Miracle-dz/UniFAR-FTUs huggingface dataset:
Combining prediction of secondary structure and solvent accessibility in proteins

Owing to the use of evolutionary information and advanced machine learning protocols, secondary structures of amino acid residues in proteins can be predicted from the primary sequence with more than 75% per‐residue accuracy for the 3‐state (i.e., helix, β‐strand, and coil) classification problem. In this work we investigate whether further progress may be achieved by incorporating the relative solvent accessibility (RSA) of an amino acid residue as a fingerprint of the overall topology of the protein. Toward that goal, we developed a novel method for secondary structure prediction that uses predicted RSA in addition to attributes derived from evolutionary profiles. Our general approach follows the 2‐stage protocol of Rost and Sander, with a number of Elman‐type recurrent neural networks (NNs) combined into a consensus predictor. The RSA is predicted using our recently developed regression‐based method that provides real‐valued RSA, with the overall correlation coefficients between the actual and predicted RSA of about 0.66 in rigorous tests on independent control sets. Using the predicted RSA, we were able to improve the performance of our secondary structure prediction by up to 1.4% and achieved the overall per‐residue accuracy between 77.0% and 78.4% for the 3‐state classification problem on different control sets comprising, together, 603 proteins without homology to proteins included in the training. The effects of including solvent accessibility depend on the quality of RSA prediction. In the limit of perfect prediction (i.e., when using the actual RSA values derived from known protein structures), the accuracy of secondary structure prediction increases by up to 4%. We also observed that projecting real‐valued RSA into 2 discrete classes with the commonly used threshold of 25% RSA decreases the classification accuracy for secondary structure prediction. While the level of improvement of secondary structure prediction may be different for prediction protocols that implicitly account for RSA in other ways, we conclude that an increase in the 3‐state classification accuracy may be achieved when combining RSA with a state‐of‐the‐art protocol utilizing evolutionary profiles. The new method is available through a Web server at http://sable.cchmc. org. Proteins 2005. © 2005 Wiley‐Liss, Inc.
Correlation between urinary nickel and testosterone plasma values in workers occupationally exposed to urban stressors.

BACKGROUND The purpose of this study is to assess whether occupational exposure to low doses of nickel (Ni) present in urban air can cause alterations in the concentration of plasma testosterone in workers of the Municipal Police of a large Italian city assigned to different types of outdoor tasks. METHODS 359 male subjects were included in the study and divided on the basis of job, age, length of service and smoking habits. The dosage of the atmospheric Ni was performed by personal dosimetries on a sample of the workers included in the study. For each worker included in the study the dosage of whole blood Ni and of the plasma testosterone was carried out. The total sample was subjected to the independent-samples T-test and the Mann-Whitney U test for variables with 2 modes (smoking cigarette) and the ANOVA test and the Kruskal Wallis test for variables with more than 2 modes (age, length of service and job function). The correlation of Pearson with p at 2 wings between the variables was evaluated in the total sample and after subdivision on the basis of smoking and on the basis of the job. After taking into account the major confounding factors the multiple linear regression was performed on the total sample and after breakdown by tasks. RESULTS The correlation between the values of urinary Ni and the values of plasma testosterone on the total sample and for all classes of subdivision was found constantly negative. These results were confirmed by multiple linear regression, which indicated the Ni as the only significant variable that can contribute to the alterations of the testosterone. CONCLUSIONS Based on the results, the Authors suggest that occupational exposure to low doses of Ni present in the urban environment is able to influence some lines of the hypothalamic-pituitary-gonadal axis in exposed workers.
Intergenerational Effects of Parental Personality and Relationship Traits on Mate Choice Among Gay Male and Lesbian Offspring

ABSTRACT Data from 33 lesbian and 54 gay male cohabiting couples were used to examine the relation between parental identification and mate selection. Theories of mate selection and parental identification are reviewed. Effects of gender and sexual orientation as they relate to parental identification and mate selection in gay male and lesbian couples also are reviewed. The results demonstrate significant associations between the similarity of perceived parental personality and relationship styling traits with those of the partner. Socio-economic status, age, and culture also were significantly associated between parents and partners. Taken together, the results demonstrate little support for any specific theory and allude to the need for further research in this area. Limitations and implications are discussed.
Prognostic significance of PD-L1 expression and tumor infiltrating lymphocyte in surgically resectable non-small cell lung cancer

