Miracle-dz/UniFAR-FTUs huggingface dataset:
Reproducibility of energy and macronutrient intake and related substrate oxidation rates in a buffet-type meal

The aim of this present study was to determine the reliability of a buffet-type meal as a measure of spontaneous energy and macronutrient intake. In addition, we evaluated the short-term effects of diet on the composition of the substrate mix oxidized postprandially. Fourteen male subjects had ad libitum access to a variety of foods from a buffet-type meal offered in the laboratory during two identical sessions. The foods comprising the test meal had varying amounts of protein, lipid and carbohydrate. The results showed that there were significant intraclass correlations (ri) for energy (ri 0·97, P = 0·0001), lipid (ri 0·97, P = 0·0001), carbohydrate (ri 0·92, P = 0·0003) and protein (ri 0·82, P = 0·0072) intake between the two meal sessions. Hunger and fullness levels measured immediately before and during 4 h after the meal were identical under the two conditions. In addition, there was no significant difference between the two sessions for RQ and resting energy expenditure, which showed significant reproducibility for measurements obtained immediately before, immediately after, as well as 30 min after, the buffet. This present study demonstrates the high reproducibility of energy and macronutrient intake and oxidation rate values obtained with a buffet-type meal in healthy male subjects and suggests that the use of this test is a reliable method for assessment of macronutrient preferences in the laboratory.
Downregulation of KiSS‐1 expression is responsible for tumor invasion and worse prognosis in gastric carcinoma

KiSS‐1 is a promising candidate tumor‐suppressor gene and may play a key role in the metastatic cascade. The expression profile and the role of KiSS‐1 in cancer progression are largely unknown in most of the cancers, including gastric cancer. In this study, KiSS‐1 expression was evaluated by RNase protection assay and localization was done by in situ hybridization in 40 gastric cancers and their adjacent normal gastric mucosa. For comparison with clinicopathologic characteristics and patient prognosis, all patients were divided into 2 groups having high and low KiSS‐1 expression by using the median as the cutoff value of KiSS‐1 expression as determined by the RNase protection assay. Gastric cancers with low KiSS‐1 had frequent venous invasion, distant metastasis and tumor recurrence. Accordingly, patients with low KiSS‐1‐expressing tumors had a significantly worse overall and disease‐free survival. In multivariate analysis, KiSS‐1 became the strongest independent prognostic factor among the conventional prognosticators for gastric cancer patients. Collectively, these findings suggest that KiSS‐1 may play a crucial role in gastric cancer invasion and could be a useful target for therapeutic intervention. © 2004 Wiley‐Liss, Inc.
Scaling out the density dependence of the α relaxation in glass-forming polymers

We show that the density and temperature dependences of the α-relaxation time of several glass-forming polymers can be described through a single scaling variable X = e(ρ)/T, where e(ρ) is well fitted by a power law ρx, x being a species-specific parameter. This implies that “fragility” is an intrinsic, density-independent property of a glass-former characterizing its super-Arrhenius slowing-down of relaxations, and it leads us to propose a modification of the celebrated Angell plot.
Turbulent structure and scaling of the inertial subrange in a stratocumulus-topped boundary layer observed by a Doppler lidar

Abstract. The turbulent structure of a stratocumulus-topped marine boundary layer over a 2-day period is observed with a Doppler lidar at Mace Head in Ireland. Using profiles of vertical velocity statistics, the bulk of the mixing is identified as cloud driven. This is supported by the pertinent feature of negative vertical velocity skewness in the sub-cloud layer which extends, on occasion, almost to the surface. Both coupled and decoupled turbulence characteristics are observed. The length and timescales related to the cloud-driven mixing are investigated and shown to provide additional information about the structure and the source of the mixing inside the boundary layer. They are also shown to place constraints on the length of the sampling periods used to derive products, such as the turbulent dissipation rate, from lidar measurements. For this, the maximum wavelengths that belong to the inertial subrange are studied through spectral analysis of the vertical velocity. The maximum wavelength of the inertial subrange in the cloud-driven layer scales relatively well with the corresponding layer depth during pronounced decoupled structure identified from the vertical velocity skewness. However, on many occasions, combining the analysis of the inertial subrange and vertical velocity statistics suggests higher decoupling height than expected from the skewness profiles. Our results show that investigation of the length scales related to the inertial subrange significantly complements the analysis of the vertical velocity statistics and enables a more confident interpretation of complex boundary layer structures using measurements from a Doppler lidar.
Simulated Annealing: Rigorous finite-time guarantees for optimization on continuous domains

