Miracle-dz/UniFAR-FTUs huggingface dataset:
Overestimation of alternative splicing caused by variable probe characteristics in exon arrays

In higher eukaryotes, alternative splicing is a common mechanism for increasing transcriptome diversity. Affymetrix exon arrays were designed as a tool for monitoring the relative expression levels of hundreds of thousands of known and predicted exons with a view to detecting alternative splicing events. In this article, we have analyzed exon array data from many different human and mouse tissues and have uncovered a systematic relationship between transcript-fold change and alternative splicing as reported by the splicing index. Evidence from dilution experiments and deep sequencing suggest that this effect is of technical rather than biological origin and that it is driven by sequence features of the probes. This effect is substantial and results in a 12-fold overestimation of alternative splicing events in genes that are differentially expressed. By cross-species exon array comparison, we could further show that the systematic bias persists even across species boundaries. Failure to consider this effect in data analysis would result in the reproducible false detection of apparently conserved alternative splicing events. Finally, we have developed a software in R called COSIE (Corrected Splicing Indices for Exon arrays) that for any given set of new exon array experiments corrects for the observed bias and improves the detection of alternative splicing (available at www.fmi.ch/groups/gbioinfo).
Is There an Assignment of Top and Bottom during Symmetry Perception?

We report data from a discrimination task in which participants had to decide whether a single-item display was either vertically symmetric or asymmetric. This decision was found to be easier when items with a top–bottom polarity were placed in an orientation where the wide end was the base of the stimulus and the narrow end was the top. The difference in reaction times between this orientation and its inversion was about 10 ms. We suggest that top and bottom labels are assigned to stimuli during the detection of bilateral symmetry.
Structural Constraints on Friendships in Old Age

The effects that widowhood or retirement have on the friendships of older people were found to vary with the prevalence of these changes in status within the age, sex, and class structure in which the individual is located. In those groups where widowhood and retirement are relatively rare either change in status places the individual in a deviant position among his peers, differentiates his interests and experiences from those of his associates, and thereby exerts a detrimental effect on friendships. In those structural contexts, however, where these changes in status are prevalent, it is the still married or employed individual who occupies a deviant position in relation to his peers and whose social life therefore tends to become more restricted.
The impact of village-based kindergarten on early literacy, numeracy, and school attendance in Solomon Islands

ABSTRACT This research, a collaboration of an international aid organisation, an institute of higher education, and an external evaluation consultant, assesses the early literacy, numeracy, and school attendance outcomes resulting from an early childhood development programme undertaken in several villages in the province of Makira, Solomon Islands. The programme was designed to enable kindergarten provision, including teacher education and development, as an early childhood development strategy. This research focused on assessing programme impact in terms of early literacy, numeracy, and school attendance for children who had participated in kindergarten in Makira Province, compared against a matched group of children in another province of Solomon Islands who did not experience the early childhood programme. The findings of the study indicate both a statistically and educationally significant impact of village-based kindergarten on children's literacy and numeracy as well as their school attendance. These findings are discussed in the context of the international literature examining early childhood education in developing countries.
Critical role of calpain in axonal damage‐induced retinal ganglion cell death

Calpain, an intracellular cysteine protease, has been widely reported to be involved in neuronal cell death. The purpose of this study is to investigate the role of calpain activation in axonal damage‐induced retinal ganglion cell (RGC) death. Twelve‐week‐old male calpstatin (an endogenous calpain inhibitor) knockout mice (CAST KO) and wild‐type (WT) mice were used in this study. Axonal damage was induced by optic nerve crush (NC) or tubulin destruction induced by leaving a gelatin sponge soaked with vinblastine (VB), a microtubule disassembly chemical, around the optic nerve. Calpain activation was assessed by immunoblot analysis, which indirectly quantified the cleaved α‐fodrin, a substrate of calpain. RGCs were retrogradely labeled by injecting a fluorescent tracer, Fluoro‐Gold (FG), and the retinas were harvested and flat‐mounted retinas prepared. The densities of FG‐labeled RGCs harvested from the WT and CAST KO groups were assessed and compared. Additionally, a calpain inhibitor (SNJ‐1945, 100 mg/kg/day) was administered orally, and the density of surviving RGCs was compared with that of the vehicle control group. The mean density of surviving RGCs in the CAST KO group was significantly lower than that observed in the WT group, both in NC and in VB. The mean density of surviving RGCs in the SNJ‐1945‐treated group was significantly higher than that of the control group. The calpain inhibitor SNJ‐1945 has a neuroprotective effect against axonal damage‐induced RGC death. This pathway may be an important therapeutic target for preventing this axonal damage‐induced RGC death, including glaucoma and diabetic optic neuropathy and other CNS diseases that share a common etiology. © 2011 Wiley Periodicals, Inc.
RevGlyph: a technique for reverting anaglyph stereoscopic videos

