Miracle-dz/UniFAR-FTUs huggingface dataset:
A hidden Markov model for progressive multiple alignment

MOTIVATION Progressive algorithms are widely used heuristics for the production of alignments among multiple nucleic-acid or protein sequences. Probabilistic approaches providing measures of global and/or local reliability of individual solutions would constitute valuable developments. RESULTS We present here a new method for multiple sequence alignment that combines an HMM approach, a progressive alignment algorithm, and a probabilistic evolution model describing the character substitution process. Our method works by iterating pairwise alignments according to a guide tree and defining each ancestral sequence from the pairwise alignment of its child nodes, thus, progressively constructing a multiple alignment. Our method allows for the computation of each column minimum posterior probability and we show that this value correlates with the correctness of the result, hence, providing an efficient mean by which unreliably aligned columns can be filtered out from a multiple alignment.
Further remarks on interpretive analysis: in response to Christine Howe

In the early 1960s several child language research papers were published that converged on a central feature of children's early sentences: the formal regularity in children's use of word order (Braine 1963, Brown & Fraser 1963, Miller & Ervin 1964, Slobin 1966). The finding was straightforward; 1to 2-year-old children use a small number of words with great frequency, in relatively fixed position, in juxtaposition with a larger number of words, each of which occurs less frequently and with different word order. It soon became clear, however, that word order is only part of the story of the child's developing language, and in the early 1970s a new group of research papers appeared that converged on another feature of children's early sentences: the semantic regularity in the meaning relations between words (Bloom 1970, Brown 1973, Schlesinger 1971). The meaning of a child's utterances is less straightforward than the formal regularity in word order in that it is less transparent in the data: the evidence of the semantics of early sentences depends upon an interpretive analysis (IA). That is, by paying attention to contextual events to what children are doing, what they are looking at, and their interactions with other persons one can infer something about what the child's behaviours mean and how they function for the child. Although there has been impressive consistency among a large number of studies as to the core of meanings expressed in children's early sentences, it has always been apparent to researchers that the interpretation of children's utterances is problematic, and, in 1976 the critique of Christine Howe (CH) represented a reaction to the IA research paradigm. This response to CH, coming as it does five years later, is intended as an evaluation of the place of that reaction in the history of ideas in the study of child language over the past decade. Since the time of the CH critique, a controversy has apparently emerged. On the one hand, the CH position has been reiterated by, for example, Rodgon (1977) and
Exploring the Learning Mechanism in Educational Games

The main aim of this paper is to evaluate the problem-based gaming model that tries to explain the learning process in educational games. The model was studied through Geometry game aimed for preschool pupils (N=24). The game relays on learning by teaching approach and involves Al-engine modeling the human concept learning structures. The qualitative analyses methods were used to explore participants learning processes and gaming strategies. The results indicated that the model describes well the problem-based gaming process in which the reflection phase seems to be a vital factor. Furthermore, the changes in playing strategies were found to enhance learning.
Characterizing Best Practices in an Extensive Reading Program

Over the course of three years, an M-reader supported extensive reading program at a small, private Japanese university grew from a tiny pilot into a fairly large-scale operation with over 2,000 participating students and approximately 60 teachers. Throughout the program, methods of implementation and assessment varied from class-to-class, as did student achievement. The researchers wanted to find out what methods and strategies were working well for both students and teachers in the program. Using data from M-reader in the form of word counts, participation rates, and number of quizzes taken, researchers identified and interviewed students achieving success in the program. Researchers also identified and interviewed teachers whose students were collectively outperform77 Characterizing Best Practices in an Extensive Reading Program Aaron P. CAMPBELL, Mami YOSHIDA, Midori TANIMURA, Andy H. CLARK, Rebecca CALMAN & Iain DAVEY ing other classes at similar levels in the program. From these interview results, researchers constructed profiles of students and teachers for whom the program was working well, highlighting the types of strategies and behaviors they had in common. Among these for students included a clear understanding of ER practices and the ability to integrate reading into their daily habits. Common practices amongst teachers were having students discuss their reading in pairs or small groups, and creating time for students to practice Silent Sustained Reading in class.
Operations on records

We define a simple collection of operations for creating and manipulating record structures, where records are intended as finite associations of values to labels. A second-order type system over these operations supports both subtyping and polymorphism. We provide typechecking algorithms and limited semantic models. Our approach unifies and extends previous notions of records, bounded quantification, record extension, and parametrization by row-variables. The general aim is to provide foundations for concepts found in object-oriented languages, within a framework based on typed lambda-calculus.
Activation of growth hormone releasing hormone (GHRH) receptor stimulates cardiac reverse remodeling after myocardial infarction (MI)

