Miracle-dz/UniFAR-FTUs huggingface dataset:
Interleukin-12 and -18 levels in peritoneal dialysate effluent correlate with the outcome of peritonitis in patients undergoing peritoneal dialysis: implications for the Type I/Type II T-cell immune response.

BACKGROUND We previously showed that a positive impact of peritoneal defense response on the outcome of peritoneal dialysis (PD)-related peritonitis is characterized by an increased pattern of peritoneal CD4/CD8 T-cell ratio with a predominant CD4(+)-T helper subtype 1 phenotype. To further explore longitudinal changes in peritoneal immunity during PD-related peritonitis, we examined the production of interleukin 12 (IL-12), IL-18, and interferon gamma (IFN-gamma) in peritoneal dialysate effluent (PDE) and kinetic expression of the transcription factors T box expressed in T cells (T-bet) and guanine adenine thymine adenine (GATA) binding protein 3 (GATA-3) in peritoneal T cells during peritonitis. Correlations between these observations and responses to antibiotics were analyzed. METHODS IL-12, IL-18, and IFN-gamma protein and IFN-gamma, T-bet, and GATA-3 messenger RNA (mRNA) were measured in PDE during various phases of peritonitis in 40 patients undergoing PD. Patients were divided into 2 groups according to whether they had a rapid versus delayed response to antibiotic treatment. RESULTS In the early phase of peritonitis, IL-12, IL-18, and IFN-gamma levels in PDE were significantly greater in the rapid-response group (P < 0.05). Changes in peritoneal IL-12 and IL-18 levels preceded changes in IFN-gamma levels. The kinetics of IFN-gamma, T-bet, and GATA-3 mRNA expression in peritoneal T cells, measured by means of real-time polymerase chain reaction, differed between the 2 groups. In the rapid-response group, IFN-gamma and T-bet mRNA expression increased, whereas that of GATA-3 decreased over time. Results were opposite in the delayed-response group, with IFN-gamma and T-bet levels decreasing and GATA-3 levels increasing over time. CONCLUSION These data suggest that local IL-12 and IL-18 production is part of a protective early immune response to PD-related peritonitis. High IL-12 and IL-18 levels in PDE during the early phase of peritonitis correlated with a predominant type 1 immune response and favorable outcome.
Pregnancy and delivery in women after Fontan palliation

Objectives: To evaluate the outcome of pregnancy in women after Fontan palliation and to assess the occurrence of infertility and menstrual cycle disorders. Design and patients: Two congenital heart disease registries were used to investigate 38 female patients who had undergone Fontan palliation (aged 18–45 years): atriopulmonary anastomosis (n = 23), atrioventricular connection (n = 5) and total cavopulmonary connection (n = 10). Results: Six women had 10 pregnancies, including five miscarriages (50%) and one aborted ectopic pregnancy. During the remaining four live-birth pregnancies clinically significant complications were encountered: New York Heart Association class deterioration; atrial fibrillation; gestational hypertension; premature rupture of membranes; premature delivery; fetal growth retardation and neonatal death. Four of seven women who had attempted to become pregnant reported female infertility: non-specified secondary infertility (n = 2), uterus bicornis (n = 1) and related to endometriosis (n = 1). Moreover, several important menstrual cycle disorders were documented. In particular, the incidence of primary amenorrhoea was high (n = 15, 40%), which resulted in a significant increase in age at menarche (14.6 (SD 2.1) years, p < 0.0001, compared with the general population). Conclusion: Women can successfully complete pregnancy after adequate Fontan palliation without important long-term sequelae, although it is often complicated by clinically significant (non-)cardiac events. In addition, subfertility or infertility and menstrual disorders were common.
Iterative multiuser joint decoding: optimal power allocation and low-complexity implementation

