Miracle-dz/UniFAR-FTUs huggingface dataset:
Full length amylin oligomer aggregation: insights from molecular dynamics simulations and implications for design of aggregation inhibitors

Amyloid oligomers are considered to play essential roles in the pathogenesis of amyloid-related degenerative diseases including type 2 diabetes. Using an explicit solvent all atomic MD simulation, we explored the stability, conformational dynamics and association force of different single-layer models of the full-length wild-type and glycine mutants of amylin (pentamer) obtained from a recent high resolution fibril model. The RMSF profile shows enhanced flexibility in the disorder (Lys1-Cys7) and turn region (Ser19-Gly23), along with smallest fluctuation at the residues (Asn14-Phe15-Leu16-Val17-His18) of β1 region and (Ala25-Ile26-Leu27-Ser28-Ser29) of the β2 region. We obtained a significant difference in backbone RMSD between the wild-type and the mutants, indicating that mutations affected the stability of the peptide. The RMSD and RMSF profiles indicate the edge and loop residues are the primary contributors to the overall conformational changes. The degree of structural similarity between the oligomers in the simulation and the fibril conformation is proposed as the possible explanation for experimentally observed shortening of the nucleation lag phase of amylin with oligomer seeding. On the basis of structure-stability findings, the β1 and β2 portions are optimal target for further anti-amyloid drug design. The MM-PBSA binding energy calculation reveals the binding of amylin: amylin strands in single layer is dominated by contributions from van der Waals interactions. The non-polar solvation term is also found to be favorable. While the electrostatic interactions and polar solvation energy was found to be favorable for the interaction for the larger aggregate and unfavorable for the smaller aggregates. A per-residue decomposition of the binding free energy has been performed to identify the residues contributing most to the self-association free energy. Residues found in the β-sheet regions were found to be key residue making the largest favorable contributions to the single-layer association. The result from our simulation could be used in rational design of new amylinomimetic agent, amylin aggregation inhibitors and amylin-specific biomarkers.
Takotsubo syndrome in a patient after renal transplantation

Summary Background Takotsubo syndrome (TTS) is a transient cardiomyopathy of unknown origin, clinically manifesting as acute coronary syndrome (ACS). This syndrome mainly occurs in postmenopausal women and has a temporary relationship with emotional or physical stress. Case Report TTS occurred in 46-year-old female patient on the first day after renal transplantation. The predominant symptoms were connected with ACS, performed with low grade troponin elevation and characteristic shape of left ventricle depicted in echocardiography. Taking into consideration the risk of the development of contrast-induced nephropathy, coronary angiography (CA) was delayed; myocardial perfusion scintigraphy and iodine-123 metaiodobenzylguanidine (123I-mIBG) myocardial uptake were performed to confirm the clinical suspicion. Myocardial perfusion scintigraphy (MPS) performed in rest condition showed normal perfusion but myocardial uptake of 123I-mIBG was impaired. Within 6 months after surgery, full recovery of all biochemical and functional parameters of the left ventricle were observed. At that time CA was done, depicting normal coronary arteries. Conclusions TTS could be diagnosed by the use of non-nephrotoxic tests – 123I-mIBG myocardial scintigraphy, MPS and echocardiography.
The Rates, Patterns and Reasons for Forming Heterosexual Interracial Dating Relationships among Asian Americans

Interracial relationships are a subject of intense popularity and controversy within the Asian American community. Asian Americans are the group with the highest interracial marriage rate in the nation, yet little is known about their dating practices. As one of the first empirical investigations of interracial dating rates among Asian Americans, this study seeks to examine the rates and patterns of interracial dating and to explain reasons for forming interracial unions. Based on a sample of 559 Asian and white students, the data suggest that studying dating patterns is an important step towards understanding and predicting intermarriage. Many similarities were found between marriage and dating patterns. However, in contrast to the out marriage literature, no sex differences were found in outdating rates and acculturation did not predict interracial dating. Propinquity was found to be the strongest predictor of interracial dating, while ethnic and sex differences in attractiveness were also important predictors.
Species Interactions in a Parasite Community Drive Infection Risk in a Wildlife Population

