Miracle-dz/UniFAR-FTUs huggingface dataset:
Resource Allocation and Power Control for D2D Communication Underlaying LTE-Advanced Networks

Device-to-device (D2D) communications has proven to be efficient in improving the network performance and releasing the traffic load of base station. D2D user equipment(DUEs) can share the same LTE resources blocks with the cellular user equipment(CUEs), but it would cause severe co-channel interference. In this paper, a resource allocation and power control scheme is proposed to reduce the impact of co-channel interference. First, adopt a resource allocation scheme based on greedy algorithm on the premise of meeting the minimum rate requirements of devices, then the path loss compensation factor matrix could be calculated according to the distance between DUEs to the base station and CUEs and used to reduce the influence. Simulation results show that the proposed algorithm has better performance in D2D user access rate and system throughput.
CORAL: Verification-Aware OpenCL Based Read Mapper for Heterogeneous Systems

Genomics has the potential to transform medicine from reactive to a personalized, predictive, preventive, and participatory (P4) form. Being a Big Data application with continuously increasing rate of data production, the computational costs of genomics have become a daunting challenge. Most modern computing systems are heterogeneous consisting of various combinations of computing resources, such as CPUs, GPUs, and FPGAs. They require platform-specific software and languages to program making their simultaneous operation challenging. Existing read mappers and analysis tools in the whole genome sequencing (WGS) pipeline do not scale for such heterogeneity. Additionally, the computational cost of mapping reads is high due to expensive dynamic programming based verification, where optimized implementations are already available. Thus, improvement in filtration techniques is needed to reduce verification overhead. To address the aforementioned limitations with regards to the mapping element of the WGS pipeline, we propose a Cross-platfOrm Read mApper using opencL (CORAL). CORAL is capable of executing on heterogeneous devices/platforms, simultaneously. It can reduce computational time by suitably distributing the workload without any additional programming effort. We showcase this on a quadcore Intel CPU along with two Nvidia GTX 590 GPUs, distributing the workload judiciously to achieve up to 2× speedup compared to when, only, the CPUs are used. To reduce the verification overhead, CORAL dynamically adapts k-mer length during filtration. We demonstrate competitive timings in comparison with other mappers using real and simulated reads. CORAL is available at: https://github.com/nclaes/CORAL.
Shape Dependent EMA Model of Nanostructured Anisotropic Materials

Heterogeneous nanostructures containing nanoparticles of various sizes and shapes have attracted significant attention in the development of nano-biosensors. Especially, plasmonic properties of such materials are advantageously exploited for the detection of biological and chemical substances. Since these media exhibit optical anisotropy, a valid homogenization procedure must be able to describe appropriately the relationship between the geometry of the inclusions and the nature of local field modes. We present a model approach for extension of the effective medium approximation (EMA) and its application to anisotropic nanostructures. The proposed model is based on a “strong-couple-dipole” (SCD) method including a volume-integral correction term in a Green tensor that enables to obtain more accurate representation of polarizability tensor. Derived depolarization factors for discs and bi-cone particles are compared with the early known shapes (spheroids, cylinders) and applied to nanostructures composed of the Fe or Au nanodots in polyacrylate.
Synapse impairment associated with enhanced apoptosis in post‐traumatic stress disorder

Synapse impairment is associated with post‐traumatic stress disorder (PTSD), which is characterized by enhanced apoptosis in the hippocampus, amygdala, and other brain regions. However, there are no detailed studies on the relationship between apoptosis and synaptic connectivity in PTSD. In this review, we discuss results from various studies describing the synaptic changes observed in the PTSD brain. A decreased number of dendrites/spines or increased number of immature spines in the hippocampus, medial prefrontal cortex, and other brain regions has been reported. Studies on axon guidance, myelination, and the cytoskeleton suggest that PTSD may involve axon overgrowth and overbranching. Apoptosis affects synapse formation; low levels of caspase maintain the balance between growth cone attraction and repulsion and inhibit axon elongation. PTSD enhances neuronal apoptosis through caspase activation, which disrupts the balance between growth cone attraction and repulsion and alters growth cone trajectory, leading to axon mistargeting. Meanwhile, caspase activation induces dendritic pruning and dendrite degeneration. These events contribute to the formation of fewer and aberrant synapses, which is associated with enhanced apoptosis in PTSD.
Genome‐wide DNA methylation and transcriptome and proteome changes in Mycobacterium tuberculosis with para‐aminosalicylic acid resistance

