Miracle-dz/UniFAR-FTUs huggingface dataset:
New Threshold and Confidence Estimates for Terminal Restriction Fragment Length Polymorphism Analysis of Complex Bacterial Communities

ABSTRACT Terminal restriction fragment length polymorphism (T-RFLP) analysis has the potential to be useful for comparisons of complex bacterial communities, especially to detect changes in community structure in response to different variables. To do this successfully, systematic variations have to be detected above method-associated noise, by standardizing data sets and assigning confidence estimates to relationships detected. We investigated the use of different standardizing methods in T-RFLP analysis of PCR-amplified 16S rRNA genes to elucidate the similarities between the bacterial communities in 17 soil and sediment samples. We developed a robust method for standardizing data sets that appeared to allow detection of similarities between complex bacterial communities. We term this the variable percentage threshold method. We found that making conclusions about the similarities of complex bacterial communities from T-RFLP profiles generated by a single restriction enzyme (RE) may lead to erroneous conclusions. Instead, the use of multiple REs, each individually, to generate multiple data sets allowed us to determine a confidence estimate for groupings of apparently similar communities and at the same time minimized the effects of RE selection. In conjunction with the variable percentage threshold method, this allowed us to make confident conclusions about the similarities of the complex bacterial communities in the 17 different samples.
Multiple Description Video Coding Based on Hierarchical B Pictures

A general multiple description video coding (MDVC) framework based on hierarchical B pictures is proposed in this paper. Two or more descriptions are generated by employing the hierarchical B pictures of H.264/AVC scalable extension, where temporal-level-based key pictures are selected in a staggered way among different descriptions. Based on this hierarchical and staggered structure, inter-description redundancy control is studied to achieve a good central/side-distortion-rate tradeoff. Moreover, to better exploit multiple complementary descriptions, a linear combination of received descriptions is employed to optimize decoding results. This proposed MDVC framework is H.264/AVC-compliant for each temporal scalable description. Some existing temporal-splitting MDVC techniques can be considered as a degraded case in the proposed structure. Experimental results validate the effectiveness of the proposed design for MDVC.
$hboxN_2$-Annealing Effects on Characteristics of Schottky-Barrier MOSFETS

Schottky-barrier (SB) heights of erbium and platinum silicides are evaluated using current-voltage and capacitance-voltage methods in the Schottky diodes. For the erbium-silicided Schottky diodes, the extracted SB heights show big differences depending on the extraction methods, due to the existence of the interface traps. The interface traps in the erbium silicide are efficiently cured by N2 annealing. Various sizes of the erbium/platinum-silicided n/p-type SB-MOSFETs are manufactured from 20 mum to 23 nm. Also, N2 annealing is applied to enhance the SB-MOSFETs' subthreshold characteristics by minimizing the interface-trap density. The manufactured SB-MOSFETs show a good drain-induced barrier thinning and subthreshold swing characteristics, due to the existence of a SB between the source and the channel, which indicates the possible application of the SB-MOSFETs in a nanoscale regime
Loss of employment and mortality

Abstract Objective: To assess effect of unemployment and early retirement on mortality in a group of middle aged British men. Design: Prospective cohort study (British Regional Heart Study). Five years after initial screening, information on employment experience was obtained with a postal questionnaire. Setting: One general practice in each of 24 towns in Britain. Subjects: 6191 men aged 40-59 who had been continuously employed for at least five years before initial screening in 1978-80: 1779 experienced some unemployment or retired during the five years after screening, and 4412 remained continuously employed. Main outcome measure: Mortality during 5.5 years after postal questionnaire. Results: Men who experienced unemployment in the five years after initial screening were twice as likely to die during the following 5.5 years as men who remained continuously employed (relative risk 2.13 (95% confidence interval 1.71 to 2.65). After adjustment for socioeconomic variables (town and social class), health related behaviour (smoking, alcohol consumption, and body weight), and health indicators (recall of doctor diagnoses) that had been assessed at initial screening the relative risk was slightly reduced, to 1.95 (1.57 to 2.43). Even men who retired early for reasons other than illness and who appeared to be relatively advantaged and healthy had a significantly increased risk of mortality compared with men who remained continuously employed (relative risk 1.87 (1.35 to 2.60)). The increased risk of mortality from cancer was similar to that of mortality from cardiovascular disease (adjusted relative risk 2.07 and 2.13 respectively). Conclusions: In this group of stably employed middle aged men loss of employment was associated with an increased risk of mortality even after adjustment for background variables, suggesting a causal effect. The effect was non-specific, however, with the increased mortality involving both cancer and cardiovascular disease.
The Role of the Tyrosine Kinase Domain of the Insulin-like Growth Factor-I Receptor in Intracellular Signaling, Cellular Proliferation, and Tumorigenesis (*)

