Miracle-dz/UniFAR-FTUs huggingface dataset:
Using Genetic Networks and Homology to Understand the Evolution of Phenotypic Traits

Homology can have different meanings for different kinds of biologists. A phylogenetic view holds that homology, defined by common ancestry, is rigorously identified through phylogenetic analysis. Such homologies are taxic homologies (=synapomorphies). A second interpretation, “biological homology” emphasizes common ancestry through the continuity of genetic information underlying phenotypic traits, and is favored by some developmental geneticists. A third kind of homology, deep homology, was recently defined as “the sharing of the genetic regulatory apparatus used to build morphologically and phylogenetically disparate features. ” Here we explain the commonality among these three versions of homology. We argue that biological homology, as evidenced by a conserved gene regulatory network giving a trait its “essential identity” (a Character Identity Network or “ChIN”) must also be a taxic homology. In cases where a phenotypic trait has been modified over the course of evolution such that homology (taxic) is obscured (e.g. jaws are modified gill arches), a shared underlying ChIN provides evidence of this transformation. Deep homologies, where molecular and cellular components of a phenotypic trait precede the trait itself (are phylogenetically deep relative to the trait), are also taxic homologies, undisguised. Deep homologies inspire particular interest for understanding the evolutionary assembly of phenotypic traits. Mapping these deeply homologous building blocks on a phylogeny reveals the sequential steps leading to the origin of phenotypic novelties. Finally, we discuss how new genomic technologies will revolutionize the comparative genomic study of non-model organisms in a phylogenetic context, necessary to understand the evolution of phenotypic traits.
Quality assurance for distance learning: a case study at Brunel University

Brunel University currently has four distance learning MSc courses, with over 500 students registered, and one undergraduate distance learning course. Some have been running for over five years, and well-established practices have been developed and provide a basis of support for the university. Quality assurance in the university has always been considered in three, equally important, ways: the curriculum and its assessment; the handling of coursework and assignments; and the liaison with students. The lesson we have learned is that a distance learning programme must be based on an existing full-time MSc programme, which is the gold standard for curriculum and its assessment, and where possible, common examinations and assessment be used. This can be further assured by scrutinisation by the associated research council. This is going to become ever more important with the increasing scrutiny by overseas governments on the academic quality of distance learning courses, which seek assurance on the comparability and quality of degrees. Quality assurance for the handling of coursework and assignments must be secure and demands a high overhead of paperwork. Detailed feedback to students on their assignments is essential, but this can, at the same time, form a quality assurance check for later progression decisions. We also copy and retain approximately 10% of the assignments for the same purpose. Rapid turnaround is essential if feedback is to be timely and therefore useful, and quality checks on processing time should be standard. Quality assurance for the procedures for liaison with distance learning students are somewhat harder to measure quantitatively. The mark of good distance learning must be its tutorial support. This demands good communications. Our own course, entitled Data Communications Systems, benefits from the high proportion of use of electronic communications, namely email, which allows fast turnaround of questions, yet is not intrusive. However, it is deemed essential that hard copy of all such correspondence is kept. Migration to other Internet support services, such as the World Wide Web, videoconferencing and groupware, is inevitable. [ABSTRACT FROM AUTHOR]
Corner detection and matching methods for brain medical image classification

many methods have been developed for corner detection and matching. However, these detection methods do not take the domain knowledge of brain medical images into account. They produce some useless corners and lose essential domain information. Moreover, existing corner matching methods do not consider the uncertainty and structure of brain medical images. And most of them are developed for 3D medical image registration, which are not applicable for 2D image classification. To address these problems, a corner detection method is firstly proposed based on hierarchical textures. Then, based on the uncertainty and structure of brain medical images, a corner matching method is developed to yield an initial and furthermore a maximum matched corner pair sequences. Finally, a similarity function is presented for classification. Experimental results show the proposed corner detection method outperforms the existing method and the classification results based on the maximum matched corner pair sequence are better than the state-of-the-art brain medical image classification methods.
Behavioral functioning in youth with inflammatory bowel disease: perceived barriers as mediator of medication adherence.

