Miracle-dz/UniFAR-FTUs huggingface dataset:
The Toll-Like Receptor/MyD88/XBP1 Signaling Axis Mediates Skeletal Muscle Wasting during Cancer Cachexia

Skeletal muscle wasting causes both morbidity and mortality of cancer patients. Accumulating evidence suggests that the markers of endoplasmic reticulum (ER) stress and unfolded protein response (UPR) pathways are increased in skeletal muscle under multiple catabolic conditions, including cancer. However, the signaling mechanisms and the role of individual arms of the UPR in the regulation of skeletal muscle mass remain largely unknown. ABSTRACT Skeletal muscle wasting causes both morbidity and mortality of cancer patients. Accumulating evidence suggests that the markers of endoplasmic reticulum (ER) stress and unfolded protein response (UPR) pathways are increased in skeletal muscle under multiple catabolic conditions, including cancer. However, the signaling mechanisms and the role of individual arms of the UPR in the regulation of skeletal muscle mass remain largely unknown. In the present study, we demonstrated that gene expression of Toll-like receptors (TLRs) and myeloid differentiation primary response gene 88 (MyD88) was increased in skeletal muscle in a Lewis lung carcinoma (LLC) model of cancer cachexia. Targeted ablation of MyD88 inhibits the loss of skeletal muscle mass and strength in LLC tumor-bearing mice. Inhibition of MyD88 attenuates the LLC-induced activation of the UPR in skeletal muscle of mice. Moreover, muscle-specific deletion of X-box binding protein 1 (XBP1), a major downstream target of IRE1α arm of the UPR, ameliorates muscle wasting in LLC tumor-bearing mice. Our results also demonstrate that overexpression of an active form of XBP1 caused atrophy in cultured myotubes. In contrast, knockdown of XBP1 inhibits myotube atrophy in response to LLC or C26 adenocarcinoma cell conditioned medium. Collectively, our results demonstrate that TLR/MyD88-mediated activation of XBP1 causes skeletal muscle wasting in LLC tumor-bearing mice.
MNM and SNM maintain but do not establish achiasmate homolog conjunction during Drosophila male meiosis

The first meiotic division reduces genome ploidy. This requires pairing of homologous chromosomes into bivalents that can be bi-oriented within the spindle during prometaphase I. Thereafter, pairing is abolished during late metaphase I, and univalents are segregated apart onto opposite spindle poles during anaphase I. In contrast to canonical meiosis, homologous chromosome pairing does not include the formation of a synaptonemal complex and of cross-overs in spermatocytes of Drosophila melanogaster. The alternative pairing mode in these cells depends on mnm and snm. These genes are required exclusively in spermatocytes specifically for successful conjunction of chromosomes into bivalents. Available evidence suggests that MNM and SNM might be part of a physical linkage that directly conjoins chromosomes. Here this notion was analyzed further. Temporal variation in delivery of mnm and snm function was realized by combining various transgenes with null mutant backgrounds. The observed phenotypic consequences provide strong evidence that MNM and SNM contribute directly to chromosome linkage. Premature elimination of these proteins results in precocious bivalent splitting. Delayed provision results in partial conjunction defects that are more pronounced in autosomal bivalents compared to the sex chromosome bivalent. Overall, our findings suggest that MNM and SNM cannot re-establish pairing of chromosomes into bivalents if provided after a chromosome-specific time point of no return. When delivered before this time point, they fortify preformed linkages in order to preclude premature bivalent splitting by the disruptive forces that drive chromosome territory formation during spermatocyte maturation and chromosome condensation during entry into meiosis I.
Deep Insight into the Transcriptome of the Single Silk Gland of Bombyx mori

