Miracle-dz/UniFAR-FTUs huggingface dataset:
A geometric algorithm to find small but highly similar 3D substructures in proteins

MOTIVATION Most biological actions of proteins depend on some typical parts of their three-dimensional structure, called 3D motifs. It is desirable to find automatically common geometric substructures between proteins to discover similarities in new structures or to model precisely a particular motif. Most algorithms for structural comparison of proteins deal with large (fold) similarities. Here, we focus on small but precise similarities. RESULTS We propose a new 3D substructure matching algorithm based on geometric hashing techniques. The key feature of the method is the introduction of a 3D reference frame attached to each residue. This allows us to reduce drastically the complexity of the recognition. Our experimental results confirm the validity of the approach and allow us to find smaller similarities than previous methods. AVAILABILITY The program uses commercial libraries and thus cannot be completely freely distributed. It can be found at ftp://www.inria. fr in the directory epidaure/Outgoing/xpennec/Prospect, but it requires a key to be run, available by request to xavier.pennec@sophia.inria. fr CONTACT Xavier.Pennec@sophia.inria. fr; Nicholas.Ayache@sophia.inria. fr
Prevalence and Associated Factors of Hypertension among Adults in Durame Town, Southern Ethiopia

Background To date, non-communicable diseases, such as cardiovascular diseases, are becoming severe public health challenges particularly in developing countries. Hypertension is a modifiable risk factor that contributes the leading role for mortality. The problem is significant in low- and middle-income countries like sub-Saharan Africa. However, there are limited studies in developing countries, particularly in Ethiopia. Hence, determining the magnitude of hypertension and identifying risk groups are important. Methods A community based cross sectional study was conducted in April 2013 among adults (age>31 years) old. A systematic sampling technique was used to select a total of 518 study participants. Data were collected after full verbal informed consent was obtained from each participant. Multivariable logistic regressions were fitted to control the effect of confounding. Adjusted Odds ratios (OR) with their 95% confidence intervals (95% CI) were calculated to measure associations. Variables having P-value <0.05 were considered as significant. Results The overall prevalence of hypertension in Durame town was 22.4% (95% CI: 18.8–26.0). Nearly 40% of hypertensive patients were newly screened. Male sex [AOR = 2.03, 95% CI; 1.05–3.93], age [AOR = 29.49, 95% CI; 10.60–81.27], salt use [AOR = 6.55, 95% CI; 2.31–18.53], eating vegetable three or fewer days per week [AOR = 2.3,95% CI; 1.17–4.51], not continuously walking at least for 10 minutes per day [AOR = 7.82, 95% CI; 2.37–25.82], having family history of hypertension [AOR = 2.46, 95%CI; 1.31–4.61] and being overweight/obese [AOR = 15.7, 95% CI 7.89–31.21)] were found to be risk factors for hypertension. Conclusions The prevalence of hypertension is found to be high. Older age, male sex, having family history of hypertension, physical inactivity, poor vegetable diet, additional salt consumption and obesity were important risk factors associated with hypertension among adults. Community level intervention measures with a particular emphasis on prevention by introducing lifestyle modifications are recommended.
Interannual variability of long-range transport as seen at the Mt. Bachelor observatory

Interannual variations in background tropospheric trace gases (such as carbon monoxide, CO) are largely driven by variations in emissions (especially wildfires) and trans- port pathways. Understanding this variability is essential to quantify the intercontinental contribution to US air quality. We investigate the interannual variability of long-range trans- port of Asian pollutants to the Northeast Pacific via measure- ments from the Mt. Bachelor Observatory (MBO: 43.98 N, 121.69 W; 2.7 km a.s.l.) and GEOS-Chem chemical trans- port model simulations in spring 2005 vs. the INTEX-B cam- paign during spring 2006. Measurements of CO at MBO were significantly enhanced during spring 2005 relative to the same time in 2006 (the INTEX-B study period); a de- cline in monthly mean CO of 41 ppbv was observed between April 2005 and April 2006. A backtrajectory-based meteoro- logical index shows that long-range transport of CO from the heavily industrialized region of East Asia was significantly greater in early spring 2005 than in 2006. In addition, spring 2005 was an anomalously strong biomass burning season in Southeast Asia. Data presented by Yurganov et al. (2008) using MOPITT satellite retrievals from this area reveal an average CO burden anomaly (referenced to March 2000- February 2002 mean values) between October 2004 through April 2005 of 2.6 Tg CO vs. 0.6 Tg CO for the same period a year later. The Naval Research Laboratory's global aerosol transport model, as well as winds from NCEP reanalysis, show that emissions from these fires were efficiently trans- ported to MBO throughout April 2005. Asian dust trans- port, however, was substantially greater in 2006 than 2005, particularly in May. Monthly mean aerosol light scattering coefficient at 532 nm ( sp) at MBO more than doubled from 2.7 Mm 1 in May 2005 to 6.2 Mm 1 in May 2006. We also evaluate CO interannual variability throughout the western US via Earth System Research Laboratory ground site data and throughout the Northern Hemisphere via MOPITT and TES satellite observations. Both in the Northeast Pacific and on larger scales, we reveal a significant decrease (from 2- 21%) in springtime maximum CO between 2005 and 2006, evident in all platforms and the GEOS-Chem model. We attribute this to (a) anomalously strong biomass burning in Southeast Asia during winter 2004 through spring 2005, and (b) the transport pattern in March and April 2006 which lim- ited the inflow of Asian pollution to the lower free tropo- sphere over western North America.
ACE2 Deficiency Enhances Angiotensin II-Mediated Aortic Profilin-1 Expression, Inflammation and Peroxynitrite Production

