Miracle-dz/UniFAR-FTUs huggingface dataset:
The Fate of Acetic Acid during Glucose Co-Metabolism by the Spoilage Yeast Zygosaccharomyces bailii

Zygosaccharomyces bailii is one of the most widely represented spoilage yeast species, being able to metabolise acetic acid in the presence of glucose. To clarify whether simultaneous utilisation of the two substrates affects growth efficiency, we examined growth in single- and mixed-substrate cultures with glucose and acetic acid. Our findings indicate that the biomass yield in the first phase of growth is the result of the weighted sum of the respective biomass yields on single-substrate medium, supporting the conclusion that biomass yield on each substrate is not affected by the presence of the other at pH 3.0 and 5.0, at least for the substrate concentrations examined. In vivo 13C-NMR spectroscopy studies showed that the gluconeogenic pathway is not operational and that [2−13C]acetate is metabolised via the Krebs cycle leading to the production of glutamate labelled on C2, C3 and C4. The incorporation of [U-14C]acetate in the cellular constituents resulted mainly in the labelling of the protein and lipid pools 51.5% and 31.5%, respectively. Overall, our data establish that glucose is metabolised primarily through the glycolytic pathway, and acetic acid is used as an additional source of acetyl-CoA both for lipid synthesis and the Krebs cycle. This study provides useful clues for the design of new strategies aimed at overcoming yeast spoilage in acidic, sugar-containing food environments. Moreover, the elucidation of the molecular basis underlying the resistance phenotype of Z. bailii to acetic acid will have a potential impact on the improvement of the performance of S. cerevisiae industrial strains often exposed to acetic acid stress conditions, such as in wine and bioethanol production.
Mix-nets: Factored Mixtures of Gaussians in Bayesian Networks with Mixed Continuous And Discrete Variables

Recently developed techniques have made it possible to quickly learn accurate probability density functions from data in low-dimensional continuous spaces. In particular, mixtures of Gaussians can be fitted to data very quickly using an accelerated EM algorithm that employs multiresolution kd-trees (Moore, 1999). In this paper, we propose a kind of Bayesian network in which low-dimensional mixtures of Gaussians over different subsets of the domain's variables are combined into a coherent joint probability model over the entire domain. The network is also capable of modeling complex dependencies between discrete variables and continuous variables without requiring discretization of the continuous variables. We present efficient heuristic algorithms for automatically learning these networks from data, and perform comparative experiments illustrating how well these networks model real scientific data and synthetic data. We also briefly discuss some possible improvements to the networks, as well as possible applications.
Peak-to-average power ratio analysis in multicarrier DS-CDMA

Multicarrier direct-sequence code-division multiple access (MC-DS-CDMA) is an attractive technique for achieving high-bit-rate wireless data transmission. Although the potentially large peak-to-average power ratio (PAPR) is an important factor for its application, there is no theoretical PAPR analysis of the transmitted signal in an MC-DS-CDMA system in the literature. The purpose of this paper is to fill such a gap. We derive a general formula for the complementary cumulative distribution function (CCDF) of the PAPR of an MC-DS-CDMA signal, giving a possible lower bound of CCDF. To achieve the lowest bound of CCDF, a criterion is proposed for optimal interleaver design in an MC-DS-CDMA system. By using two interleaver design methods as examples, simulation results demonstrate the effectiveness of the new criterion in interleaver design.
Contrast adaptation and contrast masking in human vision

After a preliminary study of visual evoked potentials (VEPs) to a test grating seen in the presence of masks at different orientations, psychophysical data are presented showing the effects of adaptation and of masking on thresholds for detecting the same test grating. The test is a vertical grating of spatial frequency 2 cycles per degree; adapting and masking gratings differ from the test either in orientation or in spatial frequency. The effects of adaptation and masking are explained by a single mechanism model that assumes: (i) adaptation and masking both alter the contrast response (or transducer) function of the mechanism that detects the test; (ii) masks, but not adaptors, stimulate the mechanism that detects the test; and (iii) a test is detectable when it raises response level by a constant amount. The model incorporates two distinct tuning functions, a broad adaptive contrast function and a narrow effective contrast function. It accounts adequately for all the data, including the location and size of the facilitative dip found in some masking functions, the constant slopes of the threshold elevation segments of adaptation functions and the varying slopes of masking functions. It also predicts the sometimes surprising joint effects of adaptation followed by masking and of two masks operating simultaneously.
A Replica Placement Algorithm for Hybrid CDN-P2P Architecture