Previous studies have reported that genome‐wide DNA methylation and differentially expressed genes and proteins are closely associated with drug resistance in Mycobacterium tuberculosis (M. tuberculosis). However, no reports have explored such associations in para‐aminosalicylic acid (PAS)‐resistant M. tuberculosis H37Rv. Here, we investigated genome‐wide methylation and transcriptome and proteome changes to explore the associations between specific genes and PAS resistance in M. tuberculosis H37Rv. The results revealed that 1,388 differentially methylated (1,161 hypermethylated and 227 hypomethylated) genes, 214 significantly differentially expressed (103 up‐ and 111 down‐regulated) genes and 137 differentially expressed (48 up‐ and 89 down‐regulated) proteins were regulated by PAS in M. tuberculosis H37Rv. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that metabolic pathways and ABC transporters were closely associated with differentially methylated and expressed genes, respectively. In addition, correlation analysis revealed that differentially methylated genes were negatively correlated with their transcriptional levels in PAS‐resistant M. tuberculosis H37Rv. Furthermore, the existence of five hypermethylated candidate genes (esxC, fabG3, fbpB, papA1 and pks2) in PAS‐resistant M. tuberculosis H37Rv was verified using protein–protein interaction analysis in the STRING database. The integrated DNA methylation and transcriptome and proteome analysis could provide valuable resources for epigenetics studies in PAS‐resistant M. tuberculosis H37Rv.
Demographic and environmental drivers of metagenomic viral diversity in vampire bats

Abstract Viruses infect all forms of life and play critical roles as agents of disease, drivers of biochemical cycles and sources of genetic diversity for their hosts. Our understanding of viral diversity derives primarily from comparisons among host species, precluding insight into how intraspecific variation in host ecology affects viral communities or how predictable viral communities are across populations. Here we test spatial, demographic and environmental hypotheses explaining viral richness and community composition across populations of common vampire bats, which occur in diverse habitats of North, Central and South America. We demonstrate marked variation in viral communities that was not consistently predicted by a null model of declining community similarity with increasing spatial or genetic distances separating populations. We also find no evidence that larger bat colonies host greater viral diversity. Instead, viral diversity follows an elevational gradient, is enriched by juvenile‐biased age structure, and declines with local anthropogenic food resources as measured by livestock density. Our results establish the value of linking the modern influx of metagenomic sequence data with comparative ecology, reveal that snapshot views of viral diversity are unlikely to be representative at the species level, and affirm existing ecological theories that link host ecology not only to single pathogen dynamics but also to viral communities.
MS-Based Approaches Enable the Structural Characterization of Transcription Factor/DNA Response Element Complex

The limited information available on the structure of complexes involving transcription factors and cognate DNA response elements represents a major obstacle in the quest to understand their mechanism of action at the molecular level. We implemented a concerted structural proteomics approach, which combined hydrogen-deuterium exchange (HDX), quantitative protein-protein and protein-nucleic acid cross-linking (XL), and homology analysis, to model the structure of the complex between the full-length DNA binding domain (DBD) of Forkhead box protein O4 (FOXO4) and its DNA binding element (DBE). The results confirmed that FOXO4-DBD assumes the characteristic forkhead topology shared by these types of transcription factors, but its binding mode differs significantly from those of other members of the family. The results showed that the binding interaction stabilized regions that were rather flexible and disordered in the unbound form. Surprisingly, the conformational effects were not limited only to the interface between bound components, but extended also to distal regions that may be essential to recruiting additional factors to the transcription machinery. In addition to providing valuable new insights into the binding mechanism, this project provided an excellent evaluation of the merits of structural proteomics approaches in the investigation of systems that are not directly amenable to traditional high-resolution techniques.
Simplified Mathematical Model of Glucose-Insulin System