Programmed death ligand 1 (PD-L1) expression is a predictive biomarker of the success of PD-1/PD-L1 inhibitor therapy for patients with advanced non-small cell lung cancer (NSCLC) but its role as a prognostic marker for early stage resectable NSCLC remains unclear. Here, we studied PD-L1 expression and tumor infiltrating lymphocytes (TILs) in surgically resectable NSCLC and correlate the finding with clinicopathological features and patient outcomes. Total of 170 archival samples of resectable NSCLC were probed for PD-L1 expression using the clone 22C3 pharmDx kit. The PD-L1 expression was determined by the Tumor Proportion Score (TPS) and classified into TPS <1%, TPS 1 to 49% and TPS ≥50%. The scoring of TILs was from hematoxylin & eosin stained tissue sections using a system for standardized evaluation of TILs in breast cancer. PD-L1 expression was compared with clinical pathological characteristics and survival outcome. Expression of PD-L1 scores of TPS ≥50%, TPS 1 to 49% and TPS <1% were observed in 10.6%, 24.7% and 64.7% of the 170 archival samples, respectively. Positive PD-L1 expression was significantly higher in patients with squamous carcinoma, in those with higher TNM stage and with the presence of TILs. Neither the PD-L1 expression, TIL status, nor their combination was an independent prognosis biomarker of survival when the data was subjected to either univariate or multivariate analysis. The incidence of PDL1 expression appears to be lower in patient with early stage resectable lung cancer. PD-L1 expression and TILs are not prognostic indicators of survival outcome in this population.
Bystander Intervention Into Crime: A Study Based on Naturally-Occurring Episodes

Thirty-two individuals who intervened in dangerous criminal episodes such as street muggings, armed robberies, and bank holdups, were interviewed at length and compared with a group of noninterveners matched for age, sex, education, and ethnic background. Interveners, in contrast to noninterveners, reported considerably more exposure to crime in terms of personal victimization and witnessing the victimizations of others. Crime interveners also were taller, heavier, and better trained to cope with crimes and emergencies, having had significantly more life-saving, medical, and police training; and were more likely to describe themselves as physically strong, aggressive, emotional, and principled. In spite of an intensive search for personality differences between the two groups, none were found. Results suggest that crime interveners are not prompted to action by notably strong humanitarian purpose or by antisocial aggressiveness, but rather act out of a sense of capability founded on training experiences and rooted in their personal strength.
'People are Plants'- a conceptual metaphor in the Hebrew Bible

Agriculture had a profound impact on the socio-economic structure of ancient Israel. Moreover, the great religious festivals were organised around an agrarian calendar. The importance of agriculture is underscored by the multiple references to plants in the Hebrew Bible. The diverse flora provided the biblical Hebrew authors with a repository of metaphors to describe the divine-human relationship and to portray the Israelites in different historical situations. Given the prevalence of plant imagery in the Hebrew Bible, this contribution endeavours to analyse the conceptual metaphor PEOPLE ARE PLANTSl/ig from a cognitive linguistic perspective. The notions of conceptual mapping and metaphorical instantiations are discussed in order to elucidate the aforementioned metaphor.
Vitamin D and vitamin D analogues for preventing fractures associated with involutional and post-menopausal osteoporosis.

