Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of Plasmid-Borne dfrA14 Trimethoprim Resistance Gene in Shigella sonnei

The most common mechanism of trimethoprim (TMP)-resistance is the acquisition of dihydrofolate reductase enzyme resistant to this drug. Previous molecular characterization of TMP-genes resistance in Chilean isolates of Shigella sonnei searching for dfrA1 and dfrA8, showed solely the presence of dfrA8 (formerly dhfrIIIc). However, these genetic markers were absent in S. sonnei strains further isolated during an outbreak in 2009. To identify the TMP-resistance gene in these strains, a genomic DNA library from a TMP-resistant (TMPR) S. sonnei representative strain for the outbreak was used to clone, select and identify a TMP-resistance marker. The TMPR clone was sequenced by primer walking, identifying the presence of the dfrA14 gene in the sul2-strA'-dfrA14-‘strA-strB gene arrangement, harbored in a native 6779-bp plasmid. The same plasmid was isolated by transforming with a ~4.2 MDa plasmid extracted from several TMPR S. sonnei strains into Escherichia coli. This plasmid, named pABC-3, was present only in dfrA14-positive strains and was homologous to a previously described pCERC-1, but different due to the absence of an 11-bp repetitive unit. The distribution of dfrA1, dfrA8, and dfrA14 TMP-resistance genes was determined in 126 TMPR S. sonnei isolates. Most of the strains (96%) carried only one of the three TMP-resistance genes assessed. Thus, all strains obtained during the 2009-outbreak harbored only dfrA14, whereas, dfrA8 was the most abundant gene marker before outbreak and, after the outbreak dfrA1 seems have appeared in circulating strains. According to PFGE, dfrA14-positive strains were clustered in a genetically related group including some dfrA1- and dfrA8-positive strains; meanwhile other genetic group included most of the dfrA8-positive strains. This distribution also correlated with the isolation period, showing a dynamics of trimethoprim genetic markers prevalent in Chilean S. sonnei strains. To our knowledge, dfrA14 gene associated to a small non-conjugative plasmid was detected for the first time in Shigella. Apparently, the strain causing the outbreak must have been introduced, changing drastically the genetic distribution of trimethoprim resistance in Chilean S. sonnei strains.
Convergence between Lesion-Symptom Mapping and Functional Magnetic Resonance Imaging of Spatially Selective Attention in the Intact Brain

The parietal regions implicated in spatially selective attention differ between patient lesion studies and functional imaging of the intact brain. We aimed to resolve this discordance. In a voxel-based lesion-symptom mapping study in 20 ischemic stroke patients, we applied the same cognitive subtraction approach as in 23 healthy volunteers who underwent functional magnetic resonance imaging (fMRI) using identical tasks and stimuli. An instructive central cue directed attention to one visual quadrant. After a brief delay, a grating appeared in that quadrant together with an irrelevant grating in an uncued quadrant. Subjects had to discriminate the orientation of the grating in the cued quadrant. Patients with a right inferior parietal lesion were significantly more impaired during contralesional versus ipsilesional orienting when stimuli were bilateral and symmetrical than when stimuli occupied diagonally opposite quadrants or two quadrants within the same hemifield. In one area, the lesion-volume map overlapped with the activity map obtained in healthy volunteers: the lower bank of the middle third of the right intraparietal sulcus (IPS). In an additional 37 healthy fMRI subjects, we disentangled the effects of symmetry, bilaterality, and spatial configuration between stimuli on activity in the volume of overlap. Only the axis of configuration between stimuli had a significant effect, with highest activity when the configuration axis was horizontal. This constitutes converging evidence from patients and cognitively intact subjects that the lower bank of the middle third of the right IPS critically contributes to attentive selection between competing stimuli in a spatially anisotropic manner.
Operations Research Techniques for Scheduling Chile's Second Division Soccer League

