Miracle-dz/UniFAR-FTUs huggingface dataset:
Improved PCR sensitivity for direct genotyping of Chlamydia trachomatis serovars by using a nested PCR

Successful amplification of omp1 DNA by PCR is crucial in the genotyping of Chlamydia trachomatis when directly performed with clinical samples (J. Lan, J. M. M. Walboomers, R. Roosendaal, G. J. van Doornum, D. M. McLaren, C. J. L. M. Meijer, and A. J. C. van den Brule, J. Clin. Microbiol. 31:1060-1065, 1993). Several primers flanking the four variable domains of the omp1 gene were selected and tested for sensitivity in several nested PCRs with serial dilutions of serovar G. The optimal sensitivity obtained was 0.1 to 0.01 inclusion-forming units, similar to that obtained in the C. trachomatis plasmid PCR. With this approach, any C. trachomatis PCR-positive sample can be typed.
2,4-D (Ethyl ester) poisoning: experience at a tertiary care centre in Northern India

2,4-Dichlorphenoxyacetic acid (2,4-D) is a selective herbicide widely used to kill broad-leaved plants in wheat cultivation. Only a few cases of documented poisoning cases with this compound have been reported from India. Since the initial manifestations are not very different from anticholinesterase poisoning, the chances of misdiagnosis are high. Anticholinesterase compounds are the most commonly used insecticides and are implicated as the commonest cause of agrochemical poisoning in India. This report aims to make physicians aware that not all cases of agrochemical poisoning are caused by anticholinesterase insecticides. Efforts must be made to correctly identify the offending compound for appropriate management.
The dynamics of breaking progressive interfacial waves

Two- and three-dimensional numerical simulations are performed to study interfacial waves in a periodic domain by imposing a source term in the horizontal momentum equation. Removing the source term before breaking generates a stable interfacial wave. Continued forcing results in a two-dimensional shear instability for waves with thinner interfaces, and a convective instability for waves with thick interfaces. The subsequent three-dimensional dynamics and mixing is dominated by secondary cross-stream convective rolls which account for roughly half of the total dissipation of wave energy. Dissipation and mixing are maximized when the interface thickness is roughly the same size as the amplitude of the wave, while the mixing efficiency is a weak function of the interface thickness. The maximum instantaneous mixing efficiency is found to be $0.36\pm 0.02$.
Structural Requirements for the BARD1 Tumor Suppressor in Chromosomal Stability and Homology-directed DNA Repair*

The BRCA1 tumor suppressor exists as a heterodimeric complex with BARD1, and this complex is thought to mediate many of the functions ascribed to BRCA1, including its role in tumor suppression. The two proteins share a common structural organization that features an N-terminal RING domain and two C-terminal BRCT motifs, whereas BARD1 alone also contains three tandem ankyrin repeats. In normal cells, the BRCA1/BARD1 heterodimer is believed to enhance chromosome stability by promoting homology-directed repair (HDR) of double strand DNA breaks. Here we have investigated the structural requirements for BARD1 in this process by complementation of Bard1-null mouse mammary carcinoma cells. Our results demonstrate that the ankyrin and BRCT motifs of BARD1 are each essential for both chromosome stability and HDR. Tandem BRCT motifs, including those found at the C terminus of BARD1, are known to form a phosphoprotein recognition module. Nonetheless, the HDR function of BARD1 was not perturbed by synthetic mutations predicted to ablate the phospho-recognition activity of its BRCT sequences, suggesting that some functions of the BRCT domains are not dependent on their ability to bind phosphorylated ligands. Also, cancer-associated missense mutations in the BRCT domains of BARD1 (e.g. C557S, Q564H, V695L, and S761N) have been observed in patients with breast, ovarian, and endometrial tumors. However, none of these was found to affect the HDR activity of BARD1, suggesting that any increased cancer risk conferred by these mutations is not because of defects in this repair mechanism.
Simple Free-Space Method for Measurement of Dielectric Constant by Means of Diffractive Optics with New Capabilities

