Miracle-dz/UniFAR-FTUs huggingface dataset:
Analysis of Five Gene Sets in Chimpanzees Suggests Decoupling between the Action of Selection on Protein-Coding and on Noncoding Elements

We set out to investigate potential differences and similarities between the selective forces acting upon the coding and noncoding regions of five different sets of genes defined according to functional and evolutionary criteria: 1) two reference gene sets presenting accelerated and slow rates of protein evolution (the Complement and Actin pathways); 2) a set of genes with evidence of accelerated evolution in at least one of their introns; and 3) two gene sets related to neurological function (Parkinson’s and Alzheimer’s diseases). To that effect, we combine human–chimpanzee divergence patterns with polymorphism data obtained from target resequencing 20 central chimpanzees, our closest relatives with largest long-term effective population size. By using the distribution of fitness effect-alpha extension of the McDonald–Kreitman test, we reproduce inferences of rates of evolution previously based only on divergence data on both coding and intronic sequences and also obtain inferences for other classes of genomic elements (untranslated regions, promoters, and conserved noncoding sequences). Our results suggest that 1) the distribution of fitness effect-alpha method successfully helps distinguishing different scenarios of accelerated divergence (adaptation or relaxed selective constraints) and 2) the adaptive history of coding and noncoding sequences within the gene sets analyzed is decoupled.
Using attribution theory to understand resilience for looked after children.

Children and young people in Public Care are one of the most at risk groups for educational failure and poor life outcomes (NCH, 2005). There is now a wealth of literature detailing predictive risk factors across a range of populations and outlining factors which contribute to resilient, adaptive outcomes in the face of risk factors (e.g. Rutter, 1990 Fonagy et al., 1994). In addition, an understanding of the processes and mechanisms involved is necessary in order to identify which, if any, of the many attributes and/or circumstances that correlate with resilience may be critical targets for effective prevention and intervention. Attributions, the causes given to events, are considered to be powerful determinants of our future actions (see Fosterling, 2001). Drawing on attribution theory and conceptualisations of optimism and self-efficacy, this research uses the Leeds Attributional Coding System (LACS) to compare high and low resilience looked after youngsters' perceptions of positive and negative events in educational, social and home contexts. Resilience was associated with how positive events were construed. High resilience (HR) youngsters made more positive attributions and tended to perceive the causes of positive outcomes optimistically, i.e. causes were relatively unchanging and wide reaching. Low resilience (LR) youngsters saw these causes as unstable and specific. HR adolescents tended to make self-efficacious controllable attributions for internal causes. LR young people were more negative about peer and carer/parent relationships, and views of school, suggesting that perceptions of more everyday contexts are more influential in resilience than major life events, such as changing school or placement, and that relationships are a key factor in positive adaptation. Furthermore, looked after adolescents tend to see themselves more frequently than non-looked after adolescents as the target of others actions. However, HR looked after youngsters are more likely to view others' actions positively.
Temporal variations in microbial activities and carbon turnover in subtidal sandy sediments

Abstract. Temporal dynamics and vertical patterns in bacterial abundances and activities were studied in a shallow subtidal sand flat in the Sylt-Romo Basin (North Frisian Wadden Sea, Germany). Extracellular enzymatic activities, bacterial carbon production and community respiration showed strong (factor of 4–5) temporal variations that were mostly related to seasonal temperature change and to changes in substrate availability. These temporal patterns in enzymatic activity were barely reflected in bacterial (200–400 mmol C m−2) and microphytobenthic biomass (800–1500 mmol C m−2) or the sedimentary carbohydrate inventory (1300–2900 mmol C m−2), suggesting that grazing controls the standing stocks of the microphytobenthic and bacterial assemblages. Despite their exposure to strong hydrodynamic forces such as tidal currents and wind-induced wave surge, the subtidal sandy sediments showed persistent vertical gradients in bacterial abundances, carbon production and extracellular enzymatic activities at all times. The vertical distribution of these parameters was tightly coupled to that of the microphytobenthos, dominated by diatoms. Despite the low organic carbon content typical for surge-exposed sandy sediments, high extracellular enzymatic activities and bacterial carbon production rates indicate a very active heterotrophic bacterial community, with a gross secondary productivity of 30–180 mmol C m−2, and a biomass turnover time of 2–18 days. Our data suggest that this high activity is supported by the rapid flux of carbohydrates from microphytobenthic primary productivity. Accordingly, the potential activities of enzymes hydrolyzing carbohydrates cover most of the total bacterial carbon demand during all seasons.
Mining Permission Request Patterns from Android and Facebook Applications