In this paper, we use operations research (OR) techniques to schedule the Second Division of the Chilean professional soccer league. The solution must satisfy a series of conditions requested by league officials. Because the teams generally travel long distances by bus, geographical restrictions are particularly important. We specify the scheduling problem and solve it using an integer linear programming (ILP) model that defines when and where each match is played, subject to constraints. For the most difficult instances, we formulate a second ILP model that generates home-away patterns and assigns them to the teams; we then run the model, which determines the match schedule. Chilean league officials have successfully used the models to schedule all five Second Division tournaments between 2007 and 2010, replacing the random scheduling methodology that they used previously. Since 2007, the two formulations have been adapted to various formats with which the Second Division has experimented; these include a quadruple round robin and a two-phase tournament with zonal and national phases. The application we present is one of a number of such projects that the authors and their colleagues developed over the past few years, and it represents an expansion of the use of OR techniques for managing tasks in Chilean soccer.
The Effect of Dietary Restriction on PhIP-Induced Mutation in the Distal Colon and B[a]P- and ENU-Induced Mutation in the Liver of the Rat

Abstract: A reduction in dietary intake has been shown to significantly increase the lifespan of rodents, lower the incidence of tumors, and reduce DNA damage. The objective of this study was to determine whether dietary restriction (DR) reduced the frequency of mutation induced by two environmentally relevant metabolically activated mutagens and one direct-acting mutagen in the lacI transgene of male and female Big Blue® rats. Both male and female rats were maintained on either an ad libitum (AL) or a 40%-reduced diet for 22 wk. The mutagenicity of a 100-mg/kg intraperitoneal injection with 2-amino-1-methyl-6-pheny-imidazo[4,5-b] pyridine (PhIP), benzo[a]pyrene (B[a]P), and N-ethyl-N- nitrosourea (ENU) was determined in the colon or liver. The results indicated that DR did not significantly alter the PhIP-induced mutant frequency in male or female colons. DR completely prevented mutagenicity induced by B[a]P in the female liver (2.6 ± 0.6 × 10-5 vs 10.9 ± 5.8 × 10-5 in AL females), yet increased the induced frequency in male livers (16.3 ± 3.7 × 10-5 vs 10.6 ± 1.5 × 10-5 in AL male livers). Although there was no difference in mutation frequency in the liver between AL and DR females treated with ENU, there was approximately a 40% decrease in induced frequency in DR males compared with AL males. These results indicate that a reduction in dietary intake has no preventive effect against PhIP-induced mutation in the colon, but has sex-dependent protective effects against B[a]P- and ENU-induced mutation in the liver.
Diffusion-weighted magnetic resonance imaging in symptomatic vertebrobasilar atherosclerosis and dissection.

BACKGROUND Acute multiple brain infarction (AMBI) pattern on diffusion-weighted imaging (DWI) is associated with arterial and cardiac sources of embolism. The DWI characteristics of patients with stroke due to vertebrobasilar arterial dissection and atherosclerotic disease have not been reported in detail. OBJECTIVE To describe the DWI stroke patterns in patients with posterior circulation occlusive disease to determine mechanisms of ischemia. DESIGN Retrospective analysis of infarct patterns in patients with symptomatic vertebrobasilar disease. SETTING Large community-based teaching hospital. PATIENTS Patients admitted with stroke due to vertebrobasilar disease were identified retrospectively. Patients were included if DWI was obtained within 7 days of symptom onset. MAIN OUTCOME MEASURE Infarct patterns were analyzed according to established templates of vascular territories. RESULTS Eleven patients with vertebral dissection and 39 patients with atherothrombosis were identified. An AMBI pattern was present in 8 (72%) of 11 patients with arterial dissections and 25 (64%) of 39 patients with atherosclerotic disease (P = .48). Distal embolism to the terminal branches of the basilar artery occurred with equal frequency in both groups and was found in half of all cases. Isolated thalamic infarction did not occur. Pontine infarction was noted in 2 (18%) of 11 patients with dissections and 18 (46%) of 39 patients with atherosclerosis (P = .09). Cerebellar border zone involvement was found in 14 (36%) of 39 patients with atherosclerosis and 4 (37%) of 11 patients with dissections (P = .6). CONCLUSIONS Large arterial disease is frequently associated with AMBI in the posterior circulation. The incidence of AMBI was comparable to that reported in the anterior circulation. This DWI study supports the importance of embolism as the main mechanism of infarction in patients with vertebrobasilar occlusive disease. On the basis of our experience, large-vessel vertebrobasilar disease rarely causes isolated small-vessel thalamic infarction.
Muscle function and functional ability improves more in community-dwelling older women with a mixed-strength training programme.