Both cardiac myocytes and cardiac stem cells (CSCs) express the receptor of growth hormone releasing hormone (GHRH), activation of which improves injury responses after myocardial infarction (MI). Here we show that a GHRH-agonist (GHRH-A; JI-38) reverses ventricular remodeling and enhances functional recovery in the setting of chronic MI. This response is mediated entirely by activation of GHRH receptor (GHRHR), as demonstrated by the use of a highly selective GHRH antagonist (MIA-602). One month after MI, animals were randomly assigned to receive: placebo, GHRH-A (JI-38), rat recombinant GH, MIA-602, or a combination of GHRH-A and MIA-602, for a 4-wk period. We assessed cardiac performance and hemodynamics by using echocardiography and micromanometry derived pressure-volume loops. Morphometric measurements were carried out to determine MI size and capillary density, and the expression of GHRHR was assessed by immunofluorescence and quantitative RT-PCR. GHRH-A markedly improved cardiac function as shown by echocardiographic and hemodynamic parameters. MI size was substantially reduced, whereas myocyte and nonmyocyte mitosis was markedly increased by GHRH-A. These effects occurred without increases in circulating levels of growth hormone and insulin-like growth factor I and were, at least partially, nullified by GHRH antagonism, confirming a receptor-mediated mechanism. GHRH-A stimulated CSCs proliferation ex vivo, in a manner offset by MIA-602. Collectively, our findings reveal the importance of the GHRH signaling pathway within the heart. Therapy with GHRH-A although initiated 1 mo after MI substantially improved cardiac performance and reduced infarct size, suggesting a regenerative process. Therefore, activation of GHRHR provides a unique therapeutic approach to reverse remodeling after MI.
False Optimism: Modernity, Class, and the Public Library in Britain in the 1960s and 1970s

In the late 1950s, the long-awaited postwar expansion in British public library services got under way. During the 1960s and 1970s, librarians and library planners became strongly optimistic about the public library's "modern" future. In keeping with the principles of egalitarianism and universalism underpinning the welfare state, a radically new philosophy, known as "community librarianship," emerged in the 1970s. Its aim was to encourage the public library to make an irreversible break with its "conservative" past and to become a truly popular institution. However, despite jettisoning a great deal of its Victorian image and embracing much of the modernity of the age, the public library was ultimately unable to live up to the visions of classlessness that library promoters had long cherished.
Light Logics and the Call-by-Value Lambda Calculus

The so-called light logics have been introduced as logical systems enjoying quite remarkable normalization properties. Designing a type assignment system for pure lambda calculus from these logics, however, is problematic. In this paper we show that shifting from usual call-by-name to call-by-value lambda calculus allows regaining strong connections with the underlying logic. This will be done in the context of Elementary Affine Logic (EAL), designing a type system in natural deduction style assigning EAL formulae to lambda terms.
Maximum Likelihood Reconstruction for Magnetic Resonance Fingerprinting

This paper introduces a statistical estimation framework for magnetic resonance (MR) fingerprinting, a recently proposed quantitative imaging paradigm. Within this framework, we present a maximum likelihood (ML) formalism to estimate multiple MR tissue parameter maps directly from highly undersampled, noisy k-space data. A novel algorithm, based on variable splitting, the alternating direction method of multipliers, and the variable projection method, is developed to solve the resulting optimization problem. Representative results from both simulations and in vivo experiments demonstrate that the proposed approach yields significantly improved accuracy in parameter estimation, compared to the conventional MR fingerprinting reconstruction. Moreover, the proposed framework provides new theoretical insights into the conventional approach. We show analytically that the conventional approach is an approximation to the ML reconstruction; more precisely, it is exactly equivalent to the first iteration of the proposed algorithm for the ML reconstruction, provided that a gridding reconstruction is used as an initialization.
Excess Inventory and Long-Term Stock Price Performance

This paper estimates the long-run stock price effects of excess inventory using nearly 900 excess inventory announcements made by publicly traded firms during 1990-2002. It examines the stock price effects starting one year before through two years after the excess inventory announcement date. Statistically significant abnormal returns are observed during the year before the announcement and on announcement. There is no evidence of statistically significant abnormal return during the two years after the announcement. I estimate that the mean (median) abnormal return due to excess inventory during the year before the announcement and on announcement is -37.22% (-27.03%). Negative abnormal returns are observed across industries, calendar time, firm size, and actions taken to deal with excess inventory. The evidence suggests that the stock market partially anticipates excess inventory situations, firms do not recover quickly from the negative effect of excess inventory, and the negative effect of excess inventory is economically and statistically significant.
Critical psychiatry and mental health : exploring the work of Suman Fernando in clinical practice

