Miracle-dz/UniFAR-FTUs huggingface dataset:
The effect of melatonin on testis histological changes and spermatogenesis indexes in mice following treatment with dexamethasone

Abstract Dexamethasone is a common medicine that is capable of causing malformation in the male reproductive system. The aim of this study was to investigate the effect of melatonin on testis histological changes and Spermatogenesis indexes in adult mice following treatment with dexamethasone. Adult male NMRI mice were divided randomly into four groups: control, dexamethasone (i.p injections, 7 mg/kg/day), dexamethasone + melatonin and melatonin (i.p injections, 20 mg/kg/day). After 7 days of treatment, the right testes were studied stereologically and the left testes were used to measure the daily sperm production (DSP). The serum levels of malondialdehyde (MDA), testosterone and total antioxidant capacity (TAC) were also measured. The left caudal epididymis was used to analyze sperm parameters. Data were analyzed using one way ANOVA and means were considered significantly different at p < 0.05. A significant decrease in the testis volume, seminiferous tubules volume, the number of spermatocytes, round and long spermatids, Spermatogenesis indexes, sperm parameters such as motility, count, viability, tail length and DSP, serum testosterone level, TAC and the body weight was found in the dexamethasone group compared to the control. Meanwhile a significant swelling of the interstitial tissue and a significant increase in the MDA level was found in the dexamethasone group compared to the control. The above parameters reached the control level in the dexamethasone + melatonin group. Melatonin can compensate for the adverse effects of dexamethasone on sperm parameters and the histology of the seminiferous tubules in mice.
The Use of the Bipedicled Deep Inferior Epigastric Perforator Flap for Unilateral Breast Reconstruction

Supplemental digital content is available in the text. Introduction The use of abdominal flaps is recognized as a very advantageous approach for breast reconstruction with gradual refinements leading from the pedicled transverse rectus abdominis musculocutaneous flap to the criterion standard deep inferior epigastric perforator (DIEP) flap and its several variations. A systematic review with meta-analysis attempts to investigate the safety of the bipedicled DIEP flap for unilateral breast reconstruction. Methods The literature search used “PubMed” database, and a relevant study conducted at the Queen Victoria Hospital was also included. The extraction of data included study type, follow-up, patients' age, body mass index, preexisting abdominal scars, timing of reconstruction, operating time, flap inset, pedicles' configuration, flap failure, revision, and complication rates. Proportions were pooled with Freeman-Tukey arcsine transformation, and meta-regression was performed to evaluate whether complication rates were modified by different variables. Results Fourteen eligible articles provided an overall sample of 486 flaps, with a median follow-up of 18.5 months. In most cases, immediate reconstruction with undivided flap was performed, with equal use of extraflap and intraflap pedicles' configuration. Only 4 cases of flap failure (0.82%) were documented, with 18% overall complications and 3% fat necrosis rate. The forest plot showed significant between-study heterogeneity, and meta-regression revealed marginal positive association between older patient and complication rate. Conclusions Bipedicled DIEP flap for unilateral breast reconstruction is a technique that maintains the complications rate relatively low in challenging postmastectomy cases. Further comparative studies are needed to substantiate the findings of this study.
Cytochrome c oxidase‐modulatory near‐infrared light penetration into the human brain: Implications for the noninvasive treatment of ischemia/reperfusion injury

Near‐infrared light (IRL) has been evaluated as a therapeutic for a variety of pathological conditions, including ischemia/reperfusion injury of the brain, which can be caused by an ischemic stroke or cardiac arrest. Strategies have focused on modulating the activity of mitochondrial electron transport chain (ETC) enzyme cytochrome c oxidase (COX), which has copper centers that broadly absorb IRL between 700 and 1,000 nm. We have recently identified specific COX‐inhibitory IRL wavelengths that are profoundly neuroprotective in rodent models of brain ischemia/reperfusion through the following mechanism: COX inhibition by IRL limits mitochondrial membrane potential hyperpolarization during reperfusion, which otherwise causes reactive oxygen species (ROS) production and cell death. Prior to clinical application of IRL on humans, IRL penetration must be tested, which may be wavelength dependent. In the present study, four fresh (unfixed) cadavers and isolated cadaver tissues were used to examine the transmission of infrared light through human biological tissues. We conclude that the transmission of 750 and 940 nm IRL through 4 cm of cadaver head supports the viability of IRL to treat human brain ischemia/reperfusion injury and is similar for skin with different skin pigmentation. We discuss experimental difficulties of working with fresh cadavers and strategies to overcome them as a guide for future studies.
From structure to function: Route to understanding lncRNA mechanism

