Miracle-dz/UniFAR-FTUs huggingface dataset:
Hexamethylbisacetamide Remodels the Human Immunodeficiency Virus Type 1 (HIV-1) Promoter and Induces Tat-Independent HIV-1 Expression but Blunts Cell Activation

ABSTRACT Hexamethylbisacetamide (HMBA) induces human immunodeficiency virus type 1 (HIV-1) gene expression in latently infected T-cell and monocytoid cell lines. We find that HMBA activation of viral expression is Tat independent but, like Tat, increases the efficiency of elongation of the HIV-1 promoter (long terminal repeat [LTR]) transcripts. Further, exposure to HMBA induces chromatin remodeling at nucleosome 1 (Nuc-1) near the start site of LTR transcription but does so without increasing histone acetylation or altering histone methylation near Nuc-1. Of note, despite enhanced proviral expression, HMBA suppressed HIV infection ex vivo in primary blood mononuclear cell (PBMC) cultures. Treatment with HMBA did not alter expression of the HIV coreceptors, CCR5 and CXCR4, in PBMCs but down-regulated CD4. Finally, HMBA interferes with cell proliferation and activation; it suppressed expression of Ki67 and CD25 and in PBMCs exposed to mitogen. As HMBA has been tested in oncology trials, its unusual properties make it a useful reagent for future studies of HIV promoter regulation and a novel prototype molecule for therapeutics that abort the latent proviral state of chronic HIV infection.
Conditional Models for Non-smooth Ranking Loss Functions

Learning to rank is an important area at the interface of machine learning, information retrieval and Web search. The central challenge in optimizing various measures of ranking loss is that the objectives tend to be non-convex and discontinuous. To make such functions amenable to gradient based optimization procedures one needs to design clever bounds. In recent years, boosting, neural networks, support vector machines, and many other techniques have been applied. However, there is little work on directly modeling a conditional probability Pr(y|x_q) where y is a permutation of the documents to be ranked and x_q represents their feature vectors with respect to a query q. A major reason is that the space of y is huge: n! if n documents must be ranked. We first propose an intuitive and appealing expected loss minimization objective, and give an efficient shortcut to evaluate it despite the huge space of ys. Unfortunately, the optimization is non-convex, so we propose a convex approximation. We give a new, efficient Monte Carlo sampling method to compute the objective and gradient of this approximation, which can then be used in a quasi-Newton optimizer like LBFGS. Extensive experiments with the widely-used LETOR dataset show large ranking accuracy improvements beyond recent and competitive algorithms.
Rho GTPase controls Drosophila salivary gland lumen size through regulation of the actin cytoskeleton and Moesin

Generation and maintenance of proper lumen size is important for tubular organ function. We report on a novel role for the Drosophila Rho1 GTPase in control of salivary gland lumen size through regulation of cell rearrangement, apical domain elongation and cell shape change. We show that Rho1 controls cell rearrangement and apical domain elongation by promoting actin polymerization and regulating F-actin distribution at the apical and basolateral membranes through Rho kinase. Loss of Rho1 resulted in reduction of F-actin at the basolateral membrane and enrichment of apical F-actin, the latter accompanied by enrichment of apical phosphorylated Moesin. Reducing cofilin levels in Rho1 mutant salivary gland cells restored proper distribution of F-actin and phosphorylated Moesin and rescued the cell rearrangement and apical domain elongation defects of Rho1 mutant glands. In support of a role for Rho1-dependent actin polymerization in regulation of gland lumen size, loss of profilin phenocopied the Rho1 lumen size defects to a large extent. We also show that Ribbon, a BTB domain-containing transcription factor functions with Rho1 in limiting apical phosphorylated Moesin for apical domain elongation. Our studies reveal a novel mechanism for controlling salivary gland lumen size, namely through Rho1-dependent actin polymerization and distribution and downregulation of apical phosphorylated Moesin.
Retroperitoneoscopic Radical Nephrectomy in Obese Patients: Outcomes and Considerations

