Miracle-dz/UniFAR-FTUs huggingface dataset:
Estimating the history of mutations on a phylogeny

Evolution is a historical process that has left its signature on the molecules and morphology of living organisms. Attempts to better understand the specific and general features of evolution involve making inferences about the past from these tell-tale signs (Felsenstein, 1985; Brooks and McLennan, 1991; Harvey and Pagel, 1991; Pagel, 1999). Ancestral state reconstruction is a powerful tool in this endeavor, as exemplified by its application to a wide array of questions (e.g. Langley and Fitch, 1974; Gillespie, 1991; Templeton, 1996; Messier and Stewart, 1997; Bishop et al., 2000). Traditionally, ancestral reconstruction has relied on well-understood approaches such as parsimony. However, the last decade has seen an excited flurry of research into statistical approaches as exemplified by the contents of this volume and the primary literature. In a general sense, most methods for ancestral reconstruction have focused on reconstructing the ancestral states at the internal nodes of a phylogeny. Often we are not interested in particular nodes of the phylogeny but the whole history of a character. In this chapter we focus on a Bayesian method for estimating these histories on phylogenies (we refer to a complete description of a character’s history as its mutational path). Mutational path methods differ most notably from other approaches in their ability to estimate not only the ancestral states at the internal nodes of a phylogeny but also the order and timing of mutational changes on the phylogeny. Our goal here is to provide a concise introduction to the statistical tools necessary for estimating mutational histories and making inferences from these histories, and to provide some examples of the power of this recent approach.
Mining slang and urban opinion words and phrases from cQA services: an optimization approach

Current opinion lexicons contain most of the common opinion words, but they miss slang and so-called urban opinion words and phrases (e.g. delish, cozy, yummy, nerdy, and yuck). These subjectivity clues are frequently used in community questions and are useful for opinion question analysis. This paper introduces a principled approach to constructing an opinion lexicon for community-based question answering (cQA) services. We formulate the opinion lexicon induction as a semi-supervised learning task in the graph context. Our method makes use of existing opinion words to extract new opinion entities (slang and urban words/phrases) from community questions. It then models the opinion entities in a graph context to learn the polarity of the new opinion entities based on the graph connectivity information. In contrast to previous approaches, our method not only learns such polarities from the labeled data but also from the unlabeled data and is more feasible in the web context where the dictionary-based relations (such as synonym, antonym, or hyponym) between most words are not available for constructing a high quality graph. The experiments show that our approach is effective both in terms of the quality of the discovered new opinion entities as well as its ability in inferring their polarity. Furthermore, since the value of opinion lexicons lies in their usefulness in applications, we show the utility of the constructed lexicon in the sentiment classification task.
Women's leadership development strategic practices for women and organizations.

This article presents a comprehensive perspective of leadership development that addresses the unique needs of women in organizations. The authors propose 7 categories of leadership development practice and examine the opportunities and obstacles in each of these practices for women. The authors offer recommendations for consulting psychologists and human resources professionals targeted to female clients and to organizational practices in order to advance women’s leadership development. Finally, the authors discuss the overarching themes emanating from their research and implications for women and leadership development.
Plant-bacterium interactions analyzed by proteomics

The evolution of the plant immune response has resulted in a highly effective defense system that is able to resist potential attack by microbial pathogens. The primary immune response is referred to as pathogen associated molecular pattern (PAMP) triggered immunity and has evolved to recognize common features of microbial pathogens. In response to the delivery of pathogen effector proteins, plants acquired R proteins to fight against pathogen attack. R-dependent defense response is important in understanding the biochemical and cellular mechanisms and underlying these interactions will enable molecular and transgenic approaches for crops with increased biotic resistance. Proteomic analyses are particularly useful for understanding the mechanisms of host plant against the pathogen attack. Recent advances in the field of proteome analyses have initiated a new research area, i.e., the analysis of more complex microbial communities and their interaction with plant. Such areas hold great potential to elucidate, not only the interactions between bacteria and their host plants, but also of bacteria-bacteria interactions between different bacterial taxa, symbiotic, pathogenic bacteria, and commensal bacteria. During biotic stress, plant hormonal signaling pathways prioritizes defense over other cellular functions. Some plant pathogens take advantage of hormone dependent regulatory system by mimicking hormones that interfere with host immune responses to promote virulence (vir). In this review, it is discussed the cross talk that plays important role in response to pathogens attack with different infection strategies using proteomic approaches.
Modulation of episodic renin release during sleep in humans.

