Miracle-dz/UniFAR-FTUs huggingface dataset:
Synthetic testosterone derivatives modulate rat P2X2 and P2X4 receptor channel gating

P2X receptors (P2XRs) are ATP‐gated cationic channels that are allosterically modulated by numerous compounds, including steroids and neurosteroids. These compounds may both inhibit and potentiate the activity of P2XRs, but sex steroids such as 17β‐estradiol or progesterone are reported to be inactive. Here, we tested a hypothesis that testosterone, another sex hormone, modulates activity of P2XRs. We examined actions of native testosterone and a series of testosterone derivatives on the gating of recombinant P2X2R, P2X4R and P2X7R and native channels expressed in pituitary cells and hypothalamic neurons. The 17β‐ester derivatives of testosterone rapidly and positively modulate the 1 µM ATP‐evoked currents in P2X2R‐ and P2X4R‐expressing cells, but not agonist‐evoked currents in P2X7R‐expressing cells. In general, most of the tested testosterone derivatives are more potent modulators than endogenous testosterone. The comparison of chemical structures and whole‐cell recordings revealed that their interactions with P2XRs depend on the lipophilicity and length of the alkyl chain at position C‐17. Pre‐treatment with testosterone butyrate or valerate increases the sensitivity of P2X2R and P2X4R to ATP by several fold, reduces the rate of P2X4R desensitization, accelerates resensitization, and enhances ethidium uptake by P2X4R. Native channels are also potentiated by testosterone derivatives, while endogenously expressed GABA receptors type A are inhibited. The effect of ivermectin, a P2X4R‐specific allosteric modulator, on deactivation is antagonized by testosterone derivatives in a concentration‐dependent manner. Together, our results provide evidence for potentiation of particular subtypes of P2XRs by testosterone derivatives and suggest a potential role of ivermectin binding site for steroid‐induced modulation.
Objection Classification Based on Estimation of Foreground Distribution

This paper presents a novel methodology for recognizing object categories based on the estimation of image foreground distribution. We offer insight into how the matting technique can be applied in the image retrieval field and how spatial cues can be incorporated into bag-of-features approach in a proper way. The spatial cues indicate distribution of foreground objects or background environments. In our approach, a formalized framework is offered: an image descriptor is defined as a weighted concatenation of features extracted on different patches of an image, and the weights here are set to be foreground distribution values in corresponding patches. Experiments on challenging object categorization image sets demonstrate the effectiveness of this framework.
Survival and clinical prognostic factors in metastatic non‐clear cell renal cell carcinoma treated with targeted therapy: A multi‐institutional, retrospective study using the Korean metastatic renal cell carcinoma registry

The optimal treatment strategy for metastatic non‐clear cell renal cell carcinoma (mNCCRCC) is still elusive and mainly extrapolated from evidence available for metastatic clear cell renal cell carcinoma. The aim of the study was therefore to investigate the survival outcomes and prognostic factors affecting survival in patients with mNCCRCC treated with targeted therapy.
HOP is a monomer: Investigation of the oligomeric state of the co‐chaperone HOP

The co‐chaperone Hsp70‐Hsp90 organizing protein (HOP) plays a central role in protein folding in vivo, binding to both Hsp70 and Hsp90 and bringing them together in a functional complex. Reports in the literature concerning the oligomeric state of HOP have been inconsistent—is it a monomer, dimer, or higher order oligomer? Knowing the oligomeric state of HOP is important, because it places limits on the number and types of multiprotein complexes that can form during the folding cycle. Thus, the number of feasible models is simplified. Here, we explicitly investigate the oligomeric state of HOP using three complementary methods: gel filtration chromatography, sedimentation equilibrium analytical ultracentrifugation (AUC), and an in vivo coexpression assay. We find that HOP does not behave like a monomeric globular protein on gel filtration. Rather its behavior is consistent with it being either an elongated monomer or a dimer. We follow‐up on these studies using sedimentation equilibrium AUC, which separates on the basis of molecular weight (MW), independent of shape. Sedimentation equilibrium AUC clearly shows that HOP is a monomer, with no indication of higher MW species. Finally, we use an in vivo coexpression assay that also supports the conclusion that HOP is a monomer.
Design of Conformance Testing Framework for IP-Based Wireless Sensor Networks

