bluuebunny/crossref_metadata_2025_split huggingface dataset:
Investigation of a facile plasma-driven method for in situ cleaning of metal-based contamination
Authors: WANG 王 Sishu 思蜀 , YANG 杨 Li 黎 , PU 蒲 Guo 国 , LIU 刘 Jianxing 建星 , JING 荆 Wenna 文娜 , GOU 芶 Fujun 富均 , CHEN 陈 Shuwei 曙嵬 , CHEN 陈 Bo 波 , CHEN 陈 Jianjun 建军 , YE 叶 Zongbiao 宗标 , WEI 韦 Jianjun 建军 
Published: June 2022

Abstract
Self-cleaning of tin contaminants was realized utilizing a self-driven hydrogen plasma. Cleaning rates of 0.7–6 nm min−1 were achieved for removal of discontinuous tin particles at different powers. The analysis of topography and cross-sectional morphology revealed that the removal of tin particles was achieved through top-down cleaning with hydrogen plasma, where the upper part of spherical tin particles was always more intensely cleaned under the synergistic effect of hydrogen atoms and ions due to the vertical incidence of ions to the substrate during the whole cleaning process. Redeposition of tin atoms caused by physical sputtering and its promotion of the chemical cleaning effect was observed for the first time. Reflectance recovery measurements during cleaning and surface analysis of the substrate after cleaning indicated that nondestructive cleaning with a reflectance loss of less than 1% can be achieved at a relatively low power of 120 W. Plasma-induced substrate damage, such as holes and valleys, reduced the reflectance of the substrate when cleaning was performed at a high power greater than 120 W, so this method should only be considered for application under conditions without substrate exposure. This study provides a comprehensive understanding of the removal of discontinuous tin particles using the in situ self-driven plasma cleaning method, and also provides meaningful guidance for the extension of this method in other potential fields of application.
4-Phenylbutyrate restored γ-aminobutyric acid uptake and reduced seizures in SLC6A1 patient variant-bearing cell and mouse models
Authors: Nwosu Gerald , Mermer Felicia , Flamm Carson , Poliquin Sarah , Shen Wangzhen , Rigsby Kathryn , Kang Jing Qiong 
Published: June 2022

Abstract
We have studied the molecular mechanisms of variants in solute carrier Family 6 Member 1 associated with neurodevelopmental disorders, including various epilepsy syndromes, autism and intellectual disability. Based on functional assays of solute carrier Family 6 Member 1 variants, we conclude that partial or complete loss of γ-amino butyric acid uptake due to reduced membrane γ-amino butyric acid transporter 1 trafficking is the primary aetiology. Importantly, we identified common patterns of the mutant γ-amino butyric acid transporter 1 protein trafficking from biogenesis, oligomerization, glycosylation and translocation to the cell membrane across variants in different cell types such as astrocytes and neurons. We hypothesize that therapeutic approaches to facilitate membrane trafficking would increase γ-amino butyric acid transporter 1 protein membrane expression and function. 4-Phenylbutyrate is a Food and Drug Administration-approved drug for paediatric use and is orally bioavailable. 4-Phenylbutyrate shows promise in the treatment of cystic fibrosis. The common cellular mechanisms shared by the mutant γ-amino butyric acid transporter 1 and cystic fibrosis transmembrane conductance regulator led us to hypothesize that 4-phenylbutyrate could be a potential treatment option for solute carrier Family 6 Member 1 mutations. We examined the impact of 4-phenylbutyrate across a library of variants in cell and knockin mouse models. Because γ-amino butyric acid transporter 1 is expressed in both neurons and astrocytes, and γ-amino butyric acid transporter 1 deficiency in astrocytes has been hypothesized to underlie seizure generation, we tested the effect of 4-phenylbutyrate in both neurons and astrocytes with a focus on astrocytes. We demonstrated existence of the mutant γ-amino butyric acid transporter 1 retaining wildtype γ-amino butyric acid transporter 1, suggesting the mutant protein causes aberrant protein oligomerization and trafficking. 4-Phenylbutyrate increased γ-amino butyric acid uptake in both mouse and human astrocytes and neurons bearing the variants. Importantly, 4-phenylbutyrate alone increased γ-amino butyric acid transporter 1 expression and suppressed spike wave discharges in heterozygous knockin mice. Although the mechanisms of action for 4-phenylbutyrate are still unclear, with multiple possibly being involved, it is likely that 4-phenylbutyrate can facilitate the forward trafficking of the wildtype γ-amino butyric acid transporter 1 regardless of rescuing the mutant γ-amino butyric acid transporter 1, thus increasing γ-amino butyric acid uptake. All patients with solute carrier Family 6 Member 1 variants are heterozygous and carry one wildtype allele, suggesting a great opportunity for treatment development leveraging wildtype protein trafficking. The study opens a novel avenue of treatment development for genetic epilepsy via drug repurposing.
Conserved QTL and chromosomal inversion affect resistance to columnaris disease in 2 rainbow trout (Oncorhyncus mykiss) populations
Authors: Calboli Federico C F , Koskinen Heikki , Nousianen Antti , Fraslin Clémence , Houston Ross D , Kause Antti 
Published: June 2022

