Miracle-dz/UniFAR-FTUs huggingface dataset:
Module Discovery by Exhaustive Search for Densely Connected, Co-Expressed Regions in Biomolecular Interaction Networks

Background Computational prediction of functionally related groups of genes (functional modules) from large-scale data is an important issue in computational biology. Gene expression experiments and interaction networks are well studied large-scale data sources, available for many not yet exhaustively annotated organisms. It has been well established, when analyzing these two data sources jointly, modules are often reflected by highly interconnected (dense) regions in the interaction networks whose participating genes are co-expressed. However, the tractability of the problem had remained unclear and methods by which to exhaustively search for such constellations had not been presented. Methodology/Principal Findings We provide an algorithmic framework, referred to as Densely Connected Biclustering (DECOB), by which the aforementioned search problem becomes tractable. To benchmark the predictive power inherent to the approach, we computed all co-expressed, dense regions in physical protein and genetic interaction networks from human and yeast. An automatized filtering procedure reduces our output which results in smaller collections of modules, comparable to state-of-the-art approaches. Our results performed favorably in a fair benchmarking competition which adheres to standard criteria. We demonstrate the usefulness of an exhaustive module search, by using the unreduced output to more quickly perform GO term related function prediction tasks. We point out the advantages of our exhaustive output by predicting functional relationships using two examples. Conclusion/Significance We demonstrate that the computation of all densely connected and co-expressed regions in interaction networks is an approach to module discovery of considerable value. Beyond confirming the well settled hypothesis that such co-expressed, densely connected interaction network regions reflect functional modules, we open up novel computational ways to comprehensively analyze the modular organization of an organism based on prevalent and largely available large-scale datasets. Availability Software and data sets are available at http://www.sfu. ca/~ester/software/DECOB.zip.
An Analysis of English–Spanish Cognates as a Source of General Academic Language

Three analyses of Spanish–English cognates were conducted, with the purpose of identifying features that might facilitate or inhibit bilingual students' cognate recognition and cross-language transfer of vocabulary knowledge. Results revealed that both the General Service List and the Academic Word List (AWL) contain a substantial number of English–Spanish cognates, a high percentage of which can be categorized by 1 of 20 cognate patterns. Orthographic and phonological transparencies were analyzed, suggesting that cognates are more transparent in terms of orthography than phonology. A frequency analysis indicated that most AWL cognates are more common in Spanish than in English. Results suggest that carefully designed cognate instruction may provide Spanish-speaking students with a “cognate advantage” in comprehending English academic texts.
Screening for dementia and investigating its causes.

OBJECTIVE To examine, from the perspective of primary care physicians, the value of mental status findings and ancillary tests in diagnosing dementia or its causes. DATA SOURCES Studies identified using MEDLINE and bibliographies of pertinent articles. STUDY SELECTION Selection based on availability of information on specific findings or tests, the criterion standard used to confirm diagnoses, the disease spectrum, and the richness of the reported data. DATA EXTRACTION Data collected on sensitivity and specificity. In many cases, the originally reported data are re-analyzed to illustrate the usefulness of alternative cut-off values or to answer specific clinical questions. Likelihood ratios estimated to summarize test results. DATA SYNTHESIS Probability of dementia is greatly reduced (likelihood ratio, 0.06 to 0.2) when either normal serial 7s, 7-digit span, 3-item recall, or clock drawing test results are obtained; abnormal results only moderately increase the odds of disease. Low (less than or equal to 20), intermediate (21 to 25), or high (greater than or equal to 26) scores on the Mini-Mental State Examination (MMSE) increase (likelihood ratio greater than or equal to 8.2), have little effect (likelihood ratio, 1.3 to 2.4), or decrease (likelihood ratio, 0.06 to 0.1) the odds of disease. The usefulness of tests to investigate the cause of dementia varies depending on the pretest probability of the specific condition. CONCLUSIONS Several useful methods exist to screen for cognitive impairment, and clinicians need to be familiar with the strengths and limitations of their preferred screening methods. In investigating the cause of dementia, routinely obtaining a VDRL test, cerebral imaging studies, serum cobalamin level, or folate level is unwarranted.
The McDonaldization of Academic Libraries and the Values of Transformational Change