We consider a canonical model for coded code-division multiple access (CDMA) with random spreading, where the receiver makes use of iterative belief-propagation (BP) joint decoding. We provide simple density-evolution analysis in the large-system limit (large number of users) of the performance of the BP decoder and of some suboptimal approximations based on interference cancellation (IC). Based on this analysis, we optimize the received user signal-to-noise ratio (SNR) distribution in order to maximize the system spectral efficiency for given user channel codes, channel load (users per chip), and target user bit-error rate (BER). The optimization of the received SNR distribution is obtained by solving a simple linear program and can be easily incorporated into practical power control algorithms. Remarkably, under the optimized SNR assignment, the suboptimal minimum mean-square error (MMSE) IC-based decoder performs almost as well as the more complex BP decoder. Moreover, for a large class of commonly used convolutional codes, we observe that the optimized SNR distribution consists of a finite number of discrete SNR levels. Based on this observation, we provide a low-complexity approximation of the MMSE-IC decoder that suffers from very small performance degradation while attaining considerable savings in complexity. As by-products of this work, we obtain a closed-form expression of the multiuser efficiency (ME) of power-mismatched MMSE filters in the large-system limit, and we extend the analysis of the symbol-by-symbol maximum a posteriori probability (MAP) multiuser detector in the large-system limit to the case of nonconstant user powers and nonuniform symbol prior probabilities.
Annals of the New York Academy of Sciences Graded Specialization within and between the Anterior Temporal Lobes

Considerable evidence from different methodologies has identified the anterior temporal lobes (ATLs) as key regions for the representation of semantic knowledge. Research interest is now shifting to investigate the roles of different ATL subregions in semantic representation, with particular emphasis on the functions of the left versus right ATLs. In this review, we provide evidence for graded specializations both between and within the ATLs. We argue (1) that multimodal, pan-category semantic representations are supported jointly by both left and right ATLs, yet (2) that the ATLs are not homogeneous in their function. Instead, subtle functional gradations both between and within the ATLs emerge as a consequence of differential connectivity with primary sensory/motor/limbic regions. This graded specialization account of semantic representation provides a compromise between theories that posit no differences between the functions of the left and right ATLs and those that posit that the left and right ATLs are entirely segregated in function. Evidence for this graded account comes from converging sources, and its benefits have been exemplified in formal computational models. We propose that this graded principle is not only a defining feature of the ATLs but is also a more general neurocomputational principle found throughout the temporal lobes.
Oxygen: an anti-inflammatory drug.

• Vol 9 • December 2007 874 Impaired tissue oxygenation and cellular hypoxia are major components in the pathophysiology of a large variety of clinical conditions, including acute and chronic ischemia, wounds and tissue trauma, infections, physical and chemical injuries, as well as inflammatory joint and connective tissue diseases [1]. Tissue hypoxia triggers an inflammatory response. Mechanisms of the intimate relationship between hypoxia and inflammation are gradually being elucidated and are expected to lead to the development of new treatment modalities to alleviate local destruction and also harness the systemic effects of exaggerated inflammatory response [1]. Evidently, the purpose of hypoxia-induced inflammation is to combat invasive microorganisms, clear tissue debris, and enhance tissue repair. However, too often the delicate balance between beneficial and potentially detrimental consequences of inflammation is impaired, causing local tissue damage and frequently culminating in a systemic inflammatory response that involves many organs and may lead to multiple organ dysfunction and failure [2]. In light of the key role of tissue hypoxia in the initiation and propagation of local and systemic inflammatory responses, evaluating the effects of treatment with oxygen at high ambient partial pressures in these conditions is called for. Inhalation of oxygen increases oxygen delivery. A small addition to oxygen delivery is attained by an increase in hemoglobin saturation to 100%, and a significantly higher increment is achieved by physically dissolved oxygen in the plasma. The amount of dissolved oxygen increases in direct proportion to the ambient pressure. Altogether, this accounts for a rather modest (~10%) increase in arterial blood oxygen content during inhalation of 100% oxygen at normal atmospheric pressure, and a 30% increase during hyperbaric exposure to oxygen at 3 atmospheres [3,4]. The amount of physically dissolved oxygen in the plasma during exposure to 100% oxygen at 3 atmospheres (about 6 vol%) is sufficient to meet the average requirements of the tissues by means of dissolved oxygen alone. It should be emphasized, however, that the predominant change in oxygen availability to tissues during exposure to hyperoxia is not solely dependent upon the increase in oxygen content but is determined by the much more significant increase in arterial blood oxygen partial pressure. This increases from around 90 mmHg while breathing air at normal atmospheric pressure to values five to sevenfold higher while breathing 100% oxygen at normal atmospheric pressure, and may reach values higher than 2000 mmHg during hyperbaric exposure at 3 atmospheres. This rather dramatic increase in arterial blood oxygen pressures and the manifold increase in oxygen partial pressure gradient from the blood to the tissues account for the markedly facilitated diffusion of oxygen to tissues during hyperoxic exposures and to significantly improved tissue oxygenation [3,4].
Oxidative Regulation of Large Conductance Calcium-Activated Potassium Channels

