Miracle-dz/UniFAR-FTUs huggingface dataset:
Hepatitis B virus in alcoholic liver disease with hepatocellular carcinoma

Walter et al. (1) recently reported negative Southern blot analyses for hepatitis B virus (HBV) DNA in alcoholic cirrhosis with or without hepatocellular carcinoma (HCC). They conclude that they have no evidence for HBV DNA being involved in the tumor. This result is at variance from that previously obtained by our group in French HBsAg-negative alcoholic patients with HCC (2, 3). Walter et al. believe that this difference is not related to epidemiological differences or to variations in the sensitivity of the procedure; therefore, they suggest that lack of specificity might account for our previous results. The observation made by Walter et al. may certainly be valid and is obviously important to consider. However, we would like to underline the following points. First, only 13% (a very low figure, indeed) of the subjects with HCC in the study of Walter et al. had antiHBs and/or anti-HBc, as against 50% in our subjects. Therefore, the authors should admit epidemiological differences between the two studies. Secondly, we have been able to demonstrate the specificity of our HBV DNA detection in HBsAg-negative sera and liver; indeed, liver DNA extracted from HBsAgnegative subjects included in our previous studies was tested in the laboratory of Professor Koike (Tokyo), and our results were confirmed (Koike, personal communiable to amplify HBV DNA sequences specifically from these samples (6); recently, we successfully achieved cloning and partial sequencing of these isolates (6). Therefore, we believe that we have obtained strong evidence for the presence of HBV DNA sequences (in a low percentage of tumorous cells) in many of our HBsAgnegative patients with HCC in France. We would be highly interested to exchange liver DNA samples with Dr. Walter and colleagues to avoid any uncertain conclusion by either of our two groups.
Mutation of the Rab6 Homologue of Saccharomyces cerevisiae, YPT6, Inhibits Both Early Golgi Function and Ribosome Biosynthesis*

A screen was designed to identify temperature-sensitive mutants of Saccharomyces cerevisiae, whose transcription of both ribosomal RNA and ribosomal protein genes is repressed at the nonpermissive temperature. The gene from one such mutant was cloned by complementation. The gene encodes a predicted product that is nearly 65% identical to the human GTPase, Rab6, and is likely to be identical to the yeast gene YPT6. It is essential for growth only at elevated temperatures. The mutant strain is partially defective in the maturation of the vacuolar protein carboxypeptidase Y, as well as in the secretion of invertase, which accumulates as a core-glycosylated form characteristic of the endoplasmic reticulum or the cis-Golgi, suggesting that Ypt6p is involved in an early step of the secretory pathway, earlier than that reported for the mammalian Rab6. The mutant protein, a truncation at codon 64 of 215, has a stronger phenotype than the null allele of YPT6. Four other mutants selected for defective ribosome synthesis at the nonpermissive temperature were also found to have defects in carboxypeptidase Y maturation, giving emphasis to our previous finding that a functional secretory pathway is essential for continued ribosome synthesis. Cloning of extragenic suppressors of the ts allele of YPT6 has revealed two additional proteins that influence the secretory pathway: Ssd1p, a suppressor of many mutations, and Imh1p, which bears some homology to the C-terminal portion of the cytoskeletal proteins integrin and myosin.
Kinetics of Chromium Sorption on Biomass Fungi from Aqueous Solution

The kinetics of chromium ions sorption from aqueous solution on fungi biomass have been investigated in a batch system. The experimental data were analysed based on an intraparticle diffusion equation and a pseudo-second-order mechanism, in order to predict the constant rate of sorption and the equilibrium capacity with the effect of initial chromium ions concentration, temperature and initial solution pH. The results indicate that the sorption mechanism is described by a pseudo-second order equation. Intraparticule diffusion was signifiant in the lower concentration systems. The sorption of chromium onto the biomass fungi sorbent is favoured at higher concentrations of chromium solution, low temperatures. An activation energy of sorption was evaluted as 11.7 Kj.mol-1 for the sorption of chromium ions on fungi biomass. The results show that the sorption of the chromium ions on fungi biomass is exothermic nature process.
Corrigendum: A Review of R-packages for Random-Intercept Probit Regression in Small Clusters

