Miracle-dz/UniFAR-FTUs huggingface dataset:
Prevalence and Genetic Diversity of Campylobacter spp. in Environmental Water Samples from a 100-Square-Kilometer Predominantly Dairy Farming Area

ABSTRACT Water samples were taken systematically from a 100-km2 area of mainly dairy farmland in northwestern England and examined for Campylobacter spp. Pulsed-field gel electrophoresis-restriction fragment length polymorphism (PFGE-RFLP) and flaA strain typing of Campylobacter jejuni and Campylobacter coli isolates were done. Data on the water source and the adjacent environment were recorded and examined as explanatory variables. Campylobacter spp. were isolated from 40.5% (n = 119) of the water samples tested. C. jejuni was isolated from 14.3%, C. coli was isolated from 18.5%, and Campylobacter lari was isolated from 4.2% of the samples. Campylobacter hyointestinalis was not isolated from any water source. The difference in prevalence between water types (trough, running, and standing) was significant (P = 0.001). C. jejuni was the species most commonly isolated from trough-water and running-water sources, while C. coli was the most frequently isolated from standing water (P < 0.001). No association was found between the presence of Escherichia coli and that of Campylobacter spp. The final multivariable logistic regression model for Campylobacter spp. included the following variables: water source, soil type, aspect, and amount of cattle fecal material in the environment (fecal pat count). Strain typing demonstrated a diverse population of C. jejuni and the presence of a common C. coli flaA type that was widely distributed throughout the area. Most of the isolates within the common flaA type were discriminated by PFGE-RFLP. These findings suggest a possible role for environmental water in the epidemiology of Campylobacter spp. in a farming environment.
The deubiquitinating enzyme USP46 regulates AMPA receptor ubiquitination and trafficking

Alpha‐amino‐3‐hydroxy‐5‐methyl‐4‐isoxazolepropionic acid receptor (AMPARs) are the primary mediators for inter‐neuronal communication and play a crucial role in higher brain functions including learning and memory. Our previous work demonstrated that AMPARs are subject to ubiquitination by the E3 ligase Nedd4, resulting in EPS15‐mediated receptor internalization and Ubiquitin (Ub)–proteasome pathway (UPP)‐dependent degradation. Protein ubiquitination is a highly dynamic and reversible process, achieved via the balance between ubiquitination and deubiquitination. However, deubiquitination of mammalian AMPARs and the responsible deubiquitinating enzymes remain elusive. In this study, we identify USP46 as the deubiquitinating enzyme for AMPARs. We find that AMPARs are subject to K63 type ubiquitination, and USP46 is able to deubiquitinate AMPARs in vivo and in vitro. In heterologous cells and neurons, expression of USP46 results in a significant reduction in AMPAR ubiquitination, accompanied by a reduced rate in AMPAR degradation and an increase in surface AMPAR accumulation. By contrast, knockdown of USP46 by RNAi leads to elevated AMPAR ubiquitination and a reduction in surface AMPARs at synapses in neurons. Consistently, miniature excitatory postsynaptic currents recordings show reduced synaptic strength in neurons expressing USP46‐selective RNAi. These results demonstrate USP46‐mediated regulation of AMPAR ubiquitination and turnover, which may play an important role in synaptic plasticity and brain function.
Clinical outcome of acute nonvariceal upper gastrointestinal bleeding after hours: the role of urgent endoscopy