Karen P. Nicholson is Manager, Information Literacy, at the University of Guelph, a PhD student at the University of Western Ontario, and a faculty member with the ACRL’s Information Literacy Immersion programs; e-mail: kanichol@uoguelph.ca. The author would like to thank Wendy Holliday, Dr. Pamela J. McKenzie, Courtney Waugh, and the reviewers for their insightful comments on an earlier version of this essay. © 2015 Karen P. Nicholson, Attribution-NonCommercial (http://creativecommons.org/licenses/ by-nc/3.0/) CC BY-NC. In his article “The McDonaldization of Academic Libraries? ” Brian Quinn explores to what extent and to what effect academic libraries have become “McDonaldized,” according to the concept developed by sociologist George Ritzer.1 Quinn identifies a number of ways in which the four dimensions of McDonaldization—efficiency, calculability, predictability, and control (typically realized through the substitution of technology for human labor)—are evident in academic libraries. Tiered reference service, self-check machines, and self-guided tours all represent ways in which libraries have sought to become more efficient. “Just-in-time” approaches to collection development—including a greater reliance on interlibrary loan and document delivery services, part of a larger trend toward access over ownership—and standardized approaches to information literacy instruction also provide greater efficiencies. Calculability is represented in the focus on quantity, such as inputs (like financial resources, number of staff, gate counts, number of volumes) and outputs (for instance, circulation stats, online transactions), as a surrogate for quality. McDonaldization is also apparent in the growing predictability of academic libraries’ collections resulting from the use of approval plans and journal aggregator databases. Likewise, Quinn suggests, most libraries offer the same suite of core services. Finally, in addition to their hierarchical structure and reliance on rules and regulations—typical of bureaucratic systems, and in itself a form of social control—the increasing use of technology in libraries serves as a mechanism of rationalization and control. Although Quinn concedes that “there are obvious advantages in maintaining a wellorganized and efficient work environment,” ultimately, he sees the “bureaucratic, McDonaldized environment” characteristic of academic libraries as a form of irrationality:
Educational Pathways into the Middle Class(es)

Although the close relationship between education and the middle class has long been recognised in the sociology of education, its various dimensions have rarely been examined in detail. Through investigating the educational histories and occupational destinations of 199 recruits into the middle class, this paper explores whether there is any clear connection between educational pathway and occupational location. In particular, it analyses the cohort's various careers against suggested cleavages within the middle class (professional/managerial, symbolic/material, public/private). The data indicate that educational pathways influence occupational locations along a number of directions. Some schools, notably those that are private and academically selective, feed a greater proportion of students into high-status universities and out into high-status occupations. However, in terms of the level of occupation, the status of university seems more important than the school. Whether a school is public or private does not appear to have influenced the choice of a managerial or professional career path, but school sector may contribute to horizontal differentiation of middle classes in terms of whether they take up employment in the public or private sector. The data suggest that schools reflect and reinforce contrasting allegiances to private and public forms of educational provision that then influence sectors of employment and political preferences.
Perception des visages et reconnaissance de la physionomie dans l'agnosie des visages

Resume L'agnosie des visages (prosopagnosie) peut etre observee (tres rarement) apres certaines lesions cerebrales : les patients ne peuvent plus reconnaitre les personnes familieres a la vue de leurs visages. Plusieurs auteurs soutiennent que la perturbation est limitee aux visages et insistent sur la dissociation de ce stimulus parmi les donnees visuelles. Ceci a conduit a emettre Vhypothese de la specificite du « stimulus visage ». Pour d'autres auteurs, l'essentiel du trouble reside plutot dans l'echec de l'evocation du caractere familier et de la reconnaissance de l'individualite lors de l'apprehension visuelle des objets. On analyse ici les travaux de neuropsychologie pathologique realises sur des groupes de patients leses et sur des sujets prosopagnosiques. Les mecanismes de la prosopagnosie ne sont pas eclaircis mais l'analyse de ces difficultes revele des dissociations, importantes a prendre en compte dans les modeles de traitements perceptivo-cognitifs et d'acces aux representations internes (categorisation et individualisation; extraction d'indices locaux et perception de physionomie; apprehension de la nouveaute et de la familiarite). Mots clefs : neuropsychologie, agnosie des visages, reconnaissance des visages, traitements visuo-cognitifs, representation visuo-imagee.
Age and motives for volunteering: Further evidence

