Miracle-dz/UniFAR-FTUs huggingface dataset:
SurfaceGenie: A web-based application for prioritizing cell-type specific marker candidates

Cell surface proteins play critical roles in a wide range of biological functions and disease processes through mediation of contacts and signals between a cell and its environment. Owing to their biological significance and accessibility, cell surface proteins are attractive targets for developing tools and strategies to identify, study, and manipulate specific cell types of interest. Applications ranging from immunophenotyping and immunotherapy to targeted drug delivery and in vivo imaging are enabled by exploitation of cell-type specific surface proteins. Despite their utility and relevance, the unique combination of molecules present at the cell surface are not yet described for most cell types. While modern mass spectrometry approaches have proven invaluable for generating discovery-driven, empirically derived snapshot views of surface proteins, significant challenges remain when analyzing these often-large datasets for the purpose of identifying candidate markers that are most applicable for downstream applications. To overcome these challenges, we developed GenieScore, a prioritization metric that integrates a consensus-based prediction of cell surface localization with user-input data to rank-order candidate cell-type specific surface markers. In this report, we outline the development of this prioritization strategy and demonstrate its utility for analyzing human and rodent data from proteomic and transcriptomic experiments in the areas of cancer, stem cell, and islet biology. The calculation of GenieScores, as well as additional scoring algorithm permutations that enable prioritization of co-expressed and intracellular cell-type specific candidate markers, is made accessible via the freely available SurfaceGenie web-application at www.cellsurfer. net/surfacegenie.
Multiple nuclear localization sequences in SRSF4 protein

SRSF4 is one of the members of serine‐/arginine (SR)‐rich protein family involved in both constitutive and alternative splicing. SRSF4 is localized in the nucleus with speckled pattern, but its nuclear localization signal was not determined. Here, we have identified nuclear localization signals (NLSs) of SRSF4 by using a pyruvate kinase fusion system. As expected, arginine‐/serine (RS)‐rich domain of SRSF4 confers nuclear localization activity when it is fused to PK protein. We then further delineated the minimum sequences for nuclear localization in RS domain of SRSF4. Surprisingly, RS‐rich region does not always have a nuclear localization activity. In addition, basic amino acid stretches that resemble to classical‐type NLSs were identified. These results strongly suggest that SRSF4 protein uses two different nuclear import pathways with multiple NLSs in RS domain.
Angiotensin (1-7) Decreases Myostatin-Induced NF-κB Signaling and Skeletal Muscle Atrophy

Myostatin is a myokine that regulates muscle function and mass, producing muscle atrophy. Myostatin induces the degradation of myofibrillar proteins, such as myosin heavy chain or troponin. The main pathway that mediates protein degradation during muscle atrophy is the ubiquitin proteasome system, by increasing the expression of atrogin-1 and MuRF-1. In addition, myostatin activates the NF-κB signaling pathway. Renin–angiotensin system (RAS) also regulates muscle mass. Angiotensin (1-7) (Ang-(1-7)) has anti-atrophic properties in skeletal muscle. In this paper, we evaluated the effect of Ang-(1-7) on muscle atrophy and signaling induced by myostatin. The results show that Ang-(1-7) prevented the decrease of the myotube diameter and myofibrillar protein levels induced by myostatin. Ang-(1-7) also abolished the increase of myostatin-induced reactive oxygen species production, atrogin-1, MuRF-1, and TNF-α gene expressions and NF-κB signaling activation. Ang-(1-7) inhibited the activity mediated by myostatin through Mas receptor, as is demonstrated by the loss of all Ang-(1-7)-induced effects when the Mas receptor antagonist A779 was used. Our results show that the effects of Ang-(1-7) on the myostatin-dependent muscle atrophy and signaling are blocked by MK-2206, an inhibitor of Akt/PKB. Together, these data indicate that Ang-(1-7) inhibited muscle atrophy and signaling induced by myostatin through a mechanism dependent on Mas receptor and Akt/PKB.
Analysis of the transgene insertion pattern in a transgenic mouse strain using long-read sequencing

