Miracle-dz/UniFAR-FTUs huggingface dataset:
Effect of Coinfection With STDs and of STD Treatment on HIV Shedding in Genital‐Tract Secretions: Systematic Review and Data Synthesis

Objective: To determine whether coinfection with sexually transmitted diseases (STD) increases HIV shedding in genital‐tract secretions, and whether STD treatment reduces this shedding. Design: Systematic review and data synthesis of cross‐sectional and cohort studies meeting predefined quality criteria. Main Outcome Measures: Proportion of patients with and without a STD who had detectable HIV in genital secretions, HIV load in genital secretions, or change following STD treatment. Results: Of 48 identified studies, three cross‐sectional and three cohort studies were included. HIV was detected significantly more frequently in participants infected with Neisseria gonorrhoeae (125 of 309 participants, 41%) than in those without N gonorrhoeae infection (311 of 988 participants, 32%; P = 0.004). HIV was not significantly more frequently detected in persons infected with Chlamydia trachomatis (28 of 67 participants, 42%) than in those without C trachomatis infection (375 of 1149 participants, 33%; P = 0.13). Median HIV load reported in only one study was greater in men with urethritis (12.4 × 104 versus 1.51 × 104 copies/ml; P = 0.04). In the only cohort study in which this could be fully assessed, treatment of women with any STD reduced the proportion of those with detectable HIV from 39% to 29% (P = 0.05), whereas this proportion remained stable among controls (15‐17%). A second cohort study reported fully on HIV load; among men with urethritis, viral load fell from 12.4 to 4.12 × 104 copies/ml 2 weeks posttreatment, whereas viral load remained stable in those without urethritis. Conclusion: Few high‐quality studies were found. HIV is detected moderately more frequently in genital secretions of men and women with a STD, and HIV load is substantially increased among men with urethritis. Successful STD treatment reduces both of these parameters, but not to control levels. More high‐quality studies are needed to explore this important relationship further.
Emotional Sequelae of Abortion: Implications for Clinical Practice

The literature is summarized on normative reactions to abortion and factors that increase risk of negative emotional sequelae. Four areas of inquiry for identifying psychotherapeutic issues in regard to abortion are elaborated, including: (a) characteristics of the woman prior to and at the time of the abortion, (b) the nature of social support and the cultural milieu around the abortion, (c) characteristics of the medical environment and abortion procedure, and (d) events subsequent to the abortion which may have aroused post-decisional conflict. The implications of the research literature for psychotherapeutic treatment of women who have had abortions are discussed.
Estimating landmark locations from geo-referenced photographs

The problem of estimating the positions of landmarks using a mobile robot equipped with a camera has intensively been studied in the past. In this paper, we consider a variant of this problem in which the robot should estimate the locations of observed landmarks based on a sparse set of geo-referenced images for which no heading information is available. Sources for such kind of data are image portals such as Flickr or Google Image Search. We formulate the problem of estimating the landmark locations as an optimization problem and show that it is possible to accurately localize the landmarks in real world settings.
De novo synthesis of estrogen in pregnant uterus is critical for stromal decidualization and angiogenesis

Implantation is initiated when the embryo attaches to the uterine luminal epithelium during early pregnancy. Following this event, uterine stromal cells undergo steroid hormone-dependent transformation into morphologically and functionally distinct decidual cells in a unique process known as decidualization. An angiogenic network is also formed in the uterine stromal bed, critically supporting the early development of the embryo. The steroid-induced mechanisms that promote stromal differentiation and endothelial proliferation during decidualization are not fully understood. Although the role of ovarian progesterone as a key regulator of decidualization is well established, the requirement of ovarian estrogen (E) during this process remains unresolved. Here we show that the expression of P450 aromatase, a key enzyme that converts androgens to E, is markedly induced in mouse uterine stromal cells undergoing decidualization. The aromatase then acts in conjunction with other steroid biosynthetic enzymes present in the decidual tissue to support de novo synthesis of E. This locally produced E is able to support the advancement of the stromal differentiation program even in the absence ovarian E in an ovariectomized, progesterone-supplemented pregnant mouse model. Administration of letrozole, a specific aromatase inhibitor, to these mice blocked the stromal differentiation process. Gene expression profiling further revealed that the intrauterine E induces the expression of several stromal factors that promote neovascularization in the decidual tissue. Collectively, these studies identified the decidual uterus as a novel site of E biosynthesis and uncovered E-regulated maternal signaling pathways that critically control uterine differentiation and angiogenesis during early pregnancy.
The Recent Advance of Molecularly Imprinted on-Line Solid Phase Extraction and its Application in Sample Pretreatment - A Mini Review