The Hybrid CDN-P2P architecture, or HCDN, which combines the complementary advantages of CDN and P2P networks, has been proposed to reduce the deployment cost and to improve the quality of service in file sharing and video streaming applications. A replica placement algorithm (RPA) decides where to replicate the specific data. Existing RPAs for pure CDN do not work efficiently in the HCDN architecture because they do not take into consideration the contribution of the peers at the P2P distribution level. In this article, a heuristic RPA that takes into account the effects of P2P distribution is proposed for HCDN. The performance of our proposed algorithm is evaluated and the impact of some key metrics is analyzed. The experimental result shows the clear performance benefits of our approach.
Clinical Features and Laboratory Diagnosis of Infection with the Potential Bioterrorism Agents Burkholderia Mallei and Burkholderia Pseudomallei

Burkholderia mallei and Burkholderia pseudomallei are the causative organisms of Glanders and Melioidosis, respectively. Although now rare in Western countries, both organisms have recently gained much interest because of their unique potential as bioterrorism agents. These organisms are less familiar to medical and laboratory personnel than other select bioterrorism bacterial agents and thus heightened awareness of Glanders and Melioidosis is crucial in order to enable adequate emergency preparedness and response to deliberate release of B. mallei and B. pseudomallei. The microbiological diagnosis of both species in the clinical laboratory is complicated. This paper reviews the various challenges and pitfalls associated with the diagnosis of Melioidosis and Glanders in the clinical setting, with emphasis on the role of sentinel laboratories.
Ibotenate Lesions of the Diagonal Band of Broca Attenuate Baroreceptor Sensitivity of Rat Supraoptic Vasopressin Neurons

Previous electrophysiological studies in the rat suggest that neurons in the diagonal band of Broca participate in baroreceptor‐induced suppression of the spontaneous activity of vasopressin‐secreting neurons in the hypothalamic supraoptic nucleus. In order to test this hypothesis, extracellular recordings were obtained from phasically‐active vasopressin neurons in the supraoptic nucleus of anesthetized rats injected at least 3 days previously with ibotenic acid (1.25 μg/250 nl) in the diagonal band of Broca, the medial and lateral septum, or the median preoptic nucleus. In normal rats, brief increases in blood pressure produced by injections of metaraminol (10 μg/10 μl iv) that were sufficient to activate peripheral baroreceptors, suppressed the activity of a majority (21 tested, 19 suppressed) of phasically‐active vasopressin‐secreting neurons. In rats with ibotenic acid lesions of the diagonal band of Broca, the number of phasically‐active neurons that were baroreceptor‐sensitive was significantly reduced (21 tested, 8 suppressed) while lesions of the medial and lateral septum (17 tested, 16 suppressed) or the median preoptic nucleus (21 tested, 20 suppressed) had no effect. The results support the hypothesis that diagonal band of Broca neurons participate in a central pathway mediating the inhibitory effects of peripheral baroreceptor stimulation on the activity of vasopressin‐secreting neurons in the rat supraoptic nucleus.
Comparative Evaluation of MPT83 (Rv2873) for T Helper-1 Cell Reactivity and Identification of HLA-Promiscuous Peptides in Mycobacterium bovis BCG-Vaccinated Healthy Subjects

