Miracle-dz/UniFAR-FTUs huggingface dataset:
Occurrence of virulence factors and antimicrobial resistance in Pasteurella multocida strains isolated from slaughter cattle in Iran

A total of 30 Pasteurella multocida strains isolated from 333 pneumonic and apparently health slaughter cattle were examined for capsule biosynthesis genes and 23 virulence-associated genes by polymerase chain reaction (PCR). The disc diffusion technique was used to determine antimicrobial resistance profiles among the isolates. Of the isolates, 23 belonged to capsular type A, 5 to capsular type D and two isolates were untypeable. The distribution of the capsular types in pneumonic lungs and in apparently health lungs was statistically similar. All virulence genes tested were detected among the isolates derived from pneumonic lungs; whereas isolates derived from apparently health lungs carried 16 of the 23 genes. The frequently detected genes among isolates from pneumonic lungs were exbD, hgbA, hgbB, ompA, ompH, oma87, and sodC; whereas tadD, toxA, and pmHAS genes occurred less frequently. Most of the adhesins and superoxide dismutases; and all of the iron acquisition and protectin proteins occurred at significantly (p ≤ 0.05) higher frequencies in isolates from pneumonic lungs. Isolates from apparently healthy lungs didn't carry the following genes; hsf-1, hsf-2, tadD, toxA, nanB, nanH, and pmHAS. One adhesion (hsf-1) and two iron acquisition (exbD and tonB) genes occurred at significantly (p ≤ 0.05) higher frequencies among capA isolates. All the P. multocida isolates were susceptible to ciprofloxacin, co-trimoxazole, doxycycline, enrofloxacin, nitrofurantoin, and tetracyclines. Different proportions of the isolates were however resistant to ampicillin, amoxicillin, erythromycin, lincomycin, penicillin, rifampin, streptomycin, and florfenicol. Our results reveal presence of virulence factors (VFs) in P. multocida strains isolated from symptomatic and asymptomatic bovids. A higher frequency of the factors among isolates from symptomatic study animals may suggest their role in pathogenesis of P. multocida-associated bovine respiratory disease (BRD). The results further reveal occurrence of antimicrobial resistance among some isolates. Control strategies for this pathogen, which could include development of an effective vaccine, are warranted so as to mitigate the social and economic consequences attributable to natural infections with this bacterium.
Soft emissions and the equivalence of BFKL and CCFM final states

This article demonstrates that the BFKL and CCFM equations, despite their different physical content, lead to equivalent results for any final-state observable at leading single-logarithmic order. A novel and fundamental element is the treatment also of the soft (z→1 divergent) part of the splitting function in the CCFM equation.
In Vivo Correction of Complement Regulatory Protein Deficiency with an Inhibitor Targeting the Red Blood Cell Membrane1

Because of the complement system’s involvement in many human diseases and potential complications associated with its systemic blockade, site-specific regulation of this effector system is an attractive concept. We report on further developments of such an approach using a single-chain Ab fragment as a vehicle to deliver complement regulatory proteins to a defined cell type. In a model system in which RBCs deficient in complement receptor 1-related gene/protein y (Crry) are rapidly cleared after injection into wild-type animals by a complement-dependent mechanism, we selectively reconstituted these cells with N- and C-terminally targeted recombinant forms of Crry. Transfusion of Crry-coated knockout RBCs into C57BL/6 mice extended their in vivo half-life from <5 min to ∼2 days. Maintenance of protective levels of Crry (by a combined treatment of donor and recipient RBCs) led to nearly normal RBC survival. Uniform in vitro and in vivo coating of the RBCs and the more efficient complement inhibitory capacity of C-terminally tagged Crry were other interesting features of this experimental system. These results suggest the possibility of using the single-chain Ab fragment-mediated targeting concept of complement regulatory proteins to restrict complement inhibition to the site of its excessive activation.
Managing dyslipidemia in HIV/AIDS patients: challenges and solutions

