Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevention of False Resistance Results Obtained in Testing the Susceptibility of Mycobacterium tuberculosis to Pyrazinamide with the Bactec MGIT 960 System Using a Reduced Inoculum

ABSTRACT The susceptibility of 211 clinical isolates of Mycobacterium tuberculosis complex (201 M. tuberculosis and 10 Mycobacterium bovis isolates) to pyrazinamide (PZA) was assessed by the nonradiometric Bactec MGIT 960 system (M960). Detection of PZA resistance was followed by a repeat testing using a reduced inoculum (RI) of 0.25 ml instead of 0.5 ml. According to the first M960 analysis, resistance was observed in 55 samples. In the RI assay, 32 samples turned out to be susceptible and 23 proved to be resistant (58.2% false positivity). The Bactec 460 assay confirmed as resistant those strains detected by the RI assay, while discrepant results were found susceptible. Mutation analysis performed on 13 M. tuberculosis isolates detected pncA mutations in 11 samples. On the basis of our data, we suggest using the RI assay to confirm all PZA resistance results obtained with the standard M960 assay. Further studies are required to confirm our findings.
Design, Modeling and Synthesis of 1,2,3-Triazole-Linked Nucleoside-Amino Acid Conjugates as Potential Antibacterial Agents

Copper-catalyzed azide-alkyne cycloadditions (CuAAC or click chemistry) are convenient methods to easily couple various pharmacophores or bioactive molecules. A new series of 1,2,3-triazole-linked nucleoside-amino acid conjugates have been designed and synthesized in 57-76% yields using CuAAC. The azido group was introduced on the 5'-position of uridine or the acyclic analogue using the tosyl-azide exchange method and alkylated serine or proparylglycine was the alkyne. Modeling studies of the conjugates in the active site of LpxC indicate they have promise as antibacterial agents.
Variability in Vowel Production within and between Days

Although the acoustic variability of speech is often described as a problem for phonetic recognition, there is little research examining acoustic-phonetic variability over time. We measured naturally occurring acoustic variability in speech production at nine specific time points (three per day over three days) to examine daily change in production as well as change across days for citation-form vowels. Productions of seven different vowels (/EE/, /IH/, /AH/, /UH/, /AE/, /OO/, /EH/) were recorded at 9AM, 3PM and 9PM over the course of each testing day on three different days, every other day, over a span of five days. Results indicate significant systematic change in F1 and F0 values over the course of a day for each of the seven vowels recorded, whereas F2 and F3 remained stable. Despite this systematic change within a day, however, talkers did not show significant changes in F0, F1, F2, and F3 between days, demonstrating that speakers are capable of producing vowels with great reliability over days without any extrinsic feedback besides their own auditory monitoring. The data show that in spite of substantial day-to-day variability in the specific listening and speaking experiences of these participants and thus exposure to different acoustic tokens of speech, there is a high degree of internal precision and consistency for the production of citation form vowels.
Optional that indicates production difficulty: evidence from disfluencies

Optional word omission, such as that omission in complement and relative clauses, has been argued to be driven by production pressure (rather than by comprehension). One particularly strong production-driven hypothesis states that speakers insert words to buy time to alleviate production difficulties. I present evidence from the distribution of disfluencies in non-subjectextracted relative clauses arguing against this hypothesis. While word omission is driven by production difficulties, speakers may use that as a collateral signal to addressees, informing them of anticipated production difficulties. In that sense, word omission would be subject to audience design (i.e. catering to addressees’ needs).
Effects of inhaled beclomethasone dipropionate on respiratory function in horses with chronic obstructive pulmonary disease (COPD).