Transgene insertion patterns are critical for the analysis of transgenic animals because the influence of transgenes may change depending on the insertion pattern (such as copy numbers and orientations of concatenations) and the insertion position in the genome. We previously reported a genomic walking strategy to locate transgenes in the genomes of transgenic mice (Exp. Anim. 53: 103–111, 2004) and to analyze transgene insertion patterns (Exp. Anim. 55: 65–69, 2006). With such strategies, however, we could not determine the copy number of transgenes or global genome modification induced by transgene insertion due to read-length limitation. In this study, we used a long-read sequencer (MinION, Oxford Nanopore Technologies) to overcome this limitation. We obtained 922,210 reads using MinION with genomic DNA from a transgenic mouse strain (4C30, Proc. Jpn. Acad. Ser. B. Phys. Biol. Sci. 87: 550–562, 2011). Among the reads, we found one 21,457-bp read containing the transgene using a local BLAST search. Nucleotide dot plot analysis revealed that the transgene was inserted in the genome as a tandem concatemer with an almost entire construct (15–3,508 of 3,508 bp) and a partial fragment (4–660, 657 bp). Ensembl’s BLAST search against the C57BL/6N genome revealed a 9,388-bp deletion at the insertion position in the intron of the Sgcd gene, confirming that mutations such as a large genomic deletion could occur at the time of transgene insertion. Thus, long-read sequencers are useful tools for the analysis of transgene insertion patterns.
Mental Demands at the Workplace - are Information Load, Time Control, and Exploration associated with Depressiveness?

OBJECTIVE According to Self Determination Theory, autonomy and competence are two essential basic human needs. It is the aim of this study to show that mental demands at the workplace (WPMDs) which address those basic needs can protect employees against depressiveness. METHODS Using a sample of 346 working participants (average age 56.2), we derived three WPMDs (Information Load, Time Control, Exploration) via principal component analysis. We then analyzed in how far they predict depressiveness, and in how far this mechanism is mediated by perceived fit between job and person (PJF). RESULTS Time Control and Exploration significantly reduced depressiveness, and the relationship between Exploration and depressiveness was mediated by PJF. CONCLUSIONS Our results emphasize the importance of addressing basic human needs at the workplace, and the relevance of PJF for employee mental health.
Gut Microbiota Is the Key to the Antidepressant Effect of Chaihu-Shu-Gan-San

Accumulating evidence highlights the link between gut microbiota and depression. As an antidepressant herbal drug in clinic, Chaihu-Shu-Gan-San (CSGS) has also been used in China for the treatment of various gastrointestinal disorders. Therefore, we hypothesize that the gut microbiota might be involved in the effect of CSGS. Here, we investigated the antidepressant effects of CSGS against chronic variable stress (CVS)-induced depression rats with and without antibiotic treatment using 16S rRNA gene sequencing and ultra-performance liquid chromatography coupled with time of flight mass spectrometry (UPLC-Q-TOF/MS) based metabolomics approaches. As a result, the prominent effects of CSGS against the depression-like behavioral disorder of CVS-induced rats were significantly weakened when the gut microbiota was changed after oral administration of the broad-spectrum antibiotic. The mediation of CSGS on hippocampal levels of serotonin (5-HT) and glutamic acid (Glu) was also receded with the antibiotic treatment. Further investigation on the diversity of microbiome indicated that the improvement effect of CSGS on gut microbiota dysbiosis—especially the phylum level of Firmicutes—was attenuated after the CSGS combined antibiotic treatment. Moreover, 3-hydroxypicolinic acid (H4) and inosine (H8) in the hippocampus were considered as important biomarkers for depression and are also associated with gut microbiota mediated CSGS efficacy. Taken together, our current study indicated that gut microbiota is a critical factor in the antidepressant effect of CSGS, which improve depression-related metabolic disturbance partly through gut microbiota.
Visual function evaluation for low vision patients with advanced glaucoma

