Miracle-dz/UniFAR-FTUs huggingface dataset:
Clinical experience in using polymerase chain reaction for rapid diagnosis of pulmonary tuberculosis.

BACKGROUND Polymerase chain reaction (PCR) techniques have revolutionized the diagnosis of tuberculosis (TB). PCR has significantly improved the sensitivity and specificity of existing diagnostic methods. In this study, we report our experience using a modified IS6110-based nested PCR assay for rapid diagnosis of pulmonary TB. METHODS A total of 327 respiratory specimens from 275 patients suspected of having pulmonary TB at Taipei Veterans General Hospital were tested using the nested PCR assay, acid-fast smear and culture for the presence of Mycobacterium tuberculosis complex (MTB). Nested PCR was performed with IS6110-based primers specific for MTB. We reviewed the medical records of patients and analyzed the clinical features. The PCR results were compared with the final clinical diagnosis. RESULTS We identified MTB in 167 of 327 samples by the nested PCR assay. No non-tuberculous Mycobacterium (NTM) was identified among the clinical samples. Diagnosis by PCR took about 6 hours in this study. The sensitivity and specificity compared with culture were 94.7% and 100%, respectively for the smear-positive, culture-positive samples, and 76.7% and 98.6% for the smear-negative, culture-positive samples. The overall sensitivity, specificity, positive and negative predictive values, compared with culture results, were 91.7%, 98.6%, 98.8% and 90.6%, respectively. Two specimens positive by PCR and negative by culture were taken from patients on anti-TB drug therapy. These specimens were culture-positive before anti-TB drug therapy. After resolution of the discrepancies by studying the patients' clinical data, both specificity and positive predictive value reached 100%. CONCLUSIONS The results indicated that this in-house nested PCR assay is a rapid and sensitive method for diagnosing pulmonary TB. It is also good for excluding infections caused by NTM.
Ribonucleotide Reductase Regulation in Response to Genotoxic Stress in Arabidopsis1[W]

Ribonucleotide reductase (RNR) is an essential enzyme that provides dNTPs for DNA replication and repair. Arabidopsis (Arabidopsis thaliana) encodes three AtRNR2-like catalytic subunit genes (AtTSO2, AtRNR2A, and AtRNR2B). However, it is currently unclear what role, if any, each gene contributes to the DNA damage response, and in particular how each gene is transcriptionally regulated in response to replication blocks and DNA damage. To address this, we investigated transcriptional changes of 17-d-old Arabidopsis plants (which are enriched in S-phase cells over younger seedlings) in response to the replication-blocking agent hydroxyurea (HU) and to the DNA double-strand break inducer bleomycin (BLM). Here we show that AtRNR2A and AtRNR2B are specifically induced by HU but not by BLM. Early AtRNR2A induction is decreased in an atr mutant, and this induction is likely required for the replicative stress checkpoint since rnr2a mutants are hypersensitive to HU, whereas AtRNR2B induction is abolished in the rad9-rad17 double mutant. In contrast, AtTSO2 transcription is only activated in response to double-strand breaks (BLM), and this activation is dependent upon AtE2Fa. Both TSO2 and E2Fa are likely required for the DNA damage response since tso2 and e2fa mutants are hypersensitive to BLM. Interestingly, TSO2 gene expression is increased in atr versus wild type, possibly due to higher ATM expression in atr. On the other hand, a transient ATR-dependent H4 up-regulation was observed in wild type in response to HU and BLM, perhaps linked to a transient S-phase arrest. Our results therefore suggest that individual RNR2-like catalytic subunit genes participate in unique aspects of the cellular response to DNA damage in Arabidopsis.
Cross-Cultural Adaptation of the Lumbar North American Spine Society Questionnaire for Italian-Speaking Patients With Lumbar Spinal Disease