This work has explored the socioemotional selectivity theory (Cartensen, 1995) with the purpose of evaluating how people selectively optimize their activities involving social investments as they increase in age, investing more in self-relevant and emotionally meaningful goals. Specifically, the purpose of this study was to test hypotheses derived from the socioemotional selectivity theory regarding the effects of age on motives for volunteering. The Volunteer Functions Inventory (Clary et al., 1998) was completed by 214 volunteers affiliated with different organizations. Results indicated that, as age increases, career, understanding and making friends volunteer motivations decrease, while social and values volunteer motivations increase. Possible implications for volunteer management in organizations are analyzed.
Emergence of a new norovirus GII.6 variant in Japan, 2008–2009

Norovirus (NoV) is recognized as one of the most common causative agents of diarrhea disease in young children. A total of 187 fecal specimens collected from non‐hospitalized children with acute gastroenteritis in Shizuoka, Japan during July 2008 to June 2009 were investigated for the presence of diarrhea viruses by a multiplex RT‐PCR. Diarrhea viruses were overall detected in 158 of 187 (84.5%). Of the viruses detected, NoV was the most prevalent (55.6%). Most of the NoV sequences belonged to GII.4 (53.8%). NoV GII.6 emerged as the second most common strain (40.4%). The full‐length capsid sequences of five representative Shizuoka GII.6 strains were compared with all 12 GII.6 strains available in GenBank database between 1990 and 2009. At least three distinct GII.6 subclusters (a–c) appeared in different parts of the world. Shizuoka GII.6 strains formed their own subcluster c, distinct from other complete GII.6 reference sequences. The Shizuoka strains had significant amino acid divergence, particularly in the P2 domain up to 10.9–17.5% and contained eight unique mutations in the P domains, compared with subcluster a and b viruses. The homology model showed that the eight mutations were predicted to be located at the surface‐exposed P1 and P2 domains. The data suggest the emergence of a new NoV GII.6 variant in Shizuoka, with a high level of genetic variation. J. Med. Virol. 84: 1089–1096, 2012. © 2012 Wiley Periodicals, Inc.
Is M82 X-1 Really an Intermediate-Mass Black Hole? X-Ray Spectral and Timing Evidence

Ultraluminous X-ray sources (ULXs) with apparent luminosities up to hundreds of times the Eddington luminosity for a neutron star have been discovered in external galaxies. The existence of intermediate-mass black holes has been proposed to explain these sources. We present evidence for an intermediate-mass black hole in the ULX M82 X-1 based on the spectral features and timing (quasi-periodic oscillation [QPO]) properties of the X-radiation from this source. We revisited XMM-Newton and Rossi X-Ray Timing Explorer (RXTE) data for M82 X-1 obtained in 2001 and 1997 for XMM and RXTE, respectively. We show for these observations that the source is either in transition or in a high/soft state with photon spectral indices 2.1 and 2.7, respectively. We confirm the early determination of the QPO frequency ν ≈ 55 mHz in this source by Strohmayer & Mushotzky and identify this as the low-frequency QPO for the source. We apply a new method to determine the black hole mass of M82 X-1. The method uses the index-QPO low-frequency correlation that has been recently established in Galactic black hole candidates GRS 1915+105, XTE J1550-564, 4U 1630-47, and others. Using scaling arguments and the correlation derived from the consideration of Galactic black holes, we conclude that M82 X-1 is an intermediate black hole with a mass of the order of 1000 M☉.
Understanding pretence and understanding action

