Miracle-dz/UniFAR-FTUs huggingface dataset:
Pathogenic mechanisms of Campylobacter jejuni : regulation of Campylobacter invasion antigen B

by Gary Andrew Flom, M.S. Washington State University May 2004 Chair: Michael E. Konkel Campylobacter jejuni, a Gram-negative, spiral shaped bacterium is the leading cause of gastroenteritis in humans worldwide. However, little is known regarding the mechanisms Campylobacter employs to cause disease. Previous work has shown that Campylobacter jejuni secretes a set of proteins known as the Campylobacter invasion antigens (Cia proteins). Recent research has shown that the flagella apparatus acts as a type III secretion system allowing the delivery of the Cia proteins to intestinal epithelial cells. Furthermore, research has shown that the expression of the cia genes is upregulated in the presence of bile salts and fetal bovine serum. Given that an environmental signal was required to induce the expression of the cia genes, I sought to determine how the cia genes were regulated. I generated single crossover mutants of ten of the response regulators and one AraC-like transcriptional activator that are present in the Campylobacter NCTC 11168 genome. Upon subjecting the single crossover mutants to secretion assays, I determined that Cj0890c, Cj1024c (flgR), and Cj1042c (AraC-like) were secretion negative and may play a role in the regulation of the cia genes. Next, I generated double crossover mutants to validate this secretion negative phenotype. In addition I generated double crossover mutants of s and s, Cj0061c (fliA) and Cj0670 (rpoN). Secretion assays of
The effects of gender, age, schooling, and cultural background on the identification of facial emotions: a transcultural study

ABSTRACT Background: Social cognition tasks, such as identification of emotions, can contribute to the diagnosis of neuropsychiatric disorders. The wide use of Facial Emotion Recognition Test (FERT) is hampered by the absence of normative dataset and by the limited understanding of how demographic factors such as age, education, gender, and cultural background may influence the performance on the test. Methods: We analyzed the influence of these variables in the performance in the FERT from the short version of the Social and Emotional Assessment. This task is composed by 35 pictures with 7 different emotions presented 5 times each. Cognitively healthy Brazilian participants (n = 203; 109 females and 94 males) underwent the FERT. We compared the performance of participants across gender, age, and educational subgroups. We also compared the performance of Brazilians with a group of French subjects (n = 60) matched for gender, age, and educational level. Results: There was no gender difference regarding the performance on total score and in each emotion subscore in the Brazilian sample. We found a significant effect of aging and schooling on the performance on the FERT, with younger and more educated subjects having higher scores. Brazilian and French participants did not differ in the FERT and its subscores. Normative data for employing the FERT in Brazilian population is presented. Conclusions: Data here provided may contribute to the interpretation of the results of FERT in different cultural contexts and highlight the common bias that should be corrected in the future tasks to be developed.
Mutation Spectrum of the ABCA4 Gene in a Greek Cohort with Stargardt Disease: Identification of Novel Mutations and Evidence of Three Prevalent Mutated Alleles

Aim To evaluate the frequency and pattern of disease-associated mutations of ABCA4 gene among Greek patients with presumed Stargardt disease (STGD1). Materials and Methods A total of 59 patients were analyzed for ABCA4 mutations using the ABCR400 microarray and PCR-based sequencing of all coding exons and flanking intronic regions. MLPA analysis as well as sequencing of two regions in introns 30 and 36 reported earlier to harbor deep intronic disease-associated variants was used in 4 selected cases. Results An overall detection rate of at least one mutant allele was achieved in 52 of the 59 patients (88.1%). Direct sequencing improved significantly the complete characterization rate, that is, identification of two mutations compared to the microarray analysis (93.1% versus 50%). In total, 40 distinct potentially disease-causing variants of the ABCA4 gene were detected, including six previously unreported potentially pathogenic variants. Among the disease-causing variants, in this cohort, the most frequent was c.5714+5G>A representing 16.1%, while p.Gly1961Glu and p.Leu541Pro represented 15.2% and 8.5%, respectively. Conclusions By using a combination of methods, we completely molecularly diagnosed 48 of the 59 patients studied. In addition, we identified six previously unreported, potentially pathogenic ABCA4 mutations.
Involvement of GABAergic and Adrenergic Neurotransmissions on Paraventricular Nucleus of Hypothalamus in the Control of Cardiac Function

