Miracle-dz/UniFAR-FTUs huggingface dataset:
Structures of Tyr188Leu mutant and wild-type HIV-1 reverse transcriptase complexed with the non-nucleoside inhibitor HBY 097: inhibitor flexibility is a useful design feature for reducing drug resistance.

The second generation Hoechst-Bayer non-nucleoside inhibitor, HBY 097 (S-4-isopropoxycarbonyl-6-methoxy-3-(methylthiomethyl)-3, 4-dihydroqui noxalin-2(1H)-thione), is an extremely potent inhibitor of HIV-1 reverse transcriptase (RT) and of HIV-1 infection in cell culture. HBY 097 selects for unusual drug-resistance mutations in HIV-1 RT (e.g. Gly190Glu) when compared with other non-nucleoside RT inhibitors (NNRTIs), such as nevirapine, alpha-APA and TIBO. We have determined the structure of HBY 097 complexed with wild-type HIV-1 RT at 3.1 A resolution. The HIV-1 RT/HBY 097 structure reveals an overall inhibitor geometry and binding mode differing significantly from RT/NNRTI structures reported earlier, in that HBY 097 does not adopt the usual butterfly-like shape. We have determined the structure of the Tyr188Leu HIV-1 RT drug-resistant mutant in complex with HBY 097 at 3.3 A resolution. HBY 097 binds to the mutant RT in a manner similar to that seen in the wild-type RT/HBY 097 complex, although there are some repositioning and conformational alterations of the inhibitor. Conformational changes of the structural elements forming the inhibitor-binding pocket, including the orientation of some side-chains, are observed. Reduction in the size of the 188 side-chain and repositioning of the Phe227 side-chain increases the volume of the binding cavity in the Tyr188Leu HIV-1 RT/HBY 097 complex. Loss of important protein-inhibitor interactions may account for the reduced potency of HBY 097 against the Tyr188Leu HIV-1 RT mutant. The loss of binding energy may be partially offset by additional contacts resulting from conformational changes of the inhibitor and nearby amino acid residues. This would suggest that inhibitor flexibility can help to minimize drug resistance.
Antimicrobial activity of plant phenols from Chlorophora excelsa and Virgilia oroboides

The anti-bacterial and anti-fungal activity of four aqueous plant extracts (1 x 10 4 μg/ml) of 2,3'4,5'-tetra hydroxy-4'-geranylstilbene (chlorophorin) and 3',4, 5' - trihydroxy - 4' - geranylstilbene (Iroko) from the tree Chlorophora excelsa and (6aR,11aR)-3-hydroxy-8,9-methylenedioxypterocarpan (Maackiain) and 7-hydroxy-4'-methoxyisoflavone (formononetin) from Virgilia oroboides were evaluated by the seeded agar overlay well diffusion method. The test organisms and bioautography used included: Bacillus coagulans, Streptococcus pneumoniae, Klebsiella pneumoniae, Escherichia coli, Mycobacteria tuberculosis, Aspergillus flavus and Fusarium verticilloides . Vancomycin, the drug of choice for these organisms was used as the control at 30 μg/ml. The extracts showed that chlorophorin at 1.95 μg/ml and Iroko at 3.125 and 6.25 μg/ml respectively were active in inhibiting the growth of S. pneumoniae and B. coagulans and not active against K. pneumoniae and E. coli. Maackiain; formononetin and formononetin acetate showed little activity against S. pneumonia, B. coagulans, K. pneumoniae and E. coli . None of the extracts showed activity against M. tuberculosis. Maackiain, formononetin, chlorophorin and Iroko inhibited F. vertiicilloides, maackiain being the most active compound. Formononetin, chlorophorin and Iroko inhibited A. flavus . A. flavus was most sensitive to chlorophorin and Iroko. The bioautography method confirmed these results and was attributed to the phenolic nature of the compounds. Keywords : Plant compounds, anti-bacterial, anti-fungal, chlorophorin, Iroko African Journal of Biotechnology Vol. 12(17), pp. 2254-2261
Entropy of Relativistic Mono-Atomic Gas and Temperature Relativistic Transformation in Thermodynamics