Insulin and insulin-like growth factor (IGF-I) receptors are heterotetrameric proteins consisting of two α- and two β-subunits and members of the transmembrane tyrosine kinase receptors. Specific ligand binding to the receptor triggers a cascade of intracellular events, which begins with autophosphorylation of several tyrosine residues of the β-subunit of the receptor. The triple cluster in the tyrosine kinase domain of the β-subunit is the earliest and major autophosphorylation site. Previous studies have shown that substitutions of these three tyrosines by phenylalanines of both insulin and IGF-I receptors practically abolish any activation of cellular signaling pathways. We have studied the effect of double tyrosine mutations on IGF-I-induced receptor autophosphorylation, activation of Shc and IRS-1 pathways, and cell proliferation and tumorigenicity. Substitution of tyrosines 1131/1135 blocks any detectable autophosphorylation, whereas substitution of tyrosines 1131/1136 or 1135/1136 only reduces autophosphorylation levels in some clones by 50%. Nevertheless, all the cells expressing IGF-I receptors with double tyrosine substitutions demonstrated markedly reduced signaling through Shc and IRS-1 pathways. In addition, they were unable to respond to IGF-I-stimulated cell growth in culture, and tumor formation in nude mice was abrogated. These data suggest that the presence of tyrosine 1131 or 1135 essential for receptor autophosphorylation, whereas the presence of each of these tyrosines is necessary for a fully functional receptor.
Methods to monitor the quaternary structure of G protein‐coupled receptors

A wide range of approaches has been applied to examine the quaternary structure of G protein‐coupled receptors, the basis of such protein–protein interactions and how such interactions might modulate the pharmacology and function of these receptors. These include coimmunoprecipitation, various adaptations of resonance energy transfer techniques, functional complementation studies and the analysis of ligand‐binding data. Each of the available techniques has limitations that restrict interpretation of the data. However, taken together, they provide a coherent body of evidence indicating that many, if not all, G protein‐coupled receptors exist and function as dimer/oligomers. Herein we assess the widely applied techniques and discuss the relative benefits and limitations of these approaches.
A mixed methods thematic review: Health‐related decision‐making by the older person

AIMS AND OBJECTIVES To undertake a mixed methods thematic literature review that explored how elderly adults approached decision-making in regard to their health care following discharge. BACKGROUND A critical time for appropriate health decisions occurs during hospital discharge planning with nursing staff. However, little is known how the 89% of elderly living at home make decisions regarding their health care. Research into older adults' management of chronic conditions emerges as an important step to potentially encourage symptom monitoring, prevent missed care and detect deterioration. All should reduce the risk of hospital re-admission. DESIGN A mixed methods thematic literature review was undertaken. The structure followed the PRISMA reporting guidelines for systematic reviews recommended by the EQUATOR network. METHODS PubMed, Cumulative Index to Nursing and Allied Health Literature (CINAHL) and Scopus online databases were searched using keywords, inclusion and exclusion criteria. References drawn from relevant publications, identified by experts and published between 1995 and 2017 were also considered. Twenty-five qualitative, quantitative and mixed methods studies and reviews were critically appraised (CASP 2013) before inclusion in the review. Analysis of each study's findings was undertaken using Braun and Clarke's (2006) steps to identify major themes and sub-themes. RESULTS Four main themes associated with health-related decision-making in the elderly were identified: "the importance of maintaining independence," "decision making style," "management of conditions at home" and "discharge planning. " CONCLUSION Health care decision preferences in the elderly emerged as highly complex and influenced by multiple factors. Development of a tool to assess these components has been recommended. RELEVANCE TO CLINICAL PRACTICE Nurses play a vital role in exploring and understanding the influence that maintaining independence has with each patient. This understanding provides an initial step toward development of a tool to assist collaboration between patients and healthcare professionals involved in their care.
The Professional Doctorate for the Engineering & Technology Profession