In order to visualize stereoscopic videos, it is necessary a pair of videos of a same scene horizontally displaced -- the stereo pair --, thus requiring twice the space to be stored. The anaglyph conversion is a technique in which color components of the stereo pair are removed, being the remaining color components joined to form a single video. With that, it is possible to reduce at least by the half the amount of data to be stored. Unfortunately, the anaglyphic video is not supported by other stereoscopic visualization methods -- they require the stereo pair. Our proposal is to create an anaglyph reversion technique that would enable to recreate the stereo pair from an anaglyph video, which could make stereo information available for other visualization methods. Such reversion is not straightforward, since during the anaglyph conversion some color data is lost. In this paper, we introduce RevGlyph, an approach to the anaglyph reversion by storing the removed color components in a special structure that we call "Color Index Table". We then discuss the results obtained from our experiments with this technique, achieving a good compression rate of 79.64% compared to the original image. The results also showed that the process does not interfere with the stereo depth perception.
Influence of Multi-Source and Multi-Temporal Remotely Sensed and Ancillary Data on the Accuracy of Random Forest Classification of Wetlands in Northern Minnesota

Wetland mapping at the landscape scale using remotely sensed data requires both affordable data and an efficient accurate classification method. Random forest classification offers several advantages over traditional land cover classification techniques, including a bootstrapping technique to generate robust estimations of outliers in the training data, as well as the capability of measuring classification confidence. Though the random forest classifier can generate complex decision trees with a multitude of input data and still not run a high risk of over fitting, there is a great need to reduce computational and operational costs by including only key input data sets without sacrificing a significant level of accuracy. Our main questions for this study site in Northern Minnesota were: (1) how does classification accuracy and confidence of mapping wetlands compare using different remote sensing platforms and sets of input data; (2) what are the key input variables for accurate differentiation of upland, water, and wetlands, including wetland type; and (3) which datasets and seasonal imagery yield the best accuracy for wetland classification. Our results show the key input variables include terrain (elevation and curvature) and soils descriptors (hydric), along with an assortment of remotely sensed data collected in the spring (satellite visible, near infrared, and thermal bands; satellite normalized vegetation index and Tasseled Cap greenness and wetness; and horizontal-horizontal (HH) and horizontal-vertical (HV) polarization using L-band satellite radar). We undertook this exploratory analysis to inform decisions by natural resource
A reanalysis of McGurk data suggests that audiovisual fusion in speech perception is subject-dependent.

Audiovisual perception of conflicting stimuli displays a large level of intersubject variability, generally larger than pure auditory or visual data. However, it is not clear whether this actually reflects differences in integration per se or just the consequence of slight differences in unisensory perception. It is argued that the debate has been blurred by methodological problems in the analysis of experimental data, particularly when using the fuzzy-logical model of perception (FLMP) [Massaro, D. W. (1987). Speech Perception by Ear and Eye: A Paradigm for Psychological Inquiry (Laurence Erlbaum Associates, London)] shown to display overfitting abilities with McGurk stimuli [Schwartz, J. L. (2006). J. Acoust. Soc. Am. 120, 1795-1798]. A large corpus of McGurk data is reanalyzed, using a methodology based on (1) comparison of FLMP and a variant with subject-dependent weights of the auditory and visual inputs in the fusion process, weighted FLMP (WFLMP); (2) use of a Bayesian selection model criterion instead of a root mean square error fit in model assessment; and (3) systematic exploration of the number of useful parameters in the models to compare, attempting to discard poorly explicative parameters. It is shown that WFLMP performs significantly better than FLMP, suggesting that audiovisual fusion is indeed subject-dependent, some subjects being more "auditory," and others more "visual. " Intersubject variability has important consequences for theoretical understanding of the fusion process, and re-education of hearing impaired people.
Long-term disease-free survivors in metastatic undifferentiated carcinoma of nasopharyngeal type.

