Miracle-dz/UniFAR-FTUs huggingface dataset:
Searching for Structure: Characterizing the Protein Conformational Landscape with Clustering-based Algorithms

The identification and characterization of the main conformations from a protein population is a challenging, inherently high-dimensional problem. We introduce the Secondary sTructural Ensembles with machine LeArning (StELa) double clustering method, which clusters protein structures based on the underlying Ramachandran plot. Our approach takes advantage of the relationship between the phi and psi dihedral angles in a protein backbone and the secondary structure of the protein. The classification of states as vectors composed of the clusters’ indices arising naturally from the Ramachandran plot, followed by the hierarchical clustering of the vectors, enables the identification of the minima from the corresponding free energy landscape (FEL) by lifting the high structure degeneracy found with existing approaches such as the RMSD-based clustering GROMOS. We compare the performance of StELa with not only GROMOS but also with CATS, the combinatorial averaged transient structure clustering method based on distributions of the phi and psi dihedral angle coordinates. Using ensembles of conformations from molecular dynamics (MD) simulations of either intrinsically disordered proteins (IDPs) of various lengths (tau protein fragments) or from local structures from a globular protein, we show that StELa is the only clustering method that identifies nearly all the minima from the corresponding FELs. In contrast, GROMOS yields a large number of clusters that cover the entire FEL and CATS, even with an additional clustering step, is unable to sample well the FEL for long IDPs and for fragments from globular proteins as it misses important minima. TOC Graphic
Mapping QTL for Yield and Its Component Traits Using Wheat (Triticum aestivum L.) RIL Mapping Population from TAM 113 × Gallagher

Understanding genetic architectures of yield and yield-related traits of wheat (Triticum aestivum L.) grown under dryland or irrigated conditions is pivotal for developing modern high-yielding germplasm and cultivars. The objectives of this study were to detect quantitative trait loci (QTL) linked to yield and yield components using a mapping population derived from ‘TAM 113’/‘Gallagher’, including 191 recombinant inbred lines (RILs). The population was grown in McGregor, College Station, and Bushland, Texas, for three consecutive years from 2019 to 2021. A high-density genetic map covering all 21 chromosomes was constructed using a set of 8,075 single nucleotide polymorphisms (SNPs) obtained using genotyping-by-sequencing (GBS). A total of 147 QTLs for 16 yield-related traits were identified, which included 16 QTLs consistently detected in multiple experiments and 8 QTLs that showed pleiotropic effects. Of them, five pleiotropic QTLs overlapped with the consistent QTL. They increased grain yield (YLD) up to 37.64 g m−2, thousand kernel weight (TKW) up to 1.33 g, harvest (HI) up to 0.97%, kernel length up to 0.08 mm, and kernel width up to 0.04 mm with Gallagher alleles and increased YLD up to 22.21 g m−2, kernels spike−1 up to 1.77, TKW up to 1.14 g, and HI up to 3.72% with TAM 113 alleles. One major and consistent QTL on chromosome 2D at 34.4 Mbp overlapped with the major photoperiod gene Ppd-D1 and was affected by multiple traits, including kernel diameter (DIAM), TKW, kernel hardness index (KHI), heading date (HD), and plant height (PH). Another QTL cluster region on 7D between 52 and 66 Mbp, encompassing one consistent and three pleiotropic QTLs. One of the pleiotropic QTLs at 52 Mbp increased YLD up to 24.16 g m−2, HI up to 1%, and DIAM up to 0.03 mm. This study dissected genetic loci associated with yield and yield-related traits, providing valuable information on wheat improvement using marker-assisted selection (MAS).
When controls matter: evidence of non-linear association between Internal Control Weaknesses and Audit Quality