Michael J. Dyrenfurth is a Professor and Graduate Programs Coordinator in the Department of of Technology Leadership and Innovation in Purdue University’s Polytechnic Institute. He is a member of the ASEE and he has served on both the ENT and the ETD Board of directors and as program chair for the ASEE ENT (2014) and the CIEC in New Orleans (2008). Previously he completed a four year term as Assistant Dean for Graduate Studies in Purdue University’s College of Technology.
Coadministration of Galanin Antagonist M40 with a Muscarinic M1 Agonist Improves Delayed Nonmatching to Position Choice Accuracy in Rats with Cholinergic Lesions

The neuropeptide galanin is overexpressed in the basal forebrain in Alzheimer’s disease (AD). In rats, galanin inhibits evoked hippocampal acetylcholine release and impairs performance on several memory tasks, including delayed nonmatching to position (DNMTP). Galanin(1–13)-Pro2-(Ala-Leu)2-Ala-NH2(M40), a peptidergic galanin receptor ligand, has been shown to block galanin-induced impairment on DNMTP in rats. M40 injected alone, however, does not improve DNMTP choice accuracy deficits in rats with selective cholinergic immunotoxic lesions of the basal forebrain. The present experiments used a strategy of combining M40 with an M1 cholinergic agonist in rats lesioned with the cholinergic immunotoxin 192IgG-saporin. Coadministration of intraventricular M40 with intraperitoneal 3-(3-S-n-pentyl-1,2,5-thiadiazol-4-yl)-1,2,5,6-tetrahydro-1-methylpyridine (TZTP), an M1 agonist, improved choice accuracy significantly more than a threshold dose of TZTP alone. These results suggest that a galanin antagonist may enhance the efficacy of cholinergic treatments for the cognitive deficits of AD.
Overexpression of vasopressin in the rat transgenic for the metallothionein-vasopressin fusion gene.

Arginine vasopressin (AVP) is a major antidiuretic hormone, the overproduction of which causes diluting hyponatremia in humans and is called the syndrome of inappropriate antidiuresis (SIAD). To study physiological changes resulting from AVP overproduction and to develop an animal model of hyponatremia, the human AVP gene was expressed under the control of the metallothionein promoter in transgenic (Tg) rats. Analyses of AVP immunoreactivity (irAVP) in the tissues revealed that the transgene is expressed mainly in the central nervous system. Gel filtration showed that irAVP in the brain and plasma was properly processed AVP. AVP purified from the brains of both Tg and control rats also exerted equal bioactivity to generate cAMP in LLC-PK1 cells. The founder rats did not show any physical or anatomical abnormalities. Under basal conditions, Tg rats had high plasma AVP levels (Tg 13.8 +/- 2.5 pg/ml; control 2.7 +/- 1.2 pg/ml; n=6 in both groups; means +/- S.E.M.), decreased urine volume, and normal plasma [Na(+)]. Hypertonic saline injected i.p. did not affect AVP secretion in Tg rats. In response to a zinc-supplemented liquid diet, plasma AVP decreased in control rats, but increased in Tg rats (Tg 32.7 +/- 2.7 pg/ml; control 1.0+/-0.1 pg/ml; n=6), resulting in hyponatremia (Tg 135.2 +/- 2.5 mEq/l; control 140.8 +/- 0.4 mEq/l; n=6). To our knowledge, this is the first transgenic animal to show diluting hyponatremia. This transgenic rat may therefore provide a useful model in which to investigate various physiological alterations resulting from the oversecretion of AVP which involve SIAD, stress response, behavior, and blood pressure.
Initial Experience of 18F-FDG PET/MRI in Thymic Epithelial Tumors: Morphologic, Functional, and Metabolic Biomarkers

