Miracle-dz/UniFAR-FTUs huggingface dataset:
Expert-Novice Differences in Memory: A Reformulation

Background: One of the most discriminating measures of expertise in multiple domains has been performance on memory tasks. In medicine, however, the relation between expertise and memory is more equivocal. Purpose: To compare and contrast the sufficiency of multiple explanations of this finding by using three probes of memory rather than the traditional free recall task alone. Methods: Students, residents, and internists were asked to read case histories and assign diagnoses before undertaking free recall, cued recall, and recognition tests. Results: Students consistently outperformed internists. Resident performance was more variable. Conclusions: Our data appear to rule out (a) the notion that expert memory for cases takes on an encapsulated form, (b) the idea that experts simply say less than students in response to a free recall task, and (c) the possibility that experts attend differentially to highly diagnostic features. The results can best be explained by the idea that students process the featural details of a case history more elaborately than do expert diagnosticians who, instead, read medical cases more holistically.
Impact of Fronto-Orbital Advancement on Frontal Sinus Volume, Morphology, and Disease in Nonsyndromic Craniosynostosis

Background: Fronto-orbital advancement for nonsyndromic craniosynostosis has been thought to injure frontal sinus buds, lead to chronic sinus disease, and influence final forehead shape. This study investigates the effect of fronto-orbital advancement in infancy on subsequent frontal sinus volume, morphology, and disease. Methods: The authors conducted a retrospective review of nonsyndromic craniosynostosis patients treated with fronto-orbital advancement in infancy with a head computed tomographic scan obtained at age 7 to 18 years. Facial trauma patients served as age-matched controls. Frontal sinus characteristics were determined using three-dimensional reconstructions. Results: The study included 33 nonsyndromic craniosynostosis patients who underwent fronto-orbital advancement (n = 20 unicoronal; n = 13 metopic) and 20 control patients. The incidence of at least unilateral pneumatization was 94 percent for fronto-orbital advancement subjects and 95 percent for control subjects. Mean frontal sinus volumes for unicoronal synostosis, metopic synostosis, and control groups were 3427 ± 2294, 4576 ± 3510, and 4157 ± 3963 mm3, respectively (p = 0.598). Asymmetry scores were as follows: unicoronal synostosis, 56 ± 35 percent; metopic synostosis, 36 ± 33 percent; and control, 23 ± 24 percent (p = 0.010). Unicoronal subjects displayed prominent asymmetry, with increased pneumatization on the unaffected side. Frontal sinus volume correlated with age at computed tomography but not with age at fronto-orbital advancement. Interrater reliability was 0.997. One fronto-orbital advancement subject and zero control subjects demonstrated computed tomographic evidence of frontal sinus disease. Conclusions: Frontal sinus volume, morphology, and disease do not differ significantly between control subjects and nonsyndromic craniosynostosis subjects following fronto-orbital advancement, but subtle differences such as increased asymmetry in the unicoronal synostosis group can be appreciated. Further research with syndromic craniosynostosis patients undergoing multiple procedures may help elucidate the association between surgical disruption and frontal sinus development. CLINICAL QUESTION/LEVEL OF EVIDENCE: Therapeutic, III.
Genetic Analysis of SH2D4A, a Novel Adapter Protein Related to T Cell-Specific Adapter and Adapter Protein in Lymphocytes of Unknown Function, Reveals a Redundant Function in T Cells1

T cell-specific adapter (TSAd) protein and adapter protein in lymphocytes of unknown function (ALX) are two related Src homology 2 (SH2) domain-containing signaling adapter molecules that have both been shown to regulate TCR signal transduction in T cells. TSAd is required for normal TCR-induced synthesis of IL-2 and other cytokines in T cells and acts at least in part by promoting activation of the LCK protein tyrosine kinase at the outset of the TCR signaling cascade. By contrast, ALX functions as a negative-regulator of TCR-induced IL-2 synthesis through as yet undetermined mechanisms. In this study, we report a novel T cell-expressed adapter protein named SH2D4A that contains an SH2 domain that is highly homologous to the TSAd protein and ALX SH2 domains and that shares other structural features with these adapters. To examine the function of SH2D4A in T cells we produced SH2D4A-deficient mice by homologous recombination in embryonic stem cells. T cell development, homeostasis, proliferation, and function were all found to be normal in these mice. Furthermore, knockdown of SH2D4A expression in human T cells did not impact upon their function. We conclude that in contrast to TSAd and ALX proteins, SH2D4A is dispensable for TCR signal transduction in T cells.
Hacking an Ambiguity Detection Tool to Extract Variation Points: an Experience Report

