Miracle-dz/UniFAR-FTUs huggingface dataset:
Concordance of Fingerstick and Venipuncture Sampling for Fertility Hormones.

1. It is not clear whether the authors used fingerstick capillary blood spotted on filter paper or serum separator cards, which is pertinent information for this study. 2. The authors modified a U.S. Food and Drug Administration (FDA)– approved assay for fingerstick analysis, rendering it a laboratory developed test that is no longer FDA-approved and requires validation.2 3. Serum and fingerstick are considered different sample types and should not be compared without prior validation, according to Clinical and Laboratory Standards Institute procedures.3 4. The concordance graphs in Figure 1 are misleading, except for anti-müllerian hormone, because the graphs compress the clinically relevant sample data. To properly demonstrate concordance, clinically relevant reference ranges should be addressed and graphed, with contrived samples identified.3 5. Showing accuracy and precision for liquid serum on an FDAapproved assay only verifies the ability of the assay to perform as manufactured and cannot be used to demonstrate accuracy and precision in fingerstick samples. 6. The working range for the fingerstick assays has a lower range of zero for each analyte. An appropriate limit of quantification needs to be established.
Pupil Dilation Progression Modulates Aberrant Social Cognition in Autism Spectrum Disorder

Progression of pupil dilation (PD) in response to visual stimuli may indicate distinct internal processes. No study has been performed on PD progression during a social cognition task. Here, we describe PD progression during the Movie for the Assessment of Social Cognition (MASC) test in n = 23 adolescents with Autism Spectrum Disorder (ASD) and n = 24 age, IQ and sex‐matched neurotypical controls (NTC). The MASC consists of 43 video sequences depicting human social interactions, each followed by a multiple‐choice question concerning characters' mental states. PD progression data were extracted by eye tracking and controlled for fixation behavior. Segmenting PD progression during video sequences by principal component analysis, three sequential PD components were unveiled. In ASD compared with NTC, a distinct PD progression was observed with increased constriction amplitude, increased dilation latency, and increased dilation amplitude that correlated with PD progression components. These components predicted social cognition performance. The first and second PD components correlated positively with MASC behavioral performance in ASD but negatively in NTC. These PD components may be interpreted as indicators of sensory‐perceptual processing and attention function. In ASD, aberrant sensory‐perceptual processing and attention function could contribute to attenuated social cognition performance. This needs to be tested by additional studies combining the respective cognitive tests and the outlined PD progression analysis. Phasic activity of the locus coeruleus–norepinephrine system is discussed as putatively shared underlying mechanism. Autism Res2019. © 2019 The Authors. Autism Research published by International Society for Autism Research published by Wiley Periodicals, Inc.
Modules for Rapid Application Development of Web-Based Information Systems (RADWIS)

Abstract This paper describes a model of modular system for Rapid Application Development of Web-based Information Systems (RADWIS). The existing modular systems on technology, framework and platform level does not fully solve the problems of functionality reuse, rapid application development and balance between the complexity, size and functionality. The proposed modular system addresses these problems in a new way. The current work fills the gap between the modular systems on the framework and platform level. The model uses flexible, reusable modules, which can be built with different technologies. They are installable and shareable with the standard dependency manager of the technology and can communicate using web services. The modules use NoSQL approaches in SQL databases. A workflow engine module, based on the Petri Nets theory, allows a graphical and formal mathematical solution for a wide variety of problems.
Transcriptomic Analysis of Mucor irregularis Containing a Negative Single-Stranded RNA Mycovirus

The fungus Mucor irregularis is a causative agent of mucormycosis. The transcriptome analysis of the isolated M. irregularis strain C3B revealed the presence of an RNA polymerase domain of a negative-polarity RNA virus. In this work, we describe the gene ontology-based annotation of the Mucor irregularis transcriptome, which includes a putative RNA mycovirus. ABSTRACT The fungus Mucor irregularis is a causative agent of mucormycosis. The transcriptome analysis of the isolated M. irregularis strain C3B revealed the presence of an RNA polymerase domain of a negative-polarity RNA virus. In this work, we describe the gene ontology-based annotation of the Mucor irregularis transcriptome, which includes a putative RNA mycovirus.
Structure-based optimization of a PDZ-binding motif within a viral peptide stimulates neurite outgrowth