The effects of beclomethasone dipropionate on pulmonary function and arterial blood gas values were investigated in horses with chronic obstructive pulmonary disease (COPD). Six mature mares, diagnosed as having COPD based on clinical signs, cytological examination of bronchoalveolar lavage and pulmonary function testing, were used. Beclomethasone dipropionate (3750 microg) was administered b.i. d. for a 2 week period with a metered dose inhaler using a mask. Pulmonary function tests and arterial blood gas analyses were performed at weekly intervals, starting before beclomethasone administration and for 4 weeks thereafter. Upper airway endoscopy and nasopharyngeal fungal cultures were performed before and after treatment. Maximal variations in transpulmonary pressure (deltaPL) were elevated in all horses at baseline. Beclomethasone administration resulted in a significant decrease in deltaPL in 5 horses, and deltaPL fell to within the normal range in 4 horses. Two weeks after the end of treatment, deltaPL was at or above baseline values in all horses. Total pulmonary resistance and elastance decreased significantly during treatment and returned to or above baseline values after the administration of beclomethasone was discontinued. At baseline, PaO2 range was 53-90 mmHg. In 4 horses with pronounced laboured breathing, PaO2 increased with treatment. One horse became reluctant to inhale the beclomethasone after one week, and only a transient improvement in respiratory function was noted in this animal. One horse developed a mild lower airway infection 24 h after the beginning of treatment, but no other possible side effects were noticed. Pharyngeal fungal cultures were negative before and after treatment. It can be concluded from the results of this study that inhaled beclomethasone dipropionate causes a marked improvement of respiratory function in horses with COPD.
Morphometric analysis of oligodendrocytes in the adult mouse frontal cortex

Oligodendrocytes (OLs), the myelinating cells of the central nervous system, have specialized morphologies that subserve their function. Numerous qualitative studies suggest that OLs in different brain regions can differ in their morphological characteristics, including number of branches and internodes, internode length, etc. However, progress in identifying and characterizing the diverse types of OLs and their distribution in the brain has been made difficult by several technical constraints. Here we report a new strategy to analyze OL morphology with a high degree of quantitative power and throughput. We used confocal microscopy and three‐dimensional cell tracing software to study OLs in the frontal cortex of mice expressing enhanced green fluorescent protein (eGFP) under the control of the proteolipid protein (Plp) gene promoter. Three‐dimensional reconstructions were then used to analyze and quantify cell morphology, including total process length, total process surface area, total internode length, number of primary processes, number of branch points, and number of internodes. In addition, these reconstructions were subjected to Sholl analysis, which allows for the quantitative measure of OL arbor complexity. By using this approach, we identified and characterized a previously undescribed population of small OLs with a compact but complex morphology that includes numerous branching processes and a large number of short internodes. Our data suggest that other populations of OLs remain to be identified and characterized and that the tools we have developed could help in the process of characterizing them. © 2007 Wiley‐Liss, Inc.
An Evaluation of HIV Elite Controller Definitions within a Large Seroconverter Cohort Collaboration

Background Understanding the mechanisms underlying viral control is highly relevant to vaccine studies and elite control (EC) of HIV infection. Although numerous definitions of EC exist, it is not clear which, if any, best identify this rare phenotype. Methods We assessed a number of EC definitions used in the literature using CASCADE data of 25,692 HIV seroconverters. We estimated proportions maintaining EC of total ART-naïve follow-up time, and disease progression, comparing to non-EC. We also examined HIV-RNA and CD4 values and CD4 slope during EC and beyond (while ART naïve). Results Most definitions classify ∼1% as ECs with median HIV-RNA 43–903 copies/ml and median CD4>500 cells/mm3. Beyond EC status, median HIV-RNA levels remained low, although often detectable, and CD4 values high but with strong evidence of decline for all definitions. Median % ART-naïve time as EC was ≥92% although overlap between definitions was low. EC definitions with consecutive HIV-RNA measurements <75 copies/ml with follow-up≥ six months, or with 90% of measurements <400 copies/ml over ≥10 year follow-up preformed best overall. Individuals thus defined were less likely to progress to endpoint (hazard ratios ranged from 12.5–19.0 for non-ECs compared to ECs). Conclusions ECs are rare, less likely to progress to clinical disease, but may eventually lose control. We suggest definitions requiring individuals to have consecutive undetectable HIV-RNA measurements for ≥ six months or otherwise with >90% of measurements <400 copies/ml over ≥10 years be used to define this phenotype.
The Incidence and Prevalence of Thyroid Disease Do Not Differ in the Multiple Sclerosis and General Populations: A Validation Study Using Administrative Data