Background/Aims: This study was performed to investigate the clinical role of urgent esophagogastroduodenoscopy (EGD) for acute nonvariceal upper gastrointestinal bleeding (ANVUGIB) performed by experienced endoscopists after hours. Methods: A retrospective analysis was performed for consecutively collected data of patients with ANVUGIB between January 2009 and December 2010. Results: A total of 158 patients visited the emergency unit for ANVUGIB after hours. Among them, 60 underwent urgent EGD (within 8 hours) and 98 underwent early EGD (8 to 24 hours) by experienced endoscopists. The frequencies of hemodynamic instability, fresh blood aspirate on the nasogastric tube, and high-risk endoscopic findings were significantly higher in the urgent EGD group. Primary hemostasis was achieved in all except two patients. There were nine cases of recurrent bleeding, and 30-day mortality occurred in three patients. There were no significant differences between the two groups in primary hemostasis, recurrent bleeding, and 30-day mortality. In a multiple linear regression analysis, urgent EGD significantly reduced the hospital stay compared with early EGD. In patients with a high clinical Rockall score (more than 3), urgent EGD tended to decrease the hospital stay, although this was not statistically significant (7.7 days vs. 12.0 days, p > 0.05). Conclusions: Urgent EGD after hours by experienced endoscopists had an excellent endoscopic success rate. However, clinical outcomes were not significantly different between the urgent and early EGD groups.
Identification of potential diagnostic markers of prostate cancer and prostatic intraepithelial neoplasia using cDNA microarray

The identification of novel genes or groups of genes expressed in prostate cancer may allow earlier diagnosis or more accurate staging of the disease. We describe the assembly and use of a 1877-member microarray representing cDNA clones from a range of prostate cancer stages and grades, precursor lesions and normal tissue. Using labelled cDNA from tumour samples obtained from TURP or radical prostatectomy, analysis of expression patterns identified many up-regulated transcripts. Cell lines were found to over-express fewer genes than diseased tissue samples. 17 known genes were found to over-express more than 4-fold in 4 or more cancers out of 15 cancers. Only 2 genes were over-expressed in 6 out of 15 cancers or more, whilst no genes were consistently found to be over-expressed in all cancer samples. Novel prostate cancer associations for several well characterized genes or full length cDNAs were identified, including PLRP1, JM27, human UbcM2, dynein light intermediate chain 2 and human homologue of rat sec61. Novel associations with high-grade PIN include: breast carcinoma fatty acid synthase and cDNA DKFZp434B0335. We shortlist and discuss the most significant over-expressed genes in prostate cancer and PIN, and highlight expression differences between malignant and benign samples. © 2001 Cancer Research Campaign http://www.bjcancer. com
Genetic Testing for Long-QT Syndrome: Distinguishing Pathogenic Mutations From Benign Variants

Background— Genetic testing for long-QT syndrome (LQTS) has diagnostic, prognostic, and therapeutic implications. Hundreds of causative mutations in 12 known LQTS-susceptibility genes have been identified. Genetic testing that includes the 3 most commonly mutated genes is available clinically. Distinguishing pathogenic mutations from innocuous rare variants is critical to the interpretation of test results. We sought to quantify the value of mutation type and gene/protein region in determining the probability of pathogenicity for mutations. Methods and Results— Type, frequency, and location of mutations across KCNQ1 (LQT1), KCNH2 (LQT2), and SCN5A (LQT3) were compared between 388 unrelated “definite” (clinical diagnostic score ≥4 and/or QTc ≥480 ms) cases of LQTS and >1300 healthy controls for each gene. From these data, estimated predictive values (percent of mutations found in definite cases that would cause LQTS) were determined according to mutation type and location. Mutations were 10 times more common in cases than controls (0.58 per case versus 0.06 per control). Missense mutations were the most common, accounting for 78%, 67%, and 89% of mutations in KCNQ1, KCNH2, and SCN5A in cases and >95% in controls. Nonmissense mutations have an estimated predictive value >99% regardless of location. In contrast, location appears to be critical for characterizing missense mutations. Relative frequency of missense mutations between cases and controls ranged from ≈1:1 in the SCN5A interdomain linker to infinity in the pore, transmembrane, and linker in KCNH2. These correspond to estimated predictive values ranging from 0% in the interdomain linker of SCN5A to 100% in the transmembrane/linker/pore regions of KCNH2. The estimated predictive value is also high in the linker, pore, transmembrane, and C terminus of KCNQ1 and the transmembrane/linker of SCN5A. Conclusions— Distinguishing pathogenic mutations from rare variants is of critical importance in the interpretation of genetic testing in LQTS. Mutation type, mutation location, and ethnic-specific background rates are critical factors in predicting the pathogenicity of novel mutations. Novel mutations in low–estimated predictive value regions such as the interdomain linker of SCN5A should be viewed as variants of uncertain significance and prompt further investigation to clarify the likelihood of disease causation. However, mutations in regions such as the transmembrane, linker, and pore of KCNQ1 and KCNH2 may be defined confidently as high-probability LQTS-causing mutations. These findings will have implications for other genetic disorders involving mutational analysis.
Modal solutions of photonic crystal fibers by using a full-vectorial finite element method