The monitoring of the composition of materials is an important problem of applied spectroscopy using optical, infrared, microwave and THz wavelength bands. MM and THz waves ensure better spatial resolution than microwaves and they can be used for material testing in media that are opaque for optical and infrared radiation. Whenever dielectric components are used in MM and THz wavebands, a precise knowledge of the dielectric properties of the material is essential. The developments original setups for dielectric material probing simultaneously at several discrete wavelengths within the same local zone are described.
The Trade System and Climate Action: Ways Forward Under the Paris Agreement

The relationship between trade policy and climate policy needs to improve in the future, in particular with a view towards implementing the Paris Agreement. With the aim of making trade policy supportive of climate action, this working paper discusses the relationship between the regimes established by the World Trade Organization (WTO) and the United Nations Framework Convention on Climate Change (UNFCCC), the provisions and pending disputes, the role of regional trade agreements as well as upcoming issues emerging from the Paris Agreement. It highlights several options for addressing the relationship between the two regimes from a legal, institutional and a policy perspective. The suggested options relate to those fields where national climate policy action has been taken during the last years and which are part of the intended nationally determined contributions (INDCs) submitted in the run-up to the Paris Agreement.Already today, many regional trade agreements include climate and environmental provisions, and could thus help prevent a regulatory race to the bottom. Moreover, the increasing number of WTO disputes over national renewable energy policy regulations points to the case-by-case nature of WTO rule application on the one hand, and to a more systemic conflict of national approaches with the WTO obligation of non-discrimination on the other.
Epidemiology of tuberculosis in Benin.

SETTING Benin, West Africa. OBJECTIVE To describe the epidemiology of tuberculosis (TB) in Benin. DESIGN Analysis of two tuberculin surveys initiated in 1987 and 1994 and of the quarterly reports of the Basic Management Units to the National Tuberculosis Programme from 1995 to 2007. RESULTS The average annual risk for a child in Benin of becoming infected with Mycobacterium tuberculosis was around 0.5% in the mid 1980s. The notification rate increased by approximately 1% each year over the observation period and was on average 35 per 100,000 population, with a male-to-female sex ratio of 1.8 and no shift in the age structure of the cases over the observation period. Human immunodeficiency virus prevalence was 14% (97% of the patients were tested). There is a strong gradient of incident notification rates from the north to the south of the country that seems to be related to the population density. CONCLUSION Both the tuberculin skin test survey results and the notification data suggest that the TB problem in Benin is much smaller than in eastern and southern African countries.
Comparative content analysis of professional, semi-professional, and user-generated restaurant reviews

ABSTRACT This study examines the content of professional, semi-professional, and user-generated reviews. By comparing these three review types, this study was able to identify characteristics and factors unique to each type of review. Although, the amount of discourse in a particular factor varied, food is clearly the most important review factor regardless of review type. Semi-professional reviews emphasize atmosphere and décor more than both newspaper and user-generated reviews, while price factors were more prevalent in semi-professional reviews and user-generated reviews than in newspaper reviews. Understanding the varied structures of review types provides guidance for both restaurateurs and review users.
Photoemission Replenishment Criterion for Inception of Negative Corona Discharges in Air

Photoemission replenishment criterion (PRC) is widely used to evaluate the onset conditions for negative corona discharges in atmospheric air. The relationship between the PRC and the air density is built up in this paper, which is validated for a wide range of electrode radii and low air densities. The total effective region responsible for photoemission is taken into account and a new geometric parameter that characterizes the photon absorption in the discharge volume is proposed, although the modification insignificantly affects the results. The numerical results agree well with Peek's experimental data for negative corona discharges in air, which are also consistent with Peek's formula for coaxial cylinders and Whitehead's formula for negative corona onset.
Optimal Haplotype Structure for Linkage Disequilibrium-Based Fine Mapping of Quantitative Trait Loci Using Identity by Descent