Objective:To determine whether obesity is associated with surgical outcome in Japanese patients undergoing retroperitoneoscopic radical nephrectomy (RRN). Patients and Methods: Between November 1999 and March 2005, we performed 98 RRN procedures for patients with renal cell carcinoma. Patients with a body mass index (BMI) of 25.0 or more were defined as obese (group A, n = 33) and those with a BMI of <25.0 were defined as non-obese (group B, n = 65), in accordance with the criteria of the Japan Society for the Study of Obesity. Patient background, degree of surgical invasiveness, and period of convalescence were compared between groups A and B. Results: No statistically significant differences were observed between the groups in terms of age, gender, tumor laterality, tumor size, and time until resumption of oral intake and ambulation. However group A had a significantly longer insufflation time (172.1 vs. 137.4 min), greater blood loss (195.3 vs. 48.4 ml) and higher renal specimen weight (440.0 vs. 306.0 g) than group B. Conclusion: Obesity is not a factor that affects patient eligibility for RRN, but is a risk factor for longer insufflation time and greater blood loss.
An Interference Aware Distributed Resource Management Scheme for CDMA-Based Wireless Mesh Backbone

In this paper, with a cross-layer design principle, we propose an interference aware distributed resource management scheme for a code-division multiple access (CDMA)-based wireless mesh backbone (consisting of a number of wireless routers at fixed sites). Specifically, benefiting from the fixed location of wireless routers, the power allocation is based on the length of the transmission path, so as to ensure a certain level of fairness among the routers. For a new call arrival, based on the maximum sustainable interference concept, each existing receiver (rather than the potential sender) estimates its experienced interference level under the hypothesis that the new call is admitted. If the interference is not tolerable, the existing receiver rejects the new call by sending a blocking-signal. The main advantages of our proposed scheme are the low control message overhead for easy implementation, and the accurate interference estimation. Simulation results are presented to evaluate the performance of our scheme.
Infinite-Horizon Policy-Gradient Estimation

Gradient-based approaches to direct policy search in reinforcement learning have received much recent attention as a means to solve problems of partial observability and to avoid some of the problems associated with policy degradation in value-function methods. In this paper we introduce GPOMDP, a simulation-based algorithm for generating a biased estimate of the gradient of the average reward in Partially Observable Markov Decision Processes (POMDPs) controlled by parameterized stochastic policies. A similar algorithm was proposed by Kimura, Yamamura, and Kobayashi (1995). The algorithm's chief advantages are that it requires storage of only twice the number of policy parameters, uses one free parameter β ∈ [0, 1] (which has a natural interpretation in terms of bias-variance trade-off), and requires no knowledge of the underlying state. We prove convergence of GPOMDP, and show how the correct choice of the parameter β is related to the mixing time of the controlled POMDP. We briefly describe extensions of GPOMDP to controlled Markov chains, continuous state, observation and control spaces, multiple-agents, higher-order derivatives, and a version for training stochastic policies with internal states. In a companion paper (Baxter, Bartlett, & Weaver, 2001) we show how the gradient estimates generated by GPOMDP can be used in both a traditional stochastic gradient algorithm and a conjugate-gradient procedure to find local optima of the average reward.
Boolean Circuits, Tensor Ranks, and Communication Complexity

We investigate two methods for proving lower bounds on the size of small-depth circuits, namely the approaches based on multiparty communication games and algebraic characterizations extending the concepts of the tensor rank and rigidity of matrices. Our methods are combinatorial, but we think that our main contribution concerns the algebraic concepts used in this area (tensor ranks and rigidity). Our main results are following. (i) An $o(n)$-bit protocol for a communication game for computing shifts, which also gives an upper bound of $o(n^2)$ on the contact rank of the tensor of multiplication of polynomials; this disproves some earlier conjectures. A related probabilistic construction gives an $o(n)$ upper bound for computing all permutations and an $O(n\log\log n)$ upper bound on the communication complexity of pointer jumping with permutations. (ii) A lower bound on certain restricted circuits of depth 2 which are related to the problem of proving a superlinear lower bound on the size of logarithmic-depth circuits; this bound has interpretations both as a lower bound on the rigidity of the tensor of multiplication of polynomials and as a lower bound on the communication needed to compute the shift function in a restricted model. (iii) An upper bound on Boolean circuits of depth 2 for computing shifts and, more generally, all permutations; this shows that such circuits are more efficient than the model based on sending bits along vertex-disjoint paths.
Polyphase tectonic inversion and its role in controlling hydrocarbon prospectivity in the Greater East Shetland Platform and Mid North Sea High, UK

