Miracle-dz/UniFAR-FTUs huggingface dataset:
Interaction of the HIV-1 Intasome with Transportin 3 Protein (TNPO3 or TRN-SR2)*

Background: TNPO3 is a key cellular factor involved in early steps of HIV-1 replication. Results: TNPO3 is highly structured, interacts with the HIV-1 intasome by engaging the C-terminal domain of integrase, and does not directly bind capsid tubes. Conclusion: TNPO3 interacts with HIV-1 intasomes and not capsid cores. Significance: Our findings aid future genetic analysis to elucidate the role of TNPO3 in HIV-1 replication. Transportin 3 (TNPO3 or TRN-SR2) has been shown to be an important cellular factor for early steps of lentiviral replication. However, separate studies have implicated distinct mechanisms for TNPO3 either through its interaction with HIV-1 integrase or capsid. Here we have carried out a detailed biophysical characterization of TNPO3 and investigated its interactions with viral proteins. Biophysical analyses including circular dichroism, analytical ultracentrifugation, small-angle x-ray scattering, and homology modeling provide insight into TNPO3 architecture and indicate that it is highly structured and exists in a monomer-dimer equilibrium in solution. In vitro biochemical binding assays argued against meaningful direct interaction between TNPO3 and the capsid cores. Instead, TNPO3 effectively bound to the functional intasome but not to naked viral DNA, suggesting that TNPO3 can directly engage the HIV-1 IN tetramer prebound to the cognate DNA. Mass spectrometry-based protein footprinting and site-directed mutagenesis studies have enabled us to map several interacting amino acids in the HIV-1 IN C-terminal domain and the cargo binding domain of TNPO3. Our findings provide important information for future genetic analysis to better understand the role of TNPO3 and its interacting partners for HIV-1 replication.
Receiver design for asymmetrically clipped optical OFDM

Asymmetrically clipped optical OFDM (ACO-OFDM) is compatible with optical intensity modulation and is well suited to bandlimited optical wireless channels. By carefully locating data on odd subcarriers and clipping the resulting time signal, ACO-OFDM guarantees non-negative output amplitudes and clipping noise orthogonal to the information. However, in the conventional receiver, clipping noise is ignored in detection and data are extracted from odd subcarriers only. In this paper, a new receiver design for ACO-OFDM is proposed which exploits the structure of the clipping noise to improve the optical power efficiency. By observing the anti-symmetry of time domain samples, a simple pairwise maximum likelihood detector is developed and is used to fix half of the received samples to zero. Simulation results show that employing the proposed detector design leads to 1.3 dB optical gain at a BER of 10−5.
Tight (Lower) Bounds for the Fixed Budget Best Arm Identification Bandit Problem

We consider the problem of \textit{best arm identification} with a \textit{fixed budget $T$}, in the $K$-armed stochastic bandit setting, with arms distribution defined on $[0,1]$. We prove that any bandit strategy, for at least one bandit problem characterized by a complexity $H$, will misidentify the best arm with probability lower bounded by $$\exp\Big(-\frac{T}{\log(K)H}\Big),$$ where $H$ is the sum for all sub-optimal arms of the inverse of the squared gaps. Our result disproves formally the general belief - coming from results in the fixed confidence setting - that there must exist an algorithm for this problem whose probability of error is upper bounded by $\exp(-T/H)$. This also proves that some existing strategies based on the Successive Rejection of the arms are optimal - closing therefore the current gap between upper and lower bounds for the fixed budget best arm identification problem.
The impact of HIV and ART on recurrent tuberculosis in a sub-Saharan setting

