Miracle-dz/UniFAR-FTUs huggingface dataset:
Organisms causing spontaneous bacterial peritonitis in children with liver disease and ascites in Southern Iran.

AIM To determine the causative agents of spontaneous bacterial peritonitis (SBP) in children with liver disease and ascites in our center. METHODS During a 2.5 year period, from September 2003 to March 2006, 12 patients with 13 episodes of SBP were studied. In all cases at the time of admission serum albumin and glucose, urinalysis and urine culture was performed. Analysis [white blood cell (WBC) count with differential, albumin, glucose], gram stain, culture by BACTEC method and antibiogram was done on ascitic fluids. Abdominal paracentesis was repeated after 48 h of antibiotic therapy for bacteriologic assay. The patients were followed for at least three months in a gastroenterology clinic. RESULTS There were 7 girls (58%) and 5 boys (42%) with a median age of 5.2 years (range, 6 mo to 16 years). All cases had positive ascitic fluid culture. Gram stain was positive in 5 (38.5%) of them. The isolated organisms were S. pneumoniae in 5 (38.5%), E. coli in 2 (15.3%), S. viridans in 2 (15.3%), and K. pneumoniae, H. influenza, Enterococci, and nontypable Streptococcus each in one (7.7%). All of them except Enterococci were sensitive to ciprofloxacin and ceftriaxone. All ascitic fluid cultures were negative after 48 h of antibiotic therapy. CONCLUSION S. pneumoniae is the most common cause of SBP in the pediatric age group and we recommend a third generation cephalosporine (e.g., Ceftriaxione or Cefotaxime) for empirical therapy in children with SBP.
Estimation of pairwise relatedness between individuals and characterization of isolation‐by‐distance processes using dominant genetic markers

A new estimator of the pairwise relatedness coefficient between individuals adapted to dominant genetic markers is developed. This estimator does not assume genotypes to be in Hardy–Weinberg proportions but requires a knowledge of the departure from these proportions (i.e. the inbreeding coefficient). Simulations show that the estimator provides accurate estimates, except for some particular types of individual pairs such as full‐sibs, and performs better than a previously developed estimator. When comparing marker‐based relatedness estimates with pedigree expectations, a new approach to account for the change of the reference population is developed and shown to perform satisfactorily. Simulations also illustrate that this new relatedness estimator can be used to characterize isolation by distance within populations, leading to essentially unbiased estimates of the neighbourhood size. In this context, the estimator appears fairly robust to moderate errors made on the assumed inbreeding coefficient. The analysis of real data sets suggests that dominant markers (random amplified polymorphic DNA, amplified fragment length polymorphism) may be as valuable as co‐dominant markers (microsatellites) in studying microgeographic isolation‐by‐distance processes. It is argued that the estimators developed should find major applications, notably for conservation biology.
Crystal structures of λ exonuclease in complex with DNA suggest an electrostatic ratchet mechanism for processivity

The λ exonuclease is an ATP-independent enzyme that binds to dsDNA ends and processively digests the 5′-ended strand to form 5′ mononucleotides and a long 3′ overhang. The crystal structure of λ exonuclease revealed a toroidal homotrimer with a central funnel-shaped channel for tracking along the DNA, and a mechanism for processivity based on topological linkage of the trimer to the DNA was proposed. Here, we have determined the crystal structure of λ exonuclease in complex with DNA at 1.88-Å resolution. The structure reveals that the enzyme unwinds the DNA prior to cleavage, such that two nucleotides of the 5′-ended strand insert into the active site of one subunit of the trimer, while the 3′-ended strand passes through the central channel to emerge out the back of the trimer. Unwinding of the DNA is facilitated by several apolar residues, including Leu78, that wedge into the base pairs at the single/double-strand junction to form favorable hydrophobic interactions. The terminal 5′ phosphate of the DNA binds to a positively charged pocket buried at the end of the active site, while the scissile phosphate bridges two active site Mg2+ ions. Our data suggest a mechanism for processivity in which wedging of Leu78 and other apolar residues into the base pairs of the DNA restricts backward movement, whereas attraction of the 5′ phosphate to the positively charged pocket drives forward movement of the enzyme along the DNA at each cycle of the reaction. Thus, processivity of λ exonuclease operates not only at the level of the trimer, but also at the level of the monomer.
Comparative Diagnostic Performance of Ultrasonography and 99mTc-Sestamibi Scintigraphy for Parathyroid Adenoma in Primary Hyperparathyroidism; Systematic Review and Meta-Analysis

