Miracle-dz/UniFAR-FTUs huggingface dataset:
Integrative Analysis of Proteomics and Transcriptomics of Longissimus dorsi with Different Feeding Systems in Yaks

Yaks (Bos grunniens) are a critical livestock breed in the plateau region, and changing the feeding system of yaks can significantly improve their growth performance. The effects of different feeding regimes on the growth performance and meat quality of yaks were comprehensively compared here. The transcriptome and proteome of the Longissimus dorsi muscle were determined using RNA-seq and Tandem Mass Tag (TMT) techniques. Indoor feeding significantly improved the growth performance (such as the average daily gain and carcass weight) and meat quality characteristics compared with traditional grazing feeding. In the grazing (Group G) vs. in-house fed group (Group HF) comparison, 40 differentially expressed genes/differentially abundant proteins exhibited the same mRNA and protein expression trends. These genes were associated with collagen binding, the lipoxygenase pathway, and the arachidonic acid metabolic process. Parallel reaction monitoring verified whether the TMT results were reliable. Moreover, some pathways, such as the AMPK signaling pathway, FoxO signaling pathway, PPAR signaling pathway, and fatty acid metabolism, were significantly enriched. These results expand our knowledge about meat quality in yaks and provide practical information and more evidence for further insight into the biological mechanisms underlying meat quality traits.
Lower Limb Exoskeleton - Energy Optimization of Bipedal Walking With Energy Recycling - Modeling and Simulation

Humans tend to use more energy to walk compared to other limb-based locomotion animals. This higher energy usage is due to “heel strikes” and “negative work” during human gait. Passive walkers elevate this phenomenon by utilizing elastic joints that absorb/reuse some of the negative work. The objective of this study is to absorb energy at one phase of the gait cycle, store it, and then release it at a later phase through the use of a lower limb exoskeleton. Knee geometry is one important factor in energy efficiency during gait. Animals with reversed knees compared to humans (backward knee), such as ostriches, exhibit improved energy efficiency. As part of this study, new energy optimization strategies were developed utilizing collision-based ground reaction forces and a discrete lagrangian. The minimal cost of transport (CoT) gait patterns were calculated with both forward-knee and backward-knee human-exoskeleton models. Simulation results show that wearing a backward-knee exoskeleton can reduce the CoT by 15% of while carrying external loads ranging from 20 to 60 kg. In addition, when the exoskeleton utilized energy recycling, the CoT was shown to be further reduced to 35%. These simulation results suggested that the optimal design for an exoskeleton aimed at utilizing energy recycling principles should incorporate backward-knee configurations much like those found in energy-efficient biped/quadruped animals.
Influence of the magnetization damping on dynamic hysteresis loops in single domain particles

This article reports on the influence of the magnetization damping on dynamic hysteresis loops in single-domain particles with uniaxial anisotropy. The approach is based on the Neel–Brown theory and the hierarchy of differential recurrence relations, which follow from averaging over the realizations of the stochastic Landau–Lifshitz equation. A new method of solution is proposed, where the resulting system of differential equations is solved directly using optimized algorithms to explore its sparsity. All parameters involved in uniaxial systems are treated in detail, with particular attention given to the frequency dependence. It is shown that in the ferromagnetic resonance region, novel phenomena are observed for even moderately low values of the damping. The hysteresis loops assume remarkably unusual shapes, which are also followed by a pronounced reduction of their heights. Also demonstrated is that these features remain for randomly oriented ensembles and, moreover, are approximately independent of te.
An Insight into the Machine-Learning-Based Fileless Malware Detection