Natural language (NL) requirements documents can be a precious source to identify variability information. This information can be later used to define feature models from which different systems can be instantiated. In this paper, we are interested in validating the approach we have recently proposed to extract variability issues from the ambiguity defects found in NL requirement documents. To this end, we single out ambiguities using an available NL analysis tool, QuARS, and we classify the ambiguities returned by the tool by distinguishing among false positives, real ambiguities, and variation points. We consider three medium sized requirement documents from different domains, namely, train control, social web, home automation. We report in this paper the results of the assessment. Although the validation set is not so large, the results obtained are quite uniform and permit to draw some interesting conclusions. Starting from the results obtained, we can foresee the tailoring of a NL analysis tool for extracting variability from NL requirement documents.
Comparative Efficacy of Famciclovir and Valacyclovir for Suppression of Recurrent Genital Herpes and Viral Shedding

Background: Daily antiviral therapy with famciclovir and valacyclovir has been shown to be effective in reducing both symptomatic and asymptomatic reactivation of herpes simplex virus type 2 (HSV-2) when compared to placebo. However, few comparative studies between the 2 antivirals have been performed. Objectives: To compare the clinical and virologic effects of famciclovir and valacyclovir administered as daily suppressive therapy for persons with genital herpes. Study Design: Two randomized, double-blind, placebo-controlled studies comparing daily famciclovir 250 mg bid with valacyclovir 500 mg qd were performed. Study 1 randomized 320 participants and compared the clinical effect of the drugs given for 16 weeks, and study 2 enrolled 70 HSV-2 seropositive subjects and compared the virologic effect of the drugs given for 10 weeks. Results: In study 1, the time to first recurrence was similar in famciclovir and valacyclovir recipients, hazard ratio (HR) 1.17 (95% CI, 0.78–1.76), but time to first virologically confirmed recurrence was shorter among famciclovir recipients, HR = 2.15 (95% CI, 1.00–4.60). In study 2, HSV was detected on 3.2% of days among famciclovir recipients and 1.3% of days among valacyclovir recipients, relative risk 2.33 (95% CI, 1.18–4.89). Conclusion: Valacyclovir appear to be somewhat better than famciclovir for suppression of genital herpes and associated shedding. Further comparative trials of antiviral drugs for various indications should be performed as acyclovir and penciclovir appear to have different ability to abrogate HSV reactivation.
Data representations for in-situ exploration of health and fitness data

Wearable devices that collect and generate masses of health related data, such as number of steps taken in a day and heart-rate have seen widespread adoption among general consumers. The wearers of such devices need to interpret the data being generated to ensure they meet their physical activity goals. Little is currently known about how users of such devices explore such data and the corresponding visual representations, in-situ, i.e. during the course of their physical activity. Through a series of interview sessions with users of health and fitness data, i.e., quantified-selfers, we gained an understanding of how they benefit from in-situ data exploration. Our findings reveal the wide number of in-situ tasks, data types, and requirements for designing data representations that support immediate reflection on data being collected. We further solicited the aid of professional designers to sketch visual representations for carrying out the necessary in-situ tasks identified by our users. From these exploratory studies, we derive broader implications for the design of data representations supporting in-situ exploration.
Amelogenesis Imperfecta

Amelogenesis imperfecta (AI) is a clinically and genetically heterogeneous group of diseases characterized by enamel defects. The authors have identified a large consanguineous Moroccan family segregating different clinical subtypes of hypoplastic and hypomineralized AI in different individuals within the family. Using targeted next-generation sequencing, the authors identified a novel heterozygous nonsense mutation in COL17A1 (c.1873C>T, p.R625*) segregating with hypoplastic AI and a novel homozygous 8-bp deletion in C4orf26 (c.39_46del, p.Cys14Glyfs*18) segregating with hypomineralized-hypoplastic AI in this family. This study highlights the phenotypic and genotypic heterogeneity of AI that can exist even within a single consanguineous family. Furthermore, the identification of novel mutations in COL17A1 and C4orf26 and their correlation with distinct AI phenotypes can contribute to a better understanding of the pathophysiology of AI and the contribution of these genes to amelogenesis.
Bede's ecclesiastical history of the English people