Simulated annealing is a popular method for approaching the solution of a global optimization problem. Existing results on its performance apply to discrete combinatorial optimization where the optimization variables can assume only a finite set of possible values. We introduce a new general formulation of simulated annealing which allows one to guarantee finite-time performance in the optimization of functions of continuous variables. The results hold universally for any optimization problem on a bounded domain and establish a connection between simulated annealing and up-to-date theory of convergence of Markov chain Monte Carlo methods on continuous domains. This work is inspired by the concept of finite-time learning with known accuracy and confidence developed in statistical learning theory.
Structure of sugar-bound LacY

Significance The lactose permease of Escherichia coli (LacY), a model for the major facilitator superfamily, catalyzes the symport of a galactopyranoside and an H+ across the membrane by a mechanism in which the sugar-binding site in the middle of the protein becomes alternately accessible to either side of the membrane. However, all X-ray structures thus far show LacY in an inward-facing conformation with a tightly sealed periplasmic side. Significantly, by using a double-Trp mutant, we now describe an almost occluded, outward-open conformation with bound sugar, confirming more than two decades of biochemical and biophysical findings. We also present evidence that protonated LacY specifically binds D-galactopyranosides, inducing an occluded state that can open to either side of the membrane. Here we describe the X-ray crystal structure of a double-Trp mutant (Gly46→Trp/Gly262→Trp) of the lactose permease of Escherichia coli (LacY) with a bound, high-affinity lactose analog. Although thought to be arrested in an open-outward conformation, the structure is almost occluded and is partially open to the periplasmic side; the cytoplasmic side is tightly sealed. Surprisingly, the opening on the periplasmic side is sufficiently narrow that sugar cannot get in or out of the binding site. Clearly defined density for a bound sugar is observed at the apex of the almost occluded cavity in the middle of the protein, and the side chains shown to ligate the galactopyranoside strongly confirm more than two decades of biochemical and spectroscopic findings. Comparison of the current structure with a previous structure of LacY with a covalently bound inactivator suggests that the galactopyranoside must be fully ligated to induce an occluded conformation. We conclude that protonated LacY binds d-galactopyranosides specifically, inducing an occluded state that can open to either side of the membrane.
Constructing Double-Erasure HoVer Codes Using Latin Squares

Storage applications are in urgent need of multi-erasure codes. But there is no consensus on the best coding technique. Hafner has presented a class of multi-erasure codes named HoVer codes [1]. This kind of codes has a unique data/parity layout which provides a range of implementation options that cover a large portion of the performance/efficiency trade-off space. Thus it can be applied to many scenarios by simple tuning. In this paper, we give a combinatorial representation of a family of double-erasure HoVer codes - create a mapping between this family of codes and Latin squares. We also present two families of double-erasure HoVer codes respectively based on the column-Hamiltonian Latin squares (of odd order) and a family of Latin squares of even order. Compared with the double-erasure HoVer codes presented in [1], the new codes enable greater flexibility in performance and efficiency trade-off.
Changes in von Willebrand factor-cleaving protease (ADAMTS-13) in patients with aortic stenosis undergoing valve replacement or balloon valvuloplasty