Sympathetic premotor neurons of the paraventricular hypothalamus (PVN) play a role in hemodynamics adjustments during changes in body fluid homeostasis. However, PVN contribution to the tonic control of cardiac function remains to be systematically studied. In this study, we assessed whether GABAergic and adrenergic synapses, known for being active in the PVN, are involved in the control of cardiac function. Adult male Wistar rats (250–350 g; n = 27) were anesthetized with urethane (1.2–1.4 g/kg i.p.) and underwent catheterization of femoral artery to record blood pressure and heart rate. The femoral vein was used to inject the vasoactive agents phenylephrine (10 μg/kg) and sodium nitroprusside (10 μg/kg) and to supplement anesthesia. The cardiac left ventricle was catheterized to record left ventricular pressure and its derivative. Craniotomy allowed for injections (100 nL) into the PVN of: muscimol (20 mM), bicuculline methiodide (0.4 mM), propranolol (10 mM), isoproterenol (100 μM), phentolamine (13 mM), phenylephrine (30 nM). We found that: (i) inhibition of PVN by muscimol, reduced arterial pressure, cardiac chronotropy and inotropy; (ii) disinhibition of PVN neurons by bicuculline evoked positive chronotropy and inotropy, and increase blood pressure; (iii) PVN alpha adrenergic receptors control cardiac chronotropy and inotropy; (iv) beta adrenergic receptors of the PVN do not influence cardiac function; (v) afterload does not contribute to the PVN-evoked inotropy. Our results indicate that the modulation of the activity of PVN neurons exerted by GABAergic and adrenergic mechanisms contribute to the control of cardiac function.
The alteration of T790M between 19 del and L858R in NSCLC in the course of EGFR-TKIs therapy: a literature-based pooled analysis.

Background Treatment-naive epidermal growth factor receptor (EGFR) T790M mutation is more inclined to coexist with L858R than with 19 del in non-small cell lung cancer (NSCLC) patients. However, EGFR-tyrosine kinase inhibitors (EGFR-TKIs) might alter this status. We sought to compare the prevalence of T790M upon acquired resistance to EGFR-TKIs between 19 del and L858R by assembling all existing data. Methods Electronic databases were comprehensively searched for eligible studies. The primary endpoint was the odds ratio (OR) of T790M mutation in NSCLC co-existing with L858R mutation and 19 del upon resistance to first-generation EGFR-TKIs. A random effects model was used. Stratified analysis was performed based on study type (retrospective and prospective), race (Asians and Caucasians) and sample type (tissue and plasma). Results A total of 25 studies involving 1,770 patients were included. The overall T790M existent rate was 45.25%. Post-resistance T790M was more frequent in 19 del than in L858R mutated patients (53% vs. 36%; OR 1.87; P<0.001). All outcomes of subgroup and overall analyses were similar. In contrast, we re-analyzed the previous meta-analysis, finding that the pooled rate of pretreatment T790M was 14% and 22% in 19 del and L858R respectively (OR 0.59; P<0.001). The increase of T790M rate was 2.79-fold in 19 del and only 0.63-fold in L858R in the course of EGFR-TKIs therapy. Conclusions Opposite to the situation of de novo T790M, it was observed that T790M was more frequent in exon 19 deletion than in L858R among patients with acquired resistance to EGFR-TKIs. The difference in T790M alteration between 19 del and L858R encourages development of detection or treatment strategies for the specific resistance mechanism.
Benchmarking Touchscreen Biometrics for Mobile Authentication