RNAs have emerged as a major target for diagnostics and therapeutics approaches. Regulatory nonprotein‐coding RNAs (ncRNAs) in particular display remarkable versatility. They can fold into complex structures and interact with proteins, DNA, and other RNAs, thus modulating activity, localization, or interactome of multi‐protein complexes. Thus, ncRNAs confer regulatory plasticity and represent a new layer of regulatory control. Interestingly, long noncoding RNAs (lncRNAs) tend to acquire complex secondary and tertiary structures and their function—in many cases—is dependent on structural conservation rather than primary sequence conservation.
Development of a Brief Screen to Detect Cognitive Impairment in Older Adults: The QuickSort

Sorting tests detect cognitive decline in older adults who have a neurodegenerative disorder, such as Alzheimerʼs and Parkinsonʼs disease. Although equally effective at detecting impairment as other cognitive screens (e.g. Mini‐Mental State Examination (MMSE)), sorting tests are not commonly used in this context. This study examines the QuickSort, which is a new brief sorting test that is designed to screen older adults for cognitive impairment.
The extra-vascular water pathway regulates dynamic leaf hydraulic decline and recovery in Populus nigra.

Leaf hydraulic conductance (Kleaf ) is highly dynamic and typically responds to changes in water status and irradiance. However, the relative contribution of vascular (Kx ) and extra-vascular (Kox ) water pathways to Kleaf changes in response to water potential decline and recovery in function of light conditions remains poorly investigated. We investigated the dynamic responses of leaf hydraulics in Populus nigra L. by measuring Kleaf , Kx and Kox changes under drought and upon recovery. Measurements were done at both low and high irradiance (LI and HI, respectively). Kleaf increased and became more vulnerable to dehydration under HI conditions than LI, due to marked changes of Kox . After re-watering, Kleaf recovered in parallel with Kox recovery, but Kleaf response to irradiance remained inhibited. Strong correlations between Kleaf and drought-induced membrane damage demonstrated the relevance of the cell-to-cell water pathway in driving the dynamic responses of Kleaf under drought and recovery. Our findings highlight the importance of coordination between water and light availability in modulating the overall Kleaf response to environmental conditions. This article is protected by copyright. All rights reserved.
ProteoCombiner: integrating bottom-up with top-down proteomics data for improved proteoform assessment

MOTIVATION We present a high-performance software integrating shotgun with top-down proteomic data. The tool can deal with multiple experiments and search engines. RESULTS Enable rapid and easy visualization, manual validation, and comparison of the identified proteoform sequences including the PTM characterization. AVAILABILITY We demonstrate the effectiveness of our approach on a large-scale E. coli dataset; ProteoCombiner unambiguously shortlisted proteoforms among those identified by the multiple search engines. SUPPLEMENTARY INFORMATION ProteoCombiner, a demonstration video and user tutorial are freely available at https://proteocombiner.pasteur. fr, for academic use; all data are thus available from the ProteomeXchange consortium (identifier PXD017618).
Performance, Fantasy, or Narrative: LGBTQ+ Asian American Identity Through Kpop Media and Fandom

ABSTRACT LGBTQ+ Asian Americans experience intersecting forms of oppression, and due to the limited research on this underserved population, it is important to understand their lived experiences and the factors that enhance and endanger their health. The absence of positive representations of LGBTQ+ Asian Americans in the media upholds stereotypes and feelings of invisibility that have harmful effects. Studying LGBTQ+ Asian Americans using Kpop media offers a new and timely way to understand these identities and outcomes of well-being. This study qualitatively explored how 16 college-aged LGBTQ+ Asian Americans identify with Kpop and reconstruct representations to protect themselves from negative influences surrounding their identities. Using grounded theory methodology, this study found that Kpop functions as a source of representation and social connection that supports LGBTQ+ Asian Americans. Findings also illustrate how LGBTQ+ Asian Americans engage in Kpop fan labor to create narratives that can mitigate the harmful effects of marginalization.
Altered Resting-State Neural Oscillations and Spectral Power in Children with Fetal Alcohol Spectrum Disorder.

