Miracle-dz/UniFAR-FTUs huggingface dataset:
Alpha-Toxin Induces Programmed Cell Death of Human T cells, B cells, and Monocytes during USA300 Infection

This investigation examines the influence of alpha-toxin (Hla) during USA300 infection of human leukocytes. Survival of an USA300 isogenic deletion mutant of hla (USA300Δhla) in human blood was comparable to the parental wild-type strain and polymorphonuclear leukocyte (PMN) plasma membrane permeability caused by USA300 did not require Hla. Flow cytometry analysis of peripheral blood mononuclear cells (PBMCs) following infection by USA300, USA300Δhla, and USA300Δhla transformed with a plasmid over-expressing Hla (USA300Δhla Comp) demonstrated this toxin plays a significant role inducing plasma membrane permeability of CD14+, CD3+, and CD19+ PBMCs. Rapid plasma membrane permeability independent of Hla was observed for PMNs, CD14+ and CD19+ PBMCs following intoxication with USA300 supernatant while the majority of CD3+ PBMC plasma membrane permeability induced by USA300 required Hla. Addition of recombinant Hla to USA300Δhla supernatant rescued CD3+ and CD19+ PBMC plasma membrane permeability generated by USA300 supernatant. An observed delay in plasma membrane permeability caused by Hla in conjunction with Annexin V binding and ApoBrdU Tunel assays examining PBMCs intoxicated with recombinant Hla or infected with USA300, USA300Δhla, USA300Δhla Comp, and USA300ΔsaeR/S suggest Hla induces programmed cell death of monocytes, B cells, and T cells that results in plasma membrane permeability. Together these findings underscore the importance of Hla during S. aureus infection of human tissue and specifically demonstrate Hla activity during USA300 infection triggers programmed cell death of human monocytes, T cells and B cells that leads to plasma membrane permeability.
Mining Conversational Social Video

Keywords: social media ; social computing ; user behavior ; online social video ; video blogging ; vlogging ; interpersonal perception ; first impressions ; YouTube ; social attention ; personality ; first impressions These Ecole polytechnique federale de Lausanne EPFL, n° 5781 (2013)Programme doctoral Genie electriqueFaculte des sciences et techniques de l'ingenieurInstitut de genie electrique et electroniqueLaboratoire de l'IDIAPJury: S. Susstrunk (presidente), P. Frossard, B.A. Huberman, M. Mehl Public defense: 2013-6-28 Reference doi:10.5075/epfl-thesis-5781Print copy in library catalog Record created on 2013-06-19, modified on 2016-08-09
Ventilatory protective strategies during thoracic surgery: effects of alveolar recruitment maneuver and low-tidal volume ventilation on lung density distribution.

BACKGROUND The increased tidal volume (V(T)) applied to the ventilated lung during one-lung ventilation (OLV) enhances cyclic alveolar recruitment and mechanical stress. It is unknown whether alveolar recruitment maneuvers (ARMs) and reduced V(T) may influence tidal recruitment and lung density. Therefore, the effects of ARM and OLV with different V(T) on pulmonary gas/tissue distribution are examined. METHODS Eight anesthetized piglets were mechanically ventilated (V(T) = 10 ml/kg). A defined ARM was applied to the whole lung (40 cm H(2)O for 10 s). Spiral computed tomographic lung scans were acquired before and after ARM. Thereafter, the lungs were separated with an endobronchial blocker. The pigs were randomized to receive OLV in the dependent lung with a V(T) of either 5 or 10 ml/kg. Computed tomography was repeated during and after OLV. The voxels were categorized by density intervals (i.e., atelectasis, poorly aerated, normally aerated, or overaerated). Tidal recruitment was defined as the addition of gas to collapsed lung regions. RESULTS The dependent lung contained atelectatic (56 ± 10 ml), poorly aerated (183 ± 10 ml), and normally aerated (187 ± 29 ml) regions before ARM. After ARM, lung volume and aeration increased (426 ± 35 vs. 526 ± 69 ml). Respiratory compliance enhanced, and tidal recruitment decreased (95% vs. 79% of the whole end-expiratory lung volume). OLV with 10 ml/kg further increased aeration (atelectasis, 15 ± 2 ml; poorly aerated, 94 ± 24 ml; normally aerated, 580 ± 98 ml) and tidal recruitment (81% of the dependent lung). OLV with 5 ml/kg did not affect tidal recruitment or lung density distribution. (Data are given as mean ± SD.) CONCLUSIONS The ARM improves aeration and respiratory mechanics. In contrast to OLV with high V(T), OLV with reduced V(T) does not reinforce tidal recruitment, indicating decreased mechanical stress.
CD4 T cells in murine acquired immunodeficiency syndrome: polyclonal progression to anergy