The silk gland synthesizes and secretes a large amount of protein and stores liquid silk protein at an extremely high concentration. Interestingly, silk proteins and serine protease inhibitors are orderly arranged in the silk gland lumen and cocoon shells. Silk fiber formation and the spinning mechanism have not been fully elucidated. Therefore, we conducted a comparative transcriptome analysis of seven segments of the single silk gland to characterize internal changes in the silk gland during the 5th instar of mature larvae. In total, 3121 differentially expressed genes were identified in the seven segments. Genes highly expressed in the middle silk gland (MSG) were mainly involved in unsaturated fatty acid biosynthesis, fatty acid metabolism, apoptosis—fly, and lysosome pathways, whereas genes highly expressed in the posterior silk gland (PSG) were mainly involved in ribosome, proteasome, citrate cycle, and glycolysis/gluconeogenesis pathways. Thus, the MSG and PSG differ greatly in energy source use and function. Further, 773 gradually upregulated genes (from PSG to MSG) were involved in energy metabolism, silk protein synthesis, and secretion, suggesting that these genes play an important role in silk fiber formation. Our findings provide insights into the mechanism of silk protein synthesis and transport and silk fiber formation.
Neuropeptide changes in the suprachiasmatic nucleus are associated with the development of hypertension

ABSTRACT Human postmortem studies as well as experimental animal studies indicate profound changes in neuropeptide expression in the suprachiasmatic nucleus (SCN) in several pathological conditions including hypertension. In addition, animal experimental observations show that the SCN peptides, vasopressin (AVP) and vasoactive intestinal peptide (VIP) are essential for adequate rhythmicity. These data prompted us to investigate whether changes in these neuronal populations could be the cause or consequence of hypertension. Changes in blood pressure and levels of neuropeptide expression in the SCN were determined during development of hypertension in spontaneously hypertensive rats (SHR), in 2K1C reno-vascular induced hypertensive animals and their respective controls. During the pre-hypertensive stage (5 weeks of age), the VIP and AVP content was higher and the somatostatin (SOM) content was lower in the SHR SCN. At the onset of hypertension (12 weeks of age), when blood pressure levels had just reached about 140 mmHg, AVP and SOM content in the SCN was not different anymore in SHRs compared to control, but VIP was still higher. After 16 weeks, the AVP content was decreased, but SOM was increased and the overall level of VIP in the SCN was still higher in SHRs compared to controls. None of the aforementioned changes in the SCN was observed after induction of hypertension in the 2K1C model. However, while VIP was increased in the NTS projecting medial region of the SCN in SHR animals only after the establishment of hypertension, VIP was decreased in the same region in the 2K1C induced hypertensive rats. Consequently, the present findings confirm previous studies in human and rat indicating that changes in the SCN are strongly associated with the development of hypertension. In addition, the changes in peptide content in the 2K1C animals indicate that the SCN is also able to respond to increases in blood pressure.
Crunch: integrated processing and modeling of ChIP-seq data in terms of regulatory motifs

Although it has become routine for experimental groups to apply ChIP-seq technology to quantitatively characterize the genome-wide binding of transcription factors (TFs), computational analysis procedures remain far from standardized, making it difficult to meaningfully compare ChIP-seq results across experiments. In addition, while genome-wide binding patterns must ultimately be determined by local constellations of binding sites in the DNA, current analysis is typically limited to a standard search for enriched motifs in ChIP-seq peaks. Here we present Crunch, a completely automated computational method that performs all ChIP-seq analysis from quality control through read mapping and peak detecting, and integrates comprehensive modeling of the ChIP signal in terms of known and novel binding motifs, quantifying the contribution of each motif, and annotating which combinations of motifs explain each binding peak. Applying Crunch to 128 ChIP-seq datasets from the ENCODE project we find that TFs naturally separate into ‘solitary TFs’, for which a single motif explains the ChIP-peaks, and ‘co-binding TFs’ for which multiple motifs co-occur within peaks. Moreover, for most datasets the motifs that Crunch identified de novo outperform known motifs and both the set of co-binding motifs and the top motif of solitary TFs are consistent across experiments and cell lines. Crunch is implemented as a web server (crunch.unibas.ch), enabling standardized analysis of any collection of ChIP-seq datasets by simply uploading raw sequencing data. Results are provided both in a graphical interface and as downloadable files.
Metal-insulator-metal tunnel diodes on micro/nano antennas for energy harvesting and detector applications

