Miracle-dz/UniFAR-FTUs huggingface dataset:
Sexual risk, substance use, and psychological distress in HIV-positive gay and bisexual men who also inject drugs

Objectives:Gay and bisexual men and injection drug users (IDU) are the two main groups at risk of HIV exposure in the United States, but few studies have focused on the intersection of these two groups. Little is known about HIV-positive gay and bisexual IDU. The aim of this study is to identify and compare differences in HIV transmission risk behaviors and psychological distress in HIV-positive gay and bisexual men by injection versus non-injection drug use. Methods:Data were from the baseline assessment of a randomized controlled trial of an HIV prevention intervention for HIV-positive gay and bisexual men. Results:Of the 1168 men, 236 (20%) reported injection drug use, 500 (43%) reported only non-injection drug use, and 422 (36%) reported no drug use. More of the IDU reported having sex with women, and identified themselves as ‘barebackers’ (i.e. men who intentionally have unprotected anal intercourse). IDU reported more unprotected sexual behaviors than men who did not use drugs, but their sexual risk behaviors were similar to those of men who used non-injection drugs. IDU, compared with other drug users, reported more use of non-injected methamphetamine, amphetamine, barbiturates, and gamma hydroxybutyrate. More IDU, compared with the other two groups, reported sexual abuse, anxiety, and hostility. Conclusion:HIV-positive gay and bisexual IDU are a distinct group from other HIV-positive gay and bisexual men. Prevention case management and interventions that help men cope with multiple health concerns and prevent HIV transmission are needed for this population.
DEPD: a novel database for differentially expressed proteins

SUMMARY The Differentially Expressed Protein Database was designed to store the output of comparative proteomics studies and provides a publicly available query and analysis platform for data mining. The database contains information about more than 3000 differentially expressed proteins (DEPs) manually extracted from the published literature, including relevant biological, experimental and methodological elements. Tools for visualization and functional analysis of DEPs are provided via a user-friendly webinterface. AVAILABILITY http://protchem.hunnu. edu.cn/depd/.
Bevacizumab plus 5-fluorouracil induce growth suppression in the CWR-22 and CWR-22R prostate cancer xenografts

Prostate cancer is the most common malignancy in men. Although patients with metastatic prostate cancer can benefit from androgen ablation, most of them will die of prostate cancer progression to an androgen-refractory state. In the present study, the effects of docetaxel, bevacizumab, 5-fluorouracil (5-FU), bevacizumab plus docetaxel, and bevacizumab plus 5-FU on the growth of human CWR-22 (androgen-dependent) and CWR-22R (androgen-independent) prostate carcinoma xenografts were investigated. We report that i.p. administration of 10 mg/kg docetaxel at 1-week interval, 5 mg/kg/ bevacizumab once every 2 weeks, or 12.5 mg/kg 5-FU, bevacizumab/docetaxel, or bevacizumab/5-FU weekly to severe combined immunodeficient mice bearing prostate cancer xenografts (12 mice per treatment group) for 21 days resulted in 22.5 ± 8%, 23 ± 7%, 31 ± 8%, 22 ± 6%, and 81 ± 5% growth inhibition, respectively. Greatest growth suppression was observed in bevacizumab/5-FU treatment. Bevacizumab/5-FU–induced growth suppression was associated with reduction in microvessel density, inhibition of cell proliferation; up-regulation of phosphatase and tensin homologue, p21Cip1/Waf1, p16INK4a, and p27Kip1; hypophosphorylation of retinoblastoma protein; and inhibition of Akt/mammalian target of rapamycin pathway. Our data indicate that bevacizumab/5-FU effectively inhibits angiogenesis and cell cycle progression and suggest that bevacizumab/5-FU may represent an alternative treatment for patients with prostate cancer. [Mol Cancer Ther 2007;6(8):2149–57]
Disjunctive Temporal Planning with Uncertainty