We previously described a strong concordance between nocturnal oscillations in plasma renin activity and sleep cycles. To examine whether modifying renal renin content or release influences the response to central stimuli linked to sleep stage alternation, plasma renin activity was measured every 10 minutes from 11:00 PM to 8:00 AM in three groups of six subjects. The first group received one 40 mg dose of the diuretic furosemide; the second group underwent the night experiment after 3 days on a low sodium diet; the third group received one 100 mg dose of the beta-blocker atenolol. Each subject underwent a control night when a placebo was given. The nocturnal curves were analyzed with a pulse detection program. For the control nights, 74 of the 83 sleep cycles were associated with significant plasma renin activity oscillations; non-rapid eye movement sleep occurred in the ascending portions and rapid eye movement sleep in the declining portions of the oscillations. These oscillations persisted in the three groups of subjects during the experimental nights and the relation with the sleep stages was not disturbed. Acute stimulation by furosemide amplified the oscillations and led to a general upward trend of the nocturnal profiles. Similarly, a low sodium diet, which led to a slow increase in renal renin content, provoked large oscillations with high initial levels. However, in both cases the mean relative amplitude of the oscillations, expressed as a percentage of the nocturnal means, was similar to that of the control nights and approximated 60%. (ABSTRACT TRUNCATED AT 250 WORDS)
Parents' Discourses About Language Strategies for Their Children's Preschool Bilingual Development

The study focused on immigrant parents' discourses about strategies for their children's preschool bilingual development and education. The article investigated how immigrant parents described and explained these strategies. The study was based on semi-structured interviews with 4 families. The 8 parents were Russian-speaking immigrants to Israel from the former Soviet Union. Analysis of the data showed that all the parents desired their children to maintain the heritage language and to acquire the host language. At the same time, they were realistically skeptical of achieving balanced bilingualism in their children's language development. Nevertheless, most reported clearly elaborated intervention plans to support the children's balanced bilingualism. The regulation of language interaction with the child at home occupied a central place in parents' strategies for their children's bilingual development; however, some chose bilingual kindergarten for their children, whereas others chose monolingual programs. To explain and justify this choice, parents adduced different motives and representations about trajectories of children's bilingual development.
Organizational Commitment in a Male Dominated Profession

The paper analyzes the organizational commitment of North American male andfemale accountants working in professional organizations. Unlike others, the present study controlledfor the critical variables of type of occupation, level and subject of higher education, and type of organization. The independent variables were age, gender, tenure, organizational level, cognitive affective orientation to the job, professional commitment, overalljob satisfaction, and intrinsic and e-xtrinsic need satisfaction. It was found by an analysis of covariance that women tended to have lower levels of organizational commitment than men. However, an hierarchical regression analysis indicated that sex did not significantly explain the variance beyond the demographic and cognitive-affective variables. Women were also less satisfied than men in terms of overall job satisfaction and extrinsic satisfaction.
The Effect of 29 kV X Rays on the Dose Response of Chromosome Aberrations in Human Lymphocytes