Reactive oxygen/nitrogen species are readily generated in vivo, playing roles in many physiological and pathological conditions, such as Alzheimer's disease and Parkinson's disease, by oxidatively modifying various proteins. Previous studies indicate that large conductance Ca2+-activated K+ channels (BKCa or Slo) are subject to redox regulation. However, conflicting results exist whether oxidation increases or decreases the channel activity. We used chloramine-T, which preferentially oxidizes methionine, to examine the functional consequences of methionine oxidation in the cloned human Slo (hSlo) channel expressed in mammalian cells. In the virtual absence of Ca2+, the oxidant shifted the steady-state macroscopic conductance to a more negative direction and slowed deactivation. The results obtained suggest that oxidation enhances specific voltage-dependent opening transitions and slows the rate-limiting closing transition. Enhancement of the hSlo activity was partially reversed by the enzyme peptide methionine sulfoxide reductase, suggesting that the upregulation is mediated by methionine oxidation. In contrast, hydrogen peroxide and cysteine-specific reagents, DTNB, MTSEA, and PCMB, decreased the channel activity. Chloramine-T was much less effective when concurrently applied with the K+ channel blocker TEA, which is consistent with the possibility that the target methionine lies within the channel pore. Regulation of the Slo channel by methionine oxidation may represent an important link between cellular electrical excitability and metabolism.
A probability‐based analysis of temporal and spatial co‐occurrence in grassland birds

Aim To test for non‐random co‐occurrence in 36 species of grassland birds using a new metric and the C‐score. The analysis used presence–absence data of birds distributed among 305 sites (or landscapes) over a period of 35 years. This analysis departs from traditional analyses of species co‐occurrence in its use of temporal data and of individual species’ probabilities of occurrence to derive analytically the expected co‐occurrence between paired species.
Chancroid and Haemophilus ducreyi

Haemophilus ducreyi is the causative agent of chancroid, one of the genital ulcerative diseases. H. ducreyi is the major cause of genital ulcer disease in Africa and Southeast Asia and is of increasing concern in the United States. Definitive diagnosis of chancroid requires the isolation and identification of H. ducreyi, but isolation of this organism is difficult and the available medium is not optimal for all strains. Fluorescent antibody and serologic tests are of limited value. In general, our knowledge of this organism is rather limited, and indeed, recent studies have questioned the placement of H. ducreyi in the genus Haemophilus. H. ducreyi has relatively few biochemical activities, and epidemiologic studies are limited because there are limited phenotypic markers available for strain typing. Specific virulence factors of H. ducreyi have yet to be identified. Antimicrobial resistance in H. ducreyi is of special concern, as this organism has acquired both gram-negative and gram-positive resistance determinants. In addition, some of these determinants can be mobilized and transferred to other Haemophilus species or to Neisseria gonorrhoeae.
Survival rates of parasite eggs in sludge during aerobic and anaerobic digestion