BACKGROUND Supervised training can reach a limited number of elderly people. OBJECTIVE To determine the impact of a 1-year mixed-strength training programme on muscle function (MF), functional ability (FA) and physical activity (PA). SETTING Twice-a-week hospital-based exercise classes and a once-a-week home session. PARTICIPANTS twenty-eight healthy community-dwelling men and women on the training programme and 20 controls aged over 75 years. METHODS Training with two multi-gym machines for the lower limbs at 60% of the repetition maximum (1RM). At-home subjects used elastic bands. MEASUREMENTS Maximum isometric strength of knee extensors (KE), ankle plantar flexors (PF), leg extensor power (LEP), functional reach (FR), chair rise 1 (CR1) and 10 times (CR10), bed rise (BR), six-minute walking test (6MWT), stair climbing (SC), get-up-and-go (GU&G), one-leg standing (1LS). PA was assessed with the Paqap questionnaire. RESULTS Women were significantly weaker than men at baseline: -47% for KE and -59% for PF. Training induced significant gains in MF and FA in the training females; males improved significantly only in FA. PA levels increased non-significantly (2%) in all of the training group. CONCLUSIONS Long-term mixed-strength programmes can improve MF and FA in elderly females, and FA in elderly males.
The Word Reading Test of Effort in Adult Learning Disability: A Simulation Study

The Word Reading Test (WRT) was designed to detect effort problems specific to a learning disability sample. The WRT and the Word Memory Test (WMT) were administered to two simulator and normal control groups. The WRT showed excellent receiver operating characteristics (e.g., 90% sensitivity and 100% positive predictive power) and outperformed the WMT in detecting both reading and mental speed simulators. This finding and a double dissociation between reading and speed simulators on WRT errors and reaction time suggested specific effort effects while poor effort of simulators on the WMT suggested general effort effects. Results are supportive of the WRT as a potential effort indicator in learning disability.
A Multiobjective Ant Colony System for Vehicle Routing Problem with Time Windows

This paper proposes a variation of the Multiple Ant Colony System for Vehicle Routing Problem with Time Windows (MACS-VRPTW) algorithm, which is based on an Ant Colony System approach, using two ant colonies to minimize first the number of vehicles and then the total traveled distance. As an improvement, the present work proposes to use a modified version specialized for a multiobjective context, using just one colony to get a set of Pareto optimal solutions considering three objectives at the same time, the number of vehicles, the total traveling time and the total delivery time. Experimental results validate the new approach with very good results when compared to the original MACS-VRPTW.
Dosimetric and microdosimetric study of contrast-enhanced radiotherapy with kilovolt x-rays

Kilovolt x-rays are clearly suboptimal compared to MV photon beams for radiotherapy of deep-seated tumours because of the increased attenuation in tissue, causing a rapid dose fall-off. This picture could change drastically when tumours can be labelled with contrast medium, containing high atomic number elements. This causes a significant dose enhancement to the tumour by exploiting the high cross sections for the photo-electric effect for kV x-rays. In this work, we have investigated the dosimetric and microdosimetric characteristics of kV contrast-enhanced radiation therapy (CERT) for different photon energies, contrast-medium concentrations and types (I and Gd). Two idealized patient treatment plans (head and lung) for irradiation with CT-arc beams were calculated. It is shown that the dose enhancement in tumours can be highly significant (up to about sixfold for realistic 80–120 kVp x-ray spectra and an iodine concentration of 50 mg ml−1) but that dose homogeneity in the tumour depends on photon energy, contrast-medium concentration and type, and irradiation scheme. An attempt to optimize the irradiation scheme is discussed. The microdosimetric study of the dose mean lineal energy shows that radiation quality changes in the contrast-medium-labelled region compared to homogeneous tissue are fairly small and limited to 10%. It is concluded that kV-CERT is a promising radiotherapy technique, provided contrast medium can be delivered reliably to tumours.
Growth optimal portfolios in discrete-time markets under transaction costs

