Miracle-dz/UniFAR-FTUs huggingface dataset:
A Role for the Twins Protein Phosphatase (PP2A-B55) in the Maintenance of Drosophila Genome Integrity

The protein phosphatase 2A (PP2A) is a conserved heterotrimeric enzyme that regulates several cellular processes including the DNA damage response and mitosis. Consistent with these functions, PP2A is mutated in many types of cancer and acts as a tumor suppressor. In mammalian cells, PP2A inhibition results in DNA double strand breaks (DSBs) and chromosome aberrations (CABs). However, the mechanisms through which PP2A prevents DNA damage are still unclear. Here, we focus on the role of the Drosophila twins (tws) gene in the maintenance of chromosome integrity; tws encodes the B regulatory subunit (B/B55) of PP2A. Mutations in tws cause high frequencies of CABs (0.5 CABs/cell) in Drosophila larval brain cells and lead to an abnormal persistence of γ-H2Av repair foci. However, mutations that disrupt the PP4 phosphatase activity impair foci dissolution but do not cause CABs, suggesting that a delayed foci regression is not clastogenic. We also show that Tws is required for activation of the G2/M DNA damage checkpoint while PP4 is required for checkpoint recovery, a result that points to a conserved function of these phosphatases from flies to humans. Mutations in the ATM-coding gene tefu are strictly epistatic to tws mutations for the CAB phenotype, suggesting that failure to dephosphorylate an ATM substrate(s) impairs DNA DSBs repair. In addition, mutations in the Ku70 gene, which do not cause CABs, completely suppress CAB formation in tws Ku70 double mutants. These results suggest the hypothesis that an improperly phosphorylated Ku70 protein can lead to DNA damage and CABs.
A genome-wide RNA interference screen identifies new regulators of androgen receptor function in prostate cancer cells

The androgen receptor (AR) is a mediator of both androgen-dependent and castration-resistant prostate cancers. Identification of cellular factors affecting AR transcriptional activity could in principle yield new targets that reduce AR activity and combat prostate cancer, yet a comprehensive analysis of the genes required for AR-dependent transcriptional activity has not been determined. Using an unbiased genetic approach that takes advantage of the evolutionary conservation of AR signaling, we have conducted a genome-wide RNAi screen in Drosophila cells for genes required for AR transcriptional activity and applied the results to human prostate cancer cells. We identified 45 AR-regulators, which include known pathway components and genes with functions not previously linked to AR regulation, such as HIPK2 (a protein kinase) and MED19 (a subunit of the Mediator complex). Depletion of HIPK2 and MED19 in human prostate cancer cells decreased AR target gene expression and, importantly, reduced the proliferation of androgen-dependent and castration-resistant prostate cancer cells. We also systematically analyzed additional Mediator subunits and uncovered a small subset of Mediator subunits that interpret AR signaling and affect AR-dependent transcription and prostate cancer cell proliferation. Importantly, targeting of HIPK2 by an FDA-approved kinase inhibitor phenocopied the effect of depletion by RNAi and reduced the growth of AR-positive, but not AR-negative, treatment-resistant prostate cancer cells. Thus, our screen has yielded new AR regulators including drugable targets that reduce the proliferation of castration-resistant prostate cancer cells.
A Non-Noble Metal Based Catalytic Converter for Two-Stroke, Two-Wheeler Applications

Two wheelers constitute almost three fourths of the vehicular population in developing countries like India, and consequently they are the major contributors to vehicular pollution. Catalytic converters based on nonnoble metal catalyst have been developed for 2-stroke, 2- wheelers application. In this study a modified and thermally stable alumina washcoat has been developed for application of non-noble metal catalyst. Alumina washcoat has been used on both ceramic and metallic honeycomb substrates and subsequently the perovskite type of catalyst has been synthesized in-situ on alumina washcoated substrates. Extensive characterization was carried out during development of alumina washcoat and synthesis of perovskite catalyst to establish the thermal stability of alumina washcoat and phase formation of catalysts. A number of prototypes based on alumina supported perovskite have been prepared and tested for mass conversion efficiency with respect to CO, HC and NOx. The results reveal the confirmation of performance of converter for EURO-I emission norms, which are presently applicable in India for 2-stroke, 2-wheelers. The optimized design of converter minimizes the pressure drop across the converter and the power loss of the engine is well within tolerable limits.
Synthetic detection of change point and outliers in bilinear time series models