ABSTRACT This study aimed to analyze the association between Internal Control Weaknesses (or Internal Control Deficiencies - ICDs) and Audit Quality (AQ). The article fills a gap in the national literature, as it provides evidence of an association between reported ICDs and the main AQ proxies. The study is relevant because it evinces the lack of contemporary association between reported ICDs and the AQ of listed Brazilian companies, but found a lagged association between these variables. Unlike prior studies, it was observed that the ICDs reported in the previous year can function as an Audit Red Flag in the current year, thus contributing to risk assessment by accountants, auditors, members of governance and audit committees, and regulators. The study, documentary and descriptive, with a quantitative approach, analyzed data from a sample of 257 companies listed on the Brazil Stock Exchange and Over-the-Counter Market (Brasil, Bolsa, Balcão [B3]) in the period 2010-2018. Data were assessed using regression models with panel data, logistic and negative binomial. The results showed that, although there are significant differences between the AQ proxies for companies that reported ICD and those that did not, there is no contemporary and statistically significant association between ICD disclosure and AQ proxies. However, it was observed that audit delay and the probability of being involved in an Administrative Sanctioning Procedure (ASP) are associated with the number of ICDs reported in the previous year.
Economics and Computation: An Introduction to Algorithmic Game Theory, Computational Social Choice, and Fair Division

This textbook connects three vibrant areas at the interface between economics and computer science: algorithmic game theory, computational social choice, and fair division. It thus offers an interdisciplinary treatment of collective decision making from an economic and computational perspective. Part I introduces to algorithmic game theory, focusing on both noncooperative and cooperative game theory. Part II introduces to computational social choice, focusing on both preference aggregation (voting) and judgment aggregation. Part III introduces to fair division, focusing on the division of both a single divisible resource ("cake-cutting") and multiple indivisible and unshareable resources ("multiagent resource allocation"). In all these parts, much weight is given to the algorithmic and complexity-theoretic aspects of problems arising in these areas, and the interconnections between the three parts are of central interest.
Insomnia and common mental disorder among patients with pre-existing chronic non-communicable diseases in southern Ethiopia: a survey during COVID-19 pandemic

Background COVID-19 has been causing significant mental health problems and other health-related issues. Despite the fact that COVID-19 has a significant impact on chronic disease patients, there is scant research on insomnia, common mental health disorders (CMD), and their associated factors among chronic disease patients. Objective The purpose of this study was to assess the prevalence of insomnia and common mental disorders (CMD) and their associated factors among patients with pre-existing chronic NCDs in Sidama, southern Ethiopia. Methods A multicenter cross-sectional study was undertaken between June 1 and September 1, 2021. The study included 633 participants. CMD and insomnia were assessed using a 20-item Self-Reported Questionnaire (SRQ-20) and a 7—item Insomnia Severity Index (ISI) scale, respectively. To describe the various variables, descriptive statistics were used. We performed multivariable logistic regression analysis to identify independent factors associated with CMD and insomnia. A value of p < 0.05 was considered statistically significant at a 95% confidence interval. Results The prevalence of insomnia and CMD was found to be 39.3% and 46.8%, respectively. Being merchant (AOR = 0.33; 95% CI = 0.13, 0.82), having a diagnosis of diabetes mellitus (AOR = 1.89; 95% CI = 1.04, 3.46), comorbid diagnosis (AOR = 3.96; 95% CI = 2.27, 6.89), low social support (poor (AOR = 3.37; 95% CI = 1.51, 7.57) and moderate (AOR = 3.13; 95% CI = 1.46, 6.69)), symptoms of insomnia (AOR = 12.08; 95% CI = 7.41, 19.72) and poor quality of life (QOL) (AOR = 1.67; 95% CI = 1.04, 2.72) were independent predictors of CMD. We also found out that, having cardiovascular disorders (CVDs) (AOR = 2.48; 95% CI = 1.18, 5.19), CMD (AOR = 12.09; 95% CI = 7.46, 19.61), and poor QOL (AOR = 2.04; 95% CI = 1.27, 3.26) were significantly associated with insomnia symptoms. Conclusion Our study suggests that substantially high prevalence of CMD and insomnia. Significant association between CMD and occupation, diagnosis, comorbidity, social support, insomnia, and QOL were found. We also revealed that having CVDs, CMD, and poor QOL were significantly associated with insomnia symptoms. Therefore, dealing with the mental health problems of patients with chronic NCDs is an essential component of public health intervention during the COVID-19 pandemic.
Coexistent GLIM-Defined Malnutrition and Sarcopenia Increase the Long-Term Mortality Risk in Hospitalized Patients with Decompensated Cirrhosis