Study Design. A cross-cultural adaptation and cross-sectional study of a sample of lumbar spine patients, with a subsample followed prospectively for retest reliability. Objectives. To assess the Italian version instrument reliability and validity. Summary of Background Data. The orthopaedic outcome measurements have been usually focused on objective parameters as radiograph measures or other technical aspects. However, these parameters are weakly related with outcomes that are more relevant to patients as functional status and symptoms. In the last ten years, the patient-oriented measures have become an important aspect of spinal clinical outcome evaluation. The most common instruments to assess patient perspective are self-administered questionnaires that must be validated by a widely accepted process to evaluate reliability and validity, which are fundamental for every instrumental measure. Methods. The North American Spine Society (NASS) questionnaire was culturally adapted for Italian-speaking people following the Guillemin criteria. The Italian version was tested on 74 consecutive patients who were referred to the authors’ department and suffered from low back pain with leg irradiation. The results were compared with other validated patient-oriented measures. Forty-eight-hour retests were performed on a subsample of 45 patients. Results. The questionnaire was favorably accepted by patients. The lumbar spine pain and disability and neurogenic symptoms subscales showed a high correlation with other patient-oriented measures, as hypothesized, and it also showed good values on test-retest. Conclusions. The questionnaire should be considered for patient health status monitoring and for clinical trials.
Psychometric Evaluation of the Midlife Women’s Symptom Index in Multiethnic Groups

The Midlife Women’s Symptom Index (MSI) was designed to measure menopausal symptoms specifically in a multiethnic sample of midlife women. This study involved a psychometric property test to evaluate MSI among 512 multiethnic groups of midlife women (White, Hispanic, African American, and Asian American). Across the ethnic groups, the MSI had an adequate internal consistency in all subdomains except psychosomatic symptoms. The item—total correlation coefficients of lost weight and nosebleeds were lower than . 20 among all ethnic groups. The discriminant validity was confirmed among all ethnic groups except Asian Americans. Overall, the MSI may work better for Whites compared with other ethnic groups. Additional studies with diverse groups of multiethnic midlife women are needed, however, to confirm the psychometric properties of the MSI because the samples tended to be a select group.
Dual Diagnosis and Suicide Risk in a Spanish Outpatient Sample

The present study compares dual-diagnosis patients with other groups of psychiatric patients to determine the differential characteristics in suicide risk and other clinical variables between them. During 2008 in Madrid, 837 outpatients were evaluated in addiction and mental health services. Three comparison groups were created according to current diagnosis: (i) dual patients, (ii) patients with substance use disorders but no other mental disorders, and (iii) patients with mental disorders but no substance use disorders. A multinomial logistic regression model was built to explore the risk associated with dual diagnosis. Criteria for dual diagnosis were met at the time of the study by 440 patients (52.6%). Dual patients showed several demographic and clinical differences and a higher risk for suicide than the other two comparison groups. Further research is needed to define suicide preventive strategies for dual patients.
A Probabilistic Approach for Deriving Acceptable Human Intake Limits and Human Health Risks from Toxicological Studies: General Framework

The use of uncertainty factors in the standard method for deriving acceptable intake or exposure limits for humans, such as the Reference Dose (RfD), may be viewed as a conservative method of taking various uncertainties into account. As an obvious alternative, the use of uncertainty distributions instead of uncertainty factors is gaining attention. This paper presents a comprehensive discussion of a general framework that quantifies both the uncertainties in the no-adverse-effect level in the animal (using a benchmark-like approach) and the uncertainties in the various extrapolation steps involved (using uncertainty distributions). This approach results in an uncertainty distribution for the no-adverse-effect level in the sensitive human subpopulation, reflecting the overall scientific uncertainty associated with that level. A lower percentile of this distribution may be regarded as an acceptable exposure limit (e.g., RfD) that takes account of the various uncertainties in a nonconservative fashion. The same methodology may also be used as a tool to derive a distribution for possible human health effects at a given exposure level. We argue that in a probabilistic approach the uncertainty in the estimated no-adverse-effect-level in the animal should be explicitly taken into account. Not only is this source of uncertainty too large to be ignored, it also has repercussions for the quantification of the other uncertainty distributions.
Environmental and spatial drivers of taxonomic, functional, and phylogenetic characteristics of bat communities in human-modified landscapes

