Miracle-dz/UniFAR-FTUs huggingface dataset:
[Characterization of the rpoB gene mutations in clinical isolates of rifampicin-resistant Mycobacterium tuberculosis].

OBJECTIVES Characterization and frequency of the rpoB gene mutations associated with rifampin resistance in Mycobacterium tuberculosis clinical isolates in Sevilla. METHODS Characterization of rpoB mutations in 21 rifampicin-resistant strains of M. tuberculosis isolated during a three-year period (1994-1996) by three different molecular methods: a nonradioactive Single-strand conformation polymorphism (SSCP) analysis, DNA sequence analysis and a commercial method the line probe assay InnoLiPA. RESULTS Five distinct rpoB mutations were identified. Ser531-->Leu mutation was detected in 14 strains (66.7%), H526-->Asp in 3 strains (14.3%), Ans512-->Ser in 1 strain (4.8%), Glu513-->Leu in 1 strain (4.8%). A nine nucleotide deletion (codon 510-513) was found in one strain (4.8%) while in the remaining resistant strain (4.8%) no mutation was detected. CONCLUSIONS The frequency of the different mutations found in the rpoB gene, associated with rifampicin resistance in Mycobacterium tuberculosis clinical isolates in Seville, are similar to those previously reported. However, two new mutations has been detected: a nine nucleotide deletion (codon 510-513), and the Asn512-->Ser point mutation. The characterization of the mutations in the rpoB gene could serve as epidemiological marker for the rifampicin resistant clinical isolates of M. tuberculosis.
Regulatory Overlap and Functional Redundancy among Bacillus subtilis Extracytoplasmic Function σ Factors

ABSTRACT Bacillus subtilis encodes seven extracytoplasmic function (ECF) σ factors that regulate partially overlapping regulons related to cell envelope homeostasis and antibiotic resistance. Here, we investigated their physiological role by constructing a mutant set of single, double, triple, and quadruple ECF σ factor deletions in the undomesticated B. subtilis strain NCIB3610. This mutant set was subsequently screened for defects in motility, multicellular differentiation, and sensitivity to more than 200 chemicals by using Phenotype MicroArrays. A quadruple mutant strain, harboring deletions of the sigV, sigY, sigZ, and ylaC gene, behaved indistinguishably from the wild-type strain, indicative of either regulatory redundancy or very specific functions of these four ECF σ factors. In contrast, a triple mutant, inactivated for the sigM, sigW, and sigX genes (but none of the corresponding double mutants), showed a biphasic growth behavior and a complete loss of multicellular differentiation, as judged by both colony formation and the inability to form a pellicle. This triple mutant also displayed a greatly increased sensitivity to detergents and several cell wall antibiotics including β-lactams, polymyxin B, and d-cycloserine. In several cases, these antibiotic-sensitive phenotypes are significantly enhanced in the triple mutant strain relative to strains lacking only one or two σ factors.
Prevalence of and factors associated with head impact during falls in older adults in long-term care

Background: Falls cause more than 60% of head injuries in older adults. Lack of objective evidence on the circumstances of these events is a barrier to prevention. We analyzed video footage to determine the frequency of and risk factors for head impact during falls in older adults in 2 long-term care facilities. Methods: Over 39 months, we captured on video 227 falls involving 133 residents. We used a validated questionnaire to analyze the mechanisms of each fall. We then examined whether the probability for head impact was associated with upper-limb protective responses (hand impact) and fall direction. Results: Head impact occurred in 37% of falls, usually onto a vinyl or linoleum floor. Hand impact occurred in 74% of falls but had no significant effect on the probability of head impact (p = 0.3). An increased probability of head impact was associated with a forward initial fall direction, compared with backward falls (odds ratio [OR] 2.7, 95% confidence interval [CI] 1.3–5.9) or sideways falls (OR 2.8, 95% CI 1.2–6.3). In 36% of sideways falls, residents rotated to land backwards, which reduced the probability of head impact (OR 0.2, 95% CI 0.04–0.8). Interpretation: Head impact was common in observed falls in older adults living in long-term care facilities, particularly in forward falls. Backward rotation during descent appeared to be protective, but hand impact was not. Attention to upper-limb strength and teaching rotational falling techniques (as in martial arts training) may reduce fall-related head injuries in older adults.
Bank Income Smoothing, Institutions and Corruption