Solid phase extraction (SPE) is a sample pretreatment technique which is increasingly popular and widely used. However, most of the traditional SPE material has poor selectivity. Molecular imprinting is an emerging technology for the preparation of functionalized materials with molecular recognition ability. Using the imprinted polymers as new sorbent, a molecularly imprinted on-line solid phase extraction coupled with chromatography or other techniques has become one of the most interesting applications of MIP, which has not only the extraction efficiency of SPE but also the high selectivity of imprinted polymers. This paper focuses on the recent states, advantages and outlooks of molecularly imprinted on-line solid phase extraction in sample pretreatment. This mini review may promote the extensive application of MIP in food safety.
The effect of the mixing routes of biodegradable polylactic acid and polyhydroxybutyrate nanocomposites and compatibilised nanocomposites

Biodegradable nanocomposites comprising of organically modified montmorillonite-reinforced polylactic acid (PLA) and polyhydroxybutyrate (PHB) were assessed. This study investigates different nanocomposites mixing techniques as methods of achieving exfoliation. The incorporation of reverse flow mixing sections resulted in an increase in exfoliation of nanoclay platelets in PLA nanocomposites. PHB nanocomposites were shown to be more sensitive to thermal degradation and therefore benefited from a reduction in the number of processing steps utilised. Further development of the process was observed with the incorporation of compatibilisers for both polymers which led to considerable improvements in terms of mechanical properties exhibiting superior flexural properties. It was shown using x-ray diffraction that improvements in intercalation was observed which affected the compostability of both composites. Composites with increased interlayer spacing degraded faster and the nanocomposites in general degraded at a faster rate than the virgin polymers.
Should I Stay or Should I Go? Improving Event Recommendation in the Social Web

This paper focuses on the recommendation of events in the Social Web, and addresses the problem of finding if, and to which extent, certain features, which are peculiar to events, are relevant in predicting the users' interests and should thereby be taken into account in recommendation. We consider in particular three "additional" features that are usually shown to users within social networking environments: reachability from the user location, the reputation of the event in the community, and the participation of the user's friends. Our study is aimed at evaluating whether adding this information to the description of the event type and topic, and including in the user profile the information on the relevance of these factors, can improve our capability to predict the user's interest. We approached the problem by carrying out two surveys with users, who were asked to express %with a score their interest in a number of events. We then trained, by means of linear regression, a scoring function defined as a linear combination of the different factors, whose goal was to predict the user scores. We repeated this experiment under different hypotheses on the additional factors, in order to assess their relevance by comparing the predictive capabilities of the resulting functions. The compared results of our experiments show that additional factors, if properly weighted, can improve the prediction accuracy with an error reduction of 4.1%. The best results were obtained by combining content-based factors and additional factors in a proportion of approximately 10:4.
Efficient Infectious Cell Culture Systems of the Hepatitis C Virus (HCV) Prototype Strains HCV-1 and H77

ABSTRACT The first discovered and sequenced hepatitis C virus (HCV) genome and the first in vivo infectious HCV clones originated from the HCV prototype strains HCV-1 and H77, respectively, both widely used in research of this important human pathogen. In the present study, we developed efficient infectious cell culture systems for these genotype 1a strains by using the HCV-1/SF9_A and H77C in vivo infectious clones. We initially adapted a genome with the HCV-1 5′UTR-NS5A (where UTR stands for untranslated region) and the JFH1 NS5B-3′UTR (5-5A recombinant), including the genotype 2a-derived mutations F1464L/A1672S/D2979G (LSG), to grow efficiently in Huh7.5 cells, thus identifying the E2 mutation S399F. The combination of LSG/S399F and reported TNcc(1a)-adaptive mutations A1226G/Q1773H/N1927T/Y2981F/F2994S promoted adaptation of the full-length HCV-1 clone. An HCV-1 recombinant with 17 mutations (HCV1cc) replicated efficiently in Huh7.5 cells and produced supernatant infectivity titers of 104.0 focus-forming units (FFU)/ml. Eight of these mutations were identified from passaged HCV-1 viruses, and the A970T/I1312V/C2419R/A2919T mutations were essential for infectious particle production. Using CD81-deficient Huh7 cells, we further demonstrated the importance of A970T/I1312V/A2919T or A970T/C2419R/A2919T for virus assembly and that the I1312V/C2419R combination played a major role in virus release. Using a similar approach, we found that NS5B mutation F2994R, identified here from culture-adapted full-length TN viruses and a common NS3 helicase mutation (S1368P) derived from viable H77C and HCV-1 5-5A recombinants, initiated replication and culture adaptation of H77C containing LSG and TNcc(1a)-adaptive mutations. An H77C recombinant harboring 19 mutations (H77Ccc) replicated and spread efficiently after transfection and subsequent infection of naive Huh7.5 cells, reaching titers of 103.5 and 104.4 FFU/ml, respectively. IMPORTANCE Hepatitis C virus (HCV) was discovered in 1989 with the cloning of the prototype strain HCV-1 genome. In 1997, two molecular clones of H77, the other HCV prototype strain, were shown to be infectious in chimpanzees, but not in vitro. HCV research was hampered by a lack of infectious cell culture systems, which became available only in 2005 with the discovery of JFH1 (genotype 2a), a genome that could establish infection in Huh7.5 cells. Recently, we developed in vitro infectious clones for genotype 1a (TN), 2a (J6), and 2b (J8, DH8, and DH10) strains by identifying key adaptive mutations. Globally, genotype 1 is the most prevalent. Studies using HCV-1 and H77 prototype sequences have generated important knowledge on HCV. Thus, the in vitro infectious clones developed here for these 1a strains will be of particular value in advancing HCV research. Moreover, our findings open new avenues for the culture adaptation of HCV isolates of different genotypes.
Understanding the impact of pre-analytic variation in haematological and clinical chemistry analytes on the power of association studies