Background Assembly of species into communities following human disturbance (e.g., deforestation, fragmentation) may be governed by spatial (e.g., dispersal) or environmental (e.g., niche partitioning) mechanisms. Variation partitioning has been used to broadly disentangle spatial and environmental mechanisms, and approaches utilizing functional and phylogenetic characteristics of communities have been implemented to determine the relative importance of particular environmental (or niche-based) mechanisms. Nonetheless, few studies have integrated these quantitative approaches to comprehensively assess the relative importance of particular structuring processes. Methods We employed a novel variation partitioning approach to evaluate the relative importance of particular spatial and environmental drivers of taxonomic, functional, and phylogenetic aspects of bat communities in a human-modified landscape in Costa Rica. Specifically, we estimated the amount of variation in species composition (taxonomic structure) and in two aspects of functional and phylogenetic structure (i.e., composition and dispersion) along a forest loss and fragmentation gradient that are uniquely explained by landscape characteristics (i.e., environment) or space to assess the importance of competing mechanisms. Results The unique effects of space on taxonomic, functional and phylogenetic structure were consistently small. In contrast, landscape characteristics (i.e., environment) played an appreciable role in structuring bat communities. Spatially-structured landscape characteristics explained 84% of the variation in functional or phylogenetic dispersion, and the unique effects of landscape characteristics significantly explained 14% of the variation in species composition. Furthermore, variation in bat community structure was primarily due to differences in dispersion of species within functional or phylogenetic space along the gradient, rather than due to differences in functional or phylogenetic composition. Discussion Variation among bat communities was related to environmental mechanisms, especially niche-based (i.e., environmental) processes, rather than spatial mechanisms. High variation in functional or phylogenetic dispersion, as opposed to functional or phylogenetic composition, suggests that loss or gain of niche space is driving the progressive loss or gain of species with particular traits from communities along the human-modified gradient. Thus, environmental characteristics associated with landscape structure influence functional or phylogenetic aspects of bat communities by effectively altering the ways in which species partition niche space.
Cardiovascular risk among patients on clopidogrel anti-platelet therapy after placement of drug-eluting stents is modified by genetic variants in both the CYP2C19 and ABCB1 genes

Summary Long-term (at least one year) dual anti-platelet therapy incorporating aspirin and clopidogrel is currently recommended following percutaneous coronary intervention with placement of a drug-eluting stent (DES). Genetic variants in both the ABCB1 and CYP2C19 genes have been associated with cardiovascular events among patients on clopidogrel. We examined the concurrent contribution of the CYP2C19 *2 and *17 alleles and the ABCB1 3435 alleles to one-year clinical risk among patients (n=1,034 on clopidogrel therapy following the placement of a DES. For CYP2C19*2, event rates were 8.4%, 10.9% and 44.4% for patients with 0, 1 and 2 *2 alleles, respectively (p=0.016). ABCB1 3435 was not associated with events in univariate analysis. However, 72% of patients with a *2 variant also possessed the ABCB1 3435 C allele; among these patients (*2/C genotype) the event rate for myocardial infarction (MI) was 14.2% vs. 6.9% for those lacking both *2 and C alleles (p=0.027) and for MI/death, 16.9% vs. 9.6% (p=0.046). Overall for all genotypes, the presence of the gain-of-function (protective) *17 allele significantly reduced the one-year rate of MI from 11.1% to 7.0% (p=0.045) and trended to reduce the combined rate of MI/death from 13.8% to 10.5% (p=0.182). In conclusion, the ABCB1 3435 locus and the *2 allele combine to impart a significant trend toward increased risk. This trend was largely reversed by the simultaneous carriage of one or two *17 alleles. These findings suggest that assessment of a combined genotype may improve risk assessment.
Effect of Aerosol Surface Lubricants on the Abundance and Richness of Selected Forest Insects Captured in Multiple-Funnel and Panel Traps