Driven by planning problems with both disjunctive constraints and contingency, we define the Disjunctive Temporal Problem with Uncertainty (DTPU), an extension of the DTP that includes contingent events. Generalizing existing work on Simple Temporal Problems with Uncertainty, we divide the time-points into controllable and uncontrollable classes, and propose varying notions of controllability to replace the notion of consistency.
Scalarization versus indicator-based selection in multi-objective CMA evolution strategies

While scalarization approaches to multi- criteria optimization become infeasible in the case of many objectives, for few objectives the benefits of population- based methods compared to a set of independent single- objective optimization trials on scalarized functions are not obvious. The multi-objective covariance matrix adaptation evolution strategy (MO-CMA-ES) is a powerful algorithm for real-valued multi-criteria optimization. This population- based approach combines mutation and strategy adaptation from the elitist CMA-ES with multi-objective selection. We empirically compare the steady-state MO-CMA-ES with different scalarization algorithms, in which the elitist CMA-ES is used as single-objective optimizer. Although only bicriteria benchmark problems are considered, the MO-CMA-ES performs best in the overall comparison. However, if the scalarized problems have a structure that can easily be exploited by the CMA-ES and that is less apparent in the vector-valued fitness function, the CMA- ES with scalarization outperforms the population-based approach.
A two-step approach to restorable dynamic QoS routing

Aiming at minimizing the combined bandwidth cost of a pair of disjoint active and backup paths, a popular approach to designing restorable dynamic QoS routing schemes is based on integer linear programming (ILP) formulation. Owing to the very different natures of active and backup paths, we found this approach problematic. In this paper, we propose a simple alternative approach, called two-step routing. In the first step, active path is found using the widest-shortest path (WSP) routing. In the second step, the corresponding backup path is determined using one of the three variants of shortest-widest path (SWP) routing, basic-SWP, approximate-SWP and composite-SWP. Combining both steps, three novel restorable routing algorithms, SBW, SAW and SCW, are obtained. Comparing with the existing best-known algorithms, we show that our two-step routing approach yields noticeably lower call blocking probability, shorter active path length, and adjustable backup path length (depending on the SWP variant adopted). Besides, our two-step routing approach gives a much shorter running time than the ILP approach, which makes it more attractive for dynamic routing.
Coffin-Lowry syndrome

Males with Coffin-Lowry syndrome typically have severe to profound intellectual disability and delayed development. Affected women may be cognitively normal, or they may have intellectual disability ranging from mild to profound. Beginning in childhood or adolescence, some people with this condition experience brief episodes of collapse when excited or startled by a loud noise. These attacks are called stimulus-induced drop episodes (SIDEs).
Effect of By-product Feed-based Silage Feeding on the Performance, Blood Metabolites, and Carcass Characteristics of Hanwoo Steers (a Field Study)

This study was conducted to determine the effects of feeding by-product feed (BF)-based silage on the performance, blood metabolite parameters, and carcass characteristics of Hanwoo steers. The BF-based silage was composed of 50% spent mushroom substrate, 21% recycled poultry bedding, 15% cut ryegrass straw, 10.8% rice bran, 2% molasses, 0.6% bentonite, and 0.6% microbial additive (on a wet basis), and ensiled for over 5 d. Fifteen steers were allocated to three diets during the growing and fattening periods (3.1 and 9.8 months, respectively): a control diet (concentrate mix and free access to rice straw), a 50% BF-based silage diet (control diet+50% of maximum BF-based silage intake), and a 100% BF-based silage diet (the same amount of concentrate mix and ad libitum BF-based silage). The BF-based silage was fed during the growing and fattening periods, and was replaced with larger particles of rice straw during the finishing period. After 19.6 months of the whole period all the steers were slaughtered. Compared with feeding rice straw, feeding BF-based silage tended (p = 0.10) to increase the average daily gain (27%) and feed efficiency (18%) of the growing steers, caused by increased voluntary feed intake. Feeding BF-based silage had little effect on serum constituents, electrolytes, enzymes, or the blood cell profiles of fattening steers, except for low serum Ca and high blood urea concentrations (p<0.05). Feeding BF-based silage did not affect cold carcass weight, yield traits such as back fat thickness, longissimus muscle area, yield index or yield grade, or quality traits such as meat color, fat color, texture, maturity, marbling score, or quality grade. However, it improved good quality grade (1+ and 1++) appearance rates (60% for the control group vs 100% for the BF-based silage-fed groups). In conclusion, cheap BF-based silage could be successfully used as a good quality roughage source for beef cattle.
Design, Deployment, and Use of the DETER Testbed