Objective: Ultrasonography (US) and parathyroid scintigraphy (PS) with 99mTc-MIBI are common methods for preoperative localization of parathyroid adenomas but there discrepancies exist with regard to diagnostic accuracy. The aim of the study was to compare PS and US for localization of parathyroid adenoma with a systematic review and meta-analysis of the literature. Methods: Pub Med, Scopus (EMbase), Web of Science and the reference lists of all included studies were searched up to 1st January 2016. The search strategy was according PICO characteristics. Heterogeneity between the studies was accounted by P < 0.1. Point estimates were pooled estimate of sensitivity, specificity and positive predictive value of SPECT and ultrasonography with 99% confidence intervals (CIs) by pooling available data. Data analysis was performed using Meta-DiSc software (version 1.4). Results: Among 188 studies and after deletion of duplicated studies (75), a total of 113 titles and abstracts were studied. From these, 12 studies were selected. The meta-analysis determined a pooled sensitivity for scintigraphy of 83% [99% confidence interval (CI) 96.358 -97.412] and for ultra-sonography of 80% [99% confidence interval (CI) 76-83]. Similar results for specificity were also obtained for both approache. Conclusion: According this meta- analysis, there were no significant differences between the two methods in terms of sensitivity and specificity. There were overlaps in 99% confidence intervals. Also features of the two methods are similar.
The role of pro‐inflammatory and immunoregulatory cytokines in tendon healing and rupture: new insights

Owing to limited self‐healing capacity, tendon ruptures and healing remain major orthopedic challenges. Increasing evidence suggests that post‐traumatic inflammatory responses, and hence, cytokines are involved in both cases, and also in tendon exercise and homeostasis. This review summarizes interrelations known between the cytokines interleukin (IL)‐1β, tumor necrosis factor (TNF)α, IL‐6 and vascular endothelial growth factor (VEGF) in tendon to assess their role in tendon damage and healing. Exogenic cytokine sources are blood‐derived leukocytes that immigrate in damaged tendon. Endogenous expression of IL‐1β, TNFα, IL‐6, IL‐10 and VEGF was demonstrated in tendon‐derived cells. As tendon is a highly mechanosensitive tissue, cytokine homeostasis and cell survival underlie an intimate balance between adequate biomechanical stimuli and disturbance through load deprivation and overload. Multiple interrelations between cytokines and tendon extracellular matrix (ECM) synthesis, catabolic mediators e.g. matrix‐degrading enzymes, inflammatory and angiogenic factors (COX‐2, PGE2, VEGF, NO) and cytoskeleton assembly are evident. Pro‐inflammatory cytokines affect ECM homeostasis, accelerate remodeling, amplify biomechanical adaptiveness and promote tenocyte apoptosis. This multifaceted interplay might both contribute to and interfere with healing. Much work must be undertaken to understand the particular interrelation of these inflammatory and regulatory mediators in ruptured tendon and healing, which has relevance for the development of novel immunoregulatory therapeutic strategies.
Multiple Actions of Neurturin Correlate with Spatiotemporal Patterns of Ret Expression in Developing Chick Cranial Ganglion Neurons

The neurotrophic effects of neurturin (NRTN) on chick cranial ganglia were evaluated at various embryonic stages in vitro and related to its receptor expression. NRTN promoted the outgrowth and survival of ciliary ganglion neurons at early embryonic (E) stages (E6–E12), trigeminal ganglion neurons at midstages (E9–E16), and vestibular ganglion neurons at late stages (E12–E16). NRTN had no positive effects on cochlear ganglion neurons throughout development. In accordance with the time and order of onset in NRTN responsiveness, Ret protein was first detected in ciliary ganglia at E6, subsequently in trigeminal ganglia at E9, and in vestibular ganglia at E12. Ret was absent in E16 ciliary ganglia as well as in cochlear ganglia at all developmental stages that were tested. Exogenous application of retinoic acid induced NRTN responsiveness and Ret protein expression from E9 vestibular ganglion neurons, suggesting that retinoic acid can regulate Ret protein expression in peripheral sensory neurons in vitro. Ret was confined to the neuron cell body, whereas GFRα was localized predominantly in peripheral and central neurite processes. No noticeable change in GFRα expression was seen in any cranial ganglia throughout the developmental stages that were tested (E6–E16). These results demonstrate that NRTN exerts neurotrophic effects on different cranial ganglia at different developmental stages and that the onset and offset of NRTN responsiveness are regulated mainly by the spatiotemporal patterns of Ret, but not of GFRα receptors. The results also substantiate the recently emerging view that NRTN may be an essential target-derived neurotrophic factor for parasympathetic neurons during development.
Habitual Floor Activities Increase Risk of Knee Osteoarthritis