Abstract Schmid, E. , Regulla, D. , Kramer, H-M. and Harder, D. The Effect of 29 kV X Rays on the Dose Response of Chromosome Aberrations in Human Lymphocytes. Radiat. Res. 158, 771–777 (2002). The induction of chromosome aberrations in human lymphocytes irradiated in vitro with X rays generated at a tube voltage of 29 kV was examined to assess the maximum low-dose RBE (RBEM) relative to higher-energy X rays or 60Co γ rays. Since blood was taken from the same male donor whose blood had been used for previous irradiation experiments using widely varying photon energies, the greatest possible accuracy was available for such an estimation of the RBEM, avoiding the interindividual variations in sensitivity or differences in methodology usually associated with interlaboratory comparisons. The magnitude of the linear coefficient α of the linear-quadratic dose–effect relationship obtained for the production of dicentric chromosomes by 29 kV X rays (α = 0.0655 ± 0.0097 Gy−1) confirms earlier observations of a strong increase in α with decreasing photon energy. Relating this value to previously published values of α for the dose–effect curves for dicentrics obtained in our own laboratory, RBEM values of 1.6 ± 0.3 in comparison with weakly filtered 220 kV X rays, 3.0 ± 0.7 compared to heavily filtered 220 kV X rays, and 6.1 ± 2.5 compared to 60Co γ rays have been obtained. These data emphasize that the choice of the reference radiation is of fundamental importance for the RBEM obtained. A special survey of the RBEM values obtained by different investigators in the narrow quality range from about 30 to 350 kV X rays indicates that the present RBE is in fairly good agreement with previously published findings for the induction of chromosome aberrations or micronuclei in human lymphocytes but differs from recently published findings for neoplastic transformation in a human hybrid cell line.
Middle Managers, Strategic Sensemaking, and Discursive Competence

This paper seeks to better understand the way middle managers contribute strategically to the development of an organization by examining how they enact the strategic roles allocated to them, with particular reference to strategic change. Through vignettes drawn from the authors' current research, a framework is developed that shows two situated, but interlinked, discursive activities, ‘performing the conversation’ and ‘setting the scene’, to be critical to the accomplishment of middle manager sensemaking. Language use is key, but needs to be combined with an ability to devise a setting in which to perform the language. The paper shows how middle managers knowledgeably enact these two sets of discursive activities by drawing on contextually relevant verbal, symbolic, and sociocultural systems, to allow them to draw people from different organizational levels into the change as they go about their day-to-day work.
Serine Protease-mediated Host Invasion by the Parasitic Nematode Steinernema carpocapsae*

Steinernema carpocapsae is an insect parasitic nematode used in biological control, which infects insects penetrating by mouth and anus and invading the hemocoelium through the midgut wall. Invasion has been described as a key factor in nematode virulence and suggested to be mediated by proteases. A serine protease cDNA from the parasitic stage was sequenced (sc-sp-1); the recombinant protein was produced in an Escherichia coli system, and a native protein was purified from the secreted products. Both proteins were confirmed by mass spectrometry to be encoded by the sc-sp-1 gene. Sc-SP-1 has a pI of 8.7, a molecular mass of 27.3 kDa, a catalytic efficiency of 22.2 × 104 s−1 m−1 against N-succinyl-Ala-Ala-Pro-Phe-pNA, and is inhibited by chymostatin (IC 0.07) and PMSF (IC 0.73). Sc-SP-1 belongs to the chymotrypsin family, based on sequence and biochemical analysis. Only the nematode parasitic stage expressed sc-sp-1. These nematodes in the midgut lumen, prepared to invade the insect hemocoelium, expressed higher levels than those already in the hemocoelium. Moreover, parasitic nematode sense insect peritrophic membrane and hemolymph more quickly than they do other tissues, which initiates sc-sp-1 expression. Ex vivo, Sc-SP-1 was able to bind to insect midgut epithelium and to cause cell detachment from basal lamina. In vitro, Sc-SP-1 formed holes in an artificial membrane model (Matrigel), whereas Sc-SP-1 treated with PMSF did not, very likely because it hydrolyzes matrix glycoproteins. These findings highlight the S. carpocapsae-invasive process that is a key step in the parasitism thus opening new perspectives for improving nematode virulence to use in biological control.
Local disciplines, local cultures: praise and criticism in British and Spanish history book reviews

