Miracle-dz/UniFAR-FTUs huggingface dataset:
Multisite Comparison of Anti-Human Immunodeficiency Virus Microbicide Activity in Explant Assays Using a Novel Endpoint Analysis

ABSTRACT Microbicide candidates with promising in vitro activity are often advanced for evaluations using human primary tissue explants relevant to the in vivo mucosal transmission of human immunodeficiency virus type 1 (HIV-1), such as tonsil, cervical, or rectal tissue. To compare virus growth or the anti-HIV-1 efficacies of candidate microbicides in tissue explants, a novel soft-endpoint method was evaluated to provide a single, objective measurement of virus growth. The applicability of the soft endpoint is shown across several different ex vivo tissue types, with the method performed in different laboratories, and for a candidate microbicide (PRO 2000). The soft-endpoint method was compared to several other endpoint methods, including (i) the growth of virus on specific days after infection, (ii) the area under the virus growth curve, and (iii) the slope of the virus growth curve. Virus growth at the assay soft endpoint was compared between laboratories, methods, and experimental conditions, using nonparametric statistical analyses. Intra-assay variability determinations using the coefficient of variation demonstrated higher variability for virus growth in rectal explants. Significant virus inhibition by PRO 2000 and significant differences in the growth of certain primary HIV-1 isolates were observed by the majority of laboratories. These studies indicate that different laboratories can provide consistent measurements of anti-HIV-1 microbicide efficacy when (i) the soft endpoint or another standardized endpoint is used, (ii) drugs and/or virus reagents are centrally sourced, and (iii) the same explant tissue type and method are used. Application of the soft-endpoint method reduces the inherent variability in comparisons of preclinical assays used for microbicide development.
Integrating Conventional and Participatory Breeding Approaches in Assessment of Common Bean Varieties for Farmer Preffered Traits

It is estimated that over 75% of rural households in Tanzania depend on common bean (Phaseolus vulgaris L.) for daily subsistence. Recently, farmers have been increasingly looking for improved bean varieties which meet specific market demands characterized with yellow seed colour, early maturing and/or adapted to local agro-ecologies. Study focused on assessing the performance of bean varieties for agronomic traits through variety and environmental interactions by identifying high yielding, ealy maturing and market demand seed classes among the tested materials. For testing adaptability and stability, experiments were conducted in low to high altitudes for two consecutive years using randomized complete block design (RCBD) with three replicates. Eight common bean varieties KG98, Navy line 1, KATB9, SABRYT, KATB1, Lyamungu 85, JESCA and Calima Uyole were used. Absolute, matrix and pairwise ranking were used integratively for farmers’ and researcher’s assessment and selection. Participatory variety selection approach gave farmers an opportunity to assess and select varieties from a range of near finished materials in the breeding process. As part of the Farmers’ participatory variety selection process, seventeen participants as among the consumers 46% being women were selected to participate in a focused group discussion. Results revealed that, days to flowering, days to maturity and yield across the tested environments showed significant differences (p ≤ 0.05) as well as yield and diseases interactions for genotype, environment and season. Field data and farmers’ assessment data showed two varieties of KATB1 (yellow round) and KATB9 (red round) for better performance (high yield) and grain preference respectively. It showed that, early maturing; seed type and marketability varieties are highly demanded by bean farmers in Tanzania.
The complexity of homomorphism and constraint satisfaction problems seen from the other side

We give a complexity theoretic classification of homomorphism problems for graphs and, more generally, relational structures obtained by restricting the left hand side structure in a homomorphism. For every class C of structures, let HOM(C, /spl I.bar/) be the problem of deciding whether a given structure A /spl isin/ C has a homomorphism to a given (arbitrary) structure B. We prove that, under some complexity theoretic assumption from parameterized complexity theory, HOM(C, /spl I.bar/) is in polynomial time if, and only if, the cores of all structures in C have bounded tree-width (as long as the structures in C only contain relations of bounded arity). Due to a well known correspondence between homomorphism problems and constraint satisfaction problems, our classification carries over to the latter.
A standardized approach for the assessment of the lower uterine segment at first trimester by transvaginal ultrasound: a flash study

