Miracle-dz/UniFAR-FTUs huggingface dataset:
Dynamics Govern Specificity of a Protein-Protein Interface: Substrate Recognition by Thrombin

Biomolecular recognition is crucial in cellular signal transduction. Signaling is mediated through molecular interactions at protein-protein interfaces. Still, specificity and promiscuity of protein-protein interfaces cannot be explained using simplistic static binding models. Our study rationalizes specificity of the prototypic protein-protein interface between thrombin and its peptide substrates relying solely on binding site dynamics derived from molecular dynamics simulations. We find conformational selection and thus dynamic contributions to be a key player in biomolecular recognition. Arising entropic contributions complement chemical intuition primarily reflecting enthalpic interaction patterns. The paradigm “dynamics govern specificity” might provide direct guidance for the identification of specific anchor points in biomolecular recognition processes and structure-based drug design.
The challenge of teen nutrition: An ecological view of socio-cognitive influences on urban, African-American adolescent diet quality

Title of Document: THE CHALLENGE OF TEEN NUTRITION: AN ECOLOGICAL VIEW OF SOCIOCOGNITIVE INFLUENCES ON URBAN, AFRICAN-AMERICAN ADOLESCENT DIET QUALITY Margaret Mary Wrobleski, Doctor of Philosophy, 2010 Directed By: Assistant Professor, Nancy Atkinson, Department of Public and Community Health The routine food choices that adolescents make impact their nutritional status, health, and their risk of developing chronic illnesses such as heart disease, cancer, and osteoporosis in the future. Nutrient requirements during adolescence are comparable to those in early infancy, emphasizing the importance of a high quality diet for healthy growth and development. A myriad of personal, social, and environmental factors influence adolescents in shaping their dietary intake and quality of diet. Lowincome, African-American adolescents in Baltimore were identified as having suboptimal nutritional intake compared to national dietary recommendations. This study explored the dynamic and relative contributions that factors within three environmental levels (personal, social, and community) made as predictors of diet quality in a sample of low-income, urban African-American adolescents using an integrated Social Cognitive Theory (SCT) / ecological theoretical framework. It was hypothesized that 1) the personal, social, and community environmental levels of dietary influences would all significantly contribute to diet quality, with community environment making the largest relative contribution; 2) self-efficacy for healthy eating moderated the relationship between parental beliefs about nutrition and diet quality; and 3) self-efficacy for healthy eating moderated the relationship between peer eating behaviors and diet quality. There have been very few studies using an integrated SCT/ecological model to explore the dietary influences on adolescent nutrition, especially on this demographic. The significant influence the SCT construct of observational learning has on adolescents was evidenced in this study by the positive relationship found between diet quality, parental beliefs about nutrition, and peer eating behavior. Younger participants in early adolescence and females were predominately guided by their parents’ beliefs about nutrition, while males in this study appeared to identify more with their peers’ nutrition-related behaviors. This study revealed that parents and peers play important roles in AfricanAmerican adolescents’ food choices and subsequent diet quality. Nutrition interventions should focus on parent-teen interactions and on improving the dietary habits of parents so they may be more effective role models for youth. Nutrition promotion research targeting young African-American men may consider using group interactive behavioral interventions with peers that build and reinforce peer modeling of positive nutrition behaviors. THE CHALLENGE OF TEEN NUTRITION: AN ECOLOGICAL VIEW OF SOCIO-COGNITIVE INFLUENCES ON URBAN, AFRICAN-AMERICAN ADOLESCENT DIET QUALITY
Quantum hydrodynamic model for the nonlinear electron dynamics in thin metal films

A quantum hydrodynamic (fluid) model, derived from the Wigner-Poisson equations, is used to investigate the ultrafast electron dynamics in thin metal films. The hydrodynamic equations, which include exchange and correlation effects, can be combined into a single nonlinear Schr\"odinger-type equation. The fluid model is first benchmarked against a density-functional calculation for the ground state, with good agreement between the two approaches. The ultrafast nonlinear electron dynamics is then investigated and compared to recent semiclassical results obtained with a Vlasov-Poisson approach.
Resource‐based habitat associations in a neotropical liana community

1. Lianas are a conspicuous element of many tropical forests, accounting for up to 40% of woody stem density and 20% of species richness in seasonal forests. However, lianas have seldom been surveyed at sufficiently large spatial scales to allow an assessment of the importance of habitat variables in structuring liana communities.
Aides incitatives et dterminants des embauches des tablissements passs 35 heures