Bede's Ecclesiastical History of the English People was completed in 731 and still ranks among the most popular of history books. By the end of the eighth century, copies of it were to be found in many parts of England and on the Continent, some of which are still extant. If it were not for Bede's History we should know little about the Anglo-Saxon invasion and the beginnings of Christianity in England, and such familiar names as Edwin and Oswald, Cuthbert and Chad, Hilda and Caedmon would be almost forgotten. First published in 1969, Colgrave and Mynors's edition made use for the first time of the mid-eighth-century manuscript now in Leningrad, provided a survey of the extant manuscripts, and a new translation; it also brought up to date Plummer's invaluable edition. This revised edition takes into account J.M. Wallace-Hadrill's Bede's Ecclesiastical History of the English People: A Historical Commentary (Oxford Medieval Texts, 1988), enabling the reader to use the two in conjunction.
Neural Variational Inference For Topic Models

Topic models are one of the most popular methods for learning representations of text, but a major challenge is that any change to the topic model requires mathematically deriving a new inference algorithm. A promising approach to address this problem is neural variational inference (NVI), but they have proven difficult to apply to topic models in practice. We present what is to our knowledge the first effective neural variational inference method for latent Dirichlet allocation (LDA), tackling the problems caused for NVI by the Dirichlet prior and by component collapsing. We find that NVI matches traditional methods in accuracy with much better inference time. Indeed, because of the inference network, we find that it is unnecessary to pay the computational cost of running variational optimization on test data. Because NVI is black box, it is readily applied to new topic models. As a dramatic illustration of this, we present a new topic model called ProdLDA, that replaces the mixture model in LDA with a product of experts. By changing only one line of code from LDA, we find that ProdLDA yields much more interpretable topics, even if LDA is trained via collapsed Gibbs sampling.
Decorrelating Detectors for a Dual Rate Synchronous DS/CDMA System

This paper addresses the use of decorrelating detectors for a dual rate DS/CDMA system that serves both low bit rate and high bit rate users. We assume that in an interval of duration T0, a low rate user transmits one bit while a high rate user transmits M bits. Applying a standard decorrelator to the interval of duration T0 yields an M bit processing delay for high rate users and a computational complexity that grows with M. In this paper, we propose a decorrelator that generates bit decisions for each high rate user in every subinterval of duration T0/M. To decode a low rate user, a soft decoding rule applies maximal ratio combining on M separate decorrelated outputs of each low rate user. The soft decoding dual rate decorrelator eliminates the bit processing delay for high rate users and also reduces the computational complexity of a standard decorrelator. Further, it is shown that the asymptotic efficiency of the standard decorrelator is greater than or equal to the proposed decorrelator. By evaluation, it is observed that when the signature sequences have good correlation properties, the proposed soft decoding decorrelator is found to perform nearly as well as the standard decorrelator. However, when the signature sequences have high cross-correlation, then the proposed decorrelator suffers in terms of bit error rate while retaining the near-far resistance property.
Mining Gene-Disease Relationships from Biomedical Literature: Weighting Proteinprotein Interactions and Connectivity

MOTIVATION The promises of the post-genome era disease-related discoveries and advances have yet to be fully realized, with many opportunities for discovery hiding in the millions of biomedical papers published since. Public databases give access to data extracted from the literature by teams of experts, but their coverage is often limited and lags behind recent discoveries. We present a computational method that combines data extracted from the literature with data from curated sources in order to uncover possible gene-disease relationships that are not directly stated or were missed by the initial mining. METHOD An initial set of genes and proteins is obtained from gene-disease relationships extracted from PubMed abstracts using natural language processing. Interactions involving the corresponding proteins are similarly extracted and integrated with interactions from curated databases (such as BIND and DIP), assigning a confidence measure to each interaction depending on its source. The augmented list of genes and gene products is then ranked combining two scores: one that reflects the strength of the relationship with the initial set of genes and incorporates user-defined weights and another that reflects the importance of the gene in maintaining the connectivity of the network. We applied the method to atherosclerosis to assess its effectiveness. RESULTS Top-ranked proteins from the method are related to atherosclerosis with accuracy between 0.85 to 1.00 for the top 20 and 0.64 to 0.80 for the top 90 if duplicates are ignored, with 45% of the top 20 and 75% of the top 90 derived by the method, not extracted from text. Thus, though the initial gene set and interactions were automatically extracted from text (and subject to the impreciseness of automatic extraction), their use for further hypothesis generation is valuable given adequate computational analysis.
The effect of long-term instruction on a Brazilian learner's pronunciation of regular verbs ending in -ed