ABSTRACT MPT83 (Rv2873), a surface lipoprotein excreted in the culture of Mycobacterium tuberculosis, is immunoreactive in antibody assays in humans and animals and provides protection as a combined DNA vaccine in mice and cattle. This study was undertaken to determine the reactivity of MPT83 in T helper 1 (Th1)-cell assays, i.e., antigen-induced proliferation and gamma interferon (IFN-γ) secretion, using peripheral blood mononuclear cells (PBMCs) obtained from Mycobacterium bovis bacillus Calmette-Guérin (BCG)-vaccinated and/or M. tuberculosis-infected healthy subjects. PBMCs were tested with complex mycobacterial antigens and pools of synthetic peptides corresponding to MPT63, MPT83, MPB70, LppX, PPE68, CFP10, and ESAT-6. The results showed that MPT83 is among the strongest Th1 cell antigens of M. tuberculosis, and it was recognized equally strongly by BCG-vaccinated and by BCG-vaccinated and M. tuberculosis-infected healthy subjects. Furthermore, HLA heterogeneity of the responding donors suggested that MPT83 was presented to Th1 cells by several HLA-DR molecules. The analysis of the mature MPT83 sequence (amino acids [aa] 1 to 220) and its 14 overlapping synthetic peptides for binding prediction to HLA class II molecules and actual recognition of the peptides by PBMCs from HLA-DR-typed subjects in antigen-induced proliferation and IFN-γ assays suggested that Th1 cell epitopes were scattered throughout the sequence of MPT83. In addition, the HLA-promiscuous nature of at least three peptides, i.e., P11 (aa 151 to 175), P12 (aa 166 to 190), and P14 (aa 196 to 220), was suggested by HLA-DR binding predictions and recognition by HLA-DR heterogeneous donors in Th1 cell assays. These results support the inclusion of MPT83 in an antigen cocktail to develop a new antituberculosis vaccine.
After revision anterior cruciate ligament reconstruction, who returns to sport? A systematic review and meta-analysis

Background Return to sport and to pre-injury level represents an important outcome after both primary and revision anterior cruciate ligament (ACL) reconstructions. Purpose The aim of the present meta-analysis was to determine the return to sport rate after revision ACL reconstruction. Material and methods A systematic search was performed of the MEDLINE, Embase and the Cochrane Central Register of Controlled Trials Databases. All the studies that reported return to sport, return to pre-injury sport level and return to high level/competitive sport was considered for the meta-analysis. The overall pooled mean of post-operative knee laxity and pooled rate of positive pivot-shift and objective International Knee Documentation Committee (IKDC) categories was calculated as well. Results Overall, 472 abstracts were identified and screened for inclusion and only 16 studies reported the rate of return to any level of sport activity at the final follow-up of 4.7 years (range 1.0–13.2 years), showing a pooled rate of 85.3% (CI 79.7 to 90.2). The return to pre-injury sport level was achieved in 53.4% (CI 37.8 to 68.7) of cases. Normal or quasi-normal objective IKDC, less than 5 mm of side-to-side difference at arthrometric evaluations and grade I-II pivot-shift test were reported in 84%, 88% and 93% patients, respectively. Conclusions In spite of almost 8 patients out of 10 returning to sport after revision ACL reconstruction and showing good stability, only half of the patients returned to the same pre-injury sport level.
Altered Neuronal Excitability in Cerebellar Granule Cells of Mice Lacking Calretinin

Calcium-binding proteins such as calretinin are abundantly expressed in distinctive patterns in the CNS, but their physiological function remains poorly understood. Calretinin is expressed in cerebellar granule cells, which provide the major excitatory input to Purkinje cells through parallel fibers. Calretinin-deficient mice exhibit dramatic alterations in motor coordination and Purkinje cell firing recorded in vivo through unknown mechanisms. In the present study, we used patch-clamp recording techniques in acute slice preparation to investigate the effect of a null mutation of the calretinin gene on the intrinsic electroresponsiveness of cerebellar granule cells at a mature developmental stage. Calretinin-deficient granule cells exhibit faster action potentials and generate repetitive spike discharge showing an enhanced frequency increase with injected currents. These alterations disappear when 0.15 mm of the exogenous fast-calcium buffer BAPTA is infused in the cytosol to restore the calcium-buffering capacity. A proposed mathematical model demonstrates that the observed alterations of granule cell excitability can be explained by a decreased cytosolic calcium-buffering capacity resulting from the absence of calretinin. This result suggests that calcium-binding proteins modulate intrinsic neuronal excitability and may therefore play a role in information processing in the CNS.
Posttraumatic Stress Disorder in the Child of an Adult Burn Victim: A Case Report and Review of the Literature

