Miracle-dz/UniFAR-FTUs huggingface dataset:
Emergence of Resistance in Normal Human Aerobic Commensal Flora during Telithromycin and Amoxicillin-Clavulanic Acid Treatments

ABSTRACT Mean fecal global yeast counts increased similarly during 7 days of treatment with telithromycin (800 mg once daily) or amoxicillin-clavulanic acid (amoxiclav) (1 g of amoxicillin and 125 mg of clavulanic acid 3 times daily) in human volunteers and decreased slowly thereafter. On skin, coagulase-negative staphylococci of decreased susceptibility (DS) to telithromycin increased in the telithromycin group, whereas those with DS to methicillin increased in the amoxiclav group. A similar antibiotic-related shift towards homologous DS was observed for oral nongroupable streptococci (NGS), but in addition, the prevalence of NGS resistant to both classes of antibiotics was significantly greater in the amoxiclav group at days 8 (P < 0.01) and 45 (P < 0.015).
Parallel Symbolic Factorization for Sparse LU with Static Pivoting

This paper presents the design and implementation of a memory scalable parallel symbolic factorization algorithm for general sparse unsymmetric matrices. Our parallel algorithm uses a graph partitioning approach, applied to the graph of $|A|+|A|^T$, to partition the matrix in such a way that is good for sparsity preservation as well as for parallel factorization. The partitioning yields a so-called separator tree which represents the dependencies among the computations. We use the separator tree to distribute the input matrix over the processors using a block cyclic approach and a subtree to subprocessor mapping. The parallel algorithm performs a bottom-up traversal of the separator tree. With a combination of right-looking and left-looking partial factorizations, the algorithm obtains one column structure of $L$ and one row structure of $U$ at each step. The algorithm is implemented in C and MPI. From a performance study on large matrices, we show that the parallel algorithm significantly reduces the memory requirement of the symbolic factorization step, as well as the overall memory requirement of the parallel solver. It also often reduces the runtime of the sequential algorithm, which is already relatively small. In general, the parallel algorithm prevents the symbolic factorization step from being a time or memory bottleneck of the parallel solver.
Efficient biotechnological approach for lentiviral transduction of induced pluripotent stem cells

Induced pluripotent stem (iPS) cells are generated from differentiated adult somatic cells by reprogramming them. Unlimited self-renewal, and the potential to differentiate into any cell type, make iPS cells very promising candidates for basic and clinical research. Furthermore, iPS cells can be genetically manipulated for use as therapeutic tools. DNA can be introduced into iPS cells, using lentiviral vectors, which represent a helpful choice for efficient transduction and stable integration of transgenes. In this study, we compare two methods of lentiviral transduction of iPS cells, namely, the suspension method and the hanging drop method. In contrast to the conventional suspension method, in the hanging drop method, embryoid body (EB) formation and transduction occur concurrently. The iPS cells were cultured to form EBs, and then transduced with lentiviruses, using the conventional suspension method and the hanging drop method, to express miR-128 and green fluorescent protein (GFP). The number of transduced cells were assessed by fluorescent microscopy and flow cytometry. MTT assay and real-time PCR were performed to determine the cell viability and transgene expression, respectively. Morphologically, GFP+ cells were more detectable in the hanging drop method, and this finding was quantified by flow cytometric analysis. According to the results of the MTT assay, cell viability was considerably higher in the hanging drop method, and real-time PCR represented a higher relative expression of miR-128 in the iPS cells introduced with lentiviruses in drops. Altogether, it seems that lentiviral transduction of challenging iPS cells using the hanging drop method offers a suitable and sufficient strategy in their gene transfer, with less toxicity than the conventional suspension method.
Antibiotic Resistance in CampylobacterStrains Isolated from Animals, Foods, and Humans in Spain in 1997–1998