Mathematical modelling of glucose-insulin system is very important in medicine as a necessary tool to understand the homeostatic control of human body. It can also be used to design clinical trials and in the evaluation of the diabetes prevention. In the last three decades so much work has been done in this direction. One of the most notable models is the global six compartment-mathematical model with 22 ordinary differential equations due to John Thomas Sorensen. This paper proposes a more simplified three compartment-mathematical model with only 6 ordinary differential equations by introducing a tissue compartment comprising kidney, gut, brain and periphery. For model parameter identification, we use inverse problems technique to solve a specific optimal control problem where data are obtained by solving the global model of John Thomas Sorensen. Numerical results show that the proposed model is adaptable to data and can be used to adjust diabetes mellitus type I or type II for diabetic patients.
The ethylene receptors CpETR1A and CpETR2B cooperate in the control of sex determination in Cucurbita pepo

Abstract High-throughput screening of an ethyl methanesulfonate-generated mutant collection of Cucurbita pepo using the ethylene triple-response test resulted in the identification of two semi-dominant ethylene-insensitive mutants: etr1a and etr2b. Both mutations altered sex determination mechanisms, promoting conversion of female into bisexual or hermaphrodite flowers, and monoecy into andromonoecy, thereby delaying the transition to female flowering and reducing the number of pistillate flowers per plant. The mutations also altered the growth rate and maturity of petals and carpels in pistillate flowers, lengthening the time required for flowers to reach anthesis, as well as stimulating the growth rate of ovaries and the parthenocarpic development of fruits. Whole-genome sequencing allowed identification of the causal mutation of the phenotypes as two missense mutations in the coding region of CpETR1A and CpETR2B, each one corresponding to one of the duplicates of ethylene receptor genes highly homologous to Arabidopsis ETR1 and ETR2. The phenotypes of homozygous and heterozygous single- and double-mutant plants indicated that the two ethylene receptors cooperate in the control of the ethylene response. The level of ethylene insensitivity, which was determined by the strength of each mutant allele and the dose of wild-type and mutant etr1a and etr2b alleles, correlated with the degree of phenotypic changes in the mutants.
The Effect of stiffness variation of electrospun fiber meshes of multiblock copolymers on the osteogenic differentiation of human mesenchymal stem cells.

Electrospinning has attracted significant attention as a method to produce cell culture substrates whose fibrous structure mimics the native extracellular matrix (ECM). In this study, the influence of E-modulus of fibrous substrates on the lineage commitment of human adipose-derived stem cells (hADSCs) was studied using fiber meshes prepared via the electrospinning of a polyetheresterurethane (PEEU) consisting of poly(ρ-dioxanone) (PPDO) and poly(ɛ-caprolactone) (PCL) segments. The PPDO: PCL weight ratio was varied from 40:60 to 70:30 to adjust the physiochemical properties of the PEEU fibers. The cells attached on stiffer PEEU70 (PPDO:PCL,= 70:30) fiber meshes displayed an elongated morphology compared to those cultured on softer fibers. The nuclear aspect ratio (width vs. length of a nucleus) of hADSCs cultured on softer PEEU40 (PPDO:PCL = 40:60) fibers was lower than on stiffer fibers. The osteogenic differentiation of hADSCs was enhanced by culturing on stiffer fibers. Compared to PEEU40, a 73% increase of osteocalcin expression and a 34% enhancement of alkaline phosphatase (ALP) activity were observed in cells on PEEU70. These results demonstrated that the differentiation commitment of stem cells could be regulated via tailoring the mechanical properties of electrospun fibers.
Growth response of the ichthyotoxic haptophyte, Prymnesium parvum Carter, to changes in sulfate and fluoride concentrations