We investigate portfolio selection problem from a signal processing perspective and study how and when an investor should diversify wealth over two assets in order to maximize the cumulative wealth. We construct portfolios that provide the optimal growth in i.i. d. discrete time two-asset markets under proportional transaction costs. As the market model, we consider arbitrary discrete distributions on the price relative vectors, which can also be used to approximate a wide class of continuous distributions. To achieve optimal growth, we use threshold portfolios, where we introduce an iterative algorithm to calculate the expected wealth. Subsequently, the corresponding parameters are optimized using a brute force approach yielding the growth optimal portfolio under proportional transaction costs in i.i. d. discrete-time two-asset markets.
The value of design rationale information

A complete and detailed (full) Design Rationale Documentation (DRD) could support many software development activities, such as an impact analysis or a major redesign. However, this is typically too onerous for systematic industrial use as it is not cost effective to write, maintain, or read. The key idea investigated in this article is that DRD should be developed only to the extent required to support activities particularly difficult to execute or in need of significant improvement in a particular context. The aim of this article is to empirically investigate the customization of the DRD by documenting only the information items that will probably be required for executing an activity. This customization strategy relies on the hypothesis that the value of a specific DRD information item depends on its category (e.g., assumptions, related requirements, etc.) and on the activity it is meant to support. We investigate this hypothesis through two controlled experiments involving a total of 75 master students as experimental subjects. Results show that the value of a DRD information item significantly depends on its category and, within a given category, on the activity it supports. Furthermore, on average among activities, documenting only the information items that have been required at least half of the time (i.e., the information that will probably be required in the future) leads to a customized DRD containing about half the information items of a full documentation. We expect that such a significant reduction in DRD information should mitigate the effects of some inhibitors that currently prevent practitioners from documenting design decision rationale.
The epidemiology of substance use among street children in resource-constrained settings: a systematic review and meta-analysis.

AIMS To compile and analyze critically the literature published on street children and substance use in resource-constrained settings. METHODS We searched the literature systematically and used meta-analytical procedures to synthesize literature that met the review's inclusion criteria. Pooled-prevalence estimates and 95% confidence intervals (CI) were calculated using the random-effects model for life-time substance use by geographical region as well as by type of substance used. RESULTS Fifty studies from 22 countries were included into the review. Meta-analysis of combined life-time substance use from 27 studies yielded an overall drug use pooled-prevalence estimate of 60% (95% CI = 51-69%). Studies from 14 countries contributed to an overall pooled prevalence for street children's reported inhalant use of 47% (95% CI = 36-58%). This review reveals significant gaps in the literature, including a dearth of data on physical and mental health outcomes, HIV and mortality in association with street children's substance use. CONCLUSIONS Street children from resource-constrained settings reported high life-time substance use. Inhalants are the predominant substances used, followed by tobacco, alcohol and marijuana.
Complete Mitochondrial DNA Diversity in Iranians

Due to its pivotal geographical location and proximity to transcontinental migratory routes, Iran has played a key role in subsequent migrations, both prehistoric and historic, between Africa, Asia and Europe. To shed light on the genetic structure of the Iranian population as well as on the expansion patterns and population movements which affected this region, the complete mitochondrial genomes of 352 Iranians were obtained. All Iranian populations studied here exhibit similarly high diversity values comparable to the other groups from the Caucasus, Anatolia and Europe. The results of AMOVA and MDS analyses did not associate any regional and/or linguistic group of populations in the Anatolia/Caucasus and Iran region pointing to close genetic positions of Persians and Qashqais to each other and to Armenians, and Azeris from Iran to Georgians. By reconstructing the complete mtDNA phylogeny of haplogroups R2, N3, U1, U3, U5a1g, U7, H13, HV2, HV12, M5a and C5c we have found a previously unexplored genetic connection between the studied Iranian populations and the Arabian Peninsula, India, Near East and Europe, likely the result of both ancient and recent gene flow. Our results for Persians and Qashqais point to a continuous increase of the population sizes from ∼24 kya to the present, although the phase between 14-24 kya is thought to be hyperarid according to the Gulf Oasis model. Since this would have affected hunter-gatherer ranges and mobility patterns and forced them to increasingly rely on coastal resources, this transition can explain the human expansion across the Persian Gulf region.
Nearest-Neighbor Search on a Time Budget via Max-Margin Trees

