Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting the lethal phenotype of the knockout mouse by integrating comprehensive genomic data

MOTIVATION The phenotypes of knockout mice provide crucial information for understanding the biological functions of mammalian genes. Among various knockout phenotypes, lethality is of great interest because those involved genes play essential roles. With the availability of large-scale genomic data, we aimed to assess how well the integration of various genomic features can predict the lethal phenotype of single-gene knockout mice. RESULTS We first assembled a comprehensive list of 491 candidate genomic features derived from diverse data sources. Using mouse genes with a known phenotype as the training set, we integrated the informative genomic features to predict the knockout lethality through three machine learning methods. Based on cross-validation, our models could achieve a good performance (accuracy = 73% and recall = 63%). Our results serve as a valuable practical resource in the mouse genetics research community, and also accelerate the translation of the knowledge of mouse genes into better strategies for studying human disease.
Investigating the Reggio Emilia Study Tour Experience: From Conversation to Insights

Taking early childhood Master’s students on a Reggio Emilia Study Tour leads to making meaning of anticipatory and after-experience reflective narrative-episodes. These narrative episodes are constructed around the phenomena of anticipating the trip as well as reflecting on the experiences during and after the study tour. The experiences are then analyzed collaboratively among researchers and participants through informal discussions. Themes in each narrative episode are explored through the written narratives and then conclusions are drawn. Anticipatory themes include eagerness to see, desire to witness the image of the child in the everyday, and a concern about adopting the Reggio approach in the U.S.; and, wanting to understand documentation processes and feeling a sense of time and space in the environments. After-experience reflections bring about themes such as change as a constant reminder of humanness and barriers in language and translation; and, questioning practices at home and constructing understanding/articulating differences as reconciliation. In the conclusion, questions linger about stretching ourselves, going on the journey as learners, and finding the in-between moments. We also find new frameworks of mind where believing and seeing in new ways lead us to not “do Reggio” and instead develop our own living organism and dynamic programs as the joy in a lifetime of work approach. In the end, finding the extraordinary in the everyday emerges as an implication for future research.
The differential contribution of maternal and paternal values to social competence of preschoolers

Multivariate analyses were conducted to clarify the nature of the influences of parental values on social behaviours of kindergarteners in the context of socio-demographic variables and sex of participants. This study included 217 mothers and 172 fathers from the same families, who completed a socio-demographic questionnaire and a new Q-sort that assesses parental values on Individualism (IND)/Collectivism (COL) and Horizontal (HOR)/Vertical (VER) continuums. To test the hypothesis of an association between parental values and children's behaviours, teachers also provided information about each child's social competence, anger-aggression, and anxiety-withdrawal in kindergarten using the Social Competence and Behavior Scale. Parents shared a greater proportion of IND/COL than VER values and mothers were more likely to emphasise IND and COL values than fathers. Mothers within IND and COL groups had more socially competent kindergartners as reported by teachers. Considering the mixed results found in the literature regarding sex differences in parenting and behaviours of children, the present results suggested that examining more closely the system of parental values might offer valuable avenues for future research on early childhood socialisation.
Heart rate and posttraumatic stress in injured children.

BACKGROUND Elevated, acute heart rate has been related to later posttraumatic stress disorder (PTSD) development in injured adults, but this has not been examined in children and adolescents. Better understanding of the relationship between acute physiological arousal and later child PTSD could help elucidate the etiology of posttrauma responses in children and might identify useful markers for PTSD risk. OBJECTIVE To evaluate the relationship between heart rate assessed in the emergency department (ED) during normal clinical care and later PTSD outcome in traumatically injured children. DESIGN Prospective cohort study assessed heart rate at ED triage and PTSD an average of 6 months' postinjury. SETTING Large, urban pediatric academic medical center in the northeastern United States. PARTICIPANTS One hundred ninety children and adolescents (aged 8-17 years) hospitalized for traffic-related injury.Main Outcome Measure Clinician-Administered PTSD Scale for Children and Adolescents. RESULTS The group of children who developed partial or full PTSD had a higher mean +/- SD heart rate at ED triage than those who did not go on to have PTSD (109.6 +/- 22.3 vs 99.7 +/- 18.0 beats per minute). Children with an elevated heart rate (defined as >/=2 SDs higher than the normal resting heart rate for their age and sex) at ED triage were more likely to meet criteria for partial or full PTSD at follow-up, even after adjusting for age, sex, and injury (adjusted odds ratio, 2.4 [95% confidence interval, 1.1-5.4]). CONCLUSION These results suggest an association between early physiological arousal and the development or persistence of PTSD symptoms in injured children and point to the importance of better understanding the interplay between physiological and psychological functioning after a traumatic stressor.
MEMORANDUM No 19 / 2001 Who Are the Advertisers ?