Inflammation and oxidative stress play a crucial role in angiotensin (Ang) II-mediated vascular injury. Angiotensin-converting enzyme 2 (ACE2) has recently been identified as a specific Ang II-degrading enzyme but its role in vascular biology remains elusive. We hypothesized that loss of ACE2 would facilitate Ang II-mediated vascular inflammation and peroxynitrite production. 10-week wildtype (WT, Ace2+/y) and ACE2 knockout (ACE2KO, Ace2−/y) mice received with mini-osmotic pumps with Ang II (1.5 mg.kg−1.d−1) or saline for 2 weeks. Aortic ACE2 protein was obviously reduced in WT mice in response to Ang II related to increases in profilin-1 protein and plasma levels of Ang II and Ang-(1–7). Loss of ACE2 resulted in greater increases in Ang II-induced mRNA expressions of inflammatory cytokines monocyte chemoattractant protein-1 (MCP-1), interleukin (IL)-1β, and IL-6 without affecting tumor necrosis factor-α in aortas of ACE2KO mice. Furthermore, ACE2 deficiency led to greater increases in Ang II-mediated profilin-1 expression, NADPH oxidase activity, and superoxide and peroxynitrite production in the aortas of ACE2KO mice associated with enhanced phosphorylated levels of Akt, p70S6 kinase, extracellular signal-regulated kinases (ERK1/2) and endothelial nitric oxide synthase (eNOS). Interestingly, daily treatment with AT1 receptor blocker irbesartan (50 mg/kg) significantly prevented Ang II-mediated aortic profilin-1 expression, inflammation, and peroxynitrite production in WT mice with enhanced ACE2 levels and the suppression of the Akt-ERK-eNOS signaling pathways. Our findings reveal that ACE2 deficiency worsens Ang II-mediated aortic inflammation and peroxynitrite production associated with the augmentation of profilin-1 expression and the activation of the Akt-ERK-eNOS signaling, suggesting potential therapeutic approaches by enhancing ACE2 action for patients with vascular diseases.
Sex-specific foraging behavior in response to fishing activities in a threatened seabird

Some seabird species have learnt to efficiently exploit fishing discards from trawling activities. However, a discard ban has been proposed as necessary in Europe to ensure the sustainability of the seas. It is of crucial importance for the management and conservation purposes to study the potential consequences of a discard ban on the foraging ecology of threatened seabirds. We assessed the influence of fishing activities on the feeding habits of 22 male and 15 female Audouin's gulls (Larus audouinii) from the Ebro Delta (Mediterranean Sea) during the breeding period using GPS loggers together with Stable Isotope Analysis (SIA), which provided new insights into their foraging behavior and trophic ecology, respectively. GPS data revealed different sex-specific foraging patterns between workdays and weekends. Females were highly consistent in that they foraged at sea throughout the week even though discarding stops at weekends. In contrast, males switched from foraging at sea during the week (when discards are produced) to an increased use of rice field habitats at weekends (when fishermen do not work). This sex-specific foraging behavior could be related to specific nutritional requirements associated with previous egg production, an energetically demanding period for females. However, on a broader time scale integrated by the SIA, both sexes showed a high degree of individual specialization in their trophic ecology. The need to obtain detailed information on the dependence and response of seabirds to fishing activities is crucial in conservation sciences. In this regard, sex-specific foraging behavior in relation to fisheries has been overlooked, despite the ecological and conservation implications. For instance, this situation may lead to sex differentiation in bycatch mortality in longlines when trawlers do not operate. Moreover, any new fisheries policy will need to be implemented gradually to facilitate the adaptation of a specialized species to a discard ban scenario.
Recognition Techniques for Online Arabic Handwriting Recognition Systems

Online recognition of Arabic handwritten text has been an on-going research problem for many years. Generally, online text recognition field has been gaining more interest lately due to the increasing popularity of hand-held computers, digital notebooks and advanced cellular phones. However, different techniques have been used to build several online handwritten recognition systems for Arabic text, such as Neural Networks, Hidden Markov Model, Template Matching and others. Most of the researches on online text recognition have divided the recognition system into these three main phases which are preprocessing phase, feature extraction phase and recognition phase which considers as the most important phase and the heart of the whole system. This paper presents and compares techniques that have been used to recognize the Arabic handwriting scripts in online recognition systems. Those techniques attempt to recognize Arabic handwritten words, characters, digits or strokes. The structure and strategy of those reviewed techniques are explained in this article. The strengths and weaknesses of using these techniques will also be discussed.
Speech recognition by normal-hearing and cochlear implant listeners as a function of intensity resolution.

