Miracle-dz/UniFAR-FTUs huggingface dataset:
Coevolution Reveals a Network of Human Proteins Originating with Multicellularity

Protein interaction networks play central roles in biological systems, from simple metabolic pathways through complex programs permitting the development of organisms. Multicellularity could only have arisen from a careful orchestration of cellular and molecular roles and responsibilities, all properly controlled and regulated. Disease reflects a breakdown of this organismal homeostasis. To better understand the evolution of interactions whose dysfunction may be contributing factors to disease, we derived the human protein coevolution network using our MatrixMatchMaker algorithm and using the Orthologous MAtrix project (OMA) database as a source for protein orthologs from 103 eukaryotic genomes. We annotated the coevolution network using protein–protein interaction data, many functional data sources, and we explored the evolutionary rates and dates of emergence of the proteins in our data set. Strikingly, clustering based only on the topology of the coevolution network partitions it into two subnetworks, one generally representing ancient eukaryotic functions and the other functions more recently acquired during animal evolution. That latter subnetwork is enriched for proteins with roles in cell–cell communication, the control of cell division, and related multicellular functions. Further annotation using data from genetic disease databases and cancer genome sequences strongly implicates these proteins in both ciliopathies and cancer. The enrichment for such disease markers in the animal network suggests a functional link between these coevolving proteins. Genetic validation corroborates the recruitment of ancient cilia in the evolution of multicellularity.
The Role of Social Norms in the Structural Model Explaining Alcohol Use Among Students

Few studies have explored the complex relationships among several factors determining alcohol use or explained how norms operate in the relationships between alcohol use and other psychological constructs. This study aims to explore the complex relationships in the proposed model explaining students' alcohol use with special emphasis on descriptive and injunctive norms. Cross-sectional data were collected from 719 university students (59.0% females; Mage = 21.25; SD = 1.99), who were asked to fill in a set of AUDIT items, cognitive and affective attitudes, descriptive and injunctive norms, self-regulation, self- -determination, drinking motives, and alcohol expectancies. Structural equation modelling was used for data analysis. It was found that (1) self-regulation was neither directly nor indirectly associated with alcohol use; (2) self-determination was indirectly associated with alcohol use through injunctive norms, attitudes and drinking motives; (3) descriptive norms were associated with alcohol use directly; (4) injunctive norms were associated with alcohol use directly as well as indirectly via alcohol expectancies, attitudes and drinking motives; (5) alcohol expectancies were associated with alcohol use directly. In addition to identifying individual associations among variables, this study also explains which factors contribute to students' alcohol use and norms and how these factors interact, which can be useful for the development of prevention programmes.
The Detection of ADHD and Malingering in Young Adults

Over the past 20 years, an increasing number of adults and college students have selfreferred for ADHD evaluations. With the rise in adult ADHD evaluations, there has been increased concern that a proportion of these adults may be malingering the symptoms of ADHD to receive external incentives such as academic accommodations and stimulant medications. Research supports the use of well-validated measures to classify malingering in non-ADHD populations, yet all available validity tests have insufficient research to support their usage to detect this population. The present study investigated the ability of the Multidimensional ADHD Rating Scale (MARS) and two published validity tests (Word Memory Test and CAT-A Infrequency scale) to detect a group of non-ADHD college students instructed to feign ADHD, and to differentiate ADHD from non-ADHD cases. Results found that the MARS Symptom Validity Index demonstrated higher sensitivity rates for simulated malingering (75.4%) at close to optimal specificity (86.8%) compared to two published tests (sensitivity < 50%). The MARS Total Symptom index differentiated ADHD from non-ADHD cases with high sensitivity (87.1%). The study provides additional support for the effectiveness of the MARS symptom, impairment, and symptom validity indices to detect simulated cases of malingering, and to differentiate ADHD from non-ADHD cases.
Proximity-based ranking of biomedical texts

Biomedical decision making and research often require relevant evidences in the huge and ever-growing biomedical literature. Retrieval of the evidences calls for a system that accepts a natural language query for a biomedical information need, and among the large number of texts retrieved for the query, ranks relevant texts higher for access or processing. However, state-of-the-art text rankers have a weakness in dealing with biomedical queries, which often consists of several correlating concepts and prefers those texts that talk about the concepts completely. In this paper, we present a technique PRE (Proximity-based Ranker Enhancer) that measures contextual completeness of query concepts appearing in a nearby area in the text, and based on the contextual completeness, assesses the term frequency (TF) of each term in the text. Therefore, those rankers that consider TF in ranking may be supplemented with PRE, without needing to change the algorithms and development processes of the rankers. Moreover, PRE is efficient to conduct the TF assessment, and neither training process nor training data is required. Empirical evaluation shows that PRE significantly improves several state-of-the-art rankers, and is better than several state-of-the-art techniques aiming at improving rankers.
Multicolor observations of the afterglow of the short/hard GRB 050724