Android and Facebook provide third-party applications with access to users' private data and the ability to perform potentially sensitive operations (e.g., post to a user's wall or place phone calls). As a security measure, these platforms restrict applications' privileges with permission systems: users must approve the permissions requested by applications before the applications can make privacy-or security-relevant API calls. However, recent studies have shown that users often do not understand permission requests and are unsure of which permissions are typical for applications. As a first step towards simplifying permission systems, we cluster a corpus of 188,389 Android applications and 27,029 Facebook applications to find patterns in permission requests. Using a method for Boolean matrix factorization to find overlapping clusters of permissions, we find that Facebook permission requests follow a clear structure that can be fitted well with only five patterns, whereas Android applications demonstrate more complex permission requests. We also find that low-reputation applications often deviate from the permission request patterns that we identified for high-reputation applications, which suggests that permission request patterns can be indicative of user satisfaction or application quality.
Can Moderate Alcohol Intake Limit the Size of Myocardial Infarction?

&NA; Several observational and epidemiologic analyses suggest that moderate drinking of alcohol (usually two drinks per day) may have beneficial effects on the heart. Specifically it may reduce the incidence of ischemic heart disease and improve the outcome after a myocardial infarction. The purpose of this study was to test the hypothesis that long‐term, moderate consumption of alcohol has a direct cardioprotective effect, reducing myocardial infarct size in rats subjected to ischemia/reperfusion. Two groups of rats were given alcohol in their drinking water at concentrations of 15% or 36%; control rats received water (n =10 for all groups). After 16 weeks of treatment, the rats were anesthetized and subjected to 60 min of coronary artery occlusion and reperfusion. The ischemic risk region (% LV) was not significantly different among groups. Infarct size (% risk zone) was 49 ± 7%, 44 ± 4%, and 50 ± 8%, respectively (p =0.79). Thus no significant differences in infarct size between control and alcohol‐fed rats were observed. There was no correlation between alcohol level and infarct size in alcohol‐treated rats (r = 0.20, p = 0.45). Arterial pressures were lower in the 36% group at baseline and throughout the study compared with the control and 15% groups, but heart rates were similar in all groups. Moderate consumption of alcohol failed to alter infarct size compared with control and thus it is unlikely that alcohol drinking has a direct myocardial‐protecting effect on the outcome of ischemia and reperfusion.
Generation and deposition of Aβ43 by the virtually inactive presenilin‐1 L435F mutant contradicts the presenilin loss‐of‐function hypothesis of Alzheimer's disease

As stated by the prevailing amyloid cascade hypothesis, Alzheimer's disease (AD) is caused by the aggregation and cerebral deposition of long amyloid‐β peptide (Aβ) species, which are released from a C‐terminal amyloid precursor protein fragment by γ‐secretase. Mutations in its catalytic subunit presenilin‐1 (PS1) increase the Aβ42 to Aβ40 ratio and are the major cause of familial AD (FAD). An opposing hypothesis states that loss of essential presenilin functions underlies the disease. A major argument for this hypothesis is the observation that the nearly inactive PS1 L435F mutant, paradoxically, causes FAD. We now show that the very little Aβ generated by PS1 L435F consists primarily of Aβ43, a highly amyloidogenic species which was overlooked in previous studies of this mutant. We further demonstrate that the generation of Aβ43 is not due to a trans‐dominant effect of this mutant on WT presenilin. Furthermore, we found Aβ43‐containing plaques in brains of patients with this mutation. The aberrant generation of Aβ43 by this particular mutant provides a direct objection against the presenilin hypothesis.
Negative-Zero-Positive Refractive Index in a Prism-Like Omega-Type Metamaterial

Negative-zero-positive index refraction was demonstrated numerically on the basis of full-wave analysis of a microstructured omega-type array and experimentally via angle resolved transmission measurement of a prism-type prototype. The experimental results are interpreted in terms of characteristic impedance and refractive index retrieved by a Fresnel inversion technique. The possibility to balance the dispersion characteristics with a negative-zero-positive index is demonstrated over X - and Ku -bands.
Distribution, structure and function of Nordic eelgrass (Zostera marina) ecosystems: implications for coastal management and conservation

This paper focuses on the marine foundation eelgrass species, Zostera marina, along a gradient from the northern Baltic Sea to the north-east Atlantic. This vast region supports a minimum of 1480 km2 eelgrass (maximum >2100 km2), which corresponds to more than four times the previously quantified area of eelgrass in Western Europe. Eelgrass meadows in the low salinity Baltic Sea support the highest diversity (4–6 spp.) of angiosperms overall, but eelgrass productivity is low (<2 g dw m-2 d-1) and meadows are isolated and genetically impoverished. Higher salinity areas support monospecific meadows, with higher productivity (3–10 g dw m-2 d-1) and greater genetic connectivity. The salinity gradient further imposes functional differences in biodiversity and food webs, in particular a decline in number, but increase in biomass of mesograzers in the Baltic. Significant declines in eelgrass depth limits and areal cover are documented, particularly in regions experiencing high human pressure. The failure of eelgrass to re-establish itself in affected areas, despite nutrient reductions and improved water quality, signals complex recovery trajectories and calls for much greater conservation effort to protect existing meadows. The knowledge base for Nordic eelgrass meadows is broad and sufficient to establish monitoring objectives across nine national borders. Nevertheless, ensuring awareness of their vulnerability remains challenging. Given the areal extent of Nordic eelgrass systems and the ecosystem services they provide, it is crucial to further develop incentives for protecting them. © 2014 The Authors. Aquatic Conservation: Marine and Freshwater Ecosystems published by John Wiley & Sons, Ltd.
DEVELOPMENT OF NONINVASIVE AND QUANTITATIVE METHODOLOGIES FOR THE ASSESSMENT OF CHRONIC ULCERS AND SCARS IN HUMANS

