bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical Feasibility of Shear Wave Dispersion Slope for Noninvasive Diagnosis of Nonalcoholic Steatohepatitis in Patients With Morbid Obesity
Authors: Kim Yeonsoo , Hwang Jiyoung , Bae Sung Hwan , Hong Seong Sook , Chang Yun-Woo , Kim Hyun-joo , Kim Sang Hyun , Jin So-Young 
Published: March 2022

Abstract
We aimed to investigate the clinical feasibility of shear wave dispersion slope for assessing nonalcoholic steatohepatitis (NASH) in patients with morbid obesity before bariatric surgery.
This prospective study collected data from 25 participants who received liver biopsy during bariatric surgery between February 2019 and December 2020. All participants underwent ultrasonography shear wave elastography before surgery and shear wave speed and shear wave dispersion slope were measured. Liver specimens were evaluated by 1 pathologist scored histologically for nonalcoholic fatty liver disease (NAFLD). Ultrasonography measurements were compared according to histopathologic findings. Diagnostic performance in differentiating NASH from NAFLD was evaluated using the area under the receiver operating characteristic curve (AUC). Median shear wave speed (1.48 vs 1.62 m/s, P = 0.014) and dispersion slope (8.40 vs 11.80 [m/s]/kHz, P = 0.004) were higher in NASH group than in NAFLD group. Shear wave dispersion slope tended to increase step by step as the severity of activity grade (P = 0.032) and hepatic fibrosis (P = 0.015) increased. The AUC of shear wave dispersion slope for differentiating NASH from NAFLD (AUC, 0.83; 95% confidence intervals, 0.66–1.00) was higher than that of shear wave speed (AUC, 0.78; 95% CI, 0.60–0.97), although it did not reach statistical significance (P = 0.729). Shear wave dispersion slope could be a feasible tool for assessing NASH in patients with morbid obesity.
Comparison of Face-to-Face Education and Multimedia Software Education on Adjustment of Patients With Intestinal Ostomy
Authors: Heidari-Beni Farshad , Esmaeilian Somayeh , Yousefi Fatemeh , Zarei Mohammad Reza , Farahani Mansoureh Ashghali 
Published: March 2022

PURPOSE:
The aim of this study was to compare the effect of face-to-face versus multimedia education on the adjustment of patients to an intestinal ostomy.

DESIGN:
Randomized clinical trial.

SUBJECT AND SETTING:
The sample comprised 135 patients with new ostomies randomly assigned to 3 groups (control, face-to-face, and multimedia education). Data were collected from November 2018 to May 2019; the study setting was Rasul-e Akram and Imam Khomeini Hospitals, Tehran, Iran.

METHODS:
The control group received no additional ostomy education. The face-to-face education group was educated individually in the hospital environment during four 3-hour sessions delivered over 4 consecutive days. The multimedia group viewed a multimedia educational program using a laptop. Data were collected at baseline and 3 months after the intervention. Data collection forms comprised a demographic questionnaire and the Ostomy Adjustment Inventory-23 (OAI-23).

RESULTS:
Before the intervention, the mean OAI-23 adjustment score did not significantly differ among the 3 groups (P = .752). Three months after the intervention, the mean score of adjustment score in the multimedia software group was significantly higher than those of the face-to-face and control groups (P = .000). In addition, the mean score of adjustment of the face-to-face education group was significantly higher than that of the control group (P = .002).

CONCLUSION:
Findings indicate that multimedia education was associated with higher levels of adjustment when compared to face-to-face teaching.
Acetic Acid Use in Chronic Wound Healing
Authors: Chen Qiuyun , Zhou Kehua 
Published: March 2022

BACKGROUND:
Acetic acid is bacteriostatic or bactericidal to many gram-negative and gram-positive microorganisms, especially Pseudomonas. Nevertheless, it has also been found to possess cytotoxic effects in concentrations as low as 0.25% inhibiting the epithelialization process during wound healing.

CASES:
In this multiple case series, we present 2 cases of chronic traumatic leg wounds treated with gauze moistened with acetic acid (0.25%), which were covered with a securing dressing and compression stockinet. Both patients were told to apply gauze moistened with acetic acid (0.25%) twice daily. In both cases, the wound progressed to blue-green drainage and wet yellow slough tissue to near-complete beefy granulation tissue. At this point, acetic acid was replaced with collagen or petrolatum dressing until complete wound closure was achieved. The treatment of these wounds illustrated successful use of acetic acid for chronic wound care.