Adults with a myriad of medical and surgical conditions are at risk for pain, delirium, and disfigurement. Needless to say, these critical illnesses are profoundly stressful for patients and their caregivers. However, physicians rarely consider the reactions of children to their parents’ illnesses. The article presents the case of a 15-year-old girl who developed posttraumatic stress disorder following her mother’s severe burn and complicated course in a critical care unit; the case is used to discuss strategies for the detection of psychological vulnerability and for the implementation of care. By learning more about the children of adult patients, by screening for interpersonal dysfunction, and by maximizing support systems, clinicians can improve function and minimize distress.
Brainstem Auditory Evoked Responses in Foals: Reference Values, Effect of Age, Rate of Acoustic Stimulation, and Neurologic Deficits

Background Age and rate of acoustic stimulation affect peak latencies in brainstem auditory evoked responses (BAER) in humans. Those effects are unknown in foals. Hypothesis/Objectives Our goals were to (1) establish reference values for BAER in foals by using 3 different stimulation protocols, (2) evaluate the effects of age and stimulation frequencies on BAER tracing in foals up to 6 months old, and (3) compare the data with BAER obtained from foals with central nervous system (CNS) disorders. Animals Thirty‐nine neurologically normal foals and 16 foals with neurologic diseases. Methods Prospective observational clinical study. BAER recorded by using 3 protocols of stimulation (11.33 repetitions per second [Hz]/70 decibel normal hearing level [dBNHL]; 11.33 Hz/90 dBNHL; 90 Hz/70 dBNHL). Results No effect of age was observed in normal foals (P > .005). No significant difference was observed for latencies and interpeak latencies (IPL) when comparing foals with neurologic diseases and normal foals (P > .05), but 78.6% of foals with neurologic diseases had an asymmetry in their tracing, reflecting a difference in conduction time between the left and right side of the brainstem. Increasing the stimulation rate did not improve detection of CNS disorders. Conclusions and Clinical Importance We propose BAER reference values for foals up to 6 months of age by using 3 protocols. Most foals with neurologic deficits had abnormal BAER tracing.
0νββ and 2νββ nuclear matrix elements, quasiparticle random-phase approximation, and isospin symmetry restoration

Within the quasiparticle random-phase approximation (QRPA) we achieve partial restoration of the isospin symmetry and hence fulfillment of the requirement that the 2νββ Fermi matrix element M^(2ν)_F vanishes, as it should, unlike in the previous version of the method. This is accomplished by separating the renormalization parameter g_pp of the particle-particle proton-neutron interaction into isovector and isoscalar parts. The isovector parameter g^(T=1)_(pp) needs to be chosen to be essentially equal to the pairing constant g_pair, so no new parameter is needed. For the 0νββ decay the Fermi matrix element M^(0ν)_F is substantially reduced, while the full matrix element M^(0ν) is reduced by ≈10%. We argue that this more consistent approach should be used from now on in the proton-neutron QRPA and in analogous methods
PARIS: Probabilistic Alignment of Relations, Instances, and Schema

One of the main challenges that the Semantic Web faces is the integration of a growing number of independently designed ontologies. In this work, we present paris, an approach for the automatic alignment of ontologies. paris aligns not only instances, but also relations and classes. Alignments at the instance level cross-fertilize with alignments at the schema level. Thereby, our system provides a truly holistic solution to the problem of ontology alignment. The heart of the approach is probabilistic, i.e., we measure degrees of matchings based on probability estimates. This allows paris to run without any parameter tuning. We demonstrate the efficiency of the algorithm and its precision through extensive experiments. In particular, we obtain a precision of around 90% in experiments with some of the world's largest ontologies.
Cardiomyocytes of Noncardiac Origin in Myocardial Biopsies of Human Transplanted Hearts

