Solving Maximum Clique Problem for Protein Structure Similarity

Computing the similarity between two protein structures is a crucial task in molecular biology, and has been extensively investigated. Many protein structure comparison methods can be modeled as maximum weighted clique problems in specific k-partite graphs, referred here as alignment graphs. In this paper we present both a new integer programming formulation for solving such clique problems and a dedicated branch and bound algorithm for solving the maximum cardinality clique problem. Both approaches have been integrated in VAST, a software for aligning protein 3D structures largely used in the National Center for Biotechnology Information, an original clique solver which uses the well known Bron and Kerbosch algorithm (BK). Our computational results on real protein alignment instances show that our branch and bound algorithm is up to 116 times faster than BK.

Investigating the role of capacitive coupling between the operating table and the return electrode of an electrosurgery unit in the modification of the current density distribution within the patients’ body

Background: Electrosurgery units are widely employed in modern surgery. Advances in technology have enhanced the safety of these devices, nevertheless, accidental burns are still regularly reported. This study focuses on possible causes of sacral burns as complication of the use of electrosurgery. Burns are caused by local densifications of the current, but the actual pathway of current within patient's body is unknown. Numerical electromagnetic analysis can help in understanding the issue. Methods: To this aim, an accurate heterogeneous model of human body (including seventy-seven different tissues), electrosurgery electrodes, operating table and mattress was build to resemble a typical surgery condition. The patient lays supine on the mattress with the active electrode placed onto the thorax and the return electrode on his back. Common operating frequencies of electrosurgery units were considered. Finite Difference Time Domain electromagnetic analysis was carried out to compute the spatial distribution of current density within the patient's body. A differential analysis by changing the electrical properties of the operating table from a conductor to an insulator was also performed. Results: Results revealed that distributed capacitive coupling between patient body and the conductive operating table offers an alternative path to the electrosurgery current. The patient's anatomy, the positioning and the different electromagnetic properties of tissues promote a densification of the current at the head and sacral region. In particular, high values of current density were located behind the sacral bone and beneath the skin. This did not occur in the case of non-conductive operating table. Conclusion: Results of the simulation highlight the role played from capacitive couplings between the return electrode and the conductive operating table. The concentration of current density may result in an undesired rise in temperature, originating burns in body region far from the electrodes. This outcome is concordant with the type of surgery-related sacral burns reported in literature. Such burns cannot be immediately detected after surgery, but appear later and can be confused with bedsores. In addition, the dosimetric analysis suggests that reducing the capacity coupling between the return electrode and the operating table can decrease or avoid this problem. © 2013 Bifulco et al.; licensee BioMed Central Ltd.

A wearable device for recording of biopotentials and body movements

Long term recording of biomedical signals such as ECG, EMG, respiration and other information (e.g. body motion) can improve diagnosis and potentially monitor the evolution of many widespread diseases. However, long term monitoring requires specific solutions, portable and wearable equipment that should be particularly comfortable for patients. The key-issues of portable biomedical instrumentation are: power consumption, long-term sensor stability, comfortable wearing and wireless connectivity. In this scenario, it would be valuable to realize prototypes using available technologies to assess long-term personal monitoring and foster new ways to provide healthcare services. The aim of this work is to discuss the advantages and the drawbacks in long term monitoring of biopotentials and body movements using textile electrodes embedded in clothes. The textile electrodes were embedded into garments; tiny shirt and short were used to acquire electrocardiographic and electromyographic signals. The garment was equipped with low power electronics for signal acquisition and data wireless transmission via Bluetooth. A small, battery powered, biopotential amplifier and three-axes acceleration body monitor was realized. Patient monitor incorporates a microcontroller, analog-to-digital signal conversion at programmable sampling frequencies. The system was able to acquire and to transmit real-time signals, within 10 m range, to any Bluetooth device (including PDA or cellular phone). The electronics were embedded in the shirt resulting comfortable to wear for patients. Small size MEMS 3-axes accelerometers were also integrated. © 2011 IEEE.