PURPOSE To review incidence and analyze profile of long-term complete responders among patients with undifferentiated carcinoma of nasopharyngeal type (UCNT) treated at a single institution. PATIENTS AND METHODS We present a cohort of 20 long-term unmaintained complete responders to chemotherapy for metastatic UCNT treated at the Institut Gustave Roussy between April 1978 and November 1996. A patient was considered a long-term survivor if he or she was disease-free for more than 36 months without treatment after obtaining a complete response by chemotherapy. Patient characteristics were as follows: sex, 17 men and three women; median age, 28 years (range, 9 to 62 years); median World Health Organization performance status, 1; and initial tumor-node-metastasis stage (International Union Against Cancer-American Joint Committee on Cancer, 1987) of T3 to T4, 60%, and of N2b to N3, 75%. Epstein-Barr virus serology was characteristic in 19 patients. Of 16 pretreated patients, 11 were pretreated by radiotherapy alone and five by chemotherapy and radiotherapy. Thirteen patients had metastatic relapses of locally controlled UCNT. Tumor sites were bone in 15 patients, lung in four, and liver (biopsy-proven) in two. Chemotherapy included the following: cisplatin, bleomycin, and fluorouracil in five patients; bleomycin, epirubicin, and cisplatin in seven patients; fluorouracil, mitomycin, epirubicin, and cisplatin in four patients; and fluorouracil, bleomycin, epirubicin, and cisplatin in one patient. Three patients were treated with platinum-based regimens before 1985. Patients received a median of six cycles (range, three to 13). Thirteen patients with bone metastases received consolidating radiotherapy. RESULTS As of June 1999, 14 of 20 patients were still alive with no evidence of disease after treatment (disease-free survival time, 82+ to 190+ months), three patients died of other causes while in complete response at 61, 109, and 208 months after treatment, and three patients died of disease at 42, 89, and 115 months after treatment. Long-term complete responses were obtained in both bone and visceral disease. CONCLUSION Our data support a curative role for chemotherapy in metastatic UCNT and are a major incentive to continue research for better combinations to increase the percentage of patients with metastatic UCNT who attain complete responses and long-term survival.
Correlates of comorbid psychopathology in children with ADHD.

OBJECTIVE To investigate correlates of internalizing and externalizing psychopathology in a clinical sample of children with attention-deficit/hyperactivity disorder (ADHD). METHOD Parent and teacher Child Behavior Checklists were administered to 300 children with ADHD to ascertain comorbid symptoms. Based on previous research, a seven-step hierarchical regression analysis was developed. Six hierarchical regression analyses were conducted with either parent or teacher Child Behavior Checklist aggression, delinquency, or anxious/depressive comorbid symptoms as dependent measures. RESULTS Controlling for (1) variables known to increase risk for ADHD child psychopathology and (2) estimated duration of ADHD, our results suggest that the presence of comorbid symptoms is influenced by age of onset. An early age of onset of ADHD was correlated with a greater rate of parent-reported child aggressive symptoms, and a later age of onset was correlated with a greater rate of parent-reported child anxious/depressive symptoms. Elevated levels of comorbid externalizing and internalizing symptoms are associated with greater ADHD symptom severity. CONCLUSIONS Comorbid externalizing and internalizing symptoms are correlated with age of ADHD onset and are related to the severity of clinical presentation in a referred sample of children with ADHD.
Investigation of Hydrogen-Sensing Characteristics of a Pd/GaN Schottky Diode

The hydrogen sensing and response characteristics of a catalytic Pd/GaN metal-semiconductor (MS) Schottky diode are systematically studied in this paper. The current-voltage characteristics, hydrogen detection sensitivity ratios, Schottky barrier height variations, adsorption heat, and transient responses for different hydrogen concentration are measured over wide temperature range. The Pd/GaN Schottky diode reveals a remarkable capability of hydrogen detection at high temperature and relatively wide operating temperature range under bipolarly applied voltages. Experimentally, extremely low hydrogen concentration for 14 ppm H2 in air can be detected. A very high hydrogen detection sensitivity ratio of 12744 and a large Schottky barrier height variation Δφb of 253 meV are obtained when a 9970 ppm H2 in air gas is introduced at 300 K. In addition, according to the van't Hoff equation, the hydrogen adsorption heat value of the studied device is calculated as -18.24 kJ mole. Finally, considerably short response time is found in the studied device.
Ascribed versus Self-Determined Identity: Critical Interpretive Inquiry into the Subjectivity of Microminority Identity

Oftentimes minorities are perceived through an external racial lens by peers and personnel in educational institutions. Furthermore, the literature often homogenizes minorities into broad racial groups such as Black, Asian, and Hispanic. This study has been designed to explore if there is a discrepancy between internal, subjective perceptions and external, institutional perceptions regarding the identity of micro-minorities (i.e., minorities who are part of very small groups or of no group at all). This qualitative critical study was conducted on the campus of a four-year university in North Carolina. Face-to-face interviews were conducted with six international students from a variety of cultural and ethnic backgrounds. Some of the participants reported not being able to identify with groups they were homogenized within by the institution based on race. Instead, they considered themselves part of very small and specific groups or of no group at all. Additional findings revealed that the way these participants perceived their identity diverged significantly from institutional perceptions: Most participants considered culture and not race as central to their identity. Furthermore, the data suggested that being part of a small minority group or no group at all results in a very different experience than being part of a larger group. I chose critical race theory as the theoretical framework for this exploratory study, which also contained a self-reflective component designed to supplement, compare, and contrast the experiences of the participants with my own.
Effect of weathering on physical and mechanical properties of hybrid nanocomposite based on polyethylene, woodflour and nanoclay

