Miracle-dz/UniFAR-FTUs huggingface dataset:
Attaching and effacing pathogen‐induced tight junction disruption in vivo

Diarrhoea is a hallmark of infections by the human attaching and effacing (A/E) pathogens, enterohaemorrhagic Escherichia coli (EHEC) and enteropathogenic E. coli (EPEC). Although the mechanisms underlying diarrhoea induced by these pathogens remain unknown, cell culture results have suggested that these pathogens may target tight junctions. Tight junctions in the colon function as physical intercellular barriers that separate and prevent mixing of the luminal contents with adlumenal regions of the epithelium. Consequently, it is thought that the disruption of intestinal epithelial tight junctions by A/E pathogens could result in a loss of barrier function in the alimentary tract; however, this remains unexamined. Here we demonstrate for the first time that A/E pathogen infection results in the morphological alteration of tight junctions during natural disease. Tight junction alteration, characterized by relocalization of the transmembrane tight junction proteins claudin 1, 3 and 5, is a functional disruption; molecular tracers, which do not normally penetrate uninfected epithelia, pass across pathogen‐infected epithelia. Functional junction disruption occurs with a concomitant increase in colon luminal water content. The effects on tissue are dependent upon the bacterial type III effector EspF (E. coli secreted protein F), because bacteria lacking EspF, while able to colonize, are defective for junction disruption and result in decreased proportions of water in the colon compared with wild‐type infection. These results suggest that the diarrhoea induced by A/E pathogens occurs as part of functional tight junction disruption.
UV-B irradiation attenuates dermal effects of botulinum toxin A: a randomized, double-blind, placebo-controlled study.

BACKGROUND Botulinum toxin type A (BoNT/A) is frequently used for cosmetic indications and hyperhidrosis. OBJECTIVES We investigated whether UV-B irradiation alleviates the BoNT/A effect on local sudomotor activity. MATERIALS AND METHODS In a randomized, double-blinded trial, the anhidrotic areas after BoNT/A (100 mU) injection 48 hours before and 14 days after UV-B irradiation were compared in six healthy volunteers. RESULTS UV-B irradiation alleviated BoNT/A effect by approximately 30% (p=.0017). The UV-B-evoked reduction of anhidrotic areas was constant over the observation period of 14 weeks. CONCLUSIONS When BoNT/A is applied intradermally, excessive exposure to UV-B and sunburn should be reconsidered. The authors have indicated no significant interest with commercial supporters.
Remediation of DDT-Contaminated Water and Soil by Using Pretreated Iron Byproducts from the Automotive Industry

The objective of this study was to quantify the effectiveness of different pretreated iron byproducts from the automotive industry to degrade DDT [(1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane] in aqueous solutions and soil slurry. Iron byproducts from automotive manufacturing were pretreated by three different methods (heating, solvent and 0.5N HCl acid washing) prior to experimentation. All pretreated irons were used at 5% (wt v− 1) to treat 0.014 mM (5 mgL− 1) of DDT in aqueous solution. Among the pretreated irons, acid pretreated iron results in the fastest destruction rates, with a pseudo first-order degradation rate of 0.364 d− 1. By lowering the pH of the DDT aqueous solution from 9 to 3, destruction kinetic rates increase more than 20%. In addition, when DDT-contaminated soil slurry (3.54 mg kg− 1) was incubated with 5% (wt v− 1) acid-pretreated iron, more than 90% destruction of DDT was observed within 8 weeks. Moreover, DDT destruction kinetics were enhanced when Fe(II), Fe(III) or Al(III) sulfate salts were added to the soil slurry, with the following order of destruction kinetics: Al(III) sulfate > Fe(III) sulfate > Fe(II) sulfate. These results provide proof-of concept that inexpensive iron byproducts of the automotive industry can be used to remediate DDT-contaminated water and soil.
Long-Term Safety of an Everolimus-Eluting Bioresorbable Vascular Scaffold and the Cobalt-Chromium XIENCE V Stent in a Porcine Coronary Artery Model