Background: Prior studies of a possible increased risk of autoimmune thyroid disease (AIT) in multiple sclerosis (MS) are inconsistent. We aimed to validate and apply administrative case definitions for the surveillance of AIT in MS. Methods: We used administrative health data to identify 4,192 persons with MS and an age-, sex- and geographically matched general population cohort (n = 20,940). We developed case definitions for AIT using International Classification of Disease-9/10 codes and prescription claims, compared them to medical records and applied them to estimate the incidence and prevalence of AIT. Results: When compared to medical records, the administrative case definition using ≥1 hospital or ≥2 physician or ≥2 prescription claims had a sensitivity of 73.5% and specificity of 98.4%. In 2005, the age-adjusted prevalence of AIT was 9.51% [95% confidence interval (CI) 8.46–10.6] in the MS population and 8.56% (95% CI 8.11–9.02) in the general population. The age-adjusted incidence of AIT per 100,000 persons per year was 422.8 (95% CI 204.4–641.3) in the MS population and 407.7 (95% CI 308.5–506.9) in the general population. From 1996 to 2005, the prevalence of AIT rose in both populations. Conclusion: Administrative data can be used for surveillance of AIT in MS. The incidence and prevalence of thyroid disease are similar in the MS and general populations.
Granulocytic sarcoma of the cervix: Is hysterectomy necessary?

Discussion Neuroendocrine carcinoma of the uterine cervix (NCC) is rare, highly aggressive and prone to metastasis. SCNCC is most common among the NCC and comprises 1 – 3% of cervical carcinoma whose aetiology and predisposing risk factors are poorly understood (Van Nagell et al. 1988). SCNCC exhibits aggressive behaviour and poor prognosis, even aft er multimodal therapy, as very limited data is available for understanding of both management and eff ective therapy. Th e occurrence of leiomyoma between the vagina and rectum is rare. Its aetiology is unknown, although there is much speculation. A MEDLINE search for articles with keywords ‘ small cell neuroendocrine carcinoma of cervix ’ in the last 10 years yielded eight reports, and a search of the entire English literature for leiomyoma between vagina and rectum yielded none. Some studies have demonstrated a relationship between HPV infection and NCC of the cervix (Stoler et al. 1991). In 2011, the Society of Gynaecological Oncology issued a clinical document summarising the available literature on NCC of the female reproductive tract. In a recent study on the 5-year survival rate of patients with FIGO stage IB1, the survival rate was 50 – 60%, which was signifi cantly poorer than the 90% rate for patients with stage IB1 of squamous cell carcinoma (Viswanathan et al. 2004). Recent retrospective data suggests that surgery may improve the clinical outcome and radiation is used with concurrent etoposide/ cisplatinum. For advanced stage disease, metastatic sites are treated with platinum-based combination chemotherapy (Dowell 2010). SCNCC have a reported 5-year survival of 36% (Sevin et al. 1996). Periodic full body imaging with CT or PET/CT to evaluate neurological symptoms, mental status changes or pulmonary metastases are necessary. Th e histopathology report is vital for the appropriate management and off ers relief to the suff ering woman. For the gynaecologist and oncologist, a lapse in diagnosis or treatment can prove disastrous. Th is case is reported for its rarity in the realms of cervical malignancy, as well as the unusual site for occurrence of a leiomyoma, between the vagina and rectum, and the concurrent presence of both.
Coevolution between Parasite Virulence and Host Life‐History Traits