Abstract: It is demonstrated that the entropy of the ideal mono-atomic gas comprising identical spherical atoms is not conserved under the Planck-Einstein like relativistic temperature transformation, as a result of the change in the number of atomic degrees of freedom. This fact supports the idea that there is no universal relativistic temperature transformation. Keywords: relativistic temperature transformation, ideal gas, entropy, degrees of freedom. PACS numbers: 05.70. -a, 95-30.Tg. Introduction The problems of relativistic thermodynamics and statistics attracted significant attention recently [1–4]. The interest to the field was boosted by modern astrophysics investigations. One of the most debated problems is the relativistic temperature transformation. The Planck-Einstein (PE) approach to the temperature transformation resulted in the well-known relation [5]: 2 0 02 11 T TcT u γ= − = (1) 2 0 02 d1d 1 dQ QcQ u γ= − = (2) where 2122( ) 1 − ⎥⎦⎤⎢⎣⎡= = − cuγ γu T and d Q are the temperature and the heat respectively. Ott in his early work concluded that the relativistic temperature transformation is at least ambiguous, because the
A new topic-bridged model for transfer learning

In real-world information systems, there are abundant unlabeled data but sparse labeled data. It is challenging to construct an adaptive model to classify a large amount of documents containing different domains. The classifiers trained from a source domain shall perform poorly for the test data in a target domain due to the domain mismatch. In this study, we build a topic-bridged latent Dirichlet allocation (TLDA) model from a variety of labeled and unlabeled documents and perform the transfer learning for document classification. The severe change of word distributions is compensated by bridging the latent topics of source and target data which are drawn by the Dirichlet priors. A variational inference procedure is performed for semi-supervised learning. In the experiments on text categorization using 20 Newsgroups dataset, the proposed TLDA model achieved higher classification performance compared to the other methods.
Sex-Specific Crossover Distributions and Variations in Interference Level along Arabidopsis thaliana Chromosome 4

In many species, sex-related differences in crossover (CO) rates have been described at chromosomal and regional levels. In this study, we determined the CO distribution along the entire Arabidopsis thaliana Chromosome 4 (18 Mb) in male and female meiosis, using high density genetic maps built on large backcross populations (44 markers, >1,300 plants). We observed dramatic differences between male and female map lengths that were calculated as 88 cM and 52 cM, respectively. This difference is remarkably parallel to that between the total synaptonemal complex lengths measured in male and female meiocytes by immunolabeling of ZYP1 (a component of the synaptonemal complex). Moreover, CO landscapes were clearly different: in particular, at both ends of the map, male CO rates were higher (up to 4-fold the mean value), whereas female CO rates were equal or even below the chromosomal average. This unique material gave us the opportunity to perform a detailed analysis of CO interference on Chromosome 4 in male and female meiosis. The number of COs per chromosome and the distances between them clearly departs from randomness. Strikingly, the interference level (measured by coincidence) varied significantly along the chromosome in male meiosis and was correlated to the physical distance between COs. The significance of this finding on the relevance of current CO interference models is discussed.
Attachment, motivations, and alcohol: Testing a dual-path model of high-risk drinking and adverse consequences in transitional clinical and student samples.

Cette etude avait pour objectif de reproduire et d'elargir un modele motivationnel de la consommation d'alcool a risque et de ses consequences (Cooper, Frone, Russell & Mudar, 1995; Read, Wood, Kahler, Maddock & Palfai, 2003), mettant a l'epreuve la notion que l'attachement est un antecedent commun aux cheminements social et affectif menant a la tendance a la consommation excessive d'alcool, definie selon deux dimensions, la consommation d'alcool a risque et ses consequences. Des etudiants en premiere annee d'universite (N = 696) et des clients inscrits pour une premiere fois a un centre de traitement de la toxicomanie (N = 213) ont rempli des questionnaires visant a etablir leur consommation d'alcool, les consequences de leur consommation, les raisons la motivant et le style d'attachement. Les resultats ont mis en relief l'importance du cheminement affectif en ce qui a trait aux modes de consommation et a la vulnerabilite aux problemes. Les resultats ont aussi permis de constater que les sujets ayant le plus haut niveau d'anxiete d'attachement etaient plus vulnerables aux consequences nefastes attribuables a la consommation d'alcool. Ces resultats ont souligne l'importance du style d'attachement a titre de facteur de risque de consommation d'alcool a risque et de ses consequences.
Child and parent characteristics, parental expectations, and child behaviours related to preschool children's interest in literacy