Golden alga Prymnesium parvum Carter is a euryhaline, ichthyotoxic haptophyte (Chromista). Because of its presumed coastal/marine origin where SO42- levels are high, the relatively high SO42- concentration of its brackish inland habitats, and the sensitivity of marine chromists to sulfur deficiency, this study examined whether golden alga growth is sensitive to SO42- concentration. Fluoride is a ubiquitous ion that has been reported at higher levels in golden alga habitat; thus, the influence of F- on growth also was examined. In low-salinity (5 psu) artificial seawater medium, overall growth was SO42—dependent up to 1000 mg l-1 using MgSO4 or Na2SO4 as source; the influence on growth rate, however, was more evident with MgSO4. Transfer from 5 to 30 psu inhibited growth when salinity was raised with NaCl but in the presence of seawater levels of SO42-, these effects were fully reversed with MgSO4 as source and only partially reversed with Na2SO4. Growth inhibition was not observed after acute transfer to 30 psu in a commercial sea salt mixture. In 5-psu medium, F- inhibited growth at all concentrations tested. These observations support the hypothesis that spatial differences in SO42- –but not F-–concentration help drive the inland distribution and growth of golden alga and also provide physiological relevance to reports of relatively high Mg2+ concentrations in golden alga habitat. At high salinity, however, the ability of sulfate to maintain growth under osmotic stress was weak and overshadowed by the importance of Mg2+. A mechanistic understanding of growth responses of golden alga to SO42-, Mg2+ and other ions at environmentally relevant levels and under different salinity scenarios will be necessary to clarify their ecophysiological and evolutionary relevance.
Calcitonin induces stem cell-like phenotype in prostate cancer cells.

Stem cell like-cancer cells drive tumor growth, metastasis, and enable the relapse of cancer following remission. Prostate stem cell-like cancer cells isolated from human prostate cancer (PC) biopsies express CD44+/α2β1hi/CD133+ cell surface markers, and can self-renew in vitro. Expression of calcitonin (CT) and its receptor (CTR) is frequently elevated in PCs and activation of CT-CTR axis in non-invasive PC cells induces an invasive phenotype. We investigated whether CT-CTR autocrine axis induces stem cell-like phenotype in PC cells. Human PC-3 cell line that expresses CT but lacks CTR was used as a model, and CT-CTR axis was activated by enforced expression of CTR. The cells were then examined for the changes in the expression of CD44 and CD133, collagen adherence, tumorigenic, metastatic and repopulating characteristics. The activation of CT-CTR axis led to a large increase in adherence to collagen, a remarkable increase of CD44 and CD133, and a strong increase in tumorigenic, metastatic and repopulation properties of PC-3 cells. However, the mutation of CTR-C PDZ-binding site in CTR almost abolished CTR-mediated increases in stem cell-like characteristics of PC-3 cells. These results support an important role for CT-CTR axis in the progression of PC from localized cancer to an aggressive form, and a majority of proinvasive CTR actions may be mediated through its interaction with its partner protein at the PDZ-binding site. These results suggest that CT/CTR can serve as a valuable target to prevent the generation of stem-like PC cells.
Taste test using an edible taste film kit: a randomised controlled trial

Objectives We developed an edible taste film test that can be stored easily as a kit. This study was conducted to confirm the agreement between the results of the edible taste film kit test and the conventional taste solution test. Design Prospective, randomised, controlled trial. Setting Single tertiary hospital. Participants Sixty-two healthy volunteers with no self-described taste problems. Interventions A randomisation scheme was used to determine the order of use of the edible taste film kit and the taste solution test for each subject. The taste solution test was performed using a cotton swab. In the taste film kit test, an edible taste film was placed on the tongue, and the subject detected the taste after the film was dissolved by saliva. Outcome measures For each test, we measured the taste identification threshold, taste detection time and total test time. Results We confirmed the consistency of the taste identification thresholds of the two tests, and the results were consistent with each other except for the bitter taste results, which used coffee in the edible taste film kit and quinine in the taste solution test. Although the detection time for each taste quality was faster for the taste solution test, the mean total time was significantly shorter for the taste film kit test than for the taste solution test (6.16±2.27 min vs 7.04±1.98 min, respectively; p=0.004). Conclusions The edible taste film kit along with the taste solution test will be useful for quantitative taste testing. Trial registration number KCT0002865.
Proteomic analysis of affinity-purified 26S proteasomes identifies a suite of assembly chaperones in Arabidopsis