A corrigendum on: A Review of R-packages for Random-Intercept Probit Regression in Small Clusters by Josephy, H. , Loeys, T. , and Rosseel, Y. (2016). Front. Appl. Math. Stat. 2, 1–13. doi: 10.3389/fams.2016. 00018
Involvement of Oxidative Stress in Suppression of Insulin Biosynthesis under Diabetic Conditions

Type 2 diabetes is characterized by pancreatic β-cell dysfunction and insulin resistance, and the number of patients has markedly increased worldwide. In the diabetic state, hyperglycemia per se and subsequent induction of oxidative stress decrease insulin biosynthesis and secretion, leading to the aggravation of Type 2 diabetes. In addition, there is substantial reduction in expression and/or activities of several insulin gene transcription factors. This process is known as β-cell glucose toxicity, which is often observed under diabetic conditions. Taken together, it is likely that oxidative stress explains, at least in part, the molecular mechanism for β-cell glucose toxicity, which is often observed in Type 2 diabetes.
Using Twitter data for demographic research

Background: Social media data is a promising source of social science data. However, deriving the demographic characteristics of users and dealing with the nonrandom, nonrepresentative populations from which they are drawn represent challenges for social scientists. Objective: Given the growing use of social media data in social science research, this paper asks two questions: 1) To what extent are findings obtained with social media data generalizable to broader populations, and 2) what is the best practice for estimating demographic information from Twitter data? Methods: Our analyses use information gathered from 979,992 geo-located Tweets sent by 22,356 unique users in South East England between 23 June and 4 July 2014. We estimate demographic characteristics of the Twitter users with the crowd-sourcing platform CrowdFlower and the image-recognition software Face++. To evaluate bias in the data, we run a series of log-linear models with offsets and calibrate the nonrepresentative sample of Twitter users with mid-year population estimates for South East England. Results: CrowdFlower proves to be more accurate than Face++ for the measurement of age, whereas both tools are highly reliable for measuring the sex of Twitter users. The calibration exercise allows bias correction in the age-, sex-, and location-specific population counts obtained from the Twitter population by augmenting Twitter data with mid-year population estimates. Contribution: The paper proposes best practices for estimating Twitter users’ basic demographic characteristics and a calibration method to address the selection bias in the Twitter population, allowing researchers to generalize findings based on Twitter to the general population.
The hypothalamic-pituitary-thyroid axis in critical illness.

In severe illness, profound changes occur in the hypothalamic-pituitary-thyroid axis. The observed decrease in serum concentration of both thyroid hormones and thyrotropin (TSH) are not compatible with a negative feedback loop and suggest a major change in setpoint regulation of the hypothalamic-pituitary-thyroid axis. This is supported by post mortem studies showing a decreased expression of thyrotropin-releasing hormone in the hypothalamic paraventricular nucleus of patients with a decreased serum T3 level. In critical illness, serum T3 may even become undetectable without giving rise to an elevated concentration of serum TSH. It is currently not clearly established whether this reflects an adaptation of the organism to illness or instead a potentially harmful condition leading to hypothyroidism at tissue level. There is thus a need for randomized clinical trials in critically ill patients to investigate whether they may benefit from a normalization of thyroid hormone concentration. Recent clinical studies in these patients involving the administration of hypothalamic peptides open up new ways of achieving this.
HIV infection among young adults with psychotic disorders.

OBJECTIVE The authors examined HIV infection among young adults with newly diagnosed psychotic disorders. METHODS The study was based on a research cohort of 320 first-admission patients aged 20-39 years in a semirural-suburban county. Research assessments and medical records were systematically reviewed for information about HIV status. RESULTS Despite the fact that few patients were tested for HIV, 12 (3.8%) of the 320 patients had a known HIV infection. In all 12 cases, the HIV infection was contracted before the onset of psychosis. AIDS was the leading cause of mortality in the 320 patients. CONCLUSIONS The HIV epidemic may be having an important effect on the etiology and the course of psychotic disorders.
Revision of the age of magnetization of the Montmartin red beds, Normandy, France