This study investigates bank income smoothing, focusing on the effect of corruption on the extent of income smoothing by African banks. I find that banks use loan loss provisions to smooth positive (non-negative) earnings particularly in the post-2008 crisis period and this behaviour is reduced by strong investor protection. Also, I find that banks in highly corrupt environments smooth their positive (non-negative) earnings as opposed to smoothing the entire profit distribution. Finally, cross-country variation in bank income smoothing is observed. The findings have implications.
Vehicle to Grid — Monte Carlo simulations for optimal Aggregator strategies

Previous work has shown that it could be profitable on some control markets to use Plug-in Hybrid Electric Vehicles (PHEV) as control power resources. This concept, where battery driven vehicles such as PHEVs provide ancillary service to the grid is commonly referred to as Vehicle to Grid (V2G). The idea is to sell the capacity and energy of the parked PHEVs on the control market. Due to the fact that cars on average are parked 92% of the day, the availability of this capacity could be very high, even though it will be highly dependent on commuting patterns in peak hours. However, as each PHEV has a very small capacity from a grid perspective, it is necessary to implement an aggregating control system, managing a large number of vehicles. This paper presents strategies for an Aggregator to fulfill control bids on the German control markets. These strategies are tested with respect to reliability, efficiency and profitability in a Monte Carlo simulation model. The model is based on available data on the distributions of commuting departure times and travel distances, as well as average driving power consumption, PHEV battery capacities and the market constraints of the secondary control market in Germany.
Quantitative EEG Findings in Different Stages of Alzheimer’s Disease

Summary: Although quantitative EEG (q-EEG) has been used in Alzheimer’s disease (AD), q-EEG changes in AD are complex because of the progressive nature of this disease. The topographical spectral power and occipital peak frequency (OPF) were compared among elderly controls, patients with mild cognitive impairment (MCI), and patients with four stages of AD. In AD patients, except those with a Clinical Dementia Rating Scale (CDR) score of 0.5, OPF was lower than that of elderly controls. Compared with elderly controls, the left anterior alpha spectral power was reduced in CDR 0.5; both posterior theta spectral powers were increased and all alpha spectral powers were reduced in CDR 1; all alpha and beta spectral powers were reduced and theta spectral power was increased in CDR 2; and all alpha and beta spectral powers were reduced and all delta and theta spectral powers were increased in CDR 3. Patients with MCI exhibited a reduction in both centrotemporal, posterior delta and left anterior, centrotemporal theta fields. The Mini-Mental State Examination (MMSE) score was related to left OPF, right posterior delta and left anterior theta spectral power, in that order. This study suggests that q-EEG in MCI shows nonoverlapping features between controls and AD patients, and AD patients show dynamic changes as the disease progresses. Finally, the left OPF is the parameter most significantly correlated with MMSE score.
The influence of traffic on air quality in an urban neighborhood: a community-university partnership.

OBJECTIVES We evaluated the spatial and temporal patterns of traffic-related air pollutants in an urban neighborhood to determine factors contributing to elevated concentrations and to inform environmental justice concerns. METHODS In the summer of 2007, we continuously monitored multiple air pollutants at a community site in the Mission Hill neighborhood of Boston, Massachusetts, and local high school students conducted mobile continuous monitoring throughout the neighborhood. We used regression models to explain variability in concentrations, considering various attributes of traffic, proximity to major roadways, and meteorology. RESULTS Different attributes of traffic explained variability in fixed-site concentrations of ultrafine particles, fine particulate matter, and black carbon, with diurnal patterns and meteorological effects indicative of a greater local effect on ultrafine particles and black carbon. Mobile monitoring demonstrated that multiple traffic variables predict elevated levels of ultrafine particles, with concentrations of ultrafine particles decreasing by 50% within 400 meters of 2 major roadways. CONCLUSIONS Unlike fine particulate matter, ultrafine particles demonstrate significant spatial and temporal variability within an urban neighborhood, contributing to environmental justice concerns, and patterns can be well characterized with a community-based participatory research design.
Outcomes of flexible ureteroscopy and laser fragmentation for treatment of large renal stones with and without the use of ureteral access sheaths: Results from a university hospital with a review of literature