Knee osteoarthritis is a major worldwide public health problem. Mechanical factors generally are considered important in its pathogenesis. Whether floor activities increase the risk of knee osteoarthritis is unclear. We performed a population-based survey to document the association of floor activities with pattern and severity of knee osteoarthritis. We identified 288 women and 288 men 40 years or older from Songkhla province in southern Thailand. We recorded their lifetime histories of four common positions in floor activities: squatting, lotus, side-knee bending, and kneeling. Involvement of osteoarthritis was categorized in three patterns: isolated patellofemoral, isolated tibiofemoral, and combined. We used multinomial logistic regression analysis adjusted for age, gender, body mass index, and smoking status to identify associations between lifetime floor activity and knee osteo-arthritis. Squatting and side-knee bending positions increased the relative risk of radiographic knee osteoarthritis. All types of floor activities except kneeling increased the risk of moderate to severe radiographic knee osteoarthritis. Squatting and lotus positions increased the relative risk of knee pain with radiographic osteoarthritis. Our data suggest habitual lifetime squatting, lotus, and side-knee bending positions increase the risk of knee osteoarthritis.Level of evidence: Level II, prognostic study. See the Guidelines for Authors for a complete description of levels of evidence.
Enhanced Rap1 Activation and Insulin Secretagogue Properties of an Acetoxymethyl Ester of an Epac-selective Cyclic AMP Analog in Rat INS-1 Cells

To ascertain the identities of cyclic nucleotide-binding proteins that mediate the insulin secretagogue action of cAMP, the possible contributions of the exchange protein directly activated by cAMP (Epac) and protein kinase A (PKA) were evaluated in a pancreatic beta cell line (rat INS-1 cells). Assays of Rap1 activation, CREB phosphorylation, and PKA-dependent gene expression were performed in combination with live cell imaging and high throughput screening of a fluorescence resonance energy transfer-based cAMP sensor (Epac1-camps) to validate the selectivity with which acetoxymethyl esters (AM-esters) of cAMP analogs preferentially activate Epac or PKA. Selective activation of Epac or PKA was achieved following exposure of INS-1 cells to 8-pCPT-2′-O-Me-cAMP-AM or Bt2cAMP-AM, respectively. Both cAMP analogs exerted dose-dependent and glucose metabolism-dependent actions to stimulate insulin secretion, and when each was co-administered with the other, a supra-additive effect was observed. Because 2.4-fold more insulin was secreted in response to a saturating concentration (10 μm) of Bt2cAMP-AM as compared with 8-pCPT-2′-O-Me-cAMP-AM, and because the action of Bt2cAMP-AM but not 8-pCPT-2′-O-Me-cAMP-AM was nearly abrogated by treatment with 3 μm of the PKA inhibitor H-89, it is concluded that for INS-1 cells, it is PKA that acts as the dominant cAMP-binding protein in support of insulin secretion. Unexpectedly, 10–100 μm of the non-AM-ester of 8-pCPT-2′-O-Me-cAMP failed to stimulate insulin secretion and was a weak activator of Rap1 in INS-1 cells. Moreover, 10 μm of the AM-ester of 8-pCPT-2′-O-Me-cAMP stimulated insulin secretion from mouse islets, whereas the non-AM-ester did not. Thus, the membrane permeability of 8-pCPT-2′-O-Me-cAMP in insulin-secreting cells is so low as to limit its biological activity. It is concluded that prior reports documenting the failure of 8-pCPT-2′-O-Me-cAMP to act in beta cells, or other cell types, need to be re-evaluated through the use of the AM-ester of this cAMP analog.
Transcription of granzyme A and B genes is differentially regulated during lymphoid ontogeny