Abstract
We present a comparative genetic analysis of the quantitative trait loci underlying resistance to warm water columnaris disease in 2 farmed rainbow trout (Oncorhynchus mykiss) populations. We provide evidence for the conservation of a major quantitative trait loci on Omy03, and the putative role played by a chromosomal rearrangement on Omy05. A total of 3,962 individuals from the 2 populations experienced a natural Flavobacterium columnare outbreak. Data for 25,823 genome-wide SNPs were generated for both cases (fatalities) and controls (survivors). FST and pairwise additive genetic relationships suggest that, despite being currently kept as separate broodstocks, the 2 populations are closely related. Association analyses identified a major quantitative trait loci on chromosome Omy03 and a second smaller quantitative trait loci on Omy05. Quantitative trait loci on Omy03 consistently explained 3–11% of genetic variation in both populations, whereas quantitative trait loci on Omy05 showed different degree of association across populations and sexes. The quantitative trait loci on Omy05 was found within a naturally occurring, 54.84 cM long inversion which is easy to tag due to a strong linkage disequilibrium between the 375 tagging SNPs. The ancestral haplotype on Omy05 was associated with decreased mortality. Genetic correlation between mortality in the 2 populations was estimated at 0.64, implying that the genetic basis of resistance is partly similar in the 2 populations. Our quantitative trait loci validation identifies markers that can be potentially used to complement breeding value evaluations to increase resistance against columnaris disease, and help to mitigate effects of climate change on aquaculture.
Predicting which genes will respond to transcription factor perturbations
Authors: Kang Yiming , Jung Wooseok J , Brent Michael R 
Published: June 2022

Abstract
The ability to predict which genes will respond to the perturbation of a transcription factor serves as a benchmark for our systems-level understanding of transcriptional regulatory networks. In previous work, machine learning models have been trained to predict static gene expression levels in a biological sample by using data from the same or similar samples, including data on their transcription factor binding locations, histone marks, or DNA sequence. We report on a different challenge—training machine learning models to predict which genes will respond to the perturbation of a transcription factor without using any data from the perturbed cells. We find that existing transcription factor location data (ChIP-seq) from human cells have very little detectable utility for predicting which genes will respond to perturbation of a transcription factor. Features of genes, including their preperturbation expression level and expression variation, are very useful for predicting responses to perturbation of any transcription factor. This shows that some genes are poised to respond to transcription factor perturbations and others are resistant, shedding light on why it has been so difficult to predict responses from binding locations. Certain histone marks, including H3K4me1 and H3K4me3, have some predictive power when located downstream of the transcription start site. However, the predictive power of histone marks is much less than that of gene expression level and expression variation. Sequence-based or epigenetic properties of genes strongly influence their tendency to respond to direct transcription factor perturbations, partially explaining the oft-noted difficulty of predicting responsiveness from transcription factor binding location data. These molecular features are largely reflected in and summarized by the gene’s expression level and expression variation. Code is available at https://github.com/BrentLab/TFPertRespExplainer.
Thigh and Calf Myosteatosis are Strongly Associated with Muscle and Physical Function in African Caribbean Men
Authors: Santanasto Adam J , Zmuda Joseph M , Cvejkus Ryan K , Gordon Christopher L , Nair Sangeeta , Carr J Jeffrey , Terry James G , Wheeler Victor W , Miljkovic Iva 
Published: June 2022