Foreword, Philip Thomas. Introduction. Part One: Critique of Western Psychiatry and Mental Health 1. Transcultural Psychiatry and Mental Health Suman Fernando 2. Racism in Psychiatry Suman Fernando 3. Ethno-racial Representations and the Burden of 'Otherness' in Mental Health Roy Moodley 4. Is there an Emancipatory Psychiatry? John Eversley Part Two: Challenges and Opportunities in Mental Health Care 5. The Challenge of Diversity to Mental Health Services David Ingleby 6. Race, Culture and Mental Health Care for Refugees Charles Watters 7. Developing Mental Health Policies that Address Race and Culture Hari Sewell 8. Religion, Culture and Mental Health Alison Gray and John Cox 9. In the Psychiatrist's Chair is Suman Fernando Charmaine Williams Part Three: Training and Development in Mental Health Practice 10. Institutional Racism as a Seminal Concept of Cultural Competency Training Jaswant Guzder 11. Multidisciplinary Training in Race and Culture in Mental Health Peter Ferns 12. Race and Cultural Diversity: The Training of Psychologists and Psychiatrists Rachel Tribe 13. An Anti-racism /Anti-oppression Framework in Mental Health Practice Martha Ocampo and Fritz Luther Pino Part Four: Transnational Contexts: Engaging the work of Suman Fernando 14. Myth of Global Mental Health Suman Fernando 15. Critical Psychiatry in Canada: Multiculturalism and the Politics of Alterity Laurence J. Kirmayer 16. Culture, Race and Ethnicity in US Psychiatry Carl C. Bell and Dominic F. McBride 17. Race, Culture, and Psychiatry in South Africa Nkokone Tema and Tholene Sodi 18. Mental Health Services in Sri Lanka Chamindra Weerackody and Suman Fernando 19. Transcultural Psychiatry and Social Entrepreneurship in Denmark Rashmi Singla 20. Culture and Mental Health in Aotearoa, New Zealand Materoa Mar and Judi Clements Part Five: Personal Reflections on Suman Fernando's Life and Work The Life and Times of Suman Fernando Ted Lo. Suman Fernando's roots in Sri Lanka Chamindra Weerackody. Suman Fernando's contribution to British Psychiatry John Cox. Satisfy my Soul: Suman Fernando's work in mental health Kamaldeep Bhui. Suman Fernando and University Mental Health Systems Sharon Mier. Suman Fernando foraging a place for disenfranchised populations in Mental Health Oliver Treacy. A 'Race' Against Time: Suman Fernando's Contribution to Clinical Psychology Zenobia Nadirshaw. Concluding Remarks: Future Directions of Psychiatry and Mental Health Suman Fernando.
Accomplishments and challenges in literature data mining for biology

We review recent results in literature data mining for biology and discuss the need and the steps for a challenge evaluation for this field. Literature data mining has progressed from simple recognition of terms to extraction of interaction relationships from complex sentences, and has broadened from recognition of protein interactions to a range of problems such as improving homology search, identifying cellular location, and so on. To encourage participation and accelerate progress in this expanding field, we propose creating challenge evaluations, and we describe two specific applications in this context.
Verbal planning in a case of ‘Dynamic Aphasia’: An impairment at the level of macroplanning

Patients with ‘dynamic aphasia’ exhibit reduced spontaneous speech despite well preserved basic language functions. This disorder may allow insights into the conceptual preparation of messages. Various cognitive approaches have located the patients' impairment at the level of preverbal message generation, including verbal planning, loss of inhibition of lexical concepts, and, most recently, generation of sequences of novel thoughts. We report the case of HK who presented with dynamic aphasia. The study had two goals: first, as HK was assessed over a longer period of time, changes in his performances could be documented which were relevant for the interpretation of the underlying disorder. The present study is the first to document changes across time and improvements of some of the skills involved in language production. Second, further investigations were carried out to clarify HK's underlying deficits. He was unimpaired on a number of ‘verbal planning’ tasks which argues for the preservation of those specific processes of verbal planning which Levelt (1989) termed ‘microplanning’. It is suggested that HK's performance may be best described as an impairment at the level of ‘macroplanning’. The deficit may lie in the generation of novel thoughts though minor modifications of this recent approach are being suggested.
Changes in Defense Mechanism Functioning During Group Therapy for Binge-Eating Disorder