Protection of neuronal homeostasis is a major goal in the management of neurodegenerative diseases. Microtubule-associated Ser/Thr kinase 2 (MAST2) inhibits neurite outgrowth, and its inhibition therefore represents a potential therapeutic strategy. We previously reported that a viral protein (G-protein from rabies virus) capable of interfering with protein–protein interactions between the PDZ domain of MAST2 and the C-terminal moieties of its cellular partners counteracts MAST2-mediated suppression of neurite outgrowth. Here, we designed peptides derived from the native viral protein to increase the affinity of these peptides for the MAST2–PDZ domain. Our strategy involved modifying the length and flexibility of the noninteracting sequence linking the two subsites anchoring the peptide to the PDZ domain. Three peptides, Neurovita1 (NV1), NV2, and NV3, were selected, and we found that they all had increased affinities for the MAST2–PDZ domain, with Kd values decreasing from 1300 to 60 nm, while target selectivity was maintained. A parallel biological assay evaluating neurite extension and branching in cell cultures revealed that the NV peptides gradually improved neural activity, with the efficacies of these peptides for stimulating neurite outgrowth mirroring their affinities for MAST2–PDZ. We also show that NVs can be delivered into the cytoplasm of neurons as a gene or peptide. In summary, our findings indicate that virus-derived peptides targeted to MAST2–PDZ stimulate neurite outgrowth in several neuron types, opening up promising avenues for potentially using NVs in the management of neurodegenerative diseases.
Taxane-based chemotherapy and risk of breast cancer-related lymphedema

Abstract Background: Many studies were performed to explore the correlation between taxane-based chemotherapy and the risk of breast cancer-related lymphedema (BCRL), however, with inconsistent results. Hence, the purpose of this study is to evaluate whether taxane-based chemotherapy is a risk factor for BCRL. Methods: A comprehensive systematic search of clinical trials published in the PubMed, Embase and the Cochrane Library databases will be conducted to identify eligible studies up to the date of December 31, 2018. We will employ risk ratios with 95% confidence intervals (95% CIs) to estimate the correlations between taxane-based chemotherapy and BCRL. Meta-analysis will be performed using Stata SE version 12.0 software. Results: The results of this systematic review and meta-analysis will provide a high-quality synthesis of existing evidence of the correlations between taxane-based chemotherapy and the risk of BCRL. Conclusion: The protocol will provide updated evidence for the use of taxane-based chemotherapy in postoperative breast cancer patients. Ethics and dissemination: It is not necessary for ethical approval because it is based on published studies. The protocol will be disseminated in a peer-reviewed journal or presented at a topic-related conference. Trial registration: This systematic review protocol has been registered with a number of CRD42019123989.
Complete Genome Sequence of Salmonella enterica Serovar Heidelberg Siphophage Sepoy

Phage Sepoy infects Salmonella enterica serovar Heidelberg, a Gram-negative bacterium that causes severe foodborne illnesses. Bacteriophages infecting this pathogen may be used as biocontrol agents for preventing Salmonella foodborne diseases. Here, we present the complete genome sequence of Sepoy, a T5-like siphophage. ABSTRACT Phage Sepoy infects Salmonella enterica serovar Heidelberg, a Gram-negative bacterium that causes severe foodborne illnesses. Bacteriophages infecting this pathogen may be used as biocontrol agents for preventing Salmonella foodborne diseases. Here, we present the complete genome sequence of Sepoy, a T5-like siphophage.
Association of Overlapping, Nonconcurrent, Surgery With Patient Outcomes at a Large Academic Medical Center: A Coarsened Exact Matching Study.