AbstractBackgroundAfrican Caribbeans have higher levels of myosteatosis than other populations; however, little is known about the impact of myosteatosis on physical function in African Caribbeans. Herein, we examined the association between regional myosteatosis of the calf, thigh, and abdomen versus physical function in 850 African-Ancestry men aged 64.2 ± 8.9 (range 50–95) living on the Caribbean Island of Tobago.MethodsMyosteatosis was measured using computed tomography and included intermuscular adipose tissue (IMAT) and muscle density levels of the thigh, calf, psoas, and paraspinous muscles. Outcomes included grip strength, time to complete 5 chair-rises, and 4-meter gait speed. Associations were quantified using separate linear models for each myosteatosis depot and were adjusted for age, height, demographics, physical activity, and chronic diseases. Beta coefficients were presented per standard deviation of each myosteatosis depot.ResultsHigher thigh IMAT was the only IMAT depot significantly associated with weaker grip strength (β = −1.3 ± 0.43 kg, p = .003). However, lower muscle density of all 4 muscle groups was associated with weaker grip strength (all p &lt; .05). Calf and thigh myosteatosis (IMAT and muscle density) were significantly associated with both worse chair rise time and gait speed (all p &lt; .05), whereas psoas IMAT and paraspinous muscle density were associated with gait speed.ConclusionMyosteatosis of the calf and thigh―but not the abdomen―were strongly associated with grip strength and performance measures of physical function in African Caribbean men. However, posterior abdominal myosteatosis may have some utility when abdominal images are all that are available.
Residential Segregation, Social Cohesion, and Aging in Place: Health and Mental Health Inequities
Authors: Smith Richard J , Baik Sol , Lehning Amanda J , Mattocks Nicole , Cheon Ji Hyang , Kim Kyeongmo 
Published: June 2022

Abstract

Background and Objectives
Research shows that living in segregated neighborhoods may have deleterious health outcomes via social, physical, and socioeconomic contexts that deepen existing inequities. However, there has been limited scholarship examining the effects of segregation on older adults, despite an increasing focus on aging in place. Guided by the Ecological Model of Aging, we examined the effects of segregation on older adults’ self-rated health and mental health, accounting for both individual characteristics and neighborhood opportunities and risks (e.g., social cohesion) and the potential moderating role of race and economic vulnerability.

Research Design and Methods
We used data from the first 4 rounds of the National Health and Aging Trends Study (2011–2014) merged with tract-level census data for a final sample size of 3,084 community-dwelling older adults in urban areas. We conducted multivariate regression analyses after conditioning on residential location selection variables.

Results
There was no significant association between neighborhood segregation and self-rated health or between segregation and anxiety and depression symptoms. Consistent with the literature, perceived social cohesion was protective of health in each model.