Two studies were carried out in an attempt to replicate an earlier but controversial set of findings that suggested that young children are able to understand pretence in a mentalistic sense (Hickling, Wellman, & Gottfried, 1997). In Study 1, 65 three-year-olds and 77 four-year-olds were asked to either judge the thoughts of an absent teddy bear, who had not witnessed a change in the original pretence stipulation, or were asked to complete a similar, standard false-belief task. Study 2 repeated the experimental procedures of the first study with 24 three-year-olds and 16 four-year-olds, with the difference that all children had to complete both tasks in a single session. The results obtained across both studies showed that 3-year-olds were unable to correctly judge the discrepant thoughts of the teddy bear, suggesting that young children do not attribute a false belief to another actor during pretend play, and that instead they view pretence in terms of overt action.
Analysis of Chemokines and Receptors Expression Profile in the Myelin Mutant Taiep Rat

Taiep rat has a failure in myelination and remyelination processes leading to a state of hypomyelination throughout its life. Chemokines, which are known to play a role in inflammation, are also involved in the remyelination process. We aimed to demonstrate that remyelination-stimulating factors are altered in the brainstem of 1- and 6-month-old taiep rats. We used a Rat RT2 Profiler PCR Array to assess mRNA expression of 84 genes coding for cytokines, chemokines, and their receptors. We also evaluated protein levels of CCL2, CCR1, CCR2, CCL5, CCR5, CCR8, CXCL1, CXCR2, CXCR4, FGF2, and VEGFA by ELISA. Sprague-Dawley rats were used as a control. PCR Array procedure showed that proinflammatory cytokines were not upregulated in the taiep rat. In contrast, some mRNA levels of beta and alpha chemokines were upregulated in 1-month-old rats, but CXCR4 was downregulated at their 6 months of age. ELISA results showed that CXCL1, CCL2, CCR2, CCR5, CCR8, and CXCR4 protein levels were decreased in brainstem at the age of 6 months. These results suggest the presence of a chronic neuroinflammation process with deficiency of remyelination-stimulating factors (CXCL1, CXCR2, and CXCR4), which might account for the demyelination in the taiep rat.
Nurturing longevity: Sociological constructions of ageing, care and the body

Abstract This paper examines assumptions that surround the way that aged care and assistance is conceptualised and discussed. Problems with the concept of care became apparent with the critique of care theory by the disability movement in the 1980s and continue to this day. Debates arose initially between those who sought to identify care as a gender-based duty that serves to burden those who take responsibility for it, and those who reject the concept as a form of socially constructed dependency. The paper considers the problematic sociological foundations of this critique – the failure to incorporate an understanding of the body into much sociological theory and the significance that the conceptualisation has for understanding the need for personal assistance in advanced old age. While the disability critique of care is firmly grounded in a sociological analysis, it overemphasises the social construction of social relations and ignores the visceral reality of the body. Longevity care, in contrast, needs to explicitly acknowledge that ageing is an embodied and physical process that generates a need for care. The conclusions are tested against recent Australian data and research on care needs and preferences amongst older people.
Exploring the Potential of Computers to Enrich Home and Community-Based Services Clients' Social Networks

Older persons receiving services in community settings, rather than Nursing Homes, are at risk of social isolation. Computer mediated communication offers technological resources that recipients of Home and Community-Based Services (HCBS) might use to reduce their social isolation. The present study involved personal interviews with 40 HCBS clients regarding their interest in communicating with members of their social networks and using computers. At the time of the interview, 30 of the 40 participants did not use computers and reported cost, lack of training, physical limitations, lack of interest and access, and fraud as the reasons for not using computers. After watching a videotape illustrating an easy-to-use computer interface that allows older persons to communicate with families and friends, 90% reported that it would be helpful for people like them. Participants said such a computer would be helpful because it would make communication with friends and family easy, it could accommodate visual and manual disabilities, and would be interesting. Eighty-five percent said they would use a system like the one they were shown if it were available to them.
Influence of three lighting regimes during ten weeks growth phase on laying performance, plasma levels- and tissue specific gene expression- of reproductive hormones in Pengxian yellow pullets