Background: Errors, introduced through poor assessment of physical measurement or because of inconsistent or inappropriate standard operating procedures for collecting, processing, storing or analysing haematological and biochemistry analytes, have a negative impact on the power of association studies using the collected data. A dataset from UK Biobank was used to evaluate the impact of pre-analytical variability on the power of association studies. Methods: First, we estimated the proportion of the variance in analyte concentration that may be attributed to delay in processing using variance component analysis. Then, we captured the proportion of heterogeneity between subjects that is due to variability in the rate of degradation of analytes, by fitting a mixed model. Finally, we evaluated the impact of delay in processing on the power of a nested case-control study using a power calculator that we developed and which takes into account uncertainty in outcome and explanatory variables measurements. Results: The results showed that (i) the majority of the analytes investigated in our analysis, were stable over a period of 36 h and (ii) some analytes were unstable and the resulting pre-analytical variation substantially decreased the power of the study, under the settings we investigated. Conclusions: It is important to specify a limited delay in processing for analytes that are very sensitive to delayed assay. If the rate of degradation of an analyte varies between individuals, any delay introduces a bias which increases with increasing delay. If pre-analytical variation occurring due to delays in sample processing is ignored, it affects adversely the power of the studies that use the data.
Integrating Meteorology into Research on Migration

Atmospheric dynamics strongly influence the migration of flying organisms. They affect, among others, the onset, duration and cost of migration, migratory routes, stop-over decisions, and flight speeds en-route. Animals move through a heterogeneous environment and have to react to atmospheric dynamics at different spatial and temporal scales. Integrating meteorology into research on migration is not only challenging but it is also important, especially when trying to understand the variability of the various aspects of migratory behavior observed in nature. In this article, we give an overview of some different modeling approaches and we show how these have been incorporated into migration research. We provide a more detailed description of the development and application of two dynamic, individual-based models, one for waders and one for soaring migrants, as examples of how and why to integrate meteorology into research on migration. We use these models to help understand underlying mechanisms of individual response to atmospheric conditions en-route and to explain emergent patterns. This type of models can be used to study the impact of variability in atmospheric dynamics on migration along a migratory trajectory, between seasons and between years. We conclude by providing some basic guidelines to help researchers towards finding the right modeling approach and the meteorological data needed to integrate meteorology into their own research.
Factor Structure of The Beck Depression Inventory in a University Sample

Factor analysis was performed on the Beck Depression Inventory with a university sample to examine its potential multidimensionality. A principal components analysis with an oblimin and varimax rotation produced a two-factor solution. These factors were labeled Cognitive–Affective and Physiological and accounted for approximately 39% of the common variance. This finding is consistent with multidimensionality of the inventory and with a similar study of college students. The commonalities of the two studies suggest the reliability (internal consistency) of the Cognitive-Affective and Physiological constructs among “minimally” depressed university samples.
Manifestations of Heterogeneity in Hardware/Software Codesign