CONCLUSION:
Our experience with these cases suggests that appearance of blue-green wound drainage and wet yellow slough tissue is a reasonable indication for the use of gauze moistened with acetic acid (0.25%). Further research is needed to test the efficacy of these principles in guiding acetic acid use in wound care.
Evaluating refugia in recent human evolution in Africa
Authors: Blinkhorn James , Timbrell Lucy , Grove Matt , Scerri Eleanor M. L. 
Published: March 2022

Homo sapienshave adapted to an incredible diversity of habitats around the globe. This capacity to adapt to different landscapes is clearly expressed within Africa, with Late PleistoceneHomo sapienspopulations occupying savannahs, woodlands, coastlines and mountainous terrain. As the only area of the world whereHomo sapienshave clearly persisted through multiple glacial-interglacial cycles, Africa is the only continent where classic refugia models can be formulated and tested to examine and describe changing patterns of past distributions and human phylogeographies. The potential role of refugia has frequently been acknowledged in the Late Pleistocene palaeoanthropological literature, yet explicit identification of potential refugia has been limited by the patchy nature of palaeoenvironmental and archaeological records, and the low temporal resolution of climate or ecological models. Here, we apply potential climatic thresholds on human habitation, rooted in ethnographic studies, in combination with high-resolution model datasets for precipitation and biome distributions to identify persistent refugia spanning the Late Pleistocene (130–10 ka). We present two alternate models suggesting that between 27% and 66% of Africa may have provided refugia to Late Pleistocene human populations, and examine variability in precipitation, biome and ecotone distributions within these refugial zones.This article is part of the theme issue ‘Tropical forests in the deep human past’.
Geobacter benzoatilyticus sp. nov., a novel benzoate-oxidizing, iron-reducing bacterium isolated from petroleum contaminated soil
Authors: Yang Guiqin , Li Yanling , Lin Annian , Zhuang Li 
Published: March 2022

A strictly anaerobic bacterial strain, designated Jerry-YXT, was isolated from petroleum-contaminated soil sampled in China. Strain Jerry-YXT was a Gram-stain-negative bacterium forming reddish colonies. It grew optimally at 30 °C and pH 7.0, and tolerated 1.0 % (w/v) NaCl. Strain Jerry-YXT was able to use fumarate, ferric citrate and ferrihydrite as electron acceptors, and ethanol, acetate and benzoate as electron donors. The major fatty acids of this strain were C16 : 0 and C16 : 1
ω7c/C16 : 1
ω6c (summed feature 3). The 16S rRNA gene sequence-based phylogenetic analysis placed this strain in the genus

Geobacter

, being most closely related to

Geobacter metallireducens

(98.2 % similarity),

Geobacter hydrogenophilus

(98.1 %) and

Geobacter grbiciae

(98.0 %). The DNA G+C content was 57.6 mol%. The average nucleotide identity and digital DNA–DNA hybridization values between the genomes of strain Jerry-YXT and

G. metallireducens

GS-15T were 81.8 and 35.4 %, respectively. The results of the polyphasic study allowed the genotypic and phenotypic differentiation of strain Jerry-YXT from its closest species, which suggested that strain Jerry-YXT represents a novel species of the genus

Geobacter

. The name for the proposed new species is Geobacter benzoatilyticus sp. nov. The type strain is Jerry-YXT (=MCCC 1K05659T=JCM 39190T).
Gap selection and steering during obstacle avoidance in pigeons
Authors: Antolin Natalia Pérez-Campanero , Taylor Graham K. 
Published: March 2022