The effects of mesothermic anaerobic or aerobic sludge digestion on survival of eggs from the roundworms Ascaris suum, toxocara canis, Trichuris vulpis, and Trichuris suis and from the rat tapeworm Hymenolepis diminuta were studied. Destruction of eggs throughout a 15-day treatment period, as well as their viabilities after reisolation, was analyzed. The laboratory model digesters used in this study were maintained at a 15-day retention schedule, partially simulating a continuously operating system. Ascaris eggs were destroyed in the anaerobic (23%) or aerobic (38%) digesters, and 11% Trichuris eggs were destroyed in the aerobic digesters. Trichuris eggs in anaerobic digesters and Toxocara eggs in either anaerobic or aerobic digesters were not destroyed. Destruction of eggs in digesters was correlated with the state of the eggs before subjection to the treatment processes; i.e., some Ascaris and Trichuris eggs were already embryonated in host intestinal contents or feces and hence past their most resistant stage. The viabilities of Ascaris and Toxocara eggs that survived the digestion processes were greater in anaerobically treated than in aerobically treated material. Eggs from Hymenolepis were nonviable before use in the experiments. However, they were more effectively destroyed in aerobic digesters than in anaerobic digesters.
Grafted Human Embryonic Progenitors Expressing Neurogenin-2 Stimulate Axonal Sprouting and Improve Motor Recovery after Severe Spinal Cord Injury

Background Spinal cord injury (SCI) is a widely spread pathology with currently no effective treatment for any symptom. Regenerative medicine through cell transplantation is a very attractive strategy and may be used in different non-exclusive ways to promote functional recovery. We investigated functional and structural outcomes after grafting human embryonic neural progenitors (hENPs) in spinal cord-lesioned rats. Methods and Principal Findings With the objective of translation to clinics we have chosen a paradigm of delayed grafting, i.e., one week after lesion, in a severe model of spinal cord compression in adult rats. hENPs were either naïve or engineered to express Neurogenin 2 (Ngn2). Moreover, we have compared integrating and non-integrating lentiviral vectors, since the latter present reduced risks of insertional mutagenesis. We show that transplantation of hENPs transduced to express Ngn2 fully restore weight support and improve functional motor recovery after severe spinal cord compression at thoracic level. This was correlated with partial restoration of serotonin innervations at lumbar level, and translocation of 5HT1A receptors to the plasma membrane of motoneurons. Since hENPs were not detectable 4 weeks after grafting, transitory expression of Ngn2 appears sufficient to achieve motor recovery and to permit axonal regeneration. Importantly, we also demonstrate that transplantation of naïve hENPs is detrimental to functional recovery. Conclusions and Significance Transplantation and short-term survival of Ngn2-expressing hENPs restore weight support after SCI and partially restore serotonin fibers density and 5HT1A receptor pattern caudal to the lesion. Moreover, grafting of naïve-hENPs was found to worsen the outcome versus injured only animals, thus pointing to the possible detrimental effect of stem cell-based therapy per se in SCI. This is of major importance given the increasing number of clinical trials involving cell grafting developed for SCI patients.
Ampicillin-Improved Glucose Tolerance in Diet-Induced Obese C57BL/6NTac Mice Is Age Dependent

Ampicillin has been shown to improve glucose tolerance in mice. We hypothesized that this effect is present only if treatment is initiated prior to weaning and that it disappears when treatment is terminated. High-fat fed C57BL/6NTac mice were divided into groups that received Ampicillin at different ages or not at all. We found that both diet and Ampicillin significantly changed the gut microbiota composition in the animals. Furthermore, there was a significant improvement in glucose tolerance in Ampicillin-treated, five-week-old mice compared to nontreated mice in the control group. At study termination, expressions of mRNA coding for tumor necrosis factor, serum amyloid A, and lactase were upregulated, while the expression of tumor necrosis factor (ligand) superfamily member 15 was downregulated in the ileum of Ampicillin-treated mice. Higher dendritic cell percentages were found systemically in high-fat diet mice, and a lower tolerogenic dendritic cell percentage was found both in relation to high-fat diet and late Ampicillin treatment. The results support our hypothesis that a “window” exists early in life in which an alteration of the gut microbiota affects glucose tolerance as well as development of gut immunity and that this window may disappear after weaning.
Wavelet linear density estimation for associated stratified size-biased sample

