Miracle-dz/UniFAR-FTUs huggingface dataset:
Costs of weaponry: Unarmed males sire more offspring than armed males in a male‐dimorphic mite

Morphological structures used as weapons in male–male competition are not only costly to develop but are also probably costly to maintain during adulthood. Therefore, having weapons could reduce the energy available for other fitness‐enhancing actions, such as post‐copulatory investment. We tested the hypothesis that armed males make lower post‐copulatory investments than unarmed males, and that this difference will be most pronounced under food‐limited conditions. We performed two experiments using the male‐dimorphic bulb mite Rhizoglyphus robini, in which males are either armed “fighters” or unarmed “scramblers. ” Firstly, we tested whether fighters and scramblers differed in their reproductive output after being starved or fed for 1 or 2 weeks. Secondly, we measured the reproductive output of scramblers and fighters (starved or fed) after one, two or three consecutive matings. Scramblers sired more offspring than fighters after 1 week, but scramblers and fighters only sired a few offspring after 2 weeks. Scramblers also sired more offspring than fighters at the first mating, and males rarely sired offspring after consecutive matings. Contrary to our hypothesis, the fecundity of starved and fed males did not differ. The higher reproductive output of scramblers suggests that, regardless of nutritional state, scramblers make larger post‐copulatory investments than fighters. Alternatively, (cryptic) female choice generally favours scramblers. Why the morphs differed in their reproductive output is unclear. Neither morph performed well relatively late in life or after multiple matings. It remains to be investigated to what extent the apparent scrambler advantage contributes to the maintenance and evolution of male morph expression.
BGJ398, A Pan-FGFR Inhibitor, Overcomes Paclitaxel Resistance in Urothelial Carcinoma with FGFR1 Overexpression

Paclitaxel (PTX) is commonly used to treat urothelial carcinoma (UC) after platinum-based chemotherapy has failed. However, single-agent taxane therapy is not sufficient to inhibit tumor progression and drug resistance in advanced UC. Epithelial-to-mesenchymal transition (EMT) induced by fibroblast growth factor receptor (FGFR)1 signaling has been proposed as a mechanism of PTX resistance, but it is unclear whether this can be overcome by FGFR1 inhibition. The present study investigated whether FGFR1 overexpression contributes to PTX resistance and whether FGFR inhibition can enhance PTX efficacy in UC. The effects of PTX combined with the FGFR inhibitor BGJ398 were evaluated in UC cell lines by flow cytometry; Western blot analysis; cell viability, migration, and colony forming assays; and RNA interference. PTX+BGJ398 induced cell cycle arrest and apoptosis in UC cells with mesenchymal characteristics was accompanied by downregulation of cyclin D1 protein and upregulation of gamma-histone 2A family member X and cleaved poly(ADP-ribose) polymerase. Additionally, PTX+BGJ398 synergistically suppressed UC cell migration and colony formation via regulation of EMT-associated factors, while FGFR1 knockdown enhanced the antitumor effect of PTX. These findings provide a basis for development of effective strategies for overcoming PTX resistance in UC through inhibition of FGFR1 signaling.
Practical kinematics for real-time implementation of continuum robots

This paper introduces new analyses and algorithms which are essential for the practical implementation of continuous backbone continuum robots. Actuator length limits strongly shape the configuration or joint space of continuum manipulators, introducing couplings which are not reflected in previously published kinematic models. These unmodeled effects significantly restrict the practical application of previously established kinematic models on continuum robot hardware. This paper presents a new analysis of the effects of actuator limits on continuum robots. Based on the new understanding of the configuration space uncovered, we derive for the first time the configuration space of continuum robots when constrained by actuator length limits. These contributions are essential for effective use of a wide range of continuum robots and have been implemented and tested on two different types of continuum robots. Results and insight gained from this implementation are presented
AMP-Activated Protein Kinase as a Key Trigger for the Disuse-Induced Skeletal Muscle Remodeling