ABSTRACT Survey and detection programs for native and exotic forest insects frequently rely on traps baited with odorants, which mediate the orientation of target taxa (e.g., the southern pine beetle, Dendroctonus frontalis Zimmermann) toward a resource (e.g., host material, mates). The influence of trap design on the capture efficiency of baited traps has received far less empirical attention than odorants, despite concerns that intercept traps currently used operationally have poor capture efficiencies for some target taxa (e.g., large woodborers). Several studies have recently demonstrated that treating traps with a surface lubricant to make them “slippery” can increase their capture efficiency; however, previously tested products can be expensive and their application time-consuming. The purpose of this study was to evaluate the effect of alternate, easier to apply aerosol lubricants on trap capture efficiency of selected forest insects. Aerosol formulations of Teflon and silicone lubricants increased both panel and multiple-funnel trap capture efficiencies. Multiple-funnel traps treated with either aerosol lubricant captured significantly more Monochamus spp. and Acanthocinus obsoletus (Olivier) than untreated traps. Similarly, treated panel traps captured significantly more Xylotrechus sagittatus (Germar), Ips calligraphus (Germar), Pissodes nemorensis (Germar), Monochamus spp. , A. obsoletus, Thanasimus dubius (F.), and Ibalia leucospoides (Hochenwarth) than untreated traps. This study demonstrates that treating multiple-funnel and panel traps with an aerosol dry film lubricant can increase their capture efficiencies for large woodborers (e.g., Cerambycidae) as well as bark beetles, a weevil, a woodwasp parasitoid and a bark beetle natural enemy (Coleoptera: Cleridae).
Lipopolysaccharide Stimulates Mitochondrial Biogenesis via Activation of Nuclear Respiratory Factor-1*

Exposure to bacterial lipopolysaccharide (LPS) in vivo damages mitochondrial DNA (mtDNA) and interferes with mitochondrial transcription and oxidative phosphorylation (OXPHOS). Because this damage accompanies oxidative stress and is reversible, we postulated that LPS stimulates mtDNA replication and mitochondrial biogenesis via expression of factors responsive to reactive oxygen species, i.e. nuclear respiratory factor-1 (NRF-1) and mitochondrial transcription factor-A. In testing this hypothesis in rat liver, we found that LPS induces NRF-1 protein expression and activity accompanied by mRNA expression for mitochondrial transcription factor-A, mtDNA polymerase γ, NRF-2, and single-stranded DNA-binding protein. These events restored the loss in mtDNA copy number and OXPHOS gene expression caused by LPS and increased hepatocyte mitotic index, nuclear cyclin D1 translocation, and phosphorylation of pro-survival kinase, Akt. Thus, NRF-1 was implicated in oxidant-mediated mitochondrial biogenesis to provide OXPHOS for proliferation. This implication was tested in novel mtDNA-deficient cells generated from rat hepatoma cells that overexpress NRF-1. Depletion of mtDNA (ρo clones) diminished oxidant production and caused loss of NRF-1 expression and growth delay. NRF-1 expression and growth were restored by exogenous oxidant exposure indicating that oxidative stress stimulates biogenesis in part via NRF-1 activation and corresponding to recovery events after LPS-induced liver damage.
Spare cutting approaches for repairing memories

This paper presents new algorithms for yield enhancement of redundant memories. These algorithms are based on the technique of spare cutting for a redundant memory chip in which repair is implemented by row/column deletion. Different approaches are proposed: some of these approaches are based on a fully exhaustive process, while others try to heuristically reduce the computational overhead involved in determining the repair-solution.
Large GABAergic neurons form a distinct subclass within the mouse dorsal cortex of the inferior colliculus with respect to intrinsic properties, synaptic inputs, sound responses, and projections

Neurons in the inferior colliculus (IC) show a remarkable diversity in their responses to sound, but it has been difficult to relate these responses to their morphology. Large cells, which are found in all subdivisions of the IC, may form an exception. We found that large neurons of the mouse dorsal cortex of the IC were GABAergic and were contacted by vesicular glutamate transporter 2‐containing somatic terminals, as previously observed for the rat IC. Large cells, which were targeted under two‐photon guidance, typically had a low input resistance in comparison with the other cells in the dorsal cortex of the IC. Large cells received short‐latency excitatory inputs and had short first‐spike latencies. These excitatory inputs were often followed by long‐latency inhibitory postsynaptic potentials. In four cells, it was possible to reconstruct the ascending axon following labeling with biocytin. We found evidence that they projected to both the ventral and the dorsal divisions of the medial geniculate body of the thalamus, but they also branched off large collaterals while passing through the brachium of the IC. Our data indicate that, owing to their somatic glutamatergic inputs, large GABAergic tectothalamic projection neurons can generate short‐latency, well‐timed, feed‐forward inhibition, which affects not only the thalamus, but also other ascending nuclei. Their remarkably homogeneous properties, which generally differed from those of the other cells in the dorsal cortex of the IC, suggest that large neurons form a distinct subclass within the dorsal cortex of the IC. J. Comp. Neurol. 521:189–202, 2013. © 2012 Wiley Periodicals, Inc.
Differential effects of the loss of intrachain- versus interchain-disulfide bonds in the cystine-knot domain of von Willebrand factor on the clinical phenotype of von Willebrand disease