Wood plastic composites have received increasing attention during the last decades, because of many advantages related to their use. However the durability of Wood plastic composites after ultraviolet exposure has become a concern. In this research, hybrid nanocomposites of polyethylene and woodflour with different concentrations of nanoclay were fabricated using melt compounding followed by injection molding. Specimens were exposed for 2000 h to ultraviolet radiation and moisture cycling in a laboratory weathering device to simulate the effects of exposure to sunlight and rain. Physical and mechanical properties of the nanocomposites were evaluated, before and after weathering. The results indicated that the water absorption of wood plastic composites increased after weathering but nanoclay reduced the intensity of weathering to some extent, through decreasing of water absorption. Also results showed that weathering decreased modulus of elasticity values, however good dispersion of clay layers resulted in fewer drop of modulus of elasticity values. Fourier transform infrared spectroscopy showed that lowest carbonyl index is related to the nano wood plastic composites with 2wt% nanoclay. Also X-Ray diffraction patterns revealed that intercalation morphology has been formed for nano particles.
New media technology acceptance by students of undergraduate language and communication courses

Last two decades have witnessed a phenomenal growth in the number of Internet users. Internet has brought revolution in each and every field of life including education. But it has been observed that some technologies have been accepted and used for a long span of time whereas there are certain technologies which have been rejected at some point of time; this behaviour is known as acceptance. In this research paper, the user acceptance of internet based new media technologies by undergraduate students in Language and Communication courses has been explored. The well-established UTAUT (Unified theory of acceptance and use of technology) model by Venkatesh has been used as the framework of the study.
A community of practice as an inclusive model to support children with social, emotional and behavioural difficulties in school contexts

ABSTRACT Many school children throughout the world who exhibit antisocial or destructive behaviour or have social, emotional and behavioural difficulties (SEBD) do not receive the support they need. As a result, they are caught up in a cycle of vulnerability. Systemic collaborative support is needed to counter this. Although in some cases teachers and other professionals join forces, interventions are usually affected by individual professionals outside the framework of inclusive education. This literature review paper explores the support children with SEBD in school contexts receive. The findings of the thematic document analysis highlight the vulnerability of children with SEBD, the success or otherwise of attempts made by various approaches and intervention programmes to provide support to these children, and the barriers to inclusive support. We argue the merits of adopting a Community of Practice as an inclusive model to support school children with SEBD. This kind of inclusive model strengthens constructive partnerships that provide these children with opportunities to acquire the social capital they need to engage meaningfully at schools and in their future life.
A rehabilitation exercise program induces severe bone mineral deficits in estrogen-deficient rats after extended disuse

ObjectiveBoth estrogen and mechanical loading regulate bone maintenance. However, mechanical overload seems less effective in enhancing bone mineral density (BMD) in estrogen-deficient women. The aim of this study was to determine whether estradiol (E2) influences early-phase bone adaptations to reambulation (REAMB) and/or rehabilitation exercises after hindlimb unloading (HLU) of ovariectomized rats. MethodsEighty-one 5-month-old female Sprague-Dawley rats were randomized into the following groups: (1) intact controls, (2) ovariectomy (OVX), (3) OVX + E2, (4) OVX + 4 weeks of HLU, (5) OVX + E2 + HLU, (6) OVX + HLU + 2 weeks of quadrupedal REAMB, (7) OVX + E2 + HLU + REAMB, (8) OVX + HLU + REAMB + supplemental climbing, jumping, and balance exercises (EX), or (9) OVX + E2 + HLU + REAMB + EX. Serial dual-energy x-ray absorptiometry scans were performed to track total body bone characteristics throughout the study, and peripheral quantitative computerized tomography was used to determine distal femoral metaphyseal bone mineral characteristics. ResultsTotal body BMD increased by 4% to 8% in all animals receiving supplemental E2, whereas BMD did not change in animals without E2. OVX reduced trabecular BMD at the femoral metaphysis, and HLU exacerbated this loss while also reducing cortical BMD. E2 protected against OVX + HLU–induced bone loss at the femoral metaphysis. Conversely, REAMB did not alter BMD, regardless of estrogen status. In the absence of E2, REAMB + EX resulted in severe bone loss after OVX + HLU, with trabecular BMD and cortical BMD measurements that were 91% and 7% below those of controls, respectively (P ⩽ 0.001). However, in the presence of E2, REAMB + EX did not negatively influence bone mineral characteristics. ConclusionsE2 protects against bone loss resulting from combined OVX + HLU of rodents. In the absence of estrogen, exercise induces disadvantageous early-phase bone adaptations after extended disuse.