Abstract This study aimed to compare various visual function parameters for evaluating the quality of life (QOL) of patients with advanced glaucoma with low vision. In total, 44 eyes of advanced glaucoma patients with low vision were included in this cross-sectional study. A moving pattern edge band program was used to assess edge detection ability and the low vision quality-of-life (LVQOL) questionnaire was used for evaluating QOL scores of subjects. Correlation analyses between QOL scores and visual functional parameters including pattern edge band unit, visual acuity (VA), and Mean deviation (MD) of perimetry were performed. The areas under receiver operating characteristic curves (AUROCs) of diverse visual functional parameters were calculated. VA and pattern edge band unit were related to LVQOL score in all subjects. For patients with a decimal VA lower than 0.1, only the pattern edge band showed a significant correlation with the QOL associated with distant activities (P = .031). However, the MD of perimetry was not related to the QOL score. After sorting subjects into 2 groups according to the LVQOL score, VA and pattern edge band unit were significantly different (P < .01 and P = .029, respectively). The AUROC for edge detection ability using pattern edge band was higher than MD of perimetry. Assessment of edge detection ability using pattern edge band was meaningful for predicting QOL associated with visual performance in patients with far-advanced glaucoma. For these patients, edge detection could be used as an additional parameter for visual function with traditional VA and perimetry.
Carpal, tarsal, and stifle skin lesion prevalence and potential risk factors in Swiss dairy cows kept in tie stalls: A cross-sectional study

The prevalence of skin lesions at the legs of dairy cows often serves as an indicator for animal welfare and is used as a measurement of adequacy of the present housing conditions. The aim of this study was to assess the prevalence of skin lesions at the carpus, tarsus, and stifle in Swiss dairy cows kept in tie stalls and to describe potential risk factors associated with the different types and severities thereof. Skin lesions and potential risk factors were assessed in 627 cows of 27 tie stall farms in a cross-sectional study. The associations of each outcome and the potential risk factors were assessed by means of logistic regression models using farm as the random factor. One odds ratio was obtained for each biologically relevant risk factor category and the final models were compared between the lesion types and locations. Tarsal lesions were recorded most frequently, with a prevalence of 62.2, 34.4, and 24.0% for moderate to severe hair loss, any severity of ulceration, and moderate to severe swelling, respectively. The prevalence of carpal lesions ranged from 54.4% for hair loss, over 7.7% for ulceration, to 6.1% for swelling, while stifle lesions were recorded less frequently with a prevalence of 18.6, 8.9, 3.4% for hair loss, ulceration, and swelling, respectively. The risk for various skin lesion types and locations significantly increased, when the concrete stall base was covered with a rubber mat and the bedding depth was low. Cows were at the lowest risk to develop skin lesions when they had more than 13 days of outdoor exercise per month. The prevalence of skin lesions in tied Swiss dairy cows is remarkably high and could possibly be reduced by providing the herd more frequent outdoor exercise and a well-cushioned, friction-absorbing and non-abrasive lying surface.
Human Fall Detection Based on Body Posture Spatio-Temporal Evolution

Abnormal falls in public places have significant safety hazards and can easily lead to serious consequences, such as trampling by people. Vision-driven fall event detection has the huge advantage of being non-invasive. However, in actual scenes, the fall behavior is rich in diversity, resulting in strong instability in detection. Based on the study of the stability of human body dynamics, the article proposes a new model of human posture representation of fall behavior, called the “five-point inverted pendulum model”, and uses an improved two-branch multi-stage convolutional neural network (M-CNN) to extract and construct the inverted pendulum structure of human posture in real-world complex scenes. Furthermore, we consider the continuity of the fall event in time series, use multimedia analytics to observe the time series changes of human inverted pendulum structure, and construct a spatio-temporal evolution map of human posture movement. Finally, based on the integrated results of computer vision and multimedia analytics, we reveal the visual characteristics of the spatio-temporal evolution of human posture under the potentially unstable state, and explore two key features of human fall behavior: motion rotational energy and generalized force of motion. The experimental results in actual scenes show that the method has strong robustness, wide universality, and high detection accuracy.
Invasion History of Sirex noctilio Based on COI Sequence: The First Six Years in China