Introduction: The synergistic impact of coexistent malnutrition and sarcopenia on morality in hospitalized patients with decompensated cirrhosis remains elusive. This prospective cohort study aimed to delineate the prevalence concerning coexistence of malnutrition and sarcopenia and the prognosticating role on long-term mortality among cirrhosis. Methods: Adult cirrhotic patients with decompensated episodes between 2019 and 2021 were consecutively enrolled. Malnutrition and sarcopenia were diagnosed according to the Global Leadership Initiative on Malnutrition (GLIM) criteria and the European Working Group on Sarcopenia in Older People (EWGSOP2) algorithm, respectively. The entire cohort was divided into three groups: non-malnutrition and non-sarcopenia (NN), malnutrition or sarcopenia, and coexistent malnutrition and sarcopenia (MS). Log-rank test and multivariate Cox regression model were utilized to evaluate survival status and independent risk factors for mortality, respectively. Results: Our findings indicated that malnutrition manifested in 44.6% of inpatients with decompensated cirrhosis, while sarcopenia presented in 16.4% of the entire cohort, indicative of a prevalence of 14.7% regarding coexistent malnutrition and sarcopenia. The Kaplan-Meier graphic demonstrated a significant difference regarding survival curves among the three groups, referring to the MS group presented with the lowest survival rate (log-rank test: p < 0.001). Moreover, coexistent malnutrition and sarcopenia were associated with nearly 4 times higher mortality risk (model 1: hazard ratio [HR] = 3.31, 95% confidence interval [CI]: 1.20–9.13, p = 0.020; model 2: HR = 4.34, 95% CI: 1.52–12.4, p = 0.006) in comparison with patients without any condition (NN group). Conclusions: Malnutrition and sarcopenia had superimposed negative impacts on inpatients with decompensated cirrhosis. It is imperative to identify this vulnerable subset to provide prompt therapeutic intervention for better prognosis.
Seas at the Millennium: An Environmental Evaluation

Part 1 The seas around Greenland, (F. Riget et al.) Norwegian coast, (J. Skei et al.) The Faroe Islands, (M. Dam et al.) The North Sea, (J.-P. Ducrotoy et al.) The English Channel, (A.D. Tappin, P.C. Reid) The Irish Sea, (R. Hartnoll) The Baltic Sea - especially southern and eastern regions, (J. Falandysz et al.) Baltic Sea, including Bothnian Sea and Bothnian Bay, (L. Kautsky, N. Kautsky) North coast of Spain, (I. Diez et al.) Southern Portugal - the Tagus and Sado estuaries, (G. Cabe adas et al.) Atlantic coast of southern Spain, (C.J. Luque et al.) The Canary Islands, (F. Garcia Montelongo et al.) The Azores, (B. Morton, J.C. Britton) Sargasso Sea and Bermuda, (A.H. Knap et al.) The Aegean Sea, (M. Dassenakis et al.) The coast of Israel, SE Mediterranean, (B. Herut, B. Galil) Adriatic Sea and Tyrrhenian Sea, (G. Cognetti et al.) Black Sea (G. Bakan, H. Buyukgungar). Gulf of Maine Nova Scotia to Cape Cod (J. Pearce). New York Bight, (J. Pearce) Chesapeake Bay - the United States' largest estuarine system, (K. Mountford) North and South Carolina coasts, (M.A. Mallin et al.) Gulf of Alaska, (B.A. Wright et al.) Southern California, (K.C. Schiff et al.) Florida Keys, (P. Dustan) Bahamas (K.C. Buchan). The northern Gulf of Mexico, (M.E. Pattillo, D.M. Nelson) Coastal management in Latin America, (A. Yanez-Arancibia) Southern Gulf of Mexico, (G.F. Vazquez et al.) Pacific coast of Mexico, (A.V. Botello et al.) Belize, (A.R. Harborne et al.) Nicaragua: Caribbean coast, (S.C. Jameson et al.) Nicaragua: Pacific coast, (S.C. Jameson et al.) El Salvador, (L. Cotsapas et al.) Jamaica, (M. Vierros) Puerto Rico, (J. Morelock et al.). (Part contents).
Opposing Effects on Descending Control of Nociception by µ and κ Opioid Receptors in the Anterior Cingulate Cortex