Background—The Absorb everolimus-eluting bioresorbable vascular scaffold (Absorb) has shown promising clinical results; however, only limited preclinical data have been published. We sought to investigate detailed pathological responses to the Absorb versus XIENCE V (XV) in a porcine coronary model with duration of implant extending from 1 to 42 months. Methods and Results—A total of 335 devices (263 Absorb and 72 XV) were implanted in 2 or 3 main coronary arteries of 136 nonatherosclerotic swine and examined by light microscopy, scanning electron microscopy, pharmacokinetics, and gel permeation chromatography analyses at various time points. Vascular responses to Absorb and XV were largely comparable at all time points, with struts being sequestered within the neointima. Inflammation was mild to moderate (with absence of inflammation at 1 month) for both devices, although the scores were greater in Absorb at 6 to 36 months. Percent area stenosis was significantly greater in Absorb than XV at all time points except at 3 months. The extent of fibrin deposition was similar between Absorb and XV, which peaked at 1 month and decreased rapidly thereafter. Histomorphometry showed expansile remodeling of Absorb-implanted arteries starting after 12 months, and lumen area was significantly greater in Absorb than XV at 36 and 42 months. These changes correlated with dismantling of Absorb seen after 12 months. Gel permeation chromatography analysis confirmed that degradation of Absorb was complete by 36 months. Conclusions—Absorb demonstrates comparable long-term safety to XV in porcine coronary arteries with mild to moderate inflammation. Although Absorb was associated with greater percent stenosis relative to XV, expansile remodeling was observed after 12 months in Absorb with significantly greater lumen area at ≥36 months. Resorption is considered complete at 36 months.
Nutrition and maternal morbidity and mortality

Nearly 600 000 women die every year from pregnancy related conditions and the maternal mortality rates (MMR = deaths per 100 000 live births) in developing countries may be as high as 1000 compared with less than ten in industrialised countries. In the light of the striking impact of deficiencies of micronutrients such as vitamin A and zinc on immune function, morbidity and mortality in children it seems reasonable to suggest that such deficiencies might play a contributing role in the high rates of morbidity and mortality in mothers. Hitherto, there has been rather little published on the contribution of malnutrition to maternal morbidity or mortality but recent results of micronutrient supplementation show a major effect of vitamin A or beta carotene supplementation on maternal mortality in Nepal and an impressive effect of a multiple micronutrient mixture on pregnancy outcome in Tanzania. There is now data showing that subclinical mastitis, a potential risk factor for mother to child transmission of HIV by increasing levels of virus in breast milk, is influenced by maternal diet in Tanzania and feeding patterns in South Africa. Considering the massive tragedy of maternal mortality the recent data provides opportunities for new, innovative nutritional interventions for the reduction of the global burden of maternal morbidity and mortality.
A novel high‐affinity human monoclonal antibody to mesothelin

Mesothelin is a glycosylphosphatidylinositol‐anchored glycoprotein that is highly expressed on the cell surface of mesothelioma, ovarian cancer and other malignant tumors. The interaction between mesothelin and CA125 (also called MUC16) may facilitate the implantation and metastasis of tumors in the peritoneal cavity. A desirable therapeutic agent involves finding a fully human monoclonal antibody (mAb) that binds to mesothelin or CA125 and inhibits their interaction. Here, we report the identification of a novel human mAb to mesothelin. HN1, a human single‐chain Fv specific for mesothelin, was isolated from a naïve human single‐chain variable fragment (scFv) phage display library. To investigate HN1 as a potential therapeutic, we generated a fully human IgG with the γ 1 heavy chain and the κ light chain and an immuntoxin by fusing the HN1 scFv to a truncated Pseudomonas exotoxin A. The HN1 IgG kills cancer cells with very strong antibody‐dependent cell‐mediated cytotoxicity. HN1 binds a conformation‐sensitive epitope in human mesothelin with high affinity (KD = 3 nM). The HN1 epitope is different from that of SS1, a mouse Fv used to develop therapeutic antibodies that are currently in clinical trials. HN1 binds to cell surface‐associated mesothelin on human mesothelioma, ovarian cancer, lung adenocarcinoma and pancreatic cancer cells. In addition, HN1 can functionally block the interaction of mesothelin and CA125 on cancer cells. Most importantly, because the HN1 immuntoxin kills mesothelin‐expressing cancer cells with high cytotoxic activity, we believe that it has significant potential for mesothelin‐expressing cancer treatment and diagnosis. Published 2010 UICC. This article is a US Government work and, as such, is in the public domain of the United States of America.
Suffixation influences receivers' behaviour in non-human primates