BACKGROUND Consumption of alcohol during pregnancy impacts fetal development and may lead to a variety of physical, cognitive, and behavioral abnormalities in childhood collectively known as fetal alcohol spectrum disorder (FASD). The FASD spectrum includes children with fetal alcohol syndrome (FAS), partial fetal alcohol syndrome (pFAS), and alcohol-related neurodevelopmental disorder (ARND). Children with a FASD or prenatal alcohol exposure (PAE) have impaired white matter, reduced structural volumes, impaired resting-state functional connectivity when measured with fMRI, and spectral hypersynchrony as infants. Magnetoencephalography (MEG) provides high temporal and good spatial resolution for examining spectral power and connectivity patterns unique from fMRI. The impact of PAE on MEG resting-state spectral power in children remains unknown. METHODS We collected 2 minutes of eyes-open and eyes-closed resting-state data in 51 children (8-12 years of age) with 3 subgroups included: 10 ARND/PAE, 15 FAS/pFAS, and 26 controls (TDC). MEG data were collected on the Elekta Neuromag system. The following spectral metrics were compared between subgroups: power, normalized power, half power, 95% power, and Shannon spectral entropy (SSE). MEG spectral data were correlated with behavioral measures. RESULTS Our results indicate children with FAS/pFAS had reduced spectral power and normalized power, particularly within the alpha frequency band in sensor parietal and source superior parietal and lateral occipital regions, along with elevated half power, 95% power, and SSE. We also found select hemisphere specific effects further indicating reduced corpus callosum connectivity in children with a FASD. Interestingly, while the ARND/PAE subgroup had significant differences from the FAS/pFAS subgroup, in many cases spectral data were not significantly different from TDC. CONCLUSIONS Our results were consistent with previous studies and provide new insight into resting-state oscillatory differences both between children with FAS and TDC, and within FASD subgroups. Further understanding of these resting-state variations and their impact on cognitive function may help provide early targets for intervention and enhance outcomes for individuals with a FASD.
ATOH8 overexpression inhibits the tumor progression and monocyte chemotaxis in hepatocellular carcinoma.

OBJECTIVE ATOH8 is reported to be associated with the progression of many tumors; however, there are remaining controversies. The aim of this study is to explore the role of ATOH8 in hepatocellular carcinoma (HCC) and its effect on monocyte chemotaxis. METHODS Bioinformatics analysis was performed based on the LIHC data in GEPIA and LinkedOmic. Fresh human liver cancer and adjacent nontumor tissue specimens were collected at the Shanghai Public Health Clinical Center. qRT-PCR was performed to determine the transcript level, and western blot analysis and ELISA were used to detect protein expression. CCK8, colony formation, wound-healing, Transwell migration and invasion assays were performed to examine cell proliferation, migration and invasion. An HCC xenograft mouse model was used to determine oncogenicity in vivo. Cell apoptosis and related markers were detected by flow cytometry. Additionally, chemotaxis was assessed by the Transwell migration assay. RESULTS ATOH8 expression is downregulated in HCC tissue and hepatoma cell lines. High expression of ATOH8 predicts a favorable prognosis. Overexpression of ATOH8 in liver cancer cells inhibits proliferation, migration and invasion in vitro, and tumor progression in nude mice. Knockdown of ATOH8 promotes proliferation of Huh7 and EMT-related proteins. Overexpression of ATOH8 increases chemosensitivity to 5-FU, which is probably caused by inhibiting the phosphorylation of AKT (Ser473). Furthermore, overexpression of ATOH8 in Huh7 reduced MCP1 to inhibit chemotactic THP-1, and promoted antitumor inflammatory cytokine (TNF-α and IFN-γ) secretion in monocytes. CONCLUSION In addition to the intrinsic oncosuppressive function of ATOH8 in the liver, ATOH8 may modulate the microenvironment to create an immune activation state. This may partly be attributed to ATOH8 inhibition of the monocyte recruitment via suppressing MCP1 expression so as to promote antitumor inflammatory cytokine secretion in monocytes.
Bioinformatics analysis to screen key prognostic genes in the breast cancer tumor microenvironment