OBJECTIVE Assess the safety of overlapping surgery before implementation of new recommendations and regulations. BACKGROUND Overlapping surgery is a longstanding practice that has not been well studied. There remains a need to analyze data across institutions and specialties to draw well-informed conclusions regarding appropriate application of this practice. METHODS Coarsened exact matching was used to assess the impact of overlap on outcomes amongst all surgical interventions (n = 61,524) over 1 year (2014) at 1 health system. Overlap was categorized as: any, beginning, or end overlap. Study subjects were matched 1:1 on 11 variables. Serious unanticipated events were studied including unplanned return to operating room, readmission, and mortality. RESULTS In all, 8391 patients (13.6%) had any overlap and underwent coarsened exact matching. For beginning/end overlap, matched groups were created (total matched population N = 4534/3616 patients, respectively). Any overlap did not predict unanticipated return to surgery (9.8% any overlap vs 10.1% no overlap; P = 0.45). Further, any overlap did not predict an increase in reoperation, readmission, or emergency room (ER) visits at 30 or 90 days (30D reoperation 3.6% vs 3.7%; P = 0.83, 90D reoperation 3.8% vs 3.9%; P = 0.84) (30D readmission 9.9% vs 10.2%; P = 0.45, 90D readmissions 6.9% vs 7.0%; P = 0.90) (30D ER 5.4% vs 5.6%; P = 0.60, 90D ER 4.8% vs 4.7%; P = 0.71). In addition, any overlap was not associated with mortality over the surgical follow-up period (90D mortality 1.7% vs 2.1%; P = 0.06). Beginning/end overlap had results similar to any overlap. CONCLUSION Overlapping, nonconcurrent surgery is not associated with an increase in reoperation, readmission, ER visits, or unanticipated return to surgery.
Magnetic resonance fingerprinting review part 2: Technique and directions

Magnetic resonance fingerprinting (MRF) is a general framework to quantify multiple MR‐sensitive tissue properties with a single acquisition. There have been numerous advances in MRF in the years since its inception. In this work we highlight some of the recent technical developments in MRF, focusing on sequence optimization, modifications for reconstruction and pattern matching, new methods for partial volume analysis, and applications of machine and deep learning.
A statistical virtual patient population for the glucoregulatory system in type 1 diabetes with integrated exercise model

Purpose We introduce two validated single (SH) and dual hormone (DH) mathematical models that represent an in-silico virtual patient population (VPP) for type 1 diabetes (T1D). The VPP can be used to evaluate automated insulin and glucagon delivery algorithms, so-called artificial pancreas (AP) algorithms that are currently being used to help people with T1D better manage their glucose levels. We present validation results comparing these virtual patients with true clinical patients undergoing AP control and demonstrate that the virtual patients behave similarly to people with T1D. Methods A single hormone virtual patient population (SH-VPP) was created that is comprised of eight differential equations that describe insulin kinetics, insulin dynamics and carbohydrate absorption. The parameters in this model that represent insulin sensitivity were statistically sampled from a normal distribution to create a population of virtual patients with different levels of insulin sensitivity. A dual hormone virtual patient population (DH-VPP) extended this SH-VPP by incorporating additional equations to represent glucagon kinetics and glucagon dynamics. The DH-VPP is comprised of thirteen differential equations and a parameter representing glucagon sensitivity, which was statistically sampled from a normal distribution to create virtual patients with different levels of glucagon sensitivity. We evaluated the SH-VPP and DH-VPP on a clinical data set of 20 people with T1D who participated in a 3.5-day outpatient AP study. Twenty virtual patients were matched with the 20 clinical patients by total daily insulin requirements and body weight. The identical meals given during the AP study were given to the virtual patients and the identical AP control algorithm that was used to control the glucose of the virtual patients was used on the clinical patients. We compared percent time in target range (70–180 mg/dL), time in hypoglycemia (<70 mg/dL) and time in hyperglycemia (>180 mg/dL) for both the virtual patients and the actual patients. Results The subjects in the SH-VPP performed similarly vs. the actual patients (time in range: 78.1 ± 5.1% vs. 74.3 ± 8.1%, p = 0.11; time in hypoglycemia: 3.4 ± 1.3% vs. 2.8 ± 1.7%, p = 0.23). The subjects in the DH-VPP also performed similarly vs. the actual patients (time in range: 75.6 ± 5.5% vs. 71.9 ± 10.9%, p = 0.13; time in hypoglycemia: 0.9 ± 0.8% vs. 1.3 ± 1%, p = 0.19). While the VPPs tended to over-estimate the time in range relative to actual patients, the difference was not statistically significant. Conclusions We have verified that a SH-VPP and a DH-VPP performed comparably with actual patients undergoing AP control using an identical control algorithm. The SH-VPP and DH-VPP may be used as a simulator for pre-evaluation of T1D control algorithms.
Extra-Cochlear Insertion in Cochlear Implantation: A Potentially Disastrous Condition.