Molecular mechanisms that trigger disuse-induced postural muscle atrophy as well as myosin phenotype transformations are poorly studied. This review will summarize the impact of 5′ adenosine monophosphate -activated protein kinase (AMPK) activity on mammalian target of rapamycin complex 1 (mTORC1)-signaling, nuclear-cytoplasmic traffic of class IIa histone deacetylases (HDAC), and myosin heavy chain gene expression in mammalian postural muscles (mainly, soleus muscle) under disuse conditions, i.e., withdrawal of weight-bearing from ankle extensors. Based on the current literature and the authors’ own experimental data, the present review points out that AMPK plays a key role in the regulation of signaling pathways that determine metabolic, structural, and functional alternations in skeletal muscle fibers under disuse.
Calcium-stimulated calcitonin - The “new standard” in the diagnosis of thyroid C-cell disease - clinically relevant gender-specific cut-off levels for an “old test”

Introduction Pentagastrin (Pg) stimulated calcitonin (sCT) was used to enhance accuracy in medullary thyroid cancer (MTC) diagnosis. As it is now unavailable, calcium (Ca) has been recommended as an alternative. The aim of this study was to define gender-specific cut-off values to predict MTC in patients with elevated basal CT (bCT) following Pg-sCT and Ca-sCT stimulation and to compare the time courses of CT release during stimulation. Materials and methods The stimulation tests were applied in 62 consecutive patients with thyroid nodules. Basal calcitonin was measured by chemiluminescent immunometric assay. All patients underwent thyroidectomy and bilateral central neck dissection. C-cell pathology was confirmed by histological and immunohistochemical evaluation. Results In 39 (0.63) patients MTC was documented while isolated C-cell hyperplasia (CCH) was identified in 23 (0.37) patients. Medullary thyroid cancer was predicted in males with bCT values > 43 pg/mL or sCT concentrations > 470 pg/mL (Pg-sCT) or > 1500 pg/mL (Ca-sCT), and in females with bCT concentrations > 23 pg/mL or sCT concentrations > 200 pg/mL (Pg-sCT) or > 780 pg/mL (Ca-sCT), respectively. Pg-sCT correctly predicted MTC in 16 (0.66) compared to 13 (0.54) after Ca-sCT in males and in 12 (0.80) compared to 11 (0.73) in females; without statistical significance. In patients with CCH or low tumor burden, there was a tendency of faster CT release after Ca stimulation (CT peak after 3min in > 60%) compared to patients with advanced MTC (CT peak after 3min in < 10%). Conclusions Using gender-specific cut-off values, Ca could replace Pg to predict MTC with similar diagnostic power.
Low-Temperature CVD Graphene Nanostructures on Cu and Their Corrosion Properties

Chemical vapor deposition (CVD) graphene is reported to effectively prevent the penetration of outer factors and insulate the underneath metals, hence achieving an anticorrosion purpose. However, there is little knowledge about their characteristics and corresponding corrosion properties, especially for those prepared under different parameters at low temperatures. Using electron cyclotron resonance chemical vapor deposition (ECR-CVD), we can successfully prepare graphene nanostructures on copper (Cu) at temperatures lower than 600 °C. Scanning electron microscopy (SEM), X-ray diffraction (XRD), Raman spectroscopy, and potentiodynamic polarization measurements were used to characterize these samples. In simulated seawater, i.e., 3.5 wt. % sodium chloride (NaCl) solution, the corrosion current density of one graphene-coated Cu fabricated at 400 °C can be 1.16 × 10−5 A/cm2, which is one order of magnitude lower than that of pure Cu. Moreover, the existence of tall graphene nanowalls was found not to be beneficial to the protection as a consequence of their layered orientation. These correlations among the morphology, structure, and corrosion properties of graphene nanostructures were investigated in this study. Therefore, the enhanced corrosion resistance in selected cases suggests that the low-temperature CVD graphene under appropriate conditions would be able to protect metal substrates against corrosion.
Joint-Level Analyses of the Back Squat With and Without Intraset Rest.

