Miracle-dz/UniFAR-FTUs huggingface dataset:
Making Cells Worthwhile: Calculations of Value in a European Consortium for Induced Pluripotent Stem Cell Banking

ABSTRACT The StemBANCC consortium was a large European consortium bringing together scientists from academic institutions and the pharmaceutical industry. The aim of the consortium was to produce 1500 induced pluripotent stem cell (iPSC) lines from participants with a variety of common, complex diseases. These cell lines were intended to help develop iPSC as tools for screening small molecule drug candidates and modelling human diseases in vitro. The scale of investment in this and other biobanks presents iPSC as a valuable commodity. However, StemBANCC was also mandated to make its making cells and data available to European researchers on a not-for-profit basis. To understand how making this quantity of stem cells and data available is configured as a valuable and worthwhile investment for the consortium partners, research materials (project documents, scientific literature and interviews with scientists working on StemBANCC) were analysed using theoretical tools from Valuation Studies. Combining STS and economic sociology, valuation studies analyse how the worth of things, ideas and phenomena result from context-specific practices of assessment and evaluation; worth incorporates moral, financial, scientific, economic. social and cultural registers of value. In this sense, practitioners evaluate the worth of the StemBANCC cells and data at a variety of sites, from participant recruitment to online databases. This provides an alternative to biovalue and similar conceptual models for theorising the generation of value in the Life Sciences.
Systems with the integer rounding property in normal monomial subrings

Let C be a clutter and let A be its incidence matrix. If the linear system x ≥ 0; x A ≤ 1 has the integer rounding property, we give a description of the canonical module and the a-invariant of certain normal subrings associated to C. If the clutter is a connected graph, we describe when the aforementioned linear system has the integer rounding property in combinatorial and algebraic terms using graph theory and the theory of Rees algebras. As a consequence we show that the extended Rees algebra of the edge ideal of a bipartite graph is Gorenstein if and only if the graph is unmixed.
Establishing a framework for blending intercultural education with differentiated instruction

Abstract Despite the fact that both intercultural education and differentiated instruction are based on the premises of inclusion, equality, and equity, most research and publications have focused on one in isolation of the other. Scholars from each tradition often use the same argumentation, propose similar strategies and reach similar conclusions. Nevertheless, the emphasis is different: while intercultural education celebrates students’ cultural backgrounds and draws upon culture for the development of effective classroom instruction and school environments, differentiated instruction focuses on academic aptitude, therefore, requiring a systematically planned curriculum and instruction that meets the needs of academically diverse learners. Differentiation of instruction focuses on the individual and its prerogative for success and happiness; intercultural education is focused on the community and therefore, it is mostly concerned about the preservation of collective identities. The aforementioned distinction helps us realise that the challenge for educators in contemporary multicultural classrooms is twofold: to sustain collective identities and to facilitate individual academic success. Visiting both approaches and utilising an eclectic approach, this paper discusses the rationale for the development of a comprehensive framework that can be useful for theory deliberation as well as a guide for instructional practice.
Evaluation of Human Papilloma Virus Diagnostic Testing in Oropharyngeal Squamous Cell Carcinoma: Sensitivity, Specificity, and Prognostic Discrimination

