Miracle-dz/UniFAR-FTUs huggingface dataset:
Gene Family Evolution across 12 Drosophila Genomes

Comparison of whole genomes has revealed large and frequent changes in the size of gene families. These changes occur because of high rates of both gene gain (via duplication) and loss (via deletion or pseudogenization), as well as the evolution of entirely new genes. Here we use the genomes of 12 fully sequenced Drosophila species to study the gain and loss of genes at unprecedented resolution. We find large numbers of both gains and losses, with over 40% of all gene families differing in size among the Drosophila. Approximately 17 genes are estimated to be duplicated and fixed in a genome every million years, a rate on par with that previously found in both yeast and mammals. We find many instances of extreme expansions or contractions in the size of gene families, including the expansion of several sex- and spermatogenesis-related families in D. melanogaster that also evolve under positive selection at the nucleotide level. Newly evolved gene families in our dataset are associated with a class of testes-expressed genes known to have evolved de novo in a number of cases. Gene family comparisons also allow us to identify a number of annotated D. melanogaster genes that are unlikely to encode functional proteins, as well as to identify dozens of previously unannotated D. melanogaster genes with conserved homologs in the other Drosophila. Taken together, our results demonstrate that the apparent stasis in total gene number among species has masked rapid turnover in individual gene gain and loss. It is likely that this genomic revolving door has played a large role in shaping the morphological, physiological, and metabolic differences among species.
All Bits Are Not Equal - A Study of IEEE 802.11 Communication Bit Errors

In IEEE 802.11 Wireless LAN (WLAN) systems, techniques such as acknowledgement, retransmission, and transmission rate adaptation, are frame-level mechanisms designed for combating transmission errors. Recently sub-frame level mechanisms such as frame combining have been proposed by the research community. In this paper, we present results obtained from our bit error study for identifying sub-frame error patterns because we believe that identifiable bit error patterns can potentially introduce new opportunities in channel coding, network coding, forward error correction (FEC), and frame combining mechanisms. We have constructed a number of IEEE 802.11 wireless LAN testbeds and conducted extensive experiments to study the characteristics of bit errors and their location distribution. Conventional wisdom dictates that bit error probability is the result of channel condition and ought to follow corresponding distribution. However our measurement results identify three repeatable bit error patterns that are not induced by channel conditions. We have verified that such error patterns are present in WLAN transmissions in different physical environments and across different wireless LAN hardware platforms. We also discuss our current hypotheses for the reasons behind these bit error probability patterns and how identifying these patterns may help improving WLAN transmission robustness.
Classroom Grading

Acritical area of concern to teachers, administrators, students, and parents is the evaluation and grading of student performance. the topic of grading takes on added significance when consideration is given to the grading of students with disabilities and to the related effects on collaboration between home and school. A national survey was conducted, with the purpose being to determine the policies of local school districts concerning grading. Specific foci included whether a policy was in effect, if modifications were made for students with disabilities, the nature of grading systems used, and communication mechanisms between home and school. A total of 550 surveys were mailed to school district superintendents, with a response rate of over 40%. The results indicated that a majority of school divisions had a policy on grading in effect and that the policies in effect included modifications for students with disabilities. Trends in terms of grading systems used and communication mechanisms employed are highlighted. The results are discussed in terms of their relationship to home-school collaboration and in the context of integrating students with disabilities into general education.
IMAGES OF THE MULTILINGUAL BRAIN: THE EFFECT OF AGE OF SECOND LANGUAGE ACQUISITION

Is it the age of second language acquisition (AoA) that primarily determines the manner of cerebral representation of multiple languages in the brain, or is it proficiency? Here, we review recent neuroimaging studies that aimed at investigating AoA effects by comparing early with late (usually with L2 acquisition onset after 6 years of age) bilinguals during a variety of language tasks on a number of languages. Most studies did indeed report AoA effects. Of particular interest is that the region mainly found to functionally differ between early and late bilinguals is the left inferior frontal gyrus, which was modulated during syntactic processing, word generation, and sentence generation. Additionally, differences were observed in gray-matter density of the posterior parietal cortex as well as in right-hemisphere involvement. Interestingly, despite some convergence of findings from a localizational point of view, underlying causes of organizational and functional differences for the effect of AoA on bilingual language processing still remain to be uncovered. Hypotheses currently used for explaining activation differences are described (notably cortical efficiency, executive control, neuroanatomical changes, and right-hemisphere involvement) in relation to AoA and language proficiency.
‘Exploitation’ in Peasant Societies: A Nepalese Example