During development, thymocytes express a number of genes typical for activated peripheral T lymphocytes, including granzymes. We have now analyzed by reverse transcription-polymerase chain reaction (RT-PCR), immunohistochemistry, and cytochemistry fetal liver cells and thymocytes at various developmental stages for the expression of granzyme A-G genes. At days 13-17 of gestation, only granzyme B but none of the other granzymes is expressed in fetal liver. In the most immature, Pgp-1+IL2R alpha-, thymocyte subpopulation mRNAs for granzymes A-C but not for granzymes D-G are detectable. Upon further differentiation via Pgp-1-IL-2R alpha + into more mature Pgp-1-IL-2R alpha- thymocytes the level of expression of granzymes A, B, and C gradually declines reaching its lowest level at the CD4+ 8+ double positive stage. In fetal thymic lobes depleted of lymphoid cells by treatment with deoxyguanosine, no transcripts for granzymes A, B, and C were found indicating that the PCR signals are derived exclusively from early precursor T/natural killer (NK) lineage cells rather than from residual stromal elements. In mature CD4+CD8- and CD4-CD8+ thymocytes, granzyme B mRNA is found at similar levels in both subsets whereas granzyme A mRNA is expressed selectively in the CD4-CD8+ subset. Enzymatic activity of granzyme A was only seen in a fraction of CD4- CD8+ thymocytes negative for heat stable antigen (HSA) but not in the more immature HSA+ fraction of CD4-CD8+ thymocytes. The data suggest that (a) granzyme B is a pro-thymocyte marker for all T/NK lineage cells; (b) granzyme A transcripts are associated with thymocytes with the potential to develop into the CD8+ lineage; and (c) granzyme A enzymatic activity is only expressed in the most mature CD4-CD8+ stage, suggesting that granzyme proteins are not involved in early stages of thymocyte development.
Pathophysiology of orthostatic hypotension after bed rest: paradoxical sympathetic withdrawal.

Although orthostatic hypotension is a common clinical syndrome after spaceflight and its ground-based simulation model, 6 degrees head-down bed rest (HDBR), the pathophysiology remains unclear. The authors' hypothesis that a decrease in sympathetic nerve activity is the major pathophysiology underlying orthostatic hypotension after HDBR was tested in a study involving 14-day HDBR in 22 healthy subjects who showed no orthostatic hypotension during 15-min 60 degrees head-up tilt test (HUT) at baseline. After HDBR, 10 of 22 subjects demonstrated orthostatic hypotension during 60 degrees HUT. In subjects with orthostatic hypotension, total activity of muscle sympathetic nerve activity (MSNA) increased less during the first minute of 60 degrees HUT after HDBR (314% of resting supine activity) than before HDBR (523% of resting supine activity, P < 0.05) despite HDBR-induced reduction in plasma volume (13% of plasma volume before HDBR). The postural increase in total MSNA continued during several more minutes of 60 degrees HUT while arterial pressure was maintained. Thereafter, however, total MSNA was paradoxically suppressed by 104% of the resting supine level at the last minute of HUT (P < 0.05 vs. earlier 60 degrees HUT periods). The suppression of total MSNA was accompanied by a 22 +/- 4-mmHg decrease in mean blood pressure (systolic blood pressure <80 mmHg). In contrast, orthostatic activation of total MSNA was preserved throughout 60 degrees HUT in subjects who did not develop orthostatic hypotension. These data support the hypothesis that a decrease in sympathetic nerve activity is the major pathophysiological factor underlying orthostatic hypotension after HDBR. It appears that the diminished sympathetic activity, in combination with other factors associated with HDBR (e.g., hypovolemia), may predispose some individuals to postural hypotension.
Effect of Magnetic Contact on Macroscopic Permeability of Soft Magnetic Composite

It is revealed that the contact of magnetic particles in soft magnetic composite (SMC) significantly increases the macroscopic permeability. It is shown that Ollendorff's formula, which assumes homogenous magnetic particles and insulation layers, underestimates the macroscopic permeability of SMC. It is suggested that the excess in the permeability is due to the local contacts among the magnetic particles. The effect of the magnetic contact is evaluated using a magnetic circuit model.
Cerebrospinal fluid neopterin in human immunodeficiency virus type 1 infection