A linkage disequilibrium-based method for fine mapping quantitative trait loci (QTL) has been described that uses similarity between individuals' marker haplotypes to determine if QTL alleles are identical by descent (IBD) to model covariances among individuals' QTL alleles for a mixed linear model. Mapping accuracy with this method was found to be sensitive to the number of linked markers that was included in the haplotype when fitting the model at a putative position of the QTL. The objective of this study was to determine the optimal haplotype structure for this IBD-based method for fine mapping a QTL in a previously identified QTL region. Haplotypes consisting of 1, 2, 4, 6, or all 10 available markers were fit as a “sliding window” across the QTL region under ideal and nonideal simulated population conditions. It was found that using haplotypes of 4 or 6 markers as a sliding “window” resulted in the greatest mapping accuracy under nearly all conditions, although the true IBD state at a putative QTL position was most accurately predicted by IBD probabilities obtained using all markers. Using 4 or 6 markers resulted in greater discrimination of IBD probabilities between positions while maintaining sufficient accuracy of IBD probabilities to detect the QTL. Fitting IBD probabilities on the basis of a single marker resulted in the worst mapping accuracy under all conditions because it resulted in poor accuracy of IBD probabilities. In conclusion, for fine mapping using IBD methods, marker information must be used in a manner that results in sensitivity of IBD probabilities to the putative position of the QTL while maintaining sufficient accuracy of IBD probabilities to detect the QTL. Contrary to expectation, use of haplotypes of 4–6 markers to derive IBD probabilities, rather than all available markers, best fits these criteria. Thus for populations similar to those simulated here, optimal mapping accuracy for this IBD-based fine-mapping method is obtained with a haplotype structure including a subset of all available markers.
Identification of the Origin of Replication of the Mycoplasma pulmonis Chromosome and Its Use in oriC Replicative Plasmids

ABSTRACT Mycoplasma pulmonis is a natural rodent pathogen, considered a privileged model for studying respiratory mycoplasmosis. The complete genome of this bacterium, which belongs to the class Mollicutes, has recently been sequenced, but studying the role of specific genes requires improved genetic tools. In silico comparative analysis of sequenced mollicute genomes indicated the lack of conservation of gene order in the region containing the predicted origin of replication (oriC) and the existence, in most of the mollicute genomes examined, of putative DnaA boxes lying upstream and downstream from the dnaA gene. The predicted M. pulmonis oriC region was shown to be functional after cloning it into an artificial plasmid and after transformation of the mycoplasma, which was obtained with a frequency of 3 × 10−6 transformants/CFU/μg of plasmid DNA. However, after a few in vitro passages, this plasmid integrated into the chromosomal oriC region. Reduction of this oriC region by subcloning experiments to the region either upstream or downstream from dnaA resulted in plasmids that failed to replicate in M. pulmonis, except when these two intergenic regions were cloned with the tetM determinant as a spacer in between them. An internal fragment of the M. pulmonis hemolysin A gene (hlyA) was cloned into this oriC plasmid, and the resulting construct was used to transform M. pulmonis. Targeted integration of this genetic element into the chromosomal hlyA by a single crossing over, which results in the disruption of the gene, could be documented. These mycoplasmal oriC plasmids may therefore become valuable tools for investigating the roles of specific genes, including those potentially implicated in pathogenesis.
Early and intensive rehabilitation predicts good functional outcomes in patients admitted to the stroke intensive care unit