Summary It was the objective of this study to determine whether reduced cleavage of von Willebrand factor (VWF) multimers following aortic valve replacement (AVR) is a consequence of reduced shear stress or postoperative changes in VWF cleavage protease (ADAMTS-13) activity. Aortic stenosis (AS) may be complicated by acquired von Willebrand disease. Aortic valve replacement (AVR) corrects the associated haematologic abnormalities. We enrolled 114 patients with severe AS scheduled for either balloon aortic valvuloplasty (BAV; n=64) or AVR (n=50). Haematologic assessments of VWF levels and activity and ADAMTS-13 were performed before and 24 hours after valve intervention. The VWF:RCo to VWF:Ag ratio, a surrogate for large VWF multimer activity, increased by 37% (p < 0.0001) after AVR and by 10% (p = 0.0002) after BAV. ADAMTS-13 activity significantly decreased after AVR (579 ± 127 to 468 ± 135 ng/ml; p<0.0001), but not after BAV (484 ± 153 to 529 ± 185 ng/ml; p = 0.10). By multivariable analysis, the change in VWF:RCo ratio after AVR was more strongly associated with the fall in ADAMTS-13 than with reduction of valve gradient; whereas the change in gradient better predicted the rise in VWF:RCo after BAV. In conclusion, both BAV and AVR reverse the haematological abnormalities of the acquired von Willebrand syndrome of AS and ADAMTS-13 levels decrease after AVR. These findings suggest that a portion of the haematologic benefit of AVR may be due to a postoperative decline in ADAMTS-13 rather than solely to relief of AS as previously thought.
Haptoglobin-α subunit as potential serum biomarker in ovarian cancer: Identification and characterization using proteomic profiling and mass spectrometry

Purpose : The objective of this study was to identify and characterize new serum biomarkers in ovarian cancer patients using mass spectrometric protein profiling and specific immunological assays. Experimental Design : Serum samples from 80 cancer patients and 91 healthy women were analyzed by surface enhanced laser desorption and ionization-mass spectrometry (MS) profiling. A candidate biomarker was purified by affinity chromatography, and its sequence was determined by liquid chromatography-tandem MS. An antibody was generated from the synthesized peptide for quantitative validation in the cases and controls. CA125 was determined and compared with the same set of specimens. Results : Using surface enhanced laser desorption and ionization, we found a serum biomarker at ∼11700 Da, which had peak intensity significantly higher in cases (1.366) compared with controls (0.208, P = 0.002), and subsequently identified this as the α chain of haptoglobin. ELISA indicated that Hp-α was ≤2-fold higher in cancer serum compared with normal, benign tumor, and other gynecological cancers ( P Conclusions : Haptoglobin-derived α subunit is a potential marker for ovarian cancer that is complementary to CA125. MS-based protein profiling is a valuable tool for screening protein markers and useful to detect post-translational modification of tumor-associated proteins or abnormal metabolic products. However, confirmation of protein identity with specific antibodies is crucial for clinical application and functional studies.
Enhanced production and organic solvent stability of a protease fromBrevibacillus laterosporus strain PAP04

A bacterial strain (PAP04) isolated from cattle farm soil was shown to produce an extracellular, solvent-stable protease. Sequence analysis using 16S rRNA showed that this strain was highly homologous (99%) to Brevibacillus laterosporus. Growth conditions that optimize protease production in this strain were determined as maltose (carbon source), skim milk (nitrogen source), pH 7.0, 40°C temperature, and 48 h incubation. Overall, conditions were optimized to yield a 5.91-fold higher production of protease compared to standard conditions. Furthermore, the stability of the enzyme in organic solvents was assessed by incubation for 2 weeks in solutions containing 50% concentration of various organic solvents. The enzyme retained activity in all tested solvents except ethanol; however, the protease activity was stimulated in benzene (74%) followed by acetone (63%) and chloroform (54.8%). In addition, the plate assay and zymography results also confirmed the stability of the PAP04 protease in various organic solvents. The organic solvent stability of this protease at high (50%) concentrations of solvents makes it an alternative catalyst for peptide synthesis in non-aqueous media.
Molecular genetics of Drosophila alpha-actinin: mutant alleles disrupt Z disc integrity and muscle insertions