Web of Parasite Interactions We live under constant assault from a variety of pathogens. Pathogen exposure will be more or less harmful depending on host factors, including immune status, and, as Telfer et al. (p. 243; see the Perspective by Lafferty) point out, the presence of co-infecting pathogens. In a time-series study of wild voles and four pathogens, co-infection had a larger effect on disease than any other factor. For example, infection with cowpox virus increased susceptibility and prolonged bacterial co-infections. Conversely, an ongoing infection with the bacterium Anaplasma reduced the rodents' susceptibility to the protozoan Babesia. In turn, chronic infection with Babesia limited susceptibility to the bacterium Bartonella. Coinfecting pathogens have specific interacting effects on host resources, immune responses, and other pathogens. Most hosts, including humans, are simultaneously or sequentially infected with several parasites. A key question is whether patterns of coinfection arise because infection by one parasite species affects susceptibility to others or because of inherent differences between hosts. We used time-series data from individual hosts in natural populations to analyze patterns of infection risk for a microparasite community, detecting large positive and negative effects of other infections. Patterns remain once variations in host susceptibility and exposure are accounted for. Indeed, effects are typically of greater magnitude, and explain more variation in infection risk, than the effects associated with host and environmental factors more commonly considered in disease studies. We highlight the danger of mistaken inference when considering parasite species in isolation rather than parasite communities.
Confounding the Commentators: How the 2010 Exit Poll Got it (More or Less) Right

Abstract An exit poll conducted on behalf of the three main UK broadcasting organizations for the 2010 general election predicted that the Liberal Democrats would win fewer seats than in 2005, a suggestion that was met with widespread disbelief amongst commentators. Not only did this forecast prove correct, but the poll’s prediction that the Conservatives would be the largest party in a hung parliament with 307 seats also proved to be spot on. This paper describes and evaluates the methodology of the poll. The key features were a focus on changes in party vote shares facilitated by conducting the poll in the same places as at the previous election, modelling of the variation in those estimated changes, and a probabilistic approach to identifying the likely outcome in seats. All three features contributed to the accuracy of the 2010 poll. The data provided a highly accurate estimate of the change in the Liberal Democrat vote. Meanwhile, a slight overestimation of the swing from Labour to the Conservatives was corrected by the modelling of changes in vote shares and the use of a probabilistic approach to seat prediction.
How We Count Hunger Matters

Hunger continues to be one of humanity's greatest challenges despite the existence of a more-than-adequate global food supply equal to 2,800 kilocalories for every person every day. In measuring progress, policy-makers and concerned citizens across the globe rely on information supplied by the Food and Agriculture Organization (FAO), an agency of the United Nations. In 2010 the FAO reported that in the wake of the 2007–2008 food-price spikes and global economic crisis, the number of people experiencing hunger worldwide since 2005–2007 had increased by 150 million, rising above 1 billion in 2009. However, in its State of Food Insecurity in the World 2012 (SOFI 12) the FAO presented new estimates, having revamped its methods and reinterpreted its hunger data back to 1990. The revised numbers for the period 1990–1992 to 2010–2012 reverse the trend to a steadily falling one. Based on the FAO's new calculations, extreme undernourishment peaked in 1990 at a record-breaking one billion, followed by a significant decline through 2006, when progress stalled but did not reverse (see chart below).
Functional Composition Paradigm and Applications

This paper presents functional composition (FC) as a new paradigm for combinational logic synthesis. FC uses a bottomup approach to synthesize Boolean functions, allowing to know the costs of intermediate sub-functions and to explore a larger number of different candidate combinations. These are advantages when compared to top-down nature of functional decomposition. FC presents great flexibility to implement algorithms with optimal or suboptimal results for different applications. Examples include exact factoring, factoring considering also the exclusive-OR operator, synthesis considering only majority and inverter functions. The proposed strategy presents good results for synthesis of Boolean functions targeting very different technologies.
Leveling the Home Advantage: Assessing the Effectiveness of Parental Involvement in Elementary School

In the past two decades, a great deal of energy has been dedicated to improving children's education by increasing parents' involvement in school. However, the evidence on the effectiveness of parental involvement is uneven. Whereas policy makers and theorists have assumed that parental involvement has wide-ranging positive consequences, many studies have shown that it is negatively associated with some children's outcomes. This article uses data from the children of the National Longitudinal Survey of Youth 1979 to estimate time-lagged growth models of the effect of several types of parental involvement on scores on elementary school achievement tests and the Behavioral Problems Index. The findings suggest that parental involvement does not independently improve children's learning, but some involvement activities do prevent behavioral problems. Interaction analyses suggest that the involvement of parents with low socioeconomic status may be more effective than that of parents with high socioeconomic status.
Muscle fat oxidative capacity is not impaired by age but by physical inactivity: association with insulin sensitivity