Context. New information on short/hard gamma-ray bursts (GRBs) is being gathered thanks to the discovery of their optical and X-ray afterglows. However, some key aspects are still poorly understood, including the collimation level of the outflow, the duration of the central engine activity, and the properties of the progenitor systems. Aims. We want to constrain the physical properties of the short GRB 050724 and of its host galaxy, and make some inferences on the global short GRB population. Methods. We present optical observations of the afterglow of GRB 050724 and of its host galaxy, significantly expanding the existing dataset for this event. We compare our results with models, complementing them with available measurements from the literature. We study the afterglow light curve and spectrum including X-ray data. We also present observations of the host galaxy. Results. The observed optical emission was likely related to the large flare observed in the X-ray light curve. The apparent steep decay was therefore not due to the jet effect. Available data are indeed consistent with low collimation, in turn implying a large energy release, comparable to that of long GRBs. The flare properties also constrain the internal shock mechanism, requiring a large Lorentz factor contrast between the colliding shells. This implies that the central engine was active at late times, rather than ejecting all shells simultaneously. The host galaxy has red colors and no ongoing star formation, consistent with previous findings on this GRB. However, it is not a pure elliptical, and has some faint spiral structure. Conclusions. GRB 050724 provides the most compelling case for association between a short burst and a galaxy with old stellar population. It thus plays a pivotal role in constraining progenitors models, which should allow for long delays between birth and explosion.
SETS Learning Efficacy to Improve Students Science Literacy Skills

Science learning aims to help students to be able to master the knowledge of scientific order. Science learning will be more meaningful for students, if students have good literacy skills. Someone has scientific literacy skills that can both understand and communicate science, and applying science knowledge in solving problems, and can make decisions based on scientific considerations. The results of international research show that the literacy rate of Indonesian students is in the low category. This study aims to determine the effectiveness of SETS learning to improve students' scientific literacy skills. The design of this study used quasi experimental with non-equivalent control group design. In general, the results of the study show that the effectiveness of SETS learning can be seen based on student learning outcomes in the experimental class showing better than control class students and increasing scientific literacy skills in each of the relatively high categories. Science literacy skills in the interaction of science, technology, and society experienced the highest increase in ability compared to other scientific literacy categories.
First-principles study of hydrogen diffusion and self-clustering below tungsten surfaces

The diffusion and self-clustering nucleation behavior of hydrogen (H) without vacancies below tungsten (W) surfaces are important for understanding the retention of deuterium (D) in W crystals exposed to high-flux and low-energy D plasma. The H migration energy and binding energy of H to self-clusters near the W(100), W(110), and W(111) surfaces have been investigated by first-principles computer simulations using density functional theory. H diffusion from adsorption sites on the W(100), W(110), and W(111) surfaces into solute sites in the bulk requires energies of at least 1.21, 1.78, and 1.80 eV, respectively, while 0.27, 0.31, and 0.24 eV for the reverse process. In addition, the lateral diffusion of H between two subsurface layers below the W surfaces has been investigated. Two H atoms at a depth of 0.08 nm below the W(110) surface have the highest binding energy, followed by H atom pairs below the W(111) and W(110) surfaces. The nucleation and stability of H clusters depend on the surface orientation. A planar configuration between the first nearest neighbor {100} planes is energetically favorable for H self-clustering below the W(100), W(110), and W(111) surfaces. The thermal stability of a platelet containing 16 H atoms below the W surfaces at 300 and 600 K was also studied by ab initio molecular dynamics simulations, which indicate that the H platelet below a W(111) surface is more stable than that below either the W(100) or the W(110) surface.The diffusion and self-clustering nucleation behavior of hydrogen (H) without vacancies below tungsten (W) surfaces are important for understanding the retention of deuterium (D) in W crystals exposed to high-flux and low-energy D plasma. The H migration energy and binding energy of H to self-clusters near the W(100), W(110), and W(111) surfaces have been investigated by first-principles computer simulations using density functional theory. H diffusion from adsorption sites on the W(100), W(110), and W(111) surfaces into solute sites in the bulk requires energies of at least 1.21, 1.78, and 1.80 eV, respectively, while 0.27, 0.31, and 0.24 eV for the reverse process. In addition, the lateral diffusion of H between two subsurface layers below the W surfaces has been investigated. Two H atoms at a depth of 0.08 nm below the W(110) surface have the highest binding energy, followed by H atom pairs below the W(111) and W(110) surfaces. The nucleation and stability of H clusters depend on the surface orientatio.
Fukumoto-Furuta invariants of plumbed homology 3-spheres