In recent years, massive development in the malware industry changed the entire landscape for malware development. Therefore, cybercriminals became more sophisticated by advancing their development techniques from file-based to fileless malware. As file-based malware depends on files to spread itself, on the other hand, fileless malware does not require a traditional file system and uses benign processes to carry out its malicious intent. Therefore, it evades conventional detection techniques and remains stealthy. This paper briefly explains fileless malware, its life cycle, and its infection chain. Moreover, it proposes a detection technique based on feature analysis using machine learning for fileless malware detection. The virtual machine acquired the memory dumps upon executing the malicious and non-malicious samples. Then the necessary features are extracted using the Volatility memory forensics tool, which is then analyzed using machine learning classification algorithms. After that, the best algorithm is selected based on the k-fold cross-validation score. Experimental evaluation has shown that Random Forest outperforms other machine learning classifiers (Decision Tree, Support Vector Machine, Logistic Regression, K-Nearest Neighbor, XGBoost, and Gradient Boosting). It achieved an overall accuracy of 93.33% with a True Positive Rate (TPR) of 87.5% at zeroFalse Positive Rate (FPR) for fileless malware collected from five widely used datasets (VirusShare, AnyRun, PolySwarm, HatchingTriage, and JoESadbox).
Subrenal Capsule Assay - SRCA: The Promising Re-Emergence of a Long-Forgotten Method in Preclinical Nuclear Medical Cancer Diagnostics

Since metastases are responsible for the majority of cancer-related death, in-depth understanding of metastatisation may provide an opportunity for the introduction of new therapeutic as well as diagnostic approaches in cancer management. Previously, preclinical research into the development and progression of malignancies has been hampered by the relative paucity of in vivo tumor models. Subrenal capsule assay (SRCA)-induced tumor-bearing experimental animal models, however, serve as potential preclinical model systems for the assessment of primary tumors and the route of metastatic spread. Several studies implementing either Hepatocarcinoma (He/De), Mesoblastic Nephroma (Ne/De), chemically induced Myeloid Leukemia (My1/De), or spontaneous Myeloid Myelomonocytic Leukemia (My2/De) cells under the left renal capsule of rats applying SRCA method were underway to study secondary tumor formation. Based on the results of this research, subrenally transplanted neoplastic cells led to the appearance of metastasis in the parathymic lymph nodes. Therefore, renal capsule/parathymic lymph node complex seems to be valuable in the in vivo evaluation of the process of metastatisation and the occurrence of secondary neoplasms. The re-emergence of this highly promising SRCA-based renal capsule/parathymic lymph node complex in preclinical nuclear medicine and experimental oncology may open a novel field towards drug trials and radiopharmaceutical development. In the present review, we provide a detailed overview of the history of SRCA as well as the series of research on the establishment of renal capsule/parathymic lymph node complex.
The Extreme Ultraviolet Spectrum of the BL Lacertae Object Markarian 421

We carried out a spectroscopic observation of the BL Lacertae object Mrk 421 with the Extreme Ultraviolet Explorer (EUVE) over an 11 day period in 1995 late April to early May (~242 ks useful time). During this period, the source underwent a flare that was detected also in X-rays and TeV γ-rays. The best continuous coverage of the flare was obtained by EUVE, which resolved the smooth rise and fall of the flux, measuring a variability of as much as a factor of ~1.5 over a span of ~2 days. The detected spectrum extended from ~65 to 100 Å and could be fitted with a power law of energy spectral index αEUV ≈ 3.5 ± 0.8 for the measured Galactic hydrogen column density. The EUV spectrum is much steeper than the mean 1.5-7.5 keV X-ray spectrum, αX = 1.63 ± 0.02, measured simultaneously by the Advanced Satellite for Cosmology and Astrophysics. Furthermore, a simple power-law fit to the observed fluxes at 85 Å and 1.5 keV (excluding the data from the first 4 days, the time of maximum variability) significantly overestimates the flux at the shortest detected EUV wavelengths. These two findings imply that strong absorption is occurring between ~65 and ~75 Å. Such absorption is quite similar to that detected previously in our observation of the BL Lacertae object PKS 2155-304. We demonstrate that this absorption can be attributed to a superposition of Doppler-smeared absorption lines originating in high-velocity, QSO-type nuclear clouds of total column density ~5 × 1021 cm-2 that are ionized by the beamed continuum of the associated relativistic jet. We identify the lines as mostly L- and M-shell transitions of Mg and Ne. The data suggest that the velocity range spanned by the clouds is relatively small (from vi ≈ 0.05c to vf ≈ 0.1c). We find that such a range is consistent with a scenario in which the clouds are initially accelerated to vi by a magnetized outflow from a nuclear accretion disk, with radiation pressure further accelerating them to vf after they enter the beamed emission cone of the jet. We also compute the expected cloud absorption lines in the UV and soft X-ray regimes and use these results to constrain the physical parameters of the clouds and their chemical composition.
Estimating the Relative Risk with Censored Data