Wireless sensor networks have gained immense popularity for decades and a new approach, IP-based WSNs, has recently emerged as a future technology advancing the era of ubiquitous computing. Thus, this paper designs a conformance testing framework suitable for IP-WSNs. The framework is an automatic testing methodology that consists of a test agent as a test executor located on the Internet side, a test manager in a gateway that manages testing jobs and test cases, and a software under test (SUT), which represents the actual target in the sensor nodes. The testing framework leverages the useful method of existing tools, complements their drawback.
Surface Approximation to Scattered Lines

A global weighted-mean approximation to scattered lines is introduced. Rational Gaussian weights are stretched along lines and standard deviations of Gaussians are selected in such a way as to produce surfaces that closely follow data along lines. When the lengths of the lines approach zero, the proposed formulation converges to that of global weighted mean approximation to scattered points. Therefore, the traditional weighted mean approximation becomes a special case of the proposed approximation. Implementation strategies are presented and examples of surface approximation using range data and polygon meshes are given.
The use of gene clusters to infer functional coupling.

Previously, we presented evidence that it is possible to predict functional coupling between genes based on conservation of gene clusters between genomes. With the rapid increase in the availability of prokaryotic sequence data, it has become possible to verify and apply the technique. In this paper, we extend our characterization of the parameters that determine the utility of the approach, and we generalize the approach in a way that supports detection of common classes of functionally coupled genes (e.g., transport and signal transduction clusters). Now that the analysis includes over 30 complete or nearly complete genomes, it has become clear that this approach will play a significant role in supporting efforts to assign functionality to the remaining uncharacterized genes in sequenced genomes.
Hydrophobized Reversed-Phase Adsorbent for Protection of Dairy Cattle against Lipophilic Toxins from Diet. Efficiensy In Vitro and In Vivo

The steady growth of inflammatory diseases of the udder in dairy cattle forces us to look for the causes of this phenomenon in the context of growing chemical pollution of the environment and feeds. Within the framework of this concept, an analysis was made of the polarity level of the three toxic impurity groups, which are commonly present in dairy cattle feeds. These impurities are presented by mycotoxins, polyaromatic hydrocarbons (PAH) and persistent organic pollutants (POP). It has been determined that 46% of studied mycotoxins (n = 1500) and 100% of studied polyaromatic hydrocarbons (n = 45) and persistent organic pollutants (n = 55) are lipophilic compounds, prone to bioaccumulation. A comparative evaluation of the sorption capacity of four adsorbents of a different nature and polarity with respect to the simplest PAH, naphthalene and lipophilic estrogenic mycotoxin, zearalenone in vitro has been carried out. The highest efficiency in these experiments was demonstrated by the reversed-phase polyoctylated polysilicate hydrogel (POPSH). The use of POPSH in a herd of lactating cows significantly reduced the transfer of aldrin, dieldrin and heptachlor, typical POPs from the “dirty dozen”, to the milk. The relevance of protecting the main functional systems of animals from the damaging effects of lipophilic toxins from feeds using non-polar adsorbents, and the concept of evaluating the effectiveness of various feed adsorbents for dairy cattle by their influence on the somatic cell count in the collected milk are discussed.
Generation of Enhanced Synthetic Off-Line Signatures Based on Real On-Line Data

One of the main challenges of off-line signature verification is the absence of large databases. A possible alternative to overcome this problem is the generation of fully synthetic signature databases, not subject to legal or privacy concerns. In this paper we propose several approaches to the synthesis of off-line enhanced signatures from real dynamic information. These synthetic samples show a performance very similar to the one offered by real signatures, even increasing their discriminative power under the skilled forgeries scenario, one of the biggest challenges of handwriting recognition. Furthermore, the feasibility of synthetically increasing the enrolment sets is analysed, showing promising results.
The Bmte Command: Methods for the Estimation of Treatment Effects when Exclusion Restrictions are Unavailable