The 26S proteasome is an essential protease that selectively eliminates dysfunctional and short-lived regulatory proteins in eukaryotes. To define the composition of this proteolytic machine in plants, we tagged either the core protease (CP) or the regulatory particle (RP) sub-complexes in Arabidopsis to enable rapid affinity purification followed by mass spectrometric analysis. Studies on proteasomes enriched from whole seedlings, with or without ATP needed to maintain the holo-proteasome complex, identified all known proteasome subunits but failed to detect isoform preferences, suggesting that Arabidopsis does not construct distinct proteasome sub-types. We also detected a suite of proteasome-interacting proteins, including likely orthologs of the yeast and mammalian chaperones Pba1, Pba2, Pba3, and Pba4 that assist in CP assembly; Ump1 that helps connect CP half-barrels; Nas2, Nas6, and Hsm3 that assist in RP assembly; and Ecm29 that promotes CP–RP association. Proteasomes from seedlings exposed to the proteasome inhibitor MG132 accumulated assembly intermediates, reflecting partially built proteasome sub-complexes associated with assembly chaperones, and the CP capped with the PA200/Blm10 regulator. Genetic analyses of Arabidopsis UMP1 revealed that, unlike in yeast, this chaperone is essential, with mutants lacking the major UMP1a and UMP1b isoforms displaying a strong gametophytic defect. Single ump1 mutants were hypersensitive to conditions that induce proteotoxic, salt and osmotic stress, and also accumulated several proteasome assembly intermediates, consistent with its importance for CP construction. Insights into the chaperones reported here should enable study of the assembly events that generate the 26S holo-proteasome in Arabidopsis from the collection of 64 or more subunits.
TCQG—Software-Defined Transmission Control Scheme in 5G Networks from Queuing Game Perspective

The efficient processing and forwarding of big data is one of the key problems and challenges facing the next generation wireless communication network. Using a software definition method to virtualize the network can improve the efficiency of network operation and reduce the cost of network operation and maintenance. A software-defined transmission control scheme was presented to solve the excessive controller flow problem for 5G networks. Based on the queuing game theory, a system model was built due to the competition among the requests of the switch. The transmission control platform was in charge of resource allocation. It got maximum social welfare under a profit-maximizing fee. In this model, the optimal queue length was calculated and discussed in a first-come-first-served and last-come-first-served with preemption discipline. The optimal queue length was obtained and the optimal admission fee was calculated. Then, the single switch single controller transmission control model was extended to the multi-switches single controller model. As a result, the social welfare of the system containing the controller’s profit and switch surplus reaches the maximum.
Identification of ZBTB24 protein domains and motifs for heterochromatin localization and transcriptional activation

Immunodeficiency, centromeric instability, facial anomalies (ICF) syndrome is a rare autosomal recessive disorder caused by mutations in either DNMT3B, ZBTB24, CDCA7, HELLS or an unknown gene(s). Among the known causative genes, ZBTB24 encodes a member of the BTB‐zinc finger (ZF) transcription factor family. The protein possesses a BTB domain, an AT‐hook and eight C2H2 ZF motifs. All ZBTB24 mutations reported in ICF patients are predicted to disrupt at least one ZF motif. Here, we show that both AT‐hook and distinct ZF motifs, particularly the 6th motif, of human and mouse ZBTB24 proteins are important for their heterochromatin localization. On the other hand, the 6th and 7th ZF motifs, and not the AT‐hook or the BTB domain, of the human and mouse proteins are essential for transcriptional activation of CDCA7, another ICF causative gene and a known target of ZBTB24. By deletion analysis of the human CDCA7 promoter, we show that two motifs for ZBTB24 binding are important for transcriptional activation of this gene. These results reveal the evolutionarily conserved domains and motifs important for the biological function of ZBTB24, which provides a basis for understanding the molecular mechanisms underlying the pathogenesis of ICF syndrome.