There are open issues related to efficient rectifying device (diode) for effective applications on energy harvesting and detectors based on micro/nano antennas. Some technological approaches have been developed to improve diode performance at Terahertz (THz) and optical frequency regimes. Diodes based on Metal-Insulator-Metal (MIM) structure is one of the best candidates for this task, mainly due to its relative simple architecture, as well as its capability to achieve high frequency operations. The tunneling current mechanism is the main effect that allows fast diode performances. However, there are challenges related to the fabrication process, due to very low thickness of its insulator barrier, usually below 3 nm. Motivated by this, in this theoretical study we design MIM diodes based on very promising insulator for THz and optical frequency operations based on Zinc Oxide (ZnO), combining with Aluminum (Al), Zinc (Zn) and Copper (Cu) metals; we analyze some basic performance features, assuming variations of the insulator thickness. Results show a critical dependence of MIM diode performance on small variations of this parameter. Therefore, this study indicates the necessity of a strict control of the manufacturing parameters.
The impact of relationship quality on life satisfaction and well-being in dementia caregiving dyads: findings from the IDEAL study

Abstract Objectives: The quality of the relationship between people with dementia and their informal caregiver maybe an important determinant of life satisfaction and well-being for both members of the dyad. Taking a dyadic perspective, the aim of this study was to examine whether self- and partner-rated relationship quality influences life satisfaction and well-being for both people with dementia and their caregivers. Design and methods: Using data from 1283 dyads in the Improving the Experience of Dementia and Enhancing Active Life (IDEAL) cohort, we examined the impact of current relationship quality on life satisfaction and well-being in dementia caregiving dyads. Data were analysed using the Actor–Partner Interdependence Model (APIM) framework. Results: Self-rated relationship quality was associated with own life satisfaction and well-being for both people with dementia and caregivers. Partner-rated relationship quality did not influence own life satisfaction or well-being for either member of the dyad. Conclusion: This study is the first to use the APIM framework to explore the dyadic associations between relationship quality and life satisfaction and well-being in a large cohort of dementia caregiving dyads. The obtained findings suggest that the individual perception of the quality of the caregiving relationship held by each member of the caregiving dyad is an important factor for that member’s life satisfaction and well-being, while the partner’s perception of relationship quality is not. The findings highlight the importance of considering the individual perspective of both the person with dementia and the caregiver and enabling each to maintain positive perceptions of relationship quality.
Effects of immediate versus gradual nicotine reduction in cigarettes on biomarkers of biological effects.

AIM A previous study showed significantly greater reductions in number of cigarettes smoked and biomarkers of toxicant and carcinogen exposure in smokers assigned to immediate reduction of nicotine in cigarettes to very low levels versus gradually over time or continued smoking of normal nicotine content cigarettes. This study examines the effects of these approaches on selected biomarkers associated with harmful biological effects. DESIGN Three-arm, randomized controlled trial. SETTING Ten United States academic institutional sites. PARTICIPANTS Daily smokers uninterested in quitting smoking with a mean (SD) age of 45.1 (13.4) years and smoking 17.1 (8.5) cigarettes/day; 43.9% (549/1250) female; 60.6% (758/1250) white ethnicity. INTERVENTIONS 1) Smoking cigarettes where nicotine content was immediately reduced to very low levels (n=503); 2) smoking cigarettes where nicotine content was gradually reduced, with dose changes occurring monthly (n=498); 3) continued smoking with normal nicotine content cigarettes (n=249). MEASUREMENTS Smokers were assessed at baseline, while smoking their usual brand cigarettes, and again at 4, 8, 12, 16 and 20 weeks. Outcomes were areas under the concentration time curve (AUC) for the period of study of biomarkers of inflammation, oxidative stress and hematological parameters. FINDINGS No consistent significant differences were observed across groups (Bayes factors showing data to be insensitive), with the only exception being red blood cell size variability, which was observed to be lower in the immediate vs. gradual nicotine reduction (mean difference -0.11; 95% CI -0.18, -0.04, p=0.004) and normal nicotine control groups (mean difference -0.15, 95% CI -0.23, -0.06, p=0.001). CONCLUSION It remains unclear whether switching to very low nicotine cigarettes leads to a short-term reduction in biomarkers of tobacco-related harm.
Integrated bioinformatics analysis of miRNA expression in Ewing sarcoma and potential regulatory effects of miR-21 via targeting ALCAM/CD166

