Miracle-dz/UniFAR-FTUs huggingface dataset:
Association of pro-ghrelin and GHS-R1A gene polymorphisms and haplotypes with heavy alcohol use and body mass.

BACKGROUND Ghrelin, an orexigenic peptide, acts on growth hormone secretagogue receptors (GHS-R1A), expressed in the hypothalamus as well as in important reward nodes such as the ventral tegmental area. Interestingly, ghrelin has been found to activate an important part of the reward systems, i.e., the cholinergic-dopaminergic reward link. Additionally, the rewarding and neurochemical properties of alcohol are, at least in part, mediated via this reward link. There is comorbidity between alcohol dependence and eating disorders. Thus, plasma levels of ghrelin are altered in patients with addictive behaviors such as alcohol and nicotine dependence and in binge eating disorder. This overlap prompted as to investigate the pro-ghrelin and GHS-R1A genes in a haplotype analysis of heavy alcohol-using individuals. METHODS A total of 417 Spanish individuals (abstainers, moderate, and heavy alcohol drinkers) were investigated in a haplotype analysis of the pro-ghrelin and GHS-R1A genes. Tag SNPs were chosen using HapMap data and the Tagger and Haploview softwares. These SNPs were then genotyped using TaqMan Allelic Discrimination. RESULTS SNP rs2232165 of the GHS-R1A gene was associated with heavy alcohol consumption and SNP rs2948694 of the same gene as well as haplotypes of both the pro-ghrelin and the GHS-R1A genes were associated with body mass in heavy alcohol consuming individuals. CONCLUSIONS The present findings are the first to disclose an association between the pro-ghrelin and GHS-R1A genes and heavy alcohol use, further strengthening the role of the ghrelin system in addictive behaviors and brain reward.
Differentiated thyroid carcinoma risk factors in French Polynesia.

BACKGROUND To investigate differentiated thyroid cancer risk factors in natives of French Polynesia is of interest because of the very high incidence of this cancer in the archipelago. MATERIALS AND METHODS To assess the role of various potential risk factors of thyroid cancer in the natives of French Polynesia we performed a case-control study. The study included almost all the French Polynesians diagnosed with differentiated thyroid carcinoma between 1981 and 2003 (n=229) and 373 French Polynesian control individuals from the general population without cancer. RESULTS Thyroid radiation dose received from nuclear fallout before the age of 15, a personal history of neck or/and head medical irradiation, obesity, tallness, large number of children, an artificial menopause, a familial history of thyroid cancer, a low dietary iodine intake, and having a spring as the main source of drinking water were found to be significant risk factors. No roles of smoking habits, alcohol consumption, iodine containing drugs, and exposure to pesticides were evidenced. CONCLUSIONS Except for smoking, differentiated thyroid carcinoma risk factors in natives of French Polynesia are similar to those in other populations. Our finding on the role of having a spring as a drinking water origin is coherent with some other studies and could be due to geological factors.
“Transforaminal Thoracic Interbody Fusion” in the Management of Lower Thoracic Spine Fracture Dislocations: Technical Note

Study Design: A case-control clinical study. Objectives: To assess the usefulness and safety of a novel reconstructive procedure known as transforaminal thoracic interbody fusion (TTIF) in the treatment of lower thoracic spine fracture dislocations, and to compare its efficacy with posterior/anterior combined surgery (PACS). Summary of Background Data: We developed a TTIF procedure for thoracic spine lesions, and obtained good clinical outcomes for degenerative disorders of the thoracic spine. However, the technique of TTIF in the lower thoracic spine fracture dislocation has never been reported. Methods: Seven consecutive patients with lower thoracic spine fracture dislocations underwent TTIF (6 males, 1 female; mean age, 32 y), and 16 consecutive patients with lower thoracic spine fracture dislocations underwent PACS (14 males, 2 females; mean age, 37 y). Surgical complications, clinical outcomes, and sagittal alignment were investigated. Bony fusion was assessed using plain and functional x-rays and computed tomography scans. Results: In the TTIF group and the PACS group, the mean operative times were 153 and 224 minutes, respectively, and the mean operative bleeding was 421 and 698 mL, respectively. All patients in the TTIF group were ambulatory within 2 days after surgery. Preoperative local sagittal alignments (kyphotic angles) were 22.9 and 22.5 degrees, respectively. Postoperative local sagittal alignments were 9.9 and 7.2 degrees, respectively. There were no instances of instrumentation failure or nonunion, and there were no serious complications such as neurological deficits in either group. In addition, a chest tube was necessary in 11 cases (69%) of PACS after thoracotomy, but was not required in any TTIF cases. Conclusions: TTIF achieves posterior rigid fixation with instrumentation, and anterior column reconstruction by interbody fusion. This procedure also enables early postoperative ambulation without respiratory problems. TTIF can be a useful option for reconstructive surgery of the lower thoracic spine after fracture dislocations.
From Culture-Medium-Based Models to Applications to Food: Predicting the Growth of B. cereus in Reconstituted Infant Formulae