Purpose. Earlier and more intense rehabilitation benefit stroke patients. Yet, studies have caution intensive therapy during acute brain injury. This study examined the rehabilitation commencement time and intensity as predictors of functional outcomes in acute stroke patients admitted to the stroke intensive care unit (ICU). Method. Sociodemographic, medical, rehabilitative and functional data were collected on 154 acute stroke patients. Regression analyses were used to identify predictors for the basic activities of daily living (Barthel Index, BI) and the walking ability at discharge. Result. Rehabilitation commencement time and intensity significantly predicted the BI score at discharge after adjusting for initial severity (National Institute of Health Stroke Scale, NIHSS) and age (p < 0.05). For the walking function at discharge, only the rehabilitation intensity was a significant predictor after adjusting for initial severity and age (p < 0.05). Furthermore, with increasing rehabilitation intensity, patients with severe stroke benefited more than those with moderate stroke. Conclusion. Rehabilitation commencement time and intensity, after adjusting for admission functional status and severity of stroke, remained to be important predictors of stroke functional outcomes. This study supported the recommendation to commence rehabilitation early and intensively and provided evidence that this claim can be extended to acute stroke patients admitted to an ICU.
Specific CD45 isoforms differentially regulate T cell receptor signaling.

Multiple isoforms of T cell CD45 tyrosine phosphatase are expressed as a result of alternative RNA splicing among extracellular exons. To discern the presence and identity of distinct functions among CD45 isoforms, we compared thymic T cell activation responses by elevating expression of two CD45 isoforms normally found on quiescent T cells. We report that CD45RABC significantly increased CD4+ thymic T cell proliferation in both a mixed lymphocyte reaction and following anti‐T cell receptor (TCR) antibody stimulation. Additionally, CD45RABC enhanced Ca2+ mobilization and phosphotyrosine accumulation, and suppressed the inhibitory effect of anti‐CD4 antibodies. By contrast, CD45R0 did not enhance TCR signaling or phosphotyrosine levels in CD4+ thymic T cells and required a TCR co‐stimulus to augment cellular proliferation. These studies provide genetic evidence that alternative CD45 isoforms are functionally distinct and disclose a unique mechanism by which T cell immunologic responsiveness can be modified.
A counterintuitive approach to treat enzyme deficiencies: use of enzyme inhibitors for restoring mutant enzyme activity

Abstract Pharmacological chaperone therapy is an emerging counterintuitive approach to treat protein deficiencies resulting from mutations causing misfolded protein conformations. Active-site-specific chaperones (ASSCs) are enzyme active-site directed small molecule pharmacological chaperones that act as a folding template to assist protein folding of mutant proteins in the endoplasmic reticulum (ER). As a result, excessive degradation of mutant proteins in the ER-associated degradation (ERAD) machinery can be prevented, thus restoring enzyme activity. Lysosomal storage disorders (LSDs) are suitable candidates for ASSC treatment, as the levels of enzyme activity needed to prevent substrate storage are relatively low. In addition, ASSCs are orally active small molecules and have potential to gain access to most cell types to treat neuronopathic LSDs. Competitive enzyme inhibitors are effective ASSCs when they are used at sub-inhibitory concentrations. This whole new paradigm provides excellent opportunity for identifying specific drugs to treat a broad range of inherited disorders. This review describes protein misfolding as a pathophysiological cause in LSDs and provides an overview of recent advances in the development of pharmacological chaperone therapy for the diseases. In addition, a generalized guidance for the design and screening of ASSCs is also presented.
Disordered Meiotic Regulation of Oocytes by Duration of Diabetes Mellitus in BBdp Rat

Diabetes mellitus (DM) disturbs normal functions from the level of cells to the level of organs. In this study, the authors explore the detrimental effects of type 1 diabetes on meiotic regulation depending on the duration of DM. In non—diabetes-prone BioBreeding (BBdr) control rats, most of the large follicles had germinal vesicle (GV)—intact oocytes. Conversely, a decrease of intact GV that was dependent on the duration of diabetic symptoms was observed; only 54% of the large follicles of diabetes-prone BB (BBdp) rats had GV-intact oocytes at 6 weeks after diabetes induction. Furthermore, some of the secondary follicles in BBdp rats also had germinal vesicle breakdown (GVB) oocytes. The nuclear status of the euglycemia BBdp rat was similar to those of the BBdr rat. In BBdp rats, the rate of meiotic progression to the metaphase II stage was significantly lower; however, the rate of segregated oocytes was significantly increased compared with controls during induction of in vitro maturation. The rate of segregated oocytes was not affected by the presence of the cumulus after chronic symptoms. These results indicate that chronic DM has a detrimental effect on meiotic regulation during folliculogenesis and results in a reduced number of competent oocytes. In addition, these data suggest that the follicle cells can resume supporting the meiotic regulation under euglycemia through insulin administration, independent of the duration of DM.
SIX-MINUTE WALK BY PEOPLE WITH CHRONIC RENAL FAILURE: Assessment of Effort by Perceived Exertion