We study user interaction with touchscreens based on swipe gestures for personal authentication. This approach has been analyzed only recently in the last few years in a series of disconnected and limited works. We summarize those recent efforts and then compare them to three new systems (based on support vector machine and Gaussian mixture model using selected features from the literature) exploiting independent processing of the swipes according to their orientation. For the analysis, four public databases consisting of touch data obtained from gestures sliding one finger on the screen are used. We first analyze the contents of the databases, observing various behavioral patterns, e.g., horizontal swipes are faster than vertical independently of the device orientation. We then explore an intra-session scenario, where users are enrolled and authenticated within the same day, and an inter-session one, where enrollment and test are performed on different days. The resulting benchmarks and processed data are made public, allowing the reproducibility of the key results obtained based on the provided score files and scripts. In addition to the remarkable performance, thanks to the proposed orientation-based conditional processing, the results show various new insights into the distinctiveness of swipe interaction, e.g., some gestures hold more user-discriminant information, data from landscape orientation is more stable, and horizontal gestures are more discriminative in general than vertical ones.
In Vitro Reconstitution

C ell biologists employ in vitro systems as useful intermediates between the biochemistry of isolated molecules and the intricate biology of intact cells. In vitro systems can be used to study cellular functions on a number of levels. On one hand, post-cellular extracts may be used so that complicated biochemical activities are preserved but cellular structures are not. This is the case for in vitro assays of protein translation (UNITS 11.2, 11.8, & 11.9), cotranslational translocation of proteins into microsomes (UNIT 11.4), posttranslational import of proteins into chloroplasts (UNIT 11.16), DNA replication (UNIT 11.5), mRNA transcription (UNIT 11.6), and mRNA splicing (UNIT 11.17). In other instances the plasma membrane of cells may be permeabilized by detergents, physical disruption, or bacterial toxins. Selective permeabilization allows the preservation of intact cellular structures. With the addition of exogenous cytosol, permeabilized cells can reconstitute endocytosis (UNIT 11.18), transport between the endoplasmic reticulum (ER) and Golgi apparatus (UNIT 11.3), nuclear protein import (UNIT 11.7), peroxisomal protein import (UNIT 11.15), and other protein trafficking pathways. Remarkably, some in vitro systems can reconstitute not only biochemical function but also structure. This is particularly true for Xenopus egg extracts (UNITS 11.10, 11.11, 11.12, & 11.13), which can assemble either nuclei or mitotic spindles de novo from appropriate added templates, such as sperm chromatin.
Loss of Akap1 Exacerbates Pressure Overload-Induced Cardiac Hypertrophy and Heart Failure

Left ventricular hypertrophy (LVH) is a major contributor to the development of heart failure (HF). Alterations in cyclic adenosine monophosphate (cAMP)-dependent signaling pathways participate in cardiomyocyte hypertrophy and mitochondrial dysfunction occurring in LVH and HF. cAMP signals are received and integrated by a family of cAMP-dependent protein kinase A (PKA) anchor proteins (AKAPs), tethering PKA to discrete cellular locations. AKAPs encoded by the Akap1 gene (mitoAKAPs) promote PKA mitochondrial targeting, regulating mitochondrial structure and function, reactive oxygen species production, and cell survival. To determine the role of mitoAKAPs in LVH development, in the present investigation, mice with global genetic deletion of Akap1 (Akap1-/-), Akap1 heterozygous (Akap1+/-), and their wild-type (wt) littermates underwent transverse aortic constriction (TAC) or SHAM procedure for 1 week. In wt mice, pressure overload induced the downregulation of AKAP121, the major cardiac mitoAKAP. Compared to wt, Akap1-/- mice did not display basal alterations in cardiac structure or function and cardiomyocyte size or fibrosis. However, loss of Akap1 exacerbated LVH and cardiomyocyte hypertrophy induced by pressure overload and accelerated the progression toward HF in TAC mice, and these changes were not observed upon prevention of AKAP121 degradation in seven in absentia homolog 2 (Siah2) knockout mice (Siah2-/-). Loss of Akap1 was also associated to a significant increase in cardiac apoptosis as well as lack of activation of Akt signaling after pressure overload. Taken together, these results demonstrate that in vivo genetic deletion of Akap1 enhances LVH development and accelerates pressure overload-induced cardiac dysfunction, pointing at Akap1 as a novel repressor of pathological LVH. These results confirm and extend the important role of mitoAKAPs in cardiac response to stress.
YNU_Deep at SemEval-2018 Task 11: An Ensemble of Attention-based BiLSTM Models for Machine Comprehension