Purpose: Human papillomavirus-16 (HPV16) is the causative agent in a biologically distinct subset of oropharyngeal squamous cell carcinoma (OPSCC) with highly favorable prognosis. In clinical trials, HPV16 status is an essential inclusion or stratification parameter, highlighting the importance of accurate testing. Experimental Design: Fixed and fresh-frozen tissue from 108 OPSCC cases were subject to eight possible assay/assay combinations: p16 immunohistochemistry (p16 IHC); in situ hybridization for high-risk HPV (HR HPV ISH); quantitative PCR (qPCR) for both viral E6 RNA (RNA qPCR) and DNA (DNA qPCR); and combinations of the above. Results: HPV16-positive OPSCC presented in younger patients (mean 7.5 years younger, P = 0.003) who smoked less than HPV-negative patients (P = 0.007). The proportion of HPV16-positive cases increased from 15% to 57% (P = 0.001) between 1988 and 2009. A combination of p16 IHC/DNA qPCR showed acceptable sensitivity (97%) and specificity (94%) compared with the RNA qPCR “gold standard”, as well as being the best discriminator of favorable outcome (overall survival P = 0.002). p16 IHC/HR HPV ISH also had acceptable specificity (90%) but the substantial reduction in its sensitivity (88%) impacted upon its prognostic value (P = 0.02). p16 IHC, HR HPV ISH, or DNA qPCR was not sufficiently specific to recommend in clinical trials when used in isolation. Conclusions: Caution must be exercised in applying HPV16 diagnostic tests because of significant disparities in accuracy and prognostic value in previously published techniques. Clin Cancer Res; 17(19); 6262–71. ©2011 AACR.
Glare and Ocular Diseases

Glare is the result of veiling luminance from the different light sources we are exposed to in our everyday lives. The luminance from glare can cause problems ranging from the discomfort of our eyes to vision loss. All individuals are affected by glare issues but those problems are intensified in patients living with ocular diseases. Therefore, understanding the effects of glare is applicable to elucidating visual function and pathology. This makes glare testing highly necessary in both clinic and research. However, there are many components involved in glare testing that makes attaining valid results difficult. This is evident in the flaws of current glare devices and the lack of a standardization of measuring glare. Despite the insufficiency of most glare devices, evaluating those weaknesses can potentially lead to a better understanding of glare and glare testing.
The structure of trust as a reflection of culture and institutional power structure: Evidence from four East Asian societies

Robert Jiqi Zhang, James H. Liu, Petar Milojev, Jiin Jung, Sy-feng Wang, Tian Xie, Hoon-seok Choi, Susumu Yamaguchi, and Hiroaki Morio School of Psychology, Massey University, Auckland, New Zealand, Faculty of Psychology, Beijing Normal University, Beijing, China, Marbella International University Centre, Marbella, Spain, Department of Psychology, Claremont Graduate University, Claremont, California, USA, Department of Psychology, Fu Jen Catholic University, New Taipei City, Taiwan, Department of Psychology, Philosophy School, Wuhan University, Wuhan, China, Department of Psychology, Sungkyunkwan University, Seoul, Republic of Korea, Graduate School of Humanities and Sociology, University of Tokyo, Bunky o, Japan, and Faculty of Informatics, Kansai University, Osaka, Japan
A Parallel Decoding Algorithm for Short Polar Codes Based on Error Checking and Correcting

We propose a parallel decoding algorithm based on error checking and correcting to improve the performance of the short polar codes. In order to enhance the error-correcting capacity of the decoding algorithm, we first derive the error-checking equations generated on the basis of the frozen nodes, and then we introduce the method to check the errors in the input nodes of the decoder by the solutions of these equations. In order to further correct those checked errors, we adopt the method of modifying the probability messages of the error nodes with constant values according to the maximization principle. Due to the existence of multiple solutions of the error-checking equations, we formulate a CRC-aided optimization problem of finding the optimal solution with three different target functions, so as to improve the accuracy of error checking. Besides, in order to increase the throughput of decoding, we use a parallel method based on the decoding tree to calculate probability messages of all the nodes in the decoder. Numerical results show that the proposed decoding algorithm achieves better performance than that of some existing decoding algorithms with the same code length.
Trends in water balance components across the Brazilian Cerrado