OBJECTIVES Cochlear implantation is an increasingly used technique for auditory rehabilitation of pediatric and adult population. Safe implantation is achieved in most cases; however, intraoperative complications and misplacement of the electrode are observed in some. The aim of this presentation was to review the characteristics of patients with extra-cochlear electrode insertion, postoperative diagnostic methods, and considerations in revision surgery. MATERIALS AND METHODS In total, 423 cases of cochlear implantation performed in our clinic between 2012 and 2018 were retrospectively analyzed and those of extra-cochlear implantation were evaluated. RESULTS Extra-cochlear insertion was found in 3 patients. The electrode was placed into the internal acoustic canal in the first case, superior semicircular canal in the second case, and internal carotid artery canal in the third case. Cochlear insertion was achieved in all cases with re-implantation, and no complication was observed. CONCLUSION This case series highlights that rare, but potentially serious, consequences of misplacement of the electrode in cochlear implantation can be successfully avoided and treated via a multidisciplinary approach.
Occupationally Tailored, Web-based, Nutrition and Physical Activity Program for Firefighters: Cluster Randomized Trial and Weight Outcome.

OBJECTIVE To determine the efficacy of an occupationally tailored, web-based health and wellness program, The First Twenty® (TF20), for weight change among volunteer firefighters. METHODS The impact of TF20 on firefighters' 6-month weight change was tested in a cluster, randomized controlled trial, using a crossover design of firefighters in 10 departments. TF20 has web-based nutrition, physical activity and behavioral health components. RESULTS An adjusted treatment induced weight loss from 1.7 to 2.8 lbs was observed for all participants and 2.3 to 3.1 lbs among overweight and obese participants. An average weight gain was observed among firefighters in the control condition and weight loss for those in the treatment condition. CONCLUSIONS TF20 supports firefighters' weight loss. Firefighters need wellness interventions to improve nutrition and physical activity given their high prevalence of obesity.
C-terminal proteolysis of the collagen VI α3 chain by BMP-1 and proprotein convertase(s) releases endotrophin in fragments of different sizes

The assembly of collagen VI microfibrils is a multistep process in which proteolytic processing within the C-terminal globular region of the collagen VI α3 chain plays a major role. However, the mechanisms involved remain elusive. Moreover, C5, the short and most C-terminal domain of the α3 chain, recently has been proposed to be released as an adipokine that enhances tumor progression, fibrosis, inflammation, and insulin resistance and has been named “endotrophin. ” Serum endotrophin could be a useful biomarker to monitor the progression of such disorders as chronic obstructive pulmonary disease, systemic sclerosis, and kidney diseases. Here, using biochemical and isotopic MS-based analyses, we found that the extracellular metalloproteinase bone morphogenetic protein 1 (BMP-1) is involved in endotrophin release and determined the exact BMP-1 cleavage site. Moreover, we provide evidence that several endotrophin-containing fragments are present in various tissues and body fluids. Among these, a large C2–C5 fragment, which contained endotrophin, was released by furin-like proprotein convertase cleavage. By using immunofluorescence microscopy and EM, we also demonstrate that these proteolytic maturations occur after secretion of collagen VI tetramers and during microfibril assembly. Differential localization of N- and C-terminal regions of the collagen VI α3 chain revealed that cleavage products are deposited in tissue and cell cultures. The detailed information on the processing of the collagen VI α3 chain reported here provides a basis for unraveling the function of endotrophin (C5) and larger endotrophin-containing fragments and for refining their use as biomarkers of disease progression.
Anti‐incretin effect: The other face of Janus in human glucose homeostasis