The study aimed at determining whether aging and/or sedentariness impairs muscle fat oxidative capacity (OXFA) and whether this was associated with increased risk to develop insulin resistance. We first examined muscle mitochondrial functions, OXFA and insulin sensitivity (ISI; evaluated during an oral glucose tolerance test) in a cross‐sectional study with 32 sedentary (S) and endurance‐trained (T), young (Y) and elderly (E) men (24.2±2.6 vs. 66.6±3.2 yr). As for mitochondrial functions, OXFA was higher in T than in S but similar between age groups (SY 41.8±11.3, TY 68.0±17.7, SE 40.1±14.1, TE 73.1±20.1 palmitate.min–1.g wet tissue–1; activity P<0.0001, age P=NS, activity × age P=NS). Similar results were obtained with ISI (SY 6.2±2.2, TY 11.4±4.4, SE 5.9±1.5, TE 11.0±3.5, activity P<0.001, age P=NS, activity × age P=NS). Stepwise regression showed that, among body composition, VO2max and muscle biochemical characteristics, OXFA was the main predictor of ISI (r=0.60, P<0.001). We subsequently showed in eight sedentary elderly subjects (63.5±3.3 yr) that OXFA and insulin sensitivity (measured using insulin clamp) improved in parallel after 8 weeks of endurance training (r=0.79, P<0.01). We concluded that mitochondrial functions, OXFA and ISI, are not impaired by age but by physical inactivity and are closely correlated.
Risk Propensity Among Liberals and Conservatives

Political conservatives, compared to liberals, are commonly thought to be more threat-sensitive and risk-averse. Using an American sample of community adults (n = 397), we investigated when conservatives and liberals might be risk-taking or risk-averse. Participants completed measures of political orientation, and perceptions of risk, expected benefits (EB) of risk, and risk-propensity, across five domains (financial, recreational, ethical, social, and health). The relation between perceptions of risk and EB and risk-propensity differed as a function of political conservatism and varied across risk domains. For example, with regard to new business ventures, conservatives were generally willing to take risks unless perceived risk was high and expected benefit was low, whereas liberals were generally unwilling to take risks unless perceived risk was low and expected benefit was high. Implications for understanding risk-taking are considered.
The Cortical Representation of Objects Rotating in Depth

The perception of motion provides valuable interpolations of the visual scene. This fundamental capacity of the visual system is evident in apparent rotation: by presenting only two images of an object rotated in space, a vivid illusion of a smooth apparent motion in three dimensions can be induced. The unseen interpolated rotation views are filled in by the visual system. In the present study, we identified the cortical network responsible for this filling-in process. We argue that cross talk between areas of the ventral and dorsal visual pathways promote the illusion of smooth apparent rotation. Most interestingly, the network represents the unseen object views. Using functional magnetic resonance adaptation, we are able to show that the cortical network selectively adapts to the illusory object views. Our findings provide strong evidence for cortical representations of three-dimensional rotating objects that are view invariant with respect to the rotation path. Furthermore, our results confirm psychophysical investigations that unseen interpolated rotation views can be primed by apparent motion. By applying functional magnetic resonance adaptation, we show for the first time cortical adaptation to unseen objects. Together, our neuroimaging study advances the understanding of the cortical mechanisms mediating the influence of motion on object processing.
Contemporaneous disequilibrium, a new hypothesis to explain the "paradox of the plankton".

The diversity of lake phytoplankton is unexpectedly high, since the epilimnion of a lake is continuously mixing and might be expected to have only one or at most a few niches for primary producers. However, a carefully replicated series of samples from Castle Lake, Calif. , showed a high degree of patchiness for many phytoplankton species, indicating that the rate of mixing is slow enough relative to the reproductive rate of the algae for many different niches to exist simultaneously. Productivity per unit biomass ratios, measured at Lake Tahoe, California-Nevada, shows that the turnover times for carbon in even this ultraoligotrophic lake are often less than 1 day. High diversity is associated with high productivity per unit biomass and high zooplankton populations in this lake.A contemporaneous disequilibrium model to explain the diversity of the lake phytoplankton is therefore highly plausible. At any one time, many patches of water exist in which one species is at a competitive advantage relative to the others. These water masses are stable enough to permit a considerable degree of patchiness to occur in phytoplankton, but are obliterated frequently enough to prevent the exclusive occupation of each niche by a single species.
Dynamics of Bacterial Communities in Two Unpolluted Soils after Spiking with Phenanthrene: Soil Type Specific and Common Responders

Considering their key role for ecosystem processes, it is important to understand the response of microbial communities in unpolluted soils to pollution with polycyclic aromatic hydrocarbons (PAH). Phenanthrene, a model compound for PAH, was spiked to a Cambisol and a Luvisol soil. Total community DNA from phenanthrene-spiked and control soils collected on days 0, 21, and 63 were analyzed based on PCR-amplified 16S rRNA gene fragments. Denaturing gradient gel electrophoresis (DGGE) fingerprints of bacterial communities increasingly deviated with time between spiked and control soils. In taxon specific DGGE, significant responses of Alphaproteobacteria and Actinobacteria became only detectable after 63 days, while significant effects on Betaproteobacteria were detectable in both soils after 21 days. Comparison of the taxonomic distribution of bacteria in spiked and control soils on day 63 as revealed by pyrosequencing indicated soil type specific negative effects of phenanthrene on several taxa, many of them belonging to the Gamma-, Beta-, or Deltaproteobacteria. Bacterial richness and evenness decreased in spiked soils. Despite the significant differences in the bacterial community structure between both soils on day 0, similar genera increased in relative abundance after PAH spiking, especially Sphingomonas and Polaromonas. However, this did not result in an increased overall similarity of the bacterial communities in both soils.
The toxbox: specific DNA sequence requirements for activation of Vibrio cholerae virulence genes by ToxT