Abstract Thick Paleozoic successions are buried under the Greater East Shetland Platform (ESP) and Mid North Sea High (MNSH), two large underexplored platform regions flanking the structural depocentres of the North Sea. Here, newly acquired broadband seismic data are interpreted to provide a novel assessment of the regional tectonostratigraphic evolution and its influence on hydrocarbon prospectivity. Numerous working reservoir units are present over these two frontier areas, together with large Paleozoic traps. Hydrocarbon charge occurs either via a likely maximum 30–40 km lateral migration from the Jurassic/Carboniferous basinal source kitchens or, possibly, via vertical/lateral migration from deeper Devono-Carboniferous source intervals. The two regions underwent a largely similar evolution, consisting of at least eight successive switch-overs between regional compression/uplift and extension/subsidence in the last 420 myr. However, on the Greater MNSH, the lack of significant Permo-Triassic rifting probably resulted in too little subsidence for the lower Carboniferous interval to reach sufficient burial depth for gas maturation. Seep and fluid escape data suggest a working ‘deep’ source in the Greater ESP. Here, the presence of localized Permo-Triassic intra-platform grabens and half-grabens provided sufficient subsidence for the oil-prone middle Devonian unit to eventually enter the oil maturation window and faults provide easy conduits for the upwards migration of oil.
Biological Crystallography Structural Studies of Pseudomonas and Chromobacterium X-aminotransferases Provide Insights into Their Differing Substrate Specificity

The crystal structures and inhibitor complexes of two industrially important ! -aminotransferase enzymes from Pseudomonas aeruginosa and Chromobacterium violaceum have been determined in order to understand the differences in their substrate specificity. The two enzymes share 30% sequence identity and use the same amino acceptor, pyruvate; however, the Pseudomonas enzyme shows activity towards the amino donor-alanine, whilst the Chromobacterium enzyme does not. Both enzymes show activity towards S-methyl-benzylamine (MBA), with the Chromobacterium enzyme having a broader substrate range. The crystal structure of the P. aeruginosa enzyme has been solved in the holo form and with the inhibitor gabaculine bound. The C. violaceum enzyme has been solved in the apo and holo forms and with gabaculine bound. The structures of the holo forms of both enzymes are quite similar. There is little conformational difference observed between the inhibitor complex and the holoenzyme for the P. aeruginosa aminotransferase. In comparison, the crystal structure of the C. violaceum gabacu-line complex shows significant structural rearrangements from the structures of both the apo and holo forms of the enzyme. It appears that the different rigidity of the protein scaffold contributes to the substrate specificity observed for the two ! -aminotransferases.
Water Vapor Radiometer-Global Positioning System Comparison Measurements and Calibration of the 20 to 32 Gigahertz Tropospheric Water Vapor Absorption Model