Parmi les etablissements passes aux 35 heures fin 2000, deux categories peuvent etre identifiees : les etablissements ayant signe une convention " Robien " ou " Aubry 1 " et ayant beneficie des aides incitatives et ceux passes aux 35 heures sans obtenir ces aides mais ayant beneficie des allegements prevus par le dispositif " Aubry 2 ". L'analyse proposee vise a identifier les determinants des creations d'emplois de ces deux categories d'etablissements ayant mis en oeuvre la reduction du temps de travail (RTT), en s'appuyant sur des donnees detaillees issues de l'enquete Passages realisee en 2001 par la Dares et l'institut BVA. L'impact de l'ampleur de la variation du temps de travail, celui de l'evolution du cout du travail et celui des gains de productivite sont successivement etudies. L'evaluation ex post souligne que ces variables, utilisees dans les modeles macroeconomiques prospectifs pour expliquer l'efficacite de la RTT sur l'emploi, influencent significativement l'ampleur des creations d'emplois de l'ensemble des etablissements passes aux 35 heures. Toutefois, leur impact est plus fort sur les etablissements ayant obtenu des aides incitatives. D'apres l'enquete Passages, les effectifs des etablissements ayant beneficie des aides incitatives ont augmente de plus de 10 % contre 4 % pour les autres. Afin d'expliquer cet ecart, on le decompose en trois parties : celle liee aux modalites observees de mise en oeuvre de la RTT, celle liee aux caracteristiques non observees des etablissements et celle provenant de l'effet de selection des etablissements les plus dynamiques. Pres de la moitie de la difference moyenne de creations d'emplois entre les etablissements ayant obtenu des aides incitatives et les autres s'explique par des disparites de mise en oeuvre de la RTT, notamment l'ampleur de la variation du temps de travail, l'evolution du cout du travail et les gains de productivite. Ainsi, la selection des etablissements les plus dynamiques n'est pas le seul element expliquant les ecarts de creations d'emplois observes.
Immigration and Incarceration: Patterns and Predictors of Imprisonment Among First- and Second-Generation Young Adults

In this chapter we aim to examine empirically the role of ethnicity, nativity and generation in relation to crime and imprisonment. Our analysis will be elaborated at two levels: First, at the national level, we will focus on the incarceration rates of young men 18 to 39, comparing differences between the foreign-born and the U.S.-born by national origin and by education, and, among the foreign-born, by length of residence in the United States. Second, at the local level, we will be relying on in-depth data collected by the Children of Immigrants Longitudinal Study (CILS) in San Diego. The decade-long study followed a large sample of first- and second-generation children of immigrants from Mexico, the Philippines, Vietnam, Laos, Cambodia, and other countries from Asia and Latin America. Unlike cross-sectional studies which cannot establish cause and effect temporal sequences, the CILS data set permits the identification of factors measured in early adolescence which predict arrest and incarceration outcomes in early adulthood. Most studies on crime and violence use cross sectional data, but understanding patterns of criminal offense over the life course requires panel data on childhood, adolescence, and adulthood experiences.
Broadband Optical Properties of Massive Galaxies: The Dispersion around the Field Galaxy Color-Magnitude Relation Out to z ∼ 0.4

Using a sample of nearly 20,000 massive early-type galaxies selected from the Sloan Digital Sky Survey, we study the color-magnitude relation for the most luminous (L ≳ 2.2L*) field galaxies in the redshift range 0.1 < z < 0.4 in several colors. The intrinsic dispersion in galaxy colors is quite small in all colors studied, but the 40 millimag (mmag) scatter in the bluest colors is a factor of 2 larger than the 20 mmag measured in the reddest bands. While each of three simple models constructed for the star formation history in these systems can satisfy the constraints placed by our measurements, none of them produce color distributions matching those observed. Subdividing by environment, we find the dispersion for galaxies in clusters to be about 11% smaller than that of more isolated systems. Finally, having resolved the red sequence, we study the color dependence of the composite spectra. Bluer galaxies on the red sequence are found to have more young stars than red galaxies; the extent of this spectral difference is marginally better described by passive evolution of an old stellar population than by a model consisting of a recent trace injection of young stars.
Truncations of level 1 of elements in the loop group of a reductive group

The aim of this article is to dene and study a new invariant of elements of loop groups that is invariant under -conjugation by a hyperspecial maximal open subgroup and that we call the truncation of level 1. We classify truncations of level 1 and describe their specialization behavior. Furthermore, we prove group-theoretic conditions for the set of -conjugacy classes obtained from elements of a given truncation of level 1 and in particular for the generic -conjugacy class in any given truncation stratum. In the last section we relate our invariant to the Ekedahl-Oort stratication of the Siegel moduli space and to generalizations to other PEL Shimura varieties.
Prespeech Vocalizations and the Emergence of Speech: A Study of 1005 Spanish Children