BACKGROUND Due to their known effects on bone metabolism, Vitamin D and related compounds have been proposed for the prevention of osteoporosis and fractures. OBJECTIVES To determine the effects of supplementation with Vitamin D or a Vitamin D analogue in the prevention of fractures of the axial and appendicular skeleton in elderly men or women with involutional or post-menopausal osteoporosis. SEARCH STRATEGY We searched MEDLINE, EMBASE, BIOSIS, CINAHL, HealthPLAN, Dissertation Abstracts, Index to UK Theses, Current Contents, and bibliographies of identified trials and reviews. Trials were also obtained from the Cochrane Musculoskeletal Injuries Group trials register. Date of the most recent search: December 1995. SELECTION CRITERIA Any randomised or quasi-randomised trial which compared Vitamin D or a Vitamin D analogue, either alone or in combination with calcium supplementation, with a placebo, no intervention, or the administration of calcium supplements, with fracture as an outcome, in elderly men or women with involutional or post-menopausal osteoporosis. DATA COLLECTION AND ANALYSIS Two reviewers independently assessed trial quality, by use of a seven item scale, and extracted data. Additional information was sought from trialists. Where possible the data were pooled. MAIN RESULTS Fourteen trials recording 13 different comparisons were included. In the only trial of Vitamin D alone, protection against hip fracture was not confirmed. Two regimens, each represented by one large trial, which showed limited evidence of efficacy in reducing the incidence of hip or other appendicular skeleton fractures were: 1) Oral Vitamin D when accompanied by calcium supplementation. 2) 1,25 dihydroxy Vitamin D (calcitriol). This appeared more effective than calcium in a direct comparison. Regimens showing limited evidence of efficacy in reducing the incidence of vertebral deformity were: 1) 1,25 dihydroxy Vitamin D (calcitriol), which appeared more effective than calcium in one large trial, and more effective than placebo from pooled results of two small trials. 2) Oral 1-alpha hydroxy Vitamin D (alfacalcidol), when administered with calcium supplements (two small trials, which lacked power to confirm a possible effect). Hypercalcaemia and gastro-intestinal symptoms, reported in less than 5% of participants, were slightly more common when Vitamin D analogues were taken. However, the risk of death was marginally less. REVIEWER'S CONCLUSIONS Uncertainty remains about the efficacy of regimens which include Vitamin D or its analogues in fracture prevention. Particularly if co-supplementation of calcium is required, significant cost differences are likely to exist between regimens. Further randomised trials with economic evaluation are desirable before community fracture prevention programmes employing Vitamin D supplementation can be confidently introduced.
An Empirical Analysis of Network Externalities in Peer-to-Peer Music Sharing Networks

Peer-to-peer file sharing networks are becoming an important medium for the distribution of information goods. However, there is little academic research into the optimal design of these networks under real-world conditions. Our research represents an initial effort to analyze the impact of positive and negative network externalities on the optimal size of these P2P networks. Our analysis uses a unique dataset collected from the six most popular OpenNap peer-to-peer networks between December 19, 2000 and April 22, 2001. We find that users contribute value to the network in terms of additional content and additional replicas of content at a diminishing rate, while they impose costs on the network in terms of congestion on shared resources at an increasing rate. Together these results suggest that the optimal size of peer-to-peer networks is bounded  at some point the costs a marginal user imposes on the network will exceed the value they provide.
Combined Effects of Green Tea Extracts, Green Tea Polyphenols or Epigallocatechin Gallate with Acarbose on Inhibition against α-Amylase and α-Glucosidase in Vitro

Green tea, green tea polyphenols and epigallocatechin gallate (EGCG) are confirmed to have beneficial effects in the treatment of diabetes mellitus, and a possible mechanism can be ascribed to their inhibitory effect against α-amylase and α-glucosidase in the digestive tract. In this paper, we first investigated the combined inhibitory effect of green tea extracts, green tea polyphenols or EGCG with acarbose on α-amylase and α-glucosidase in vitro. Our results indicated that the interaction between green tea extracts (green tea polyphenols or EGCG) and acarbose was complicated. The combination of green tea extracts, green tea polyphenols or EGCG with acarbose had a synergistic effect on α-amylase and α-glucosidase at low concentrations and the combined effect turned out to be antagonistic at high concentrations according to the Combination Index (CI) values. These findings not only provided some significant quantitative values, but also provide some valuable implications for the combined use of acarbose and GTE (GTP or EGCG) in the treatment of diabetes mellitus.
Individual responses to combined endurance and strength training in older adults.