ABSTRACT Colonization by Campylobacter strains was investigated in human, broiler, and pig fecal samples from 1997- 1998, as well as in foods of animal origin, and antibiotic susceptibility testing was carried out for these strains. Campylobacter strains were isolated in the foods of animal origin (55 of 101 samples; 54.4%), intestinal samples from broilers (85 of 105; 81%), and pigs (40 of 45; 88.9%). A total of 641 Campylobacter strains were isolated from 8,636 human fecal samples of clinical origin (7.4%). Campylobacter jejuni was the most frequently isolated species from broilers (81%) and humans (84%), and Campylobacter coli was most frequently isolated from pigs (100%). An extremely high frequency of ciprofloxacin resistance was detected amongCampylobacter strains, particularly those isolated from broilers and pigs (99%), with a slightly lower result for humans (72%); cross-resistance with nalidixic acid was almost always observed. A higher frequency of resistance to erythromycin (81.1%), ampicillin (65.7%), gentamicin (22.2%), and amikacin (21.6%) was detected in C. coli strains isolated from pigs compared to those isolated from humans (34.5, 29.3, 8.6, and 0%, respectively). A low frequency of erythromycin resistance was found in C. jejuni or C. coli isolated from broilers. A greater resistance to ampicillin and gentamicin (47.4 and 11.9%, respectively) was detected in C. jejuni isolated from broilers than in human strains (38 and 0.4%, respectively). β-Lactamase production was found in 81% of the Campylobacter strains tested, although 44% of them were characterized as ampicillin susceptible. The increasing rates of Campylobacter resistance make advisable a more conservative policy for the use of antibiotics in farm animals.
Geometric Scene Parsing with Hierarchical LSTM

This paper addresses the problem of geometric scene parsing, i.e. simultaneously labeling geometric surfaces (e.g. sky, ground and vertical plane) and determining the interaction relations (e.g. layering, supporting, siding and affinity) between main regions. This problem is more challenging than the traditional semantic scene labeling, as recovering geometric structures necessarily requires the rich and diverse contextual information. To achieve these goals, we propose a novel recurrent neural network model, named Hierarchical Long Short-Term Memory (H-LSTM). It contains two coupled sub-networks: the Pixel LSTM (P-LSTM) and the Multi-scale Super-pixel LSTM (MS-LSTM) for handling the surface labeling and relation prediction, respectively. The two sub-networks provide complementary information to each other to exploit hierarchical scene contexts, and they are jointly optimized for boosting the performance. Our extensive experiments show that our model is capable of parsing scene geometric structures and outperforming several state-of-the-art methods by large margins. In addition, we show promising 3D reconstruction results from the still images based on the geometric parsing.
Organization of Lipids in the Tear Film: A Molecular-Level View

Biophysical properties of the tear film lipid layer are studied at the molecular level employing coarse grain molecular dynamics (MD) simulations with a realistic model of the human tear film. In this model, polar lipids are chosen to reflect the current knowledge on the lipidome of the tear film whereas typical Meibomian-origin lipids are included in the thick non-polar lipids subphase. Simulation conditions mimic those experienced by the real human tear film during blinks. Namely, thermodynamic equilibrium simulations at different lateral compressions are performed to model varying surface pressure, and the dynamics of the system during a blink is studied by non-equilibrium MD simulations. Polar lipids separate their non-polar counterparts from water by forming a monomolecular layer whereas the non-polar molecules establish a thick outermost lipid layer. Under lateral compression, the polar layer undulates and a sorting of polar lipids occurs. Moreover, formation of three-dimensional aggregates of polar lipids in both non-polar and water subphases is observed. We suggest that these three-dimensional structures are abundant under dynamic conditions caused by the action of eye lids and that they act as reservoirs of polar lipids, thus increasing stability of the tear film.
Survival Advantage of Kidney Transplantation Over Dialysis in Patients With Hepatitis C: A Systematic Review and Meta-Analysis