Purpose: To provide a joint-level analysis of traditional (TS) and cluster (CS) set structure during the back-squat exercise. Methods: Eight men (24 [3] y, 177.3 [7.9] cm, 82.7 [11.0] kg, 11.9 [3.5] % body fat, and 150.3 [23.0] kg 1-repetition maximum [1RM]) performed the back-squat exercise (80%1RM) using TS (4 × 6, 2-min interset rest) and CS (4 × [2 × 3], 30-s intraset rest, 90-s interset rest), randomly. Lower-limb kinematics were collected by motion capture, as well as kinetic data by bilateral force platforms. Results: CS attenuated the loss in mean power (TS -21.6% [3.9%]; CS -12.4% [7.5%]; P = .042), although no differences in gross movement pattern (sagittal-plane joint angles) within and between conditions were observed (P ≥ .05). However, joint power produced at the hip increased from repetition (REP) 1 through REP 6 during TS, while a decrease was noted at the knee. A similar pattern was observed in the CS condition but was limited to the hip. Joint power produced at the hip increased from REP 1 through REP 3 but returned to REP 1 values before a similar increase through REP 6, resulting in differences between conditions (REP 4, P = .018; REP 5, P = .022). Conclusions: Sagittal-plane joint angles did not change in either condition, although CS elicited greater power. Differing joint power contributions (hip and knee) suggest potential central mechanism that may contribute to enhanced power output during CS and warrant further study. Practitioners should consider incorporating CS into training to promote greater power adaptations and to mitigate fatigue.
Quantitative Ultrasound Imaging Pixel Analysis of the Intrinsic Plantar Muscle Tissue between Hemiparesis and Contralateral Feet in Post-Stroke Patients

Quantitative ultrasound imaging of the muscle tissue may be applied in the neurology field, due to B-mode grayscale pixels values could be used as potential biomarkers for disease progression and intervention effects in poststroke patients. Thus, the study aim was to compare and analyze the ultrasound imaging B-mode pixels differences between the intrinsic plantar muscles cross-sectional area (CSA) in hemiparetic and contralateral feet from poststroke patients by means of the Image J software. A case-control design and a convenience sampling method were used in order to recruit 22 feet from 11 poststroke patients. This total sample was divided into 11 hemiparetic feet and 11 contralateral feet. The Image J software was used in order to evaluate the interface distance, CSA as well as measure the pixels mean, standard deviation (SD) and count from all offline images in the flexor digitorum brevis, abductor hallucis (AbH), and flexor hallucis brevis muscles. Statistically significant differences (p = 0.003) were only shown for the pixels count in the AbH muscle. The rest of outcome measurements did not show any statistically significant difference (p > 0.05). Therefore, B-mode ultrasound imaging Image J software differences for the pixels count reduction were shown in the AbH muscle between hemiparetic and contralateral feet from poststroke patients. Further studies are necessary in order to apply our findings as potential biomarkers during the stroke disease course.
Bayesian Convolutional Neural Networks with Variational Inference

We introduce Bayesian convolutional neural networks with variational inference, a variant of convolutional neural networks (CNNs), in which the intractable posterior probability distributions over weights are inferred by Bayes by Backprop. We demonstrate how this reliable variational inference method can serve as a fundamental construct for various network architectures. On multiple datasets in supervised learning settings (MNIST, CIFAR-10, CIFAR-100), our proposed variational inference method achieves performances equivalent to frequentist inference in identical architectures, while the two desiderata, a measure for uncertainty and regularization are incorporated naturally. We examine in detail how this measure for uncertainty, namely the predictive variance, can be decomposed into aleatoric and epistemic uncertainties. In the past, Bayes by Back prop has been successfully implemented in feedforward and recurrent neural networks, but not in convolutional ones. This work represents the extension of the group of Bayesian neural networks with variational inference which encompasses now all three aforementioned types of network architectures.
Training‐Induced Variations in Haematological and Biochemical Variables in Adolescent Athletes of Arab Origin Throughout an Entire Athletic Season