The current study examined the relations between children's literacy interest and parent and child characteristics (i.e. parents' education level and child's gender), parental expectations of their child's school attainment and achievement and the child's positive and problem behaviours. Participants were 61 preschoolers from predominately low‐income families enrolled in local preschool programmes. Parents completed questionnaires reporting demographic characteristics, parents' expectations and their child's literacy interest. Preschool teachers reported on children's behaviours in the classroom using standard behaviour‐rating scales. Child gender was marginally related to child literacy interest, but parent education was not significantly correlated with interest. Parents' expectation of their child's school achievement was significantly correlated with child literacy interest, but parental expectations about attainment were not. Overall, teachers' reports of children's positive and problem behaviours were correlated with child literacy interest in the expected direction. Interpretation and implications of the findings and future directions for research are discussed.
Cell coupling in mouse pancreatic β-cells measured in intact islets of Langerhans

The perforated whole-cell configuration of the patch-clamp technique was applied to functionally identified β-cells in intact mouse pancreatic islets to study the extent of cell coupling between adjacent β-cells. Using a combination of current- and voltage-clamp recordings, the total gap junctional conductance between β-cells in an islet was estimated to be 1.22 nS. The analysis of the current waveforms in a voltage-clamped cell (due to the firing of an action potential in a neighbouring cell) suggested that the gap junctional conductance between a pair of β-cells was 0.17 nS. Subthreshold voltage-clamp depolarization (to −55 mV) gave rise to a slow capacitive current indicative of coupling between β-cells, but not in non-β-cells, with a time constant of 13.5 ms and a total charge movement of 0.2 pC. Our data suggest that a superficial β-cell in an islet is in electrical contact with six to seven other β-cells. No evidence for dye coupling was obtained when cells were dialysed with Lucifer yellow even when electrical coupling was apparent. The correction of the measured resting conductance for the contribution of the gap junctional conductance indicated that the whole-cell KATP channel conductance (GK,ATP) falls from approximately 2.5 nS in the absence of glucose to 0.1 nS at 15 mM glucose with an estimated IC50 of approximately 4 mM. Theoretical considerations indicate that the coupling between β-cells within the islet is sufficient to allow propagation of [Ca2+]i waves to spread with a speed of approximately 80 μm s−1, similar to that observed experimentally in confocal [Ca2+]i imaging.
On Violence and Repression: A Relational Approach (The Government and Opposition/Leonard Schapiro Memorial Lecture, 2013)

Oppositional violence and repression are closely related. In fact, repression often produces an escalation of violence rather than controlling it. Bridging social movement studies and research on violence, the article uses a small-N, most-different research design to analyse the working of a specific mechanism at the onset of different types of political violence: escalating policing. In particular, it indicates specific causal mechanisms, related to interactions between social movements and the state, which create the conditions for some splinter groups to move underground. In order to compare left-wing, right-wing, ethno-national and religious violence, the article presents empirical references to the author's own empirical research on Italy and the Basque Country as well as a secondary analysis of the conflicts that preceded the rise of al-Qaeda.
Sketchy Decisions: Convex Low-Rank Matrix Optimization with Optimal Storage

This paper considers a fundamental class of convex matrix optimization problems with low-rank solutions. We show it is possible to solve these problem using far less memory than the natural size of the decision variable when the problem data has a concise representation. Our proposed method, SketchyCGM, is the first algorithm to offer provable convergence to an optimal point with an optimal memory footprint. SketchyCGM modifies a standard convex optimization method - the conditional gradient method - to work on a sketched version of the decision variable, and can recover the solution from this sketch. In contrast to recent work on non-convex methods for this problem class, SketchyCGM is a convex method; and our convergence guarantees do not rely on statistical assumptions.
Equilibrium, Kinetic, and Thermodynamic Studies on the Adsorption of Cadmium from Aqueous Solution by Modified Biomass Ash