We have examined the kinetics of changes that occur in the helper T cell subset during murine acquired immunodeficiency syndrome, which occurs after infection with the mix of viruses known as BM5. We find that there is expansion of the CD4 T cells by 2 wk, 50% of the CD4 T cells become large as the disease progresses, and the CD4 T cell population is increasingly comprised of cells with a memory/activated phenotype. These effects are apparent by 2 wk postinfection, and the change is nearly complete by 6-8 wk. The phenotypic shift is paralleled by the loss of the ability of the CD4 T cells to proliferate or to produce interleukin 2 (IL-2), IL-3, IL-4, and interferon gamma in response to stimulation with mitogens, superantigen, or anti-CD3. There is no obvious expansion or deletion of CD4 T cells expressing particular V beta genes, as might be expected if a conventional superantigen were driving the changes. The results suggest, however, that the total CD4 population has been driven to anergy by some potent polyclonal stimulus directly associated with viral infection.
Families of elliptic curves over cubic number fields with prescribed torsion subgroups

In this paper we construct inﬁnite families of elliptic curves with given torsion group structures over cubic number ﬁelds. This result provides explicit examples of the theoretical result recently developed by the ﬁrst two authors and A. Schweizer; they determined all the group structures which occur inﬁnitely often as the torsion of elliptic curves over cubic number ﬁelds. In fact, this paper presents an eﬃcient way of constructing such families of elliptic curves with prescribed torsion group structures over cubic number ﬁelds.
Cognitive Behavioural Therapy for Paruresis or “Shy Bladder Syndrome”: A Case Study

Background: Paruresis, or “shy bladder syndrome”, is a relatively common anxiety disorder, yet little is known about the causes of, and effective treatments for this disabling condition. Aim: This report describes a case study in which a man (Peter) presenting with paruresis was treated using formulation-driven CBT, which aimed to address the idiosyncratic processes that were maintaining his anxiety and avoidance of urinating in public. Method: Peter attended 12 sessions of CBT including one follow-up session a month after treatment had ended. Treatment involved collaboratively developing an idiosyncratic case conceptualization (identifying longitudinal and cross-sectional factors involved in the development and maintenance of his difficulties), followed by a number of standard cognitive and behavioural interventions commonly used in evidence-based CBT protocols for other anxiety disorders. Peter completed sessional outcome measures of paruresis symptomatology, anxiety, depression, social anxiety and functional impairment. Results: Peter subjectively found the intervention helpful and his scores on all of the outcome measures reduced over the course of his therapy, and were maintained at one month follow-up. Conclusions: This report adds to the scarce literature regarding effective treatments for individuals suffering with paruresis. Limitations of the design are acknowledged and ideas for further research in this area are discussed.
The early bactericidal activity of streptomycin.

SETTING Patients with sputum smear-positive, newly diagnosed pulmonary tuberculosis studied at Tygerburg Hospital, Cape Town, for their early response to streptomycin (SM). OBJECTIVE To determine the standard early bactericidal activity (EBA), namely the fall in viable counts of tubercle bacilli in 16-hour sputum collections during the first 2 days of treatment with SM. DESIGN Patients were randomised to logarithmically spaced daily doses of 7.5, 15 or 30 mg/kg SM. A comparison by standard biological assay methods was then made with previous estimations of the EBA of paromomycin in doses of 7.5 and 15 mg/kg. RESULTS An EBA of 0.133 obtained with 30 mg/kg SM differed significantly from zero (P = 0.0009), while the EBAs of 0.043 with 15 mg/kg and -0.025 with 7.5 mg/kg did not so differ. A linear regression equation of EBA = -0.2587 + 0.2627 log10 dose was obtained with significant slope (P = 0.007). Paromomycin was estimated to be 1.745 more potent than SM with wide 95% confidence limits (0.6-28.6), indicating that it cannot be considered more potent than SM. CONCLUSIONS The low EBAs show that SM has low, dose-related, bactericidal activity in cavities, consistent with results from clinical trials. If streptomycin-resistant bacilli are present, paromomycin is probably the aminoglycoside of choice.
Effect of sequential fermentations and grape cultivars on volatile compounds and sensory profiles of Danish wines.