The provocative idea that type 2 diabetes (T2D) may be a surgically treated disorder is based on accumulating evidence suggesting impressive remission rates of obesity and diabetes following bariatric surgery interventions. According to the “anti‐incretin” theory, ingestion of food in the gastrointestinal (GI) tract, apart from activating the well‐described incretin effect, also results in the parallel stimulation of a series of negative feedback mechanisms (anti‐incretin effect). The primary goal of these regulations is to counteract the effects of incretins and other postprandial glucose‐lowering adaptive mechanisms. Disruption of the equilibrium between incretins and anti‐incretins could be an additional pathway leading to the development of insulin resistance and hyperglycemia. This theory provides an alternative theoretical framework to explain the mechanisms behind the optimal effects of metabolic surgery on T2D and underlines the importance of the GI tract in the homeostatic regulation of energy balance in humans. The anti‐incretin concept is currently based on a limited amount of evidence and certainly requires further validation by additional studies. The aim of the present review is to discuss and critically evaluate recent evidence on the anti‐incretin theory, providing an insight into current state and future perspectives.
Complete Genome Sequence of Marinobacter sp. Strain JH2, Isolated from Seawater of the Kiel Fjord

Here, we present the genome sequence of the Gram-negative and rod-shaped Marinobacter sp. strain JH2, which was isolated from seawater of the Kiel Fjord in Germany. The draft genome consists of two replicons, including one chromosome (3.6 Mb) and a circular plasmid (36.7 kb). The genome harbors 3,347 protein-coding genes. ABSTRACT Here, we present the genome sequence of the Gram-negative and rod-shaped Marinobacter sp. strain JH2, which was isolated from seawater of the Kiel Fjord in Germany. The draft genome consists of two replicons, including one chromosome (3.6 Mb) and a circular plasmid (36.7 kb). The genome harbors 3,347 protein-coding genes.
Characterization of Antimicrobial, Antioxidant, and Leishmanicidal Activities of Schiff Base Derivatives of 4-Aminoantipyrine

Our main interest is the characterization of compounds to support the development of alternatives to currently marketed drugs that are losing effectiveness due to the development of resistance. Schiff bases are promising biologically interesting compounds having a wide range of pharmaceutical properties, including anti-inflammatory, antipyretic, and antimicrobial activities, among others. In this work, we have synthesized 12 Schiff base derivatives of 4-aminoantipyrine. In vitro antimicrobial, antioxidant, and cytotoxicity properties are analyzed, as well as in silico predictive adsorption, distribution, metabolism, and excretion (ADME) and bioactivity scores. Results identify two potential Schiff bases: one effective against E. faecalis and the other with antioxidant activity. Both have reasonable ADME scores and provides a scaffold for developing more effective compounds in the future. Initial studies are usually limited to laboratory in vitro approaches, and following these initial studies, much research is needed before a drug can reach the clinic. Nevertheless, these laboratory approaches are mandatory and constitute a first filter to discriminate among potential drug candidates and chemical compounds that should be discarded.
A Novel Approach to Improve Kernel SVM Classification Algorithm Using Hybrid Approach Based on Texture and Statistical Features of AlzheimerÃ¢ÂÂs Stage Using Neuro MR Image

Alzheimer’s (AD) stage classification is carried on 54 number of T2 weighted Magnetic resonance Images of the subject at different stages. Generating the statistical and textual features are collected by performing segmentation of white matter, gray matter, cerebral spinal fluid, area calculated taken as attributes for the data frame. Classification of the data is carried by Supported vector machines and multilayer perceptron algorithm and compared the result of the classification using Area under curve (AUC), Classification Accuracy (CA), F1, Precision, recall and it is observed that multilayer perceptron with a two Hidden layers having given better 100% classification accuracy kernel SVM gives 96.29% of classification accuracy, by hybrid approach it is possible to increase the kernel SVM performance to 100% classification accuracy.
Complete Genome Sequence of Duncaniella muris Strain B8, Isolated from the Feces of C57/BL6 Mice

Here, the complete genome sequence of Duncaniella muris strain B8 is presented. The anaerobic strain was isolated from the feces of C57/BL6 mice and is closely related to D. muris strain DSM 103720, which is the type strain of the recently proposed genus Duncaniella of the Muribaculaceae. ABSTRACT Here, the complete genome sequence of Duncaniella muris strain B8 is presented. The anaerobic strain was isolated from the feces of C57/BL6 mice and is closely related to D. muris strain DSM 103720, which is the type strain of the recently proposed genus Duncaniella of the Muribaculaceae.