The use of a critical voice in book reviews seems to depend on factors rooted in the discipline community reviewers belong to and on the language and culture which hosts the review. Adopting a cross-cultural perspective, this study analyses 60 book reviews from British and Spanish history journals in terms of the entities and aspects evaluated and the polarity (positive/negative) of the evaluation. Divergences are found in the distribution of positive and negative evaluation, revealing that even if in both cultures positive evaluation is more frequent, in Spanish book reviews negative evaluation is almost nonexistent. Interviews with informants show that these divergences respond to the local character of the disciplinary communities which host the reviews and to a different understanding of what this evaluative genre implies. 1
Rescuing replication and osteogenesis of aged mesenchymal stem cells by exposure to a young extracellular matrix

This study aimed to determine whether aging negatively affects MSC replication and osteogen‐esis and whether these features could be altered by exposure to an extracellular matrix (ECM) generated by marrow cells from young or old mice. A cell‐free ECM was prepared from cultured femoral marrow cells from either 3‐ or 18‐mo‐old C57BL/6 mice (young‐ECM or old‐ECM, respectively). The replication and osteo‐genesis of young or old MSCs maintained on young‐ECM vs. old‐ECM as well as plastic were examined in vitro and in vivo. We found that the frequency of MSCs in marrow from old mice, measured by colony‐forming cells, was only marginally lower than that of young mice. In contrast, defects in the self‐renewal and bone formation capacity of old MSCs were remarkable. These defects were corrected by provision of a young‐ECM but not old‐ECM. In parallel cultures maintained on a young‐ECM, the intracellular levels of reactive oxygen species from both old and young mice were reduced 30–50% compared to those maintained on old‐ECM or plastic. We concluded that aging negatively affects the formation of an ECM that normally preserves MSC function, and aged MSCs can be rejuvenated by culture on a young‐ECM. —Sun, Y. , Li, W. , Lu, Z. , Chen, Z. , Ling, J., Ran, O. , Jilka, R. L. , Chen, X. D. Rescuing replication and osteogenesis of aged mesenchymal stem cells by exposure to a young extracellular matrix. FASEB J. 25, 1474–1485 (2011). www.fasebj. org
The cortical representation of centrally presented words: A magnetic stimulation study

The right and left visual fields each project to the contralateral cerebral hemispheres. The current study aimed to investigate the extent of the functional overlap of the two hemifields along the vertical meridian. We applied repetitive transcranial magnetic stimulation (rTMS) over the left and right occipital cortex to investigate whether the foveal representation of words is bilaterally represented or is split between the two hemispheres. Employing a lateralized lexical decision task, we first showed a double dissociation between the stimulated cortical site and performance; right visual field (RVF) but not left visual field (LVF) performance was impaired when the left visual cortex was stimulated, and LVF but not RVF performance was impairred when the right visual cortex was stimulated. Unilateral stimulation also significantly impaired lexical decision latencies to centrally presented words. These findings support the suggestion that foveal representation of words is split. We discuss future strategies for the use of TMS in further tests of the split representation account.
Does satisfaction moderate the association between alternative attractiveness and exit intention in a marketing channel?

This study investigated the predicted moderating effect of satisfaction on the association between the attractiveness of the alternative relationship and exit intention in a marketing channel. The study used a variation of the Kenny and Judd structural equation technique proposed by the author. The results suggested that for channel customers with lower satisfaction, alternative attractiveness was positively associated with exit intention. When satisfaction was higher, however, alternative attractiveness had no association with exit intention. The implications of these results are discussed.
New perspectives in the treatment of hematological malignancies.

Hematologic malignancies, although all are cancers of the blood-forming organs, constitute a broad spectrum of disease. This paper focuses on a subset of hematologic malignancies: acute myelogenous leukemia and the 2 related conditions of promyelocytic leukemia and myelodysplastic syndromes; and the lymphoid malignancies, chronic lymphocytic leukemia, non-Hodgkin’s lymphoma, and multiple myeloma. Disease epidemiology, classification schemes, treatment regimens, and patient management issues are covered, with particular emphasis placed on current investigational therapies. A brief discussion of reimbursement issues also is included. (Adv Stud Med. 2007;7(4):105-118)
Perception Differences in Violence Against Child