Human immunodeficiency virus (HIV) is a chronic disease associated with dyslipidemia and insulin resistance. In addition, the administration of combination antiretroviral therapy is associated with an increase in the incidence of metabolic risk factors (insulin resistance, lipoatrophy, dyslipidemia, and abnormalities of fat distribution in HIV patients). HIV dyslipidemia is a common problem, and associated with an increase in incidence of cardiovascular disease. Further challenges in the management of HIV dyslipidemia are the presence of diabetes and metabolic syndrome, nonalcoholic fatty liver disease, hypothyroidism, chronic kidney disease, the risk of diabetes associated with statin administration, age and ethnicity, and early menopause in females. Dyslipidemia in patients with HIV is different from the normal population, due to the fact that HIV increases insulin resistance and HIV treatment not only may induce dyslipidemia but also may interact with lipid-lowering medication. The use of all statins (apart from simvastatin and lovastatin) is safe and effective in HIV dyslipidemia, and the addition of ezetimibe, fenofibrate, fish oil, and niacin can be used in statin-unresponsive HIV dyslipidemia. The management of dyslipidemia and cardiovascular disease risks associated with HIV is complex, and a certain number of patients may require management in specialist clinics run by specialist physicians in lipid disorders. Future research is needed to address best strategies in the management of hyperlipidemia with HIV infection.
Long‐term synaptic depression in the adult entorhinal cortex in vivo

The piriform cortex provides a major input to the entorhinal cortex. Mechanisms of long‐term depression (LTD) of synaptic transmission in this pathway may affect olfactory and mnemonic processing. We have investigated stimulation parameters for the induction of homosynaptic LTD and depotentiation in this pathway using evoked synaptic field potential recordings in the awake rat. In this study, 15 min of 1‐Hz stimulation induced a transient (<5 min) depression of evoked responses but did not induce LTD or depotentiation. To determine whether inhibitory and/or facilitatory mechanisms contribute to LTD induction, repetitive delivery of pairs of stimulation pulses was also assessed. Repetitive paired‐pulse stimulation with a 10‐ms interval between pulses, which activates inhibitory mechanisms during the second response, did not reliably induce LTD. However, repetitive paired‐pulse stimulation using a 30‐ms interval, which evokes marked paired‐pulse facilitation, resulted in synaptic depression that lasted ≥1 day, and which was reversible by tetanization. The selective induction of LTD by stimulation that evokes paired‐pulse facilitation suggests that strong synaptic activation is required for LTD induction. The N‐methyl‐D‐aspartate (NMDA) receptor antagonist MK‐801 (0.1 mg/kg) blocked the induction of LTD, indicating that NMDA receptor activation is required for LTD induction in this pathway. These results indicate that LTD in piriform cortex inputs to the entorhinal cortex in the awake rat is effectively induced by strong repetitive synaptic stimulation, and that this form of LTD is dependent on activation of NMDA receptors. © 2003 Wiley‐Liss, Inc.
Rapid Diagnosis of Childhood Pulmonary Tuberculosis by Xpert MTB/RIF Assay Using Bronchoalveolar Lavage Fluid

In order to evaluate the diagnostic accuracy of the Xpert MTB/RIF assay on childhood pulmonary tuberculosis (PTB) using bronchoalveolar lavage fluid (BALF), we evaluated the sensitivity, specificity, positive predictive value, and negative predictive value of Xpert MTB/RIF assay using BALF in comparison with acid-fast bacilli (AFB) microscopy and Mycobacterium tuberculosis (MTB) culture for diagnosing childhood PTB using Chinese “composite clinical reference standard” (CCRS) as reference standard. Two hundred fifty-five children with suspected PTB were enrolled at Beijing Children's Hospital from September 2010 to July 2013. Compared with Chinese CCRS, the sensitivity of AFB microscopy, MTB culture, and Xpert MTB/RIF assay was 8.4%, 28.9%, and 53.0%, respectively. The specificity of three assays was all 100%. Xpert MTB/RIF assay could detect 33.9% of cases with negative MTB culture, and 48.7% of cases with negative AFB microscopy. Younger age (<3 years), absence of BCG scar, and contact with TB patient were found significantly associated with a positive result of Xpert MTB/RIF assay. In conclusion, Xpert MTB/RIF assay using BALF can assist in diagnosing childhood PTB much faster when fiberoptic bronchoscopy is necessary according to the chest radiograph.
Genetic Polymorphisms of Ataxia Telangiectasia Mutated and Breast Cancer Risk