Abstract This study investigates 12 prespeech vocal behaviors which are taken to reflect children´s phonological, communicative and early symbolic development. It explores their development (onset, duration and extinction) and their relation to early lexical development. A structured parental questionnaire on prespeech vocalizations was developed, validated and used for the evaluation of 1005 Spanish children’s early vocal development (8–30 months). In parallel, the same children’s productive vocabulary was assessed using the vocabulary section of the European-Spanish MacArthur-Bates Communicative Development Inventories. Results highlight a global inverted U-shaped developmental pattern which emerges from the asynchronous development of the vocal behaviors examined, relating both their emergence and extinction to advances in linguistic development. Moreover, the protracted coexistence of prespeech vocalizations with early speech and their significant correlations with vocabulary size reveal a gradual transition into language. Overall results reinforce and extend previous findings on the development of prespeech vocalizations and establish their relevance as early indexes of linguistic development. Finally, positive evidence on the use of an assisted parental report method for reliably evaluating these developments is provided. Results are discussed within theoretical frameworks that conceive language as the emergent product of complex developmental processes.
Ergosterone-coupled Triazol molecules trigger mitochondrial dysfunction, oxidative stress, and acidocalcisomal Ca2+ release in Leishmania mexicana promastigotes

The protozoan parasite Leishmania causes a variety of sicknesses with different clinical manifestations known as leishmaniasis. The chemotherapy currently in use is not adequate because of their side effects, resistance occurrence, and recurrences. Investigations looking for new targets or new active molecules focus mainly on the disruption of parasite specific pathways. In this sense, ergosterol biosynthesis is one of the most attractive because it does not occur in mammals. Here, we report the synthesis of ergosterone coupled molecules and the characterization of their biological activity on Leishmania mexicana promastigotes. Molecule synthesis involved three steps: ergosterone formation using Jones oxidation, synthesis of Girard reagents, and coupling reaction. All compounds were obtained in good yield and high purity. Results show that ergosterone-triazol molecules (Erg-GTr and Erg-GTr2) exhibit an antiproliferative effect in low micromolar range with a selectivity index ~10 when compared to human dermic fibroblasts. Addition of Erg-GTr or Erg-GTr2 to parasites led to a rapid [Ca2+]cyt increase and acidocalcisomes alkalinization, indicating that Ca2+ was released from this organelle. Evaluation of cell death markers revealed some apoptosis-like indicators, as phosphatidylserine exposure, DNA damage, and cytosolic vacuolization and autophagy exacerbation. Furthermore, mitochondrion hyperpolarization and superoxide production increase were detected already 6 hours after drug addition, denoting that oxidative stress is implicated in triggering the observed phenotype. Taken together our results indicate that ergosterone-triazol coupled molecules induce a regulated cell death process in the parasite and may represent starting point molecules in the search of new chemotherapeutic agents to combat leishmaniasis.
A Design Technique for Concurrent Dual-Band Harmonic Tuned Power Amplifier

In this paper, a novel technique to design concurrent dual-band high-efficiency harmonic tuned (HT) power amplifiers (PAs) is presented. The proposed approach is based on a methodology developed to design multifrequency passive matching networks, which allows concurrent operability. The network design criterion is heavily investigated and later generalized both from the theoretical and practical point of view. The design, realization, and the complete characterization of a concurrent dual-band high-efficiency HT PA is finally described. A 1-mm gate periphery GaN HEMT device was used for the design and realization of the PA operating concurrently at 2.45 and 3.3 GHz. The measurement results have shown 53% and 46% drain efficiency at 33- and 32.5-dBm output power in the two targeted bands if operated in continuous wave single mode. In concurrent mode, 35% average efficiency was achieved with two simultaneously applied orthogonal frequency-division multiplexing signals.
OrthoDB v9.1: cataloging evolutionary and functional annotations for animal, fungal, plant, archaeal, bacterial and viral orthologs

OrthoDB is a comprehensive catalog of orthologs, genes inherited by extant species from a single gene in their last common ancestor. In 2016 OrthoDB reached its 9th release, growing to over 22 million genes from over 5000 species, now adding plants, archaea and viruses. In this update we focused on usability of this fast-growing wealth of data: updating the user and programmatic interfaces to browse and query the data, and further enhancing the already extensive integration of available gene functional annotations. Collating functional annotations from over 100 resources, and enabled us to propose descriptive titles for 87% of ortholog groups. Additionally, OrthoDB continues to provide computed evolutionary annotations and to allow user queries by sequence homology. The OrthoDB resource now enables users to generate publication-quality comparative genomics charts, as well as to upload, analyze and interactively explore their own private data. OrthoDB is available from http://orthodb.org.
Adrenoreceptors and nitric oxide in the cardiovascular system