Sirex noctilio F. (Hymenoptera: Siricidae: Siricinae), a new invasive species in China, is a significant international forestry pest which, transported via logs and related wood packing materials, has led to environmental damage and substantial economic loss in many countries around the world. It was first detected in China in 2013, and since then infestations have been found in 18 additional sites. Using a 322 bp fragment of the mitochondrial barcode gene COI, we studied the genetic diversity and structure of S. noctilio populations in both native and invaded ranges, with a specific focus in China. Twelve haplotypes were found across the native and invaded distribution of the pest, of which three were dominant; among these there were only one or two mutational steps between each pair of haplotypes. No obvious genetic structure was found other than in Chinese populations. China has a unique and dominant haplotype not found elsewhere, and compared with the rest of the world, the genetic structure of Chinese populations suggested a multiple invasion scenario.
Causes, types, etiological agents, prevalence, diagnosis, treatment, prevention, effects on human health and future aspects of bovine mastitis

Abstract Mastitis is among the most common and challenging diseases of dairy animals. It is an inflammation of udder tissues due to physical damage, chemical irritation, or infection caused by certain pathogens. Bovine mastitis has been known for ages, but its complex etiology and multi-factorial nature make it difficult to control. Mastitis may have a negative impact on human health by inducing antibiotic-resistant pathogens that may spread, which is threatening. Researchers are continuously struggling to devise suitable methods for mastitis control. Management strategies are mainly focused on disease prevention by farm management which includes proper hygiene, trained staff to monitor minor changes in the udder or milk, and better diagnostic and treatment methods. New technologies which have the potential to unravel this complicated disease include improved diagnostic tools, based on advanced genomics or proteomics, prevention, based on vaccines and immune modulators, and metabolic products of probiotics such as bacteriocins and gene therapy.
A protocol for systematic review and meta-analysis

Introduction: Thoracic diseases include a variety of common human primary malignant tumors, among which lung cancer and esophageal cancer are among the top 10 in cancer incidence and mortality. Early diagnosis is an important part of cancer treatment, so artificial intelligence (AI) systems have been developed for the accurate and automated detection and diagnosis of thoracic tumors. However, the complicated AI structure and image processing made the diagnosis result of AI-based system unstable. The purpose of this study is to systematically review published evidence to explore the accuracy of AI systems in diagnosing thoracic cancers. Methodsandanalysis:We will conduct a systematic review and meta-analysis of the diagnostic accuracy of AI systems for the prediction of thoracic diseases. The primary objective is to assess the diagnostic accuracy of thoracic cancers, including assessing potential biases and calculating combined estimates of sensitivity, specificity, and area under the receiver operating characteristic curve (AUC). The secondary objective is to evaluate the factors associated with different models, classifiers, and radiomics information. We will search databases such as PubMed/MEDLINE, Embase (via OVID), and the Cochrane Library. Two reviewers will independently screen titles and abstracts, perform full article reviews and extract study data. We will report study characteristics and assess methodological quality using the Quality Assessment of Diagnostic Accuracy Studies 2 (QUADAS-2) tool. RevMan 5.3 and Meta-disc 1.4 software will be used for data synthesis. If pooling is appropriate, we will produce summary receiver operating characteristic (SROC) curves, summary operating points (pooled sensitivity and specificity), and 95% confidence intervals around the summary operating points. Methodological subgroup and sensitivity analyses will be performed to explore heterogeneity. PROSPERO registration number: CRD42019135247 Abbreviations: AI = artificial intelligence, AUC = area under the receiver operating characteristic curve, CAD = computer-aided detection, CNN = convolutional neural networks, LDCT = low-dose helical computed tomography, SROC = summary receiver operating characteristic, SVM = support vector machine, VOI = volume of interest.
Persistent Urogenital Schistosomiasis and Its Associated Morbidity in Endemic Communities within Southern Ghana: Suspected Praziquantel Resistance or Reinfection?