ABSTRACT The concept of exploitation as applied to the relationships between peasants and their ruling élite has frequently been utilized by anthropologists to distinguish peasants from other rural cultivators. This essay, based on a single peasant community of East Nepal, illustrates that exploitation occurs at many levels and that a peasantry's relationships with the larger society may not, in fact, be as unequal as the current literature asserts. It is suggested that many characteristics frequently ascribed to the exploitative capacities of the non-peasant élite may be attributed to the system of social stratification found among the peasants themselves and to the effects of a rapidly expanding population.
Prediction of violent and sexual offences: A replication study of the VRAG in Switzerland

Abstract The Violence Risk Appraisal Guide (VRAG) is a widely used actuarial risk assessment instrument and has been validated in different countries. However, there is no investigation supporting the predictive accuracy of the VRAG in the German language area. The VRAG scores of 79 violent and sexual offenders in Switzerland were assessed based on data from their psychiatric expert opinions. The VRAG scores were compared to subsequent recidivism as shown in the official criminal records. Consistent with past research in the English language area, the VRAG yielded a satisfying predictive accuracy (ROC area = .73), demonstrating its usefulness for risk assessment of violent delinquency in the Swiss cultural and German language area.
Managing Risk, Resisting Management : Stability and Diversity in a Southern Australian Fishing Fleet

At Lakes Entrance, in Victoria (Australia), locally-based commercial fishers utilize diversification (e.g. multiple targets, fishing areas, boats, or markets) as a means of managing the risks that characterize the biological and economic environments they experience. These strategies have contributed to numerical stability of the local fleet at a time when most southeastern Australian fishing fleets are in decline. In effect, the Lakes Entrance fishing community has avoided, or at least delayed, outcomes that are explicitly intended by recent approaches to fisheries management. An implication of these observations is that the behavior of fishers, including, importantly, how they manage risk, offer lessons for fisheries managers with respect to both why their plans often fail and why different plans could be more successful.
"Research Action": Organizational Feedback, Understanding, and Change

This article focuses on the relationship between "research" and "action" as contradictory and complementary activities. Recent research and theory indicate the two may be synergistic and difficult to separate. It is suggested that mutual exchange of information between investigator and respondents is critical to both increased understanding ("research") and constructive change ("action"). The events in a case study of organizational diagnosis in a school and the outcomes of feedback of that diagnosis are examined in this context. The data indicate that information sharing improved the relationships between investigators and respondents, improved the quality of the diagnosis, and increased student involvement in school life. Some implications of the concept of "research action" for researchers and practitioners are discussed.
Religious Affiliation, Religious Attendance, and Participation in Social Change Organizations

How does religion affect an individual’s likelihood of volunteering for social change causes? This study reports on findings from an analysis of the 2005 wave of the COPPS supplement to the PSID to examine the effects of religious tradition (affiliation) and religious attendance (religiosity) on social change volunteering. We find that adherents to the more liberal Christian denominations—mainline Protestant and Catholic—are more likely to volunteer with social change organizations than are Evangelicals. We also find that adherents to other minority religions such as Judaism and Buddhism and individuals with no religious belief are all more likely to volunteer with social change organizations than are Evangelicals. We find a positive and significant relationship between religious attendance and social change volunteering, but find little difference in the effect of religious attendance on social change volunteering between Evangelicals and other religious traditions (except for Catholics).
Outcomes Among Family Caregivers of Aphasic Versus Nonaphasic Stroke Survivors

&NA; Adverse consequences are known to occur in family members responsible for providing care to stroke survivors. However, the differential effect of aphasic versus nonaphasic stroke on caregivers has not been well studied. This study compares selected outcomes (e.g., perceived task difficulty, depressive symptoms, and other negative stroke‐related outcomes) among caregivers of aphasic (n = 46) and nonaphasic (n = 113) stroke survivors. Results indicated that caregivers of aphasic survivors perceived greater difficulty with tasks and had more negative stroke‐related outcomes than caregivers of nonaphasic survivors. Communication with the survivor was rated as most upsetting and difficult by caregivers in the aphasic group, followed by managing behaviors. Lack of time for family and friends was evident. Female caregivers and caregivers of survivors with self‐care deficits also perceived greater difficulty with tasks and negative outcomes. Comprehensive assessment of the unique needs of caregivers of aphasic survivors is suggested for more individualized nursing interventions.
The Effects of Change in Family Structure and Income on Dropping Out of Middle and High School

Using a longitudinal sample of eighth graders who lived with both biological parents in 1988, we estimate the increased risk of dropping out among students whose two-parent families experienced disruption over the subsequent 4 years. We differentiate the impact on school dropout of initial family income before family disruption from income change after the marriage ends. This approach helps to disentangle two interpretations of the relation between income and family structure. Our results suggest that both measures of income are significant contributors of the risk of dropping out for children whose families became mother-only families. When income loss is taken into account, along with initial income and other family, demographic, and prior school achievement factors, there is no evidence of increased risk of dropout among children who began to live with a single mother during the 1988-1992 period.
Predicting Social Skills and Adaptability in Preschoolers with Behavior Problems