Chronic ulcers are a significant and common cause of morbidity and mortality worldwide. They disrupt the epidermis and dermis, resulting in a loss of barrier function. Keloids and hypertrophic scars (benign cutaneous tumors) represent an abnormal healing response. These fibroproliferative disorders are characterized by an overabundance of collagen and accumulation of extracellular matrix due to an imbalance between synthesis and degradation, culminating in excessive scarring. The objectives of this study were to evaluate and compare noninvasive biophysical methods for the measurement of outstanding quantitative parameters of scars and chronic ulcers, and to establish correlations between the parameters measured and the results of conventional subjective clinical evaluations. The development of new technologies, based on ultrasonography and laser Doppler, makes possible new dermatological evaluation methods. Fifteen patients (6 females and 9 males) with 15 chronic ulcers (4 diabetic ulcers, 10 venous ulcers and 1 pressure ulcer) and 30 patients (19 females and 11 males) with 30 scars (25 hypertrophic and 5 keloids) were included in this study. Clinical evaluation was performed by a dermatologist, an aesthetic surgeon and an endocrinologist. Biophysical measurements were used to assess local blood flow by laser Doppler flowmetry (Moor DRT4), thickness and echogenicity by high frequency ultrasonography (20 MHz, Dermascan C) and ulcer linear dimensions by image analysis. Our results show that blood flow within the ulcers and scars was higher than within normal skin. Also, skin thickness of chronic ulcers was decreased when compared to normal skin; the thickness of hypertrophic scars, but not of keloids, was increased in comparison to normal skin, and presented the possibility of measuring wound and scar surfaces with precision. In summary, this pilot study established the feasibility of measuring various biophysical parameters and adapted their potential utility to research on wounds.
Semi-concurrent error detection in data paths

An innovative approach for high-level synthesis of digital circuits with semi-concurrent self-checking abilities is introduced, achieving a compromise between redundancy and checking effectiveness. Attention is mainly focused on the data path, described as a general Sequencing Graph including linear paths as well as loops and branches. A reference architecture is defined; a technique allowing to reduce redundancy through resource sharing is then introduced, leading to synthesis of the self-checking architecture. An algorithm is proposed to simultaneously schedule and allocate the resources, while keeping error aliasing as reduced as possible. The desired checking periodicity is guarantee by the algorithm.
A Social Network Analysis of the IS Field: Aco-Authorship Network Study

The IS field is a fragmented field with many different research strategies and topics. To complicate this matter, there are many different publication venues and geographic locations. This study will try to look at the co-authorship social network (SN), using three different venues. One of the venues is the top journal in our field, the other a regional conference, and the third is a top French IS journal. The study will take a social network analysis (SNA) approach to see if there are differences in these venues and to take a preliminary look at the IS field. The results indicate that even though we research under the umbrella of IS, differing venues seem to have differing cliques of researchers. The divide between North American and France is also seen in how different the publication strategies seem to be between the two geographic areas.
Time counts: future time perspective, goals, and social relationships.

On the basis of postulates derived from socioemotional selectivity theory, the authors explored the extent to which future time perspective (FTP) is related to social motivation, and to the composition and perceived quality of personal networks. Four hundred eighty German participants with ages ranging from 20 to 90 years took part in the study. In 2 card-sort tasks, participants indicated their partner preference and goal priority. Participants also completed questionnaires on personal networks and social satisfaction. Older people, as a group, perceived their future time as more limited than younger people. Individuals who perceived future time as being limited prioritized emotionally meaningful goals (e.g., generativity, emotion regulation), whereas individuals who perceived their futures as open-ended prioritized instrumental or knowledge-related goals. Priority of goal domains was found to be differently associated with the size, composition, and perceived quality of personal networks depending on FTP. Prioritizing emotion-regulatory goals was associated with greater social satisfaction and less perceived strain with others when participants perceived their future as limited. Findings underscore the importance of FTP in the self-regulation of social relationships and the subjective experience associated with them.
Mutation analyses of Uroplakin II in children with renal tract malformations.