Abstract We investigate a class of nonparametric estimators of relative risk in the two-sample case of the proportional hazards model for censored data. The asymptotic distribution of these estimators is derived using influence functions. The optimal estimator in this class has the same influence functions and the same asymptotic distribution as the maximum partial likelihood estimator of Cox (1972). The behavior of the influence functions is discussed briefly, and the last section presents two examples from the literature.
The SAARC STORM: A Coordinated Field Experiment on Severe Thunderstorm Observations and Regional Modeling over the South Asian Region

This article describes a unique field experiment on Severe Thunderstorm Observations and Regional Modeling (STORM) jointly undertaken by eight South Asian countries. Several pilot field experiments have been conducted so far, and the results are analyzed. The field experiments will continue through 2016. The STORM program was originally conceived for understanding the severe thunderstorms known as nor'westers that affect West Bengal and the northeastern parts of India during the pre-monsoon season. The nor'westers cause loss of human lives and damage to properties worth millions of dollars annually. Since the neighboring South Asian countries are also affected by thunderstorms, the STORM program is expanded to cover the South Asian countries under the South Asian Association for Regional Cooperation (SAARC). It covers all the SAARC countries (Afghanistan, Bangladesh, Bhutan, India, Maldives, Nepal, Pakistan, and Sri Lanka) in three phases. Some of the science plans (monitoring the life cycle of nor'wester.
High-power (>10 W) continuous-wave operation from 100-μm-aperture 0.97-μm-emitting Al-free diode lasers

By incorporating a broad transverse waveguide (1.3 μm) in 0.97-μm-emitting InGaAs(P)/InGaP/GaAs separate-confinement-heterostructure quantum-well diode-laser structures we obtain record-high continuous-wave (cw) output powers for any type of InGaAs-active diode lasers: 10.6–11.0 W from 100-μm-wide-aperture devices at 10 °C heatsink temperature, mounted on either diamond or Cu heatsinks. Built-in discrimination against the second-order transverse mode allows pure fundamental-transverse-mode operation (θ⊥=36°) to at least 20-W-peak pulsed power, at 68×threshold. The internal optical power density at catastrophic optical mirror damage (COMD) PCOMD is found to be 18–18.5 MW/cm2 for these conventionally facet-passivated diodes. The lasers are 2-mm-long with 5%/95% reflectivity for front/back facet coating. A low internal loss coefficient (αi=1 cm−1) allows for high external differential quantum efficiency ηd (85%). The characteristic temperatures for the threshold current T0 and the differential quantum effic.
Multi-Grid Capacitive Transducers for Measuring the Surface Profile of Silicon Wafers

The measurements of wafers’ surface profile are crucial for safeguarding the fabrication quality of integrated circuits and MEMS devices. The current techniques measure the profile mainly by moving a capacitive or optical spacing sensing probe along multiple lines, which is high-cost and inefficient. This paper presents the calculation, simulation and experiment of a method for measuring the surface profile with arrayed capacitive spacing transducers. The calculation agreed well with the simulation and experiment. Finally, the proposed method was utilized for measuring the profile of a silicon wafer. The result is consistent with that measured by a commercial instrument. As a movement system is not required, the proposed method is promising for industry applications with superior cost and efficiency to the existing technology.
Identification of Potential Leishmania N-Myristoyltransferase Inhibitors from Withania somnifera (L.) Dunal: A Molecular Docking and Molecular Dynamics Investigation