Background The clinical outcomes of hepatitis C infection in kidney transplantation and maintenance dialysis patients remain controversial. Here, we conducted a systematic review and meta-analysis that aimed at comparing 5-year mortality rates between waiting list and kidney transplantation patients with hepatitis C infections. Methods We searched Medline, EMBASE, and Scopus databases published since inception to June 2011 and found nine studies with 1734 patients who were eligible for pooling. Eligible studies were cohort studies that analyzed adult end-stage renal disease patients with hepatitis C virus infection and compared death rates between waiting list and kidney transplantation. The crude risk ratio of death along with its 95% confidence interval was estimated for each study. Data were independently extracted by two reviewers. Results The pooled risk ratio of death at 5 years by using a random-effect model was 2.19 (95% confidence interval, 1.50–3.20), which significantly favored the kidney transplantation when compared with the waiting list. There was evidence of heterogeneity of death rates across studies (&khgr;2=22.6; df=8; P=0.004). From the metaregression model, age and male gender could be the source of heterogeneity or variation of treatment effects. A major cause of death in the waiting list was cardiovascular diseases, whereas infection was a major cause in the transplant group. There was no evidence of publication bias suggested by an Egger test. Conclusions This systematic review suggested that hepatitis C virus–infected patients who remain on dialysis are at higher risk of death when compared with those who received kidney transplantations.
Dynamic, power-aware scheduling for mobile clients using a transparent proxy

Mobile computers consume significant amounts of energy when receiving large files. The wireless network interface card (WNIC) is the primary source of this energy consumption. One way to reduce the energy consumed is to transmit the packets to clients in a predictable fashion. Specifically, the packets can be sent in bursts to clients, who can then switch to a lower power sleep state between bursts. This technique is especially effective when the bandwidth of a stream is small. This work investigates techniques for saving energy in a multiple-client scenario, where clients may be receiving either UDP or TCP data. Energy is saved by using a transparent proxy that is invisible to both clients and servers. The proxy implementation maintains separate connections to the client and server so that a large increase in transmission time is avoided. The proxy also buffers data and dynamically generates a global transmission schedule that includes all active clients. Results show that energy savings within 10-15% of optimal are common, with little packet loss.
Safety Verification Proofs for Physical Systems

While much progress has been made on verification of discrete systems such as computer programs, work on formal verification of continuous, physical systems has been limited. We present a technique for verification of safety properties of such systems. Our algorithm treats safety as a reachability problem, and attempts to prove that a system cannot evolve from an abstract initial state into a state in which the safety condition does not hold. This approach is inspired by qualitative simulation techniques and makes use of trajectories comprised of a sequence of qualitative states and state transitions. The applicability of the technique, however, is not limited to qualitative problems, as we can use any amount of quantitative mathematics in the system description. This paper describes the technique, presents example problems, and discusses its limitations as well as potential for use in device engineering.
Inhibition of Subjective and Physiological Sexual Arousal in Women by Clonidine

Objective The present investigation was designed to provide the first empirical examination of the effects of clonidine, a selective alpha2-adrenergic agonist, on sexual arousal in women with and without prior sympathetic nervous system (SNS) stimulation by exercise. The purpose was to help elucidate the influence of adrenergic mechanisms on sexual function in women. Methods Thirty sexually functional women participated in two experimental sessions in which subjective (self-report) and physiological (vaginal photoplethysmograph) sexual responses to erotic stimuli were measured after either clonidine (0.2 mg) or placebo administration in a randomized, double-blind, crossover protocol. Before viewing the experimental films, 15 subjects engaged in 20 minutes of intense exercise designed to elicit significant SNS activation. Results Clonidine significantly decreased vaginal pulse amplitude, vaginal blood volume, and subjective sexual responses to the erotic films in subjects who were in a state of heightened (via exercise), but not baseline (no exercise) SNS arousal. Conclusions Clonidine can significantly inhibit subjective and physiological sexual arousal in women. These findings have implications for deriving an etiological theory of sexual function in women and for understanding the effects of psychotherapeutic drugs on female sexual function.
Plasma ESR 1 Mutations and the Treatment of Estrogen Receptor – Positive Advanced Breast Cancer