Inverse Problem for Fractional Diffusion Equation

MSC 2010: 26A33, 33E12, 34K29, 34L15, 35K57, 35R30

Many Facet, Common Latent Trait Polytomous IRT Model and EM Algorithm

2000 Mathematics Subject Classification: 91E45.

On the Time Complexity of the Problem Related to Reducts of Consistent Decision Tables

In recent years, rough set approach computing issues concerning reducts of decision tables have attracted the attention of many researchers. In this paper, we present the time complexity of an algorithm computing reducts of decision tables by relational database approach. Let DS = (U, C ∪ {d}) be a consistent decision table, we say that A ⊆ C is a relative reduct of DS if A contains a reduct of DS. Let s = be a relation schema on the attribute set C ∪ {d}, we say that A ⊆ C is a relative minimal set of the attribute d if A contains a minimal set of d. Let Qd be the family of all relative reducts of DS, and Pd be the family of all relative minimal sets of the attribute d on s. We prove that the problem whether Qd ⊆ Pd is co-NP-complete. However, the problem whether Pd ⊆ Qd is in P .

To move or not to move, that is the question! Body schema and non-action oriented body representations:an fMRI meta-analytic study

Many studies have attempted to identify the different cognitive components of body representation (BR). Due to methodological issues, the data reported in these studies are often confusing. Here we summarize the fMRI data from previous studies and explore the possibility of a neural segregation between BR supporting actions (body-schema, BS) or not (non-oriented-to-action-body-representation, NA). We performed a general activation likelihood estimation meta-analysis of 59 fMRI experiments and two individual meta-analyses to identify the neural substrates of different BR. Body processing involves a wide network of areas in occipital, parietal, frontal and temporal lobes. NA selectively activates the somatosensory primary cortex and the supramarginal gyrus. BS involves the primary motor area and the right extrastriate body area. Our data suggest that motor information and recognition of body parts are fundamental to build BS. Instead, sensory information and processing of the egocentric perspective are more important for NA. In conclusion, our results strongly support the idea that different and segregated neural substrates are involved in body representations orient or not to actions.

Perceptions of family environment, body image and self-esteem of eating disordered and non-eating disordered women

This study explored the perceptions of family environment, body image and self esteem of women who suffer from anorexia nervosa, bulimia nervosa, and depression. Using a nonequivalent control group design, one hundred and fifty women with anorexia nervosa (n = 50), bulimia nervosa (n = 50), and depression (n = 50) were given the Family Environment Scale (FES) and the Eating Disorders Inventory-2 (EDI-2). The objectives of this study were to: (1) study how women with anorexia nervosa and bulimia nervosa perceive their family environment as measured by the FES; (2) compare and contrast perceptions of family environment of women with anorexia nervosa and bulimia nervosa with the control group; (3) compare and contrast perceived levels of self esteem and body image as measured by the EDI-2 of women with anorexia nervosa and bulimia nervosa with the control group; and (4) examine the perceived family environments of eating disordered and non-eating disordered women with regard to body image and self esteem. Results suggested, women who suffered from anorexia nervosa or bulimia nervosa scored significantly lower (p $<$.021) on the Expressiveness, Intellectual-Cultural Orientation, and Active-Recreational subscales of the FES. The results also indicated that women who suffered from bulimia nervosa scored significantly higher (p $<$.015) than women who suffered from anorexia nervosa on the Conflict and Independence subscales of the FES. The results of studying these three populations reflected that women who suffered from anorexia nervosa scored significantly different (p $<$.000) than women who suffered from bulimia nervosa on many of the subscales of the EDI-2. The findings of the study confirmed that women who suffered from anorexia nervosa or bulimia nervosa scored significantly different (p $<$.000) on the subscales of the EDI-2 compared to women who suffered from depression. It was also confirmed that a relationship does exist between perceptions of body image and self esteem and perceptions of family environment amongst women with anorexia nervosa and bulimia nervosa as compared to depressed women. The findings of the study indicated that women who suffered from anorexia nervosa tended to: be less expressive and independent; handle conflict less openly; have a greater drive for thinness; have greater body dissatisfaction; be more perfectionistic; and struggle more intensely with fears around maturity and social insecurity than did women who suffered from bulimia nervosa or depression. In addition, the findings of the study also suggested that women who suffered from bulimia nervosa tended to: be raised in homes where openly expressed anger is permitted amongst family members; have a lesser drive for thinness; have less body dissatisfaction; be less perfectionistic; and not struggle as intensely with fears around maturity and social insecurity as do women who suffered from anorexia nervosa, but more than women who suffer from depression. Treatment implications that may assist community college professors and counselors in meeting the special needs of this special group of women were also discussed. (Abstract shortened by UMI.) ^