Abstract Objective. The aim of this study was to analyse prospective data on flexible ureteroscopy and laser fragmentation (FURSL) of large stones (> 2 cm) to assess whether a ureteral access sheath (UAS) is necessary for the treatment of large renal stones. Materials and methods. Between March 2012 and October 2014, 43 patients with large stones underwent FURSL. Data were collected on a prospective database for patient demographics, stone characteristics and outcomes of FURSL with and without a UAS. Results. There were 27 men and 16 women with a mean age of 54 years (range 7–84 years). The cumulative stone diameter was 2.92 cm (range 2–5 cm), with an overall stone-free rate (SFR) of 83.7%. A total of 68 procedures was needed (average 1.58 procedures/patient). The overall complication rate was 8.8% (n = 6); these were Clavien class II complications associated with urinary tract infections treated with additional antibiotics. UAS was not used in 28 procedures (41.2%). Comparing outcomes in those who had a UAS versus those who did not, there were no statistical differences in SFR, complication rate or average number of procedures per patients. Conclusion. Use of a UAS does not make any difference to the SFR or complication rate for FURSL in large stones (> 2 cm) and may not be routinely needed in all cases.
Security Smells in Android

The ubiquity of smartphones, and their very broad capabilities and usage, make the security of these devices tremendously important. Unfortunately, despite all progress in security and privacy mechanisms, vulnerabilities continue to proliferate. ,,Research has shown that many vulnerabilities are due to insecure programming practices. However, each study has often dealt with a specific issue, making the results less actionable for practitioners. ,,To promote secure programming practices, we have reviewed related research, and identified avoidable vulnerabilities in Android-run devices and the security code smells that indicate their presence. In particular, we explain the vulnerabilities, their corresponding smells, and we discuss how they could be eliminated or mitigated during development. Moreover, we develop a lightweight static analysis tool and discuss the extent to which it successfully detects several vulnerabilities in about 46 000 apps hosted by the official Android market.
Identification of Escherichia coli and Shigella Species from Whole-Genome Sequences

ABSTRACT Escherichia coli and Shigella species are closely related and genetically constitute the same species. Differentiating between these two pathogens and accurately identifying the four species of Shigella are therefore challenging. The organism-specific bioinformatics whole-genome sequencing (WGS) typing pipelines at Public Health England are dependent on the initial identification of the bacterial species by use of a kmer-based approach. Of the 1,982 Escherichia coli and Shigella sp. isolates analyzed in this study, 1,957 (98.4%) had concordant results by both traditional biochemistry and serology (TB&S) and the kmer identification (ID) derived from the WGS data. Of the 25 mismatches identified, 10 were enteroinvasive E. coli isolates that were misidentified as Shigella flexneri or S. boydii by the kmer ID, and 8 were S. flexneri isolates misidentified by TB&S as S. boydii due to nonfunctional S. flexneri O antigen biosynthesis genes. Analysis of the population structure based on multilocus sequence typing (MLST) data derived from the WGS data showed that the remaining discrepant results belonged to clonal complex 288 (CC288), comprising both S. boydii and S. dysenteriae strains. Mismatches between the TB&S and kmer ID results were explained by the close phylogenetic relationship between the two species and were resolved with reference to the MLST data. Shigella can be differentiated from E. coli and accurately identified to the species level by use of kmer comparisons and MLST. Analysis of the WGS data provided explanations for the discordant results between TB&S and WGS data, revealed the true phylogenetic relationships between different species of Shigella, and identified emerging pathoadapted lineages.
2'-NH2-MPTP in Swiss Webster mice: evidence for long-term (6-month) depletions in cortical and hippocampal serotonin and norepinephrine, differential protection by selective uptake inhibitors or clorgyline and functional changes in central serotonin neurotransmission.