This paper proposes a procedure of synthetic detection for the location of a change point and outliers in bilinear time series models with a change after an unknown time point. Based on Bayesian framework, we first derive the conditional posterior distribution of the change point and from that distribution estimate the position of the change point. Then we use these results to detect the outliers in the time series before and after that change point via Gibbs sampler algorithm. Our simulation studies show that the proposed procedure is effective.
Going Deeper in Spiking Neural Networks: VGG and Residual Architectures

Over the past few years, Spiking Neural Networks (SNNs) have become popular as a possible pathway to enable low-power event-driven neuromorphic hardware. However, their application in machine learning have largely been limited to very shallow neural network architectures for simple problems. In this paper, we propose a novel algorithmic technique for generating an SNN with a deep architecture, and demonstrate its effectiveness on complex visual recognition problems such as CIFAR-10 and ImageNet. Our technique applies to both VGG and Residual network architectures, with significantly better accuracy than the state-of-the-art. Finally, we present analysis of the sparse event-driven computations to demonstrate reduced hardware overhead when operating in the spiking domain.
Modeling the LPS-induced effects on transcription factor activation and gene expression in murine macrophages

Macrophages within the liver are of particular importance for a functional defense against bacterial infection. They exhibit a complex response to lipopolysaccharide and secrete a variety of pro-inflammatory cytokines and chemokines that both coordinate the immune response and regulate activity of the macrophages, themselves. In this context, the dynamic of pathway activation and gene expression is important for a better understanding of the role of activated macrophages in healthy and diseased states. Therefore, we present a representative model of LPS-induced macrophage activation that covers the principle regulatory motifs. Based on that, we propose a simplified model with a reduced number of states and parameters that allows estimation of transcription factor activity from gene expression data and can be easily extended to describe the full spectrum of gene regulation in LPS-activated macrophages.
The Immunohistochemical Profile of Breast Cancer in Indigenous Women of Southeast Nigeria

Objective: To evaluate the hormone receptor status of breast cancer in indigenous women of southeast Nigeria. Materials and Methods: We collected data on clinical parameters and histologic characteristics - from case notes and histology reports - of women diagnosed of breast cancer and paid for immunohistochemical analyses of their formalin-fixed, paraffin wax-embedded tissue cassettes for hormone receptor status. The relevant clinical data and histologic and immunohistochemical characteristics were analyzed using predictive analytical software, version 17 (IBM, SPSS Inc., Chicago, IL, USA). Comparisons of discrete data were done using Chi-square test, with levels of significance being set at P ≤ 0.05. Result: Within the 6 years study period, 1,410 breast surgical cases were received; 28.2% (397/1,410) of which were diagnosed as breast cancers. Ultimately, 31% (123/397) of these women had IHC (ER, PR, and HER-2/neu) done on their specimens. The age range of the women was 24 to 85 years with a mean of 46.3 years. Approximately 61% (75/123) of the women were pre-menopausal. More than a third of the cancers were triple negative, 40.7% (50/123). Conclusion: We conclude that there is higher proportion of triple negative breast cancers compared to other parts of the world with therapeutic implications.
Necessary and Sufficient Conditions for Consensus of Double-Integrator Multi-Agent Systems With Measurement Noises

An average consensus protocol is proposed for continuous-time double-integrator multi-agent systems with measurement noises under fixed topologies. The time-varying control gain is employed to attenuate noises. The closed-loop system is therefore a time-varying linear stochastic differential equation. By determining the state transition matrix of this closed-loop system, the dynamic characteristics of the multi-agent system can be fully described. It is proved that in the noisy communication environment the average consensus can be achieved if and only if the communication topology is a balanced and strongly connected graph, and the time-varying control gain satisfies the stochastic approximation-type conditions. Under the proposed protocol, the position of each agent is convergent in mean square to a common random variable whose mathematical expectation is the average of initial positions and initial velocities of all agents in the system, while each agent's velocity is convergent in mean square to a common random variable whose mathematical expectation and variance are both zero.
The influence of transportation on turkey meat quality.