Nitric Oxide (NO) is a small molecule that continues to attract much attention from the scientific community. Since its discovery, it has been evident that NO has a crucial role in the modulation of vascular tone. Moreover, NO is involved in multiple signal transduction pathways thus contributing to the regulation of many cellular functions. NO effects can be either dependent or independent on cGMP, and rely also upon several mechanisms such as the amount of NO, the compartmentalization of the enzymes responsible for its biosynthesis (NOS), and the local redox conditions. Several evidences highlighted the correlation among adrenoreceptors activity, vascular redox status and NO bioavailability. It was suggested a possible crosstalk between NO and oxidative stress hallmarks in the endothelium function and adaptation, and in sympathetic vasoconstriction control. Adrenergic vasoconstriction is a balance between a direct vasoconstrictive effect on smooth muscle and an indirect vasorelaxant action caused by α2- and β-adrenergic endothelial receptor-triggered NO release. An increased oxidative stress and a reduction of NO bioavailability shifts this equilibrium causing the enhanced vascular adrenergic responsiveness observed in hypertension. The activity of NOS contributes to manage the adrenergic pathway, thus supporting the idea that the endothelium might control or facilitate β-adrenergic effects on the vessels and the polymorphic variants in β2-receptors and NOS isoforms could influence aging, some pathological conditions and individual responses to drugs. This seems to be dependent, almost in part, on differences in the control of vascular tone exerted by NO. Given its involvement in such important mechanisms, the NO pathway is implicated in aging process and in both cardiovascular and non-cardiovascular conditions. Thus, it is essential to pinpoint NO involvement in the regulation of vascular tone for the effective clinical/therapeutic management of cardiovascular diseases (CVD).
Two-Stage Team Rent-Seeking: Experimental Analysis

This paper presents a two-stage team rent-seeking model with a contest prize that is not excludable among winning team members. When early effort is a perfect substitute for late effort, early actors can free ride on their late-moving teammates. However, when early and late efforts are complements, all team members exert positive effort levels. Asymmetries in early effort reduce effort choices for all late movers. The theory is tested with laboratory experimental methods. Although subjects overinvest relative to the Nash equilibrium in all treatments, chosen effort levels provide limited support for the model. Early movers exerted higher effort in the complement treatment, and second-stage effort choices were broadly consistent with best response functions. Surprisingly, in both single-shot and repeated play environments, early movers in the substitute treatment did not free ride, choosing effort levels similar to those of late movers.
Comparative Lipidomics in Clinical Isolates of Candida albicans Reveal Crosstalk between Mitochondria, Cell Wall Integrity and Azole Resistance

Prolonged usage of antifungal azoles which target enzymes involved in lipid biosynthesis invariably leads to the development of multi-drug resistance (MDR) in Candida albicans. We had earlier shown that membrane lipids and their fluidity are closely linked to the MDR phenomenon. In one of our recent studies involving comparative lipidomics between azole susceptible (AS) and azole resistant (AR) matched pair clinical isolates of C. albicans, we could not see consistent differences in the lipid profiles of AS and AR strains because they came from different patients and so in this study, we have used genetically related variant recovered from the same patient collected over a period of 2-years. During this time, the levels of fluconazole (FLC) resistance of the strain increased by over 200-fold. By comparing the lipid profiles of select isolates, we were able to observe gradual and statistically significant changes in several lipid classes, particularly in plasma membrane microdomain specific lipids such as mannosylinositolphosphorylceramides and ergosterol, and in a mitochondrial specific phosphoglyceride, phosphatidyl glycerol. Superimposed with these quantitative and qualitative changes in the lipid profiles, were simultaneous changes at the molecular lipid species levels which again coincided with the development of resistance to FLC. Reverse transcriptase-PCR of the key genes of the lipid metabolism validated lipidomic picture. Taken together, this study illustrates how the gradual corrective changes in Candida lipidome correspond to the development of FLC tolerance. Our study also shows a first instance of the mitochondrial membrane dysfunction and defective cell wall (CW) in clinical AR isolates of C. albicans, and provides evidence of a cross-talk between mitochondrial lipid homeostasis, CW integrity and azole tolerance.
Measuring confidence and uncertainty during the financial crisis: Evidence from the CFS survey

The CFS survey covers individual situations of banks and other companies of the financial sector. This provides a rare opportunity to analyse appraisals, expectations and forecast errors of the core sector of the recent financial crisis. Following standard ways of aggregating individual survey data, we first present and introduce the CFS survey by comparing CFS indicators of confidence and predicted confidence to Ifo and ZEW indicators. The major contribution is the analysis of several indicators of uncertainty. In addition to well-established concepts, we introduce innovative measures based on the skewness of forecast errors and on the share of “no response” replies. Results show that uncertainty indicators fit quite well with patterns of real and financial time series of the time period 2007 to 2010. [REPORT]