ABSTRACTThe ability of birds to fly through cluttered environments has inspired biologists interested in understanding its underlying mechanisms, and engineers interested in applying its underpinning principles. To analyse this problem empirically, we break it down into two distinct, but related, questions: How do birds select which gaps to aim for? And how do they steer through them? We answered these questions by using a combined experimental and modelling approach, in which we released pigeons (Columbia livia domestica) inside a large hall whose open exit was separated from the release point by a curtain creating two vertical gaps—one of which was obstructed by an obstacle. We tracked the birds using a high-speed motion capture system, and found that their gap choice seemed to be biased by their intrinsic handedness, rather than determined by extrinsic cues such as the size of the gap or its alignment with the destination. We modelled the pigeons’ steering behaviour algorithmically by simulating their flight trajectories under a set of six candidate guidance laws, including those used previously to model targeted flight behaviours in birds. We found that their flights were best modelled by delayed proportional navigation commanding turning in proportion to the angular rate of the line-of-sight from the pigeon to the midpoint of the gap. Our results are consistent with this being a two-phase behaviour, in which the pigeon first heads forward from the release point before steering towards the midpoint of whichever gap it chooses to aim for under closed-loop guidance. Our findings have implications for the sensorimotor mechanisms that underlie clutter negotiation in birds, uniting this with other kinds of target-oriented behaviours including aerial pursuit.
Spatial patterning and immunosuppression of glioblastoma immune contexture in hypoxic niches
Authors: Sattiraju Anirudh , Kang Sangjo , Chen Zhihong , Marallano Valerie , Brusco Concetta , Ramakrishnan Aarthi , Shen Li , Hambardzumyan Dolores , Friedel Roland H , Zou Hongyan 
Published: March 2022

ABSTRACTGlioblastoma (GBM), a highly lethal brain cancer, is notorious for its immunosuppressive microenvironment, yet current immunotherapies are ineffective. Thus, understanding the immune contexture and governing factors of immunosuppression is crucial. Here, we identified a highly dynamic temporospatial patterning of tumor-associated macrophages (TAMs) corresponding to vascular changes in GBM: as tumor vessels transition from an initial dense regular network to later scant engorged vasculature, CD68+ TAMs shift away from perivascular regions to poorly vascularized areas. Remarkably, this process is heavily influenced by the immunocompetency of host animal, as tumor vessels in immunodeficient hosts remained dense and regular while TAMs evenly distributed. Utilizing a sensitive fluorescent reporter to track tumor hypoxia, we revealed that hypoxic niche controls immunosuppression by at least two mechanisms: first, attracting and sequestering activated TAMs in hypoxic zones, and second, reprograming entrapped TAMs towards an immunotolerant state. Indeed, entrapped TAMs also experience hypoxia and upregulate phagocytic marker Cd68 and immunotolerant genes Mrc1 and Arg1, thereby facilitating debris clearing, inflammatory containment, and immunosuppression in hypoxic zones. Mechanistically, we identified Ccl8 and IL-1β as two hypoxic niche factors released by TAMs in response to cues from hypoxic GBM cells, functioning to reinforce TAM retainment. Reciprocally, niche factors also shape the transcriptional responses of hypoxic tumor cells that exhibit quiescence and mesenchymal shift. Moreover, hypoxic niche factors are highly enriched in human GBMs, particularly mesenchymal subtype, and predict poor survival. Importantly, perturbing hypoxic niches resulted in reduced TAM sequestration and better tumor control. Together, understanding the mutual influence of immune contexture and metabolic landscape has important ramifications for improving efficacy of immunotherapies against GBM.
Evaluation of nanopore sequencing for epigenetic epidemiology: a comparison with DNA methylation microarrays
Authors: Flynn Robert , Washer Sam , Jeffries Aaron R , Andrayas Alexandria , Shireby Gemma , Kumari Meena , Schalkwyk Leonard C , Mill Jonathan , Hannon Eilis 
Published: March 2022