The Gram‐negative, curved rod Vibrio cholerae causes the severe diarrhoeal disease cholera. The two major virulence factors produced by V. cholerae during infection are the cholera toxin (CT) and the toxin‐coregulated pilus (TCP). Transcription of the genes encoding both CT and the components of the TCP is directly activated by ToxT, a transcription factor in the AraC/XylS family. ToxT binds upstream of the ctxAB genes, encoding CT, and upstream of tcpA, the first gene in a large operon encoding the components of the TCP. The DNA sequences upstream of ctxAB and tcpA that contain ToxT binding sites do not have any significant similarity other than being AT‐rich. Extensive site‐directed mutagenesis was performed on the region upstream of tcpA previously shown to be protected by ToxT, and we identified specific base pairs important for activation of tcpA transcription by ToxT. This genetic approach was complemented by copper‐phenanthroline footprinting experiments that showed protection by ToxT of the base pairs identified as most important for transcription activation in the mutagenesis experiments. Based on this new information and on previous work, we propose the presence of a ToxT‐binding motif – the ‘toxbox’– in promoters regulated by ToxT. At tcpA, two toxbox elements are present in a direct repeat configuration and both are required for activation of transcription by ToxT. The identity of only a few of the base pairs within the toxbox is important for activation by ToxT, and we term these the core toxbox elements. Lastly, we examined ToxT binding to a mutant having 5 bp inserted between the two toxboxes at tcpA and found that occupancy of both binding sites is retained regardless of the positions of the binding sites relative to each other on the face of the DNA. This suggests that ToxT binds independently as a monomer to each toxbox in the tcpA direct repeat, in accordance with what we observed previously with the inverted repeat ToxT sites between acfA and acfD.
Critical Care: A Color(full) Analysis of Care Narratives in the Schooling Experiences of Puerto Rican Girls

In this article, the author explores the intersection between race/ethnicity and caring in the educational experiences of middle school Puerto Rican girls. Critical race theory and Latino/Latina critical theory are used as data analysis frameworks because of their emphasis on the roles of race/ethnicity and racism in shaping the circumstances of individuals and institutions. The author calls for a color(full) critical care praxis that is grounded in a historical understanding of students’ lives; translates race-conscious ideological and political orientations into pedagogical approaches that benefit Latino/a students; uses caring counternarratives to provide more intimate, caring connections between teachers and the Latino communities where they work; and pays attention to caring at both the individual and institutional levels.
Early Predictors of Health-Related Quality of Life Outcomes in Polytrauma Patients with Spine Injuries: A Level 1 Trauma Center Study

Study Design Retrospective review on clinical-quality trauma registry prospective data. Objective To identify early predictors of suboptimal health status in polytrauma patients with spine injuries. Methods A retrospective review on a prospective cohort was performed on spine-injured polytrauma patients with successful discharge from May 2009 to January 2011. The Short Form 12-Questionnaire Health Survey (SF-12) was used in the health status assessment of these patients. Univariate and multivariate logistic regression models were applied to investigate the effects of the Injury Severity Score, age, blood sugar level, vital signs, brain trauma severity, comorbidities, coagulation profile, spine trauma-related neurologic status, and spine injury characteristics of the patients. Results The SF-12 had a 52.3% completion rate from 915 patients. The patients who completed the SF-12 were younger, and there were fewer patients with severe spinal cord injuries (American Spinal Injury Association classifications A, B, and C). Other comparison parameters were satisfactorily matched. Multivariate logistic regression revealed five early predictive factors with statistical significance (p ≤ 0.05). They were (1) tachycardia (odds ratio [OR] = 1.88; confidence interval [CI] = 1.11 to 3.19), (2) hyperglycemia (OR = 2.65; CI = 1.51 to 4.65), (3) multiple chronic comorbidities (OR = 2.98; CI = 1.68 to 5.26), and (4) thoracic spine injuries (OR = 1.54; CI = 1.01 to 2.37). There were no independent early predictive factors identified for suboptimal mental health-related qualify of life outcomes. Conclusion Early independent risk factors predictive of suboptimal physical health status identified in a level 1 trauma center in polytrauma patients with spine injuries were tachycardia, hyperglycemia, multiple chronic medical comorbidities, and thoracic spine injuries. Early spine trauma risk factors were shown not to predict suboptimal mental health status outcomes.