Abstract The purpose of this study was to observe and report variations in several haematological and biochemical markers throughout an entire athletic season in a large cohort of adolescent athletes of Arab origin. Blood samples were collected from 72 adolescent male athletes at 4 selected time points during their training season. Results expressed in relation to plasma volume were corrected accordingly and significant variations in several variables emerged. Initial uncorrected haematological results revealed that haematocrit (Hct) and mean cell volume (MCV) concentrations noticeably increased at the competitive period (T3) and before the start of the following preseason (T4), whereas reticulocytes equivalent (Ret-He) only rose at T4 phase (p < 0.01). Conversely, corrected red blood cells (RBC), haemoglobin (Hb) and mean cell haemoglobin concentration (MCHC) progressively decreased over the year (p < 0.001). From the electrolytes panel, sodium and chloride considerably reduced at the peak of the training period (T2) to the start of the next preseason (T4), while a significant fall in potassium was mainly observed during the competitive period (T3) (p < 0.001). Coaches and sport scientists could use the results of this study to evaluate typical variations of each age group in order to diagnose potential adverse effects of high training loads, assist in the design of training programs and/or clinical interventions that will safeguard athletes’ health, and consider the important role of plasma volume for the interpretation of results.
The EMBL Nucleotide Sequence Database

The EMBL Nucleotide Sequence Database is a comprehensive database of DNA and RNA sequences directly submitted from researchers and genome sequencing groups and collected from the scientific literature and patent applications. In collaboration with DDBJ and GenBank the database is produced, maintained and distributed at the European Bioinformatics Institute (EBI) and constitutes Europe's primary nucleotide sequence resource. Database releases are produced quarterly and are distributed on CD-ROM. EBI's network services allow access to the most up-to-date data collection via Internet and World Wide Web interface, providing database searching and sequence similarity facilities plus access to a large number of additional databases.
CMV2b-Dependent Regulation of Host Defense Pathways in the Context of Viral Infection

RNA silencing (or RNA interference, RNAi) plays direct roles in plant host defenses against viruses. Viruses encode suppressors of RNAi (VSRs) to counteract host antiviral defenses. The generation of transgenic plants expressing VSRs facilitates the understanding of the mechanisms of VSR-mediated interference with the endogenous silencing pathway. However, studying VSRs independent of other viral components simplifies the complex roles of VSRs during natural viral infection. While suppression of transgene silencing by the VSR 2b protein encoded by cucumber mosaic virus (CMV) requires 2b-small RNA (sRNA) binding activity, suppression of host antiviral defenses requires the binding activity of both sRNAs and AGOs proteins. This study, aimed to understand the functions of 2b in the context of CMV infection; thus, we performed genome-wide analyses of differential DNA methylation regions among wild-type CMV-infected, CMVΔ2b-infected, and 2b-transgenic Arabidopsis plants. These analyses, together with transcriptome sequencing and RT-qPCR analyses, show that while the majority of induced genes in 2b-transgenic plants were involved in extensive metabolic pathways, CMV-infection 2b-dependent induced genes were enriched in plant immunity pathways, including salicylic acid (SA) signaling. Together with infection with CMV mutants that expressed the 2b functional domains of sRNA or AGO binding, our data demonstrate that CMV-accelerated SA signaling depends on 2b-sRNA binding activity which is also responsible for virulence.
Diamond/Porous Titanium Nitride Electrodes With Superior Electrochemical Performance for Neural Interfacing

