bluuebunny/crossref_metadata_2025_split huggingface dataset:
Simple Video-Based Spatiotemporal Gait Analysis Is Not Better than Subjective Visual Assessment of Lameness in Dogs
Authors: Møller Julie H. , Vitger Anne D. , Poulsen Helle H. , Miles James E. 
Published: June 2021

AbstractIntroduction Visual gait analysis is prone to subjectivity, but objective analysis systems are not widely available to clinicians. Simple video analysis using high-definition recordings might enable identification of temporal or spatial variations that could permit objective and repeatable assessments of lameness in general practice.Methods Cohorts of normal and mildly to moderately lame dogs were filmed using a standardized protocol. Using freely available software, measurements of stance, swing and stride time were obtained, along with measurements of pelvic, shoulder, and head height for each limb. Symmetry ratios were calculated, and distributions of normal and lame dogs compared using Mann–Whitney U test and Kruskal–Wallis test.Results Recordings from 35 normal dogs were assessed along with 30 dogs with grade 1 to 3/5 lameness. While no consistent significant differences in temporal characteristics could be found, head height asymmetry was significantly different between lame and normal dogs (p = 0.003), with pairwise comparison showing this difference was restricted to forelimb-lame dogs (p = 0.03).Conclusion While potentially useful for patient records, use of video recordings at walking speeds for simple spatiotemporal gait analysis does not appear to offer clinically significant advantages over visual gait analysis in a typical clinical population of lame dogs.
Eco-friendly utilization to increase income and efficiency of Banggai yam farming in the Banggai Islands, Central Sulawesi, Indonesia
Authors: Jumiyati S , Possumah N , Hadid A , Bachri S , Dua P 
Published: June 2021

Abstract
Banggai yam (Dioscorea spp) is a type of tuber plant which is endemic (local specific) as native food consumed by local communities in the Banggai Islands. Previously, Banggai yam cultivation was carried out traditionally and for household consumption needs. Currently, apart from being a source of food for family farmers, they have cultivated Banggai yam for economic purposes to increase income and meet market demand. The objectives of this study are 1) To determine the comparison of income between farmers who apply the concept of eco-friendly farming with conventional farming for economic purposes only; 2). To determine the difference between eco-friendly utilization of resources and the conventional utilization of resources for economic purposes only. Data collection was carried out by survey method using a questionnaire to 15 farmers with eco-friendly farming concepts and 15 conventional farming concepts. The analysis model used is qualitative and quantitative analysis. The qualitative analysis is used to explain the different forms of eco-friendly utilization of resources with the conventional utilization of resources for economic purposes only. Meanwhile, the quantitative analysis uses comparative analysis (t-Test) to compare the income of farmers who apply the concept of eco-friendly farming with conventional farming. The results show that there are significant differences in income which are influenced by the number of costs and production that affect the efficiency of farming. Besides, the concept of eco-friendly utilization of resources also leads to productivity reorientation to increase the optimal and sustainable income of farming.
Evaluation of cages dimension to the growth of giant trevally Caranx ignobilis
Authors: Pattipeiluhu S M , Soumokil A W , Loupatty J W , Pattipeilohy Ch E , Wamir Y 
Published: June 2021

Abstract
Fish growth is one of the most target in aquaculture with right method of feeding, water quality and size of cages where they were held. In this study, a 70-day research was conducted to evaluate the effect of floating net cages dimension on growth and survival of trevally Caranx ignobilis in Ambon Inner Bay of Indonesia. A total of 90 juvenile trevallies with an average weight of 17.18 ± 1.9 g was randomly stocked in six floating net cages at three different sizes as treatments in replicate groups. Fish were fed 10% of total body mass with by catch fish twice a day to satiation. Length and weight were recorded, growth performance of fish were assessed in the form of Specific Growth Rate (SGR), Food Conversion Ratio (FCR) and Survival rate (SR). The result showed there were no significant different growth rate (SGR) at different treatments (p>0,05), with the highest SR = 100% and lowest FCR = 2.9 both in treatment C. It means the best dimension of fish rare in this research was at the biggest size of cage 200 × 150 × 100 cm 3.
Analysis of prediction of sea level rise impact based on tidal gauge and altimetry satellite on land cover area of Saparua Island, Maluku, Indonesia
Authors: Djunarsjah E , Rahma A , Ihsan  , Nusantara C A D S 
Published: June 2021