PURPOSE A combination of endurance and strength training is generally used to seek further health benefits or enhanced physical performance in older adults compared with either of the training modes alone. The mean change within a training group, however, may conceal a wide range of individual differences in the responses. The purpose, therefore, was to examine the individual trainability of aerobic capacity and maximal strength, when endurance and strength training are performed separately or concurrently. METHODS For this study, 175 previously untrained volunteers, 89 men and 86 women between the ages of 40 and 67 yr, completed a 21-wk period of either strength training (S) twice a week, endurance training (E) twice a week, combined training (ES) four times per week, or served as controls. Training adaptations were quantified as peak oxygen uptake (VO2peak) in a bicycle ergometer test to exhaustion and maximal isometric bilateral leg extension force (MVC) in a dynamometer. RESULTS A large range in training responses, similar to endurance or strength training alone, was also observed with combined endurance and strength training in both ΔVO2peak (from -8% to 42%) and ΔMVC (from -12% to 87%). There were no significant correlations between the training responses in VO2peak and MVC in the E, S, or especially in the ES group, suggesting that the same subjects did not systematically increase both aerobic capacity and maximal strength. CONCLUSIONS The goal of combined endurance and strength training--increasing both aerobic capacity and maximal strength simultaneously--was only achieved by some of the older subjects. New means are needed to personalize endurance, strength, and especially combined endurance and strength training programs for optimal individual adaptations.
The Size Distribution of Trans-Neptunian Bodies

We search 0.02 deg2 of the invariable plane for trans-Neptunian objects (TNOs) 25 AU or more distant using the Advanced Camera for Surveys (ACS) aboard the Hubble Space Telescope. With 22 ks per pointing, the search is more than 50% complete for m606W ≤ 29.2. Three new objects are discovered, the faintest with mean magnitude m = 28.3 (diameter ≈25 km), which is 3 mag fainter than any previously well-measured solar system body. Each new discovery is verified with a follow-up 18 ks observation with the ACS, and the detection efficiency is verified with implanted objects. The three detections are a factor of ∼25 less than would be expected under extrapolation of the power-law differential sky density for brighter objects, Σ(m) ≡ dN/dm dΩ ∝ 10αm with α ≈ 0.63. Analysis of the ACS data and recent TNO surveys from the literature reveals departures from this power law at both the bright and faint ends. Division of the TNO sample by distance and inclination into "classical Kuiper belt" (CKB) and "Excited" samples reveals that Σ(m) differs for the two populations at 96% confidence, and both samples show departures from power-law behavior. A double power-law Σ(m) adequately fits all data. Implications of these departures include the following: (1) The total mass of the "classical" Kuiper belt is ≈0.010 M⊕, only a few times Pluto's mass, and is predominantly in the form of ∼100 km bodies (barring a secondary peak in the mass distribution at sub–10 km sizes). The mass of Excited objects is perhaps a few times larger. (2) The Excited class has a shallower bright-end magnitude (and, presumably, size) distribution; the largest objects, including Pluto, make up tens of percent of the total mass whereas the largest CKB objects are only ∼2% of its mass. (3) The derived size distributions predict that the largest Excited body should be roughly the mass of Pluto, and the largest CKB body should have mR ≈ 20—hence, Pluto is feasibly considered to have originated from the same physical process as the Excited TNOs. (4) The observed deficit of small TNOs occurs in the size regime where present-day collisions are expected to be disruptive, suggesting extensive depletion by collisions. The Excited and CKB size distributions are qualitatively similar to some numerical models of growth and erosion, with both accretion and erosion appearing to have proceeded to more advanced stages in the Excited class than in the CKB. (5) The lack of detections of distant TNOs implies that if a mass of TNOs comparable to the CKB is present near the invariable plane beyond 50 AU, that distant population must be composed primarily of bodies smaller than ≈40 km. (6) There are too few small CKB objects for this population to be the reservoir of Jupiter-family comet precursors without a significant upturn in the population at diameters under 20 km. With optimistic model parameters and extrapolations, the Excited population could be the source reservoir. Implications of these discoveries for the formation and evolution of the outer solar system are discussed.
Amyloid Beta Precursor Protein and Prion Protein Have a Conserved Interaction Affecting Cell Adhesion and CNS Development