We firstly use GloVe to learn the distributed representations automatically from the instance, question and answer triples. Then an attentionbased Bidirectional LSTM (BiLSTM) model is used to encode the triples. We also perform a simple ensemble method to improve the effectiveness of our model. The system we developed obtains an encouraging result on this task. It achieves the accuracy 0.7472 on the test set. We rank 5th according to the official ranking.
Salamander evolution across a latitudinal cline in gape-limited predation risk

General predictions of community dynamics require that insights derived from local habitats can be scaled up to explain phenomena across geographic scales. Across these larger spatial extents, adaptation can play an increasing role in determining the outcome of species interactions. If local adaptation is common, then our ability to generalize measures of species interaction strength across communities will be limited without an additional understanding of the genetic variation underlying interaction traits. In the context of predatorprey interactions, prey individuals commonly are expected to reduce risky foraging behaviors and subsequent growth under predation threat. However, rapid growth into a large body size can defend against gape-limited predators, creating a tradeoff between increased predation risk due to elevated foraging activity and decreased predation risk due to large size. Here I combine field observations, natural selection experiments, and common garden assays to understand potential adaptations of spotted salamander Ambystoma maculatum larvae to gape-limited and gape-unconstrained predators. Field observations and natural selection trials suggested antagonistic selection on prey body size among ponds dominated by gape-limited predator salamanders A. opacum and gape-unconstrained beetle larvae Dytiscus. In common garden experiments, prey from sites with high gapelimited predation risk grew larger than those from other sites, suggesting the evolution of rapid growth into a prey size refuge. Larvae from all sites grew to a large size when exposed to the gape-limited N. viridescens predator’s kairomones. Hence, induced rapid growth into a size refuge may be an adaptive response to gape-limited predation risk. Results point to an important role for cross-community generalizations based on functional classifications of predators by their gape constraints and inter-site genetic variation in prey growth rates and behaviors.
Importance of the axial reference plane in computed tomography for dental implant surgery: cadaveric study

_Objectives The aims of the study were to assess the accuracy of dental computed tomography (CT) scans and to compare the discrepancies obtained when either the occlusal plane or the basal plane was used as the axial reference plane. _Materials and methods Thirty-nine mandibles from adult cadavers were examined. Eighteen tomographic slices were performed for each mandible, using the occlusal and the basal planes as axial reference planes. The radiographic measurements obtained using the two reference planes were compared with bone measurements taken using a digital calibrator.
Dietary and serum vitamins A and E and colorectal cancer risk in Chinese population: a case–control study

The effect of vitamin A (VA) and vitamin E (VE) on colorectal cancer (CRC) risk is controversial. The aim of this study is to examine the association between serum concentrations and dietary intakes of VA and VE and the risk of CRC in Guangdong, China. A total of 535 cases and 552 sex and age-matched (5-year interval) controls were recruited during July 2010 to September 2014. Dietary information was assessed by face-to-face interviews using a validated food frequency questionnaire. Concentrations of VA and VE were measured by high-performance liquid chromatography. Multivariable logistic regression was used to estimate the odds ratios (ORs) and 95% confidence interval (CI) after adjusting for various potential confounders. A higher intake of VA and VE was found to be associated with 52 and 43% reduction in CRC risk. The ORs of the highest quartile compared with the lowest quartile intake were 0.48 (95% CI: 0.31, 0.73, Ptrend<0.01) for VA and 0.57 (95% CI: 0.37, 0.88, Ptrend<0.01) for VE. An inverse association was also found between serum retinol and CRC risk, with an adjusted OR (95% CI) of 0.28 (0.19–0.43) (Ptrend<0.01). However, no statistically significant association was found between serum α-tocopherol and CRC risk. Stratified analysis by sex showed that serum retinol and dietary VA and VE were inversely associated with CRC risk in both sexes. This study supported the hypothesis that lower serum levels of retinol and lower intakes of VA and VE were associated with the risk of CRC in a Chinese population.
Gut Microbiota in Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis: Current Applications and Future Perspectives