Compared to humans, non-human primates have very little control over their vocal production. Nonetheless, some primates produce various call combinations, which may partially offset their lack of acoustic flexibility. A relevant example is male Campbell's monkeys (Cercopithecus campbelli), which give one call type (‘Krak’) to leopards, while the suffixed version of the same call stem (‘Krak-oo’) is given to unspecific danger. To test whether recipients attend to this suffixation pattern, we carried out a playback experiment in which we broadcast naturally and artificially modified suffixed and unsuffixed ‘Krak’ calls of male Campbell's monkeys to 42 wild groups of Diana monkeys (Cercopithecus diana diana). The two species form mixed-species groups and respond to each other's vocalizations. We analysed the vocal response of male and female Diana monkeys and overall found significantly stronger vocal responses to unsuffixed (leopard) than suffixed (unspecific danger) calls. Although the acoustic structure of the ‘Krak’ stem of the calls has some additional effects, subject responses were mainly determined by the presence or the absence of the suffix. This study indicates that suffixation is an evolved function in primate communication in contexts where adaptive responses are particularly important.
Noun phrases extraction using shallow parsing with C4.5 decision tree algorithm for Indonesian Language ontology building

Ontology describes a set of concept or entity and each relation. Ontology as knowledge representation usually has a large structure because it can cover a wide area topics. Ontology building process is divided into two subprocesses, those are term extraction and relation formation. Term extraction in ontology building is done for extracting concept or entity before each relation is obtained. Main objective in this research is to extract noun phrases using shallow parsing algorithm based on C4.5 decision tree as candidate concept or term for ontology building process in Indonesian Text. One of the advantages of using shallow parsing is it can recover syntactic information efficiently and reliably from unrestricted text. For our dataset, we use Indonesian Language online newspapers for one month. Based on our experiments, it concludes that our proposed method can perform well for Indonesian Language noun phrase identification with average F-score 84.63%.
Performance Comparison and Tuning of Virtual Machines For Sequence Alignment Software

We explore the performance cost of virtualisation for the fast growing application domain of genomics. Traditionally, scientific applications have been considered too high-performance to pay the performance cost of virtualisation. However, as the demand for computing power for genomics is ever-increasing, the cloud can become an attractive way to meet the scaling challenge presented by Next-Generation Sequencing (NGS). We seek to explore the feasibility of running an NGS pipeline in a cloud, and in doing so consider two prevalent short-read sequence alignment programs, BWA and Novoalign. We executed those applications in three separate open-source system virtualisation solutions: the KVM hypervisor, the Xen para-virtualised hypervisor, and Linux Containers. We compare the runtime in each environment against the runtime of the same system without virtualisation and measure the relative performance of each hypervisor. We investigate and reduce as much as possible any overhead, presenting tuning suggestions for cloud implementers and users. Overall, we find that the overhead introduced by virtualisation can be reduced to low single-digit percentages, a cost we believe to be more than acceptable, especially given that two of the three solutions, Xen and Containers, exhibit near-zero overhead.
Living with the unknown: Posttraumatic stress disorder in pediatric bone marrow transplantation survivors and their mothers

ABSTRACT Bone marrow transplantation (BMT) is used to treat children with various hematologic, oncologic, and metabolic diseases. Although the treatment can be lifesaving, it is also physically and psychologically demanding for both the child and caregivers. In previous studies, BMT is found to be related with anxiety, posttraumatic stress disorder (PTSD), depression, and psychosocial problems both in children and parents. The aim of this study was to investigate PTSD in pediatric BMT survivors and their mothers compared with the healthy controls. Twenty-seven BMT survivors and their mothers and 28 healthy peers and their mothers were recruited as the study group and as the comparison group, respectively. All children were interviewed using Child Posttraumatic Stress Disorder—Reaction Index (CPTSD-RI) for assessing posttraumatic stress responses. As for mothers, Clinician-Administered PTSD Scale (CAPS) was used. In healthy children and mothers, instead of BMT, the most important traumatic event reported by them was included. All data were analyzed by a neutral statistician from the Department of Biostatistics of the university. The BMT group, both children and mothers, obtained significantly higher PTSD rates than the control group (66.5% and 17.8%, respectively, in children; 57.6% and 7%, respectively, in mothers). However, there was a weak correlation between survivors' and mothers' posttraumatic stress responses. These findings suggest that BMT is a significant stressor for both children and mothers. Clinicians should be aware of psychiatric symptoms of children who underwent such a life-threatening condition. Combination of medical treatment with psychosocial support is imperative.
Five level cross connected cell for cascaded converters