We assess the water balance of the Brazilian Cerrado based on remotely sensed estimates of precipitation (TRMM), evapotranspiration (MOD16), and terrestrial water storage (GRACE) for the period from 2003 to 2010. Uncertainties for each remotely sensed data set were computed, the budget closure was evaluated using measured discharge data for the three largest river basins in the Cerrado, and the Mann‐Kendall test was used to evaluate temporal trends in the water balance components and measured river discharge. The results indicate an overestimation of discharge data, due mainly to the overestimation of rainfall by TRMM version 6. However, better results were obtained when the new release of TRMM 3B42 v7 was used instead. Our results suggest that there have been (a) significant increases in average annual evapotranspiration over the entire Cerrado of 51 ± 15 mm yr−1, (b) terrestrial water storage increases of 11 ± 6 mm yr−1 in the northeast region of the Brazilian Cerrado, and (c) runoff decreases of 72 ± 11 mm yr−1 in isolated spots and in the western part of the State of Mato Grosso. Although complete water budget closure from remote sensing remains a significant challenge due to uncertainties in the data, it provides a useful way to evaluate trends in major water balance components over large regions, identify dry periods, and assess changes in water balance due to land cover and land use change.
Effect of GnRH antagonists in FSH mildly stimulated intrauterine insemination cycles: a multicentre randomized trial.

BACKGROUND The usefulness of GnRH antagonists in mild controlled ovarian hyperstimulation (COH) and intrauterine insemination (IUI) cycles is debated. METHODS Two-hundred and ninety-nine couples with unexplained or mild male factor infertility were enrolled in this international multicentre randomized controlled trial. Women allocated to the GnRH antagonist group (n=148) received 50 IU recombinant FSH starting on day 3 of the menstrual cycle and Ganirelix 0.25 mg daily starting from the day in which a follicle with a mean diameter of 13-14 mm was visualized at ultrasound. Women allocated to the control group (n=151) were administered only 50 IU recombinant FSH starting on day 3 of the menstrual cycle. Couples were recruited only for their first treatment cycle. The primary outcome was the clinical pregnancy rate per initiated cycle. RESULTS Baseline characteristics of the two treatment groups were similar. Clinical pregnancy rates per initiated cycle in women who did and did not receive GnRH antagonists were 12.2 and 12.6%, respectively (P=1.00). The relative risk of conception (95% confidence interval) for the use of GnRH antagonists was 1.0 (0.5-1.9). CONCLUSIONS In mild COH and IUI cycles, any benefit of the use of GnRH antagonists in improving pregnancy rates is <2-fold increase.
Clinical Reasoning: Survey of Teaching Methods and Assessment in Entry-Level Physical Therapist Clinical Education

Background. Clinical reasoning skills have been identified as an integral part of physical therapist education developed in both the academic and clinical settings. There is limited understanding of clinical instructors (CIs) expectations related to the anticipated level of clinical reasoning (CR) skills achieved by students and how CR is taught and assessed in the clinic. Objective. The purpose of this research was to explore how CIs teach and assess student physical therapists' CR skills and garner an understanding of CIs' expectations related to CR skills attained at various levels of clinical experience. Design. A descriptive, cross-sectional survey was used to gather data from CIs. Methods. Participants identified from an American Physical Therapy Association database of credentialed CIs were asked to complete an 18-question electronically delivered survey. Results. A nationwide sample of 749 CIs completed the survey. The data clearly demonstrated that CIs value and recognize the importance of clinical education in the development of CR. They also value the use of engaged discussion and reflection to foster the development of reasoning skills. Most CIs did not expect students to achieve entry-level CR skills during the third year. Conclusions. Clinical instructors see the importance of clinical experiences and engaged discussion to foster the development of CR. Further research is needed to understand why most clinical educators did not expect students to achieve “entry-level” CR skills as defined by the Clinical Performance Instrument by the final year of the program.
A Conditional Random Field Approach to Unsupervised Texture Image Segmentation

An unsupervised multiresolution conditional random field (CRF) approach to texture segmentation problems is introduced. This approach involves local and long-range information in the CRF neighbourhood to determine the classes of image blocks. Like most Markov random field (MRF) approaches, the proposed method treats the image as an array of random variables and attempts to assign an optimal class label to each. While most MRFs involve only local information extracted from a small neighbourhood, our method also allows a few long-range blocks to be involved in the labelling process. This alleviates the problem of assigning different class labels to disjoint regions of the same texture and oversegmentation due to the lack of long-range interaction among the neighbouring and distant blocks. The proposed method requires no a priori knowledge of the number and types of regions/textures.
Birds of a Feather: Teams as a Screening Mechanism