Summary. A new roadcut has enabled us to sample the south-dipping limb of the Montmartin syncline for a palaeomagnetic reevaluation of an earlier result published by Jones, Van der Voo & Bonhommet. In combination with the results previously published in 1979 for the north-dipping beds of the syncline, a conclusively negative fold test is obtained. The resulting magnetization (declination/inclination =206°/-3°, α95= 12°, palaeopole at 38°S, 325°E) is interpreted to be of Late Carboniferous age, not Late Devonian as thought earlier. Simultaneously, we have re-evaluated the age of the rocks, previously thought to be Late Devonian on the basis of Acritarchs, Chitinozoans and spores. It has not been possible to reconfirm these fossils, not even in the same samples as studied originally; in contrast, the regional presence of Early Palaeozoic fossils suggests to us an age similar to that of other red beds in the Arrnorican Massif, which have been dated as Early Ordovician. The geodynamic implications of our finding that the Montmartin rocks are completely remagnetized, however, are of no great consequence for the geodynamics of the Hercynian belt. Pre-folding magnetization obtained from Silurian and Devonian rocks in Spain and Germany argue for the same conclusion as reached erroneously in our earlier study, namely that the Armorican Massif and adjacent parts of Hercynian Europe were adjointed to North America, Great Britain, the Baltic Shield and the Russian Platform since at least Late Devonian time. If a Medio-European ocean existed during the Palaeozoic, it was virtually closed before the mid-Devonian and of insignificant width during Culm deposition in Early Carboniferoirs time.
Brillouin Optical Time Domain Analysis in Silica Fibers at 850-nm Wavelength

Brillouin scattering properties of silica fibers at 850-nm wavelength were experimentally investigated using a Brillouin optical time-domain analysis scheme. In the single-mode 780-HP fiber, the Brillouin frequency shift (BFS) and full width at-half maximum of the Brillouin gain spectrum were found to be ~19795 and 90 MHz, respectively. The estimated peak Brillouin gain is 0.32 (mW)-1. The temperature and strain dependences of BFS were determined as well. Distributed sensing capability was demonstrated at a minimum spatial resolution of 1.5 m and a fiber length of 100 m. As a proof-of-principle, the temperature and strain dependences of the BFS in SFM-28 fiber have been determined at 850- and 1550-nm wavelengths, suggesting its possible use for temperature/strain discrimination.
Exercising in Herds : Treatment Size and Status Specific Peer Effects in a Randomized Exercise Intervention

In a field experiment using university students, we find that subjects who have been incentivized to exercise increase their recreation center usage more if they have more friends who have been incentivized, and less if they have more friends in the control group. Controls, however, are not influenced by their peers. Findings highlight subtle effects of randomization, indicating that the fraction treated in an experiment of this kind has a large influence on outcomes, and that spillovers may vary greatly by treatment status. The methodology is applicable to other settings and quantifies spillovers that previous approaches do not detect. We thank Kelly Bedarad, Eric Bettinger, Olivier Deschenes, Peter Kuhn, Heather Royer, Bruce Sacerdote, Jon Sonstelie, and Cathy Weinberger for helpful comments. We are grateful for funding by the Hellman Family Foundation, and excellent research assistance by Jennifer Carnan, Jennifer Schulte, Allison Nuovo, Christy Helvestine, Bonnie Queen, Jessica Evans, Natalie Brechtel, and Randi Golde. We are also grateful for assistance from Chris Clontz at the Recreation Center at the University of California, Santa Barbara.
An ex vivo investigation into the use of a plasma arc lamp when using a visible light-cured composite and a resin-modified glass poly(alkenoate) cement in orthodontic bonding.

OBJECTIVE To determine the usefulness of the plasma arc lamp in orthodontic bonding when used with both a light curable diacrylate and a resin modified glass poly(alkenoate) cement. DESIGN Ex-vivo study. METHOD 160 second premolar teeth were divided into 2 groups. 80 teeth had steel brackets bonded using Transbond XT and 80 were bonded using Fuji Ortho LC. One of four light curing regimes were used, with 20 specimens in each group: (i) 20 seconds curing with a halogen lamp; (ii) 1 second; (iii) 2 seconds or; (iv) 3 seconds with the plasma lamp. OUTCOMES Shear bond tested to failure and the force to debond (N) and locus of bond failure recorded in each case. RESULTS Force to debond increases in the case of both bonding materials as the curing time with the plasma lamp increases. The force to debond with 1 and 2 seconds with the plasma lamp was significantly lower in each case. In all instances the force to debond was lower in the case of the resin modified glass poly(alkenoate) cement specimens. Locus of bond failure was unaffected by the method and length of light curing and was generally mixed mode. CONCLUSIONS Use of the plasma arc lamp in orthodontic bonding could result in significant time saving.
Molecular and Cellular Pathobiology Oncogenic Synergism between ErbB 1 , Nucleolin , and Mutant Ras

