in the gut microbiome can affect intelligence; however, whether the relationships are causal is unknown.MethodsWe conducted a bidirectional two-sample Mendelian randomization (MR) analysis using the summary statistics from the largest GWAS meta-analysis of gut microbiota composition (n = 18,340) and intelligence (n = 269,867). Inverse-variance weighted method was used to conduct the MR analyses complemented by a range of sensitivity analyses to validate the robustness of the results. We further applied a two-step MR analysis to evaluate whether the effect of identified taxa on intelligence was mediated by regulating the brain volume.ResultsMR evidence suggested a risk effect of the genusOxalobacteron intelligence (β = –0.032; 95% confidence interval, –0.049 to –0.015;P= 1.88 ×10-4) and a protective effect of the genusFusicatenibacteron intelligence (β = 0.051; 95% confidence interval, 0.023 to 0.079;P= 3.03× 10-4). In the other direction, we did not find causal evidence of intelligence on gut microbiome composition. The mediation analysis showed that the effect of genusFusicatenibacteron intelligence was partly mediated by regulating the brain volume, with a mediated proportion of 26.7% (95% confidence interval, 4.9% to 48.5%).ConclusionsOur findings may help reshape our understanding of the microbiota-gut-brain axis and development of novel intervention approaches for preventing cognitive impairment.
Polygenic Risk for Depression and Anterior and Posterior Hippocampal Volume in Children and Adolescents
Authors: Hurtado Hailee , Hansen Melissa , Strack Jordan , Vainik Uku , Decker Alexandra L. , Khundrakpam Budhachandra , Duncan Katherine , Finn Amy S. , Mabbott Donald J. , Merz Emily C. 
Published: May 2023

AbstractBackgroundDepression has frequently been associated with smaller hippocampal volume. The hippocampus varies in function along its anterior-posterior axis, with the anterior hippocampus more strongly associated with stress and emotion processing. The goals of this study were to examine the associations among parental history of anxiety/depression, polygenic risk scores for depression (PGS-DEP), and anterior and posterior hippocampal volumes in children and adolescents. To examine specificity to PGS-DEP, we examined associations of educational attainment polygenic scores (PGS-EA) with anterior and posterior hippocampal volume.MethodsParticipants were 350 3– to 21-year-olds (46% female). PGS-DEP and PGS-EA were computed based on recent, large-scale genome-wide association studies. High-resolution, T1-weighted magnetic resonance imaging (MRI) data were acquired, and a semi-automated approach was used to segment the hippocampus into anterior and posterior subregions.ResultsChildren and adolescents with higher PGS-DEP were more likely to have a parent with a history of anxiety/depression. Higher PGS-DEP was significantly associated with smaller anterior but not posterior hippocampal volume. PGS-EA were not associated with anterior or posterior hippocampal volumes.LimitationsParticipants in these analyses were all of European ancestry.ConclusionsPolygenic risk for depression may lead to smaller anterior but not posterior hippocampal volume in children and adolescents, and there may be specificity of these effects to PGS-DEP rather than PGS-EA. These findings may inform the earlier identification of those in need of support and in the future could inform the design of more effective, personalized treatment strategies.
A network-based model ofAspergillus fumigatuselucidates regulators of development and defensive natural products of an opportunistic pathogen
Authors: Carriel Cristobal Carrera , Pyne Saptarshi , Halberg-Spencer Spencer A. , Park Sung Chul , Seo Hye-won , Schmidt Aidan , Calise Dante G. , Ané Jean-Michel , Keller Nancy P. , Roy Sushmita 
Published: May 2023

ABSTRACTAspergillus fumigatusis a notorious pathogenic fungus responsible for various harmful, sometimes lethal, diseases known as aspergilloses. Understanding the gene regulatory networks that specify the expression programs underlying this fungus’ diverse phenotypes can shed mechanistic insight into its growth, development, and determinants of pathogenicity. We used eighteen RNA-seq datasets (seventeen publicly available and one previously unpublished) ofAspergillus fumigatusto construct a comprehensive gene regulatory network resource. Our resource, named GRAsp (GeneRegulation ofAspergillus fumigatus), was able to recapitulate known regulatory pathways such as response to hypoxia, iron and zinc homeostasis, and secondary metabolite synthesis. Further, GRAsp was experimentally validated in two cases: one in which GRAsp accurately identified an uncharacterized transcription factor negatively regulating the production of the virulence factor gliotoxin and another where GRAsp revealed the bZip protein, AtfA, as required for fungal responses to microbial signals known as lipo-chitooligosaccharides. Our work showcases the strength of using network-based approaches to generate new hypotheses about regulatory relationships inAspergillus fumigatus. We also unveil an online, user-friendly version of GRAsp available to theAspergillusresearch community.