Abstract
The sea level rise phenomenon can threaten the environmental, social, and economical aspect of the coastal area. Human activities and other living beings in small islands are very dependent on the resources that are available in the islands. Indonesia as the largest archipelagic state in the world that has 17,508 islands with 99,8% of them are small islands will be directly affected by the phenomenon, which is the submergence of the islands. This research aims to determine the sea level rise trend in Saparua Island using tidal data that are obtained from tide gauge and altimetry satellite. A 12-years tide gauge data and 17-years Sea Level Anomaly (SLA) value of altimetry satellite are used in the research. The monthly average in a 12-years range of tidal station data is calculated to obtain sea level rise trend, meanwhile SLA value from the altimetry satellite observation in the form of satellite footprint is interpolated to get the SLA value across the water area as the sea level rise parameter of altimetry satellite. Then, sea level rise trend will be use to predict the impact of the sea level rise based on topographical condition of Saparua Island. Using those methods, the sea level rise value will be obtained from tide gauge and altimetry satellite in a millimeter orde.
“Toilet Paper Panic”: Uncertainty and Insecurity in Early 1970s Japan
Authors: Siniawer Eiko Maruko 
Published: June 2021

Abstract
When toilet paper disappeared from store shelves across Japan in November 1973, the housewives who searched their neighborhood markets and stood in long lines for the scarce packs were described as unwitting perpetrators of a “toilet paper panic.” The word “panic” evoked well-established notions of a social frenzy, irrational and overwrought. This article overturns a conception of panic laden with condescension and adopts, instead, a more empathetic approach to examining why a run on toilet paper and other daily necessities occurred in late 1973, and why it resonated so deeply across Japan as a “panic.” In the broader context of the early 1970s, the toilet paper scare and its characterization as a “panic” can be understood as responses to sweeping and multifaceted economic challenges that destabilized daily life and threatened to upend middle-class lifestyles. After more than fifteen years of high economic growth, that sense of middle-class comfort and security was shaken by shortages and inflation as well as mounting evidence of government ineptitude and corporate profiteering. Buffeted by insecurity and uncertainty, Japanese “middle-classness” as both an experience and an ideal had never seemed as vulnerable as it did in the early 1970s.
Modulation of frequency and height of cytosolic calcium spikes by plasma membrane anion channels in guard cells
Authors: Tahjib-Ul-Arif Md , Munemasa Shintaro , Nakamura Toshiyuki , Nakamura Yoshimasa , Murata Yoshiyuki 
Published: June 2021

ABSTRACT
Cytosolic calcium ([Ca2+]cyt) elevation activates plasma membrane anion channels in guard cells, which is required for stomatal closure. However, involvement of the anion channels in the [Ca2+]cyt elevation remains unclear. We investigated the involvement using Arabidopsis thaliana anion channel mutants, slac1-4 slah3-3 and slac1-4 almt12-1. Extracellular calcium induced stomatal closure in the wild-type plants but not in the anion channel mutant plants whereas extracellular calcium induced [Ca2+]cyt elevation both in the wild-type guard cells and in the mutant guard cells. The peak height and the number of the [Ca2+]cyt spike were lower and larger in the slac1-4 slah3-3 than in the wild type and the height and the number in the slac1-4 almt12-1 were much lower and much larger than in the wild type. These results suggest that the anion channels are involved in the regulation of [Ca2+]cyt elevation in guard cells.
PathBIX—a web server for network-based pathway annotation with adaptive null models
Authors: Castresana-Aguirre Miguel , Persson Emma , Sonnhammer Erik L L 
Published: June 2021

ABSTRACT

Motivation
Pathway annotation is a vital tool for interpreting and giving meaning to experimental data in life sciences. Numerous tools exist for this task, where the most recent generation of pathway enrichment analysis tools, network-based methods, utilize biological networks to gain a richer source of information as a basis of the analysis than merely the gene content. Network-based methods use the network crosstalk between the query gene set and the genes in known pathways, and compare this to a null model of random expectation.