A qualitative study of the clinical practice of graduates of a problem-based physical therapy program

The purpose of this study was to examine the perspectives of three graduates of a problem-based leaning (PBL) physical therapy (PT) program about their clinical practice. The study used the qualitative methods of observations, interviews, and journaling to gather the data. Three sessions of audiotaped interviews and two observation sessions were conducted with three exemplars from Nova Southeastern University PBL PT program. Each participant also maintained a reflective journal. The data were analyzed using content analysis. A systematic filing system was used by employing a mechanical means of maintaining and indexing coded data and sorting data into coded classifications of subtopics or themes. All interview transcripts, field notes from observations, and journal accounts were read, and index sheets were appropriately annotated. From the findings of the study, it was noted that, from the participants' perspectives, they were practicing at typically expected levels as clinicians. The attributes that governed the perspectives of the participants about their physical therapy clinical practice included flexibility, reflection, analysis, decision-making, self-reliance, problem-solving, independent thinking, and critical thinking. Further, the findings indicated that the factors that influenced those attributes included the PBL process, parents' value system, self-reliant personality, innate personality traits, and deliberate choice. Finally, the findings indicated that the participants' perspectives, for the most part, appeared to support the espoused efficacy of the PBL educational approach. In conclusion, there is evidence that the physical therapy clinical practice of the participants were positively impacted by the PBL curriculum. Among the many attributes they noted which governed these perspectives, problem-solving, as postulated by Barrows, was one of the most frequently mentioned benefits gained from their PBL PT training. With more schools adopting the PBL approach, this research will hopefully add to the knowledge base regarding the efficacy of embracing a problem-based learning instructional approach in physical therapy programs. ^

Invisible but not forgotten: The Afro-Argentine and Afro-Uruguayan experience from the sixteenth to the twentieth centuries

The problem to be examined in this thesis involves the supposedly overlooked history and contributions of Africans and their descendants in the River Plate countries of Argentina and Uruguay. Therefore, the primary purpose of the study is to narrate the social history of Afro-Argentines and Afro-Uruguayans from the sixteenth to the twentieth century. A secondary purpose, moreover, is to synthesize the academic literature on Blacks in the Rio de la Plata and their many cultural and other contributions to the current nation-states of Argentina and Uruguay. This thesis thereby challenges the regnant historiographical argument that African Argentines and African Uruguayans have been “forgotten” as historical actors by scholars both inside and outside the Rio de la Plata. By synthesizing the large body of historical and social science scholarship on Africans in the River Plate, as well as providing a thorough bibliography on the subject, this study attempts to proffer (to borrow the subtitle of Marvin Lewis' 1996 study of Afro-Argentine literature) “another dimension of the Black Diaspora” to the Americas. ^

Impact of a cognitive-behavioral weight control program on body weight, diet quality, and smoking cessation in weight-concerned female smokers