Ramirez and Vidakovic [(2010), ‘Wavelet Density Estimation for Stratified Size-Biased Sample’, Journal of Statistical Planning and Inference, 140, 419–432] considered an estimator of the density function based on wavelets with independent stratified random variables from weighted distributions. They proved that it is L 2-consistent. In this paper, we complete this result by determining the rate of convergence attained by a slightly modified version of their estimator (including an estimator of the normalisation parameters). Then, we explore the case when the random variables are negatively and positively associated within strata. The theory is illustrated with a simulation study.
Estimating Diffusion Network Structures: Recovery Conditions, Sample Complexity & Soft-thresholding Algorithm

Information spreads across social and technological networks, but often the network structures are hidden from us and we only observe the traces left by the diffusion processes, called cascades. Can we recover the hidden network structures from these observed cascades? What kind of cascades and how many cascades do we need? Are there some network structures which are more difficult than others to recover? Can we design efficient inference algorithms with provable guarantees? Despite the increasing availability of cascade-data and methods for inferring networks from these data, a thorough theoretical understanding of the above questions remains largely unexplored in the literature. In this paper, we investigate the network structure inference problem for a general family of continuous-time diffusion models using an [Formula: see text]-regularized likelihood maximization framework. We show that, as long as the cascade sampling process satisfies a natural incoherence condition, our framework can recover the correct network structure with high probability if we observe O(d3 log N) cascades, where d is the maximum number of parents of a node and N is the total number of nodes. Moreover, we develop a simple and efficient soft-thresholding inference algorithm, which we use to illustrate the consequences of our theoretical results, and show that our framework outperforms other alternatives in practice.
Amino Acid Substitutions in VP2 Residues Contacting Sialic Acid in Low-Neurovirulence BeAn Virus Dramatically Reduce Viral Binding and Spread of Infection

ABSTRACT Theiler's murine encephalomyelitis viruses (TMEV) consist of two groups, the high- and low-neurovirulence groups, based on lethality in intracerebrally inoculated mice. Low-neurovirulence TMEV result in a persistent central nervous system infection in mice, leading to an inflammatory demyelinating pathology and disease. Low- but not high-neurovirulence strains use sialic acid as an attachment factor. The recent resolution of the crystal structure of the low-neurovirulence DA virus in complex with the sialic acid mimic sialyllactose demonstrated that four capsid residues make contact with sialic acid through noncovalent hydrogen bonds. To systematically test the importance of these sialic acid-binding residues in viral entry and infection, we mutated three VP2 puff B amino acids proposed to make contact with sialic acid and analyzed the consequences of each amino acid substitution on viral entry and spread. The fourth residue is in the VP3-VP1 cleavage dipeptide and could not be mutated. Our data suggest that residues Q2161 and G2174 are directly involved in BeAn virus attachment to sialic acid and that substitutions of these two residues result in the loss of or reduced viral binding and hemagglutination and in the inability to spread among BHK-21 cells. In addition, a gain of function-revertant virus was recovered with the Q2161A mutation after prolonged passage in cells.
Production-Run Software Failure Diagnosis via Adaptive Communication Tracking

Software failure diagnosis techniques work either by sampling some events at production-run time or by using some bug detection algorithms. Some of the techniques require the failure to be reproduced multiple times. The ones that do not require such, are not adaptive enough when the execution platform, environment or code changes. We propose ACT, a diagnosis technique for production-run failures, that uses the machine intelligence of neural hardware. ACT learns some invariants (e.g., data communication invariants) on-the-fly using the neural hardware and records any potential violation of them. Since ACT can learn invariants on-the-fly, it can adapt to any change in execution setting or code. Since it records only the potentially violated invariants, the postprocessing phase can pinpoint the root cause fairly accurately without requiring to observe the failure again. ACT works seamlessly for many sequential and concurrency bugs. The paper provides a detailed design and implementation of ACT in a typical multiprocessor system. It uses a three stage pipeline for partially configurable one hidden layer neural networks. We have evaluated ACT on a variety of programs from popular benchmarks as well as open source programs. ACT diagnoses failures caused by 16 bugs from these programs with accurate ranking. Compared to existing learning and sampling based approaches, ACT has better diagnostic ability. For the default configuration, ACT has an average execution overhead of 8.2%.