Objective:To estimate the impact of antiretroviral therapy (ART) on the incidence of recurrent tuberculosis (TB) in an African population. Design:A long-term population cohort in Karonga District, northern Malawi. Methods:Patients who had completed treatment for laboratory-confirmed TB diagnosed since 1996 were visited annually to record vital status, ART use and screen for TB. Survival analysis estimated the effect of HIV/ART status at completion of treatment on mortality and recurrence. Analyses were stratified by time since treatment completion to estimate the effects on relapse (predominates during first year) and reinfection disease (predominates later). Results:Among 1133 index TB cases contributing 4353 person-years of follow-up, there were 307 deaths and 103 laboratory-confirmed recurrences (recurrence rate 4.6 per 100 person-years). Half the recurrences occurred in the first year since completing treatment. HIV infection increased the recurrence rate [rate ratio adjusted for age, sex, period and TB type 2.69, 95% confidence interval (CI) 1.69–4.26], but with less effect in the first year (adjusted rate ratio 1.71, 95% CI 0.87–3.35) than subsequently (adjusted rate ratio 4.2, 95% CI 2.16–8.15). Recurrence rates on ART were intermediate between those of HIV-negative individuals and HIV-positive individuals without ART. Compared with HIV-positive individuals without ART, the adjusted rate ratio was 0.74 (95% CI 0.27–2.06) in the first year, and 0.43 (95% CI 0.11–1.73) later. Conclusion:The increased incidence of TB recurrence observed in HIV-positive patients appeared to be reduced by ART. The effects are mostly on later (likely reinfection) disease so the impact of ART on reducing recurrence will be highest in high TB incidence settings.
Empowering Parents and Building Communities

This article builds and explores the hypothesis that parent and community participation in school governance can have positive impacts on community development by fostering improvements in school performance and school— community relations and by acting as a catalyst for collective action around community-development issues. It does so through case studies of reforms for school-based management that have led to the creation of school-site councils that include parents and community representatives in Kentucky, Hawaii, Chicago, and El Paso. The article finds that the hypothesized outcomes can occur where parents are given meaningful decision-making authority in schools, nongovernmental organizations provide training and advocacy for parents, and principals actively facilitate parent involvement.
Cyclic production of vesicular stomatitis virus caused by defective interfering particles.

Purified standard and defective interfering (DI) particles of vesicular stomatitis virus (VSV) were reconstituted, and the mixture was continuously passaged for six 24-hr growth periods in Chinese hamster ovary cells in suspension cultures. The cultures were monitored for cellular viability, for intracellular virus-specific RNA, for total extracellular viral particles, and for production of plaque-forming standard VSV. During the six passages, there was a cyclic, overlapping pattern of synthesis of both DI and standard VSV particles; decline in the production of standard virus was always preceded by large amounts of DI particles. Intracellular virus-specific RNA synthesis reflected the pattern of production of extracellular particles. Viral antigens represented by nucleocapsids accumulated in cells when DI particles were being produced in large quantities. These nucleocapsids contained RNA of DI particles. Under other conditions, infected cells were able to survive longer than usual and were resistant to superinfection by standard VSV. Preliminary evidence indicates that this resistance was due to surface interference. Therefore, a wide variety of different interactions between virus and host occurs simply by varying the total concentration of viral particles and the relative concentrations of standard and DI particles in these preparations.
The neuroendocrine effects of venlafaxine in healthy subjects

Venlafaxine hydrochloride represents a novel chemical class of antidepressant compounds. In preclinical studies it had monoamine uptake inhibitory properties. It specifically inhibited the uptake of serotonin (5‐HT) norepinephrine (NE) and dopamine (DA) in rat brain synaptosomes. Previous studies showed that various classes of psychotropic drugs with different effects on central aminergic systems exhibit distinct neuroendocrine profiles. In this study we investigated the effect of ascending doses of venlafaxine (12.5 mg, 25 mg, 50 mg, 75 mg orally) on neuroendocrine function in six healthy male subjects, using a single‐blind, placebo‐controlled study design. After the ascending doses of venlafaxine there could be demonstrated descriptively an influence on GH, and prolactin after the higher doses of venlafaxine. The cortisol secretion was statistically significantly influenced by venlafaxine, and showed a dose‐dependent increased. These neuroendocrine effects of venlafaxine may be interpreted as being a result of 5‐HT and NE reuptake‐inhibition properties of the substance. Evidence for a DA reuptake‐inhibition was not found as DA‐agonists lead to an inhibition of prolactin secretion.
Snap-together visualization: can users construct and operate coordinated visualizations?