Results
We developed PathBIX, a novel web application for network-based pathway analysis, based on the recently published ANUBIX algorithm which has been shown to be more accurate than previous network-based methods. The PathBIX website performs pathway annotation for 21 species, and utilizes prefetched and preprocessed network data from FunCoup 5.0 networks and pathway data from three databases: KEGG, Reactome, and WikiPathways.

Availability
https://pathbix.sbc.su.se/

Contact
erik.sonnhammer@scilifelab.se

Supplementary information
Supplementary data are available at Bioinformatics Advances online.
MHCVision: estimation of global and local false discovery rate for MHC class I peptide binding prediction
Authors: Pearngam Phorutai , Sriswasdi Sira , Pisitkun Trairak , Jones Andrew R 
Published: June 2021

Abstract

Motivation
MHC-peptide binding prediction has been widely used for understanding the immune response of individuals or populations, each carrying different MHC molecules as well as for the development of immunotherapeutics. The results from MHC-peptide binding prediction tools are mostly reported as a predicted binding affinity (IC50) and the percentile rank score, and global thresholds e.g. IC50 value &lt; 500 nM or percentile rank &lt; 2% are generally recommended for distinguishing binding peptides from non-binding peptides. However, it is difficult to evaluate statistically the probability of an individual peptide binding prediction to be true or false solely considering predicted scores. Therefore, statistics describing the overall global false discovery rate (FDR) and local FDR, also called posterior error probability (PEP) are required to give statistical context to the natively produced scores.

Result
We have developed an algorithm and code implementation, called MHCVision, for estimation of FDR and PEP values for the predicted results of MHC-peptide binding prediction from the NetMHCpan tool. MHCVision performs parameter estimation using a modified expectation maximization framework for a two-component beta mixture model, representing the distribution of true and false scores of the predicted dataset. We can then estimate the PEP of an individual peptide’s predicted score, and conversely the probability that it is true. We demonstrate that the use of global FDR and PEP estimation can provide a better trade-off between sensitivity and precision over using currently recommended thresholds from tools.

Availability and implementation
https://github.com/PGB-LIV/MHCVision.

Supplementary information
Supplementary data are available at Bioinformatics online.
Acquired pulmonary vein stenosis resulting in haemoptysis: a case series
Authors: Talmor Nina , Massera Daniele , Small Adam , Ramachandran Abhinay , Argilla Michael , Staniloae Cezar S , Latson Larry A , Halpern Dan G 
Published: June 2021

Abstract

Background
Acquired pulmonary vein stenosis (PVS) is an infrequent complication of atrial fibrillation ablation that is often misdiagnosed due to predominant respiratory symptoms. It can result in pulmonary venous hypertension, with varying presentations, ranging from shortness of breath to haemoptysis.

Case summary
We report two patients with a history of paroxysmal atrial fibrillation treated with radiofrequency ablation and pulmonary vein (PV) isolation, who subsequently developed PVS. Case 1 initially presented with indolent symptoms of shortness of breath and cough. He was initially diagnosed with and treated for pneumonia. In contrast, Case 2 presented with massive haemoptysis, requiring intubation and intensive care unit admission. Both patients were eventually diagnosed with PVS by computed tomography. They were treated with PV angioplasty and stenting.

Discussion
While previously limited to the congenital heart disease population, PVS is occurring more frequently now in adult patients as a complication of ablation procedures. It is most effectively treated with angioplasty and stent implantation but has a high rate of recurrence.
Atrial fibrillation and risk of venous thromboembolism: a Swedish Nationwide Registry Study
Authors: Hornestam Björn , Adiels Martin , Wai Giang Kok , Hansson Per-Olof , Björck Lena , Rosengren Annika 
Published: June 2021