Abstract Objectives: To evaluate the reproducibility of a standardized approach to lower uterine segment (LUS) imaging by transvaginal ultrasound at 11–14 weeks. Methods: This was a “flash” study lasting for 1 month. Obstetrician-sonographers performing more than 50 first trimester ultrasounds per year participated. All consecutive women attending for their 11–14 weeks scan were included. A standardized, transvaginal approach to the imaging of LUS was defined. The sonographers recorded one or two images of the LUS. The quality of the images was assessed by sonographers and reviewed by an independent fetal medicine specialist using the same scoring system. Inter and intra-reviewer variability was assessed. Results: Seventy-one sonographers and 851 pregnant women participated. The mean (±SD) and medium (IQR) scores attributed by sonographer versus reviewer were 5.01 (±0.92) and 5 [4–6] versus 4.68 (±1.14) and 5 [4–5.24], p = 0.08. The mean [95% CI] difference of −0.33 [−2.6;2] was recorded. There was good, moderate and poor agreement in 74.4%, 16.7% and 8.9% cases, respectively. Variability in inter-reviewer and intra-reviewer was low with the mean [95% CI] difference of −0.1 [−1.6;1.4] and −0.1 [−1.4;1.2] respectively. Conclusions: A standardized approach to LUS imaging at 11–14 weeks is feasible and highly reproducible in a large population.
Toll-Like Receptor 3 is Associated With the Risk of HCV Infection and HBV-Related Diseases

AbstractThere are inconsistent data on the association of risk of hepatitis virus infection and hepatitis virus-related diseases with the toll-like receptor 3 (TLR3) gene.Several common polymorphism sites were targeted to assess the risk of HBV infection, HCV infection, and HBV-related diseases.Meta-analysis combining data for 3547 cases and 2797 controls from 8 studies was performed in this study. Pooled ORs were calculated to measure the risk of hepatitis virus infection and hepatitis virus-related diseases. Fixed-effects pooled ORs were calculated using the Mantel-Haenszel method.The TLR3 gene was associated with a significantly increased risk of HBV-related diseases among 1355 patients and 1130 controls ([pooled OR, [95%CI]: 1.30, [1.15–1.48] for dominant; 1.77, [1.35–2.31] for recessive; 1.28 [1.16–1.41] for allele frequency). Subgroup analyses by a polymorphism site indicated an increased risk of HCV infection in relation to the TT/CT genotypes of rs3775291 (1.50 [1.11–2.01]), and a decreased risk ascribed to the T allele (0.20 [0.16–0.25]). We also noted an association between rs3775291 and significantly increased risk of HBV-related diseases (2.23 [1.55–3.21]). No significant inter-study heterogeneity or publication bias was detected in the analyses.These data suggest a likely effect on the risk to infect HCV and develop HBV-related diseases for the TLR3 gene. Large-scale studies with racially diverse populations are required to validate these findings.
Place-and-route impact on the security of DPL designs in FPGAs

Straightforward implementations of cryptographic algorithms are known to be vulnerable to attacks aimed not at the mathematical structure of the cipher but rather at the weak points of the electronic devices which implement it. These attacks, known as side-channel attacks, have proved to be very powerful in retrieving secret keys from any kind of unprotected electronic device. Amongst the various protection strategies, side-channel hiding is very popular and well studied. The principle of information hiding is to make any leak constant, thus uncorrelated to the device internal secrets. The so-called ldquodual-rail with precharge logicrdquo (DPL) style is indicated to achieve that goal. For DPL protection to be effective, it further requires a carefully balanced layout so as to obtain equal propagation delays and power consumption on both rails. In this article, we study to which extent the differential place-and-route constraints must be strict in FPGA technology. We describe placement techniques suitable for Xilinx and Altera FPGAs, and quantify the gain of balance they confer. On the one hand, we observed that Xilinx fitting tool achieves naturally good balancing results. On the other hand, the symmetry can be greatly improved with Altera devices, using a manual placement, leading to unprecedented dual netlists balancing.
Modulation of the Arrestin-Clathrin Interaction in Cells