Leishmaniasis is a group of infectious diseases caused by Leishmania protozoa. The ineffectiveness, high toxicity, and/or parasite resistance of the currently available antileishmanial drugs has created an urgent need for safe and effective leishmaniasis treatment. Currently, the molecular-docking technique is used to predict the proper conformations of small-molecule ligands and the strength of the contact between a protein and a ligand, and the majority of research for the development of new drugs is centered on this type of prediction. Leishmania N-myristoyltransferase (NMT) has been shown to be a reliable therapeutic target for investigating new anti-leishmanial molecules through this kind of virtual screening. Natural products provide an incredible source of affordable chemical scaffolds that serve in the development of effective drugs. Withania somnifera leaves, roots, and fruits have been shown to contain withanolide and other phytomolecules that are efficient anti-protozoal agents against Malaria, Trypanosoma, and Leishmania spp. Through a review of previously reported compounds from W. somnifera-afforded 35 alkaloid, phenolic, and steroid compounds and 132 withanolides/derivatives, typical of the Withania genus. These compounds were subjected to molecular docking screening and molecular dynamics against L. major NMT. Calycopteretin-3-rutinoside and withanoside IX showed the highest affinity and binding stability to L. major NMT, implying that these compounds could be used as antileishmanial drugs and/or as a scaffold for the design of related parasite NMT inhibitors with markedly enhanced binding affinity.
Immunomodulation of B Lymphocytes by Prebiotics, Probiotics and Synbiotics: Application in Pathologies

Introduction: Prebiotics, probiotics and synbiotics are known to have major beneficial effects on human health due to their ability to modify the composition and the function of the gut mucosa, the gut microbiota and the immune system. These components largely function in a healthy population throughout different periods of life to confer homeostasis. Indeed, they can modulate the composition of the gut microbiota by increasing bacteria strands that are beneficial for health, such as Firmicute and Bifidobacteria, and decreasing harmful bacteria, such as Enteroccocus. Their immunomodulation properties have been extensively studied in different innate cells (dendritic cells, macrophages, monocytes) and adaptive cells (Th, Treg, B cells). They can confer a protolerogenic environment but also modulate pro-inflammatory responses. Due to all these beneficial effects, these compounds have been investigated to prevent or to treat different diseases, such as cancer, diabetes, allergies, autoimmune diseases, etc. Regarding the literature, the effects of these components on dendritic cells, monocytes and T cells have been studied and presented in a number of reviews, but their impact on B-cell response has been less widely discussed. Conclusions: For the first time, we propose here a review of the literature on the immunomodulation of B-lymphocytes response by prebiotics, probiotics and synbiotics, both in healthy conditions and in pathologies. Discussion: Promising studies have been performed in animal models, highlighting the potential of prebiotics, probiotics and synbiotics intake to treat or to prevent diseases associated with B-cell immunomodulation, but this needs to be validated in humans with a full characterization of B-cell subsets and not only the humoral response.
Effects of Brimonidine on Microglia Morphology in the Transient Retinal Ischemia Model

Background: This study aimed to investigate the effects of brimonidine on microglia cell morphology by creating a transient retinal ischemia model in rats. Methods: In the right eyes of male Wistar rats (n = 12), a transient retinal ischemia model was created. The rats were divided into three groups: (1) eyes treated with topical brimonidine in the transient retinal ischemia model, (2) shamtreated eyes, and (3) control eyes. Four main phenotypes (ramified, primed, reactive, and amoeboid-phagocytic) of Iba-1 positive microglia cells were examined in the retinal layers. Results: In the transient retinal ischemia model, the number of Iba-1 positive microglia cells was 100.67 ± 7.50 cells in the sham group and 57.67 ± 14.64 cells in the topical brimonidine group. The decrease in the total number of Iba-1 positive microglial cells was statistically significant (p < 0.05). When we compared ramified and primed microglia cells, there was no statistically significant difference between the groups. The number of amoeboidphagocytic microglial cells was 9.5 ± 1.29 cells in the sham treatment group and 2.25 ± 0.50 cells in the topical brimonidine group (p < 0.05). There was a statistically significant decrease in the number of reactive and amoeboid cells. Conclusion: Studies in the central nervous system in rats demonstrated that cell metabolism and functions were changed after acute injury and that microglia transformed from a ramified form to an amoeboid-phagocytic form. In this study, the decrease in the transition of cells from ramified to reactive and amoeboid forms showed us that topical brimonidine treatment could have neuroinflammation suppressor features.
Epigenetic methylation changes: implication as biomarkers in oral and maxillofacial area cancers