OBJECTIVES To examine the relationship between behavioral functioning specific to levels of attention and conduct problems and prescription medication adherence in youth with inflammatory bowel disease (IBD), and examine the mediational role of perceived barriers to adherence. Identifying potentially malleable factors associated with poor adherence such as behavioral functioning and barriers may guide treatment. METHODS 85 adolescents with IBD and their parents completed measures of adherence, attention and conduct problems, and barriers. To examine mediation models, indirect effects were tested using bootstrapping procedures outlined by Preacher & Hayes (2004, 2008). RESULTS The majority of participants reported normative levels of attention and conduct problems. Higher levels of attention problems, conduct problems, and barriers were negatively associated with adherence. Bootstrapping procedures indicated that barriers mediated the effects of behavioral functioning on adherence. CONCLUSIONS Barriers may be a proximal factor contributing to the relationship between everyday behavioral functioning and adherence in youth with IBD.
Hyperplasia, partial hepatectomy, and the carcinogenicity of aflatoxin B1

Generalized cellular hyperplasia has long been associated as a factor in the causation of liver cancer. Parenchymal cell hyperplasia resulting from hepatotoxins, viruses, parasites, or malnutrition is exceedingly variable as to when it occurs, its extent, and its duration. Partial hepatectomy has been used as an experimental tool precisely because the timing and extent of hyperplasia can be known and controlled. With regards to aflatoxin B1 (AFB1) carcinogenesis, partial hepatectomy has produced variable results. An explanation appears to reside in the hepatotoxic properties of AFB1 that enhance the early stages of carcinogenesis. © 2003 Wiley‐Liss, Inc.
Ontology evolution as reconfiguration-design problem solving

In this paper we present an approach to model ontology evolution as reconfiguration-design problem solving. The problem is reduced to a graph search where the nodes are evolving ontologies and the edges represent the changes that transform the source node into the target node. The search is guided by the constraints provided partially by a user and partially by a set of rules defining ontology consistency. In this way we allow a user to specify an arbitrary request declaratively and ensure its resolving. The approach is implemented in the KAON framework and the evaluation study shows its benefits.
Tumor marker utility grading system: a framework to evaluate clinical utility of tumor markers.

Introduction of tumor markers into routine clinical practice has been poorly controlled, with few criteria or guidelines as to how such markers should be used. We propose a Tumor Marker Utility Grading System (TMUGS) to evaluate the clinical utility of tumor markers and to establish an investigational agenda for evaluation of new tumor markers. A Tumor Marker Utility Grading Worksheet has been designed. The initial portion of this worksheet is used to clarify the precise characteristics of the marker in question. These characteristics include the marker designation, the molecule and/or substance and the relevant alteration from normalcy, the assay format and reagents, the specimen type, and the neoplastic disease for which the marker is being evaluated. To determine the clinical utility of each marker, one of several potential uses must be designated, including risk assessment, screening, differential diagnosis, prognosis, and monitoring clinical course. For each of these uses, associations between marker assay results and expected biologic process and end points must be determined. However, knowledge of tumor marker data should contribute to a decision in practice that results in a more favorable clinical outcome for the patient, including increased overall survival, increased disease-free survival, improvement in quality of life, or reduction in cost of care. Semiquantitative utility scales have been developed for each end point. The only markers recommended for use in routine clinical practice are those that are assigned utility scores of "++" or " " on a 6-point scale (ranging from 0 to ) in the categories relative to more favorable clinical outcomes. Each utility score assignment should be supported by documentation of the level of evidence used to evaluate the marker. TMUGS will establish a standardized analytic technique to evaluate clinical utility of known and future tumor markers. It should result in improved patient outcomes and more cost-efficient investigation and application of tumor markers.
Marginal zone B cells exhibit unique activation, proliferative and immunoglobulin secretory responses

Mouse splenic B cells can be separated based on their distinctive expression of cell surface antigens. Marginal zone (MZ) B cells are CD38high CD21high CD23low/−, while follicular (FO) B cells are CD21int CD23int and newly formed (NF) B cells are CD21dim/− CD23−. Exploiting these phenotypic distinctions, we isolated the three B cell subsets and assessed their other phenotypic differences and functional capabilities in vitro. FO B cells proliferate more than the other B cell subsets in response to either IgM or CD38 cross‐linking. MZ B cells proliferate better than FO B cells when stimulated with lipopolysaccharide (LPS), sub‐optimal levels of LPS and CD38 cross‐linking or CD40 ligation. When NF, FO and MZ B cells were stimulated with either LPS or LPS and interleukin‐4, MZ B cells secreted more IgM and IgG3 than the other two subsets. Similarly, calcium fluxes measured within MZ B cells are larger in amplitude and more sustained after B cell receptor cross‐linking than those found in the other two subsets. Collectively, these results indicate that CD38high CD21high CD23low/− MZ B cells are specially suited to play a unique role in response to antigens delivered to the MZ area.
A Novel Recommender System Based on Fuzzy Set and Rough Set Theory

Recommender System is an effective means of handling information overload and can provide personalized service as a useful information tool in e-commerce. In this paper, a novel automatic recommender system is proposed based on fuzzy c-means algorithm and rough set theory, including three main steps: data discretization, rules establishing and fuzzy reasoning. A method for fitting the results of FCM clustering is put forward by membership function and using it with attributes to achieve data discretization, in order to avoid the processing that each input data have to carry clustering operation for discretization. Using rough set theory, it can accelerate the speed of fuzzy reasoning through rules reduction with choosing closely relating attributes for commodity. Fuzzy reasoning method is also applied into commodity recommender system. Lastly, a case study conducted by the presented method is given, and the results show that this model can provide valuable advice for potential users and it is also an effective way for recommendation.
A mass shooting at Port Arthur, Tasmania, Australia: a study of its impact on early pregnancy losses using a conception time-based methodology.