Predictive models of the growth of foodborne organisms are commonly based on data generated in laboratory medium. It is a crucial question how to apply the predictions to realistic food scenarios. A simple approach is to assume that the bias factor, i.e., the ratio between the maximum specific growth rate in culture medium and the food in question is constant in the region of interest of the studied environmental variables. In this study, we investigate the validity of this assumption using two well-known link functions, the square-root and the natural logarithm, both having advantageous properties when modeling the variation of the maximum specific growth rate with temperature. The main difference between the two approaches appears in terms of the respective residuals as the temperature decreases to its minimum. The model organism was Bacillus cereus. Three strains (B594, B596, and F4810/72) were grown in Reconstituted Infant Formulae, while one of them (F4810/72) was grown also in culture medium to calculate the bias factor. Their growth parameters were estimated using viable count measurements at temperatures ranging from 12 to 25°C. We utilized the fact that, if the bias factor is independent of the temperature, then the minimum growth temperature parameter of the square-root model of Ratkowsky et al. (1982) is the same for culture medium and food. We concluded, supported also by mathematical analysis, that the Ratkowsky model works well but its rearrangement for the natural logarithm of the specific growth rate is more appropriate for practical regression. On the other hand, when analyzing mixed culture data, available in the ComBase database, we observed a trend different from the one generated by pure cultures. This suggests that the identity of the strains dominating the growth of mixed cultures depends on the temperature. Such analysis can increase the accuracy of predictive models, based on culture medium, to food scenarios, bringing significant saving for the food industry.
The Paradox of Success at a No-Excuses School

No recent reform has had so profound an effect as no-excuses schools in increasing the achievement of low-income black and Hispanic students. In the past decade, no-excuses schools—whose practices include extended instructional time, data-driven instruction, ongoing professional development, and a highly structured disciplinary system—have emerged as one of the most influential urban school-reform models. Yet almost no research has been conducted on the everyday experiences of students and teachers inside these schools. Drawing from 18 months of ethnographic fieldwork inside one no-excuses school and interviews with 92 school administrators, teachers, and students, I argue that even in a school promoting social mobility, teachers still reinforce class-based skills and behaviors. Because of these schools’ emphasis on order as a prerequisite to raising test scores, teachers stress behaviors that undermine success for middle-class children. As a consequence, these schools develop worker-learners—children who monitor themselves, hold back their opinions, and defer to authority—rather than lifelong learners. I discuss the implications of these findings for market-based educational reform, inequality, and research on noncognitive skills.
Effects of near‐future ocean acidification, fishing, and marine protection on a temperate coastal ecosystem