The DETER testbed provides infrastructure for conducting medium-scale repeatable experiments in computer security, especially experiments that involve malicious code. Built using Utah's EMULAB, the DETER testbed has been configured and extended to provide stronger assurances for isolation and containment. This paper provides information on the capabilities of the DETER testbed and discusses the lessons learned from its deployment. Our strategies for containment are described and future plans discussed.
Scalable Data Mining Algorithms in Computational Biology and Biomedicine

1School of Computer Science and Technology, Tianjin University, Tianjin 300354, China 2Institute of Informatics, Silesian University of Technology, 44-100 Gliwice, Poland 3Department of Mathematics and Statistics and Department of Agronomy, Horticulture, and Plant Science, BioSNTR, South Dakota State University, Brookings, SD 57007, USA 4Center for Bioinformatics and Systems Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
RGAP: A Rough Set, Genetic Algorithm and Particle Swarm Optimization based Feature Selection Approach

Feature selection plays an important role in improving the classification accuracy by handling redundant or irrelevant features present in the dataset. Various soft computing based hybrid approaches like neuro-fuzzy, genetic-fuzzy, rough set-neuro etc. are proposed by researchers to perform feature selection. The existing approaches gives higher complexity and computational cost with low classification accuracy. Hence to improve the complexity and classification accuracy, a hybrid approach based on Genetic Algorithm (GA), Particle Swarm Optimization (PSO) and Rough Set Theory (RST) to perform feature selection is proposed. In the proposed approach, GA is used as a searching algorithm. To explore search space more efficiently, GA is combined with a PSO based local search operation. Rough Set Attribute Reduction (RSAR) method based on RST is used to compute core reducts. The proposed algorithm is tested on various benchmark datasets. Satisfactory improvements in terms of complexity and classification accuracy have been achieved.
WARM: Improving NAND flash memory lifetime with write-hotness aware retention management

Increased NAND flash memory density has come at the cost of lifetime reductions. Flash lifetime can be extended by relaxing internal data retention time, the duration for which a flash cell correctly holds data. Such relaxation cannot be exposed externally to avoid altering the expected data integrity property of a flash device. Reliability mechanisms, most prominently refresh, restore the duration of data integrity, but greatly reduce the lifetime improvements from retention time relaxation by performing a large number of write operations. We find that retention time relaxation can be achieved more efficiently by exploiting heterogeneity in write-hotness, i.e., the frequency at which each page is written. We propose WARM, a write-hotness aware retention management policy for flash memory, which identifies and physically groups together write-hot data within the flash device, allowing the flash controller to selectively perform retention time relaxation with little cost. When applied alone, WARM improves overall flash lifetime by an average of 3.24× over a conventional management policy without refresh, across a variety of real I/O workload traces. When WARM is applied together with an adaptive refresh mechanism, the average lifetime improves by 12.9×, 1.21× over adaptive refresh alone.
Depth Modulation of the Attentional Repulsion Effect

Shifts of attention can cause mislocalisation of visual objects. A brief cue that attracts attention can cause a shift in the perceived location of a subsequently presented visual object—specifically, moving it away from the focus of attention (attentional repulsion). In the present study we investigated whether depth would influence the magnitude of attentional repulsion by presenting peripheral visual cues in different depth planes from the target or fixation. In experiment 1 the results showed that the magnitude of the attentional repulsion was larger when the cue was presented at the depth plane farther away from the target and fixation. In experiment 2 we presented the fixation point in the same depth plane as the nearest cues and found larger repulsion effects when the cues were presented in depth planes farther away from the fixation. In experiment 3 no depth modulation was observed when the fixation was presented in the same depth plane with the farthest cues. Taken together, when the cues were presented in the depth plane farther away from the fixation, the magnitude of the attentional repulsion effect increased. It is speculated that the residual coarser spatial representation in the space farther from the fixation plane or the enhanced attentional process for the space closer than the fixation may be responsible for the larger attentional repulsion effect.
Spitzer’s Mid-Infrared View on an Outer-Galaxy Infrared Dark Cloud Candidate toward NGC 7538