Abstract MicroRNAs (miRNAs) play essential functions in pathogenesis of Ewing sarcoma (ES). However, the molecular mechanisms responsible for ES occurrence and development through the regulation of miRNAs remain largely unknown. This study is aimed to explore the differential expressed miRNAs and mRNAs that play vital roles in ES. GSE80201 miRNA and GSE68776 mRNA microarray dataset were selected to carry out a series of bioinformatics analysis such as GEO 2R, gene ontology, pathway enrichment analysis, Venn analysis and PPI network construction to predict hub genes. Furthermore, using quantitative real-time PCR, RNA interference and luciferase reporter assay we demonstrated that activated leukocyte cell adhesion molecule (ALCAM/CD166) is a direct target of miR-21-3p in human ES cell lines. Our results suggest that the miR-21/CD166 axis has the potential to serve as both diagnostic markers and therapeutic targets for ES.
Endothelial Function is improved by Inducing Microbial Polyamine Production in the Gut: A Randomized Placebo-Controlled Trial

Recently, it was demonstrated that spermidine-induced autophagy reduces the risk of cardiovascular disease in mice. Intestinal bacteria are a major source of polyamines, including spermidine. We previously reported that the intake of both Bifidobacterium animalis subsp. lactis (Bifal) and arginine (Arg) increases the production of putrescine, a spermidine precursor, in the gut. Here, we investigated the effects of Bifal and Arg consumption on endothelial function in healthy subjects. Healthy individuals with body mass index (BMI) near the maximum value in the “healthy” range (BMI: 25) (n = 44) were provided normal yogurt containing Bifal and Arg (Bifal + Arg YG) or placebo (normal yogurt) for 12 weeks in this randomized, double-blinded, placebo-controlled, parallel-group comparative study. The reactive hyperemia index (RHI), the primary outcome, was measured using endo-peripheral arterial tone (EndoPAT). The change in RHI from week 0 to 12 in the Bifal + Arg YG group was significantly higher than that in the placebo group, indicating that Bifal + Arg YG intake improved endothelial function. At week 12, the concentrations of fecal putrescine and serum putrescine and spermidine in the Bifal + Arg YG group were significantly higher than those in the placebo group. This study suggests that consuming Bifal + Arg YG prevents or reduces the risk of atherosclerosis.
Maternal, but not paternal or grandparental, caffeine intake is associated with childhood obesity and adiposity: The Lifeways Cross-Generation Cohort Study.

BACKGROUND Maternal caffeine intake is associated with adverse birth outcomes, but its long-term influence on offspring adiposity outcomes is not well studied. Furthermore, few studies have investigated paternal and grandparental caffeine intake in relation to offspring outcomes. OBJECTIVE To study the associations between maternal, paternal, and grandparental caffeine intake and offspring childhood adiposity. DESIGN The core study sample consists of 558 mother-child pairs from the Lifeways Study. Caffeine intake was derived from relevant food items in a self-administered validated food frequency questionnaire in early pregnancy. Children's body mass index (BMI) and waist circumference (WC) were measured at 5- and 9-y follow-up. Childhood overall and central obesity were defined as age- and sex-specific BMI z-score > International Obesity Task Force cut-off and WC z-score > 90th percentile, respectively. Multiple linear and logistic regressions were used to assess associations. RESULTS Study mothers had a mean age of 30.8 y and a mean prepregnancy BMI (kg/m2) of 23.7. In adjusted models, maternal caffeine intake was associated with a higher offspring BMI z-score [β (95% CI): 0.13 (0.06, 0.21) for year 5 and 0.17 (0.04, 0.29) for year 9; per 100 mg/d increment in maternal caffeine intake], WC z-score [β (95% CI): 0.09 (0.01, 0.17) for year 5 and 0.19 (0.05, 0.32) for year 9], and a higher risk of offspring overall obesity [OR (95% CI): 1.32 (1.11, 1.57) for year 5 and 1.44 (1.10, 1.88) for year 9] and central obesity [1.28 (1.02, 1.60) for year 5 and 1.62 (1.12, 2.34) for year 9]. The influence was stronger for coffee caffeine than tea caffeine. No consistent associations were observed for paternal and grandparental caffeine intake. CONCLUSIONS Maternal antenatal, but not paternal or grandparental, caffeine intake is associated with higher offspring adiposity and obesity risk at age 5 and 9 y, with stronger associations observed for coffee caffeine. This prospective observational study was registered at the ISRCTN Registry as ISRCTN16537904.
Health-Promoting Components in Fermented Foods: An Up-to-Date Systematic Review