Abstract Mostly, people who apply violence do not realize the effects of it, especially child victims give strong emotional responses to violence. Behaviors without any intention of abuse or neglect can mostly be seen among the people, who are dealing with children intensely like teachers and parents. Aim of this work is to determine the perception differences of parents, teachers and children in violence. Revised form of Childhood Trauma Questionnaire and also 17 parameters related to violence were applied to children, parents and teachers and then their answers were compared with each other. Questionnaires were responded by 411 children, 135 parents and 85 teachers. In each three groups, it was noticed that the ratio of perception of violence in parameters related to physical violence was higher than in parameters related to emotional violence. While the teachers had the highest perception of violence, children had the lowest perception of violence. Sensitiveness in perception of violence and education on this subject are not enough to stop violence. It must be prevented to apply violence in society for an aim of discipline and education and violence must not be seen as a way of teaching good manners. It also must not be applied as a tool for solving problems, gaining power and control. The rights of violence victims, especially children’s rights must be protected and there must be intimidating sanctions for people who practice violence on the others. Key Words: Child abuse, behavior, neglect, victim
Myocardial 123metaiodobenzylguanidine uptake in genetic Parkinson's disease

Myocardial 123Metaiodobenzylguanidine (MIBG) enables the assessment of postganglionic sympathetic cardiac innervation. MIBG uptake is decreased in nearly all patients with Parkinson's disease (PD). Our objective was to evaluate MIBG uptake in patients with genetic PD. We investigated MIBG uptake in 14 patients with PD associated with mutations in different genes (Parkin, DJ‐1, PINK1, and leucine‐rich repeat kinase 2 ‐LRRK2), in 15 patients with idiopathic PD, and 10 control subjects. The myocardial MIGB uptake was preserved in 3 of the 4 Parkin‐associated Parkinsonisms, in 1 of the 2 patients with DJ‐1 mutations, in 1 of the 2 brothers with PINK1 mutations, in 3 of the 6 unrelated patients with Gly2019Ser mutation in the LRRK2 gene, whereas it was impaired in all patients with idiopathic PD. MIBG was preserved in all control subjects. Our study shows that myocardial MIGB uptake was normal in 8 of 14 patients with genetic PD, suggesting that cardiac sympathetic denervation occurs less frequently in genetic PD than in idiopathic PD. Our findings also demonstrate that MIGB uptake has a heterogeneous pattern in genetic PD, because it was differently impaired in patients with different mutations in the same gene or with the same gene mutation. © 2007 Movement Disorder Society
Surveillance of HCC Patients after Liver RFA: Role of MRI with Hepatospecific Contrast versus Three-Phase CT Scan—Experience of High Volume Oncologic Institute

Purpose. To compare the diagnostic accuracy of hepatospecific contrast-enhanced MRI versus triple-phase CT scan after radiofrequency ablation (RFA) in hepatocellular carcinoma (HCC) patients. Methods. Thirty-four consecutive HCC patients (42 hepatic nodules) were treated with percutaneous RFA and underwent MR and CT scans. All patients were enrolled in a research protocol that included CT with iodized contrast medium injection and MR with hepatospecific contrast medium injection. All patients were restaged within four weeks and at 3 months from ablation. The images were reviewed by four different radiologists to evaluate tumor necrosis, residual or recurrence disease, and evidence of new foci. Results. Thirty-two nodules were necrotic after treatment; 10 showed residual disease. Six new HCCs were identified. At first month followup CT has identified 34 necrotic lesions and 8 residual diseases; no new foci were recognized. At MRI instead, 32 complete necrotic lesions were identified, 10 lesions showed residual disease, and 2 new HCCs were found. At three months, CT demonstrated 33 completely necrotic lesions, 9 residual diseases, and 2 new HCCs. MR showed 31 complete necrotic lesions, 11 cases of residual disease, and 6 new HCCs. Conclusions. Hepatospecific contrast-enhanced MRI is more effective than multiphase CT in assessment of HCC treated with RFA.