AbstractMost epigenetic epidemiology to date has utilized microarrays to identify positions in the genome where variation in DNA methylation is associated with environmental exposures or disease. However, these profile less than 3% of DNA methylation sites in the human genome, potentially missing affected loci and preventing the discovery of disrupted biological pathways. Third generation sequencing technologies, including Nanopore sequencing, have the potential to revolutionise the generation of epigenetic data, not only by providing genuine genome-wide coverage but profiling epigenetic modifications direct from native DNA. Here we assess the viability of using Nanopore sequencing for epidemiology by performing a comparison with DNA methylation quantified using the most comprehensive microarray available, the Illumina EPIC array. We implemented a CRISPR-Cas9 targeted sequencing approach in concert with Nanopore sequencing to profile DNA methylation in three genomic regions to attempt to rediscover genomic positions that existing technologies have shown are differentially methylated in tobacco smokers. Using Nanopore sequencing reads, DNA methylation was quantified at 1,779 CpGs across three regions, providing a finer resolution of DNA methylation patterns compared to the EPIC array. The correlation of estimated levels of DNA methylation between platforms was high. Furthermore, we identified 12 CpGs where hypomethylation was significantly associated with smoking status, including 10 within the AHRR gene. In summary, Nanopore sequencing is a valid option for identifying genomic loci where large differences in DNAm are associated with a phenotype and has the potential to advance our understanding of the role differential methylation plays in the aetiology of complex disease.
Drawing the experience dynamics of meditation
Authors: Jachs Barbara , Camino Garcia Manuel , Canales-Johnson Andrés , Bekinschtein Tristan A. 
Published: March 2022

AbstractSubjective experiences are hard to capture quantitatively without losing depth and nuance, and subjective report analyses are time-consuming, their interpretation contested. We describe Temporal Experience Tracing, a method that captures relevant aspects of the unified conscious experience over a continuous period of time. The continuous multidimensional description of an experience allows us to computationally reconstruct common experience states. Applied to data from 852 meditations – from novice (n=20) and an experienced (n=12) meditators practising Breathing, Loving-Kindness and Open-Monitoring meditation – we reconstructed four recurring experience states with an average duration of 6:46 min (SD = 5:50 min) and their transition dynamics. Three of the experience states assimilated the three meditation styles practiced, and a fourth experience state represented a common low-motivational, ‘off-task’ state for both groups. We found that participants in both groups spent more time in the task-related experience state during Loving Kindness meditation than other meditation styles and were less likely to transition into an ‘off-task’ experience state during Loving Kindness meditation than during Breathing meditation. We demonstrate that drawing the dynamics of experience enables the quantitative analysis of subjective experiences, transforming the time dimension of the stream of consciousness from narrative to measurable.
Campylobacter jejuni modulates reactive oxygen species production and NADPH oxidase 1 expression in human intestinal epithelial cells
Authors: Hong Geunhye , Davies Cadi , Omole Zahra , Liaw Janie , Grabowska Anna D. , Canonico Barbara , Corcionivoshi Nicolae , Wren Brendan , Dorrell Nick , Elmi Abdi , Gundogdu Ozan 
Published: March 2022

AbstractCampylobacter jejuni is the major bacterial cause of foodborne gastroenteritis worldwide. Mechanistically, how this pathogen interacts with intrinsic defence machinery of human intestinal epithelial cells (IECs) remains elusive. To address this, we investigated how C. jejuni counteracts the intracellular and extracellular reactive oxygen species (ROS) in IECs. Our work shows that C. jejuni differentially regulates intracellular and extracellular ROS production in human T84 and Caco-2 cells. C. jejuni downregulates the transcription and translation of Nicotinamide adenine dinucleotide phosphate (NAPDH) oxidase (Nox1), a key ROS-generating enzyme in IECs and antioxidant defence genes cat and sod1. Furthermore, inhibition of Nox1 by diphenylene iodonium (DPI) and siRNA reduced C. jejuni ability to interact, invade and intracellularly survive within T84 and Caco-2 cells. Collectively, these findings provide mechanistic insight into how C. jejuni modulates the IEC defence machinery.
GenErode: a bioinformatics pipeline to investigate genome erosion in endangered and extinct species
Authors: Kutschera Verena E. , Kierczak Marcin , van der Valk Tom , von Seth Johanna , Dussex Nicolas , Lord Edana , Dehasque Marianne , Stanton David W. G. , Khoonsari Payam Emami , Nystedt Björn , Dalén Love , Díez-del-Molino David 
Published: March 2022