Modal solutions for photonic crystal fibers (PCFs) with circular air holes in a hexagonal matrix are presented, using a rigorous full-vectorial finite element-based approach. The effective indices, mode field profiles, spot-sizes, modal hybridness, modal birefringence and group velocity dispersion values have been determined for a representative range of PCFs and the results obtained are shown and conclusions drawn. The effect of the structural asymmetry and modal confinement on the optimization of the modal birefringence is also thoroughly studied and presented here. The effect of total power on the effective indices and spot-sizes of nonlinear PCFs is also presented.
The Phylogenetics and Ecology of the Orthopoxviruses Endemic to North America

The data presented herein support the North American orthopoxviruses (NA OPXV) in a sister relationship to all other currently described Orthopoxvirus (OPXV) species. This phylogenetic analysis reaffirms the identification of the NA OPXV as close relatives of “Old World” (Eurasian and African) OPXV and presents high support for deeper nodes within the Chordopoxvirinae family. The natural reservoir host(s) for many of the described OPXV species remains unknown although a clear virus-host association exists between the genus OPXV and several mammalian taxa. The hypothesized host associations and the deep divergence of the OPXV/NA OPXV clades depicted in this study may reflect the divergence patterns of the mammalian faunas of the Old and New World and reflect a more ancient presence of OPXV on what are now the American continents. Genes from the central region of the poxvirus genome are generally more conserved than genes from either end of the linear genome due to functional constraints imposed on viral replication abilities. The relatively slower evolution of these genes may more accurately reflect the deeper history among the poxvirus group, allowing for robust placement of the NA OPXV within Chordopoxvirinae. Sequence data for nine genes were compiled from three NA OPXV strains plus an additional 50 genomes collected from Genbank. The current, gene sequence based phylogenetic analysis reaffirms the identification of the NA OPXV as the nearest relatives of “Old World” OPXV and presents high support for deeper nodes within the Chordopoxvirinae family. Additionally, the substantial genetic distances that separate the currently described NA OPXV species indicate that it is likely that many more undescribed OPXV/NA OPXV species may be circulating among wild animals in North America.
Influence of Plant Growth Regulators on In Vitro Shoot Multiplication and Plantlet Formation in Cassia angustifolia Vahl

An effective and improved plant regeneration system was successfully developed using shoot tip explants taken from a two years old mature plant of Cassia angustifolia. The effect of different cytokinins, [6-benzyladenine (BA), Kinetin (Kin) and thidiazuron (TDZ)] at different concentrations (0.5-10 µM) were evaluated as augmented with Murashige and Skoog (MS 1962) medium. Among all the cytokinins tested, TDZ (5.0 µM) was optimum in inducing multiple shoots as compared to BA and Kin. The rate of shoot multiplication was increased when optimal concentration (5.0 µM) of BA and Kin was tested with different concentration (0.1-1.0 µM) of Indole-3- acetic acid (IAA). Among all the combinations tested, the maximum rate of shoot multiplication was obtained on MS medium supplemented with 5.0 µM BA and 0.5 µM IAA. The number of the shoots and shoot length developed in TDZ was increased when transferred to MS medium devoid of TDZ. After every subculture, rate of the shoot multiplication and shoot length showed increment and continued even after fifth subculture without any decline rate. In vitro rooting in regenerated shoots were best obtained in half-strength MS medium supplemented with 2.0 µM indole-3- butyric acid (IBA). Plantlets with well-developed shoot and roots were successfully hardened off in earthen pots containing garden soil and grown in greenhouse with 80% survival rate.
Assessing Bacterial Interactions Using Carbohydrate-Based Microarrays