Background: The efficiency of descending pain modulation, commonly assessed with the conditioned pain modulation procedure, is diminished in patients with chronic pain. The authors hypothesized that the efficiency of pain modulation is controlled by cortical opioid circuits. Methods: This study evaluated the effects of µ opioid receptor activation in the anterior cingulate cortex on descending control of nociception, a preclinical correlate of conditioned pain modulation, in male Sprague-Dawley rats with spinal nerve ligation–induced chronic pain or in sham-operated controls. Additionally, the study explored the consequences of respective activation or inhibition of κ opioid receptor in the anterior cingulate cortex of naive rats or animals with neuropathic pain. Descending control of nociception was measured as the hind paw withdrawal response to noxious pressure (test stimulus) in the absence or presence of capsaicin injection in the forepaw (conditioning stimulus). Results: Descending control of nociception was diminished in the ipsilateral, but not contralateral, hind paw of rats with spinal nerve ligation. Bilateral administration of morphine in the anterior cingulate cortex had no effect in shams but restored diminished descending control of nociception without altering hypersensitivity in rats with neuropathic pain. Bilateral anterior cingulate cortex microinjection of κ opioid receptor antagonists, including nor-binaltorphimine and navacaprant, also re-established descending control of nociception in rats with neuropathic pain without altering hypersensitivity and with no effect in shams. Conversely, bilateral injection of a κ opioid receptor agonist, U69,593, in the anterior cingulate cortex of naive rats inhibited descending control of nociception without altering withdrawal thresholds. Conclusions: Anterior cingulate cortex κ opioid receptor activation therefore diminishes descending control of nociception both in naive animals and as an adaptive response to chronic pain, likely by enhancing net descending facilitation. Descending control of nociception can be restored by activation of μ opioid receptors in the anterior cingulate cortex, but also by κ opioid receptor antagonists, providing a nonaddictive alternative to opioid analgesics. Navacaprant is now in advanced clinical trials. Microinjection of κ opioid receptor antagonists into the anterior cingulate cortex of nerve injured rats restored descending control of nociception, an endogenous pain control circuit. Microinjection of selective κ opioid receptor agonists reduced descending control of nociception in sham injured rats confirming the importance of the κ opioid receptor in regulating endogenous pain control.
Extreme Sea Level Analysis in Coastal Waters around Korean Peninsula Using Empirical Simulation Technique

The estimation of the extreme sea level is necessary in the design of offshore or coastal structures. In this paper, the storm surge data calculated numerically at 52 harbors around the Korean Peninsula are analyzed by using annual maximum series(AMS), peaks over threshold(POT) and empirical simulation technique(EST). The maximum likelihood method was used to estimate the parameters in both AMS and POT models. The Generalized Pareto distribution was used and Chi-square and Kolmogorov-Smirnov goodness-of-fit tests were performed with the acceptable significance level 5%. The extreme sea levels were also evaluated by EST including tide effect, showing similar results as given by Jeong et al.(2008).
Range expansion is both slower and more variable with rapid evolution across a spatial gradient in temperature

Rapid evolution in colonizing populations can alter our ability to predict future range expansions. Recent theory suggests that the dynamics of replicate range expansions are less variable, and hence more predictable, with increased selection at the expanding range front. Here, we test whether selection from environmental gradients across space produces more consistent range expansion speeds, using the experimental evolution of replicate duckweed populations colonizing landscapes with and without a temperature gradient. We found that range expansion across a temperature gradient was slower on average, with range-front populations displaying higher population densities, and genetic signatures and trait changes consistent with directional selection. Despite this, we found that with a spatial gradient range expansion speed became more variable and less consistent among replicates over time. Our results therefore challenge current theory, highlighting that chance can still shape the genetic response to selection to influence our ability to predict range expansion speeds.
Effects of management objectives and rules on marine conservation outcomes