Purpose: ESR1 mutations are selected by prior aromatase inhibitor (AI) therapy in advanced breast cancer. We assessed the impact of ESR1 mutations on sensitivity to standard therapies in two phase III randomized trials that represent the development of the current standard therapy for estrogen receptor–positive advanced breast cancer. Materials and methods: In a prospective-retrospective analysis, we assessed ESR1 mutations in available archived baseline plasma from the SoFEA (Study of Faslodex Versus Exemestane With or Without Arimidex) trial, which compared exemestane with fulvestrant-containing regimens in patients with prior sensitivity to nonsteroidal AI and in baseline plasma from the PALOMA3 (Palbociclib Combined With Fulvestrant in Hormone Receptor–Positive HER2-Negative Metastatic Breast Cancer After Endocrine Failure) trial, which compared fulvestrant plus placebo with fulvestrant plus palbociclib in patients with progression after receiving prior endocrine therapy. ESR1 mutations were analyzed by multiplex digital polymerase chain reaction. Results: In SoFEA, ESR1 mutations were found in 39.1% of patients (63 of 161), of whom 49.1% (27 of 55) were polyclonal, with rates of mutation detection unaffected by delays in processing of archival plasma. Patients with ESR1 mutations had improved progression-free survival (PFS) after taking fulvestrant (n = 45) compared with exemestane (n = 18; hazard ratio [HR], 0.52; 95% CI, 0.30 to 0.92; P = .02), whereas patients with wild-type ESR1 had similar PFS after receiving either treatment (HR, 1.07; 95% CI, 0.68 to 1.67; P = .77). In PALOMA3, ESR1 mutations were found in the plasma of 25.3% of patients (91 of 360), of whom 28.6% (26 of 91) were polyclonal, with mutations associated with acquired resistance to prior AI. Fulvestrant plus palbociclib improved PFS compared with fulvestrant plus placebo in both ESR1 mutant (HR, 0.43; 95% CI, 0.25 to 0.74; P = .002) and ESR1 wild-type patients (HR, 0.49; 95% CI, 0.35 to 0.70; P < .001). Conclusion: ESR1 mutation analysis in plasma after progression after prior AI therapy may help direct choice of further endocrine-based therapy. Additional confirmatory studies are required.
Baseline NIH Stroke Scale Responses Estimate the Probability of Each Particular Stroke Subtype

Background: Emergency treatment of ischemic stroke should ideally be mechanism specific, but acute subtype diagnosis is problematic. Since different subtypes often are associated with specific patterns of neurological deficits, we hypothesize that scores on baseline NIH stroke scale (NIHSS) items may help emergently stratify patients by their probability of having a particular stroke subtype. Methods: We performed multivariate polytomous logistic regression analyses on 1,281 patients enrolled in the Trial of ORG 10172 in Acute Stroke Treatment (TOAST). We tested the predictive value of individual items to the baseline NIHSS exam, and syndromic combinations of those items, in anticipating the TOAST stroke subtype at 3 months adjusting for atrial fibrillation. We then used the most significant NIHSS items to construct a predictive model. Results: The NIHSS items that discriminate between stroke subtypes are language, neglect, visual field and brachial predominance of weakness. Among patients without atrial fibrillation, a normal score for these 4 variables conveys a 46% chance of lacunar stroke, 12% of atherothrombotic stroke and 10% of cardioembolism. This pattern gradually reverses with increased numbers of abnormal responses. Those with abnormalities in all 4 items have a 0.1% chance of lacunar stroke, 50% of atherothrombotic stroke and 39% of cardioembolism. Conclusions: Language, neglect, visual fields and brachial predominance of weakness in the baseline NIHSS help discriminate between subtypes, particularly between lacunar and nonlacunar strokes. Clinical trials testing interventions aimed to particular stroke mechanisms may use these NIHSS items to emergently stratify patients based on their probability of having a particular stroke subtype.
Aerobic exercise alters skeletal muscle molecular responses to resistance exercise.