We recently demonstrated that nonvisual arrestins interact via a C-terminal binding domain with clathrin and function as adaptor proteins to promote β2-adrenergic receptor (β2AR) internalization. Here, we investigated the potential utility of a mini-gene expressing the clathrin-binding domain of β-arrestin (β-arrestin (319–418)) to function as a dominant-negative with respect to β2AR internalization and compared its properties with those of β-arrestin and β-arrestin-V53D, a previously reported dominant-negative mutant.In vitro studies demonstrated that β-arrestin-V53D bound better to clathrin than β-arrestin but was significantly impaired in its interaction with phosphorylated G protein-coupled receptors. In contrast, whereas β-arrestin (319–418) also bound well to clathrin it completely lacked receptor binding activity. When coexpressed with the β2AR in HEK293 cells, β-arrestin (319–418) effectively inhibited agonist-promoted receptor internalization, whereas β-arrestin-V53D was only modestly effective. However, both constructs significantly inhibited the stimulation of β2AR internalization by β-arrestin in COS-1 cells. Interestingly, immunofluorescence microscopy analysis reveals that both β-arrestin (319–418) and β-arrestin-V53D are constitutively localized in clathrin-coated pits in COS-1 cells. These results indicate the potential usefulness of β-arrestin (319–418) to effectively block arrestin-clathrin interaction in cells and suggest that this construct may prove useful in further defining the mechanisms involved in G protein-coupled receptor trafficking.
Prediction of functional regulatory SNPs in monogenic and complex disease

Next‐generation sequencing (NGS) technologies are yielding ever higher volumes of human genome sequence data. Given this large amount of data, it has become both a possibility and a priority to determine how disease‐causing single nucleotide polymorphisms (SNPs) detected within gene regulatory regions (rSNPs) exert their effects on gene expression. Recently, several studies have explored whether disease‐causing polymorphisms have attributes that can distinguish them from those that are neutral, attaining moderate success at discriminating between functional and putatively neutral regulatory SNPs. Here, we have extended this work by assessing the utility of both SNP‐based features (those associated only with the polymorphism site and the surrounding DNA) and gene‐based features (those derived from the associated gene in whose regulatory region the SNP lies) in the identification of functional regulatory polymorphisms involved in either monogenic or complex disease. Gene‐based features were found to be capable of both augmenting and enhancing the utility of SNP‐based features in the prediction of known regulatory mutations. Adopting this approach, we achieved an AUC of 0.903 for predicting regulatory SNPs. Finally, our tool predicted 225 new regulatory SNPs with a high degree of confidence, with 105 of the 225 falling into linkage disequilibrium blocks of reported disease‐associated genome‐wide association studies SNPs. Hum Mutat 32:1183–1190, 2011. ©2011 Wiley‐Liss, Inc.
Disturbances of menstruation in hypothyroidism

Most thyroid textbooks describe hypo‐thyroidism resulting in changes in the length of the menstrual cycle and in the amount of bleeding. Our experience at a busy thyroid clinic had given a picture which differs from that presented in the literature. The aim of this study was to determine the frequency and type of menstrual irregularities in premenopausal hypothyroid patients.
Efficacy and Complication Rates of Full‐Thickness Skin Graft Repair of Lower Extremity Wounds After Mohs Micrographic Surgery

Background Repair of below‐the‐knee lower extremity defects after Mohs micrographic surgery (MMS) that are not amenable to primary closure can be challenging given the high propensity for complications. No criterion standard exists for management of these wounds, but secondary‐intention healing, partial‐ and full‐thickness skin grafts (FTSGs), and various flaps are possible options to manage these wounds. Few data exist on the efficacy of FTSG repairs for lower extremity wounds. Objectives Assess the efficacy and complications rates of FTSG repairs for lower extremity wounds after MMS. Methods This was a retrospective review of 80 FTSG repairs performed after MMS. Data were derived from 45 cases at Beth Israel Deaconess Medical Center and 35 cases at University of California, San Diego (UCSD) Medical Center. Results Seventy‐two of 80 cases (90%) had full graft survival, six (7.5%) had partial failure, and two (2.5%) had complete failure. In the cases where grafts had failed, wounds healed by secondary intention without further complications. Other complications included infections in nine (11%) cases and hematoma formation in two (2.5%). Conclusion FTSG is a consistent and safe reconstructive option for the management of lower extremity wounds after MMS.
In Vivo Measurement of Indole-3-acetic Acid Decarboxylation in Aging Coleus Petiole Sections.