Multiple coordinated visualizations enable users to rapidly explore complex information. However, users often need unforeseen combinations of coordinated visualizations. Snap-together visualization (Snap) enables users to rapidly and dynamically construct coordinated? visualization interfaces, customized for their data, without programming. Users U001load data into desired visualizations, then construct coordinations between them for brushing and linking, overview and detail view, drill down, etc. Snap formalizes a conceptual model of visualization coordination based on the relational data model. Visualization developers can easily Snap-enable their independent visualizations using a simple API.Empirical evaluation reveals benefits, cognitive issues and usability concerns with coordination concepts and Snap. Two user studies explore coordination construction and operation. Data-savvy users successfully, enthusiastically and rapidly constructed powerful coordinated? visualization interfaces of their own. Operating an overview-and-detail coordination reliably improved user performance by 30? 80% over detail-only and uncoordinated interfaces for most tasks.
Gender Dimensions of Support for Elderly in Vietnam

Although women and the elderly are assumed to be disadvantaged in much of the world, systematic empirical studies of gender differences in well-being among the elderly are rare. This article examines gender differences in elderly support and socio-economic well-being in Vietnam using census and survey data. Sources of support examined include work, nonfamilial support, and especially familial support including living arrangements. The authors consider the gender of the support recipient and provider. Substantial regional differences in the patriarchal/patrilineal family system, manifested in the wide regional variation in coresidence with married sons rather than daughters, make Vietnam a particularly interesting context for the study. The receipt of intergenerational transfers shows little variation across gender once the mediating effect of marital status differences is controlled. Gender differences in economic well-being, as measured by household wealth and self-perceptions of economic satisfaction, are modest, especially when marital status and age are controlled.
Phytoplankton Dynamics: from the Behavior of Cells to a Transport Equation

We present models of the dynamics of phytoplankton aggregates. We start with an individual-based model in which aggregates can grow, divide, joint and move randomly. Passing to infinity with the number of individuals, we obtain a model which describes the space-size dis- tribution of aggregates. The density distribution function satisfies a non-linear transport equation, which contains terms responsible for the growth of phytoplankton aggregates, their fragmentation, coagulation, and diffusion.
Structure of the normal rat larynx

Recent studies have shown the rat larynx to be an important organ in the evaluation of irritancy of inhaled materials. Serial sections and scanning electron microscope observations have clarified its basic structure. In particular the cartilage pattern and the distribution of the epithelia lining the lumen have been determined. There are 2 specialised epithelia-stratified squamous (found in areas subject to wear) and ciliated pseudostratified columnar (which produces and transports mucus). Always intervening between these is an unspecialised epithelium, the non-ciliated columnar. The marked variation in type of epithelium over a short distance within the larynx emphasises the need to take sections in the same plane when comparing different specimens.
A delicate balance: role of MMP-9 in brain development and pathophysiology of neurodevelopmental disorders

The extracellular matrix (ECM) is a critical regulator of neural network development and plasticity. As neuronal circuits develop, the ECM stabilizes synaptic contacts, while its cleavage has both permissive and active roles in the regulation of plasticity. Matrix metalloproteinase 9 (MMP-9) is a member of a large family of zinc-dependent endopeptidases that can cleave ECM and several cell surface receptors allowing for synaptic and circuit level reorganization. It is becoming increasingly clear that the regulated activity of MMP-9 is critical for central nervous system (CNS) development. In particular, MMP-9 has a role in the development of sensory circuits during early postnatal periods, called ‘critical periods. ’ MMP-9 can regulate sensory-mediated, local circuit reorganization through its ability to control synaptogenesis, axonal pathfinding and myelination. Although activity-dependent activation of MMP-9 at specific synapses plays an important role in multiple plasticity mechanisms throughout the CNS, misregulated activation of the enzyme is implicated in a number of neurodegenerative disorders, including traumatic brain injury, multiple sclerosis, and Alzheimer’s disease. Growing evidence also suggests a role for MMP-9 in the pathophysiology of neurodevelopmental disorders including Fragile X Syndrome. This review outlines the various actions of MMP-9 during postnatal brain development, critical for future studies exploring novel therapeutic strategies for neurodevelopmental disorders.
Corporate fraud: an analysis of Malaysian securities commission enforcement releases