ABSTRACT Increasing evidence has shown that the tumor microenvironment (TME) plays an important role in tumor occurrence and development and can also affect patient prognosis. In this study, we screened key prognostic genes in the breast cancer (BC) TME by analyzing the immune and stromal scores of tumor samples to detect differentially expressed genes (DEGs) and also constructed a TME-related prognostic model. First, we obtained mRNA-Seq and related clinical information for patients with BC from The Cancer Genome Atlas (TCGA) and calculated the stromal and immune scores of tumor tissues using the ESTIMATE algorithm. Next, we performed functional enrichment analysis and generated protein–protein interaction networks from the DEGs that were highly related to the TME. Finally, Cox proportional hazards regression analysis was performed on BC datasets from TCGA, and analyses were conducted on infiltrating immune cells and the human protein atlas. Together, these analyses indicated that the KLRB1 and SIT1 genes could be used as independent prognostic factors for BC, while risk score, age, and clinical stage could be used as prognostic factors. In summary, we found that the prognosis of BC is closely related to immune regulation in the TME. Graphical abstract
Integrative genomic phylogeography reveals signs of mitonuclear incompatibility in a natural hybrid goby population

Hybridization between divergent lineages generates new allelic combinations. One mechanism that can hinder the formation of hybrid populations is mitonuclear incompatibility, that is, dysfunctional interactions between proteins encoded in the nuclear and mitochondrial genomes (mitogenomes) of diverged lineages. Theoretically, selective pressure due to mitonuclear incompatibility can affect genotypes in a hybrid population in which nuclear genomes and mitogenomes from divergent lineages admix. To directly and thoroughly observe this key process, we de novo sequenced the 747‐Mb genome of the coastal goby, Chaenogobius annularis, and investigated its integrative genomic phylogeographics using RNA‐sequencing, RAD‐sequencing, genome resequencing, whole mitogenome sequencing, amplicon sequencing, and small RNA‐sequencing. Chaenogobius annularis populations have been geographically separated into Pacific Ocean (PO) and Sea of Japan (SJ) lineages by past isolation events around the Japanese archipelago. Despite the divergence history and potential mitonuclear incompatibility between these lineages, the mitogenomes of the PO and SJ lineages have coexisted for generations in a hybrid population on the Sanriku Coast. Our analyses revealed accumulation of nonsynonymous substitutions in the PO‐lineage mitogenomes, including two convergent substitutions, as well as signals of mitochondrial lineage‐specific selection on mitochondria‐related nuclear genes. Finally, our data implied that a microRNA gene was involved in resolving mitonuclear incompatibility. Our integrative genomic phylogeographic approach revealed that mitonuclear incompatibility can affect genome evolution in a natural hybrid population.
Constraint Satisfaction Driven Natural Language Generation: A Tree Search Embedded MCMC Approach

Generating natural language under complex constraints is a principled formulation towards controllable text generation. We present a framework to allow specification of combinatorial constraints for sentence generation. We propose TSMC, an efficient method to generate high likelihood sentences with respect to a pre-trained language model while satisfying the constraints. Our approach is highly flexible, requires no task-specific train- ing, and leverages efficient constraint satisfaction solving techniques. To better handle the combinatorial constraints, a tree search algorithm is embedded into the proposal process of the Markov Chain Monte Carlo (MCMC) to explore candidates that satisfy more constraints. Compared to existing MCMC approaches, our sampling approach has a better mixing performance. Experiments show that TSMC achieves consistent and significant improvement on multiple language generation tasks.
Effects of Applications on Computer Tablet for Cognitive Training in Stroke Patients