PURPOSE This study assessed the influence of an acute aerobic exercise bout on molecular responses to subsequent resistance exercise (RE). METHODS Nine physically active men performed a 45-min one-legged cycle ergometry exercise and 4 × 7 maximal concentric-eccentric knee extensions for each leg 6 h later. Thus, one limb was subjected to aerobic and resistance exercise (AE+RE), and the contralateral limb to resistance exercise (RE) only. Knee extensor peak power was determined. Biopsies were obtained from the m vastus lateralis before (PRE) and 15 min (POST1) and 3 h after RE. Analysis determined glycogen content, mRNA levels (vascular endothelial growth factor, peroxisome proliferator-activated receptor-γ coactivator-1, muscle RING-finger protein-1, atrogin-1, myostatin), and phosphorylated proteins (mammalian target of rapamycin, p70S6 kinase, ribosomal protein S6, eukaryotic elongation factor 2). RESULTS Peak power was similar in AE + RE and RE. After RE, the time course of glycogen utilization and protein signaling was similar across legs. However, phosphorylation of mammalian target of rapamycin and p70S6 kinase was elevated in AE + RE versus RE (main effect, P < 0.05). Vascular endothelial growth factor and peroxisome proliferator-activated receptor-γ coactivator-1 were higher in AE + RE than in RE at PRE and POST1 (P < 0.05). Myostatin was lower in AE + RE versus RE at PRE and POST1 (P < 0.05) and downregulated after resistance exercise only. Atrogin-1 was higher in AE + RE than in RE at PRE and POST1 (P < 0.05) and decreased after RE in AE + RE. Muscle RING-finger protein-1 was similar across legs. No difference for any marker was evident 3 h after RE. CONCLUSIONS These results suggest that acute aerobic exercise alters molecular events regulating muscle protein turnover during the early recovery period from subsequent RE.
The role of radioactive iodine-125 seed localization in breast-conserving therapy following neoadjuvant chemotherapy.

BACKGROUND Neoadjuvant chemotherapy (NAC) is increasingly used in the framework of breast-conserving therapy (BCT). Localization of the initial tumor is essential to guide surgical resection after NAC. This study describes the results obtained with I-125 seed localization in BCT including NAC. PATIENTS AND METHODS Between January 2009 and December 2010, 85 patients treated with NAC and BCT after I-125 seed localization were included. Radiological and pathological response and resection margins were retrospectively evaluated. RESULTS BCT was carried out in 85 patients without secondary local excisions. Nineteen patients with unifocal tumors and seven patients with multifocal tumors showed a complete pathological response (P = 0.18). Tumor-free resection margins were obtained in 78 patients (50 patients with unifocal and 28 patients with multifocal tumors, P = 0.27). Focally involved margins were found in four patients (two patients with a unifocal and two patients with a multifocal tumor, P = 0.27). A subsequent mastectomy was carried out in three patients (two patients with multifocal tumors, P = 0.29). CONCLUSIONS BCT after NAC can be carried out successfully after initial localization with I-125 seeds in both unifocal and multifocal breast tumors with complete resection rates of >90%.
Internal models of reaching and grasping

One of the most distinguishing features of cognitive systems is the ability to predict the future course of actions and the results of ongoing behaviors, and in general to plan actions well in advance. Neuroscience has started examining the neural basis of these skills with behavioral or animal studies and it is now relatively well understood that the brain builds models of the physical world through learning. These models are sometimes called 'internal models', meaning that they are the internal rehearsal (or simulation) of the world enacted by the brain. In this paper we investigate the possibility of building internal models of human behaviors with a learning machine that has access to information in principle similar to that used by the brain when learning similar tasks. In particular, we concentrate on models of reaching and grasping, and we report on an experiment in which biometric data collected from human users during grasping was used to train a support vector machine. We then assess to what degree the models built by the machine are faithful representations of the actual human behaviors. The results indicate that the machine is able to predict reasonably well human reaching and grasping, and that prior knowledge of the object to be grasped improves the performance of the machine, while keeping the same computational cost.
Electronic Communications of the EASST Volume 59 ( 2013 ) Special Issue of the First Workshop on Patterns Promotion and Anti-patterns Prevention ( PPAP 2013 ) Analysing Anti-patterns Static Relationships with Design Patterns

Anti-patterns are motifs that are usually thought to be good solutions to some design or implementation problems, but back-fires badly when applied. Previous studies have reported that anti-patterns make object oriented systems hard to maintain. Anti-patterns motifs usually have dependencies with other classes in the system. In this paper, we propose to analyse these dependencies (with in particular design patterns) in order to understand how developers can maintain programs containing anti-patterns. To the best of our knowledge, no substantial investigation of anti-pattern dependencies with design patterns has been done before. This paper presents the results of a study that we performed on three different systems, ArgoUML, JFreeChart, and XercesJ, written in Java, and of size ranges from 1,191 to 3,325 classes, to analyse the static relationships between anti-patterns and design patterns. We found that these relationships (1) exist, but (2) are temporary and (3) classes participating in such relationships are more change-prone but less fault-prone than other anti-pattern classes.