We present a new Stata command, bmte (bias-minimizing treatment effects), that implements two new estimators proposed in Millimet and Tchernis (2013, Journal of Applied Econometrics 28: 982–1017) and designed to estimate the effect of treatment when selection on unobserved variables exists and appropriate exclusion restrictions are unavailable. In addition, the bmte command estimates treatment effects from several alternative estimators that also do not rely on exclusion restrictions for identification of the causal effects of the treatment, including the following: 1) Heckman's two-step estimator (1976, Annals of Economic and Social Measurement 5: 475–492; 1979, Econometrica 47: 153–161); 2) a control function approach outlined in Heckman, LaLonde, and Smith (1999, Handbook of Labor Economics 3: 1865–2097) and Navarro (2008, The New Palgrave Dictionary of Economics [Palgrave Macmillan]); and 3) a more recent estimator proposed by Klein and Vella (2009, Journal of Applied Econometrics 24: 735–762) that exploits heteroskedasticity for identification. By implementing two new estimators alongside preexisting estimators, the bmte command provides a picture of the average causal effects of the treatment across a variety of assumptions. We present an example application of the command following Millimet and Tchernis (2013, Journal of Applied Econometrics 28: 982–1017).
Gravitational Waves from Extragalactic Inspiraling Binaries: Selection Effects and Expected Detection Rates

We examine the selection effects that determine how the population of inspiraling binary compact objects (BCOs) is reflected by those potentially observed with ground-based interferometers like LIGO. We lay the groundwork for the interpretation of future observations in terms of constraints on the real population and, correspondingly, binary star evolution models.To determine the extragalactic population of inspiraling binaries, we combine data on distance and blue luminosity from galaxy catalogs with current models of the Galactic BCO mass distribution to simulate the physical distribution of binaries in the nearby universe. We use Monte Carlo methods to determine the fraction of binaries observable by the LIGO detectors from each galaxy as a function of the BCO chirp mass. We examine separately the role of source distance, sky position, time of detection, and binary system chirp mass on the detection efficiency and selection effects relevant to the three LIGO detectors. Finally, we discuss the implications of the nearby geography of space on anticipated gravitational wave detection and compare our results to those of previous studies, which have assumed uniform galaxy volume density and fixed chirp mass for BCOs. From these considerations, actual BCO inspiral observations or significant upper limits on the coalescence rate anticipated in the near future by ground-based interferometers can be used to improve our knowledge of the Galactic binary inspiral rate and to constrain models of radio pulsar characteristics and binary star evolution channels leading to neutron star or black hole binaries.
Assessment of the Impact of Plug-in Electric Vehicles on Distribution Networks

Plug-in electric vehicles (PEVs) present environmental and energy security advantages versus conventional gasoline vehicles. In the near future, the number of plug-in electric vehicles will likely grow significantly in the world. Despite the aforementioned advantages, the connection of PEV to the power grid poses a series of new challenges for electric utilities. This paper proposes a comprehensive approach for evaluating the impact of different levels of PEV penetration on distribution network investment and incremental energy losses. The proposed approach is based on the use of a large-scale distribution planning model which is used to analyze two real distribution areas. Obtained results show that depending on the charging strategies, investment costs can increase up to 15% of total actual distribution network investment costs, and energy losses can increase up to 40% in off-peak hours for a scenario with 60% of total vehicles being PEV.
String Methods for Folk Tune Genre Classification

In folk song research, string methods have been widely used to retrieve highly similar tunes or to perform tune family classification. In this study, we investigate how various string methods perform on a fundamentally different classification task, which is to classify folk tunes into genres, the genres being the dance types of the tunes. A new data set Dance-9 is therefore introduced. The different string method classification accuracies are compared with each other and also with n-gram models and global feature models which have been proven to be useful in previous folk song research. They are shown to yield similar results to the global feature models, but are outperformed by the n-gram models.
A Look at Targeted Attacks Through the Lense of an NGO