The gut environment and gut microbiome dysbiosis have been demonstrated to significantly influence a range of disorders in humans, including obesity, diabetes, rheumatoid arthritis, and multiple sclerosis (MS). MS is an autoimmune disease affecting the central nervous system (CNS). The etiology of MS is not clear, and it should involve both genetic and extrinsic factors. The extrinsic factors responsible for predisposition to MS remain elusive. Recent studies on MS and its animal model, experimental autoimmune encephalomyelitis (EAE), have found that gastrointestinal microbiota may play an important role in the pathogenesis of MS/EAE. Thus, gut microbiome adjustment may be a future direction of treatment in MS. In this review, we discuss the characteristics of the gut microbiota, the connection between the brain and the gut, and the changes in gut microbiota in MS/EAE, and we explore the possibility of applying microbiota therapies in patients with MS.
Variants of PEAR1 Are Associated With Outcome in Patients With ACS and Stable CAD Undergoing PCI

Introduction: Platelet endothelial aggregation receptor 1 (PEAR1) triggers platelet aggregation and is expressed in platelets and endothelial cells. Genome-wide association studies (GWAS) showed an association between platelet function and single-nucleotide polymorphisms (SNPs) in PEAR1. Methods: In 582 consecutive patients with stable coronary artery disease (CAD) or acute coronary syndrome (ACS) scheduled for PCI and treated with ASA and Clopidogrel, Prasugrel, or Ticagrelor, SNP analysis for rs12566888, rs2768759, rs41273215, rs3737224, and rs822442 was performed. During a follow-up period of 365 days after initial PCI, all patients were tracked for a primary endpoint, defined as a combined endpoint consisting of either time to death, myocardial infarction (MI) or ischemic stroke. All cause mortality, MI and ischemic stroke were defined as secondary endpoints. Results: Multivariable Cox model analysis for the primary endpoint revealed a significantly increased risk in homozygous PEAR1 rs2768759 minor allele carriers (hazard ratio, 3.16; 95% confidence interval, 1.4–7.13, p = 0.006). Moreover, PEAR1 rs12566888 minor allele carriers also showed an increased risk in all patients (hazard ratio, 1.69; 95% confidence interval, 0.87–3.27, p = 0.122), which was marginally significant in male patients (hazard ratio, 2.12; 95% confidence interval, 1.02–4.43, p = 0.045; n = 425). Conclusions: To the best of our knowledge, this is the first study showing that distinct genetic variants of PEAR1 are associated with cardiovascular prognosis in high risk patients undergoing PCI and treated with dual anti platelet therapy.
A Place to Call Home: A Synthesis of Delta Smelt Habitat in the Upper San Francisco Estuary

We used a combination of published literature and field survey data to synthesize the available information about habitat use by delta smelt Hypomesus transpacificus, a declining native species in the San Francisco Estuary. Delta smelt habitat ranges from San Pablo and Suisun bays to their freshwater tributaries, including the Sacramento and San Joaquin rivers. In recent years, substantial numbers of delta smelt have colonized habitat in Liberty Island, a north Delta area that flooded in 1997. The species has a more upstream distribution during spawning as opposed to juvenile rearing periods. Post-larvae and juveniles tend to have a more downstream distribution during wetter years. Delta smelt are most common in low-salinity habitat ( 12 NTU) and moderate temperatures (7 °C to 25 °C). They do not appear to have strong substrate preferences, but sandy shoals are important for spawning in other osmerids. The evidence to date suggests that they generally require at least some tidal flow in their habitats. Delta smelt also occur in a wide range of channel sizes, although they seem to be rarer in small channels (<15 m wide). Nonetheless, there is some evidence that open water adjacent to habitats with long water-residence times (e.g. tidal marsh, shoal, low-order channels) may be favorable. Other desirable features of delta smelt habitat include high calanoid copepod densities and low levels of submerged aquatic vegetation (SAV) and the toxic algae Microcystis. Although enough is known to plan for large-scale pilot habitat projects, these efforts are vulnerable to several factors, most notably climate change, which will change salinity regimes and increase the occurrence of lethal temperatures. We recommend restoration of multiple geographical regions and habitats coupled with extensive monitoring and adaptive management. An overall emphasis on ecosystem processes rather than specific habitat features is also likely to be most effective for recovery of the species.