The i.p. administration of 1-methyl-4-(2'-aminophenyl)-1,2,3,6-tetrahydropyridine (2'-NH2-MPTP; 4 x 20 mg/kg) to Swiss Webster mice caused substantial decreases in cortical and hippocampal 5-hydroxytryptamine (5-HT), 5-hydroxyindoleacetic acid and norepinephrine (NE) measured 1 week post-treatment. Compared with the authors' previously reported results in C57BL/6 mice, these effects were significantly greater in hippocampus (80-90% vs. 60%) and of a similar magnitude in frontal cortex (60-75%). A long-term study showed that cortical and hippocampal 5-HT, 5-hydroxyindoleacetic acid and NE were still decreased 40% to 50% 6 months after treatment. Regional brain dopamine was essentially unchanged during the 6-month period. Pretreatment with the 5-HT-selective uptake inhibitors, fluoxetine or paroxetine, or with the NE-selective uptake inhibitor, desipramine, prevented decreases in cortical and hippocampal 5-HT and NE, respectively, 3 weeks after 2'-NH2-MPTP (4 x 20 mg/kg). In addition, pretreatment with the monoamine oxidase type-A inhibitor, clorgyline, also prevented the more modest decreases in 5-HT and NE caused by 4 x 15 mg/kg 2'-NH2-MPTP. Selegiline, a monoamine oxidase-B inhibitor, did not provide similar protection. Lastly, 2'-NH2-MPTP administered 3 weeks earlier, abolished hypothermia caused by the serotonin agonist, m-chlorophenylpiperazine, which provided preliminary evidence for an associated functional change in the central serotonergic system. Together, these data suggest that 2'-NH2-MPTP is a novel agent capable of producing long-lasting depletions in forebrain 5-HT and NE but not dopamine in two different strains of mice by some mechanisms that resemble those of the parent dopamine-depleting neurotoxin, MPTP.
Prediction of Severe Acute Pancreatitis at Admission to Hospital Using Artificial Neural Networks

Background/Aims: Artificial neural networks (ANNs) are non-linear pattern recognition techniques, which can be used as a tool in medical decision-making. The aim of this study was to construct and validate an ANN model for early prediction of the severity of acute pancreatitis (AP). Methods: Patients treated for AP from 2002 to 2005 (n = 139) and from 2007 to 2009 (n = 69) were analyzed to develop and validate the ANN model. Severe AP was defined according to the Atlanta criteria. Results: ANNs selected 6 of 23 potential risk variables as relevant for severity prediction, including duration of pain until arrival at the emergency department, creatinine, hemoglobin, alanine aminotransferase, heart rate, and white blood cell count. The discriminatory power for prediction of progression to a severe course, determined from the area under the receiver-operating characteristic curve, was 0.92 for the ANN model, 0.84 for the logistic regression model (p = 0.030), and 0.63 for the APACHE II score (p < 0.001). The numbers of correctly classified patients for a sensitivity of 50 and 75% were significantly higher for the ANN model than for logistic regression (p = 0.002) and APACHE II (p < 0.001). Conclusion: The ANN model identified 6 risk variables available at the time of admission, including duration of pain, a finding not being presented as a risk factor before. The severity classification developed proved to be superior to APACHE II.
Can Johnny finally encrypt?: evaluating E2E-encryption in popular IM applications

Recently, many popular Instant-Messaging (IM) applications announced support for end-to-end encryption, claiming confidentiality even against a rogue operator. Is this, finally, a positive answer to the basic challenge of usable-security presented in the seminal paper, 'Why Johnny Can't Encrypt'? Our work evaluates the implementation of end-to-end encryption in popular IM applications: WhatsApp, Viber, Telegram, and Signal, against established usable-security principles, and in quantitative and qualitative usability experiments. Unfortunately, although participants expressed interest in confidentiality, even against a rogue operator, our results show that current mechanisms are impractical to use, leaving users with only the illusion of security. Hope is not lost. We conclude with directions which may allow usable end-to-end encryption for IM applications.
A new epidemic focus of zoonotic cutaneous leishmaniasis in central Iran