We seek to explain why TV advertising is dominated by a few product categories. We apply a model of the TV industry that encompasses both the product markets and the market for TV viewers to discuss who will advertise on TV. Under the assumption that viewers dislike advertising, entailing a contagion effect in advertising, we find that less profitable firms not only will advertise less than highly profitable firms but will choose not to advertise at all. (77 words) *This is a revised version of parts of our previous paper, “TV Advertising, Programming Investments, and Product-Market Oligopoly”. We are indebted to Philippe Cyrenne, Ted Frech, Jean Gabszewicz, Laurent Linnemer, and seminar participants at the Universities of Calgary, California-Berkeley, California-Santa Barbara, and Colorado, at Northwestern University and Copenhagen Business School, and at the 2000 meetings of CEA (Vancouver), EEA (Bolzano), and EARIE (Lausanne), for helpful comments. Part of this research is financed by the Norwegian Competition Authority and the Norwegian Ministry of Government Administration through SNF (The Foundation for Research in Economics and Business Administration). Part of Nilssen’s research was done during a visit at the Haas School of Business at the University of California, Berkeley. Part of Sørgard’s research was done during a visit at the Department of Economics at the University of California, Santa Barbara. The hospitality of the two institutions, as well as travel grants from the Research Council of Norway and the U.S.-Norway Fulbright Foundation for Educational Exchange, are gratefully acknowledged.
Strategyproofness in the large as a desideratum for market design

We propose a criterion of approximate strategyproofness (SP), called strategyproof in the large (SP-L). A mechanism is SP-L if, for any agent, any probability distribution of the other agents' reports, and any > 0, in a large enough market the agent maximizes his expected payo to within by reporting his preferences truthfully. Conceptually, SP-L distinguishes between two kinds of non-SP mechanisms: those where pro table misreports vanish as the market grows large in our sense, and those where pro table misreports persist even for agents who regard the mechanism's prices as exogenous. Our main result shows that, under some assumptions, SP-L is approximately costless to satisfy in large markets relative to Bayes-Nash or Nash implementability. The assumptions include anonymity, private values, and a continuity condition. We interpret the result as justifying SP-L as a second-best desideratum, especially for problems for which the bene ts of SP design are compelling (e.g., compliance with the Wilson doctrine) yet it is known that mechanisms that are exactly SP are unattractive. We illustrate with examples from assignment, auctions, and matching. ∗For helpful discussions we are grateful to Nabil Al-Najjar, Susan Athey, Aaron Bodoh-Creed, Gabriel Carroll, Je Ely, Alex Frankel, Drew Fudenberg, Matt Gentzkow, Jason Hartline, John Hat eld, Richard Holden, Ehud Kalai, Emir Kamenica, Fuhito Kojima, Scott Kominers, Jacob Leshno, Jon Levin, Paul Milgrom, Roger Myerson, David Parkes, Parag Pathak, Nicola Persico, Andy Postlewaite, Canice Prendergast, Ilya Segal, Eran Shmaya, Lars Stole, Glen Weyl, and especially Al Roth. We are grateful to seminar audiences at Ohio State, the MFI Conference on Matching and Price Theory, UCLA, Chicago, AMMA 2011, Boston College, the NBER Conference on Market Design, Duke / UNC, Michigan, Carnegie Mellon / Pittsburgh, Montreal, Berkeley, Northwestern and Rochester. †Harvard University, azevedo@fas.harvard. edu. ‡University of Chicago Booth School of Business, eric.budish@chicagobooth.edu. STRATEGYPROOFNESS IN THE LARGE 1
Silicon enhances suberization and lignification in roots of rice (Oryza sativa)