We have isolated a Drosophila melanogaster alpha-actinin gene and partially characterized several mutant alleles. The Drosophila protein sequence is very similar (68% identity) to those of chicken alpha- actinin isoforms, but less closely related (30% identity) to Dictyostelium alpha-actinin. The gene is within subdivision 2C of the X chromosome, coincident with 15 lethal (1)2Cb mutations. At least four alleles, l(1)2Cb1, l(1)2Cb2, l(1)2Cb4, and l(1)2Cb5 are interrupted by rearrangement breakpoints and must be null. In all four cases, hemizygous mutants complete embryogenesis and do not die until the second day of larval growth, signifying that either the role of alpha- actinin in nonmuscle cells is redundant or that a distinct and only distantly related gene encodes the non-muscle isoform. Allelic but less severely affected fliA mutants are apparently due to point mutations, and develop into adults having thoracic muscle abnormalities. EM of mutant muscles reveals that Z discs and myofibrillar attachments are disrupted, whereas epithelial "tendon" cells are less affected. We discuss these phenotypes in the light of presumed in vivo alpha-actinin functions.
Slow, Decorrelated Features for Pretraining Complex Cell-like Networks

We introduce a new type of neural network activation function based on recent physiological rate models for complex cells in visual area V1. A single-hidden-layer neural network of this kind of model achieves 1.50% error on MNIST. We also introduce an existing criterion for learning slow, decorrelated features as a pretraining strategy for image models. This pretraining strategy results in orientation-selective features, similar to the receptive fields of complex cells. With this pretraining, the same single-hidden-layer model achieves 1.34% error, even though the pretraining sample distribution is very different from the fine-tuning distribution. To implement this pretraining strategy, we derive a fast algorithm for online learning of decorrelated features such that each iteration of the algorithm runs in linear time with respect to the number of features.
Seasonal variability of prevalence and occurrence of multiple infections shape the population structure of Crithidia bombi, an intestinal parasite of bumblebees (Bombus spp.)

Ergonomic growth phases of annual social insect societies strongly influence horizontally transmitted parasites. Herein, we focused on the impact of temporal changes in host demography on the population structure of a horizontally transmitted parasite. Seasonal fluctuations in prevalence and the occurrence of multiple infections of the gut parasite Crithidia bombi were analyzed in repeatedly sampled populations of two common bumblebee (Bombus spp.) species. Prevalence of C. bombi was greatest in the middle of the foraging season and coincided with the maximal occurrence of multiple infections. Both decline later in the season. The genetic structure of the parasite population also showed strong seasonal fluctuations with a drastic decline in effective population size and an increase in linkage disequilibrium when infection rates were highest. These effects are mainly attributable to significant changes in parasite allele frequencies leading to selection of specific alleles and increasing the frequency of homozygote genotypes in the middle of the season. Within host, competition between parasite genotypes might explain the observed pattern leading to selection of these alleles, and thus a boost of homozygote genotypes in the middle of the season. Toward the end of the season, selection appears to relax and we observed a recovery in linkage equilibrium, as well as an increase in effective population size. This might be explained by genetic exchange in these trypanosomes in natural populations.
Short‐ and long‐duration responses to levodopa during the first year of levodopa therapy

We examined the response to 2–hour levodopa infusions in 18 Parkinson's disease subjects before starting long‐term levodopa treatment and after 6 and 12 months of treatment using tapping speed as an index of bradykinesia. The long‐duration response (LDR), measured as the increase in baseline (overnight without levodopa) tapping speed, increased by 29 ± 18 at 6 months and by 35 ± 24 at 12 months. The magnitude of the short‐duration response (SDR) to a 2‐hour levodopa infusion after an overnight levodopa withdrawal did not differ at 6 and 12 months (16 ± 18 and 20±13 taps/min) from that before long‐term levodopa (21±taps/min). However, when levodopa was withheld for 3 days, it was evident that the SDR magnitude was increasing in magnitude (19, 23, and 31 taps/min at 0, 6, and 12 months). Duration of SDR did not change. A diurnal motor pattern with faster tapping speeds in the morning and slower in the evening was apparent on the days no levodopa was administered. These observations indicate (1) the LDR is responsible for much of the sustained response to levodopa during the first year of treatment, (2) the SDR magnitude increases but is obscured by the LDR, and (3) a diurnal pattern of motor function is present that may be partially responsible for the poorer motor function in the afternoons and evenings.
Association between smoking and mortality: Khon Kaen cohort study, Thailand.