BACKGROUND There has been an increasing interest in the use of selected non-Saccharomyces yeasts in co-culture with Saccharomyces cerevisiae. In this work, three non-Saccharomyces yeast strains (Metschnikowia viticola, Metschnikowia fructicola and Hanseniaspora uvarum) indigenously isolated in Denmark were used in sequential fermentations with S. cerevisiae on three cool-climate grape cultivars, Bolero, Rondo and Regent. During the fermentations, the yeast growth was determined as well as key oenological parameters, volatile compounds and sensory properties of finished rosé wines. RESULTS The different non-Saccharomyces strains and cool-climate grape cultivars produced wines with a distinctive aromatic profile. A total of 67 volatile compounds were identified, including 43 esters, 14 alcohols, five acids, two ketones, a C13-norisoprenoid, a lactone and a sulfur compound. The use of M. viticola in sequential fermentation with S. cerevisiae resulted in richer berry and fruity flavours in wines. The sensory plot showed a more clear separation among wine samples by grape cultivars compared with yeast strains. CONCLUSION Knowledge on the influence of indigenous non-Saccharomyces strains and grape cultivars on the flavour generation contributed to producing diverse wines in cool-climate wine regions. © 2017 Society of Chemical Industry.
Decline in Homophone Spelling Associated with Loss of Semantic Influence on Spelling in Alzheimer′s Disease

The homophone spellings of 20 subjects with Alzheimer's disease (AD) and mild dementia were compared to those of matched normal controls. Both groups were tested once (Time 1) and then again 9 months to 1 year later (Time 2). At Time 1, AD subjects misspelled more homophones than the control group and the discrepancy between the two groups' performances significantly increased by Time 2. Two types of errors were tabulated: homophone confusions (i.e. an inappropriate yet correctly spelled homophone given the context, such as spelling doe, given the context "bake the bread dough") and other spelling errors (e.g. doue, dogh). The relationship between homophone confusions and confrontation naming increased from Time 1 to Time 2. In contrast, the relationship between the number of spelling errors (that were not homophone confusions) and confrontation naming performance was not significant at Time 2. One subgroup of 3 subjects showed an increase in homophone confusions and confrontational naming errors and not more spelling errors. Another subgroup of 4 subjects showed neither an increase in homophone confusions nor in confrontational naming errors, but did show an increase in spelling errors. Based on these results, we suggest that homophone confusions are primarily due to impairment of semantic access to a functional orthographic output lexicon. Other spelling errors may reflect post-linguistic spelling deficits without a significant change in the use of semantic input for spelling homophones.
Fast plane detection in disparity maps

We propose a new method for fast detection of planar patches in disparity maps. We first use a region growing algorithm on random seeds. This approach is similar to the one introduced in [1] for fast line segment detection in images. Then, the parameter-free criterion introduced in [2] is used to keep only the patches that are planar. The main advantage of our method is to be able to estimate the disparity map precision which is usually a critical parameter in other methods. This method is specially well suited to 3D reconstruction of urban environments from low-baseline aerial or satellite stereo pairs where a piecewise-planar model can be applied.
Tolerating byzantine faults in transaction processing systems using commit barrier scheduling