To evaluate the role of genetic polymorphisms of ataxia telangiectasia mutated (ATM) in the etiology of breast cancer, a hospital-based case-control study was conducted in Korea. Nine-hundred ninety-six histologically confirmed incident breast cancer cases and 1,181 cancer-free controls were recruited in Seoul between 1995 and 2003. Genotypes of the ATM polymorphisms-5144A>T, IVS21+1049T>C, IVS33−55T>C, IVS34+60G>A, and 3393T>G were determined by the 5′-nuclease assay. Individual haplotypes were estimated from genotype data by a Bayesian method. Five ATM alleles were found to be in strong linkage disequilibrium (D′ > 0.82; P < 0.001). Haplotype frequencies were significantly different between cases and controls (χ2 test, P < 0.001). The ATM IVS21+1049 TC or CC, IVS34+60 GA or AA, and 3393 TG or GG genotypes were associated with increased breast cancer risk, particularly in premenopausal women [odds ratios (OR), 1.51; 95% confidence interval (CI), 1.11-2.05; OR, 1.42; 95% CI, 1.08-1.88; and OR, 1.37; 95% CI, 1.04-1.80, respectively]. Compared with diploid of TCCAG:TCCAG, the most common haplotype, the ATTGT:ATTGT was associated with decreased risk of breast cancer with borderline significance (OR, 0.77; 95% CI, 0.58-1.04) and TCCAG:ATCGT and ATTGT:ACCAG were associated with increased breast cancer risk (OR, 2.30; 95% CI, 1.18-4.48 and OR, 2.43; 95% CI, 1.1.07-5.52, respectively) after adjusting for age, education, age at first full-term pregnancy, parity, family history of breast cancer, alcohol consumption, and smoking. As the number of ATTGT haplotype decreased, the risk of breast cancer increased (P for trend <0.01). Our results thus suggest that genetic polymorphisms of ATM play an important role in the development of breast cancer in Korean women.
Disease Detection or Public Opinion Reflection? Content Analysis of Tweets, Other Social Media, and Online Newspapers During the Measles Outbreak in the Netherlands in 2013

Background In May 2013, a measles outbreak began in the Netherlands among Orthodox Protestants who often refuse vaccination for religious reasons. Objective Our aim was to compare the number of messages expressed on Twitter and other social media during the measles outbreak with the number of online news articles and the number of reported measles cases to answer the question if and when social media reflect public opinion patterns versus disease patterns. Methods We analyzed measles-related tweets, other social media messages, and online newspaper articles over a 7-month period (April 15 to November 11, 2013) with regard to topic and sentiment. Thematic analysis was used to structure and analyze the topics. Results There was a stronger correlation between the weekly number of social media messages and the weekly number of online news articles (P<.001 for both tweets and other social media messages) than between the weekly number of social media messages and the weekly number of reported measles cases (P=.003 and P=.048 for tweets and other social media messages, respectively), especially after the summer break. All data sources showed 3 large peaks, possibly triggered by announcements about the measles outbreak by the Dutch National Institute for Public Health and the Environment and statements made by well-known politicians. Most messages informed the public about the measles outbreak (ie, about the number of measles cases) (93/165, 56.4%) followed by messages about preventive measures taken to control the measles spread (47/132, 35.6%). The leading opinion expressed was frustration regarding people who do not vaccinate because of religious reasons (42/88, 48%). Conclusions The monitoring of online (social) media might be useful for improving communication policies aiming to preserve vaccination acceptability among the general public. Data extracted from online (social) media provide insight into the opinions that are at a certain moment salient among the public, which enables public health institutes to respond immediately and appropriately to those public concerns. More research is required to develop an automatic coding system that captures content and user’s characteristics that are most relevant to the diseases within the National Immunization Program and related public health events and can inform official responses.
The Essential Turing

Many physicists would agree that, had it not been for rasterization, the exploration of IPv7 might never have occurred. In fact, few end-users would disagree with the simulation of red-black trees. Our focus in our research is not on whether the location-identity split and congestion control are generally incompatible, but rather on exploring a novel application for the analysis of systems ( Juge ).
GERp 95 , a Membrane-associated Protein that Belongs to a Family of Proteins Involved in Stem Cell Differentiation