Previous research has indicated that antemortem stress factors can influence the development of pale, soft, and exudative (PSE) meat in swine as well as in turkeys. Such antemortem factors can include environmental temperatures, relative humidity, preslaughter handling practices, and transportation. However, the effect of transportation on meat quality of turkeys has not been extensively studied. Eighty Nicholas male turkeys (21 wk of age) were divided into two groups and were either transported in coops on a flatbed trailer for 3 h immediately prior to processing or processed without transportation. Breast muscle samples were collected for pH (0, 2, 24 h), L* value (2, 24 h), drip loss, and cook loss. Additionally, breast fillets were marinated and cooked to determine marination uptake, retention, and cook loss. The breast muscles from transported turkeys had significantly higher muscle pH at 0, 2, and 24 h; significantly lower L* values at 2 and 24 h; significantly higher marination retention (i.e., lower drip loss after marination); and significantly lower cook loss in the marinated fillets compared with fillets of the nontransported turkeys. There were no significant differences in drip loss and cook loss of the nonmarinated fillets or the marination uptake percentage between the transported and nontransported turkeys. These results suggest that transporting turkeys immediately before processing does not induce PSE meat and may actually improve water-holding properties.
Radio Resource Management in Machine-to-Machine Communications—A Survey

In futuristic wireless communications, a massive number of devices need to access networks with diverse quality of service (QoS) requirements. It is estimated that the number of connected devices will exceed 20 billions in 2020, and machine-to-machine (M2M) devices will account for nearly half of total connected devices. However, existing cellular systems and wireless standards, designed primarily for human-to-human (H2H) communications focusing on reducing access latency, increasing data rate, and system throughput, are not well suited for M2M communications that require massive connections, diverse QoS requirements, and low energy consumption. Radio resource management (RRM) in conventional H2H communications aims at improving spectrum efficiency and energy efficiency. Similarly, RRM also plays a vital role in M2M communications. In this paper, we make a comprehensive survey on state-of-the-art research activities on RRM in M2M communications. First, we discuss the issues on RRM for machine-type communications in LTE/LTE-A cellular networks including access control, radio resource allocation, power management, and the latest 3GPP standards supporting M2M communications. Acknowledging the fact that a single technology can not support all M2M applications, we discuss RRM issues for unlicensed band radio access technologies in M2M capillary networks, including IEEE 802.11ah, Bluetooth low energy, ZigBee, and smart metering networks. We also survey M2M RRM methods in heterogeneous networks consisting of cellular networks, capillary networks, and ultra dense networks. Finally, we review recent standard activities and discuss the open issues and research challenges.
Cryopreservation of rooster sperm.

Successful cryopreservation of sperm requires: 1) selection of proper diluent; 2) selection of the best cryoprotectant; 3) determination of freezing and thawing rates for optimum retention of fertilization potential; and 4) removal of any materials deleterious to fertility (e.g., glycerol) before insemination. An economically useful process must allow recovery of sperm with sufficient fertilization capacity to enable maximum use of any given superior male. A series of experiments tested a novel semen freezing container (BioPore CryoCell container) having physical characteristics that permit reproducible freezing and thawing plus facile removal of glycerol from the sample after processing. Experiments tested the effect of: a) residual glycerol; b) initial glycerol concentrations on retention of fertility when samples were frozen and thawed at 6 C/min; c) Beltsville Poultry Semen Extender and Minnesota A buffers used during the dialysis procedure; and d) dialysis time. Respectively, the results were: a) . 8% (vol/vol) reduced fertility by 5 to 10%; b) 12% glycerol was superior to 10% and 8% glycerol; c) no difference was observed between the two buffers; and d) 90 and 120 min were both superior to 60 min. Numerous pools of rooster sperm cryopreserved in CryoCell containers and dialyzed after thawing in a prototype BioStore environmental control chamber for 90 or 120 min resulted in a mean fertility of 55.6%. This mean fertility of frozen-thawed sperm was based on 3,263 eggs laid by 400 hens on Days +1 through 9 after inseminations on Days -1, 2, and 5. It is likely that broiler stocks might have lower fertility than that obtained from the Barred Plymouth Rock males and the Single Comb White Leghorn females used in these studies. Nevertheless, the procedure described is the first to consistently result in > 50% fertilized eggs as a result of conventional intravaginal insemination (< 200 x 10(6) sperm in 100 microL extender) of sperm processed after thawing by a procedure amenable to the scaleup required for commercial applications.
Effective optical constants of silver nanofilms calculated in wide frequency range