BACKGROUND Uroplakin (UP) proteins cover urothelial apical surfaces. Mice lacking UPIIIa have elevated urothelial permeability and congenital renal tract anomalies, and UPIIIa mutations have been reported in children with kidney and ureter malformations. Mice with null mutation of another UP family member, UPII, are often born with congenital hydronephrosis. We hypothesized that UPII mutations may be present in humans with renal tract malformations. METHODS Mutations were sought, using direct sequencing of the five UPII exons, in 42 children with diverse renal tract anomalies. RESULTS No UPII abnormalities were detected in 41 patients, whereas one index case had a heterozygous frameshift change which, if expressed, would generate a truncated protein. This Caucasian child presented with vesicoureteric reflux (VUR), bilateral nephropathy and renal failure. The genetic change was also found in the index case's mother who had normal renal ultrasonography, but it was absent in 150 healthy Caucasian control individuals (96 assessed by direct sequencing and another 54 assessed by restriction digests). UPII was immunolocalized in urothelium of the normal human embryonic renal pelvis in a pattern similar to UPIIIa. CONCLUSION This study offers no definitive support for UPII mutations causing human renal tract malformations. In rare patients, UPII variants might be implicated in pathogenesis when acting in conjunction with other yet-to-be-defined, genetic or environmental modifying factors.
Sticky Prices in the United States

It has often been argued that prices are sticky in the United States. However, the empirical papers that have claimed to support this view have not reflected any formal behavioral theory. This paper presents a theory that justifies price stickiness, namely, that firms, fearing to upset their customers, attribute a cost to price changes. The rational expectations equilibrium of an economy with many such firms is presented, estimated with postwar U.S. data, and tested against alternative hypotheses. The results largely support the model. Furthermore, the hypothesis that prices are not sticky is rejected by U.S. data.
Auditing management practices in schools: Recurring communication problems and solutions

Purpose – Over the past ten years, most Dutch high schools have been confronted with mergers, curriculum reforms, and managerial changes. As a result, the pressure on the schools' communication systems has increased and several problems have emerged. This paper aims to examine recurring clusters of communication problems in high schools.Design/methodology/approach – A multi‐method communication audit was conducted within three large high schools in The Netherlands. Data were collected using network analysis, the critical incident technique, and the Communication Satisfaction Questionnaire.Findings – The communication audits uncovered six major clusters of communication problems that require management's attention. These problems vary from a lack of participation in decision making to employees feeling under appreciated. While some of these problems could be solved by creating more awareness within the organization, others require more structural changes and long‐range planning.Originality/value – The stud.
uPAR-targeted multimodal tracer for pre- and intraoperative imaging in cancer surgery

Pre- and intraoperative diagnostic techniques facilitating tumor staging are of paramount importance in colorectal cancer surgery. The urokinase receptor (uPAR) plays an important role in the development of cancer, tumor invasion, angiogenesis, and metastasis and over-expression is found in the majority of carcinomas. This study aims to develop the first clinically relevant anti-uPAR antibody-based imaging agent that combines nuclear (111In) and real-time near-infrared (NIR) fluorescent imaging (ZW800-1). Conjugation and binding capacities were investigated and validated in vitro using spectrophotometry and cell-based assays. In vivo, three human colorectal xenograft models were used including an orthotopic peritoneal carcinomatosis model to image small tumors. Nuclear and NIR fluorescent signals showed clear tumor delineation between 24h and 72h post-injection, with highest tumor-to-background ratios of 5.0 ± 1.3 at 72h using fluorescence and 4.2 ± 0.1 at 24h with radioactivity. 1-2 mm sized tumors could be clearly recognized by their fluorescent rim. This study showed the feasibility of an uPAR-recognizing multimodal agent to visualize tumors during image-guided resections using NIR fluorescence, whereas its nuclear component assisted in the pre-operative non-invasive recognition of tumors using SPECT imaging. This strategy can assist in surgical planning and subsequent precision surgery to reduce the number of incomplete resections.
Local Political Context and Negative Campaigns

ABSTRACT Research into the intended and unintended consequences of negative campaigns has spawned a variety of approaches and a variety of contradictory findings. This paper suggests that some of the contradictions are likely due to methodological issues. First, we examine the use of elite assessment as an improved means of operationalizing the tone of political campaigns. Second, several hypotheses about the mediating effects of local electoral culture are tested. That is, we first derive a measure of negativity from the perceptions of newspaper editors and reporters who covered the 1998 congressional campaigns in the USA, and then merge this information with the 1998 NES data to measure the effects on respondents in different electoral subcultures. We find that the unintended effects of negative campaigns are more pronounced in U.S. states with little or no history of partisan competition. We conclude that elite assessment should be considered as a method for measuring a race's “negativity” and that context is a key component in sorting out the “unintended effects” mystery.