ABSTRACT The ability to exercise among 20 people with chronic renal failure was assessed on three tests by measuring the distance walked in 6 min, heart rate change from pre-exercise to postexercise and perceived exertion. Test 1 was conducted to minimize practice effects. Ten participants received exercise coaching for 3 mo between Tests 2 and 3, and 10 individuals were in a control group. Distance walked was highly correlated on the three tests; heart rate change and perceived exertion were only slightly less consistent. Three people changed their perceived exertion by more than one point between Tests 2 and 3, and these changes obscured differences between the exercise and control groups. Exclusion of data for those who changed by more than one point equalized perceived exertion changes in the two groups and revealed a significant (P < 0.05) increase in distance in the exercise group (+21.8 m) but not in the control group (+1.5 m). The study demonstrates that, although perceived exertion ratings are intended for use in incremental exercise testing, they are also valuable for assessing consistency v change in the effort of individual participants in single-intensity testing, such as a self-paced walk.
PROBLEM TO PETITION RIGHTS TO ISLAMIC INHERITANCE – PRACTICAL SOLUTION FOUND ELSEWHERE THAN THE LEGAL SYSTEM OF MALAYSIA

Dampen by their failure to completely replace all Islamic Laws in the Malay States by the English Common Laws, the British vested more authority on the Civil courts to handle inheritance cases and wills, thus stripping the Syariah courts of their authority to distribute Islamic inheritance. The current legal system of Malaysia is laced with British influences that have caused many conflicting constitutional issues. The current legal system can neither accommodate a smooth and fluent administration and distribution of Islamic inheritance nor can it allow for a single Syariah-compliant system to exist. Muslims will continue to endure spending lots of money and time on the process flows of the inheritance unless the legal system is free of all British influences. This predicament is a problem that is seriously in need of a practical solution that lies in venues other than the legal system, one of which is the use of network flow model which is researched on by this current on-going study.
A development of fuzzy control of hybrid energy system using ultracapacitor

Fuzzy control for improving the performance of hybrid power application is presented. The hybrid power system consists of battery and ultracapacitor (UC). It can be expected that the improvement of system efficiency and the long duration period of the energy storage can be achieved by using battery as a main storage and UC as an auxiliary source. UC are electrical energy storage devices which have dynamics features of high power density, very fast power recycling capability and have mechanical robustness. In a short term power applications, this type of energy storage system is widely used for improving power consumption especially when charge and discharge time recovery are critical. However the voltage offer by UC is depending on their operating condition. Thus a power dc-dc converter is required as well as high dynamics control technique should be selected to get the best operating of UC. Therefore in this paper the new fuzzy control technique is being used to control the power flow of UC to supply the transient power demand for a proposed hybrid system. The bidirectional DC-DC converter is used to connect the UC with the battery for the controlled instantaneous electric power flow. The proposed control technique applied in this hybrid system has been verified by the simulation during various condition of the load.
A joint space formulation for compliant motion control of robot manipulators

This paper presents a joint space formulation for robot manipulator's hybrid motion/force control. The motivations come from 1) extending the previous work to general (either constrained or redundant) robots; and 2) improving the robustness against disturbances originated at the joint level. Contact geometry and closed-loop dynamics are derived in this paper, also a joint space hybrid control scheme is proposed. At the end, we show some simulation results to verify the applicability of our theory on a constrained (4-degree-of-freedom) robot WAM.