The concentration of indoleacetic acid (IAA) in plant tissues is regulated, in part, by its rate of decarboxylation. However, the commonly used in vitro assays for IAA oxidase may not accurately reflect total in vivo decarboxylation rates. A method for measuring in vivo decarboxylation was utilized in which (14)CO(2) is collected following uptake of [1-(14)C]IAA by excised tissue sections. After a 30-minute equilibration period, the evolution of (14)CO(2) was found to follow an approximately linear course with respect to both time and tissue weight.Decarboxylation rates were measured by this method in petiole sections of the Princeton clone of Coleus blumei Benth. Both the (14)CO(2) evolved per milligram tissue and the percent of [1-(14)C]IAA uptake decarboxylated were highest in sections from the youngest petioles tested, and declined in the older tissue. Thin layer chromatography of acetonitrile extracts from the [1-(14)C]IAA-treated petioles showed a decreasing amount of free IAA and an increase at the retardation factor of indoleacetylaspartate in the older sections. The decreased decarboxylation rates in the older petioles may be attributable to a generally lower metabolic rate and increased protection of the IAA by conjugation.
Step-Size Adaptation Based on Non-Local Use Selection Information

The performance of Evolution Strategies (ESs) depends on a suitable choice of internal strategy control parameters. Apart from a fixed setting, ESs facilitate an adjustment of such parameters within a self-adaptation process. For stepsize control in particular, various adaptation concepts were evolved early in the development of ESs. These algorithms mostly work very efficiently as long as the relative sensitivities of the parameters to be optimized are known. If this scaling is not known, the strategy has to adapt individual step-sizes for the parameters. In general, the number of necessary step-sizes (variances) equals the dimension of the problem. In this case, step-size adaptation proves to be difficult. The algorithm presented in this paper is a development based on the derandomized scheme of mutative step-size control. The new adaptation concept uses information accumulated from the preceding generations with an exponential fading of old information instead of using information from the current generation only. Compared to the conventional adaptation scheme, this enables a less locally determined step-size control and allows a much faster adaptation of individual step-sizes without increasing disturbing random effects and without additional evaluations of the fitness function. The adaptation of the general step-size can be improved as well.
Impact of Educational Sessions for Epileptic Children Mothers on Their knowledge, Adherence to Antiepileptic Drugs and Seizures Severity among their Children

Background: Epilepsy is a chronic medical condition, which requires long term management. Adherence to antiepileptic drugs (AEDs) is crucial for preventing the risk of recurrent seizures. Aim of this study is to examine the impact of educational Sessions on maternal knowledge, adherence to antiepileptic drugs and seizure severity among their epileptic children. Methods: A quasi experimental design (pre, post three month and follow up after six month) was conducted on 100 mothers with their epileptic children who willing to participate at inpatient unit and outpatient clinic of neurology department at Mansoura University Children's hospital. Three tools were used to collect the required data; structured interview questionnaire, medication adherence scale and seizure severity scale, then educational sessions was developed according to mothers needs. Results: More than half of the studied mothers (59%) have poor knowledge and only (3%) of them have good knowledge. As regard adherence to antiepileptic drugs about three quarters of mothers (73%) are nonadherent. Also seventy two (72%) of children has moderate severity of epilepsy, (15%) has sever level and only (13%) has mild level of epilepsy severity before intervention, but after three and six month of intervention57% &44% of mothers had good knowledge, the majority of them 95% & 98% respectively become adherent to drugs administration and the severity level of seizure among children were decreased. Also (91%) of mothers reported that forgetness is the major causes of nonadherence to antiepileptic drug administration. Conclusion: An improvement in mean score of mothers' knowledge, their adherence to antiepileptic drugs and seizure severity occurred among their children after three and six month of intervention than before. Recommendation: Educational efforts and reinforcement must be continuous to meet the needs of the mothers and their children during various stages of the disease.
Psychiatric Symptoms in Dermatology Patients