This paper describes the design, implementation, and evaluation of areplication scheme to handle Byzantine faults in transaction processing database systems. The scheme compares answers from queries and updates on multiple replicas which are unmodified, off-the-shelf systems, to provide a single database that is Byzantine fault tolerant. The scheme works when the replicas are homogeneous, but it also allows heterogeneous replication in which replicas come from different vendors. Heterogeneous replicas reduce the impact of bugs and security compromises because they are implemented independently and are thus less likely to suffer correlated failures. The main challenge in designing a replication scheme for transactionprocessing systems is ensuring that the different replicas execute transactions in equivalent serial orders while allowing a high degreeof concurrency. Our scheme meets this goal using a novel concurrency control protocol, commit barrier scheduling (CBS). We have implemented CBS in the context of a replicated SQL database, HRDB(Heterogeneous Replicated DB), which has been tested with unmodified production versions of several commercial and open source databases as replicas. Our experiments show an HRDB configuration that can tolerate one faulty replica has only a modest performance overhead(about 17% for the TPC-C benchmark). HRDB successfully masks several Byzantine faults observed in practice and we have used it to find a new bug in MySQL.
Correction for “ Myc and mTOR converge on a common node in protein synthesis control that confers synthetic lethality in Myc-driven cancers

MEDICAL SCIENCES Correction for “Myc and mTOR converge on a common node in protein synthesis control that confers synthetic lethality in Myc-driven cancers,” by Michael Pourdehnad, Morgan L. Truitt, Imran N. Siddiqi, Gregory S. Ducker, Kevan M. Shokat, and Davide Ruggero, which appeared in issue 29, July 16, 2013, of Proc Natl Acad Sci USA (110:11988–11993; first published June 26, 2013; 10.1073/pnas.1310230110). The authors note that Fig. 5 appeared incorrectly. The corrected figure and its legend appear below.
Effect of ammonium and nitrate on ferric chelate reductase and nitrate reductase in Vaccinium species.

BACKGROUND AND AIMS Most Vaccinium species have strict soil requirements for optimal growth, requiring low pH, high iron availability and nitrogen primarily in the ammonium form. These soils are limited and are often located near wetlands. Vaccinium arboreum is a wild species adapted to a wide range of soils, including high pH, low iron, and nitrate-containing soils. This broader soil adaptation in V. arboreum may be related to increased efficiency of iron or nitrate uptake compared with the cultivated Vaccinium species. METHODS Nitrate, ammonium and iron uptake, and nitrate reductase (NR) and ferric chelate reductase (FCR) activities were compared in two Vaccinium species grown hydroponically in either nitrate or ammonia, with or without iron. The species studied were the wild V. arboreum and the cultivated V. corymbosum interspecific hybrid, which exhibits the strict soil requirements of most Vaccinium species. RESULTS Ammonium uptake was significantly greater than nitrate uptake in both species, while nitrate uptake was greater in the wild species, V. arboreum, compared with the cultivated species, V. corymbosum. The increased nitrate uptake in V. arboreum was correlated with increased root NR activity compared with V. corymbosum. The lower nitrate uptake in V. corymbosum was reflected in decreased plant dry weight in this species compared with V. arboreum. Root FCR activity increased significantly in V. corymbosum grown under iron-deficient conditions, compared with the same species grown under iron-sufficient conditions or with V. arboreum grown under either iron condition. CONCLUSIONS V. arboreum appears to be more efficient in acquiring nitrate compared with V. corymbosum, possibly due to increased NR activity and this may partially explain the wider soil adaptation of V. arboreum.
Plasticity in animal personality traits: does prior experience alter the degree of boldness?

Theoreticians predict that animal ‘personality’ traits may be maladaptive if fixed throughout different contexts, so the present study aimed to test whether these traits are fixed or plastic. Rainbow trout (Onchorhyncus mykiss) were given emboldening or negative experiences in the forms of watching bold or shy individuals responding to novelty or winning or losing fights to examine whether prior experience affected boldness. Bold individuals that lost fights or watched shy demonstrators became more shy by increasing their latency to approach a novel object, whereas shy observers that watched bold demonstrators remained cautious and did not modify their responses to novelty. Shy winners became bolder and decreased their latency to approach a novel object, but shy losers also displayed this shift. In comparison, control groups showed no change in behaviour. Bold fishes given negative experiences reduced their boldness which may be an adaptive response; however, shy fishes may base their strategic decisions upon self-assessment of their relative competitive ability and increase their boldness in situations where getting to resources more quickly ensures they outcompete better competitors.
A Note on the Complexity of L p Minimization