Background: schistosomiasis is a neglected tropical disease caused by helminths of the genus Schistosoma. The disease has a worldwide distribution, with more cases occurring in Africa. Urogenital schistosomiasis caused by S. haematobium with its associated morbidity is prevalent in many areas of Ghana. Praziquantel is still the recommended drug of choice for schistosomiasis treatment, although a number of studies have reported sub-therapeutic effects and associated treatment failure. The current study, therefore, assessed whether persistent schistosomiasis, with its associated morbidity among children living in endemic areas within the Greater Accra Region of Ghana, is as a result of reinfection or suspected praziquantel resistance. Methodology: this was a longitudinal study involving a baseline and follow-up sampling after praziquantel treatment. Urine samples were collected from school children (whose parents had also consented) for the detection of S. haematobium ova using a sedimentation technique. The morbidity parameters were examined with urine chemistry strips, as well as microscopy. Viability was assessed using a modified hatchability technique, vital staining (0.4% trypan blue and 1% neutral red) and fluorescent (Hoechst 33258) microscopy. Infected individuals were treated with a single dose of praziquantel (40mg/kg). Resampling to determine reinfection was done sixth months post-treatment, after evidence of total egg clearance. For possible resistance assessment, egg counts and viability testing were conducted on the positive samples at the baseline, as well as weekly post-treatment follow-ups for 12 weeks. Results: out of the 420 school children sampled, 77 were initially positive but, after the sixth month sampling for reinfection assessment, eight out of the initial positives were infected again, giving a reinfection percentage of 10.4%. No suspected praziquantel resistance was recorded in the 21 positives detected out of the 360 sampled for suspected resistance assessment. The egg reduction rate increased weekly in the follow-up samples with a gradual reduction in the egg count. The study also recorded a gradual decrease in the percentage of live eggs after the first week; with all viability testing methods used complimenting each other. The morbidity parameters (proteinuria, haematuria and pyuria) changed between the baseline and post-treatment samples, eventually reducing to zero. Conclusions: the outcome of this study suggests that the persistent schistosomiasis, with its associated morbidity observed in these endemic communities, is not likely to be as a result of praziquantel resistance, but reinfection. Even though there was no suspected resistance observed in the study, there remains the need to continuously intensify the monitoring of praziquantel in other endemic communities.
Substance Use and Exposure to Adverse Childhood Experiences in Undergraduate and Graduate Nursing Students

BACKGROUND: Substance misuse remains a public health crisis and contributor to morbidity and mortality. The nursing workforce is not immune to the impacts of substance misuse as rates are thought to mirror those of the general population. Additionally, as substance misuse often begins in adolescence or early adulthood, prevalence of misuse among practicing nurses highlights the fact that students are also at risk. OBJECTIVES: The purpose of this study was to examine rates and patterns of substance use and adverse childhood experience (ACE) exposure among nursing students while also examining associations between substance use and ACE exposure. METHOD: This study utilizes a cross-sectional and descriptive design through the provision of email surveys to nursing students. Email surveys consisting of the Alcohol Use Disorders Identification Test, the Drug Abuse Screening Tool 10-item survey, the ACE Questionnaire, and a demographic inquiry were distributed via Qualtrics survey software. RESULTS: A total of 662 individuals participated in the survey, the majority of whom self-identified as female, were undergraduate students, and were between 18 and 21 years. Moderate- to high-risk alcohol use was identified in 20% of students, while moderate- to high-risk drug use was identified in 3.6% of students. More than half of students endorsed exposure to at least one ACE. Significant associations were found between the Drug Abuse Screening Tool 10-item survey and the ACE Questionnaire. CONCLUSIONS: The results of this study have significant implications for nursing educators and must inform groundwork for the development of policies and interventions that are evidence based, nonpunitive, and trauma informed.