Infrared dark clouds (IRDCs) represent the earliest observed stages of clustered star formation, characterized by large column densities of cold and dense molecular material observed in silhouette against a bright background of mid-IR emission. Up to now, IRDCs were predominantly known toward the inner Galaxy where background infrared emission levels are high. We present Spitzer observations with the Infrared Array Camera toward object G111.80+0.58 (G111) in the outer Galactic plane, located at a distance of ~3 kpc from us and ~10 kpc from the Galactic center. Earlier results show that G111 is a massive, cold molecular clump very similar to IRDCs. The mid-IR Spitzer observations unambiguously detect object G111 in absorption. We have identified for the first time an IRDC in the outer Galaxy, which confirms the suggestion that cluster-forming clumps are present throughout the Galactic plane. However, against a low mid-IR background such as the outer Galaxy it takes some effort to find them.
IP-address lookup using LC-tries

There has been a notable interest in the organization of routing information to enable fast lookup of IP addresses. The interest is primarily motivated by the goal of building multigigabit routers for the Internet, without having to rely on multilayer switching techniques. We address this problem by using an LC-trie, a trie structure with combined path and level compression. This data structure enables us to build efficient, compact, and easily searchable implementations of an IP-routing table. The structure can store both unicast and multicast addresses with the same average search times. The search depth increases as /spl Theta/(log log n) with the number of entries in the table for a large class of distributions, and it is independent of the length of the addresses. A node in the trie can be coded with four bytes. Only the size of the base vector, which contains the search strings, grows linearly with the length of the addresses when extended from 4 to 16 bytes, as mandated by the shift from IP version 4 to IP version 6. We present the basic structure as well as an adaptive version that roughly doubles the number of lookups/s. More general classifications of packets that are needed for link sharing, quality-of-service provisioning, and multicast and multipath routing are also discussed. Our experimental results compare favorably with those reported previously in the research literature.
EVALUATION OF AN ENZYME IMMUNOASSAY TEST FOR THE DIAGNOSIS OF CHLAMYDIA PSITTACI INFECTION IN FREE-RANGING KOALAS (PHASCOLARCTOS CINEREUS) IN SOUTHEASTERN QUEENSLAND, AUSTRALIA

The IDEIA Chlamydia Test, a commercially available antigen-capture enzyme-linked immunosorbent assay (ELISA) test, based on a monoclonal antibody for the detection of chlamydia in clinical specimens, was evaluated in a population of 65 free-ranging koalas in southeastern Queensland determined to be infected with Chlamydia psittaci. Compared to isolation of the organism in tissue culture, the sensitivity of the IDEIA test ranged from 3 to 11%, and the specificity from 90 to 97%. The results indicated that the IDEIA test is unsuitable for use as a diagnostic screening test for C. psittaci in free-ranging koalas.
A novel family of fluorescent hypoxia sensors reveal strong heterogeneity in tumor hypoxia at the cellular level