We evaluated cerebrospinal fluid (CSF) concentrations of neopterin, a putative marker of activated macrophages, in 97 subjects infected with human immunodeficiency virus type 1 who had a spectrum of neurological complications. The highest CSF neopterin concentrations occurred in those with neurological opportunistic infections, primary central nervous systems lymphoma, and acquired immunodeficiency syndrome (AIDS) dementia complex. In general, the CSF concentration of neopterin was independent of CSF cell count and blood‐brain barrier disruption to albumin. In the patients with AIDS dementia complex, CSF neopterin concentrations correlated with severity of disease and decreased in conjunction with clinical improvement following treatment with zidovudine. These results suggest that CSF neopterin, although not disease‐specific, may be useful as a surrogate marker for the presence of AIDS dementia complex and its response to antiviral therapy.
Dose-Volume Analysis of Lung and Heart according to Respiration in Breast Cancer Patients Treated with Breast Conserving Surgery

Purpose Adjuvant radiotherapy of breast cancer using a photon tangential field incurs a risk of late heart and lung toxicity. The use of free breathing (FB), expiration breath hold (EBH), and deep inspiration breath hold (DIBH) during tangential breast radiotherapy as a means of reducing irradiated lung and heart volume was evaluated. Methods In 10 women with left-sided breast cancer (mean age, 44 years) post-operative computed tomography (CT) scanning was done under different respiratory conditions using FB, EBH, and DIBH in 3 CT scans. For each scan, an optimized radiotherapy plan was designed with 6 MV photon tangential fields encompassing the clinical target volume after breast-conserving surgery. Results The results of dose-volume histograms were compared using three breathing pattern techniques for the irradiated volume and dose to the heart. A significant reduction dose to the irradiated heart volume for the DIBH breathing technique was compared to FB and EBH breathing techniques (p<0.05). Conclusion This study demonstrated that the irradiated heart volume can be significantly reduced in patients with left-sided breast cancer using the DIBH breathing technique for tangential radiotherapy.
Phase recovery by unwrapping: applications to music signal processing

This paper introduces a novel technique for reconstructing the phase of modified spectrograms of audio signals. From the analysis of mixtures of sinusoids we obtain relationships between phases of successive time frames in the Time-Frequency (TF) domain. Instantaneous frequencies are estimated locally to encompass the class of non-stationary signals such as vibratos. This technique ensures the horizontal coherence (over time) of the partials. The method is tested on a variety of data and demonstrates better performance than traditional consistency-based approaches. We also introduce an audio restoration framework and obtain results that compete with other state-of-the-art methods. Finally, we apply this phase recovery method to an audio source separation task where the spectrograms of the isolated components are known. We propose to use the phase unwrapping estimate to initialize a source separation iterative procedure. Experiments conducted on realistic music pieces demonstrate the effectiveness of such a method for various music signal processing tasks.
Occupational Neurological Disorders in Korea

The purpose of this article was to provide a literature review of occupational neurological disorders and related research in Korea, focusing on chemical hazards. We reviewed occupational neurological disorders investigated by the Occupational Safety and Health Research Institute of Korean Occupational Safety and Health Agency between 1992 and 2009, categorizing them as neurological disorders of the central nervous system (CNS), of the peripheral nervous system (PNS) or as neurodegenerative disorders. We also examined peer-reviewed journal articles related to neurotoxicology, published from 1984 to 2009. Outbreaks of occupational neurological disorder of the CNS due to inorganic mercury and carbon disulfide poisoning had helped prompt the development of the occupational safety and health system of Korea. Other major neurological disorders of the CNS included methyl bromide intoxication and chronic toxic encephalopathy. Most of the PNS disorders were n-hexane-induced peripheral neuritis, reported from the electronics industry. Reports of manganese-induced Parkinsonism resulted in the introduction of neuroimaging techniques to occupational medicine. Since the late 1990s, the direction of research has been moving toward degenerative disorder and early effect of neurotoxicity. To understand the early effects of neurotoxic chemicals in the preclinical stage, more follow-up studies of a longer duration are necessary.
Statistical Machine Translation Features with Multitask Tensor Networks

We present a three-pronged approach to improving Statistical Machine Translation (SMT), building on recent success in the application of neural networks to SMT. First, we propose new features based on neural networks to model various non-local translation phenomena. Second, we augment the architecture of the neural network with tensor layers that capture important higher-order interaction among the network units. Third, we apply multitask learning to estimate the neural network parameters jointly. Each of our proposed methods results in significant improvements that are complementary. The overall improvement is +2.7 and +1.8 BLEU points for Arabic-English and Chinese-English translation over a state-of-the-art system that already includes neural network features.