Summary Von Willebrand factor (VWF) contains a large number of cysteine residues, which all form disulfide bonds. Mutations of cysteines located in the cystine-knot (CK) domain of VWF have been identified in both qualitative type 2A (IID) and quantitative type 3 vonWillebrand disease (VWD). Our objective was to test the hypothesis that the difference in phenotype is related to whether the mutated cysteine residue is involved in either interchain- or intrachain-disulfide-bond formation. The effects of three cysteine mutations which are all located in the CK-domain of VWF, C2773S (type 2A(IID)), C2739Y (type 3), and C2754W (type 3), were studied by transient expression in 293T cells. Cotransfection of wild-type (wt) and C2773S VWF constructs reproduced the plasma phenotype of heterozygous type 2A(IID) patients, with normal to high levels of VWF antigen (VWF:Ag), absence of high-molecular-weight multimers, and the presence of intervening bands between the normal multimers.In contrast, single transfections of C2739Y or C2754W resulted in a quantitativeVWF defect with lowVWF:Ag levels, and co-transfections of wt and mutant constructs resulted in a 50% reduction of VWF:Ag and only a minor effect on VWF multimerization. We demonstrated N-terminal dimerization of VWF-C2773S and both Nand C-terminal dimerization of VWF-C2754W. Our data suggest that loss of a single disulfide bond in the CK-domain ofVWF leads toa recessive, quantitativeVWF deficiency if an intrachain-disulfide bond is involved, and to a dominant-negative, qualitative defect of VWF if an interchain-disulfide bond is involved.
CpG DNA and immunotherapy of allergic airway diseases

Atopic asthma is a highly prevalent and serious health problem for which no therapy currently offers the hope of a cure. Preindustrialized and rural populations appear relatively protected from the asthma epidemic; the hygiene hypothesis ascribes this protection to the effects of microbes and microbial products. An important immunostimulant component of microbes is DNA; bacterial DNA contains sequence motifs centred on the CpG dinucleotide, which are suppressed in mammalian DNA. Oligonucleotides containing these motifs (CpG ODN), like bacterial DNA, promote Th1 and regulatory‐type immune responses. Using CpG ODN, we and others have demonstrated in murine studies that CpG ODN are effective in preventing the development of atopic airways disease. Moreover, when administered in conjunction with experimental allergen, they promote the reversal of established eosinophilic inflammation. These data suggest that CpG ODN may be a novel therapeutic tool for the treatment of atopic asthma.
Protection of Microgrids During Utility Voltage Sags

Microgrids are systems with clusters of microgenerators, which are installed for distributed power generation. When interfaced to the utility grid, microgrids are exposed to common utility power-quality disturbances. In particular, during utility-voltage sags, large line currents can flow along distribution feeders connecting the micro- and utility grids. To limit this flow of large line currents and, hence, protect the microgrids, this paper proposes two current-limiting algorithms, namely, the RL feedforward and flux-charge-model feedback algorithms, for controlling a series inverter connected between the micro- and utility grids during utility voltage sags. Both methods function by inserting a large virtual RL or L impedance in series with the distribution feeder to limit the line-current flow. Detailed descriptions, controller designs, and comparisons of both algorithms are presented. Phasor analyses of both methods are also presented to show how the inserted RL or L values can be optimally tuned to improve the inverter damping performance and minimize its injected voltages and circulating power under all operation conditions. Lastly, both methods have been tested in simulation and in experiments using an emulated laboratory microgrid system