Proposed here is an alternate Five-level four-quadrant cascaded multilevel converter cell configuration that compared to the other cell configurations, for dc fault current limitation, will be more compact and avoid the external dc breaker. Loss comparison on cells with dc fault blocking capability for the cascaded converter is also presented.
MiDAS: the field guide to the microbes of activated sludge

The Microbial Database for Activated Sludge (MiDAS) field guide is a freely available online resource linking the identity of abundant and process critical microorganisms in activated sludge wastewater treatment systems to available data related to their functional importance. Phenotypic properties of some of these genera are described, but most are known only from sequence data. The MiDAS taxonomy is a manual curation of the SILVA taxonomy that proposes a name for all genus-level taxa observed to be abundant by large-scale 16 S rRNA gene amplicon sequencing of full-scale activated sludge communities. The taxonomy can be used to classify unknown sequences, and the online MiDAS field guide links the identity to the available information about their morphology, diversity, physiology and distribution. The use of a common taxonomy across the field will provide a solid foundation for the study of microbial ecology of the activated sludge process and related treatment processes. The online MiDAS field guide is a collaborative workspace intended to facilitate a better understanding of the ecology of activated sludge and related treatment processes—knowledge that will be an invaluable resource for the optimal design and operation of these systems. Database URL: http://www.midasfieldguide. org
Single hepatocellular carcinoma smaller than 2 cm: are ethanol injection and radiofrequency ablation equally effective?

BACKGROUND/AIM The impact of radiofrequency ablation (RFA) and percutaneous ethanol injection (PEI) on survival in patients with small hepatocellular carcinoma (HCC) is unclear. We compared their efficacy in cirrhotics with single HCC ≤2 cm. PATIENTS AND METHODS Two hundred forty-four cirrhotics with single HCC ≤2 cm treated with PEI (108 cases) or RFA (136 cases) were enrolled in the study. Eighty-one patients in each group were selected for propensity score matching analysis. RESULTS The five-year survival was not significantly different (64.7% in PEI and 72.9% in RFA group) but the 5-year recurrence (73.3% in PEI and 49% in RFA group, p=0.023) and local tumor progression (49% in PEI and 30.1% in RFA group, p=0.018) were higher in the PEI group. CONCLUSION PEI and RFA are equally effective in treating HCCs smaller than 2 cm in terms of 5-year survival, despite higher cumulative and local recurrence rates, in patients treated with PEI.
Expression of the p53 family in lung cancer.