Natural biomass ash of agricultural residuals was collected from a power plant and modified with hexagonal mesoporous silica and functionalized with 3-aminopropyltriethoxysilane. The physicochemical and morphological properties of the biomass ash were analyzed by ICP-OES, SEM, TEM-EDS, FTIR, and BET analysis. The adsorption behavior of the modified product for Cd2+ in aqueous solution was studied as a function of pH, initial metal concentration, equilibrium time, and temperature. Results showed that the specific surface area of the modified product was 9 times that of the natural biomass ash. The modified biomass ash exhibited high affinity for Cd2+ and its adsorption capacity increased sharply with increasing pH from 4.0 to 6.0. The maximum adsorption capacity was 23.95 mg/g in a pH 5 solution with an initial metal concentration of 50 mg/L and a contact time of 90 min. The adsorption of Cd2+ onto the modified biomass ash was well fitted to the Langmuir model and it followed pseudo-second-order kinetics. Thermodynamic analysis results showed that the adsorption of Cd2+ was spontaneous and endothermic in nature. The results suggest that the modified biomass ash is promising for use as an inexpensive and effective adsorbent for Cd2+ removal from aqueous solution.
Autocrine endothelin-3 / endothelin receptor B signaling maintains cellular and molecular properties of tumorigenic glioblastoma stem cells

1. Department of Surgery/Surgical Oncology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California. 2. Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China 3. Cancer Institute, Zhejiang University, Hangzhou, Zhejiang, P.R. China 4. Department of Neurosurgery, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California. 5. Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 6. Department of Medicine/Hematology-Oncology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 7. Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 8. Department of Neurology, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 9. Department of Psychiatry, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California 10. Jonsson Comprehensive Cancer Center, University of California Los Angeles, Los Angeles, California.
Revisiting the Role of H+ in Chemotactic Signaling of Sperm

Chemotaxis of sperm is an important step toward fertilization. During chemotaxis, sperm change their swimming behavior in a gradient of the chemoattractant that is released by the eggs, and finally sperm accumulate near the eggs. A well established model to study chemotaxis is the sea urchin Arbacia punctulata. Resact, the chemoattractant of Arbacia, is a peptide that binds to a receptor guanylyl cyclase. The signaling pathway underlying chemotaxis is still poorly understood. Stimulation of sperm with resact induces a variety of cellular events, including a rise in intracellular pH (pHi) and an influx of Ca2+; the Ca2+ entry is essential for the chemotactic behavior. Previous studies proposed that the influx of Ca2+ is initiated by the rise in pHi. According to this proposal, a cGMP-induced hyperpolarization activates a voltage-dependent Na+/H+ exchanger that expels H+ from the cell. Because some aspects of the proposed signaling pathway are inconsistent with recent results (Kaupp, U.B., J. Solzin, J.E. Brown, A. Helbig, V. Hagen, M. Beyermann, E. Hildebrand, and I. Weyand. 2003. Nat. Cell Biol. 5:109–117), we reexamined the role of protons in chemotaxis of sperm using kinetic measurements of the changes in pHi and intracellular Ca2+ concentration. We show that for physiological concentrations of resact (<25 pM), the influx of Ca2+ precedes the rise in pHi. Moreover, buffering of pHi completely abolishes the resact-induced pHi signal, but leaves the Ca2+ signal and the chemotactic motor response unaffected. We conclude that an elevation of pHi is required neither to open Ca2+-permeable channels nor to control the chemotactic behavior. Intracellular release of cGMP from a caged compound does not cause an increase in pHi, indicating that the rise in pHi is induced by cellular events unrelated to cGMP itself, but probably triggered by the consumption and subsequent replenishment of GTP. These results show that the resact-induced rise in pHi is not an obligatory step in sperm chemotactic signaling. A rise in pHi is also not required for peptide-induced Ca2+ entry into sperm of the sea urchin Strongylocentrotus purpuratus. Speract, a peptide of S. purpuratus may act as a chemoattractant as well or may serve functions other than chemotaxis.
Add prior knowledge to speaker recognition