A panel of mAbs was elicited against intracellular membrane fractions from rat pancreas. One of the antibodies reacted with a 95-kDa protein that localizes primarily to the Golgi complex or the endoplasmic reticulum (ER), depending on cell type. The corresponding cDNA was cloned and sequenced and found to encode a protein of 97.6 kDa that we call GERp95 (Golgi ER protein 95 kDa). The protein copurifies with intracellular membranes but does not contain hydrophobic regions that could function as signal peptides or transmembrane domains. Biochemical analysis suggests that GERp95 is a cytoplasmically exposed peripheral membrane protein that exists in a protease-resistant complex. GERp95 belongs to a family of highly conserved proteins in metazoans and Schizosaccharomyces pombe. It has recently been determined that plant and Drosophila homologues of GERp95 are important for controlling the differentiation of stem cells (Bohmert et al., 1998; Cox et al., 1998; Moussian et al., 1998). In Caenorhabditis elegans, there are at least 20 members of this protein family. To this end, we have used RNA interference to show that the GERp95 orthologue in C. elegans is important for maturation of germ-line stem cells in the gonad. GERp95 and related proteins are an emerging new family of proteins that have important roles in metazoan development. The present study suggests that these proteins may exert their effects on cell differentiation from the level of intracellular membranes.
Long-term surgical results with aneurysms involving the ophthalmic segment of the carotid artery.

OBJECT Because of the anatomical complexity of the paraclinoid region, the surgical treatment of aneurysms arising in the C(6) segment of the internal carotid artery is extremely challenging. The authors' aim in this study was to describe the extended clinical follow-up and assess the short-term and long-term effectiveness of surgical treatment for these aneurysms, focusing on the clinical outcome and degree of aneurysm occlusion and recurrence. METHODS The authors retrospectively analyzed the clinical records for patients treated surgically between 1973 and 2004 at the University of Rome, "La Sapienza. " Aneurysms were classified into the following 3 groups according to the site where they arose: the anteromedial, anterior or anterolateral, and posteromedial wall of the C(6) segment. RESULTS Of the 108 aneurysms in 104 patients treated, 63 (58%) were large or giant. Eighty-eight aneurysms in 84 patients were clipped, 16 underwent a high-flow bypass, 2 were trapped, 1 was wrapped, and 1 was left untreated. The mean follow-up was 126 months; 47 patients had a follow-up of > 10 years. Of the 88 aneurysms that were clipped, 6 (6.8%) had an incomplete occlusion that required an immediate reoperation in 1 case and at 2 years in another. Overall 6 patients (5.8%) had surgery-related permanent complications. CONCLUSIONS Mortality and morbidity rates depend mainly on the patient's preoperative Hunt and Hess grade subarachnoid hemorrhage, whereas surgical morbidity principally reflects excessive manipulation of the optic nerve or ischemic problems due to excessive temporary trapping undertaken without adequate neuroprotection. In expert hands, surgery (clipping and bypass procedures) is a definitive treatment for C(6) aneurysms and has an acceptable complication rate.
Improving Speech Recognition by Revising Gated Recurrent Units

Speech recognition is largely taking advantage of deep learning, showing that substantial benefits can be obtained by modern Recurrent Neural Networks (RNNs). The most popular RNNs are Long Short-Term Memory (LSTMs), which typically reach state-of-the-art performance in many tasks thanks to their ability to learn long-term dependencies and robustness to vanishing gradients. Nevertheless, LSTMs have a rather complex design with three multiplicative gates, that might impair their efficient implementation. An attempt to simplify LSTMs has recently led to Gated Recurrent Units (GRUs), which are based on just two multiplicative gates. This paper builds on these efforts by further revising GRUs and proposing a simplified architecture potentially more suitable for speech recognition. The contribution of this work is two-fold. First, we suggest to remove the reset gate in the GRU design, resulting in a more efficient single-gate architecture. Second, we propose to replace tanh with ReLU activations in the state update equations. Results show that, in our implementation, the revised architecture reduces the per-epoch training time with more than 30% and consistently improves recognition performance across different tasks, input features, and noisy conditions when compared to a standard GRU.
Isoform-level gene signature improves prognostic stratification and accurately classifies glioblastoma subtypes