Hypoxia is an intensively investigated condition with profound effects on cell metabolism, migration, and angiogenesis during development and disease. Physiologically, hypoxia is linked to tissue homeostasis and maintenance of pluripotency. Hypoxia also contributes to pathologies including cardiovascular diseases and cancer. Despite its importance, microscopic visualization of hypoxia is largely restricted to the detection of reductively activated probes by immunostaining. Here, we describe a novel family of genetically encoded fluorescent sensors that detect the activation of HIF transcription factors reported by the oxygen‐independent fluorescent protein UnaG. It comprises sensors with different switching and memory behavior and combination sensors that allow the distinction of hypoxic and reoxygenated cells. We tested these sensors on orthotopically transplanted glioma cell lines. Using a cranial window, we could visualize hypoxia intravitally at cellular resolution. In tissue samples, sensor activity was detected in regions, which were largely devoid of blood vessels, correlated with HIF‐1α stabilization, and were highly heterogeneous at a cellular level. Frequently, we detected recently reoxygenated cells outside hypoxic areas in the proximity of blood vessels, suggestive of hypoxia‐promoted cell migration.
WASP-3b: a strongly irradiated transiting gas-giant planet

We report the discovery of WASP-3b, the third transiting exoplanet to be discovered by the WASP and SOPHIE collaboration. WASP-3b transits its host star USNO-B1.0 1256−0285133 every 1.846 834 ± 0.000 002 d. Our high-precision radial velocity measurements present a variation with amplitude characteristic of a planetary-mass companion and in phase with the light curve. Adaptive optics imaging shows no evidence for nearby stellar companions, and line-bisector analysis excludes faint, unresolved binarity and stellar activity as the cause of the radial velocity variations. We make a preliminary spectroscopic analysis of the host star and find it to have T eff = 6400 ± 100 K and log g = 4.25 ± 0.05 which suggests it is most likely an unevolved main-sequence star of spectral type F7-8V. Our simultaneous modelling of the transit photometry and reflex motion of the host leads us to derive a mass of 1.76 +0.08 −0.14 MJ and radius 1.31 +0.07 −0.14 RJ for WASP-3b. The proximity and relative temperature of the host star suggests that WASP-3b is one of the hottest exoplanets known, and thus has the potential to place stringent constraints on exoplanet atmospheric models.
Dimensionality Reduction for the Control of Powered Upper Limb Prostheses

Myoelectric prosthesis control is difficult to achieve, because the optimal selection of features from a set, extracted from a myoelectric signal, is known as being a very challenging problem in prosthetic control. Dimensionality reduction means to retain MES information, that is important for class discrimination and to discard irrelevant data. Dimensionality reduction strategies can be categorized into feature selection and feature projection methods according to their objective functions. This work brings forward a statistical cluster analysis technique, which we call the "Guilin Hills selection method". The goal of our efforts is to control electrically powered upper limb prostheses with a minimum number of sensors and a low-power processor. The paper introduces the method and brings forward exemplar results for the selection of two time-domain features. With the proposed method, we can clearly distinguish four hand-positions from myoelectric signals of two sensors. The method also suggests feature combinations that lead to less robust classifications but require fewer sensors
Sampling Large Databases for Association Rules

Discovery of association rules . is an important database mining problem. Current algorithms for finding association rules require several passes over the analyzed database, and obviously the role of I/O overhead is very significant for very large databases. We present new algorithms that reduce the database activity considerably. The idea is to pick a Random sample, to find using this sample all association rules that probably hold in the whole database, and then to verify the results with the rest of the database. The algorithms thus produce exact association rules, not approximations based on a sample. The approach is, however, probabilistic, and in those rare cases where our sampling method does not produce all association rules, the missing rules can be found in a second pass. Our experiments show that the proposed algorithms can find association rules very efficiently in only one database
Startle Habituation and Midfrontal Theta Activity in Parkinson Disease

The ability to adapt to aversive stimuli is critical for mental health. Here, we investigate the relationship between habituation to startling stimuli and startle-related activity in medial frontal cortex as measured by EEG in both healthy control participants and patients with Parkinson disease (PD). We report three findings. First, patients with PD exhibited normal initial startle responses but reduced startle habituation relative to demographically matched controls. Second, control participants had midfrontal EEG theta activity in response to startling stimuli, and this activity was attenuated in patients with PD. Finally, startle-related midfrontal theta activity was correlated with the rate of startle habituation. These data indicate that impaired startle habituation in PD is a result of attenuated midfrontal cognitive control signals. Our findings could provide insight into the frontal regulation of startle habituation.