Background/Aim Squamous cell carcinoma (SCC) is the most frequent cancer of the head and neck area in the oral cavity. Epigenetic alterations in oral and maxillofacial area cancers are urgently needed to be investigated, as the observed changes might have crucial diagnostic value for personalized medicine. Methods Our study aimed to identify the most frequently hypermethylated tumor suppressor gene promoters in OSCC, followed by correlation analysis with the patients’ survival. We evaluated the methylation status of the promoters in a panel of 22 tumor suppressor genes in Romanian (n=9) and Bulgarian (n=12) patient groups suffering from oral and maxillofacial area cancers. The extracted DNA was further digested through EpiTect Methyl II PCR Array System containing methylation-sensitive and methylation-dependent restriction enzymes, followed by specific amplification of the products obtained by qPCR and data analysis using the online platform provided by the producer. Results Different methylation patterns were observed in the tumor suppressor genes’ promoters. Among them, the methylation profile of Cccnd2, Chd1, Cdh13, Cdkn1c, Neurog1, Gstp1, and Runx3 genes further correlated with overall survival rates. Conclusions Our data emphasize that epigenetic alterations are responsible for the clinical heterogeneity of oral and maxillofacial area cancers and significantly impact on patient survival. Additional investigation on a larger patient cohort should validate these potential biomarkers.
Branched structures on Riemann surfaces

Following results of Gunning on geometric realizations of projective structures on Riemann surfaces, we investigate more fully certain generalizations of such structures. We define the notion of a branched analytic cover on a Riemann surface M (of genus g) and specialize this to the case of branched projective and affine structures. Establishing a correspondence between branched projective and affine structures on M and the classical projective and affine connections on M we show that if a certain linear homogeneous differential equation involving the connection has only meromorphic solutions on M then the connection corresponids to a branched structure on M. Utilizing this fact we then determine classes of positive divisors on M such that for each divisor z in the appropriate class the branched structures having z as their branch locus divisor form a nonempty affine variety. Finally we apply some of these results to study the structures on a fixed Riemann surface of genus 2.
Multi-Functional Time Expanded Graph: A Unified Graph Model for Communication, Storage, and Computation for Dynamic Networks Over Time

Space-air-ground integrated network (SAGIN) aided multi-tier computing network can be modelled as a dynamic and predictable network. For the SAGIN aided multi-tier computing network, the traditional time expanded graph (TEG) can only jointly model communication and storage capability, as well as one computing function for one mission flow within one same node. However, for multiple computing functions for one mission flow in one same node, TEG is not applicable. In this paper, for SAGIN aided multi-tier computing networks, we propose an multi-functional time expanded graph (MF-TEG) to jointly model the communication, storage, and computation capability of nodes where multiple computing functions for one mission flow in one same node can be characterized. Specifically, based on TEG, for each node having computation functions, we adopt the virtual network graph (VNG) to virtually decompose it into three virtual components: sub-virtual node, virtual computing nodes, and virtual transmission links, where the virtual computing node provides the computing function. We characterize the amount of data flow on each link and also present four kinds of fundamental constraints for the data flow in the MF-TEG for joint communication, storage, and computing function: computation capacity constraints, communication capacity constraints, storage capacity constraints, and flow conservation constraints. We provide one example of using MF-TEG to model the SAGIN aided multi-tier computing network with a service function chain (SFC), where satellite nodes could provide communication, storage, and multiple computing functions for one mission flow in one same node, where TEG is not valid. Furthermore, simulation results show that for SAGIN aided multi-tier computing network, the proposed MF-TEG model significantly outperforms the snapshot graph-aided VNG (SSG-aided VNG) model. The reason for that is only communication and computation capability is considered by the SSG-aided VNG model, while storage capability is not exploited.
Bayesian analysis of the SUR Tobit model

This paper develops a practical sampling scheme for Bayesian analysis of correlated censored data using the seemingly unrelated Tobit regressions model. Posterior inference is performed via the Gibbs sampler with data augmentation algorithm. In particular, the relevant full conditional distributions needed in the use of Gibbs sampler are derived. The method is then applied to a real data set on the determination of the payments of cash and stock dividends.