Collocated measurements of opacity (from water vapor radiometer (WVR) brightness temperatures) and wet path delay (from ground-based tracking of Global Positions System (GPS) satellites) are used to constrain the model of atmospheric water vapor absorption in the 20 to 32 GHz band. A difierential approach is presented in which the slope of opacity-versus-wet delay data is used as the absorption model constraint. This technique minimizes the efiects of radiometric calibration errors and oxygen model uncertainties in the derivation of a best-flt vapor absorption model. A total of approximately 5 months of data were obtained from two experiment sites. At the Cloud and Radiation Testbed (CART) site near Lamont, Oklahoma, three independent WVRs provided near-continuous opacity measurements over the interval from July through September 1998. At NASA’s Goldstone tracking station in the California desert, two WVRs obtained opacity data over the September through October 1997 interval. At both sites, a GPS receiver and surface barometer obtained the data required for deriving the zenith wet delays over the same time frames. Measured values of the opacity-versus-wet delay slope parameter were obtained at four WVR frequencies (20.7, 22.2, 23.8, and 31.4 GHz) and compared with predictions of three candidate absorption models referenced in the recent literature. With one exception, all three models provide agreement within approximately 5 percent of the opacity-versus-wet delay slope measurements at all WVR frequencies at both sites. One model provides agreement for all channels at both sites to the 2 to 3 percent level. This accuracy is su‐cient to meet the requirements of the tropospheric calibration system now being deployed at Goldstone to support the Cassini Gravitational Wave Experiment.
Anti-Müllerian hormone inhibits initiation of growth of human primordial ovarian follicles in vitro.

BACKGROUND Anti-Müllerian hormone (AMH) inhibits the initiation of the development and early growth of mouse ovarian follicles. Furthermore, the ovarian follicle pool diminishes prematurely in AMH-knockout mice. In this study, we examined whether AMH plays a similar role in humans, controlling ovarian follicle growth. METHODS Human ovarian cortical tissue biopsy specimens were cut into small pieces and cultured for 7 days in medium containing rat recombinant AMH at 0, 10, 30 or 100 ng/ml. The developmental stages and viability of the follicles were evaluated from histological sections. RESULTS Similar to previous studies, significant initiation of follicle growth was observed in almost all culture media, as demonstrated by a significantly smaller proportion of primordial follicles (14-26%) compared with non-cultured control tissue (56%). The exception was tissue in medium supplemented with AMH at 100 ng/ml. Here, the proportion of primordial follicles was not significantly different from that in non-cultured tissue; furthermore, it was significantly greater than that in vehicle control cultures and cultures containing AMH at 10 ng/ml, indicating the inhibition of growth initiation. Viability was unaffected by the presence of AMH when compared with tissues in control media. CONCLUSIONS Recombinant AMH at a concentration of 100 ng/ml has an inhibitory effect on early human ovarian follicular development in vitro, suppressing the initiation of primordial follicle growth.
The Extraretinal Eyelet of Drosophila: Development, Ultrastructure, and Putative Circadian Function

Circadian rhythms can be entrained by light to follow the daily solar cycle. In Drosophila melanogaster a pair of extraretinal eyelets expressing immunoreactivity to Rhodopsin 6 each contains four photoreceptors located beneath the posterior margin of the compound eye. Their axons project to the region of the pacemaker center in the brain with a trajectory resembling that of Bolwig's organ, the visual organ of the larva. A lacZ reporter line driven by an upstream fragment of the developmental gap geneKrüppel is a specific enhancer element for Bolwig's organ. Expression of immunoreactivity to the product oflacZ in Bolwig's organ persists through pupal metamorphosis and survives in the adult eyelet. We thus demonstrate that eyelet derives from the 12 photoreceptors of Bolwig's organ, which entrain circadian rhythmicity in the larva. Double labeling with anti-pigment-dispersing hormone shows that the terminals of Bolwig's nerve differentiate during metamorphosis in close temporal and spatial relationship to the ventral lateral neurons (LNv), which are essential to express circadian rhythmicity in the adult. Bolwig's organ also expresses immunoreactivity to Rhodopsin 6, which thus continues in eyelet. We compared action spectra of entrainment in different fly strains: in flies lacking compound eyes but retaining eyelet (so1), lacking both compound eyes and eyelet (so1;gl60j ), and retaining eyelet but lacking compound eyes as well as cryptochrome (so1;cryb ). Responses to phase shifts suggest that, in the absence of compound eyes, eyelet together with cryptochrome mainly mediates phase delays. Thus a functional role in circadian entrainment first found in Bolwig's organ in the larva is retained in eyelet, the adult remnant of Bolwig's organ, even in the face of metamorphic restructuring.
Development of a Colorectal Cancer Screening Intervention for Iranian Adults: Appling Intervention Mapping