This paper studies the informational content of elective teams in a dynamic principal/multiple-agents framework with adverse selection. Two agents with different employment histories are paid their conditional expected marginal product. They observe their types (good or bad), and choose between working together or separately. We characterize the distributions on agents' types, nature and wages such that teams are formed exclusively by good-type agents, with and without side payments. As employment records matter when idiosyncratic contributions are difficult to isolate, a good-type agent prefers not to jeopardize his reputation by teaming up with a bad-type agent. Cet article etudie le contenu informationel des equipes facultatives, dans le cadre d'un modele dynamique de principal-agent avec selection adverse. Deux agents ayant des historiques d'emploi differents recoivent leur produit marginal espere conditionnel. Ils observent leurs types (bon ou mauvais) et doivent decider s'ils veulent travailler ensemble ou separement. Nous caracterisons la distribution sur les types, les chocs de la nature et les salaires pour lesquelles des equipes sont formees exclusivement par deux agents de bon type, avec ou sans paiements lateraux. Parce que les dossiers d'emploi sont valorises lorsque les contributions individuelles sont difficiles a evaluer, un agent de bon type refuse de mettre en peril sa reputation en formant une equipe avec un agent de mauvais type.
Simulated X-ray galaxy clusters at the virial radius: Slopes of the gas density, temperature and surface brightness profiles

Using a set of hydrodynamical simulations of nine galaxy clusters with masses in the range 1.5 x 10 14 < M vir < 3.4 x 10 15 M ⊙ , we have studied the density, temperature and X-ray surface brightness profiles of the intracluster medium in the regions around the virial radius. We have analysed the profiles in the radial range well above the cluster core, the physics of which are still unclear and matter of tension between simulated and observed properties, and up to the virial radius and beyond, where present observations are unable to provide any constraints. We have modelled the radial profiles between 0.3R 200 and 3R 200 with power laws with one index, two indexes and a rolling index. The simulated temperature and [0.5-2] keV surface brightness profiles well reproduce the observed behaviours outside the core. The shape of all these profiles in the radial range considered depends mainly on the activity of the gravitational collapse, with no significant difference among models including extraphysics. The profiles steepen in the outskirts, with the slope of the power-law fit that changes from -2.5 to -3.4 in the gas density, from -0.5 to -1.8 in the gas temperature and from -3.5 to -5.0 in the X-ray soft surface brightness. We predict that the gas density, temperature and [0.5-2] keV surface brightness values at R 200 are, on average, 0.05, 0.60, 0.008 times the measured values at 0.3R 200 . At 2R 200 , these values decrease by an order of magnitude in the gas density and surface brightness, by a factor of 2 in the temperature, putting stringent limits on the detectable properties of the intracluster-medium (ICM) in the virial regions.
Novel Glutaredoxin Activity of the Yeast Prion Protein Ure2 Reveals a Native-like Dimer within Fibrils*

Ure2 is the protein determinant of the Saccharomyces cerevisiae prion [URE3]. Ure2 has structural similarity to glutathione transferases, protects cells against heavy metal and oxidant toxicity in vivo, and shows glutathione-dependent peroxidase activity in vitro. Here we report that Ure2 (which has no cysteine residues) also shows thiol-disulfide oxidoreductase activity similar to that of glutaredoxin enzymes. This demonstrates that disulfide reductase activity can be independent of the classical glutaredoxin CXXC/CXXS motif or indeed an intrinsic catalytic cysteine residue. The kinetics of the glutaredoxin activity of Ure2 showed positive cooperativity for the substrate glutathione in both the soluble native state and in amyloid-like fibrils, indicating native-like dimeric structure within Ure2 fibrils. Characterization of the glutaredoxin activity of Ure2 sheds light on its ability to protect yeast from heavy metal ion and oxidant toxicity and suggests a role in reversible protein glutathionylation signal transduction. Observation of allosteric enzyme behavior within amyloid-like Ure2 fibrils not only provides insight into the molecular structure of the fibrils but also has implications for the mechanism of [URE3] prion formation.
Research Paper No . 2006 / 15 International Convergence or Higher Inequality in Human Development ? Evidence for 1975 to 2002