Background Reports from the health center of Yazd province of increasing cutaneous leishmaniasis (CL) cases led us to carry out an epidemiological study using standard techniques in Ardakan County, central Iran, during 2001. Patients and Methods Data was collected on the prevalence of scars and ulcers over a period of 14 months among 621 households in three villages around Ardakan County. Smears were prepared by scraping the edges of the ulcers. We collected the same data on all school children aged 7 to 11 years old in the area. To determine the reservoir host of the disease, rodents and dogs were caught and examined. Sandflies were collected biweekly from indoor and outdoor locations in the study area, and then identified. Parasites isolated from human and rodents were characterized by RAPD-PCR technique. Results The prevalence of scars and ulcers were 30.4% and 24.6%, respectively, in 3024 individuals in the three villages. Individuals 10 to 14 years of age were the most highly infected age group, with a rate of 28.4%. Males and females were equally infected. Examination of 892 students in primary schools showed a rate of 22.9% for scars and 23.7% for ulcers. Meriones libycus (42.2%) and Rhombomys opimus (57.8%) were present around the villages. Both were infected with Leishmania. Three of 19 M. libycus (15.7%) and 3 out of 26 R. opimus (11.5%) had positive results. The active season of sandflies was late April to late November. Phlebotomus papatasi and Sergentomyia sintoni were the dominant species indoors and outdoors. Natural leptomonad infection was found in P. caucasicus and S. sintoni from gerbil and Jird burrows. Conclusion Based on this survey, there is an epidemic of zoonotic CL in the area, with Leishmania major as the agent, M. libycus and R. opimus as the reservoir hosts, and most probably Phlebotomus papatasi as the vector because about 77% of indoor sandflies were of this species.
Identification and analysis of long‐range electrostatic effects in proteins by computer modeling:Aspartate transcarbamylase

While ion pairs are readily identified in crystal structures, longer range electrostatic interactions cannot be identified from the three‐dimensional structure alone. These interactions are likely to be important in large, multisubunit proteins that are regulated by allosteric interactions. In this paper, we show that these interactions are readily detected by electrostatic modeling, using, as an example, unliganded Escherichia coli aspartate transcarbamylase, a widely studied allosteric enzyme with 12 subunits and a molecular weight of 310 kD. The Born, dipolar, and site‐site interaction terms of the free energy of protonation of the 810 titratable sites in the holoenzyme were calculated using the multigrid solution of the nonlinear Poisson‐Boltzmann equation. Calculated titration curves are in good agreement with experimental titration curves, and the structural asymmetry observed in the crystal structure is readily apparent in the calculated free energies and pK1/2 values. Most of the residues with pK1/2 values that differ substantially from those of model compounds are buried in the low dielectric medium of the protein, particularly at the intersubunit interfaces. The dependence of the site‐site interaction free energies on distance is complex, with a steep dependence at distances less than 5 Å and a more shallow dependence at longer distances. Interactions over distances of 6 to 15 Å require a bridging residue and are often not apparent in the structure. The network of interactions between ionizable groups extends across and between subunits and provides a potential mechanism for transmitting long‐range structural effects and allosteric signals. © 1996 Wiley‐Liss, Inc.
Effect of temperature on the transmission of orbiviruses by the biting midge, Culicoides sonorensis

Abstract The influence of temperature on the likelihood of Culicoides sonorensis Wirth & Jones (Diptera: Ceratopogonidae) transmitting African horse sickness virus (AHSV) serotypes 4 and 6, bluetongue virus (BTV) serotypes 10 and 16 and epizootic haemorrhagic disease of deer virus (EHDV) serotype 1 was investigated. Extrinsic incubation periods (EIP), vector competence and vector survival were determined at 15, 20, 25 and 30°C. The effect of humidity on vector survival was also investigated by maintaining adult C. sonorensis at 40, 75 and 85% r.h. at each temperature. Higher temperatures were associated with a shorter EIP for all virus serotypes except AHSV6, to which C. sonorensis was orally refractory, increased vector competence for AHSV4 and EHDV1, but not for BTV10 or BTV16, and a reduction in vector survival. Humidity interacted with temperature in influencing vector survival, such that at low temperatures, lower humidity (40 and 75% r.h.) was detrimental for survival (up to 18% reduction in longevity), whereas at high temperatures, high humidity (85% r.h.) was detrimental (up to 36% reduction in longevity). In general, the transmission potential of C. sonorensis for AHSV4, EHDV1, BTV10 and BTV16 was greater at higher temperatures, because although vector survival was reduced, this was more than compensated for by the accompanying decrease in duration of the EIP.