Purpose The aim of this study was to investigate the value of morphologic, functional, and metabolic biomarkers acquired concurrently at PET/MRI in patients with thymic epithelial tumors. Patients and Methods During 1 year, 9 patients with suspected thymic epithelial tumors at contrast-enhanced chest CT were prospectively enrolled and underwent preoperative 18F-FDG PET/MRI. Two chest radiologists prospectively reviewed the CT and MRI scans of PET/MRI in consensus, and 2 nuclear physicians reviewed the PET images. Visual assessment of the tumor morphology, functional biomarkers such as apparent diffusion coefficient from diffusion-weighted images, and metabolic biomarkers (including SUVmax, metabolic tumor volume, total lesion glycolysis, and heterogeneity index) were recorded. All patients underwent operation, and their pathologic reports served as the reference standard. Results Thymic epithelial tumors were demonstrated in all 9 patients at pathologic examination. Tumor contour (P = 0.012) and shape (P = 0.033) had an association with the World Health Organization subtype, and the presence of septum (P = 0.048) on MRI scans had an association with the Masaoka stage. In terms of functional and metabolic biomarkers, SUVmax (&rgr; = 0.683, P = 0.042) and SUV/apparent diffusion coefficient (&rgr; = 0.703, P = 0.035) correlated with the Masaoka stage. Metabolic tumor volume (P = 0.024), heterogeneity index (P = 0.024), and total lesion glycolysis (P = 0.048) were useful for classification between low- and high-risk thymic epithelial tumors. Conclusions Although limited by the small number of patients enrolled, morphologic, functional, and metabolic biomarkers derived from PET/MRI scans were useful for the stratification of thymic epithelial tumors.
Controls of EGF‐induced morphological transformation of human bronchial epithelial cells

Human bronchial epithelial cells, both normal primary (NHBE) and the BEAS‐2B line, respond to epidermal growth factor (EGF) by extruding lengthy filaments, or filapodia. The morphological transformation of BEAS‐2B cells maximized at 48 h using 1–10 nM EGF. EGF‐induced filapodia extension was inhibited by co‐exposure to transforming growth factor beta, which did not affect tyrosine phosphorylation of the EGF receptor (EGFR). Inhibition was also effected by phorbol myristoyl acetate (PMA), which reduced the rate of EGFR tyrosine phosphorylation. Dibutyryl‐cAMP had no effect, whereas the protein kinase inhibitor H‐89 stimulated the EGF response. The ability to regulate cellular responses to EGF by hormonal and chemical approaches has implications for current investigations into the roles of EGF in lung growth, differentiation, and wound repair. © 2001 Wiley‐Liss, Inc.
Modulation by ellagic acid of DCA‐induced developmental toxicity in the zebrafish (Danio rerio)

The ability of ellagic acid (EA) to modulate dichloroacetic acid (DCA)‐induced developmental toxicity and oxidative damage was examined in zebrafish embryos. Embryos were exposed to 20 mM EA administered concomitantly with 32 mM DCA at 4 hours postfertilization (hpf) and 20 h later. Embryos were observed through 144 hpf for developmental malformations, and production of superoxide anion (SA) and nitric oxide (NO) was determined in embryonic homogenates. DCA was shown to produce developmental abnormalities and significant levels of SA and NO in zebrafish embryos. EA exposure alleviated the developmental malformations observed in treated embryos and decreased the levels of SA and NO in those same embryos. Less than 10% of DCA + EA exposed embryos showed developmental malformations compared to 100% of embryos treated with DCA alone. Animals in this group that developed malformations were shown to have fewer defects than those treated with DCA only. Taken together, the results confirm the involvement of oxidative stress in the developmental toxicity of DCA in zebrafish embryos, and suggest possible protection against those effects with the use of antioxidants. © 2006 Wiley Periodicals, Inc. J Biochem Mol Toxicol 20:183–190, 2006; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/jbt.20135
Undergraduate musculoskeletal examination teaching by trained patient educators--a comparison with doctor-led teaching.