Alterations in the ErbB family of growth factor receptors, their signaling components, and mutational activation of Ras proteins are major contributors to malignant transformation. Recently, mutant Ras was shown to be capable of activating ErbB receptors in a ligand-independent manner. Furthermore, it was observed that nucleolin, a transcriptional regulator and ribosome biogenesis factor, can bind both K-Ras and the cytoplasmic tail of ErbB receptors to enhance ErbB receptor activation. However, the functional significance of these interactions to cancer pathogenesis has not been probed. Here, we show that endogenous nucleolin interacts simultaneously in vivo with endogenous Ras and ErbB1 (EGFR) in cancer cells. The C-terminal 212 amino acids of nucleolin were determined to be sufficient to interact with ErbB1 and all Ras protein isoforms (H-, N-, and KRas). Nucleolin partially colocalizes with Ras at the plasma membrane. Moreover, activated but not wild-type Ras facilitates nucleolin interaction with ErbB1 and stabilizes ErbB1 receptor levels. Most importantly, these three oncogenes synergistically facilitate anchorage-independent cell growth in vitro and tumor growth in vivo. Our findings suggest strategies to target nucleolin as a general approach to inhibiting ErbBand Ras-driven cancers. Cancer Res; 71(6); 2140–51. 2011 AACR.
The G‐beta subunit MGB1 is involved in regulating multiple steps of infection‐related morphogenesis in Magnaporthe grisea

Trimeric G‐proteins transmit extracellular signals to various downstream effectors (e.g. MAP kinases) in eukaryotes. In the rice blast fungus Magnaporthe grisea, the Pmk1 MAP kinase is essential for appressorium formation and infectious growth. The pmk1 deletion mutant fails to form appressoria but still responds to exogenous cAMP for tip deformation. Since gene disruption mutants of three Gα subunits still form appressoria and are phenotypically different from pmk1 mutants, it is likely that the Pmk1 pathway is activated by Gβ in M. grisea. In this study, we isolated and characterized the MGB1 gene that encodes the G subunit in M. grisea. Mutants disrupted in MGB1 were reduced in conidiation. Conidia from mgb1 mutants were defective in appressorium formation and failed to penetrate or grow invasively on rice leaves. Exogenous cAMP induced appressorium formation in mgb1 mutants, but these appressoria were abnormal in shape and could not penetrate. The intracellular cAMP level was reduced in mgb1 mutants and the defects in conidiation and hyphal growth were partially suppressed with 1 mM cAMP. Transformants expressing multiple copies of MGB1 were able to form appressoria on hydrophilic surfaces. Our results suggest that MGB1 may be involved in the cAMP signalling for regulating conidiation, surface recognition and appressorium formation. The Pmk1 pathway may be the downstream target of MGB1 for regulating penetration and infectious hyphae growth in M. grisea.
Cochlear implantation in children with auditory neuropathy spectrum disorders

Abstract Aim To present the outcomes of cochlear implantation (CI) in children with auditory neuropathy spectrum disorders (ANSD). Materials and methods The pre- and post-CI hearing outcomes in children with ANSD were retrospectively evaluated. Performance was assessed with categories of auditory performance (CAP) and the Manchester spoken language development scale (MSLDS). Results Full data were available in 27 implanted children with ANSD with average age at implantation 35.4 months (range 19–68 months). Nine children were implanted bilaterally, while 13 were bimodal. The pre-CI CAP and MSLDS scores were 2.5 (range 0–5) and 2.5 (range 0–6), while the post-CI scores 5.8 (range 2–9) and 7.7 (range 3–10), respectively. Conclusions Although the outcome of CI in children with ANSD might vary, it is favourable in most of the cases. CI seems a justified hearing rehabilitation option for children with ANSD and limited benefits from conventional hearing aids.
Dietary inclusion of whole soy foods results in significant reductions in clinical risk factors for osteoporosis and cardiovascular disease in normal postmenopausal women