STUDY QUESTION Does an acute calamity in a community cause early miscarriage and is this association the same for male and female fetuses? SUMMARY ANSWER Estimated losses of 29.5% of first trimester pregnancies in the affected region could be associated with an acute calamity, with no statistically significant difference in estimated losses by fetal sex. WHAT IS KNOWN ALREADY There are very few studies on the impact of a calamity on early pregnancy loss and its differential effects on male and female fetuses. A decline in the human sex ratio at birth associated with the events of 9/11 in New York has been documented. STUDY DESIGN, SIZE, DURATION This is a retrospective descriptive study of birth register data in Tasmania, Australia, from 1991 to 1997, covering the period in which the calamity occurred. The register contains data on all pregnancies that proceeded to >20 weeks gestation. The conception date was calculated by subtracting gestational age from birth date. We estimated that 40 318 pregnancies were conceived in the period 1991-1996 inclusive. These were aggregated to 4-weekly blocks classified by region and sex. PARTICIPANTS/MATERIALS, SETTING, METHODS The acute calamity was at Port Arthur, Tasmania, Australia. On 28 April 1996, a gunman opened fire on visitors and staff in a tourist cafe. A very stressful 20 h period, ended with 35 people dead and 22 injured. A negative binomial regression model was used to assess the association between this calamity and pregnancy loss. This loss is evidenced by a shortfall in the registration of pregnancies that were in their first trimester at the time of the calamity. MAIN RESULTS AND THE ROLE OF CHANCE We estimated a shortfall of 29.5% or 229 registered pregnancies among those in the first trimester at the time of the calamity (P < 0.001), in the region surrounding the calamity site. There was no sex effect in this shortfall (P = 0.911). There was no corresponding shortfall in other parts of Tasmania (P = 0.349). LIMITATIONS, REASONS FOR CAUTION The study is descriptive and cannot produce causal inferences. These first trimester miscarriages are estimated statistically and it is understood that gestational age is an estimate. The use of maternal residential postcodes at birth as a surrogate for geographic area or space assumes that the mother has not moved into the postcode area after the calamity and before the reporting of a birth. WIDER IMPLICATIONS OF THE FINDINGS The results of this study suggest that calamities bring about significant pregnancy loss affecting both sexes. The methodology presented of inferring conception date from birth date and using this for analysis, provides a more accurate assessment of first trimester pregnancy losses than raw birth data or sex ratio at birth.
A prefetching technique for irregular accesses to linked data structures

Prefetching offers the potential to improve the performance of linked data structure (LDS) traversals. However, previously proposed prefetching methods only work well when there is enough work processing a node that the prefetch latency can be hidden, or when the LDS is long enough and the traversal path is known a priori. This paper presents a prefetching technique called prefetch arrays which can prefetch both short LDS, as the lists found in hash tables, and trees when the traversal path is nor known a priori. We offer two implementations, one software-only and one which combines software annotations with a prefetch engine in hardware. On a pointer-intensive benchmark suite, we show that our implementations reduce the memory stall lime by 23% to 51% for the kernels with linked lists, while the other prefetching methods cause reductions that are substantially less. For binary-trees, our hardware method manages to cut nearly 60% of the memory stall time even when the traversal path is not known a priori. However, when the branching factor of the tree is too high, our technique does not improve performance. Another contribution of the paper is that we quantify pointer-chasing found in interesting applications such as OLTP, Expert Systems, DSS, and JAVA codes and discuss which prefetching techniques are relevant to use in each case.
Black Professors Managing Mentorship: Implications of Applying Social Exchange Frameworks to Analyses of Student Interactions and Their Influence on Scholarly Productivity