BACKGROUND To compare the core hand and knee examination skills gained by undergraduates taught either by trained patient educators (PEs) or by doctors. METHODS A total of 50 final year medical students were randomized to receive training from PEs or doctors. Group A were taught hand examination by a PE with rheumatoid arthritis, and knee examination by a PE with osteoarthritis. Group B was taught hand and knee examination by a consultant rheumatologist plus an untrained patient with appropriate signs. All students were taught an established core skills set in small group workshops. Students then undertook two validated objective structured clinical examination (OSCE) stations with two blinded assessors. Pre- and post-teaching questionnaires established the students' self-reported levels of skills (SRS) and a student evaluation of teaching (SET). The study was analysed as an equivalence trial. A mean difference in OSCE scores of 10% was assumed to be of educational significance. RESULTS Although the SET scores of both groups were high, the doctor-led group received higher scores. Aside from this, the two student groups did not differ significantly. There were no significant differences in mean hand OSCE (mean difference = 0.88, P = 0.28, 95% CI = -0.73 to 2.49) or knee OSCE (mean difference = 0.28, P = 0.7, 95% CI = -1.19 to 1.75) scores. Both the upper and lower confidence intervals for each mean difference fell within the 10% range (-2.8 to 2.8 for the hand, and -2.5 to 2.5 for the knee) and equivalence was assumed. CONCLUSIONS Adequately trained PEs can deliver clearly structured undergraduate skills, teaching with equivalent learning outcomes to those of rheumatology consultants. PEs are a valuable development to augment musculoskeletal education in the face of expanding student numbers.
Modeling Missingness for Time-to-Event Data: A Case Study in Osteoporosis

Abstract Clinical trials of long duration are often hampered by high dropout rates, making statistical inference and interpretation of results difficult. Statistical inference should be based on models selected according to whether missingness is independent of response [missing completely at random (MCAR)], or depends on response either through observed responses only [missing at random (MAR)] or through unobserved responses [nonignorable missing (NIM)]. If the dropout rate is high and little is known about the dropout mechanism, plausible nonignorable missing scenarios should be investigated as a sensitivity tool, offering the data analyst an understanding of the robustness of conclusions. Modeling missingness is illustrated by an analysis of an interval censored time-to-event outcome from a 5-year clinical trial on fracture response in osteoporosis in which the overall dropout rate was substantial. In this article, we provide an overview of a reanalysis accounting for possible nonignorable missingness, emphasize the importance of modeling the dropout and response mechanisms jointly, and highlight critical points arising in missing data problems.
Interaction of lipopolysaccharides of Helicobacter pylori with basement membrane protein laminin

The ability of hemagglutinating and poorly hemagglutinating strains of the gastroduodenal pathogen Helicobacter pylori to bind 125I-radiolabelled laminin was quantitated in a liquid phase assay. Although all strains bound laminin, some hemagglutinating strains were good binders of laminin (maximum of 31% binding), whereas poorly hemagglutinating strains bound intermediate to small amounts of laminin (minimum of 6% binding). Since a hydrophobic component of the bacterium has been reported to be involved in binding of laminin (T. J. Trust, P. Doig, L. Emödy, Z. Kienle, T. Wadström, and P. O'Toole, Infect. Immun. 59:4398-4404, 1991), we investigated the role of lipopolysaccharide (LPS) in the interaction of both types of strains with laminin. Although the extent of inhibition varied among strains, laminin binding to hemagglutinating and poorly hemagglutinating strains was inhibited with homologous and heterologous smooth-form LPS. The ability of heterologous rough-form LPS to produce inhibition comparable to that shown by smooth-form LPS indicated that the O side chain of H. pylori LPS was not involved in the interaction. Further inhibition experiments with dephosphorylated LPS, isolated core oligosaccharide, and free lipid A suggested that a phosphorylated structure in the core oligosaccharide mediates the interaction of a hemagglutinating strain of H. pylori with laminin, whereas a conserved nonphosphorylated structure in the core oligosaccharide mediates the interaction of a poorly hemagglutinating strain. Furthermore, we showed that the interaction of H. pylori LPS with 125I-radiolabelled laminin in a solid phase assay was saturable, specific, and inhibitable with unlabelled laminin. It was postulated that the initial recognition and binding of laminin by H. pylori may occur through LPS and that subsequently a more specific interaction with a lectin-like adhesin on the bacterial surface occurs.