Economic crime (i.e. corporate fraud) has a significant impact on business. This study analyzes the fraud cases reported by the Malaysian Securities Commission. Frauds involving market manipulation and/or illegal share trading are the most common types of fraud reported over the 6 years analyzed. The highest number of frauds reported involved investment and fund holding companies. Alarmingly the results indicate quite a high number of frauds cases are committed by management. The higher number of Chinese perpetrators may be due to fact that they are the dominant group in Malaysian business. The result also shows that more than half of companies involved with fraud are privately held companies in the investment/fund/finance sector. The results of this study highlight general characteristic of perpetrators (person and company) that commit fraud which could help the regulators in their monitoring and enforcement activities. To investors, this would help in analyzing their business investment or portfolio risk. Keywords—Corporate fraud, economic crime, fraud characteristic, perpetrators
Prediction of the bulking phenomenon in wastewater treatment plants

The control and prediction of wastewater treatment plants poses an important goal: to avoid breaking the environmental balance by always keeping the system in stable operating conditions. It is known that qu litative information — coming from microscopic examinations and subjective remarks — has a deep influence on the activated sludge process. In particular, on the total amount of effluent suspended solids, one of the measures of overall plant performance. The search for an input–output model of this variable and the prediction of sudden increases (bulkingepisodes) is thus a central concern to ensure the fulfillment of current discharge limitations. Unfortunately, the strong interrelation between variables, their heterogeneity and the very high amount of missing information makes the use of traditional techniques difficult, or even impossible. Through the combined use of several methods — rough set theory and artificial neural networks, mainly — reasonable prediction models are found, which also serve to show the different importance of variables and provide insight into the process dynamics. q 2000 Elsevier Science Ltd. All rights reserved.
Incisional Hernia in Women: Predisposing Factors and Management Where Mesh is not Readily Available

Background/Aim: Incisional hernia is still relatively common in our practice. The aim of the study was to identify risk factors associated with incisional hernia in our region. The setting is the Obafemi Awolowo University Teaching Hospitals Complex, Ile-Ife, Nigeria during a period when prosthetic mesh was not readily available. Patients and Methods: All the women who presented with incisional hernia between 1996 and 2005 were prospectively studied using a standard form to obtain information on pre-hernia (index) operations and possible predisposing factors. They all had open surgical repair and were followed up for 18-60 months. Results: Forty-four women were treated during study period. The index surgeries leading to the hernias were emergency caesarian section 26/44 (59.1%), emergency exploratory laparotomy 6/44 (13.6%), and elective surgeries 12/44 (27.3%). Major associated risk factors were the use of wrong suture materials for fascia repair, midline incisions, wound sepsis, and overweight. Conclusion: For elective surgeries, reduction of weight should be encouraged when appropriate, and transverse incisions are preferred. Absorbable sutures, especially chromic catgut, should be avoided in fascia closure. Antibiotics should be used for complicated obstetric cases.
IXPs: Mapped?

Internet exchange points (IXPs) are an important ingredient of the Internet AS-level ecosystem—a logical fabric of the Internet made up of about 30,000 ASes and their mutual business relationships whose primary purpose is to control and manage the ﬂow of traﬃc. Despite the IXPs’ critical role in this fabric, little is known about them in terms of their peering matrices (i.e., who peers with whom at which IXP) and corresponding traﬃc matrices (i.e., how much traf-ﬁc do the diﬀerent ASes that peer at an IXP exchange with one another). In this paper, we report on an Internet-wide traceroute study that was speciﬁcally designed to shed light on the unknown IXP-speciﬁc peering matrices and involves targeted traceroutes from publicly available and geographically dispersed vantage points. Based on our method, we were able to discover and validate the existence of about 44K IXP-speciﬁc peering links—nearly 18K more links than were previously known. In the process, we also classiﬁed all known IXPs depending on the type of information required to detect them. Moreover, in view of the currently used inferred AS-level maps of the Internet that are known to miss a signiﬁcant portion of the actual AS relationships of the peer-to-peer type, our study provides a new method for augmenting these maps with IXP-related peering links in a systematic and informed manner.
Analyzing the influential people in Sina Weibo dataset