Many high-profile applications pose high-dimensional nearest-neighbor search problems. Yet, it still remains difficult to achieve fast query times for state-of-the-art approaches which use multidimensional trees for either exact or approximate search, possibly in combination with hashing approaches. Moreover, a number of these applications only have a limited amount of time to answer nearest-neighbor queries. However, we observe empirically that the correct neighbor is often found early within the tree-search process, while the bulk of the time is spent on verifying its correctness. Motivated by this, we propose an algorithm for finding the best neighbor given any particular time limit, and develop a new data structure, the max-margin tree, to achieve accurate results even with small time budgets. Max-margin trees perform better in the limited-time setting than current commonly-used data structures such as the kd-tree and more recently developed data structures like the RP-tree.
Outpatient management of childhood asthma by paediatrician or asthma nurse: randomised controlled study with one year follow up

Background: Until now, care provided by asthma nurses has been additional to care provided by paediatricians. A study was undertaken to compare nurse led outpatient management of childhood asthma with follow up by a paediatrician. Methods: Seventy four children referred because of insufficient control of persistent asthma were randomly allocated to 1 year follow up by a paediatrician or asthma nurse. The main outcome measure was the percentage of symptom-free days. Additional outcome measures were airway hyperresponsiveness, lung function, daily dose of inhaled corticosteroids (ICS), number of exacerbations, number of additional visits to the general practitioner, absence from school, functional health status, and disease specific quality of life. Results: There were no significant differences at the end of the 1 year study period between the two treatment groups in percentage of symptom-free days (mean difference 2.5%; 95% CI −8.8 to 13.8), airway hyperresponsiveness (log10 PD20 0.06; −0.19 to 0.32), functional health status (10.1; −0.3 to 19.8), disease specific quality of life of patients (0.08; −0.9 to 0.7), and disease specific quality of life of caregivers (0.09; −0.2 to 0.3), nor in any other outcome parameters. Most outcome parameters improved considerably over the 1 year study period. These improvements were achieved although the daily dose of ICS was reduced by a mean of 26% compared with the dose received by children at referral. All parents were satisfied with the asthma care received. Conclusions: After initial assessment in a multidisciplinary clinic, childhood asthma can be successfully managed by an asthma nurse in close cooperation with a paediatrician. During close follow up by paediatrician or asthma nurse, asthma control improved despite a reduction in ICS dose.
Labial soft tissue volume evaluation of different techniques for ridge preservation after tooth extraction: a randomized controlled clinical trial.

OBJECTIVE To volumetrically evaluate soft tissue changes of different ridge preservation techniques compared to spontaneous healing 6 months after tooth extraction. MATERIALS AND METHODS In each of 40 patients, one single-rooted tooth was extracted and four treatment modalities were randomly assigned to the following groups (n = 10 each): A) ß-tricalcium-phosphate-particles with a polylactid coating (ß-TCP), B) demineralized bovine bone mineral with 10% collagen covered with a collagen matrix (DBBM-C/CM), C) DBBM with 10% collagen covered with an autogenous soft tissue punch graft (DBBM-C/PG), D) spontaneous healing (control). Impressions were obtained before extraction and 6 months later, casts were digitized and volumetric changes at the buccal soft tissues were determined. One-way anova was performed and pair-wise Wilcoxon rank sum test with Bonferroni-Holm method was applied for comparison of differences between two groups. RESULTS After 6 months, horizontal contour changes accounted for -1.7 ± 0.7 mm (A), -1.2 ± 0.5 mm (B), -1.2 ± 0.7 mm (C) and -1.8 ± 0.8 mm (D). None of the group comparisons reached statistical significance. CONCLUSIONS Six months after tooth extraction all groups revealed a horizontal volume change in the buccal soft tissue contour. Application of DBBM-C/CM or DBBM-C/PG reduced the amount of volume resorption compared to ß-TCP or spontaneous healing without reaching statistically significant difference.