Prior knowledge helps to make the speaker recognition system more reliable and robust. This paper presents a uniform framework of feature-level fusion to incorporate the prior knowledge for speaker recognition using gender information based on dynamic Bayesian network (DBN). DBNs are a new statistical approach, with the ability to handle hidden variables and missing data in a principled way with high extensibility. And thus, DBNs can describe the prior knowledge conveniently. Our contribution is to apply DBNs to construct a general feature-level fusion to combine the general acoustic feature like MFCC and prior information like gender into a single DBN for speaker identification. In our framework, gender information become additional observed data to influence both hidden variables and observed acoustic data. Experimental evaluation over a subnet of YOHO corpus show promising results.
Quality-based model for effective and robust multi-user pay-as-you-go ontology matching

Using a pay-as-you-go strategy, we allow for a community of users to validate mappings obtained by an automatic ontology matching system using consensus for each mapping. The ultimate objectives are effectiveness—improving the quality of the obtained alignment (set of mappings) measured in terms of F-measure as a function of the number of user interactions—and robustness—making the system as much as possible impervious to user validation errors. Our strategy consisting of two major steps: candidate mapping selection, which ranks mappings based on their perceived quality, so as to present first to the users those mappings with lowest quality, and feedback propagation, which seeks to validate or invalidate those mappings that are perceived to be “similar” to the mappings already presented to the users. The purpose of these two strategies is twofold: achieve greater improvements earlier and minimize overall user interaction. There are three important features of our approach. The first is that we use a dynamic ranking mechanism to adapt to the new conditions after each user interaction, the second is that we may need to present each mapping for validation more than once—revalidation—because of possible user errors, and the third is that we propagate a user’s input on a mapping immediately without first achieving consensus for that mapping. We study extensively the effectiveness and robustness of our approach as several of these parameters change, namely the error and revalidation rates, as a function of the number of iterations, to provide conclusive guidelines for the design and implementation of multi-user feedback ontology matching systems.
Green One Pot Solvent-Free Synthesis of Pyrano[2,3-c]-Pyrazoles and Pyrazolo[1,5-a]Pyrimidines

Pyrano[2,3-c]pyrazoles are obtained via mixing ethyl acetoacetate, hydrazine hydrate, aldehydes or ketones and malononitrile in the absence of solvent. These same products were also obtained by reacting arylidenemalononitriles 3 with 3-methyl-2-pyrazolin-5-ones. NOE difference experiments confirmed that these products exist solely in the 2H form. Similar treatments of 3-amino-2-pyrazolin-5-one with arylidene-malononitrile afforded adduct 6. Similarly mixing ethyl cyanoacetate, hydrazine hydrate, aldehydes, with malononitrile gave the same product 6. A novel synthesis of 4-oxo-4H-pyrano[2,3-c]pyrazole (8) could be achieved via reacting 3-methyl-2-pyrazolin-5-one with a mixture of cyanoacetic acid and acetic anhydride. Similar treatment of 3-aminopyrazole 11 with the benzylidene-malononitrile produced the pyrazolo[2,3-a]pyrimidines 12a,b.
High Performance FPGA Implementation of Elliptic Curve Cryptography over Binary Fields

In this paper, we propose a high performance hardware implementation architecture of elliptic curve scalar multiplication over binary fields. The proposed architecture is based on the Montgomery ladder method and uses polynomial basis for finite field (FF) arithmetic. A single Karatsuba multiplier runs with no idle cycle significantly increases the performance of FF multiplication while spending small amount of hardware resources, and other FF operations performed in parallel with the FF multiplier. The optimized circuits lead to a lesser area requirement compared to other high performance implementations. An implementation for the National Institute of Standards and Technology (NIST) recommended curve with degree 163 is shown, the proposed design can reach 121 MHz with 10,417 slices when implemented on Xilinx Virtex-4 XC4VLX200 FPGA device, the total time required for one elliptic curve scalar multiplication is 9.0 μs.