Understanding ecosystem responses to global and local anthropogenic impacts is paramount to predicting future ecosystem states. We used an ecosystem modeling approach to investigate the independent and cumulative effects of fishing, marine protection, and ocean acidification on a coastal ecosystem. To quantify the effects of ocean acidification at the ecosystem level, we used information from the peer‐reviewed literature on the effects of ocean acidification. Using an Ecopath with Ecosim ecosystem model for the Wellington south coast, including the Taputeranga Marine Reserve (MR), New Zealand, we predicted ecosystem responses under 4 scenarios: ocean acidification + fishing; ocean acidification + MR (no fishing); no ocean acidification + fishing; no ocean acidification + MR for the year 2050. Fishing had a larger effect on trophic group biomasses and trophic structure than ocean acidification, whereas the effects of ocean acidification were only large in the absence of fishing. Mortality by fishing had large, negative effects on trophic group biomasses. These effects were similar regardless of the presence of ocean acidification. Ocean acidification was predicted to indirectly benefit certain species in the MR scenario. This was because lobster (Jasus edwardsii) only recovered to 58% of the MR biomass in the ocean acidification + MR scenario, a situation that benefited the trophic groups lobsters prey on. Most trophic groups responded antagonistically to the interactive effects of ocean acidification and marine protection (46%; reduced response); however, many groups responded synergistically (33%; amplified response). Conservation and fisheries management strategies need to account for the reduced recovery potential of some exploited species under ocean acidification, nonadditive interactions of multiple factors, and indirect responses of species to ocean acidification caused by declines in calcareous predators.
What are the factors determining authorship and the order of the authors' names? A study among authors of the Nederlands Tijdschrift voor Geneeskunde (Dutch Journal of Medicine).

CONTEXT Although criteria justifying authorship of scientific medical articles have been formulated, it is not well known how authorship is established in practice. OBJECTIVES To assess the criteria for authorship used by authors of original articles in Nederlands Tijdschrift voor Geneeskunde (NTVG, the Dutch Journal of Medicine), and to determine whether the criteria for authorship of the International Committee of Medical Journal Editors (ICMJE) are known and applied. DESIGN Survey questionnaire. SETTING Editorial office of the NTVG. PARTICIPANTS All 450 authors of 115 original articles published in 1995. MAIN OUTCOME MEASURES Author's contribution to study design, material, collection of data, statistics, and writing. RESULTS Of 362 forms returned, 352 could be analyzed (78.2% response rate). The 5 questions most frequently answered affirmatively were ICMJE criteria: critical reading (86.1 % of the authors), approval of the final version (84.7%), study design (74.7%), study conception (64.2%), and revision (63.4%). Authors rated their contribution 2 points higher than did their coauthors. Interestingly, 64% of the respondents met the ICMJE criteria, although 60% of the respondents did not know them. CONCLUSION Authorship was mostly in accordance with ICMJE criteria although many authors were not familiar with them.
Prediction of protein solvent profile using SVR

We describe a support vector regression (SVR) approach to predict the accessible surface area (ASA) of a protein from its sequence. Our approach encodes each protein residue as a vector of amino acid propensities derived from a multiple alignment of the subject protein with homologous proteins. The vector consists of the log-likelihood ratios of each of the twenty amino acids in the residue's multiple alignment column. Using a reference set of proteins of known structure and, hence, known ASA, we trained an SVR model. Each training sample consists of the fifteen log-likelihood vectors in a window of width fifteen surrounding a residue, along with the "true" ASA value, computed from the known structure. To apply the model to proteins of unknown structure, only the subject protein sequence is required. Our method uses PSI-BLAST to simultaneously determine a set of (putative) homologs and compute the log-likelihood vectors needed to encode the subject protein. We show that this method provides substantially improved accuracy in predicting ASA when compared with an earlier method.
The effect of frequency adaptation according to the attenuation coefficient and focus depth on radiation force amplitude and estimated displacements

In remote dynamic elastography, amplitudes of generated displacement fields are directly related to the amplitude of the radiation force. Therefore, displacement improvement for better tissue characterization requires the optimization of the radiation force by increasing the push duration and/or the excitation amplitude of the transducer. The main problem of this approach is that the Food and Drug Administration (FDA) thresholds for medical applications, and transducer limitations may be easily exceeded. In the present study, the effect of the frequency used for the generation of radiation force on the amplitude of the displacement field is investigated. The aim is to apply the adaptive radiation force to increase the displacement amplitude. We found that amplitudes of displacements generated by adapted radiation force sequences are greater than those generated by non-adapted ones. The obtained gains were between 20% and 158% depending on the focus depths and the attenuation of the tested phantom. The signal to noise ratio was also improved by more than four times. We conclude that frequency adaptation is a complementary technique that may be used for the optimization of displacement amplitude. This technique can be used safely to optimize the deposited local acoustic energy, without increasing the risk of damaging tissues and transducers.
Bayesian Inference With Muller C-Elements