We discuss the Lp (0 ≤ p < 1) minimization problem arising from sparse solution construction and compressed sensing. For any fixed 0 < p < 1, we prove that finding the global minimal value of the problem is strongly NP-Hard, but computing a local minimizer of the problem can be done in polynomial time. We also develop an interior-point potential reduction algorithm with a provable complexity bound and demonstrate preliminary computational results of effectiveness of the algorithm.
PoMo: An Allele Frequency-Based Approach for Species Tree Estimation

Incomplete lineage sorting can cause incongruencies of the overall species-level phylogenetic tree with the phylogenetic trees for individual genes or genomic segments. If these incongruencies are not accounted for, it is possible to incur several biases in species tree estimation. Here, we present a simple maximum likelihood approach that accounts for ancestral variation and incomplete lineage sorting. We use a POlymorphisms-aware phylogenetic MOdel (PoMo) that we have recently shown to efficiently estimate mutation rates and fixation biases from within and between-species variation data. We extend this model to perform efficient estimation of species trees. We test the performance of PoMo in several different scenarios of incomplete lineage sorting using simulations and compare it with existing methods both in accuracy and computational speed. In contrast to other approaches, our model does not use coalescent theory but is allele-frequency based. We show that PoMo is well suited for genome-wide species tree estimation and that on such data it is more accurate than previous approaches.
Differences in evoked EEG by transcranial magnetic stimulation at various stimulus points on the head

The combination of transcranial magnetic stimulation (TMS) and electroencephalogram (EEG) is an effective tool for investigating the cortical reactivity and the functional connectivity in the brain. In our previous study, we reported a method of removing stimulus artifact during TMS with Sample-and-Hold circuit and EEG activity evoked by TMS could be measured successfully. In addition to this method, independent component analysis (ICA) was also applied to recorded EEG data in order to remove the stimulus artifact from for off-line analysis. By using these methods, short latency (< 15 ms) EEG responses to TMS could be obtained. In this paper, we focused on the propagation of EEG activity elicited by TMS. We observed both the EEG topography and the distribution of the current density over the whole head by changing the stimulus site. When motor cortex was stimulated, the propagation of EEG activity to contralateral hemisphere could be clearly observed. However, when posterior parietal cortex was stimulated, no or less propagation of EEG responses could be recognized. These results suggest that the responses evoked by TMS over motor cortex propagate to contralateral hemisphere along the axon through the corpus callosum.
Differential microRNA-34a expression and tumor suppressor function in retinoblastoma cells.

PURPOSE The role of miR-34a, a p53-regulated microRNA, in retinoblastoma (RB) was investigated. METHODS The expression of miR-34 family members in RB cells was determined by semiquantitative RT-PCR and real-time qPCR. Regulation of miR-34a expression by p53-activating compounds was determined by qPCR analysis. The tumor suppressor functions of miR-34a in RB cell lines were determined by tetrazolium-based cell growth assay and by caspase-3/7 and activated caspase-3 apoptotic activity assays. Additive growth inhibitory properties of miR-34a in combination with topotecan were determined by cell growth assay. miR-34a targets in RB cells were identified by real-time qPCR expression analysis of previously reported and GenMiR++-predicted mRNAs. RESULTS Differential miR-34a and miR-34b expression was observed in RB cell lines and tumor samples. miR-34a expression could be increased in Y79 cells, but not Weri-Rb1 cells, after p53 activation. This differential regulation was not caused by genomic alterations at the miR-34a p53 binding site or mature gene. Exogenous miR-34a inhibited Y79 and Weri-Rb1 cell growth and increased apoptotic activity in Y79 cells. Increased inhibition of Y79 and Weri-Rb1 cell growth was observed with combination miR-34a and topotecan treatment. mRNA expression changes were observed in 7 of 7 previously reported and 13 of 18 GenMiR++-predicted miR-34a targets after transfection of Y79 cells with miR-34a compared with negative control microRNA. CONCLUSIONS miR-34a functions as a tumor suppressor in RB cells and is a potential therapeutic target. Differential expression, regulation, and activity of miR-34a in RB cells may suggest further p53 pathway inactivation in RB.