AbstractAimsAtrial fibrillation (AF) is associated with arterial thromboembolism, mainly ischaemic stroke, while venous thromboembolism (VTE) in AF is less well studied. The aim of this study, therefore, was to examine the relationship between AF and VTE, including pulmonary embolism (PE) and deep venous thrombosis (DVT).Methods and resultsAF cases without previous VTE, ischaemic stroke or pulmonary arterial hypertension were identified from the Swedish Inpatient Registry between 1987 and 2013 and compared to two population controls per case without AF matched for age, sex, and county with respect to the incidence of VTE, PE, and DVT. In total, 463 244 AF cases were compared to 887 336 population controls. In both men and women, VTE rates were higher among AF patients the first 30 days after an AF diagnosis [40.2 vs. 5.7 in men and 55.7 vs. 6.6 in women per 1000 person-years at risk, respectively; hazard ratios 6.64 (95% confidence interval, 5.74–7.69) and 7.56 (6.47–8.83)]; and then decreasing, simultaneously with an increasing number of AF patients being treated with oral anticoagulation. VTE risk was similar to controls after 9 months in men but remained slightly elevated in women.ConclusionAF is strongly associated with an increased risk of VTE during the first months after diagnosis. Introduction of anticoagulant therapy soon after AF diagnosis might reduce the risk of VTE as well as of ischaemic stroke.
Gastroesophageal reflux disease: recent innovations in endoscopic assessment and treatment
Authors: Chen Sheng , Du Feng , Zhong Changqing , Liu Caifang , Wang Xiaoying , Chen Yan , Wang Gang , Gao Xiaopei , Zhang Lu , Li Lianyong , Wu Wei 
Published: June 2021

Abstract
Innovations in endoscopy have brought about some impressive improvements in diagnosing and treating gastroesophageal reflux disease (GERD). GERD, as one of the most prevalent gastrointestinal disorders in the world, has always been on the cutting edge of endoscopic interventions. A primary diagnosis of GERD is based on symptoms and an initial trial of proton-pump inhibitor (PPI) therapy, which is devoid of adequately instructive value for therapeutic strategies. Endoscopy and optional biopsies can be used to directly observe and determine the abnormal structural and pathophysiological damage in the esophagus. The emergence of minimally invasive endoscopic therapy fills the gap between patients who are reluctant or insensitive to PPIs and candidates who are not indicated for surgical anti-reflux fundoplication. In this review, we discuss the utility of endoscopy and biopsy in patients with persistent GERD-related manifestations after proper medical anti-reflux treatment. Moreover, we portray a landscape of four current endoscopic GERD therapies and clarify the merits and disadvantages of each technique. Future research needs to concentrate on stratifying GERD patients based on personal conditions and elucidating the primary pathophysiology of GERD.
Integrated geological and gravity modelling to improve 3-D model harmonization—Methods and benefits for the Saxony-Anhalt/Brandenburg cross-border region (North German Basin)
Authors: Mueller Christian Olaf , Wächter Jacob , Jahnke Christoph , Pueyo Morer Emilio L , Riefstahl Florian , Malz Alexander 
Published: June 2021

SUMMARYAs 3-D geological models become more numerous and widely available, the opportunity arises to combine them into large regional compilations. One of the biggest challenges facing these compilations is the connection and alignment of individual models, especially in less explored areas or across political borders. In this regard, gravity modelling is suitable for revealing additional subsurface information that can support a harmonization of structural models. Here, we present an integrated geological and gravity modelling approach to support the harmonization process of two geological 3-D models of the North German Basin in the cross-border region between the federal states of Saxony-Anhalt and Brandenburg. Gravity gradient calculation, filtering and Euler deconvolution are utilized to reveal new insights into the local fault system and gravity anomaly sources. The independent models are merged and harmonized during 3-D forward and inverse gravity modelling. Herein, density gradients for individual layers are incorporated in the framework of model parametrization. The resulting geological 3-D model consists of harmonized interfaces and is consistent with the observed gravity field. To demonstrate the plausibility of the derived model, we discuss the new geophysical findings on the sedimentary and crustal structures of the cross-border region in the context of the regional geological setting. The cross-border region is dominated by an NW–SE oriented fault system that coincides with the Elbe Fault System. We interpret a low-density zone within the basement of the Mid-German Crystalline Rise as a northward continuation of the Pretzsch–Prettin Crystalline Complex into the basement of the North German Basin. Additionally, we observe two types of anticlines within the basin, which we link to provinces of contrasting basement rigidity. Our gravity modelling implies that the Zechstein salt has mostly migrated into the deeper parts of the basin west of the Seyda Fault. Finally, we identify a pronounced syncline that accommodates a narrow and up to 800 m deep Cenozoic basin.
The Lines That Held Us: Assessing Racial and Socioeconomic Disparities in SARS-CoV-2 Testing
Authors: Hsiao Chu J , Patel Aditi G M , Fasanya Henrietta O , Stoffel Michelle R , Beal Stacy G , Winston-McPherson Gabrielle N , Campbell Sean T , Cotten Steven W , Crews Bridgit O , Kuan Kevin , Lapedis Cathryn J , Mathias Patrick C , Peck Palmer Octavia M , Greene Dina N 
Published: June 2021