AbstractBackgroundMany wild species have suffered drastic population size declines over the past centuries, which have led to ‘genomic erosion’ processes characterized by reduced genetic diversity, increased inbreeding, and accumulation of harmful mutations. Yet, genomic erosion estimates of modern-day populations often lack concordance with dwindling population sizes and conservation status of threatened species. One way to directly quantify the genomic consequences of population declines is to compare genome-wide data from pre-decline museum samples and modern samples. However, doing so requires computational data processing and analysis tools specifically adapted to comparative analyses of degraded, ancient or historical, DNA data with modern DNA data as well as personnel trained to perform such analyses.ResultsHere, we present a highly flexible, scalable, and modular pipeline to compare patterns of genomic erosion using samples from disparate time periods. The GenErode pipeline uses state-of-the-art bioinformatics tools to simultaneously process whole-genome re-sequencing data from ancient/historical and modern samples, and to produce comparable estimates of several genomic erosion indices. No programming knowledge is required to run the pipeline and all bioinformatic steps are well-documented, making the pipeline accessible to users with different backgrounds. GenErode is written in Snakemake and Python3 and uses Conda and Singularity containers to achieve reproducibility on high-performance compute clusters. The source code is freely available on GitHub (https://github.com/NBISweden/GenErode).ConclusionsGenErode is a user-friendly and reproducible pipeline that enables the standardization of genomic erosion indices from temporally sampled whole genome re-sequencing data.
Estimating spatially variable and density-dependent survival using open-population spatial capture-recapture models
Authors: Milleret Cyril , Dey Soumen , Dupont Pierre , Turek Daniel , de Valpine Perry , Bischof Richard 
Published: March 2022

AbstractOpen-population spatial capture-recapture (OPSCR) models use the spatial information contained in individual detections collected over multiple consecutive occasions to estimate occasion-specific density, but also demographic parameters. OPSCR models can also estimate spatial variation in vital rates, but such models are neither widely used nor thoroughly tested. We developed a Bayesian OSPCR model that not only accounts for spatial variation in survival using spatial covariates, but also estimates local density-dependent effects on survival within a unified framework. Using simulations, we show that OPSCR models provide sound inferences on the effect of spatial covariates on survival, including multiple competing sources of mortality, each with potentially different spatial determinants. Estimation of local density-dependent survival was possible but required more data due to the greater complexity of the model. Not accounting for spatial heterogeneity in survival led to positive bias in abundance estimates (up to 10% relative bias). We provide a set of features in R package nimbleSCR that allow computationally efficient fitting of Bayesian OPSCR models with spatially varying survival. The ability to make population-level inferences of spatial variation in survival is an essential step towards a fully spatially-explicit OPSCR model that can disentangle the role of multiple spatial drivers on population dynamics.Open Research statementcode to reproduce the analysis is available on github;https://github.com/Cyril-Milleret/Public/tree/master/SpatialSurvivalOPSCR
Cholinergic forebrain activation improves cognition, boosts neurotrophin receptors, and lowers Aβ42 levels in the cerebral cortex of 5xFAD mice
Authors: Kumro Jacob , Tripathi Ashutosh , Lei Yun , Sword Jeremy , Callahan Patrick , Terry Alvin , Lu Xin-yun , Kirov Sergei , Pillai Anilkumar , Blake David T 
Published: March 2022

AbstractThe biological basis of Alzheimer’s dementia has been hypothesized in terms of basal forebrain cholinergic decline, and in terms reflecting the neuropathologies surrounding beta amyloid and tau. To shed light on the contributions of these different biological elements, we performed five month intermittent stimulation of the basal forebrain, which projects to the cortical mantle, in 5xFAD Alzheimer’s model mice and wild-type littermates, and subjected mice to behavioral testing and tissue analysis. The 5xFAD mice performed worse in water maze testing than their littermates. Stimulation improved both classes of mice, and removed performance differences between genotypes by the fifth testing day. Stimulated groups had two to four-fold increases in immunoblot measures of each of the neurotrophin receptors tropomyosin receptor kinase A and B. Stimulation also led to lower tissue Aβ42 and beta amyloid cleavage enzyme 1 in 5xFAD mice. Despite the lack of strong direct projections from the basal forebrain stimulation region to the hippocampus, the hippocampal tissues in stimulated mice had more nerve growth factor receptor, and lower levels of beta secretase for amyloid. These data support a causal relation between forebrain cholinergic pathways and cognitive decline dependent on Aβ42. Activation of cholinergic brain pathways improves neurotrophin pathways and reduces Aβ42 accumulation. The recruitment of both classes of neurotrophin receptors in the process suggests a serine protease cleavage intermediary between cholinergic response and neurotrophin activation.