We present an empirical analysis of targeted attacks against a human-rights Non-Governmental Organization (NGO) representing a minority living in China. In particular, we analyze the social engineering techniques, attack vectors, and malware employed in malicious emails received by two members of the NGO over a four-year period. We find that both the language and topic of the emails were highly tailored to the victims, and that sender impersonation was commonly used to lure them into opening malicious attachments. We also show that the majority of attacks employed malicious documents with recent but disclosed vulnerabilities that tend to evade common defenses. Finally, we find that the NGO received malware from different families and that over a quarter of the malware can be linked to entities that have been reported to engage in targeted attacks against political and industrial organizations, and Tibetan NGOs.
AppA: a web server for analysis, comparison, and visualization of contact residues and interfacial waters of antibody–antigen structures and models

Abstract The study of contact residues and interfacial waters of antibody–antigen (Ab-Ag) structures could help in understanding the principles of antibody–antigen interactions as well as provide guidance for designing antibodies with improved affinities. Given the rapid pace with which new antibody–antigen structures are deposited in the protein databank (PDB), it is crucial to have computational tools to analyze contact residues and interfacial waters, and investigate them at different levels. In this study, we have developed AppA, a web server that can be used to analyze and compare 3D structures of contact residues and interfacial waters of antibody–antigen complexes. To the best of our knowledge, this is the first web server for antibody–antigen structures equipped with the capability for dissecting the contributions of interfacial water molecules, hydrogen bonds, hydrophobic interactions, van der Waals interactions and ionic interactions at the antibody–antigen interface, and for comparing the structures and conformations of contact residues. Various examples showcase the utility of AppA for such analyses and comparisons that could help in the understanding of antibody–antigen interactions and suggest mutations of contact residues to improve affinities of antibodies. The AppA web server is freely accessible at http://mspc.bii. a-star.edu. sg/minhn/appa.html.
gpart: human genome partitioning and visualization of high-density SNP data by identifying haplotype blocks

Abstract Summary For the analysis of high-throughput genomic data produced by next-generation sequencing (NGS) technologies, researchers need to identify linkage disequilibrium (LD) structure in the genome. In this work, we developed an R package gpart which provides clustering algorithms to define LD blocks or analysis units consisting of SNPs. The visualization tool in gpart can display the LD structure and gene positions for up to 20 000 SNPs in one image. The gpart functions facilitate construction of LD blocks and SNP partitions for vast amounts of genome sequencing data within reasonable time and memory limits in personal computing environments. Availability and implementation The R package is available at https://bioconductor.org/packages/gpart. Supplementary information Supplementary data are available at Bioinformatics online.
Information extraction from high resolution SAR data for urban scene understanding

The high complexity and the increased importance of geometry in growing resolution synthetic aperture radar (SAR) data in urban environments poses a limit on the usability of lattice-based scene models. Geometrical models based on marked point processes can be employed to provide better descriptions of the scene. A Gibbs potential based on a hierarchical Bayesian description of the direct model of the acquisition is defined on the process: an a-priori measure of plausibility for the scene takes into account interactions between scene objects, while a Bayesian likelihood term is based on the decomposition of scene objects into basic elements and on their mapping in the data space. Multiple reflections of the radar signals are considered and exploited. The resulting detectability measure is compared to a hypothesis in a likelihood ratio. The resulting posterior potential is optimized by Monte Carlo methods. The resulting algorithm is applied on a diverse set of single submeter resolution SAR intensity images on urban scenes, providing descriptions of the 3-d structure of the imaged urban areas in terms of separate objects.
Preparation and biodistribution study of 67Ga-gallium calcitonin