Abstract

Background
Racial disparities in SARS-CoV-2 prevalence are apparent. Race is a sociocultural construct, necessitating investigation into how sociocultural factors contribute.

Methods
This cross-sectional study linked laboratory data of adult patients between February 29 and May 15, 2020 with socio-demographics variables from the 2018 American Community Survey (ACS). Medical sites included healthcare organizations in Michigan, New York, North Carolina, California, Florida, Pennsylvania, and Washington. Race was treated as a proxy for racism and not biological essentialism. Laboratory data included patient age, sex, race, ethnicity, test result, test location, and residential ZIP code. ACS data included economic and educational variables contributing to an SES Index, population density, proportion Medicaid, and racial composition for corresponding ZIP code. Associations between race/socioeconomic variables and test results were examined using odds ratios (OR).

Results
Of 126 452 patients [mean (SD) age 51.9 (18.4) years; 52 747 (41.7%) men; 68 856 (54.5%) White and 27 805 (22.0%) Black], 18 905 (15.0%) tested positive. Of positive tests, 5238 (SD 27.7%) were White and 7223 (SD 38.2%) were Black. Black race increased the odds of a positive test; this finding was consistent across sites [OR 2.11 (95% CI 1.95–2.29)]. When subset by race, higher SES increased the odds of a positive test for White patients [OR 1.10 (95% CI 1.05–1.16)] but decreased the odds for Black patients [OR 0.92 (95% CI 0.86–0.99)]. Black patients, but not White patients, who tested positive overwhelmingly resided in more densely populated areas.

Conclusions
Black race was associated with SARS-CoV-2 positivity and the relationship between SES and test positivity differed by race, suggesting the impact of socioeconomic status on test positivity is race-specific.
Evaluation of Three Commercial and Two Non-Commercial Immunoassays for the Detection of Prior Infection to SARS-CoV-2
Authors: Nilles Eric J , Karlson Elizabeth W , Norman Maia , Gilboa Tal , Fischinger Stephanie , Atyeo Caroline , Zhou Guohai , Bennett Christopher L , Tolan Nicole V , Oganezova Karina , Walt David R , Alter Galit , Simmons Daimon P , Schur Peter , Jarolim Petr , Woolley Ann E , Baden Lindsey R 
Published: June 2021

Abstract

Background
Serological testing provides a record of prior infection with SARS-CoV-2, but assay performance requires independent assessment.

Methods
We evaluated 3 commercial (Roche Diagnostics pan-IG, and Epitope Diagnostics IgM and IgG) and 2 non-commercial (Simoa and Ragon/MGH IgG) immunoassays against 1083 unique samples that included 251 PCR-positive and 832 prepandemic samples.

Results
The Roche assay registered the highest specificity 99.6% (3/832 false positives), the Ragon/MGH assay 99.5% (4/832), the primary Simoa assay model 99.0% (8/832), and the Epitope IgG and IgM 99.0% (8/830) and 99.5% (4/830), respectively. Overall sensitivities for the Simoa, Roche pan-IG, Epitope IgG, Ragon/MGH IgG, and Epitope IgM were 92.0%, 82.9%, 82.5%, 64.5% and 47.0%, respectively. The Simoa immunoassay demonstrated the highest sensitivity among samples stratified by days postsymptom onset (PSO), &lt;8 days PSO (57.69%) 8–14 days PSO (93.51%), 15–21 days PSO (100%), and &gt; 21 days PSO (95.18%).

Conclusions
All assays demonstrated high to very high specificities while sensitivities were variable across assays.