The beneficial element silicon (Si) may affect radial oxygen loss (ROL) of rice roots depending on suberization of the exodermis and lignification of sclerenchyma. Thus, the effect of Si nutrition on the oxidation power of rice roots, suberization and lignification was examined. In addition, Si-induced alterations of the transcript levels of 265 genes related to suberin and lignin synthesis were studied by custom-made microarray and quantitative Real Time-PCR. Without Si supply, the oxidation zone of 12 cm long adventitious roots extended along the entire root length but with Si supply the oxidation zone was restricted to 5 cm behind the root tip. This pattern coincided with enhanced suberization of the exodermis and lignification of sclerenchyma by Si supply. Suberization of the exodermis started, with and without Si supply, at 4–5 cm and 8–9 cm distance from the root tip (drt), respectively. Si significantly increased transcript abundance of 12 genes, while two genes had a reduced transcript level. A gene coding for a leucine-rich repeat protein exhibited a 25-fold higher transcript level with Si nutrition. Physiological, histochemical, and molecular-biological data showing that Si has an active impact on rice root anatomy and gene transcription is presented here.
Palatine Mucosa of Aging and Experimentally Induced Diabetic Aging Rabbits: Light-Microscopic, Scanning Electron Microscopic and Transmission Electron Microscopic Qualitative Study

Background: Data associating palatine mucosa, microvascular architecture, aging and diabetes mellitus are few, so the aim of the present study was to examine these conditions structurally and ultrastructurally. Methods: We used 18 female rabbits, aged about 2 years at the beginning of the experiment, distributed into 2 groups: aging diabetic and aging animals, prepared by three different methodologies: light microscopy, scanning electron microscopy and transmission electron microscopy. The samples were stained with hematoxylin-eosin for light microscopy, and for scanning electron microscopy, we used Mercox® Cl-2B vascular corrosion casts. For transmission electron microscopy, the specimens were fixed and embedded in Epon 812 resin. Results: Under light microscopy, we noted small amounts of underdeveloped connective papillae and significant flattened areas through the epithelium-connective tissue interface in the aging diabetic group. Larger blood vessels were deeply located in the palatine mucosa, branching off in the direction of the epithelium-connective tissue interface. Capillaries followed the interface contour. In both groups, vascular corrosion casts revealed capillaries sprouting out in disorganized rows but parallel between themselves. ‘Hair-pin’ capillary loops and convoluted capillary loops were noted. Conclusion: The aging diabetic group showed rarefying microvasculature areas with complex tortuous capillary loops. Transmission electron microscopy results showed that the aging diabetic group presented small cytoplasmatic projections directed to the vessel lumen and micropinocytic vesicle, i.e. caveolas. Epithelium-connective tissue interface, connective papillae, microangioarchitecture, and information about endothelial cells alterations were observed in the aging diabetic and aging animals.
Old Ideas in New Skins: Examining Discourses of Diversity on the Websites of 10 Urban-Serving Universities

Deficit discourse, the idea that minorities "lack" intellectually, runs through current ideas about diversity in higher education. Diversity is viewed as a policy that helps the deficient. Recent litigation about diversity, Fisher v. University of Texas (2013), embodied the alignment of deficit and diversity. This study examined portrayals, visual and textual, of diversity on the websites of ten urban-serving universities, using a method of critical discourse analysis and a lens of critical race theory, to uncover the ways they defined diversity and if notions of deficit were attached. This study also addressed the ways these universities, a part of the Coalition of Urban-Serving Universities, discussed their communities and if deficit was attached. Diversity was defined as deficient racial minorities and communities as well as diversity as tokens and a form of compliance. The findings of this study show that these college websites, through their portrayals of racial minorities as deficient, duplicate inequality and encourage the maintenance of White hegemony.
Genes and Gene Ontologies Common to Airflow Obstruction and Emphysema in the Lungs of Patients with COPD