The importance of intensity resolution in terms of the number of intensity steps needed for speech recognition was assessed for normal-hearing and cochlear implant listeners. In experiment 1, the channel amplitudes extracted from a six-channel continuous interleaved sampling (CIS) processor were quantized into 2, 4, 8, 16, or 32 steps. Consonant recognition was assessed for five cochlear implant listeners, using the Med-El/CIS-link device, as a function of the number of steps in the electrical dynamic range. Results showed that eight steps within the dynamic range are sufficient for reaching asymptotic performance in consonant recognition. These results suggest that amplitude resolution is not a major factor in determining consonant identification. In experiment 2, the relationship between spectral resolution (number of channels) and intensity resolution (number of steps) in normal-hearing listeners was investigated. Speech was filtered through 4-20 frequency bands, synthesized as a linear combination of sine waves with amplitudes extracted from the envelopes of the bandpassed waveforms, and then quantized into 2-32 levels to produce stimuli with varying degrees of intensity resolution. Results showed that the number of steps needed to achieve asymptotic performance was a function of the number of channels and the speech material used. For vowels, asymptotic performance was obtained with four steps, while for consonants, eight steps were needed for most channel conditions, consistent with our findings in experiment 1. For sentences processed though 4 channels, 16 steps were needed to reach asymptotic performance, while for sentences processed through 16 channels, 4 steps were needed. The results with normal-hearing listeners on sentence recognition point to an inverse relationship between spectral resolution and intensity resolution. When spectral resolution is poor (i.e., a small number of channels is available) a relatively fine intensity resolution is needed to achieve high levels of understanding. Conversely, when the intensity resolution is poor, a high degree of spectral resolution is needed to achieve asymptotic performance. The results of this study, taken together with previous findings on the effect of reduced dynamic range, suggest that the performance of cochlear implant subjects is primarily limited by the small number (four to six) of channels received, and not by the small number of intensity steps or reduced dynamic range.
“The efficiency of alternative control mechanisms in a MTO three-stage tandem production/inventory system”

In this work we develop a SD model for a make-to-order (MTO) three-stage capacitated production/inventory system. We employ a production order release mechanism affiliated with the automated pipeline inventory and order based production control system (APIOBPCS) policies family. The production rates at each stage are defined under alternative policies. One of the policies considers the human behavior in the decision making process. The robustness of the alternative policies is investigated through the dynamic response of the system under step and pulse changes in demand. Finally, the efficiency of the alternative policies is examined by means of six performance criteria.
Exchange Rate Regimes, Foreign Exchange Volatility, and Export Performance in Central and Eastern Europe: Just Another Blur Project?

This paper attempts to analyze the direct impact of exchange rate volatility on the export performance of ten Central and Eastern European transition economies as well as its indirect impact via changes in exchange rate regimes. Not only aggregate but also bilateral and sectoral export flows are studied. To this end, we first analyze shifts in exchange rate volatility linked to changes in the exchange rate regimes and second, use these changes to construct dummy variables we include in our export function. The results suggest that the size and the direction of the impact of forex volatility and of regime changes on exports vary considerably across sectors and countries and that they may be related to specific periods.
An Approach to Control of Human Leg Switched Dynamics

This article describes the approach to control of human leg dynamical model as a switched linear system. The control scheme consists of fractional and integral order PID controllers. In the paper we analyze the responses of the system depending on the above-mentioned controllers. We focus our attention on angular displacements only. The angular velocity maybe arbitrary. Additionally, we present the method how to design a human leg as the switched linear system. In this case the switching rule is state-dependent. Finally, we present two illustrative examples for two different trajectories.
Second-harmonic generation in optically trapped nonlinear particles with pulsed lasers.