Fermented foods have long been produced according to knowledge passed down from generation to generation and with no understanding of the potential role of the microorganism(s) involved in the process. However, the scientific and technological revolution in Western countries made fermentation turn from a household to a controlled process suitable for industrial scale production systems intended for the mass marketplace. The aim of this paper is to provide an up-to-date review of the latest studies which investigated the health-promoting components forming upon fermentation of the main food matrices, in order to contribute to understanding their important role in healthy diets and relevance in national dietary recommendations worldwide. Formation of antioxidant, bioactive, anti-hypertensive, anti-diabetic, and FODMAP-reducing components in fermented foods are mainly presented and discussed. Fermentation was found to increase antioxidant activity of milks, cereals, fruit and vegetables, meat and fish. Anti-hypertensive peptides are detected in fermented milk and cereals. Changes in vitamin content are mainly observed in fermented milk and fruits. Fermented milk and fruit juice were found to have probiotic activity. Other effects such as anti-diabetic properties, FODMAP reduction, and changes in fatty acid profile are peculiar of specific food categories.
A Repair Method of Point Cloud with Big Hole

The repair of point cloud with big hole is a challenge research in computer graphics. In our paper, we present a divisional repair method based on feature lines, including hole boundary lines, ridge and valley lines. First, these feature lines are obtained and reconstructed. In order to maintain the original contour shapes, the big hole is divided into several small holes based on the features lines. Then control points sequence of NURBS surface fitting is obtained. Finally, the hole is repaired by fitting every small hole. The experiment results show that our method not only recovers the initial shape-skeleton of hole, but also maintains its sharp features.
A Hybrid Genetic and Particle Swarm Optimization Algorithms for Dynamic Facility Layout Problem with Multiple Transporters

Nowadays, manufacturing plants should be agile to changes their production mix plan based on dynamic demands. Here, layout design significantly could impact on manufacturing efficiency. When the flows of materials between departments embed variability during the planning horizon, this problem is known as the dynamic facility layout problem (DFLP). This paper extends such problem with considering multiple transporters, which commonly are used for transportation tasks among facilities. Hence, we extended the classical DFLP objective function in such a way that could encounter total combined rearrangement, material handling and transporting costs. Firstly, the relevant mathematical model is presented and then hybrid metaheuristic algorithms based on particle swarm optimization (PSO)and genetic algorithm (GA)presented to solve such problem efficiently. To achieve reliable results, a Taguchi's design of experiments is applied to calibrate initial parameters. Also, a few small-sized problems are solved using the CPLEX software. Analysis of the results shows that the proposed hybrid PSO algorithms have good solution quality according to the objective function and CPU time rather than hybrid GA and proved the effectiveness of this algorithm on the set of test problems.
Conformal Parameterization by Minimizing Distortion Energy

Planar parameterization of triangulated surface meshes is used to find an isomorphic mapping between a discrete 3D surface and a planar patch, a crucial problem in computer graphics, computer aided design and digital geometric processing. This paper introduces an algorithm for parameterizing 3D meshes by minimizing the angle and area distortion energy. The parameterization algorithm traverses the mesh in a region growing way and is able to yield results with less global distortion. Various applications are tested to illustrate the effectiveness of the techniques proposed in this paper.
A Cluster-Based Handoff for Vehicular Ad-hoc Network

The development of smart vehicular nodes has increased the demand of various infotainment and sensor dependent services that provides comfort to vehicular drivers. This brings in the necessity of development in Vehicular Network. To provide seamless services for the fast moving vehicles they need to have uninterrupted connection with the network. Efficient and optimized handoff strategies in VANET helps to maintain the continuous uninterrupted connection. This also decrease the amount of packet loss thus ensuring higher Quality of Service. In this work a Cluster Based Vehicular Handoff is proposed. The proposed clustering technique is executed using k-means clustering. Cluster heads are selected using the formulated utility function. Simulation analysis is carried out in NS3.0 and SUMO. The proposed work reduces both load from a single backbone device and packet loss during handoff by proactively caching packets intended for the node that is participating in the handoff process.