Chronic obstructive pulmonary disease (COPD) is a major public health problem with increasing prevalence worldwide. The primary aim of this study was to identify genes and gene ontologies associated with COPD severity. Gene expression profiling was performed on total RNA extracted from lung tissue of 18 former smokers with COPD. Class comparison analysis on mild (n = 9, FEV1 80–110% predicted) and moderate (n = 9, FEV1 50–60% predicted) COPD patients identified 46 differentially expressed genes (p<0.01), of which 14 genes were technically confirmed by quantitative real-time-PCR. Biological replication in an independent test set of 58 lung samples confirmed the altered expression of ten genes with increasing COPD severity, with eight of these genes (NNMT, THBS1, HLA-DPB1, IGHD, ETS2, ELF1, PTGDS and CYRBD1) being differentially expressed by greater than 1.8 fold between mild and moderate COPD, identifying these as candidate determinants of COPD severity. These genes belonged to ontologies potentially implicated in COPD including angiogenesis, cell migration, proliferation and apoptosis. Our secondary aim was to identify gene ontologies common to airway obstruction, indicated by impaired FEV1 and KCO. Using gene ontology enrichment analysis we have identified relevant biological and molecular processes including regulation of cell-matrix adhesion, leukocyte activation, cell and substrate adhesion, cell adhesion, angiogenesis, cell activation that are enriched among genes involved in airflow obstruction. Exploring the functional significance of these genes and their gene ontologies will provide clues to molecular changes involved in severity of COPD, which could be developed as targets for therapy or biomarkers for early diagnosis.
MicroRNAs Classify Different Disease Behavior Phenotypes of Crohn's Disease and May Have Prognostic Utility

Background:There is a dire need for reliable prognostic markers that can guide effective therapeutic intervention in Crohn's disease (CD). We examined whether different phenotypes in CD can be classified based on colonic microRNA (miRNA) expression and whether miRNAs have prognostic utility for CD. Methods:High-throughput sequencing of small and total RNA isolated from colon tissue from patients with CD and controls without Inflammatory Bowel Disease (non-IBD) was performed. To identify miRNAs associated with specific phenotypes of CD, patients were stratified according to disease behavior (nonstricturing, nonpenetrating; stricturing; penetrating), and miRNA profiles in each subset were compared with those of the non-IBD group. Validation assays were performed using quantitative reverse transcription polymerase chain reaction. These miRNAs were further evaluated by quantitative reverse transcriptase polymerase chain reaction on formalin-fixed, paraffin-embedded tissue (index biopsies) of patients with nonpenetrating CD at the time of diagnosis that either retained the nonpenetrating phenotype or progressed to penetrating/fistulizing CD. Results:We found a suite of miRNAs, including miR-31-5p, miR-215, miR-223-3p, miR-196b-5p, and miR-203 that stratify patients with CD according to disease behavior independent of the effect of inflammation. Furthermore, we also demonstrated that expression levels of miR-215 in index biopsies of patients with CD might predict the likelihood of progression to penetrating/fistulizing CD. Finally, using a novel statistical simulation approach applied to colonic RNA-sequencing data for patients with CD and non-IBD controls, we identified miR-31-5p and miR-203 as candidate master regulators of gene expression profiles associated with CD. Conclusions:miRNAs may serve as clinically useful prognostic markers guiding initial therapy and identifying patients who would benefit most from effective intervention.
UnlimitedHand: Input and Output Hand Gestures with Less Calibration Time