Background/Context Past research has focused on benefits that students reap from mentoring, but less attention has been focused on the faculty experience. Studies on faculty and mentorship tend to highlight the costs that can negatively influence faculty productivity rather than addressing any benefits they may accrue. Black faculty may be at particularly high risk for these challenges, considering their high rates of service and mentorship. By examining the nature of mentoring, this study clarifies how certain types of developmental relationships may distract, but also potentially contribute to the scholarly success of, Black professors. Purpose/Objective/Research Question/Focus of Study The purpose of this study is to explore how Black faculty experience and perceive specific types of interactions within their mentoring relationships, especially in relation to their scholarly productivity. Setting Data were collected at two large predominantly White research universities of similar size, type, and mission: Oceanside University and Column University (pseudonyms). Population/Participants/Subjects A total of 17 Oceanside professors (10 males, 7 females) and 11 Column professors (6 males, 5 females) agreed to participate. Five participants were assistant, 11 were associate, and 12 were full professors. The largest proportion of faculty taught in the social sciences (n = 12), followed by professional programs (n = 5). Research Design This research is a qualitative multi–case study that uses pattern matching to analyze transcripts of 60- to 90-minute interviews with faculty participants. Findings/Results Interactions with students were perceived as having both costs and benefits, which had varying influence on productivity based on the type of interaction between the faculty member and the student. Collaborative activities (productive exchanges) have the potential to increase faculty productivity; however, interactions that are focused primarily on student development (generalized exchanges) can be rewarding, yet appear more likely to distract from research and limit scholarly productivity. Conclusions/Recommendations Although Black professors participating in this study perceived themselves as more likely to counsel students (generalized exchanges), they did not note that they were more likely to collaborate with students, particularly on research. Thus, rather than suggesting that Black faculty have slower rates of advancement and higher rates of attrition because they spend too much time working with students, this study suggests that perhaps their diminished outcomes stem from both frequency and form of interaction. Findings suggest that policy makers and institutional leaders, in addition to supporting Black professors as they work with students, could consider ways to foster the ability of Black professors to simultaneously counsel and collaborate with students as they develop strategies to encourage faculty promotion and retention.
Evaluation of synchronous-rectification efficiency improvement limits in forward converters

Design trade-offs for different implementations of the forward power converter with synchronous rectifiers are presented, and effects of the synchronous rectifier driving method on the conversion efficiency are evaluated. Specifically, the merits and limitations of the RCD-clamp and active-clamp reset approaches for a power converter with self-driven synchronous rectifiers are discussed. Estimates of the upper limits of the efficiency improvements of the discussed synchronous rectification approaches relative to the Schottky diode implementation are derived. Finally, experimental comparisons of efficiencies for an offline, 3.3 V/20 A forward power converter power stage are presented and compared with the theoretically estimated ones. >
Falls among Community-Dwelling Older Adults: Determining the Relationship between Social Networks and the Risk for falls

Falls among community-dwelling older adults: Determining the relationship between social networks and the risk for falls Sikhrakar, Smita, M.Sc. Minnesota State University, Mankato, 2015. 71 pp. Falls among community-dwelling older adults is a big public health problem, which have an effect on older adults’ health, independence, and quality of life. The purpose of this study was to determine the relationship between social networks and the risk for falls among communitydwelling older adults. This was a descriptive correlational study, which utilized a cross-sectional survey for the data collection. The dependent and independent variable of this study were the risk for falls among the community-dwelling older adults, and the strength and type of social networks respectively. In this study, 218 community-dwelling older adults were recruited, who were living in the south-central Minnesota in the United States. A paper survey was distributed, which included the Demographic Tool, Fall Risk Questionnaire, and Lubben Social Network Scale. However, the total number of participants who completed the survey was 184 older adults. The results of this study showed that there is a weak negative relationship between the strength of social networks and the risk for falls, but was not statistically significant. It is recommended to conduct future research with the inclusion of gender as an independent variable to understand their impact on the relationship between social networks and the risk for falls. In the future, a tool that measures the impact of structural and functional dimensions of social networks on the risk for falls is necessary to understand the relationship between social networks and the risk for falls.
Radio environment map as enabler for practical cognitive radio networks

Latest regulations on TV white space communications and emerging trends of spectrum access through geolocation databases relax the regulatory constraints on Cognitive Radios (CRs). Geolocation databases are designed to store information related to incumbents, and CRs are envisioned to consult this database before spectrum access. Spectrum occupancy and related environment information can be constructed using these geolocation databases. In that regard, Radio Environment Map (REM) is a promising tool that provides a practical means for the realization of cognitive radio networks (CRNs). It constructs a comprehensive map of the CRN by utilizing multi-domain information from geolocation databases, characteristics of spectrum use, geographical terrain models, propagation environment, and regulations. REMs contribute to cognition engines by building long-term knowledge via processing spectrum measurements collected from sensors to estimate the state of locations where there is no measurement data. In addition, REM utilizes feedback from the CRs and can apply various learning tools. The vision is to design CRNs such that CRs, though being simple devices without advanced cognitive functionalities, can become cognitive via REMs and operate in an efficient manner. In this paper, an overview of the REM concept is presented in various dimensions ranging from its architecture and stored information to REM construction techniques as well as REM quality metrics.