The study was conducted to optimize lighting schedule for pre-pubertal (12 to 22 weeks) Chinese native breed Pengxian yellow pullet. A total of 414 healthy pullets (10 weeks), with similar body weight were randomly distributed into three groups (n = 138) and housed in individual cages for up to 12 weeks of age in light controlled rooms and provided normal lighting schedule (10L:14D). At 12 to 18 weeks of age, pullets were housed in three rooms, having varying lighting schedule viz. G1 (8L: 16D), G2 (10L:14D), or G3 (12L:12D). From 19th week onwards lighting schedule was gradually increased every week in incremental manner till all groups started receiving 16L:8D lighting schedule. The age at first egg, weight of first egg laid, percent peak hen day egg production, concentration of plasma luteinizing and follicle-stimulating hormones and expression of genes regulating synthesis or/and secretion of hypothalamic gonadotropin-releasing hormone-I (GnRH-I), and pituitary LH-β and FSH-β were studied during experimental period (12 to 43 weeks of age) of this study. The result indicated that pullets of long day length (G3) group had higher plasma levels of FSH and LH and also better mRNA expression that regulates synthesis or/and secretion of GnRH-I, FSH-β, and LH-β before egg laying. The age at first egg (151.3 days) in pullets of G3 group receiving longer lighting hours (12L:12D) was 8.8 days less (P<0.05) compared to pullets of G1 group, while it was 6.9 days less (P>0.05) compared to G2. However, significantly higher (P<0.05) plasma levels of LH and FSH in pullets of G1 as compared to pullets belonging to G3 group corresponded with the higher (P<0.05) cumulative egg production during the experimental period, while these attributes in G2 group didn’t differ from either G1 or G3 groups. Pullets of G1 group had significantly higher levels (P<0.05) of GnRH-I, FSH-β, and LH-β mRNA abundances at 43 weeks of age than other two groups and this corresponded with the percent (hen day) peak egg production (75.38%) in pullets in this G1 group that was attained at 32 weeks of age, while the peak production of 71.24% was attained at 30 weeks of age in G3 group. There was no effect of lighting schedule on body weight of pullets, recorded during experimental period, at all occasions; belonging to three groups (G1,G2 and G3) and receiving varying hours of photo-stimulation (P>0.05). It was inferred that the optimum lighting schedule for Chinese native breed Pengxian yellow pullets during 10 weeks of pre-pubertal growth period is short hours of photo-stimulation (i.e 8L:16D).
Return to the Zombie Gadgets: Undermining Destructive Code Reads via Code Inference Attacks

The concept of destructive code reads is a new defensive strategy that prevents code reuse attacks by coupling fine-grained address space layout randomization with a mitigation for online knowledge gathering that destroys potentially useful gadgets as they are disclosed by an adversary. The intuition is that by destroying code as it is read, an adversary is left with no usable gadgets to reuse in a control-flow hijacking attack. In this paper, we examine the security of this new mitigation. We show that while the concept initially appeared promising, there are several unforeseen attack tactics that render destructive code reads ineffective in practice. Specifically, we introduce techniques for leveraging constructive reloads, wherein multiple copies of native code are loaded into a process' address space (either side-by-side or one-after-another). Constructive reloads allow the adversary to disclose one code copy, destroying it in the process, then use another code copy for their code reuse payload. For situations where constructive reloads are not viable, we show that an alternative, and equally powerful, strategy exists: leveraging code association via implicit reads, which allows an adversary to undo in-place code randomization by inferring the layout of code that follows already disclosed bytes. As a result, the implicitly learned code is not destroyed, and can be used in the adversary's code reuse attack. We demonstrate the effectiveness of our techniques with concrete instantiations of these attacks against popular applications. In light of our successes, we argue that the code inference strategies presented herein paint a cautionary tale for defensive approaches whose security blindly rests on the perceived inability to undo the application of in-place randomization.