BACKGROUND p53 is mutated in about 50% of various malignant diseases including lung cancer. The p53 family consists of p53, p73 and p63. Although transactivating protein isoforms display p53-like functions, the deltaNp73 or deltaNp63 isoforms act toward p53 in a dominantly negative way. The aim of this study was to detect p53, deltaNp73 and deltaNp63 expressions in lung cancer and to evaluate the relationship between the expression levels of the proteins and the prognosis of patients with resectable lung cancer. MATERIALS AND METHODS Immunohistochemistry was employed to analyze the protein expression of p53, deltaNp73 and deltaNp63 in paraffin-embedded tumor samples from 132 well-characterized lung cancer patients. The correlation among the expression levels of p53, deltaNp73 and deltaNp63, clinical variables and survival outcome was analyzed. RESULTS Positive expressions of p53, deltaNp73 and deltaNp63 were detected in the tumor cells in 52, 77 and 44 of the 132 patients, respectively (39.4%, 58.3% and 33.3%) with lung cancer. The incidence of p53 positive expression was 54.5% and 27.6% in patients with squamous cell carcinoma and adenocarcinoma, respectively (p = 0.03). The incidence of a positive expression of deltaNp73 was 64.5% and 43.6% in male and female patients, respectively (p = 0.03). The incidence of deltaNp63 positive expression was 68.2% and 15.8% in the patients with squamous cell carcinoma and adenocarcinoma, respectively (p < 0.0001). The expressions of p53 and deltaNp63 were not found to significantly affect survival. However, lung cancer patients with a positive deltaNp73 expression had a poorer prognosis than those with a negative deltaNp73 expression. In addition, multivariate analysis indicated that a positive expression of deltaNp73 was a significantly independent factor for predicting a poor prognosis (p < 0.0001, risk ratio = 3.38). CONCLUSION Clinical evidence that the p53 family is frequently overexpressed in lung cancer specimens, especially deltaNp63 in squamous cell carcinoma, was provided. The expression of deltaNp73 may be a useful marker for predicting a poor prognosis in resectable lung cancer. Understanding how groups of lung cancer cell genes are coordinately expressed in response to physiological, immunological and micro-environmental stimuli remains an important goal. A better understanding of the gene expression profiles of tumors may help to identify molecular targets, such as deltaNp73, for effective therapy.
Outpatient Removal of Tunneled Dialysis Catheters by Nephrology Fellows in Training at a Veterans Affairs Medical Center

Background Removal of tunneled dialysis catheters (TDC) usually occurs in dedicated procedure suites and is performed relatively rarely at the bedside. Scarce evidence exists in the literature to assess the safety and success of this procedure when performed during supervised academic training. Patients and Methods We conducted a retrospective chart review of all TDC removals performed on an outpatient basis by nephrology fellows under faculty supervision during a 5-year period at an academic Veterans Affairs Medical Center. Data were collected regarding patient demographics, basic laboratory studies, pertinent clinical information and procedure-related variables. We evaluated the safety, success and complication rate of this procedure. Results We identified 72 TDC removals that met the above criteria. Mean age was 63 ± 10 years. All patients were male and hypertensive, 68% were diabetic and 69% were African-American. Overall, 88% of procedures were performed in end-stage renal disease (ESRD) patients, while the rest had needed temporary dialysis for acute kidney injury. Notably, 49 patients (68%) were taking one or more of aspirin, clopidogrel or warfarin at the time of TDC removal. Overall complication rate was low (<2%). There was no increase in risk of bleeding, even in subjects receiving anti-platelet therapy; only one of the 49 patients (2%) had a minor bleeding complication. Conclusions Outpatient TDC removal by trainees was successful and safe in the vast majority of cases (99%). We propose that TDC removal skills should be actively pursued and acquired by all nephrology fellows. This would expand the scope of practice for future general nephrologists and facilitate timely patient care.
Scaling Memory-Augmented Neural Networks with Sparse Reads and Writes

Neural networks augmented with external memory have the ability to learn algorithmic solutions to complex tasks. These models appear promising for applications such as language modeling and machine translation. However, they scale poorly in both space and time as the amount of memory grows — limiting their applicability to real-world domains. Here, we present an end-to-end differentiable memory access scheme, which we call Sparse Access Memory (SAM), that retains the representational power of the original approaches whilst training efficiently with very large memories. We show that SAM achieves asymptotic lower bounds in space and time complexity, and find that an implementation runs 1,000 x faster and with 3,000x less physical memory than non-sparse models. SAM learns with comparable data efficiency to existing models on a range of synthetic tasks and one-shot Omniglot character recognition, and can scale to tasks requiring 100,000s of time steps and memories. As well, we show how our approach can be adapted for models that maintain temporal associations between memories, as with the recently introduced Differentiable Neural Computer.
Filterbank transceivers optimizing information rate in block transmissions over dispersive channels

Optimal FIR transmit and receive filterbanks are derived for block based data transmissions over frequency-selective AGN channels by maximizing mutual information subject to a fixed transmit-power constraint. The inherent flexibility of the proposed transceivers is exploited to derive as special cases, zero-forcing and minimum mean-square error solutions. The potential of the proposed scheme is illustrated and compared to discrete multi-tone (DMT).