Epidemiological models generally explore the evolution of parasite life‐history traits, namely, virulence and transmission, against a background of constant host life‐history traits. However, life‐history models have predicted the evolution of host traits in response to parasitism. The coevolution of host and parasite life‐history traits remains largely unexplored. We present an epidemiological model, based on resource allocation theory, that provides an analysis of the coevolution between host reproductive effort and parasite virulence. This model allows for hosts with either a fixed (i.e., genetic) or conditional (i.e., a phenotypically plastic) response to parasitism. It also considers superinfections. We show that parasitism always favors increased allocation to host reproduction, but because of epidemiological feedbacks, the evolutionarily stable host reproductive effort does not always increase with parasite virulence. Superinfection drives the evolution of parasite virulence and acts on the evolution of the host through parasite evolution, generally leading to higher host reproductive effort. Coevolution, as opposed to cases where only one of the antagonists evolves, may generate correlations between host and parasite life‐history traits across environmental gradients affecting the fecundity or the survival of the host. Our results provide a theoretical framework against which experimental coevolution outcomes or field observations can be contrasted.
Nitrate Sensing and Metabolism Modulate Motility, Biofilm Formation, and Virulence in Pseudomonas aeruginosa

ABSTRACT Infection by the bacterial opportunist Pseudomonas aeruginosa frequently assumes the form of a biofilm, requiring motility for biofilm formation and dispersal and an ability to grow in nutrient- and oxygen-limited environments. Anaerobic growth by P. aeruginosa is accomplished through the denitrification enzyme pathway that catalyzes the sequential reduction of nitrate to nitrogen gas. Mutants mutated in the two-component nitrate sensor-response regulator and in membrane nitrate reductase displayed altered motility and biofilm formation compared to wild-type P. aeruginosa PAO1. Analysis of additional nitrate dissimilation mutants demonstrated a second level of regulation in P. aeruginosa motility that is independent of nitrate sensor-response regulator function and is associated with nitric oxide production. Because motility and biofilm formation are important for P. aeruginosa pathogenicity, we examined the virulence of selected regulatory and structural gene mutants in the surrogate model host Caenorhabditis elegans. Interestingly, the membrane nitrate reductase mutant was avirulent in C. elegans, while nitrate sensor-response regulator mutants were fully virulent. The data demonstrate that nitrate sensing, response regulation, and metabolism are linked directly to factors important in P. aeruginosa pathogenesis.
Goals as Reference Points

We argue that goals serve as reference points and alter outcomes in a manner consistent with the value function of Prospect Theory (Kahneman & Tversky, 1979; Tversky & Kahneman, 1992). We present new evidence that goals inherit the properties of the value function-not only a reference point, but also loss aversion and diminishing sensitivity. We also use the value function to explain previous empirical results in the goal literature on affect, effort, persistence, and performance.
Differences Across and Within Countries in Instructional Time and Achievements in Math, Science, and Reading: A Causal Link?

There are large differences across countries in instructional time in schooling institutions. Can these differences explain some of the differences across countries in pupils‘ achievements in different subjects? While research in recent years provides convincing evidence about the effect of several inputs in the education production function, there is limited evidence on the effect of classroom instructional time. Such evidence is of policy relevance in many countries, and it became very concrete recently as President Barrack Obama announced the goal of extending the school week and year as a central objective in his proposed education reform for the US. In this paper, I estimate the effects of instructional time on students‘ academic achievement in math, science and reading. I estimate nonlinear instructional time effects controlling for unobserved heterogeneity of both pupils and schools. The evidence from a sample of 15 year olds from over fifty countries that participated in PISA 2006 consistently shows that instructional time has a positive and significant effect on test scores. The effect is large relative to the standard deviation of the within pupil test score distribution. I obtain similar evidence from a sample of 10 and 13 year olds in Israel. The OLS results are highly biased upward but the within student estimates are very similar across groups of developed and middle-income countries and age groups. Evidence from primary and middle schools in Israel is similar to the evidence from OECD countries. However, the estimated effect of instructional time in the sample of developing countries is much lower than the effect size in the developed countries. I also show that the productivity of instructional time is higher in countries that implemented school accountability measures, and in countries that give schools autonomy in hiring and firing teachers.
Novel mechatronics design for a robotic fish