Discussion and Implications
Our findings highlight the need for more rigorous research on segregation and older residents that utilize longitudinal and spatial data. Our findings also have implications for policies and programs that aim to support the ability to age in place for older adults who have different racial identities and live in different neighborhood contexts. Because social cohesion can be a protective factor for older adults’ health and mental health, policymakers and practitioners should support initiatives to increase social cohesion.
Serum Protein Electrophoresis Reference Intervals for Six Species of Wild-Sampled Sharks in South Florida
Authors: Shinder Samantha L , Cray Carolyn , Hammerschlag Neil , Merly Liza 
Published: June 2022

Abstract
Serum proteins found in the blood have been used as diagnostic markers in both human and animal medicine. Evaluating proteins in the blood of sharks may be a valuable way to assess shark health. The purpose of this study was to perform serum protein electrophoresis from non-lethal blood samples of wild sharks and establish baseline values for six species off South Florida: blacknose (Carcharhinus acronotus), blacktip (C. limbatus), bull (C. leucas), lemon (Negaprion brevirostris), sandbar (C. plumbeus), and tiger shark (Galeocerdo cuvier). Two hundred and fifty-one serum samples were collected between 2015–2018 along with sex determination and morphometric measurements. Agarose gel analysis was performed using mammalian protein fraction delimits albumin, alpha 1-globulins, alpha 2-globulins, beta globulins, and gamma globulins alternatively defined as fractions 1–5. Reference electrophoretic profiles were established for each species, revealing the dominance of protein fractions 3 and 4. The fraction 3:4 ratio was determined for each shark and reference intervals for total solids, protein fractions, and fraction 3:4 ratio are reported for each species. There were no significant differences in total solids or protein fractions between males and females of any species. In both blacktip sharks and bull sharks, total solids were positively correlated with body size, but not in the other species evaluated. In blacknose sharks, the fraction 3:4 ratio was positively correlated with body condition. Results suggest that there may be differences in total solids values across dry and wet seasons for some species. Newly established reference intervals can now be utilized in future research to evaluate the health of captive sharks and to investigate the health status of individuals in the wild as well as relate health measures to environmental conditions.
Repeated Genetic Targets of Natural Selection Underlying Adaptation of Fishes to Changing Salinity
Authors: Velotta Jonathan P , McCormick Stephen D , Whitehead Andrew , Durso Catherine S , Schultz Eric T 
Published: June 2022

SynopsisEcological transitions across salinity boundaries have led to some of the most important diversification events in the animal kingdom, especially among fishes. Adaptations accompanying such transitions include changes in morphology, diet, whole-organism performance, and osmoregulatory function, which may be particularly prominent since divergent salinity regimes make opposing demands on systems that maintain ion and water balance. Research in the last decade has focused on the genetic targets underlying such adaptations, most notably by comparing populations of species that are distributed across salinity boundaries. Here, we synthesize research on the targets of natural selection using whole-genome approaches, with a particular emphasis on the osmoregulatory system. Given the complex, integrated and polygenic nature of this system, we expected that signatures of natural selection would span numerous genes across functional levels of osmoregulation, especially salinity sensing, hormonal control, and cellular ion exchange mechanisms. We find support for this prediction: genes coding for V-type, Ca2+, and Na+/K+-ATPases, which are key cellular ion exchange enzymes, are especially common targets of selection in species from six orders of fishes. This indicates that while polygenic selection contributes to adaptation across salinity boundaries, changes in ATPase enzymes may be of particular importance in supporting such transitions.
Impact of overexpressing NADH kinase on glucoamylase production in Aspergillus niger
Authors: Li Lin-Xiang , Yu Le-Yi , Wang Bin , Pan Li 
Published: June 2022

Abstract
Glucoamylase has a wide range of applications in the production of glucose, antibiotics, amino acids, and other fermentation industries. Fungal glucoamylase, in particular, has attracted much attention because of its wide application in different industries, among which Aspergillus niger is the most popular strain producing glucoamylase. The low availability of NADPH was found to be one of the limiting factors for the overproduction of glucoamylase. In this study, 3 NADH kinases (AN03, AN14, and AN17) and malic enzyme (maeA) were overexpressed in aconidial A. niger by CRISPR/Cas9 technology, significantly increasing the size of the NADPH pool, resulting in the activity of glucoamylase was improved by about 70%, 50%, 90%, and 70%, respectively; the total secreted protein was increased by about 25%, 22%, 52%, and 26%, respectively. Furthermore, the combination of the mitochondrial NADH kinase (AN17) and the malic enzyme (maeA) increased glucoamylase activity by a further 19%. This study provided an effective strategy for enhancing glucoamylase production of A. niger.
Rapid early progression (REP) of glioblastoma is an independent negative prognostic factor: Results from a systematic review and meta-analysis
Authors: Waqar Mueez , Roncaroli Federico , Lehrer Eric J , Palmer Joshua D , Villanueva-Meyer Javier , Braunstein Steve , Hall Emma , Aznar Marianne , De Witt Hamer Philip C , D’Urso Pietro I , Trifiletti Daniel , Quiñones-Hinojosa Alfredo , Wesseling Pieter , Borst Gerben R 
Published: June 2022