Bayesian inference is a powerful approach for integrating independent conflicting information for decision-making. Though an important component of robotic, biological, and other sensory-motors systems, general-purpose computers perform Bayesian inference with limited efficiency. Here we show that Bayesian inference can be efficiently performed with stochastic signals, which are particularly adapted to novel low power nanodevices that exhibit faults and device variations. A simple Muller C-element directly implements Bayes' rule. Complex inferences are performed by C-element trees, which compute the probability of an event based on multiple independent sources of evidence. A naïve Bayesian spam filter circuit is demonstrated as a pedagogical application, and design techniques for improving circuit functionality are described. Limitations of this structure are discussed in terms of signal autocorrelation. The stochastic inference structure is exceptionally robust to faults, an essential feature of decision circuits, and can therefore leverage the increased efficiency of emerging nanodevices. This hardware implementation of Bayesian inference is extremely area and power efficient, with an area-energy-delay product several orders of magnitude less than the conventional floating point implementation. These results open a pathway for a direct stochastic hardware implementation of Bayesian inference, enabling a new class of embedded decision circuits for robotics and medical applications.
Bromide and nitrate movement through undisturbed soil columns.

Field experiments often assume that Br-, 14NO3(-)-N, and 15NO3(-)-N have similar leaching kinetics. This study tested this assumption. Twenty-four undisturbed soil columns (15-cm diameter) were collected from summit-shoulder, backslope, and footslope positions of a no-tillage field with a corn (Zea mays L.)-soybean [Glycine max (L.) Merr. ] rotation. Each of the landscape positions had a different soil series. After conditioning the columns with 4 L of 0.01 M CaCl2 (2 pore volumes), 15N-labeled Ca(NO3)2 and KBr were applied to the soil surface and leached with 4 L of 0.01 M CaCl2. Leachate was collected, weighed, and analyzed for NO3(-)-N, NH4(+)-N, 15N, 14N, and Br-. The total amount of 15NO3(-)-N and 14NO3(-)-N collected in 1000, 2000, and 3000 mL of leachate was similar. These data suggest that 15N discrimination during leaching did not occur. Bromide leached faster through the columns than NO3(-)-N. The more rapid transport of Br- than NO3(-)-N was attributed to lower Br- (0.002 +/- 0.036 mg kg(-1)) than NO3(-)-N (0.17 +/- 0.03 mg kg(-1)) sorption. Results from this study suggest that (i) if Br- is used to estimate NO3(-)-N leaching loss, then NO3(-)-N leaching losses may be overestimated by 25%; (ii) the potential exists for landscape position to influence anion retention and movement in soil; and (iii) 15N discrimination was not detected during the leaching process.
Gallic acid–PAMAM and gallic acid–phospholipid conjugates, physicochemical characterization and in vivo evaluation

Abstract Gallic acid (GA) is a naturally occurring compound with valuable antioxidant activity. Its oral bioavailability is limited by its high metabolism and rapid clearance. In this paper, GA was conjugated with two different materials, phosphatidylcholine (PC) and polyamidoamine (PAMAM) dendrimer. The prepared conjugates were characterized by FTIR, DSC, and SEM. Also, they were tested for drug content and in vitro drug release. It was found that GA conjugation with both materials have significantly prolonged its release up to 12 h. In vivo hepatoprotective activity of free and conjugated GA was studied in rats after carbon tetrachloride (CCl4)-induced oxidative damage in rat liver through measurement of different liver marker enzymes (aspartate aminotransferase (AST), alanine aminotransferase (ALT)), in addition to the total protein and albumin level in rat serum. Also, histopathological examination of liver cell of all rat groups was done. Results showed that both prepared conjugates have significantly reduced the hepatic marker enzymes accompanied by normalizing total protein and albumin levels in rat serum and with respect to CCl4-induced group (p < .05). Histopathological examination showed that pretreatment of rats with GA–PC or GA–PAMAM before CCL4 could reduce the induced cellular histopathological changes. It appears that conjugation of GA could enhance its bioavailability and increase its hepatoprotective effect.
Molecular aspects of the biophysical CO2-concentrating mechanism and its regulation in marine diatoms