With the increasingly rapid growth of micro-blogging services, influence analysis is becoming a very important topic in this area. Sina Weibo, one of the largest mirco-blogging services in China, has provided a new operation comment-only, which allows users to give feedback on a post without forwarding. However, most of existing works focus on Twitter, which fail to consider this new operation. In paper, we propose a new influence measurement method called WeiboRank on Sina Weibo which applies comment-only operation to help researchers to find ignored influential users who have big influential in comment dimension. Furthermore we analyze why a particular user is influential based on tracing the source of influence to find out which aspects contribute to influence. Our experiments based on a subset of a whole Sina Weibo datatset, which includes three-month records of 22,514,394 users. We conduct extensive experiments and results show that we can accurately find the most influential individuals among entire social networks, while the running time of the algorithm increases linearly with any increase in data size, which is suitable for large scale networks.
Coadministration of Lopinavir/Ritonavir and Phenytoin Results in Two-Way Drug Interaction Through Cytochrome P-450 Induction

Summary:Lopinavir/ritonavir (LPV/RTV) is a CYP3A4 inhibitor and substrate; it also may induce cytochrome P-450 (CYP) isozymes. Phenytoin (PHT) is a CYP3A4 inducer and CYP2C9/CYP2C19 substrate. This study quantified the pharmacokinetic (PK) drug interaction between LPV/RTV and PHT. Open-label, randomized, multiple-dose, PK study in healthy volunteers. Subjects in arm A (n = 12) received LPV/RTV 400/100 mg twice daily (BID) (days 1–10), followed by LPV/RTV 400/100 mg BID + PHT 300 mg once daily (QD) (days 11–22). Arm B (n = 12) received PHT 300 mg QD (days 1–11), followed by PHT 300 mg QD + LPV/RTV 400/100 mg BID (days 12–23). Plasma samples were collected on day 11 and day 22; PK parameters were compared by geometric mean ratio (GMR, day 22:day 11). P values <0.05 were considered significant. Following PHT addition, LPV area under the concentration-time curve (AUC0-12h) decreased from 70.9 ± 37.0 to 49.6 ± 25.1 μg·h/mL (GMR 0.67, P = 0.011) and C0h decreased from 6.0 ± 3.2 to 3.6 ± 2.3 μg/mL (GMR 0.54, P = 0.001). Following LPV/RTV addition, PHT AUC0-24h decreased from 191.0 ± 89.2 to 147.8 ± 104.5 μg·h/mL (GMR 0.69, P = 0.009) and C0h decreased from 7.0 ± 4.0 to 5.3 ± 4.1 μg/mL (GMR 0.66, P = 0.033). Concomitant LPV/RTV and PHT use results in a 2-way drug interaction. Phenytoin appears to increase LPV clearance via CYP3A4 induction, which is not offset by the presence of low-dose RTV. LPV/RTV may increase PHT clearance via CYP2C9 induction. Management should be individualized to each patient; dosage or medication adjustments may be necessary.
Carcass Characteristics and Qualitative Meat Traits of the Padovana Breed of Chicken

The aim of this study was to describe meat quality and carcass characteristics of the Padovana breed of chicken. The Padovana chicken is a historical fancy breed found in the Veneto region of Italy and produces meat that is typical to some local markets. The experiment reported here involved 60 chickens reared in an organic production system where housing was an indoor pen with access to a grass paddock. Experimental chicks were randomly selected from May 17 and 24, 2001 hatches and slaughtered at 150 and 180 days of age, respectively. Meat from 30 chickens (16 males and 14 females) from each slaughter age was stored for subsequent analysis of breast and thigh meat quality. Males were consistently heavier then females for live; without blood and feathers; eviscerated with head; neck, and legs; carcass; breast; and right thigh weight. There were no differences between males and females for chemical composition of the breast except for percentages of dry matter and ash (female > male). Generally, overall weights were greater at 180 then 150 days of age, whereas there was no difference between ages for breast chemical composition except for % protein (180 > 150). The breast and thigh had a low value of brightness and a distinctive blue meat color. The fatty acid profile of the breast consisted of a high percentage of polyunsaturated fatty acids. There were no differences between sexes for fatty acids, except for C16:0, C18:3w3 (female > male) and C18:1w7t, C20:4w6 (male > female).