DEDICATION To my family whose support and encouragement have been invaluable. v AKNOWLEDGEMENTS I would like to thank my advisor, David H. Arnold, for his many years of guidance, support, and encouragement. I am certain that I would not be the researcher I am today without his support. I would also like to thank Lisa Harvey for her service, advice, and guidance throughout my graduate career and especially during my dissertation. I would also like to extend my gratitude to the members of my committee, Erik Cheries and Sara Whitcomb, for their helpful comments and suggestions on all stages of this project.
Amoxicillin, clarithromycin, and omeprazole based targeted nanoparticles for the treatment of H. pylori

The aim of the present study was to develop and characterize targeted sustained release nanoparticles of chitosan–glutamic acid conjugates containing triple therapy for Helicobacter pylori to improve its therapeutic effect and reduce its dose-related side effect. The chitosan–glutamate nanoparticles were prepared by using the ionotropic gelation method. The particle sizes of systems ranged between 550 nm and 900 nm. Percent drug entrapment and release profiles of amoxicillin, clarithromycin, and omeprazole in simulated gastric fluid (pH 1.2) were determined using high-performance liquid chromatography. The maximum % drug entrapment and % yield of formulations were about 60–90% and 73–88%, respectively. The stability of the drugs was assessed in simulated gastric fluid (pH 1.2). In vitro antibacterial efficacy of optimized formulations containing monotherapy and triple therapy on isolated culture of H. pylori was assessed. In vivo clearance study and histopathological study were also carried out on Swiss albino mice to evaluate the efficacy of triple therapy containing targeted nanosystem for the treatment of H. pylori. The proposed delivery system holds promise at optimizing the treatment of H. pylori.
The state of cell block variation and satisfaction in the era of molecular diagnostics and personalized medicine

Background: In the recent past, algorithms and recommendations to standardize the morphological, immunohistochemical and molecular classification of lung cancers on cytology specimens have been proposed, and several organizations have recommended cell blocks (CBs) as the preferred modality for molecular testing. Based on the literature, there are several different techniques available for CB preparation-suggesting that there is no standard. The aim of this study was to conduct a survey of CB preparation techniques utilized in various practice settings and analyze current issues, if any. Materials and Methods: A single E-mail with a link to an electronic survey was distributed to members of the American Society of Cytopathology and other pathologists. Questions pertaining to the participants’ practice setting and CBs-volume, method, quality and satisfaction-were included. Results: Of 95 respondents, 90/95 (94%) completed the survey and comprise the study group. Most participants practice in a community hospital/private practice (44%) or academic center (41%). On average, 14 CBs (range 0-50; median 10) are prepared by a laboratory daily. Over 10 methods are utilized: Plasma thrombin (33%), HistoGel (27%), Cellient automated cell block system (8%) and others (31%) respectively. Forty of 90 (44%) respondents are either unsatisfied or sometimes satisfied with their CB quality, with low-cellular yield being the leading cause of dissatisfaction. There was no statistical significance between the three most common CB preparation methods and satisfaction with quality. Discussion: Many are dissatisfied with their current method of CB preparation, and there is no consistent method to prepare CBs. In today's era of personalized medicine with an increasing array of molecular tests being applied to cytological specimens, there is a need for a standardized protocol for CB optimization to enhance cellularity.
Moving shadows: suggestions for ethnography in globalised cultures

Purpose – Traditional notions of culture have become unicorns: assumed creatures of the past, whose authenticity seems increasingly doubtful. It is required of us to rethink the boundaries of culture and social science; to develop our understanding of interdependency and instability in cultural life. In order to incorporate possible discourses, the practice of research must also change. This paper discusses some problems associated with ethnography in global cultures.Design/methodology/approach – I begin by presenting a brief history of ethnography as a method for investigating unconceptualised groups. Following this, through reference to my own research, I argue that the foundations of this methodology can be developed to include the broad networks of influences extant in contemporary cultures. To this end, I consider a solution that poses the researcher as a locus of investigation from which the relationships that construct a culture may be collated and interpretations built.Findings – The research acco.
Ultrasonic tissue characterization for the differentiation of parotid gland tumors