Genetic and biochemical mechanisms linking onset or progression of Alzheimer Disease and prion diseases have been lacking and/or controversial, and their etiologies are often considered independent. Here we document a novel, conserved and specific genetic interaction between the proteins that underlie these diseases, amyloid-β precursor protein and prion protein, APP and PRP, respectively. Knockdown of APP and/or PRNP homologs in the zebrafish (appa, appb, prp1, and prp2) produces a dose-dependent phenotype characterized by systemic morphological defects, reduced cell adhesion and CNS cell death. This genetic interaction is surprisingly exclusive in that prp1 genetically interacts with zebrafish appa, but not with appb, and the zebrafish paralog prp2 fails to interact with appa. Intriguingly, appa & appb are largely redundant in early zebrafish development yet their abilities to rescue CNS cell death are differentially contingent on prp1 abundance. Delivery of human APP or mouse Prnp mRNAs rescue the phenotypes observed in app-prp-depleted zebrafish, highlighting the conserved nature of this interaction. Immunoprecipitation revealed that human APP and PrPC proteins can have a physical interaction. Our study reports a unique in vivo interdependence between APP and PRP loss-of-function, detailing a biochemical interaction that considerably expands the hypothesized roles of PRP in Alzheimer Disease.
How You Describe a Group Shows How Biased You Are

The aim of the present research was to show that the level of linguistic abstraction used when describing group behaviors affects inferences about the speaker’s degree of bias toward that group. Participants used a speaker’s description of a group to judge that person’s communicative intentions (Study 1) and attitudes (Study 2) toward the group. The results show that speakers who use abstract terms are perceived as more biased than speakers who use concrete terms.
Fossils of Reionization in the Local Group

We use a combination of high-resolution gas dynamics simulations of high-redshift dwarf galaxies and dissipationless simulations of a Milky Way-sized halo to estimate the expected abundance and spatial distribution of the dwarf satellite galaxies that formed most of their stars around z ~ 8, evolving only little since then. Such galaxies can be considered "fossils" of the reionization era, and studying their properties could provide a direct window into the early, pre-reionization stages of galaxy formation. We show that ~5%-15% of the objects existing at z ~ 8 do indeed survive until the present in a Milky Way-like environment without significant evolution. This implies that it is plausible that the fossil dwarf galaxies do exist in the Local Group. Because such galaxies form their stellar systems early during the period of active merging and accretion, they should have a spheroidal morphology regardless of their current distance from the host galaxy. Their observed counterparts should therefore be identified among the dwarf spheroidal galaxies. We show that both the expected luminosity function and the spatial distribution of dark matter halos that are likely to host fossil galaxies agree reasonably well with the observed distributions of the luminous (LV ≳ 106 L☉) Local Group fossil candidates near the host galaxy (d ≲ 200 kpc). However, the predicted abundance is substantially larger (by a factor of 2-3) for fainter galaxies (LV < 106 L☉) at larger distances (d ≳ 300 kpc). We discuss several possible explanations for this discrepancy.
Nonlinear economic Model Predictive Control for SI engines based on Sequential Quadratic Programming

This paper proposes a model predictive torque control strategy for Spark Ignition (SI) engines with external Exhaust Gas Recirculation (EGR). The proposed Nonlinear (economic) Model Predictive Controller (NMPC) tries to minimize fuel consumption with given Indicate Mean Effective Pressure (IMEP) tracking reference and abnormal combustion constraints like knock and combustion stability. A Nonlinear Programming (NLP) problem is formulated and solved using Sequential Quadratic Programming (SQP) to obtain the desired control actions. The SQP exploits the Gauss-Newton like structure of the real time NLP problem to simplify computation of Hessian matrix. Simulation results demonstrate that the proposed model predictive IMEP control can track the IMEP reference for engine cycles without active constraints (with a RMS tracking error of 1.1%). When the IMEP reference conflicts with constraints, the SQP MPC can efficiently find close to optimal control actions that are similar to those from off-line feed forward calibration.