This paper presents a novel mechatronics design for a 3D swimming robotic fish, namely MT1 (Mechanical Tail) robotic fish. It has a novel tail structure which uses only one motor to generate fish-like swimming motion using C-bends tail shapes. This design enables MT1 to become the first small size robotic fish (<0.5m in length) and be able to dive over 3 meters deep in water. An effective control method with only 5 parameters is proposed to control its 3D swimming behaviours. Experimental results are presented to show the feasibility and good performance of the proposed control algorithms.
Analysis of the Effects of Cannabinoids on Synaptic Transmission between Basket and Purkinje Cells in the Cerebellar Cortex of the Rat

The hypothesis of the present work was that activation of CB1 cannabinoid receptors inhibits GABAergic neurotransmission between basket and Purkinje cells in the cerebellar cortex. The aim was to test this hypothesis under near-physiological conditions. Action potentials of basket cells and spontaneous inhibitory postsynaptic currents (sIPSCs) in synaptically coupled Purkinje cells were recorded simultaneously in rat brain slices. The cannabinoid agonists (R)-(+)-[2,3-dihydro-5-methyl-3-[(morpholinyl) methyl] pyrrolo[1,2,3-de]-1,4-benzoxazinyl]-(1-naphthalenyl)methanone mesylate (WIN 55212-2) and (-)-cis-3-[2-hydroxy-4-(1,1-dimethylheptyl)-phenyl]-trans-4-(3-hydroxy-propyl)-cyclohexanol (CP55940) decreased the amplitude of sIPSCs occurring simultaneously with basket cell action potentials and lowered the success rate of synaptic transmission. These effects were prevented by the CB1 receptor antagonist N-piperidino-5-(4-chlorophenyl)-1-(2,4-dichloro-phenyl)-4-methyl-3-pyrazole-carboxamide (SR141716). Depolarization of Purkinje cells also led to suppression of neurotransmission; prevention of this suppression by CP55940 and SR141716 indicates that endocannabinoids released from Purkinje cells were involved. WIN 55212-2 lowered the amplitude of autoreceptor currents recorded in basket cells (autoreceptor currents are due to the action of GABA released from axon terminals on GABAA autoreceptors of the same axon terminals); this is novel proof of the presynaptic action of cannabinoids. Autoreceptor current experiments also indicated that endogenous cannabinoids are not released by basket cell axon terminals. A presynaptic action is additionally supported by the observation that WIN 55212-2 lowered the frequency of miniature IPSCs recorded in the presence of tetrodotoxin and the calcium ionophore ionomycin. In conclusion, activation of CB1 receptors by exogenous cannabinoids and by endogenous cannabinoids released by Purkinje cells presynaptically inhibits GABAergic neurotransmission between basket and Purkinje cells. This was demonstrated under near-physiological conditions: transmitter release was elicited by action potentials generated by spontaneously firing intact presynaptic neurons.
Timing and style of Late Quaternary glaciation in northeastern Tibet

Glacial successions in the Anyemaqen and Nianbaoyeze Mountains of northeastern Tibet are reassessed and new glacial chronologies are presented for these regions. Cosmogenic radionuclide and optically stimulated luminescence dating indicates that two glacial advances occurred in marine isotope stage (MIS)-3 and MIS-2. In the Anyemaqen Mountains, a third advance occurred in the Early Holocene. We suggest that glaciation was synchronous in the Anyemaqen and Nianbaoyeze Mountains, as well as in other glaciated areas of Tibet and the Himalaya that are influenced by the Asian monsoon. The maximum extent of glaciation occurred early in the last glacial cycle (MIS-3) during a time of increased insolation when the monsoon intensified and supplied abundant precipitation, as snow at high altitude, to feed high-altitude glaciers. This suggests that precipitation, as snow, is fundamental in controlling glaciation in these regions. However, the occurrence of glacial advances during the insolation minimum of MIS-2 suggests that, despite reduced precipitation at this time, the annual temperatures were cold enough to maintain positive glacier mass balances. The numerically defined chronologies for the Anyemaqen and Nianbaoyeze Mountains presented here provide a framework for comparing glacial advances in other parts of high Asia.