Abstract

Background
In patients with newly diagnosed glioblastoma, rapid early progression (REP) refers to tumor regrowth between surgery and postoperative chemoradiotherapy. This systematic review and meta-analysis appraised previously published data on REP to better characterize and understand it.

Methods
Systematic searches of MEDLINE, EMBASE and the Cochrane database from inception to October 21, 2021. Studies describing the incidence of REP—tumor growth between the postoperative MRI scan and pre-radiotherapy MRI scan in newly diagnosed glioblastoma were included. The primary outcome was REP incidence.

Results
From 1590 search results, 9 studies were included with 716 patients. The median age was 56.9 years (IQR 54.0–58.8 y). There was a male predominance with a median male-to-female ratio of 1.4 (IQR 1.1–1.5). The median number of days between MRI scans was 34 days (IQR 18–45 days). The mean incidence rate of REP was 45.9% (range 19.3%–72.0%) and significantly lower in studies employing functional imaging to define REP (P &lt; .001). REP/non-REP groups were comparable with respect to age (P = .99), gender (P = .33) and time between scans (P = .81). REP was associated with shortened overall survival (HR 1.78, 95% CI 1.30–2.43, P &lt; .001), shortened progression-free survival (HR 1.78, 95% CI 1.30–2.43, P &lt; .001), subtotal resection (OR 6.96, 95% CI 4.51–10.73, P &lt; .001) and IDH wild-type versus mutant tumors (OR 0.20, 95% CI 0.02–0.38, P = .03). MGMT promoter methylation was not associated with REP (OR 1.29, 95% CI 0.72–2.28, P = .39).

Conclusions
REP occurs in almost half of patients with newly diagnosed glioblastoma and has a strongly negative prognostic effect. Future studies should investigate its biology and effective treatment strategies.
The Politicization of Ivermectin Tweets During the COVID-19 Pandemic
Authors: Diaz Marlon I , Hanna John J , Hughes Amy E , Lehmann Christoph U , Medford Richard J 
Published: June 2022

Abstract

Background
We explore the ivermectin discourse and sentiment in the United States with a special focus on political leaning through the social media blogging site Twitter.

Methods
We used sentiment analysis and topic modeling to geospatially explore ivermectin Twitter discourse in the United States and compared it to the political leaning of a state based on the 2020 presidential election.

Results
All modeled topics were associated with a negative sentiment. Tweets originating from democratic leaning states were more likely to be negative.

Conclusions
Real-time analysis of social media content can identify public health concerns and guide timely public health interventions tackling disinformation.
Long COVID in the Long Run—23-Month Follow-up Study of Persistent Symptoms
Authors: Helmsdal Gunnhild , Hanusson Katrin Dahl , Kristiansen Marnar Fríðheim , Foldbo Billa Mouritsardóttir , Danielsen Marjun Eivindardóttir , Steig Bjarni á , Gaini Shahin , Strøm Marin , Weihe Pál , Petersen Maria Skaalum 
Published: June 2022

Abstract
Symptoms of long coronavirus disease (COVID) were found in 38% of 170 patients followed for a median of 22.6 months. The most prevalent symptoms were fatigue, affected taste and smell, and difficulties remembering and concentrating. Predictors for long COVID were older age and number of symptoms in the acute phase. Long COVID may take many months, maybe years, to resolve.