Understanding the relative effectiveness and enabling conditions of different area‐based management tools is essential for supporting efforts that achieve positive biodiversity outcomes as area‐based conservation coverage increases to meet newly set international targets. We used data from a coastal social–ecological monitoring program in 6 Indo‐Pacific countries to analyze whether social, ecological, and economic objectives and specific management rules (temporal closures, fishing gear‐specific, species‐specific restrictions) were associated with coral reef fish biomass above sustainable yield levels across different types of area‐based management tools (i.e., comparing those designated as marine protected areas [MPAs] with other types of area‐based management). All categories of objectives, multiple combinations of rules, and all types of area‐based management had some sites that were able to sustain high levels of reef fish biomass—a key measure for coral reef functioning—compared with reference sites with no area‐based management. Yet, the same management types also had sites with low biomass. As governments advance their commitments to the Kunming–Montreal Global Biodiversity Framework and the target to conserve 30% of the planet's land and oceans by 2030, we found that although different types of management can be effective, most of the managed areas in our study regions did not meet criteria for effectiveness. These findings underscore the importance of strong management and governance of managed areas and the need to measure the ecological impact of area‐based management rather than counting areas because of their designation.
Axial Length Control Is Associated With a Choroidal Thickness Increase in Myopic Adolescents After Orthokeratology

Supplemental Digital Content is Available in the Text. Objective: To investigate the changes in choroidal thickness and axial length after orthokeratology in adolescents with low-to-moderate myopia and to explore the relationship between choroidal thickness and axial length variation. Methods: Thirty eyes with low-to-moderate myopia were retrospectively studied, and optometric data were collected before and after 6 months of continuous orthokeratology. Axial length and choroidal and foveal thicknesses were measured using optical biometry and enhanced depth imaging–spectral domain optical coherence tomography, respectively. Results: Axial length in the low myopia group increased (P<0.001) after 6 months of orthokeratology, and the variation was greater than that in the moderate myopia group (P<0.05). The subfoveal choroidal thickness in low and moderate myopia groups increased (P<0.01), and the variation was greater in the moderate myopia group (P<0.05). Choroidal thickness in all seven measured spots increased, with the variation of subfovea, nasal 1 mm to fovea, and temporal 1 mm to fovea being statistically significant (P<0.001, P<0.05, and P<0.05). The change in axial length was negatively associated with subfoveal and average choroidal thicknesses (P<0.01). Conclusion: Adolescents with moderate myopia presented better axial length control after 6 months of orthokeratology. The choroidal thickness of low and moderate myopic eyes increased, and the variation was more significant in moderate myopic eyes. The axial length control effects can be associated with an increase in the subfoveal and average choroidal thickness.
The coreceptor CD 2 uses plasma membrane microdomains to transduce signals in T cells

The Rockefeller University Press $30.00 J. Cell Biol. www.jcb. org/cgi/doi/10.1083/jcb.200809136 Cite by DOI: 10.1083/jcb.200809136 JCB 1 of 14 Correspondence to Ronald D. Vale: vale@cmp.ucsf. edu Abbreviations used in this paper: APC, antigen-presenting cell; cSMAC, central SMAC; CTB, cholera toxin subunit B; GPI, glycosylphosphatidylinositol; ITAM, immunoreceptor tyrosine-based activation motif; SMAC, supramolecular activation cluster; TCR, T cell receptor; TIRF, total internal reflection fluorescence. Introduction
Ecology and palaeoecology of benthic foraminifera

Life processes stable isotope studies population dynamics relationship between living and dead assemblages Atlantic seaboard of North America gulf of Mexico and Caribbean Atlantic seaboard of South America Atlantic seaboard of Europe and Africa Atlantic ocean Mediterranean Indian ocean western margin of the Pacific ocean eastern margin of the Pacific ocean Pacific ocean Southern ocean Arctic ocean summary of modern distribution patterns and characteristics of assemblages palaeoecology. Appendices: methods ecological data for selected genera faunal reference list.