BACKGROUND Despite anti-smoking campaigns, smoking prevalence among Thai males aged 30 or older is high, at around 50%. The purpose of this study was to determine the relationship between smoking and mortality in a rural Thai community. MATERIALS AND METHODS Subjects enrolled into the Khon Kaen cohort study between 1990 and 2001 were followed up for their vital status until 16th March 2012. The death resource was from the Bureau of Policy and Strategy, Ministry of Interior, Thailand. A Cox proportional hazards model was used to analyse the association between smoking and death, controlling for age, education level and alcohol drinking, and confidence intervals were calculated using the floating risk method. RESULTS The study recruited 5,962 male subjects, of whom 1,396 died during a median 13.5 years of follow-up. Current smokers were more likely to die than never smokers after controlling for age, education level and alcohol drinking (HR, 95%CI: 1.41, 1.32- 1.51), and the excess mortality was greatest for lung cancer (HR, 95%CI: 3.51, 2.65-4.66). However, there was no increased risk with increasing dose of tobacco, and no difference in risk between smokers of yamuan (hand- rolled cigarettes) and manufactured tobacco. CONCLUSION Mortality from cancer, particularly lung cancer, and from all causes combined is dependent on smoking status among men in rural Thailand, but the relative risks are lower than have been reported from studies in high income countries, where the tobacco epidemic is more established.
External geophysics, Climate and Environment Impact of the hydrological cycle on past climate changes: three illustrations at different time scales

We investigate in the paper the impact of the hydrologic cycle on climate at different periods. The aim is to illustrate how the changes in moisture transport, precipitation pattern, and weathering may alter, at regional or global scales, the CO 2 and climate equilibriums. We choose three climate periods to pinpoint intricate relationshi ps between water cycle and climate. The illustrations are the following. ( i) The onset of ice-sheet build-up, 115 kyr BP . We show that the increased thermal meridian gradient of SST allows large moisture advection over the North American continent and provides appropriate conditions for perennial snow on the Canadian Archipelago. (ii) The onset of Indian Monsoon at the end of the Tertiary . We demonstrate that superimposed to the Tibetan Plateau, the shrinkage of the Tethys, since Oligocene, plays a major role to explain changes in the geographical pattern of the southeastern Asian Monsoon. (iii) The onset of Global Glaciation(750 Ma). We show that the break-up of Rodinia occurring at low latitudes is an important feature to explain how the important precipitation increase leads to weathering and carbon burial, which contribute to decrease atmospheric CO2 enough to produce a snows ball Earth. All these periods have been simulated with a hierarchy of models appropriate to quantify the water cycle impact on climate. To cite this
Antimicrobial resistance testing of Helicobacter pylori: A comparison of etest and disk diffusion methods

Summary Routine antimicrobial resistance testing of Helicobacter pylori is more commonly performed since the correlation between metronidazole resistance and failure to eradicate using this drug, has been made. While resistance testing of H. pylori by Etest is simple to perform, it is expensive compared to disk diffusion methods. In this study the Etest was compared with a modified Kirby‐Bauer disk diffusion (NCCLS) method for routine resistance screening of H. pylori. Fifty one pre‐treatment isolates were tested against amoxycillin, metronidazole, tetracycline and erythromycin by both Etest and disk diffusion using NCCLS guideline strength disks. Clarithromycin was tested by Etest only. Nitroimidazole and macrolide resistance were detected using the modified Kirby‐Bauer disk diffusion method which correlated with Etest minimum inhibitory concentration (MIC). Resistance rates were 49% for metronidazole and 8% for clarithromycin. Cross resistance occurs with macrolides against H. pylori and allows testing of erythromycin to predict resistance to clarithromycin. The very low MICs obtained with H. pylori against amoxycillin and tetracycline require the use of Etest or lower strength disk methods to be used.Abbreviations: NCCLS, National Committee for Clinical Laboratory Standards.