Carbohydrates play a crucial role in host-microorganism interactions and many host glycoconjugates are receptors or co-receptors for microbial binding. Host glycosylation varies with species and location in the body, and this contributes to species specificity and tropism of commensal and pathogenic bacteria. Additionally, bacterial glycosylation is often the first bacterial molecular species encountered and responded to by the host system. Accordingly, characterising and identifying the exact structures involved in these critical interactions is an important priority in deciphering microbial pathogenesis. Carbohydrate-based microarray platforms have been an underused tool for screening bacterial interactions with specific carbohydrate structures, but they are growing in popularity in recent years. In this review, we discuss carbohydrate-based microarrays that have been profiled with whole bacteria, recombinantly expressed adhesins or serum antibodies. Three main types of carbohydrate-based microarray platform are considered; (i) conventional carbohydrate or glycan microarrays; (ii) whole mucin microarrays; and (iii) microarrays constructed from bacterial polysaccharides or their components. Determining the nature of the interactions between bacteria and host can help clarify the molecular mechanisms of carbohydrate-mediated interactions in microbial pathogenesis, infectious disease and host immune response and may lead to new strategies to boost therapeutic treatments.
Colossal positive magneto-resistance in oxygen deficient Ca4Mn3O10

Huge change of resistance by an external magnetic field, i.e. colossal magneto-resistance effect, has been a long-lived theme of research due to both fundamental science and device applications. Here we report colossal positive magneto-resistance (> 1200% at a temperature of 4K and a magnetic field of 9 T) discovered in oxygen deficient Ca4Mn3O10 phase. The structural, magnetic and magneto transport properties are discussed.
Efficiency of Different Endodontic Irrigation and Activation Systems in Removal of the Smear Layer: A Scanning Electron Microscopy Study

Introduction: This in vitro study was designed to evaluate and compare different endodontic irrigation and activation systems for removal of the intracanal smear layer. Methods and Materials: Forty recently extracted, non-carious human intact single rooted premolars were selected and divided into five groups (n=10) according to the root canal irrigation systems; syringe and needle irrigation (CTR), sonic irrigation, passive ultrasonic irrigation (PUI) and EndoVac irrigation system. All groups were prepared to #40 apical size with K-files. Each sample was subjected to final irrigation by using four different irrigation/activation systems. After splitting the samples, one half of each root was selected for examination under scanning electron microscope (SEM). The irrigation systems were compared using the Fisher's exact test with the level of significance set at 0.05. Results: The four groups did not differ from each other in the coronal and mid-root parts of the canal. In the apical part of the canal none of the methods could completely remove all the smear layer but EndoVac system showed significantly better removal of smear layer and debris than the other methods. Conclusion: Within the limitations of the present study, the EndoVac system cleaned the apical part of the canal more efficiently than sonic, ultrasonic and syringe and needle irrigation.
Optimal control for discrete-time singular systems with multiplicative-noise and input delay

This paper deals with the finite-horizon linear quadratic (LQ) optimal control problem for the discrete-time singular systems with multiplicative-noise and input delay. Firstly, by utilizing the incremental analysis method, the maximum principle is established for the singular stochastic system in discrete-time form. Then a sufficient criterion is given which guarantees not only the existence but also the uniqueness of the optimal controller. With such kind of controllers designed, the mathematical expectation of the cost function reaches its minimum value which is also given in explicit form. The criteria obtained in this paper are presented in the recursive equality form, which can be verified easily by effective algorithms. A numerical example is provided in the end of the paper which demonstrates the effectiveness of the obtained theoretical results.
A Selective Overview of Issues on Classification, Causation, and Early Intensive Behavioral Intervention for Autism