Numerous devices that either track hand gestures or provide haptic feedback have been developed with the aim of manipulating objects within Virtual Reality(VR) and Augmented Reality(AR) environments. However, these devices implement lengthy calibration processes to ease out individual differences. In this research, a wearable device that simultaneously recognizes hand gestures and outputs haptic feedback: UnlimitedHand is suggested. Photo-reflectors are placed over specific muscle groups on the forearm to read in hand gestures. For output, electrodes are placed over the same muscles to control the user's hand movements. Both sensors and electrodes target main muscle groups responsible for moving the hand. Since the positions of these muscle groups are common between humans, UnlimitedHand is able to reduce the time spent on performing calibration.
Antibacterial activity in bovine lactoferrin-derived peptides

Several peptides sharing high sequence homology with lactoferricin B (Lf-cin B) were generated from bovine lactoferrin (Lf) with recombinant chymosin. Two peptides were copurified, one identical to Lf-cin B and another differing from Lf-cin B by the inclusion of a C-terminal alanine (lactoferricin). Two other peptides were copurified from chymosin-hydrolyzed Lf, one differing from Lf-cin B by the inclusion of C-terminal alanyl-leucine and the other being a heterodimer linked by a disulfide bond. These peptides were isolated in a single step from chymosin-hydrolyzed Lf by membrane ion-exchange chromatography and were purified by reverse-phase high-pressure liquid chromatography (HPLC). They were characterized by N-terminal Edman sequencing, mass spectrometry, and antibacterial activity determination. Pure lactoferricin, prepared from pepsin-hydrolyzed Lf, was purified by standard chromatography techniques. This peptide was analyzed against a number of gram-positive and gram-negative bacteria before and after reduction of its disulfide bond or cleavage after its single methionine residue and was found to inhibit the growth of all the test bacteria at a concentration of 8 microM or less. Subfragments of lactoferricin were isolated from reduced and cleaved peptide by reverse-phase HPLC. Subfragment 1 (residues 1 to 10) was active against most of the test microorganisms at concentrations of 10 to 50 microM. Subfragment 2 (residues 11 to 26) was active against only a few microorganisms at concentrations up to 100 microM. These antibacterial studies indicate that the activity of lactoferricin is mainly, but not wholly, due to its N-terminal region.
INTERVIEWS WITH ELDERLY PEDESTRIANS INVOLVED IN ROAD ACCIDENTS

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Relatório de estágio - Instituto Português de Oncologia

This report aims to expose all that was done during the internship at Instituto Português de Oncologia Francisco Gentil (IPOFG) within the scope of the Masters in Physical Therapy, Women's Health specialty. This also aims to demonstrate the gains achieved both at personal and professional levels, as well as demonstrating the importance of physiotherapy in this increasingly vital area that is Oncology. The report is divided into five sections: internship performance report, presenting of a case study, concluding remarks, the tutor's opinion and curriculum vitae (CV) presentation. The first section begins with a characterization of the internship unit. This characterization is comprised of a description of the internship unit in the context of the National Health Plan, which is followed by a brief description of the installations, and a SWOT analysis of the unit. Next, a characterization of patients is made, where their needs are demonstrated in terms of what is described in the literature and in terms of what was observed in the internship unit. It is also described the role of the physiotherapist in Oncology and specifically the role that this professional represents on the Rehabilitation Service of the IPOFG. Three patient records, that were evaluated and treated, are presented to highlight the characteristics and needs of the oncologic patients and demonstrate the role of the physiotherapist in health care provision to this population. The intervention is then analyzed through critical analysis of three papers. Subsequently, a critical analysis of the intervention done in the internship unit based on the best available scientific evidence is presented. Further in this first section an improvement for the internship unit is proposed. This improvement is based on the SWOT analysis conducted and the raised needs. A personal SWOT analysis is also performed as a means of personal reflection and the learning contract, drawn up before the start of the stage, is exposed. The learning contract reevaluations, carried out during the internship, are also presented as well as the feedbacks obtained by other professionals and patients. Finally, a reflection on all the learning process is performed.