Introduction: In order to develop a radiolabeled calcitonin (CT) derivative for receptor imaging studies, CT was successively labeled with 67Ga-gallium chloride. Methods: The best results of the conjugation were obtained by the addition of 0.5 ml of a CT nasal pharmaceutical solution (1100 IU) to a glass tube pre-coated with DTPA-dianhydride (0.01 mg) at 25°C with continuous mild stirring for 30 min. Results: After solid phase purification of the radiolabeled hormone, instant thin layer chromatography (ITLC) showed radiochemical purity of higher than 95 % at optimized conditions (specific activity =67-134 KBq/IU, labeling efficiency 70%). 67Ga-DTPA-CT mainly accumulates in the liver. Conclusion: Preliminary in vivo studies (ID/g%) in male wild-type rats showed significant liver uptake of the tracer after 24 hours. 67Ga-DTPA-CT can be a suitable probe for biodistribution study of CT receptors in various physiological as well as neoplastic lesions with over-expressed calcitonin receptors.
A Study of Role Stressors and Job Satisfaction: The Case of MNCs in Collectivist Context

Job stressors in organizational studies are commonly known as role stressors. These include role overload (RO), role conflict (RC), role ambiguity (RA) and job insecurity (JI). We explored the predicting role of these stressors on the overall level of job stress (JS) and job satisfaction (JSF). Moreover, we tested the role of JS as a mediator between the relationship of role stressors and JSF in a multinational corporation (MNC) in a non-western collectivist context (Pakistan). We obtained data through field surveys from 173 engineering employees from the electrical, mechanical, safety and chemical divisions. Role stressors significantly predicted overall level of JS and JSF. JS was also found to partially mediate the relationship between role stressors and JSF. The study findings suggest that foreign ownership needs to focus not only on the economic value, but also the organizational and job design to mitigate the detrimental role of selected stressors. The results of this study have important implications for MNCs in general, and in developing countries in particular. Theoretical and managerial implications are discussed with recommendations.
Helicobacter pylori Mutations Detected by Next-Generation Sequencing in Formalin-Fixed, Paraffin-Embedded Gastric Biopsy Specimens Are Associated with Treatment Failure

Helicobacter pylori antibiotic resistance is widespread and increasing worldwide. Routine detection of H. pylori mutations that invoke antimicrobial resistance may be a useful approach to guide antimicrobial therapy and possibly avert treatment failure. ABSTRACT Helicobacter pylori antibiotic resistance is widespread and increasing worldwide. Routine detection of H. pylori mutations that invoke antimicrobial resistance may be a useful approach to guide antimicrobial therapy and possibly avert treatment failure. In this study, formalin-fixed, paraffin-embedded (FFPE) gastric biopsy specimens from a cohort of individuals from northern Ohio in the United States were examined using a next-generation sequencing (NGS) assay to detect H. pylori mutations that are known to confer resistance to clarithromycin, levofloxacin, and tetracycline. From January 2016 to January 2017, 133 H. pylori-infected gastric biopsy specimens were identified histologically and subsequently analyzed by NGS to detect mutations in gyrA, 23S rRNA, and 16S rRNA genes. The method successfully detected H. pylori in 126 of 133 cases (95% sensitivity). Mutations conferring resistance were present in 92 cases (73%), including 63 cases with one mutation (50%) and 29 cases with mutations in multiple genes (23%). Treatment outcomes were available in 58 cases. Sixteen of the 58 cases failed therapy (28%). Therapy failure correlated with the number of mutated genes: no failure in cases with no mutations (0/15), 19% (5/27) failure in cases with one gene mutation, and 69% (11/16) failure in cases with more than one mutated gene. Common 23S rRNA mutations (A2142G or A2413G) were present in 88% (14/16) of failed cases as opposed to in only 10% (4/42) of eradicated cases (P < 0.001). This NGS assay can be used on remnant specimens collected during standard-of-care testing to detect mutations that correlate with increased risk of treatment failure. A prospective study is needed to determine if the risk of treatment failure can be decreased by using this assay to guide antibiotic therapy.