The optical properties of Ag ultrathin films in dependence of their thickness are studied theoretically in a wavelength range 0.3 - 10 μm. The extinction coefficient (k) and refractive index (n) for thin Ag films with smooth surface structure are calculated with software package VASP. It was found the effect of growth of extinction coefficient and shift of its peak into long wavelength range with the thickness increasing. The effect is explained by the significant increasing of the surface electron states. Refractive index n is increased with the wavelength growth and attains saturation value ns at the wavelength λs. The thicker the films the higher the magnitude of ns and the larger the wavelength λs. Our results of calculations of k(λ) are in a good agreement with experimental data from ref. [25]. The difference in magnitudes of n obtained experimentally and theoretically can be explained by the formation of Ag nanoclusters on the surface of sputtered film.
Heating and Compression Bandage Treatment Is Effective for Chronic Lymphedema with Dermatolymphangioadenitis-A Case-Controlled Study.

BACKGROUND To investigate the therapeutic effect of far infrared rays and compression bandaging in the treatment of chronic lymphedema with dermatolymphangioadenitis (DLA). METHODS Between 2005 and 2013, 106 patients with chronic lymphedema with DLA treated at the Shanghai Ninth People's Hospital were retrospectively reviewed. These patients were divided into an infrared and a bandaging group (80 patients, group 1) and bandaging only group (26 patients, group 2). Outcome measures include DLA frequency, patients' subjective feedback with regards to their symptoms, and the relationship between continuous elastic compression bandaging and relapse of DLA. RESULTS The frequency of DLA in group 1 and group 2 were significantly reduced after treatment (p = 0.000 and 0.004, respectively). Seventy five percent (60) of patients in group 1 and 19% (5) of patients in group 2 suffered no further episodes of DLA during the follow-up period. In group 1, over 90% of patients reported a subjective improvement in their symptoms and the relapse rate was shown to be lower using elastic compression bandaging when higher pressures were applied. CONCLUSION Heating with compression bandaging can be an effective treatment strategy to reduce DLA and improve the quality of life for those patients with chronic lymphedema associated with DLA.
Gene Expression as a Dosimeter in Irradiated Drosophila melanogaster

Abstract Biological indicators would be of use in radiation dosimetry in situations where an exposed person is not wearing a dosimeter, or when physical dosimeters are insufficient to estimate the risk caused by the radiation exposure. In this work, we investigate the use of gene expression as a dosimeter. Gene expression analysis was done on 15,222 genes of Drosophila melanogaster (fruit flies) at days 2, 10, and 20 postirradiation, with X-ray exposures of 10, 1000, 5000, 10,000, and 20,000 roentgens. Several genes were identified, which could serve as a biodosimeter in an irradiated D. melanogaster model. Many of these genes have human homologues. Six genes showed a linear response (R2 > 0.9) with dose at all time points. One of these genes, inverted repeat-binding protein, is a known DNA repair gene and has a human homologue (XRCC6). The lowest dose, 10 roentgen, is very low for fruit flies. If the lowest dose is excluded, 13 genes showed a linear response with dose at all time points. This includes 5 of 6 genes that were linear with all radiation doses included. Of these 13 genes, 4 have human homologues and 8 have known functions. The expression of this panel of genes, particularly those with human homologues, could potentially be used as the biological indicator of radiation exposure in dosimetry applications.
Claudin-18–mediated YAP activity regulates lung stem and progenitor cell homeostasis and tumorigenesis