The concept of convergence is extended to the human development index. Evidence of weak absolute convergence is found over 1975-2002. The results are robust and verified by various conditional β-convergence models and also supported by the evidence of weak σ-convergence. Population weighted analyses provide support for polarization in the human development index amongst developing countries but a slight reduction in world inequality. The dynamics of regional analysis reveal a movement of sub-Saharan Africa towards the low band of human development with Asia and Latin America making progress. High immobility of the early part of the period is followed by considerable upward and downward mobility in the latter part indicating a possible case of the ‘twin peaks’ type of polarization.
Novel Unsupervised Auditory Filterbank Learning Using Convolutional RBM for Speech Recognition

To learn auditory filterbanks, recently, we have proposed an unsupervised learning model based on convolutional restricted Boltzmann machine (RBM) with rectified linear units. In this paper, theory, training algorithm of our proposed model, and detailed analysis of learned filterbank are being presented. Learning of the model with different databases shows that the model is able to learn cochlear-like impulse responses that are localized in frequency-domain. An auditory-like scale obtained from filterbanks learned from clean and noisy datasets resembles the Mel scale, which is known to mimic perceptually relevant aspect of speech. We have experimented with both cepstral (denoted as ConvRBM-CC) as well as filterbank features (denoted as ConvRBM-BANK). On large vocabulary continuous speech recognition task, we achieved relative improvement of 7.21-17.8% in word error rate (WER) compared to Mel frequency cepstral coefficient (MFCC) features and 1.35-6.82% compared to Mel filterbank (FBANK) features. On AURORA 4 multicondition training database, the relative improvement in WER by 4.8-13.65% was achieved using a Hybrid Deep Neural Network-Hidden Markov Model (DNN-HMM) system with ConvRBM-CC features. Using ConvRBM-BANK features, we achieve absolute reduction of 1.25-3.85% in WER on AURORA 4 test sets compared to FBANK features. A context-dependent DNN-HMM system further improves performance with a relative improvement of 3.6-4.6% on an average for bigram 5k and tri-gram 5k language models. Hence, our proposed learned filterbank performs better than traditional MFCC and Mel-filterbank features for both clean and multicondition automatic speech recognition (ASR) tasks. A system combination of ConvRBM-BANK and FBANK features further improve performance in all ASR tasks. Cross-domain experiments where subband filters trained on one database are used for the ASR task of another database show that model learns generalized representations of speech signals.
An Ab Initio Approach to the Solar Coronal Heating Problem

We present an ab initio approach to the solar coronal heating problem by modeling a small part of the solar corona in a computational box using a three-dimensional MHD code including realistic physics. The observed solar granular velocity pattern and its amplitude and vorticity power spectra, as reproduced by a weighted Voronoi tessellation method, are used as a boundary condition that generates a Poynting flux in the presence of a magnetic field. The initial magnetic field is a potential extrapolation of a SOHO/MDI high-resolution magnetogram, and a standard stratified atmosphere is used as a thermal initial condition. Except for the chromospheric temperature structure, which is kept nearly fixed, the initial conditions are quickly forgotten because the included Spitzer conductivity and radiative cooling function have typical timescales much shorter than the time span of the simulation. After a short initial start-up period, the magnetic field is able to dissipate (3-4) × 106 ergs cm-2 s-1 in a highly intermittent corona, maintaining an average temperature of ~106 K, at coronal density values for which simulated images of the TRACE 171 and 195 Å passbands reproduce observed photon count rates.