Summary The 30-item General Health Questionnaire (GHQ) (Goldberg, 1972) was administered to 196 consecutive new dermatology out-patients and 40 consecutive admissions to dermatology beds. Thirty per cent of the outpatients and 60 per cent of the in-patients obtained high scores, while half the high scorers in each group scored high on the Wakefield Self-Assessment Depression Scale (Snaith et al, 1971). These findings suggest that dermatology out-patients have a higher prevalence of psychiatric disorder than the general population, and dermatology in-patients a higher prevalence than general medical in-patients. High GHQ scores were associated with (a) diagnoses of acne, eczema, psoriasis or alopecia; with (b) extensive lesions on exposed parts of the body; and with (c) the use of high potency topical steroid. We indicate other areas that might be profitably explored in a full-scale study.
Excess Baggage for Birds: Inappropriate Placement of Tags on Gannets Changes Flight Patterns

Devices attached to flying birds can hugely enhance our understanding of their behavioural ecology for periods when they cannot be observed directly. For this, scientists routinely attach units to either birds' backs or their tails. However, inappropriate payload distribution is critical in aircraft and, since birds and planes are subject to the same laws of physics during flight, we considered aircraft aerodynamic constraints to explain flight patterns displayed by northern gannets Sula bassana equipped with (small ca. 14 g) tail- and back-mounted accelerometers and (larger ca. 30 g) tail-mounted GPS units. Tail-mounted GPS-fitted birds showed significantly higher cumulative numbers of flap-glide cycles and a higher pitch angle of the tail than accelerometer-equipped birds, indicating problems with balancing inappropriately placed weights with knock-on consequences relating to energy expenditure. These problems can be addressed by carefully choosing where to place tags on birds according to the mass of the tags and the lifestyle of the subject species.
Contour Smoothing Algorithm Based on Bezier Curves and Application

In the process of plotting contours by rectangular grids, many polylines appeared in the contour map. To improve it, this paper uses cubic Bezier curves to fit contours. First, scan all the known points and divide them into groups of 4. Then, draw cubic Bezier curves in groups. But cuspidal points turn up. And to avoid cuspidal points, de Casteljau Algorithm has been used. Add a new point at the middle position of the third and the fourth point in the previous group. Add another point at the middle position of the first and the second point in the next group. So there are three points between adjacent cubic Bezier curves. Plot another curve following the idea of de Casteljau Algorithm during these three points. Experiments show a combination of these two methods brings pretty good result.
A Decision-Making Framework and Simulator for Sustainable Electric Energy Systems

In this paper, we propose a new framework for the organization of the electric power industry, based on extensive use of information technology (IT) and on interactive decision making, where consumers and distributed producers join the traditional actors, utilities in particular, in making decisions. While many ideas considered in this paper have been put forward in recent years, such as the need to manage intermittency of renewable resources by means of proactive forecasting, and coordination with responsive demand and storage, we introduce a possible systematic IT-enabled mechanism necessary for the actual implementation of these technologies. We point out that in order to achieve a long-term sustainable energy utilization, it is essential to provide on-line information to internalize the value of just-in-time, just-in-place, and just-in-context distributed adaptation across the entire supply chain, ranging from the smallest consumers and energy providers, through their aggregators and system coordinators. We illustrate using our model-based novel simulator, how a carefully designed multidirectional and multitemporal information exchange could enable sustainable decision making while accounting for unique needs and capabilities of various resources and users. At the same time, information incentivizes the resources and users to contribute to system-wide sustainability objectives at value. We illustrate the dependence of such decisions-driven industry evolution on the industry rules (choice of performance objectives), as well as on the operating and planning practices for implementing the industry rules (temporal and spatial factors). Our model-based simulator could be used as a means of designing novel regulation defining rules, rights, and responsibilities regarding the type and rate of information to be exchanged in support of sustainable industry evolution.