Pulsed lasers are used for simultaneous single-beam three-dimensional optical trapping of and second-harmonic generation in 50-100-nm nonlinear particles. The emission power of the frequency-doubled light, the trapping stability, and the particle degradation are investigated for KTP and LiNbO(3) particles trapped by 25-kHz-repetition-rate Q-switched Nd:YAG and 76-MHz mode-locked Ti:sapphire l a s e r s . Typically 1 pW-10 nW of frequency-doubled light is detected from stably trapped particles. The particles may be used as probes for nonintrusively scanned near-field optical microscopy.
Comparison of MMPI-A Characteristics of Adolescent Sex Offenders and Juvenile Delinquents

In this study, scores on the Minnesota Multiphasic Personality Inventory for Adolescents (MMPI-A) were compared between two groups of juvenile delinquents: those who have been charged with sexually based offenses and those who have not. Through analysis of personality profiles as assessed by this test, this study sought to determine what differences there were, if any, between adolescents who have been adjudicated for sexual offenses as opposed to their non-sex offending peers. The final sample consisted of 542 juvenile delinquents, ages 12-18, involved in Department of Juvenile Justice treatment programs in northern Florida. This sample was divided into sex offenders (n=79) and non-sex offenders (n=463) based on current and past charges. We hypothesized that sexual offenders would have higher scores on scales indicating difficulty relating to peers (e.g. depression, social introversion) and that non-sex offenders would score higher on measures indicating difficulty aligning with authority. Results of statistical analysis supported our first hypothesis, revealing two significant differences between delinquent groups on scale 0 (Social Introversion) and scale 7 (Psychasthenia). There were also notable differences on several of the Harris-Lingoes subscales, further indicating that sexual offenders exhibit more shy and introverted personalities than their non-sex offending counterparts. There were no differences directly supporting our second hypothesis. These findings indicate that there may be salient differences in peer interaction styles between these two groups of offenders. With this knowledge, assessment and treatment could focus more attention on the salient personality characteristics found when using broad measures of personality and address the social introversion found in sex offenders. ( en )
Variability and Consistency in the Idiosyncratic Selection of Fillers in Japanese Monologues: Gender Differences

This study is a linguistic study on idiosyncrasy using speaker classification technique as an analytical tool. The goals of this study are to find out 1) to what extent Japanese filler words (e.g. um, you know in English) carry individual idiosyncratic information; 2) if there are any differences in the degree/nature of idiosyncrasy between the sexes; and 3) what contributes to the identified gender differences, if there are any. Based purely on the individual selection of fillers, we report in this study that 1) speaker discrimination performance was better in the male (ca. 85% accuracy) than the female (ca. 75% accuracy) speakers by approximately 10%, and 2) the poorer performance of the female speakers was due to the larger within– speaker differences in the female speakers than the male speakers. That is, the selection of fillers by female speakers is more variable, speech by speech, than that by male speakers, even under similar conditions (e.g. same type of audience and the same degree of formality). We also discuss that the findings of the current study agree with the previously–reported differences between the sexes in language use.
Faceting Artifact Analysis for Computer Graphics

The faceting signal, defined in this paper as the difference signal between a rendering of the original geometric model and a simplified version of the geometric model, is responsible for the faceting artifacts commonly observed in the renderings of coarse geometric models. In this paper, we analyze the source of the faceting signal and develop a perceptual metric for the visibility of the faceting signal.
The role of radiation in organizing convection in weak temperature gradient simulations

Using a cloud system resolving model with the large scale parameterized by the weak temperature gradient approximation, we investigated the influence of interactive versus noninteractive radiation on the characteristics of convection and convective organization. The characteristics of convecting environments are insensitive to whether radiation is interactive compared to when it is not. This is not the case for nonconvecting environments; interactive radiative cooling profiles show strong cooling at the top of the boundary layer which induces a boundary layer circulation that ultimately exports moist entropy (or analogously moist static energy) from dry domains. This upgradient transport is associated with a negative gross moist stability, and it is analogous to boundary layer circulations in radiative convective equilibrium simulations of convective self‐aggregation. This only occurs when radiation cools interactively. Whether radiation is static or interactive also affects the existence of multiple equilibria‐steady states which either support precipitating convection or which remain completely dry depending on the initial moisture profile. Interactive radiation drastically increases the range of parameters which permit multiple equilibria compared to static radiation; this is consistent with the observation that self‐aggregation in radiative‐convective equilibrium simulations is more readily attained with interactive radiation. However, the existence of multiple equilibria in absence of interactive radiation suggests that other mechanisms may result in organization.
Strategic capacity choice under uncertainty: the impact of market structure on investment and welfare

We analyze a market game where firms choose capacities under uncertainty about future market conditions and make output choices after uncertainty has unraveled. We show existence and uniqueness of equilibrium under imperfect competition and establish that capacity choices by strategic firms are generally too low from a welfare point of view. We also demonstrate that strategic firms choose even lower capacities if they anticipate competitive spot market pricing (e.g. due to regulatory intervention). We finally illustrate how the model can be used to assess the impact of electricity market liberalization on total capacity and welfare by fitting it to the data of the German electricity market.