Background—Cell replacement therapy with stem cells able to differentiate into cardiomyocytes has been discussed as a method for remodeling damaged myocardium. A physiological or pathophysiological situation in which this phenomenon might be relevant is not known. We studied the origin of cardiomyocytes in myocardial biopsies of male patients that had undergone sex-mismatched cardiac transplantation to determine whether cells containing a Y chromosome (and therefore being of recipient origin) are able to differentiate into cardiomyocytes. Methods and Results—Myocardial biopsies (n=21) were obtained from the right ventricles of male patients (n=13) who had undergone sex-mismatched heart transplantation. Tissue from 1 nontransplanted male and myocardial biopsies from sex-matched heart–transplanted patients served as controls. Cells from donor and recipient origins were identified by fluorescence in situ hybridization with the use of specific probes for X and Y chromosomes on paraffin sections of the biopsies. Cell types were identified by using immunostaining procedures on the same tissue sections. Cardiomyocytes of recipient origin were detected in 8 of 13 male recipients of female hearts. They were connected by gap junctions with adjacent myocytes. Of the cardiomyocyte nuclei, 0.16±0.04% (mean±SEM, median 0.09%) contained the Y-chromosomal marker. There was no detectable correlation with the extent or number of rejection episodes, time of transplantation, or medical treatment regimen. Conclusions—These results show that regeneration by cells of noncardiac origin (differentiated into cardiomyocytes and physiologically linked to neighboring myocytes) can be detected even in small myocardial biopsies. This may lead to new diagnostic and therapeutic strategies in the treatment of myocardial infarction, inflammatory heart disease, and/or heart failure.
Novel Perfused Compression Bioreactor System as an in vitro Model to Investigate Fracture Healing

Secondary bone fracture healing is a physiological process that leads to functional tissue regeneration via endochondral bone formation. In vivo studies have demonstrated that early mobilization and the application of mechanical loads enhances the process of fracture healing. However, the influence of specific mechanical stimuli and particular effects during specific phases of fracture healing remain to be elucidated. In this work, we have developed and provided proof-of-concept of an in vitro human organotypic model of physiological loading of a cartilage callus, based on a novel perfused compression bioreactor (PCB) system. We then used the fracture callus model to investigate the regulatory role of dynamic mechanical loading. Our findings provide a proof-of-principle that dynamic mechanical loading applied by the PCB can enhance the maturation process of mesenchymal stromal cells toward late hypertrophic chondrocytes and the mineralization of the deposited extracellular matrix. The PCB provides a promising tool to study fracture healing and for the in vitro assessment of alternative fracture treatments based on engineered tissue grafts or pharmaceutical compounds, allowing for the reduction of animal experiments.
Spondyloarthritis research Consortium of Canada magnetic resonance imaging index for assessment of sacroiliac joint inflammation in ankylosing spondylitis.

OBJECTIVE To develop a feasible magnetic resonance imaging (MRI)-based scoring system for sacroiliac joint inflammation in patients with ankylosing spondylitis (AS) that requires minimal scan time, does not require contrast enhancement, evaluates lesions separately at each articular surface, and limits the number of sacroiliac images that are scored. METHODS A scoring method based on the assessment of increased signal denoting bone marrow edema on T2-weighted STIR sequences was used. MRI films were assessed blindly in random order at 2 sites by multiple readers. Intra- and interreader reliability was assessed by intraclass correlation coefficient (ICC); the 24-week response of patients with AS randomized to placebo:infliximab (3:8) was assessed by effect size and standardized response mean. The reliability and responsiveness of the scoring method were compared for STIR and gadolinium diethylenetriaminepentaacetic (Gd-DTPA)-enhanced MRI sequences. RESULTS We scanned 11 patients with AS with clinically active disease and 11 additional patients randomized to the trial of infliximab therapy. ICC for total sacroiliac joint STIR score ranged from 0.90 to 0.98 (P < 0.00001) and interobserver ICC for combined readers from the 2 sites was 0.84 (P < 0.0001). ICC for change scores was lower for STIR (ICC 0.53) than for Gd-DTPA-enhanced sequences (ICC 0.79). Responsiveness was poor, although fusion was evident in one-third of patients who received treatment (placebo:infliximab) and inflammation scores were low. CONCLUSION The Spondyloarthritis Research Consortium of Canada MRI index is a feasible and reproducible index for measuring sacroiliac joint inflammation in patients with AS.