Robust devices for chronic neural stimulation demand electrode materials which exhibit high charge injection (Qinj) capacity and long-term stability. Boron-doped diamond (BDD) electrodes have shown promise for neural stimulation applications, but their practical applications remain limited due to the poor charge transfer capability of diamond. In this work, we present an attractive approach to produce BDD electrodes with exceptionally high surface area using porous titanium nitride (TiN) as interlayer template. The TiN deposition parameters were systematically varied to fabricate a range of porous electrodes, which were subsequently coated by a BDD thin-film. The electrodes were investigated by surface analysis methods and electrochemical techniques before and after BDD deposition. Cyclic voltammetry (CV) measurements showed a wide potential window in saline solution (between −1.3 and 1.2 V vs. Ag/AgCl). Electrodes with the highest thickness and porosity exhibited the lowest impedance magnitude and a charge storage capacity (CSC) of 253 mC/cm2, which largely exceeds the values previously reported for porous BDD electrodes. Electrodes with relatively thinner and less porous coatings displayed the highest pulsing capacitances (Cpulse), which would be more favorable for stimulation applications. Although BDD/TiN electrodes displayed a higher impedance magnitude and a lower Cpulse as compared to the bare TiN electrodes, the wider potential window likely allows for higher Qinj without reaching unsafe potentials. The remarkable reduction in the impedance and improvement in the charge transfer capacity, together with the known properties of BDD films, makes this type of coating as an ideal candidate for development of reliable devices for chronic neural interfacing.
Bayesian Model Based Clustering Analysis: Application to a Molecular Dynamics Trajectory of the HIV-1 Integrase Catalytic Core

This work describes the application of a Bayesian method for clustering protein conformations sampled during a molecular dynamics simulation of the HIV-1 integrase catalytic core. A clustering analysis is carried out under the assumption of normal distribution without fixing the number of clusters in advance. Some performance measures, such as posterior probability and class cross entropy, are used to determine the most probable set of clusters. The Bayesian clustering method results in meaningful groups identifying transitions between conformational ensembles. The dihedral angles involved in such transitions are also examined in detail. The conformations in high dimensional space are projected into 3D space employing a multidimensional scaling technique to provide a visual inspection.
Role of Overexpressed Transcription Factor FOXO1 in Fatal Cardiovascular Septal Defects in Patau Syndrome: Molecular and Therapeutic Strategies

Patau Syndrome (PS), characterized as a lethal disease, allows less than 15% survival over the first year of life. Most deaths owe to brain and heart disorders, more so due to septal defects because of altered gene regulations. We ascertained the cytogenetic basis of PS first, followed by molecular analysis and docking studies. Thirty-seven PS cases were referred from the Department of Pediatrics, King Abdulaziz University Hospital to the Center of Excellence in Genomic Medicine Research, Jeddah during 2008 to 2018. Cytogenetic analyses were performed by standard G-band method and trisomy13 were found in all the PS cases. Studies have suggested that genes of chromosome 13 and other chromosomes are associated with PS. We, therefore, did molecular pathway analysis, gene interaction, and ontology studies to identify their associations. Genomic analysis revealed important chr13 genes such as FOXO1, Col4A1, HMGBB1, FLT1, EFNB2, EDNRB, GAS6, TNFSF1, STARD13, TRPC4, TUBA3C, and TUBA3D, and their regulatory partners on other chromosomes associated with cardiovascular disorders, atrial and ventricular septal defects. There is strong indication of involving FOXO1 (Forkhead Box O1) gene—a strong transcription factor present on chr13, interacting with many septal defects link genes. The study was extended using molecular docking to find a potential drug lead for overexpressed FOXO1 inhibition. The phenothiazine and trifluoperazine showed efficiency to inhibit overexpressed FOXO1 protein, and could be potential drugs for PS/trisomy13 after validation.
Towards a Neurocognitive Model of Visual Perception

Natural and artiﬁcial vision systems differ considerably in their underlying hardware and their method of information processing. Nevertheless, biological concepts are relevant, adaptable and useful in solving hard computer vision problems. This paper presents a biologically-inspired active vision framework that emulates early visual processing at the neuronal level to accomplish a range of visual tasks. Its emergent behavior is found to be qualitatively similar to humans in certain contexts, and performance is shown to be comparable to computer vision algorithms on a saliency detection task. A neurocognitive model of visual perception based on this framework is motivated.