Molecular stratification of tumors is essential for developing personalized therapies. Although patient stratification strategies have been successful; computational methods to accurately translate the gene-signature from high-throughput platform to a clinically adaptable low-dimensional platform are currently lacking. Here, we describe PIGExClass (platform-independent isoform-level gene-expression based classification-system), a novel computational approach to derive and then transfer gene-signatures from one analytical platform to another. We applied PIGExClass to design a reverse transcriptase-quantitative polymerase chain reaction (RT-qPCR) based molecular-subtyping assay for glioblastoma multiforme (GBM), the most aggressive primary brain tumors. Unsupervised clustering of TCGA (the Cancer Genome Altas Consortium) GBM samples, based on isoform-level gene-expression profiles, recaptured the four known molecular subgroups but switched the subtype for 19% of the samples, resulting in significant (P = 0.0103) survival differences among the refined subgroups. PIGExClass derived four-class classifier, which requires only 121 transcript-variants, assigns GBM patients’ molecular subtype with 92% accuracy. This classifier was translated to an RT-qPCR assay and validated in an independent cohort of 206 GBM samples. Our results demonstrate the efficacy of PIGExClass in the design of clinically adaptable molecular subtyping assay and have implications for developing robust diagnostic assays for cancer patient stratification.
Urinary Placental Growth Factor : A Promising Marker for Screening Preeclampsia

The present study is aimed to ascertain whether preeclampsia is associated with changes in serum levels of vascular endothelial growth factor (VEGF), placental growth factor (PlGF), soluble fms-like tyrosine kinase -1 (sFlt-1) and urine excretion levels of PlGF in Indian patients. Serum and urine samples were obtained from 40 women with preeclampsia and 40 normotensive, non-proteinuric pregnant women as control and the levels of these factors were analyzed using enzymelinked immunosorbent assay (ELISA). The serum levels of VEGF (mean ± SD 170.53 ± 36.56 Vs 254.61 ± 47.394 pg/ml, p<0.0001), PlGF (mean ± SD 236.77 ± 93.70 Vs 744.98 ± 168.55 pg/ml, p<0.0001) and the urinary levels of PlGF (mean ± SD 30.08 ± 9.42 Vs 77.70 ± 24.70 pg/ml, p<0.0001) were significantly lower where as serum levels of sFlt-1 were significantly higher (median (range) 11295.25 (2936.2 – 37818) Vs 2893.20 (1180.436706.6) pg/ml, p<0.0001) in preeclamptic patients as compared to the control. In conclusion, preeclampsia is associated with alterations in serum and urinary angiogenic factors. The longitudinal measurement of these angiogenic factors in serum might be ideal for ascertaining the risk of preeclampsia, but measuring the levels of PlGF in the urine during routine antenatal care could be a simpler and non-invasive factor, if it can be used as definite, informative screening marker for preeclampsia.
Improved grindability and gold liberation by microwave pretreatment of a free-milling gold ore

Abstract The gravity concentration of gold is very efficient if the metal is fully liberated and the particle size of the gold is relatively coarse. Liberation is usually achieved by comminution, but due to the association of the gold with the other minerals in the ore, overgrinding occurs in conventional comminution circuits and slime generation leads to inefficient recovery. The liberation of minerals can be improved by adding grinding aids, which modify the mechanical properties of the ore and allow breakage at lower stress levels. In this research, microwave pretreatment was used to augment the grinding of a free-milling gold ore containing quartz, silicates and iron oxides. Under microwave irradiation, selective heating of the different mineral components resulted in thermal stresses that caused cracking. These intergranular and transgranular fractures were confirmed by scanning electron microscopy. After microwave processing, the grindability of the ore was improved and the crushing strength and the Bond Work Index were reduced by 31˙2% and 18˙5%, respectively. In addition to the enhanced grindability, gold was released from the matrix of the host minerals at a coarser size, resulting in a significant increase in free gold recovery by gravity concentration. For a gold ore with a head grade of 6˙4 gt−1, the gold recovery improved from about 28% to 40% after microwave pretreatment.