Objectives: To study the effects of a computer tablet applications for cognitive training on cognitive functions in stroke patients. Study design: A quasi-experimental, one group, pretest-post-test design. Setting: Occupational Therapy Unit of Thammasat University Hospital Subjects: Fifteen patients with first stroke and cognitive impair - ment, aged between 35-70 years, and duration of stroke less than a year, who received occupational therapy service from December 2018 to June 2019 Methods: Participants were selected by purposive sampling. The mini-mental state examination (MMSE)-Thai 2002 was used to screen for cognitive impairments. Participants received a tablet computer-based cognitive training under supervision of an occupational therapist 3 times per week for 6 consecutive weeks. They underwent the Digit Span Test, the Thai Cognitive-Percep-tual Test (Thai-CPT) and the Dynamic Loewenstein Occupational Therapy Cognitive Assessment (DLOTCA) before and after the training period. Descriptive statistics and non-parametric Wilcoxon Signed Ranks Test were used to analyze data. Results: The average age (SD) of the participants was 58 (11.39) year old. The male:female ratio was 1.1:1. The improvement of attention, memory and executive functions reached statistical significance ( p < 0.05). Conclusion: The tablet applications for cognitive training which were used in this study improved attention, memory and executive functions in stroke patients.
Domain Adversarial Transfer Learning for Generalized Tool Wear Prediction

Given its demonstrated ability in analyzing and revealing patterns underlying data, Deep Learning (DL) has been increasingly investigated to complement physics-based models in various aspects of smart manufacturing, such as machine condition monitoring and fault diagnosis, complex manufacturing process modeling, and quality inspection. However, successful implementation of DL techniques relies greatly on the amount, variety, and veracity of data for robust network training. Also, the distributions of data used for network training and application should be identical to avoid the internal covariance shift problem that reduces the network performance applicability. As a promising solution to address these challenges, Transfer Learning (TL) enables DL networks trained on a source domain and task to be applied to a separate target domain and task. This paper presents a domain adversarial TL approach, based upon the concepts of generative adversarial networks. In this method, the optimizer seeks to minimize the loss (i.e., regression or classification accuracy) across the labeled training examples from the source domain while maximizing the loss of the domain classifier across the source and target data sets (i.e., maximizing the similarity of source and target features). The developed domain adversarial TL method has been implemented on a 1-D CNN backbone network and evaluated for prediction of tool wear propagation, using NASA's milling dataset. Performance has been compared to other TL techniques, and the results indicate that domain adversarial TL can successfully allow DL models trained on certain scenarios to be applied to new target tasks.
Software Deception Steering through Version Emulation

Determined cyber adversaries often strategize their attacks by carefully selecting high-value target machines that host insecure (e.g., unpatched) legacy software. In this paper, we propose a moving-target approach to thwart and countersurveil such adversaries, wherein live (non-decoy) enterprise software services are automatically modified to deceptively emulate vulnerable legacy versions that entice attackers. A game-theoretic framework chooses which emulated software stacks, versions, configurations, and vulnerabilities yield the best defensive payoffs and most useful threat data given a specific attack model. The results show that effective movement strategies can be computed to account for pragmatic aspects of deception, such as the utility of various intelligence-gathering actions, impact of vulnerabilities, performance costs of patch deployment, complexity of exploits, and attacker profile.
INTEGRATION OF SOLAR TRACKER AND MAXIMUM POWER POINT TRACKING FOR IMPROVING PHOTOVOLTAIC (PV)SYSTEM EFFICIENCY

This paper presents a method to integrate the solar tracker and the maximum power point tracking (MPPT) to improve the photovoltaic (PV) system efficiency. The integrated system provides a closed-loop solar tracker without the sensors. Instead of using the solar sensor, the output power of the MPPT is employed as the feedback signal to the solar tracker. The solar tracker estimates the solar azimuth and elevation angles using an astronomical algorithm based on the latitude, longitude and the date-time of the local site. To improve the solar tracking accuracy, the fuzzy logic controller is employed to adjust the angle according to the power slope of maximum power with respect to the solar tracker angle. From the simulation results, the proposed method increases the PV energy by 23.23% compared to the fixed PV panel. It improves the efficiency of the existing integrated solar tracker by 0.25% based on the simulation models.