ObjectiveTo determine the effects of dietary inclusion of soy foods on clinical markers for cardiovascular disease (CVD) and osteoporosis in normal postmenopausal women. DesignThis was a single open-group prospective clinical intervention. Forty-two normal postmenopausal women consumed three daily servings for 12 consecutive weeks of whole soy foods containing approximately 60 mg/d of isoflavones. Blood and urine specimens were obtained at baseline and after 12 weeks of dietary intervention. ResultsSerum and urine levels of individual and total isoflavones increased significantly (7–19 fold, p < 0.001) from baseline. A significant increase (9.3%, p < 0.05) in the mean lag-time of low-density lipoprotein cholesterol oxidation was seen and was positively correlated with serum phytoestrogens (p < 0.05). Significant increases were found in mean levels of high-density lipoprotein cholesterol (HDLc) (3.7%, p < 0.05) and serum osteocalcin (10.2%, p < 0.025). Significant decreases were observed in total cholesterol:HDLc ratios (5.5%, p < 0.006) and mean urinary N-telopeptide excretion (13.9%, p < 0.02). Urinary excretion of total isoflavones was negatively correlated with very-low-density lipoprotein cholesterol, triglycerides, and total cholesterol:HDLc ratios (p < 0.04). No significant changes from baseline in HDLc peroxidation, total cholesterol, triglycerides, low-density lipoprotein cholesterol, very-low-density lipoprotein cholesterol, bone-specific alkaline phosphatase, follicle-stimulating hormone, or estradiol levels were observed. ConclusionsDietary inclusion of whole soy foods containing 60 mg/d of isoflavones results in significant serum levels of phytoestrogens and reductions in several key clinical risk factors for CVD and osteoporosis in normal postmenopausal women. Long-term, placebo-controlled clinical trials are needed to evaluate the effect of phytoestrogens on the clinical endpoints of CVD and osteoporosis in this population.
Patient Self-Report of Disability of the Upper Extremity following Osteocutaneous Radial Forearm Free Flap Harvest

Background: The authors critically analyzed long-term upper extremity outcome after harvest of an osteocutaneous radial forearm free flap by correlating any restrictions in range of motion and strength with patient self-report of disability. Methods: Twelve patients who had at least 1 year since surgery were evaluated with a functional examination and with the Disability of the Arm, Shoulder, and Hand questionnaire. Functional capacity was quantified by comparing range of motion of the thumbs, digits, and wrists along with pronation and supination of bilateral forearms. Pinch and grip strength measurements were obtained. Results: Range of motion in full active wrist extension, wrist flexion, forearm supination, and thumb interphalangeal flexion averaged 83 percent (p = 0.01), 82 percent (p = 0.01), 83 percent (p = 0.03), and 88 percent (p = 0.03), respectively, that of the nonflap arm. Three patients demonstrated thumb opposition limited to the ring finger. Increasing scores on the questionnaire (mean, 16.6; range, 0 to 69), indicating a worsening disability, were correlated with decreasing wrist flexion (p < 0.01; Spearman correlation coefficient, 0.77) and decreasing wrist extension (p = 0.09; Spearman correlation coefficient, 0.51) of the flap arm. Radiographs revealed one malunion secondary to a postoperative pathologic fracture in the patient with the worst questionnaire score. Three patients (25 percent) stated explicitly that harvest of the osteocutaneous radial forearm free flap had created a disability. Conclusions: Objective reductions in wrist, forearm, and/or thumb range of motion are frequent after harvest of an osteocutaneous radial forearm free flap. Wrist range of motion has the greatest impact on patient self-report of disability and may in a minority of patients be perceived as causing a clinically significant disability.
Novel Toluene Elimination System in a Toluene-Tolerant Microorganism

ABSTRACT In studies of Pseudomonas putida IH-2000, a toluene-tolerant microorganism, membrane vesicles (MVs) were found to be released from the outer membrane when toluene was added to the culture. These MVs were found to be composed of phospholipids, lipopolysaccharides (LPS), and very low amounts of outer membrane proteins. The MVs also contained a higher concentration of toluene molecules (0.172 ± 0.012 mol/mol of lipid) than that found in the cell membrane. In contrast to the wild-type strain, the toluene-sensitive mutant strain 32, which differs from the parent strain in LPS and outer membrane proteins, did not release MVs from the outer membrane. The toluene molecules adhering to the outer membrane are eliminated by the shedding of MVs, and this system appears to serve as an important part of the toluene tolerance system of IH-2000.