Recent major progress in the study of the homology cobordism group of homology 3-spheres is related to the work of Fukumoto, Furuta, and Ue on their w-invariant. We identify the w-invariant with the μ-invariant of Neumann and Siebenmann for all plumbed homology spheres. This leads to proving that all Seifert fibered and some classes of plumbed homology spheres with nontrivial Rohlin invariant have infinite order in the homology cobordism group.
Comparative measurements of inverse spin Hall effects and magnetoresistance in YIG/Pt and YIG/Ta

We report on a comparative study of spin Hall related effects and magnetoresistance in YIG$|$Pt and YIG$|$Ta bilayers. These combined measurements allow to estimate the characteristic transport parameters of both Pt and Ta layers juxtaposed to yttrium iron garnet (YIG): the spin mixing conductance ${G}_{\ensuremath{\uparrow}\ensuremath{\downarrow}}$ at the YIG$|$normal metal interface, the spin Hall angle ${\ensuremath{\Theta}}_{\mathrm{SH}}$, and the spin diffusion length ${\ensuremath{\lambda}}_{\mathrm{sd}}$ in the normal metal. The inverse spin Hall voltages generated in Pt and Ta by the pure spin current pumped from YIG excited at resonance confirm the opposite signs of spin Hall angles in these two materials. Moreover, from the dependence of the inverse spin Hall voltage on the Ta thickness, we extract the spin diffusion length in Ta, found to be ${\ensuremath{\lambda}}_{\mathrm{sd}}^{\mathrm{Ta}}=1.8\ifmmode\pm\else\textpm\fi{}0.7$ nm. Both the YIG$|$Pt and YIG$|$Ta systems display a similar variation of resistance upon magnetic field orientation, which can be explained in the recently developed framework of spin Hall magnetoresistance.
Graded Attractors: Configuring Context-Dependent Workspaces for Ideation

Thought is an essential aspect of mental function, but remains very poorly understood. In this paper, we take the view that thought is a response process – the emergent and dynamic configuration of structured response, i.e., ideas, by composing response elements, i.e., concepts, from a repertoire under the influence of afferent information, internal modulation and evaluative feedback. We hypothesize that the process of generating ideas occurs at two levels: 1) The identification of a context-specific subset – or workspace – of concepts from the larger repertoire; and 2) The configuration of plausible/useful ideas within this workspace. Workspace configuration is mediated by a dynamic selector network (DSN), which is an internal attention/working memory system. Each unit of the DSN selectively gates a subset of concepts, so that any pattern of activity in the DSN defines a workspace. The configuration of efficient and flexible workspaces is mediated by dynamical structures termed graded attractors – attractors where the set of active units can be varied in systematic order by inhibitory modulation. A graded attractor in the DSN can project a selective bias – a “searchlight” – onto the concept repertoire to define a specific workspace, and inhibitory modulation can be used to vary the breadth of this workspace. As it experiences various contexts, the cognitive system can configure a set of graded attractors, each covering a domain of similar contexts. In this paper, we focus on a mechanism for configuring context-specific graded attractors, and evaluate its performance over a set of contexts with varying degrees of similarity. In particular, we look at whether contexts are clustered appropriately into a minimal number of workspaces based on the similarity of the responses they require. While the focus in this paper is on semantic workspaces, the model is broadly applicable to other cognitive response functions such as motor control or
Boundary identification of events in clinical named entity recognition

The problem of named entity recognition in the medical/clinical domain has gained increasing attention do to its vital role in a wide range of clinical decision support applications. The identification of complete and correct term span is vital for further knowledge synthesis (e.g., coding/mapping concepts thesauruses and classification standards). This paper investigates boundary adjustment by sequence labeling representations models and post-processing techniques in the problem of clinical named entity recognition (recognition of clinical events). Using current state-of-the-art sequence labeling algorithm (conditional random fields), we show experimentally that sequence labeling representation and post-processing can be significantly helpful in strict boundary identification of clinical events.
Nitrogen deposition alters plant–fungal relationships: linking belowground dynamics to aboveground vegetation change