Autism is a behaviorally defined disorder that comprises a controversial diagnostic category due to heterogeneity in symptomatology, causation, and etiology and significant variance in response to intervention. In this article, the authors provide a brief overview of the clinical category and a summary of diagnostic developments with respect to the American Psychiatric Association’s Diagnostic and Statistical Manual of Mental Disorders.Regarding causation and etiology, they briefly discuss selected perspectives from the fields of cognitive neuroscience and neuropsychology. The article concludes with a summary of effective behavioral strategies for the treatment of children with autism. This section highlights the importance of early intensive behavioral intervention and includes a discussion of some important aspects of this approach.
Central Amino Acid Sensing in the Control of Feeding Behavior

Dietary protein quantity and quality greatly impact metabolic health via evolutionary-conserved mechanisms that ensure avoidance of amino acid imbalanced food sources, promote hyperphagia when dietary protein density is low, and conversely produce satiety when dietary protein density is high. Growing evidence supports the emerging concept of protein homeostasis in mammals, where protein intake is maintained within a tight range independently of energy intake to reach a target protein intake. The behavioral and neuroendocrine mechanisms underlying these adaptations are unclear. While peripheral factors are able to signal amino acid deficiency and abundance to the brain, the brain itself is exposed to and can detect changes in amino acid concentrations, and subsequently engages acute and chronic responses modulating feeding behavior and food preferences. In this review, we will examine the literature describing the mechanisms by which the brain senses changes in amino acids concentrations, and how these changes modulate feeding behavior.
Artificial ligand binding within the HIF2α PAS-B domain of the HIF2 transcription factor

The hypoxia-inducible factor (HIF) basic helix–loop–helix Per-aryl hydrocarbon receptor nuclear translocator (ARNT)-Sim (bHLH-PAS) transcription factors are master regulators of the conserved molecular mechanism by which metazoans sense and respond to reductions in local oxygen concentrations. In humans, HIF is critically important for the sustained growth and metastasis of solid tumors. Here, we describe crystal structures of the heterodimer formed by the C-terminal PAS domains from the HIF2α and ARNT subunits of the HIF2 transcription factor, both in the absence and presence of an artificial ligand. Unexpectedly, the HIF2α PAS-B domain contains a large internal cavity that accommodates ligands identified from a small-molecule screen. Binding one of these ligands to HIF2α PAS-B modulates the affinity of the HIF2α:ARNT PAS-B heterodimer in vitro. Given the essential role of PAS domains in forming active HIF heterodimers, these results suggest a presently uncharacterized ligand-mediated mechanism for regulating HIF2 activity in endogenous and clinical settings.
Behavioral and psychological symptoms in Taiwanese patients with Alzheimer's disease

Objective: To investigate the prevalence of and risk factors for behavioral and psychological symptoms in Taiwanese Alzheimer's disease (AD) patients. Method: Consecutive AD patients from the Memory Clinic of the Taipei Veterans General Hospital were studied. Cognitive function was evaluated using the Chinese version of the Cognitive Abilities Screening Instrument. Primary caregivers were interviewed for the Clinical Dementia Rating scale, the Barthel Index, and the Alzheimer's Deficit Scale. Behavioral and psychological symptoms were assessed using the Behavioral Pathology in Alzheimer's Disease Rating Scale. Results: Of the 142 participants, 73 (50.7%) had at least one delusion. The most frequent delusion was delusion of theft (N = 43, 30.3%). Thirty-five patients (24.6%) experienced hallucination. Fifty-seven patients (40.1%) had activity disturbances and 39 (27.5%) had aggression. Patients were divided into two subgroups according to the presence or absence of each cluster of symptoms, namely, delusions, hallucinations, activity disturbance, aggression, diurnal rhythm change, affective symptoms, and anxiety. There was no significant correlation between age, age at onset of dementia, number of years of education, and duration of illness and each cluster of symptoms. Correlation between severity of behavioral and psychological symptoms of dementia and cognitive decline was noted. Conclusions: This study revealed a high prevalence of behavioral and psychological symptoms of dementia in Taiwanese patients with AD and suggests that these symptoms are associated with cognitive deficit.