Many people use smoking as a weight control mechanism and do not want to quit because they fear weight gain. These weight-concerned smokers tend to be female, are significantly less likely to stop smoking, are less likely to join smoking cessation programs, and will relapse more often than smokers who are not weight-concerned. Research suggests that a woman’s confidence in her ability to control her weight after quitting relates positively with her intention to quit smoking. Likewise, success in smoking cessation has been associated with increased self-efficacy for weight control. It has been shown that success in changing one negative health behavior may trigger success in changing another, causing a synergistic effect. Recently research has focused on interventions for weight-concerned smokers who are ready to quit smoking. The present study investigated the effect of a cognitive based weight control program on self-efficacy for weight control and the effect on smoking behavior for a group of female weight concerned smokers. Two hundred and sixteen subjects who wanted to lose weight but who were not ready to quit smoking were recruited to participate in a 12-week, cognitive-behavioral weight control program consisting of twelve one-hour sessions. Subjects were randomly assigned to either (1) the weight-control program (intervention group), or (2) the control group. Results of this study demonstrated that subjects in the intervention group increased self-efficacy for weight control, which was associated with improved healthy eating index scores, weight loss, increased self-efficacy for quitting smoking, a decrease in number of cigarettes smoked and triggered positive movement in stage of change towards smoking cessation compared to the control subjects. For these subjects, positive changes in self-efficacy for one behavior (weight control) appeared to have a positive effect on their readiness to change another health behavior (smoking cessation). Further study of the psychological variables that influence weight-concerned female smokers’ decisions to initiate changes in these behaviors and their ability to maintain those changes are warranted.

Comparison of snail density, standing stock, and body size between Caribbean karst wetlands and other freshwater ecosystems

Synthesizing data from multiple studies generates hypotheses about factors that affect the distribution and abundance of species among ecosystems. Snails are dominant herbivores in many freshwater ecosystems, but there is no comprehensive review of snail density, standing stock, or body size among freshwater ecosystems. We compile data on snail density and standing stock, estimate body size with their quotient, and discuss the major pattern that emerges. We report data from 215 freshwater ecosystems taken from 88 studies that we placed into nine categories. Sixty-five studies reported density, seven reported standing stock, and 16 reported both. Despite the breadth of studies, spatial and temporal sampling scales were limited. Researchers used 25 different sampling devices ranging in area from 0.0015 to 2.5 m2. Most ecosystem categories had similar snail densities, standing stocks, and body sizes suggesting snails shared a similar function among ecosystems. Caribbean karst wetlands were a striking exception with much lower density and standing stock, but large body size. Disparity in body size results from the presence of ampullariids in Caribbean karst wetlands suggesting that biogeography affects the distribution of taxa, and in this case size, among aquatic ecosystems. We propose that resource quality explains the disparity in density and standing stock between Caribbean karst wetlands and other categories. Periphyton in Caribbean karst wetlands has high carbon-to-phosphorous ratios and defensive characteristics that inhibit grazers. Unlike many freshwater ecosystems where snails are key grazers, we hypothesize that a microbial loop captures much of the primary production in Caribbean karst wetlands.

S Corporations Can Benefit Many Closely-Held Hospitality Firms

In his discussion - S Corporations Can Benefit Many Closely-Held Hospitality Firms - by John M. Tarras, Assistant Professor, School of Hotel, Restaurant & Institutional Management at Michigan State University, Assistant Professor Tarras initially offers: “Organization as an S corporation has many advantages for hospitality firms since passage of the Tax Reform Act of 1986. The author discusses those advantages and lists the disadvantages as well.” In the opening paragraphs Tarras alludes to the relationship between hospitality firms, S corporations, and the Tax Reform Act of 1986, and then defines what an S corporation is. “An S corporation is a form of business entity that combines many of the tax advantages of partnerships with the legal attributes of a corporation, including limited liability for its shareholders. Its name is obtained from a subchapter of the Internal Revenue Code. Except for tax purposes, the S corporation is treated in the same manner as any regular corporation. Like a partnership, income and losses for an S corporation are generally passed through directly to shareholders for inclusion on their individual returns. An S corporation thus avoids the double tax problem facing regular corporations.” There are certain criteria to be met and caveats to be avoided in qualifying for S corporation status. Tarras lists and cites these for you. “Due to the complicated nature of S corporations, the election may be inadvertently terminated if the eligibility requirements are violated,” Tarras expands and cites. As the article suggests at the outset, there are advantages and disadvantages to S corporation status; the author outlines some examples for you. “Traditionally, the S corporation has been used by hospitality firms wishing to avoid the "double tax" problem of a regular corporation,” Tarras informs you. “Regular corporations are taxed once at the corporate level, and again at the shareholder level when income is distributed to shareholders in the form of dividends.” Tarras advises you as to why an S corporation is an advantage in this situation. “Since the S corporation generally is not subject to any corporate taxes, it generally makes no difference whether distributions to shareholders of S corporations are characterized as compensation or dividends,” thus the double tax is avoided. This is just one such positive illustration. Assistant Professor Tarras wants you to know: “Perhaps the most important reason to consider the S corporation has to do with the downward revision of tax rates for both individuals and corporations.” He highlights a case study for you. Some of the disadvantages of S corporation affiliation are the caveats alluded to earlier. They include, “the limitation of an S corporation of 35 shareholders,” Tarras cites. “Also, there are limits as to who may own stock in an S corporation.” These are but two of the limitations of an S corporation. Tarras closes with a further glimpse of the down-sides of an S corporation.