Claudins, the integral tight junction (TJ) proteins that regulate paracellular permeability and cell polarity, are frequently dysregulated in cancer; however, their role in neoplastic progression is unclear. Here, we demonstrated that knockout of Cldn18, a claudin family member highly expressed in lung alveolar epithelium, leads to lung enlargement, parenchymal expansion, increased abundance and proliferation of known distal lung progenitors, the alveolar epithelial type II (AT2) cells, activation of Yes-associated protein (YAP), increased organ size, and tumorigenesis in mice. Inhibition of YAP decreased proliferation and colony-forming efficiency (CFE) of Cldn18–/– AT2 cells and prevented increased lung size, while CLDN18 overexpression decreased YAP nuclear localization, cell proliferation, CFE, and YAP transcriptional activity. CLDN18 and YAP interacted and colocalized at cell-cell contacts, while loss of CLDN18 decreased YAP interaction with Hippo kinases p-LATS1/2. Additionally, Cldn18–/– mice had increased propensity to develop lung adenocarcinomas (LuAd) with age, and human LuAd showed stage-dependent reduction of CLDN18.1. These results establish CLDN18 as a regulator of YAP activity that serves to restrict organ size, progenitor cell proliferation, and tumorigenesis, and suggest a mechanism whereby TJ disruption may promote progenitor proliferation to enhance repair following injury.
Fine-mapping, novel loci identification, and SNP association transferability in a genome-wide association study of QRS duration in African Americans.

The electrocardiographic QRS duration, a measure of ventricular depolarization and conduction, is associated with cardiovascular mortality. While single nucleotide polymorphisms (SNPs) associated with QRS duration have been identified at 22 loci in populations of European descent, the genetic architecture of QRS duration in non-European populations is largely unknown. We therefore performed a genome-wide association study (GWAS) meta-analysis of QRS duration in 13,031 African Americans from ten cohorts and a transethnic GWAS meta-analysis with additional results from populations of European descent. In the African American GWAS, a single genome-wide significant SNP association was identified (rs3922844, P = 4 × 10-14) in intron 16 of SCN5A, a voltage-gated cardiac sodium channel gene. The QRS-prolonging rs3922844 C allele was also associated with decreased SCN5A RNA expression in human atrial tissue (P = 1.1 × 10-4). High density genotyping revealed that the SCN5A association region in African Americans was confined to intron 16. Transethnic GWAS meta-analysis identified novel SNP associations on chromosome 18 in MYL12A (rs1662342, P = 4.9 × 10-8) and chromosome 1 near CD1E and SPTA1 (rs7547997, P = 7.9 × 10-9). The 22 QRS loci previously identified in populations of European descent were enriched for significant SNP associations with QRS duration in African Americans (P = 9.9 × 10-7), and index SNP associations in or near SCN5A, SCN10A, CDKN1A, NFIA, HAND1, TBX5 and SETBP1 replicated in African Americans. In summary, rs3922844 was associated with QRS duration and SCN5A expression, two novel QRS loci were identified using transethnic meta-analysis, and a significant proportion of QRS-SNP associations discovered in populations of European descent were transferable to African Americans when adequate power was achieved.
Impact of noise correlation on multimodality

In this paper, we consider the problem of estimating an unknown random scalar observed by two modalities. We study two scenarios using mutual information and mean square error. In the first scenario, we consider that the noise correlation is known and examine its impact on the information content of two modalities. In the second scenario we quantify the information loss when the considered value of the noise correlation is wrong. It is shown that the noise correlation usually enhances the estimation accuracy and increases information. However, the performance declines if the noise correlation is misdefined, and the two modalities may jointly convey less information than one single modality.