We identify three distinct types of hardware/software codesign: 1. Joint design of an instruction-set architecture and its program. 2. Synthesis of hardware and/or software from a common specification. These can be viewed as manifestations of heterogeneity in the design methodology. The first type concerns the joint synthesis of a data-path and its controller, two conceptually distinct parts of a processor [Pau93]. The heterogeneity in this approach is limited to distinguishing the datapath from its controller. In type 2, a unified representation of an application is mapped into some mixture of implementation technologies. For example, a dataflow graph could be partitioned, and the separate partitions could be fed to hardware and software synthesis tools [Kal93]. The software components execute on commodity processors , or possibly on processors synthesized as in type 1. A hierarchical finite state machine could also be converted to hardware or software implementations [Har90]. If concurrent FSMs are used, then a mixture of hardware implementations might be attractive. In type 2, the heterogeneity is limited to distinguishing implementation technologies; the model of computation is unified. In type 3, the design representation need not be unified. Distinct models of computation can be used for different parts of the design. The model of computation for each component would be chosen on the basis of the properties of that component. For instance, dataflow would be used for signal processing, and hierarchical FSMs for control. A typical application could combine both models of computation. Within each model of computation, types 1 or 2 might apply in synthesizing the implementations. Type 3 addresses a large cross section of system-level design problems. In the signal processing domain, for example, most applications combine some hard-real-time numerical processing of signals with much more dynamic control. In applications such as modems, wireless communication systems, video phones, voice mail systems, voice recognition systems, disk-drive controllers, and data compression, one or more signal processing kernels are invoked in response to outside stimuli. For example, a modem needs to negotiate a common transmission format with another modem when a connection is established, or when a wireless device moves from one service area to another. Type 1 is fundamentally still a chip-level design problem. It can be viewed as an approach to high-level synthesis. In this paper, we concentrate on system-level problems, and hence on types 2 and 3. In this context, four key problems emerge: • partitioning • synthesis • …
Modeling Antibiotic Tolerance in Biofilms by Accounting for Nutrient Limitation

ABSTRACT A mathematical model of biofilm dynamics was used to investigate the protection from antibiotic killing that can be afforded to microorganisms in biofilms based on a mechanism of localized nutrient limitation and slow growth. The model assumed that the rate of killing by the antibiotic was directly proportional to the local growth rate. Growth rates in the biofilm were calculated by using the local concentration of a single growth-limiting substrate with Monod kinetics. The concentration profile of this metabolic substrate was calculated by solving a reaction-diffusion problem. The model predicted the following features: stratified patterns of growth with zones of no growth in the biofilm interior, slow killing of biofilm microorganisms that was further retarded as the initial biofilm thickness increased, nonuniform spatial patterns of killing inside the biofilm, biofilm killing rates that decrease in a nonlinear way as the concentration of the growth-limiting substrate feeding the biofilm is decreased, and heightened tolerance when external mass transfer resistance is manifested. This modeling study also provides motivation for further investigation of a hypothetical cell state in which damaged cells score as nonviable but continue to consume substrate. The existence of such a cell state can further retard biofilm killing, according to the simulations. The results support the important contributions of nutrient limitation and slow growth to the antibiotic tolerance of microorganisms in biofilms.
Akt Kinase Activation Blocks Apoptosis in Intestinal Epithelial Cells by Inhibiting Caspase-3 after Polyamine Depletion*

Apoptosis plays a critical role in the maintenance of gut mucosal homeostasis and is regulated by numerous factors including polyamines. Although the exact roles of polyamines in apoptotic pathway are still unclear, inhibition of polyamine synthesis promotes the resistance of intestinal epithelial cells to apoptosis. Akt is a serine-threonine kinase that has been established as an important intracellular signaling in regulating cell survival. The current studies test the hypothesis that polyamines are involved in the control of Akt activity in normal intestinal epithelial cells (IEC-6 line) and that activated Akt mediates suppression of apoptosis following polyamine depletion. Depletion of cellular polyamines by α-difluoromethylornithine induced levels of phosphorylated Akt and increased Akt kinase activity, although it had no effect on expression of total Akt, pERK, p38, and Bcl-2 proteins. This activated Akt was associated with both decreased levels of active caspase-3 and increased resistance to tumor necrosis factor-α/cycloheximide-induced apoptosis. Inactivation of Akt by either treatment with LY294002 or ectopic expression of a dominant negative Akt mutant (DNMAkt) not only enhanced the caspase-3 activation in polyamine-deficient cells but also prevented the increased resistance to tumor necrosis factor-α/cycloheximide-induced apoptosis. Phosphorylation of glycogen synthase kinase-3, a downstream target of Akt, was also increased in α-difluoromethylornithine-treated cells, which was prevented by inactivation of Akt by LY294002 or DNMAkt overexpression. These results indicate that polyamine depletion induces the Akt activation mediating suppression of apoptosis via inhibition of caspase-3 in normal intestinal epithelial cells.
Effect of Catalytic Material in Environment Pollution Treatment

Some catalytic materials can be utilized in environment pollution treatment. The material of ceramisite can be used in dye wastewater treatment process with its good properties. When they were filled in the high voltage discharge reactor, the ceramsite pellets were polarized, and partial discharge could take place beside every pellet, which would promote methylene blue degeneration in the dye wastewater. And when the solution pH>ceramsite pHzpc, the ceramsite surface presented the electronegativity and the ceramsite could adsorb more methylene blue, and removal rate increased.