Participation in a positive youth development program and multi -problem alternative high school students' transformative goals: An investigation of the theoretical and methodological utility and validity of the Transformative Goal Attainment (TGAS)

There is a growing body of literature that provides evidence for the efficacy of positive youth development programs in general and preliminary empirical support for the efficacy of the Changing Lives Program (CLP) in particular. This dissertation sought to extend previous efforts to develop and preliminarily examine the Transformative Goal Attainment Scale (TGAS) as a measure of participant empowerment in the promotion of positive development. Consistent with recent advances in the use of qualitative research methods, this dissertation sought to further investigate the utility of Relational Data Analysis (RDA) for providing categorizations of qualitative open-ended response data. In particular, a qualitative index of Transformative Goals, TG, was developed to complement the previously developed quantitative index of Transformative Goal Attainment (TGA), and RDA procedures for calculating reliability and content validity were refined. Second, as a Stage I pilot/feasibility study this study preliminarily examined the potentially mediating role of empowerment, as indexed by the TGAS, in the promotion of positive development. ^ Fifty-seven participants took part in this study, forty CLP intervention participants and seventeen control condition participants. All 57 participants were administered the study's measures just prior to and just following the fall 2003 semester. This study thus used a short-term longitudinal quasi-experimental research design with a comparison control group. ^ RDA procedures were refined and applied to the categorization of open-ended response data regarding participants' transformative goals (TG) and future possible selves (PSQ-QE). These analyses revealed relatively strong, indirect evidence for the construct validity of the categories as well as their theoretically meaningful structural organization, thereby providing sufficient support for the utility of RDA procedures in the categorization of qualitative open-ended response data. ^ In addition, transformative goals (TG) and future possible selves (PSQ-QE), and the quantitative index of perceived goal attainment (TGA) were evaluated as potential mediators of positive development by testing their relationships to other indices of positive intervention outcome within a four-step method involving both analysis of variance (ANOVA and RMANOVAs) and regression analysis. Though more limited in scope than the efforts at the development and refinement of the measures of these mediators, the results were also promising. ^

Hope comes in many forms:out-group expressions of hope override low support and promote reconciliation in conflicts

In conflicts, political attitudes are based to some extent on the perception of the outgroup as sharing the goal of peace and supporting steps to achieve it. However, intractable conflicts are characterized by inconsistent and negative interactions, which prevent clear messages of outgroup support. This problem calls for alternative ways to convey support between groups in conflict. One such method is emotional expressions. The current research tested whether, in the absence of outgroup support for peace, observing expressions of outgroup hope induces conciliatory attitudes. Results from two experimental studies, conducted within the Israeli-Palestinian conflict, revealed support for this hypothesis. Expressions of Palestinian hope induced acceptance of a peace agreement through Israeli hope and positive perceptions of the proposal when outgroup support expressions were low. Findings demonstrate the importance of hope as a means of conveying information within processes of conflict resolution, overriding messages of low outgroup support for peace.