Nitrogen (N) deposition rates are increasing globally due to anthropogenic activities. Plant community responses to N are often attributed to altered competitive interactions between plants, but may also be a result of microbial responses to N, particularly root‐associated fungi (RAF), which are known to affect plant fitness. In response to N, Deschampsia cespitosa, a codominant plant in the alpine tundra at Niwot Ridge (CO), increases in abundance, while Geum rossii, its principal competitor, declines. Importantly, G. rossii declines with N even in the absence of its competitor. We examined whether contrasting host responses to N are associated with altered plant–fungal symbioses, and whether the effects of N are distinct from effects of altered plant competition on RAF, using 454 pyrosequencing. Host RAF communities were distinct (only 9.4% of OTUs overlapped). N increased RAF diversity in G. rossii, but decreased it in D. cespitosa. D. cespitosa RAF communities were more responsive to N than G. rossii RAF communities, perhaps indicating a flexible microbial community aids host adaptation to nutrient enrichment. Effects of removing D. cespitosa were distinct from effects of N on G. rossii RAF, and D. cespitosa presence reversed RAF diversity response to N. The most dominant G. rossii RAF order, Helotiales, was the most affected by N, declining from 83% to 60% of sequences, perhaps indicating a loss of mutualists under N enrichment. These results highlight the potential importance of belowground microbial dynamics in plant responses to N deposition.
Programmable enforcement framework of information flow policies

We propose a programmable framework that can be easily instantiated to enforce a large variety of information flow properties. Our framework is based on the idea of secure multi-execution in which multiple instances of the controlled program are executed in parallel. The information flow property of choice can be obtained by simply implementing programs that control parallel executions. We present the architecture of the enforcement mechanism and its instantiations for non-interference (NI) (from Devriese and Piessens), non-deducibility (ND) (from Sutherland) and some properties proposed by Mantel, such as removal of inputs (RI) and deletion of inputs (DI), and demonstrate formally soundness and precision of enforcement for these properties.
Effects of seat position on perception of power in Chinese traditional culture

In China, some rituals show that power is represented by seat positions. The current study empirically investigated the relationship between seat position and perception of power, and the cultural differences in this relationship. In Experiment 1, participants were asked to arrange seats for people with different power. The results showed that seats for high-power people were placed facing the door while others’ seats were placed with their backs to the door. In Experiment 2, a priming task was employed to test the link between seat position and perception of power. Results revealed that after pictures of the seat facing the door were primed, judgments for high-power words were more accurate and faster than for low-power words, as compared to priming with the condition of the seat with its back to the door. A Stroop task was employed in Experiment 3 to explore cultural differences. Results showed that Chinese participants judged highpower words faster in the congruent trials than in the incongruent trials, but no such difference was found in African participants. These findings suggest that the concept of power can be partly represented by seat position in China.
The Relationship Between Psychological Contract Breach and Job-Related Attitudes Within a Manufacturing Plant

This study investigates the relationship between psychological contract breach (PCB) and three employee attitudes, namely organizational citizenship behavior (OCB), trust in the organization, and intention to leave the job. The study was carried out in an industrial plant in the chemical sector situated in Malta, which was in the process of a takeover from a multinational. Survey data were collected from 258 employees, representing 47% of the workforce in the plant. Results indicate that PCB is negatively related to trust and positively related to the intention to leave the job. The negative relationship between PCB and trust is stronger among female employees. On the other hand, the positive relation between PCB and intention to leave the job is strongest among workers with longer tenure. PCB is only moderately related to OCB among female workers. A number of conceptual and managerial implications are highlighted.
Impact of the sentinel node frozen section result on the probability of additional nodal metastases as predicted by the MSKCC nomogram in breast cancer.

OBJECTIVE Sentinel lymph node frozen section is used to obviate the need for a second operation in breast cancer patients with involved nodes. However, the overall sensitivity, specificity and accuracy of sentinel lymph node frozen section are debated, and the impact of sentinel lymph node frozen section positivity on the risk of additional nodal metastases is not known and was the focus of this investigation. METHODS We used our hospital record system to identify 176 sentinel lymph node biopsies done out of 354 cases of Stage T1-3N0 breast cancers managed from 2005 to 2007 and evaluated the sentinel lymph node frozen section results against the predictions of additional nodal metastases based on the Memorial Sloan-Kettering Breast Cancer Nomogram which is a validated tool for this purpose. RESULTS Sentinel lymph node metastases size was an independent predictor of sentinel lymph node frozen section sensitivity and those with macrometastases had 15 times the odds (odds ratio, 15.4; 95% confidence interval, 3.4-69.1) of having a true-positive frozen section when compared with those with micrometastases. The breast cancer nomogram predicted that the latter patients have a very low probability of additional nodal metastases with a median probability at 10% (inter-quartile range, 7-14%). CONCLUSIONS A negative sentinel lymph node frozen section is also associated with a low probability of additional nodal metastases. Additional prognostic factors in the breast cancer nomogram are of little clinical impact because the most predictive factor in the nomogram is the method of detection.