The first ultrasonic tissue characterization system for the computerized differentiation of tumors of the parotid gland is presented. The system is based on a multifeature tissue charac- terization approach involving spectrum and texture parameters and using fuzzy inference systems as higher order classifiers. Baseband ultrasound echo data were acquired during conven- tional ultrasound imaging examinations of the salivary glands. Several tissue-describing parameters were calculated within numerous small regions of interest in order to evaluate local spectral and textural tissue properties. The parameters were pro- cessed by an adaptive network-based fuzzy inference system using the results of conventional histology after parotidectomy as the gold standard. Cases of parotid gland tumors and alterations include basal cell adenomas, monomorphic adenomas, pleomor- phic adenomas, adenoid cysts, cysts and canaliculous adenomas. The results of the classification procedure are presented as a numerical score indicating the probability of a certain tumor or alteration for each parotid gland. In a pilot study, the system was evaluated on 23 cases of benign and malignant parotid gland tumors of patients undergoing parotidectomy. The ROC curve area given as the cross-validation mean and cross-validation standard deviation is AROC=0.95±0.07 when using four-fold cross-validation over cases and differenti- ating between various malignant and benign parotid gland tumors as the positive target group and monomorphic adenomas as the negative target group. An exceptional equal error rate of EEER=0.92±0.08 is achieved for the same setup. Some alterations which are of benign nature were counted to the positive group, as they occur too seldom to achieve a high probability for being considered safe if left untreated.
Network News: The Role of Race in Source Selection and Story Topic

The theory of incognizant racism posits that journalists cover the White community differently than communities of color, and the study's results indicate that this difference is also reflected in the choice and use of on-camera sources in network news stories. A quantitative content analysis of network news programs in 2005 revealed that Whites dominated television news coverage, comprising more than three quarters of sources. Nearly 90% of network news reporters were also White. Elite sources such as experts, company spokespeople, and government officials were overwhelmingly White, whereas minority sources appeared most often as private individuals or ordinary citizens. In addition, White sources clearly dominated all story topics, with a majority presence in every case, except for foreign affairs stories in which foreign sources made up the bulk of sound bites. Minority sources were scattered more sparingly across story topics, barely making a showing in some, such as stories about science/technology, foreign affairs, and electoral politics. Black and Hispanic sources appeared most often in stories about accidents/disasters/weather events, in both pre-Hurricane Katrina and post-Hurricane Katrina samples. Results indicated that minority reporters were more likely to use minority sources in their stories than White reporters.
Abnormal Termination of Ca2+ Release Is a Common Defect of RyR2 Mutations Associated With Cardiomyopathies

Rationale: Naturally occurring mutations in the cardiac ryanodine receptor (RyR2) have been associated with both cardiac arrhythmias and cardiomyopathies. It is clear that delayed afterdepolarization resulting from abnormal activation of sarcoplasmic reticulum Ca2+ release is the primary cause of RyR2-associated cardiac arrhythmias. However, the mechanism underlying RyR2-associated cardiomyopathies is completely unknown. Objective: In the present study, we investigate the role of the NH2-terminal region of RyR2 in and the impact of a number of cardiomyopathy-associated RyR2 mutations on the termination of Ca2+ release. Methods and Results: The 35-residue exon-3 region of RyR2 is associated with dilated cardiomyopathy. Single-cell luminal Ca2+ imaging revealed that the deletion of the first 305 NH2-terminal residues encompassing exon-3 or the deletion of exon-3 itself markedly reduced the luminal Ca2+ threshold at which Ca2+ release terminates and increased the fractional Ca2+ release. Single-cell cytosolic Ca2+ imaging also showed that both RyR2 deletions enhanced the amplitude of store overload-induced Ca2+ transients in HEK293 cells or HL-1 cardiac cells. Furthermore, the RyR2 NH2-terminal mutations, A77V, R176Q/T2504M, R420W, and L433P, which are associated with arrhythmogenic right ventricular displasia type 2, also reduced the threshold for Ca2+ release termination and increased fractional release. The RyR2 A1107M mutation associated with hypertrophic cardiomyopathy had the opposite action (ie, increased the threshold for Ca2+ release termination and reduced fractional release). Conclusions: These results provide the first evidence that the NH2-terminal region of RyR2 is an important determinant of Ca2+ release termination, and that abnormal fractional Ca2+ release attributable to aberrant termination of Ca2+ release is a common defect in RyR2-associated cardiomyopathies.
Is Central Origin of Muscle Fatigue Distinguished Solely in Finger Tapping Performance?

Ischemia in presence of drug induced long QT syndrome 2 (LQTS2) predisposes the tissue to Torsade de pointes (TdP). Reentrant arrhythmias occurring during phase 1B of ischemia have been primarily associated with areas of cellular uncoupling and hyperkalaemia. This study aims to investigate how a region of lowered gap junction conductance (GJC) in presence of LQTS2 can initiate a TdP. Here, a discrete grid of 250x100 cells interconnected using GJCs is taken representing a portion of the transmural wall with anisotropic conduction velocities. LQTS2 is introduced by reducing the potassium current (IKr) of all cells to 50%. An ischemic zone is located almost in the centre of the mid myocardium layer in the form of an elliptic inhomogeneity with varying percentage reduction of GJC compared to the surrounding. Results show that reduction of intercellular conductance in a midmyocardial island can cause a non-sustained reentrant arrhythmia to develop due to premature pacing beats. Addition of hyperkalaemic conditions in the ischemic zone has the effect of prolonging the arrhythmia.