Objective: This study examined change in defensive mechanism functioning during group psychodynamic interpersonal psychotherapy (GPIP) for women with binge-eating disorder (BED). Procedure: Women with BED (N = 85) received 16 weeks of GPIP. Five group therapy sessions (sessions 1, 3, 8, 12, and 16) from each of the 12 groups were video recorded and transcribed. Participants were rated on an observer-based measure of defensive functioning, the Defense Mechanism Rating Scale (DMRS). Symptom outcomes were assessed pre- and posttreatment. Results: Overall defensive functioning (ODF) scores improved significantly during group treatment, with specific defense level improvements in high adaptive, major image distorting, and action defenses. The linear increase in ODF mediated a decrease in binge-eating episodes and depressive symptoms. Reverse mediation was also noted. A cubic growth curve best modeled ODF data such that ODF improved in the early stage, followed by a slower rate of improvement in the middle stage, and a further increase in rate of improvement at the end of treatment. Discussion: Change in defense mechanism functioning may be an important aspect of group psychotherapy that is related to improved symptoms for women with BED who receive GPIP. The cubic trend that represented nonlinear growth in ODF is consistent with psychodynamic theory and a stage model of psychotherapy.
Measurement of renin in human plasma.

In order to obtain a simple measurement of the concentration of renin in human plasma, kinetic studies have been performed for the following enzymatic reactions: hog renin reacting with cat angiotensinogen, human renin reacting with cat angiotensinogen, and human renin reacting with human angiotensinogen. The reaction kinetics of the competition between human and cat angiotensinogen for human renin have also been investigated.From the result of these studies a micro-method was devised characterized by a precisely defined concentration of the angiotensinogen during the reaction, controlled activity of the angiotensinases, and gentle preparative treatments.The principle consists of mixing cat plasma angiotensinogen with the human plasma to be tested, and then determining the velocity of the reduction of the concentration of cat angiotensinogen during the reaction. The concentration of angiotensinogen is measured by transforming it to angiotensin under conditions where the angiotensin is stable. After an add.
The relationship between the development of musculoskeletal disorders, body mass index, and academic stress in Bahraini University students

Background There are many mechanisms in which stress can lead to weight gain thus high a BMI. The endocrine and inflammatory pathway can directly increase abdominal adiposity. Another way in which stress leads to weight gain is through changes in health behaviors. The study aimed to investigate the prevalence of musculoskeletal disorders (MSDs) among healthy students of Ahlia University, and to determine the relationship between the development of MSDs and academic stressors and body mass index. Methods Self-administered questionnaires were distributed to 94 students aged 18-26 years who were enrolled at various Ahlia University colleges and met other inclusion criteria. The students responded to the standardized Nordic musculoskeletal questionnaire and the modified College Student Stress Inventory regarding musculoskeletal symptoms and academic stressors. Height and weight measurements were also obtained to determine body mass index. Results A total of 77.66% reported MSDs in one or more body part, with the prevalence being higher among women than among men. The 7-day prevalence of MSDs severe enough to interfere with activities of daily living was 60.64%, and 44.68% by female and male students, respectively. There was a significant relationship between academic stress and MSDs in the neck, shoulders, lower back, and hips, while the relationship between MSDs, and body mass index, academic stress, and grade point average was not significant. Conclusions The prevalence of MSDs among Ahlia University students was found to be high. Apart from the positive correlation between academic stress and MSDs in certain body parts, other correlations were not significant.
Transcriptional Regulation by Triiodothyronine of the UDP-glucuronosyltransferase Family 1 Gene Complex in Rat Liver

This study demonstrates that the expression of the phenol UDP-glucuronosyltransferase 1 gene (UGT1A1) is regulated at the transcriptional level by thyroid hormone in rat liver. Following 3,5,3′-triiodo-l-thyronine (T3) stimulation in vivo, there is a gradual increase in the amount of UGT1A1 mRNA with maximum levels reached 24 h after treatment. In comparison, induction with the specific inducer, 3-methylcholanthrene (3-MC), results in maximal levels of UGT1A1 mRNA after 8 h of treatment. In primary hepatocyte cultures, the stimulatory effect of both T3 and 3-MC is also observed. This induction is suppressed by the RNA synthesis inhibitor actinomycin D, indicating that neither inducer acts at the level of mRNA stabilization. Indeed, nuclear run-on assays show a 3-fold increase in UGT1A1 transcription after T3treatment and a 6-fold increase after 3-MC stimulation. This transcriptional induction by T3 is prevented by cycloheximide in primary hepatocyte cultures, while 3-MC stimulation is only partially affected after prolonged treatment with the protein synthesis inhibitor. Together, these data provide evidence for a transcriptional control of UGT1A1 synthesis and indicate that T3 and 3-MC use different activation mechanisms. Stimulation of the UGT1A1 gene by T3 requiresde novo protein synthesis, while 3-MC-dependent activation is the result of a direct action of the compound, most likely via the aromatic hydrocarbon receptor complex.