Background: While the incidence rate of the colorectal cancer (CRC) has been increasing over the last three decades in Iran, very limited interventions to increase CRC screening have been developed for Iranian population. The purpose of this study was to describe the use of Intervention Mapping (IM) for applying theory and evidence and considering local contexts to develop a CRC screening program among adults in Iran. Materials and Methods: From April 2014 to July 2016 following the IM process, six steps were formulated and implemented. First a need assessment was conducted involving relevant stakeholders and using focus groups discussions (n=10), individual interviews (n=20), and a household survey (n= 480). Then a matrix of change objectives was developed for each behavioral outcome and theoretical methods and their practical applications were identified to guide intervention development and implementation. A multi-component intervention was developed and piloted. Decision on suitable parts of intervention was made based on feedback of pilot study. Finally, evaluation plan including process and outcome evaluation was generated and conducted to inform future scale up. Results: The needs assessment highlighted factors affecting CRC screening including knowledge, self efficacy, social support and perceived benefit and barriers (financial problems, fear of detection of cancer and etc). Results of needs assessment were used to develop next steps IM. The program utilized methods like information delivery, modeling, and persuasion. Practical applications included video presentation, group discussion, role playing and postcards. This program was assessed through a cluster-randomized controlled trial. Results showed that there were significant differences in CRC screening uptake between intervention groups and control (P<0.001). Conclusions: IM is a useful process in the design of a theory-based intervention addressing CRC screening among Iranian population.
Incidence of Anterior Pituitary Deficiency after Radiotherapy at an Early Age: Study in Retinoblastoma

ABSTRACT. Thirty‐one patients treated for retinoblastoma in the first few years (3 months to 3 years and 6 months) of life were studied 2 to 15 years later. Radiotherapy delivered 1300 to 6 500 rads to the hypothalamo‐pituitary area. Growth deficiency was documented in 30 % of all cases. Other pituitary deficiencies were the exception. The critical dose for GH insufficiency is between 2000 and 3000 rads, as in older children or adults. Our study does not support the hypothesis that the hypothalamo‐pituitary area is more sensitive to radiation at an early age. Furthermore, conservative therapy of retinoblastoma leads to double lateral irradiation and will increase the number of GH deficient children after retinoblastoma.
Males’ Ability to Report Their Partner’s Contraceptive Use at Last Sex in a Nationally Representative Sample: Implications for Unintended Pregnancy Prevention Evaluations

Addressing and enabling the role of males in contraceptive choices may facilitate efforts to reduce unintended pregnancy rates and disparities in the United States, but little is known about males’ ability to report their partners’ contraceptive use. Data from the 2011-2013 National Survey of Family Growth from 2,238 males aged 15 to 44 years who had vaginal sex with a noncohabiting or nonmarital partner and were not seeking pregnancy were examined to tabulate the proportion of males able to report whether their partner used a specific contraceptive method use at last sex (PCM) by sociodemographic and sexual history characteristics. Logistic regression was used to assess odds of being unable to report PCM, adjusting for age and sexual history factors. Most (95.0%) were able to report PCM, with no difference by age group (chi-square = 7.27, p = .281) in unadjusted analyses. Males with a new sex partner (14.8% of the sample), compared with those with an established sex partner, had significantly higher odds of being unable to report PCM in bivariate (11.7% vs. 3.7%, chi-square = 39.39, p < .001) and multivariable (adjusted odds ratio [AOR]: 3.17, 95% confidence interval [CI: 1.74, 5.65]) analyses. Those whose last sexual encounter was more than 3 months ago also had higher odds of being unable to report in bivariate (OR: 1.74, 95% CI [1.05, 2.87]) and multivariable analyses (AOR: 2.04, 95% CI [1.04, 4.03]). Most men were able report PCM, but reporting was significantly lower among men with new sex partners. To inform future research and evaluation relying on male report, validation studies comparing male report with partner report, specifically among new couples, are needed.