Diatoms operate a CO2-concentrating mechanism (CCM) that drives upwards of 20% of annual global primary production. Recent progress in CCM research in the marine pennate diatom Phaeodactylum tricornutum revealed that this diatom directly takes up HCO3- from seawater through low-CO2-inducible plasma membrane HCO3- transporters, which belong to the solute carrier (SLC) 4 family. Apart from this, studies of carbonic anhydrases (CAs) in diatoms have revealed considerable diversity in classes and localization among species. This strongly suggests that the CA systems, which control permeability and flux of dissolved inorganic carbon (DIC) by catalysing reversible CO2 hydration, have evolved from diverse origins. Of particular interest is the occurrence of low-CO2-inducible external CAs in the centric marine diatom Thalassiosira pseudonana, offering a strategy of CA-catalysed initial CO2 entry via passive diffusion, contrasting with active DIC transport in P. tricornutum. Molecular mechanisms to transport DIC across chloroplast envelopes are likely also through specific HCO3- transporters, although details have yet to be elucidated. Furthermore, recent discovery of a luminal θ-CA in the diatom thylakoid implied a common strategy in the mechanism to supply CO2 to RubisCO in the pyrenoid, which is conserved among green algae and some heterokontophytes. These results strongly suggest an occurrence of convergent coevolution between the pyrenoid and thylakoid membrane in aquatic photosynthesis.
A text to speech synthesizer using acoustic unit based concatenation for any Indian language of Devanagari script

This paper presents the prosody improvement in acoustic unit based concatenation of any language of Devanagari script. In Text to Speech synthesis system syllable-based synthesis is quite intelligible as compared to di-phone based systems. The system so developed accept the written text of any language of Devanagari script via MS word utility through MATLAB which then converted into Romanized script under text analysis. Tokenization is performed on Romanized script, for the identification of respective phoneme, syllable and diphthong acoustic units. Using the prepared database of acoustic units, these speech segments undergo concatenation using modified TD-PSOLA technique only at the disjoint points. The proposed work is performed on selecting units based on acoustic framework. The efficient use of TDPSOLA technique synthesizes the speech signal which bears the high degree of accuracy and intelligibility to understand and hear clearly like human speech.
Consistent production of a higher TH1:TH2 cytokine ratio by stimulated T cells in men compared with women.

OBJECTIVE To evaluate the T helper 1 (T(H)1)/T helper 2 (T(H)2) lymphocyte cytokine profiles in women and men and to study the in vitro effects of sex hormones on lymphocyte secretion of cytokines. METHODS Analysis of serum concentration and lymphocyte synthesis of T(H)1 (gamma interferon (INF-gamma) and interleukin 2 (IL-2)) and T(H)2 (interleukin 4 (IL-4) and interleukin 10 (IL-10)) cytokines was performed in 20 women and 15 men. Analysis of modifications in cytokine secretion induced by supplementation of lymphocyte culture with increasing concentrations of sex hormones was carried out. RESULTS Higher levels of INF-gamma and IL-2 and lower levels of IL-4 and IL-10 were detected in the phytohemagglutinin-stimulated lymphocyte culture supernatants of men compared with women; the INF-gamma:IL-4 ratio was significantly higher in men. In women, similar concentrations of all the cytokines were detected in culture supernatants obtained during the follicular and the luteal phases. The addition of sex hormones did not modify the concentration of cytokines in supernatants of phytohemagglutinin-stimulated T-cell cultures. CONCLUSIONS Women present a predominant T(H)2 cytokine profile, which could be involved in immune responses characterized principally by the secretion of antibodies. This could be a factor implicated in the higher concentration of immunoglobulins or the increased prevalence of autoimmune diseases detected in females.