Diferentemente de estudos anteriores, o presente estudo tem como objetivo principal investigar o efeito da instrucao na pronuncia de verbos regulares terminados em - ed produzidos por uma brasileira, graduanda de Letras/Ingles ao longo de aproximadamente dois anos. Assim como em estudos anteriores, este estudo tambem avaliou a influencia do contexto fonologico anterior, ortografia e proficiencia na producao destes verbos. Os resultados demonstram que, depois de tres semestres de estudo de pronuncia do ingles, de duas sessoes de instrucao de 90 minutos cada sobre a pronuncia do - ed e de instrucao sobre a producao das consoantes do ingles, a insercao de epentese vocalica, frequentemente usada por brasileiros aprendizes de ingles, diminuiu, corroborando estudos anteriores. Os resultados tambem mostram que os contextos nao-vozeados, exceto /t/, induziram maior insercao de epentese vocalica do que os vozeados, exceto /d/, corroborando estudos anteriores, e que verbos, nos quais /t/ e /d/ eram contextos anteriores, foram corretamente produzidos na grande maioria dos casos. A ortografia destes verbos tambem pareceu induzir a producao da epentese vocalica enquanto que o aumento na proficiencia na lingua pareceu colaborar para diminuir este efeito.
Predictive State Recurrent Neural Networks

We present a new model, called Predictive State Recurrent Neural Networks (PSRNNs), for filtering and prediction in dynamical systems. PSRNNs draw on insights from both Recurrent Neural Networks (RNNs) and Predictive State Representations (PSRs), and inherit advantages from both types of models. Like many successful RNN architectures, PSRNNs use (potentially deeply composed) bilinear transfer functions to combine information from multiple sources, so that one source can act as a gate for another. These bilinear functions arise naturally from the connection to state updates in Bayes filters like PSRs, in which observations can be viewed as gating belief states. We show that PSRNNs can be learned effectively by combining backpropogation through time (BPTT) with an initialization based on a statistically consistent learning algorithm for PSRs called two-stage regression (2SR). We also show that PSRNNs can be can be factorized using tensor decomposition, reducing model size and suggesting interesting theoretical connections to existing multiplicative architectures such as LSTMs. We applied PSRNNs to 4 datasets, and showed that we outperform several popular alternative approaches to modeling dynamical systems in all cases.
Performance of Klebsiella oxytoca to Generate Electricity from POME in Microbial Fuel Cell

This study is aimed to evaluate the electricity generation from microbial fuel cell (MFC) and to analyze the microbial community structure of city wastewater and anaerobic sludge to enhance the MFC performance. MFCs, enriched with palm oil mill effluent (POME) were employed to harvest electricity by innoculating of Klebsiella oxytoca , collected from city wastewater and other microbes from anaerobic sludge (AS). The MFC showed maximum power density of 207.28 mW/m 3 with continuous feeding of POME using microbes from AS. Subsequent replacement with Klebsiella oxytoca resulted maximum power density of 1236 mW/m 3 by utilizing complex substrate POME which was six times higher as compared to MFC operated with AS. Based on Biolog gene III analysis, relatively higher abundance of Klebsiella oxytoca was detected in the city wastewater. Predominant microorganisms such as Gammaproteobacteria, Azospiraoryzae, Acetobacterperoxydans and Solimonasvariicoloris were isolated from palm oil anaerobic sludge as well as from biofilm of MFC. Enriched electrochemically active bacteria Klebsiella oxytoca showed better performance to generate electricity from complex POME substrates compare to AS. These results demonstrate that the power output of MFCs can be increased significantly using Klebsiella oxytoca .
Histogenesis of sarcomatoid urothelial carcinoma of the urinary bladder: evidence for a common clonal origin with divergent differentiation

The histogenesis of sarcomatoid urothelial carcinoma, a rare neoplasm with bidirectional epithelial and mesenchymal differentiation, has been a matter of controversy. To clarify its origin, we analysed the status of X‐chromosome inactivation in sarcomatoid urothelial carcinomas from 10 female patients and examined losses of heterozygosity (LOH) in these specimens and in additional 20 tumours from male patients. Six polymorphic microsatellite markers where genetic alterations occur frequently in early or advanced stages of urothelial carcinomas, including D3S3050, D8S261, IFNA, D9S177, D11S569 and TP53, were investigated in the current study. The identical pattern of non‐random X‐chromosome inactivation in both carcinomatous and sarcomatous components was identified in five of eight informative female patients, and the remaining three informative cases showed a random, but concordant, pattern of X‐chromosome inactivation. The concordant X‐chromosome inactivation results in all eight informative cases support the concept of a monoclonal origin of both components of this biphasic neoplasm. Among the tumours demonstrating loss of heterozygosity, high incidences of an identical pattern of allelic loss between carcinomatous and sarcomatous components were identified in genetic alterations associated with early carcinogenesis: 86% at D8S261, 78% at D11S569, 75% at D9S177 and 57% at IFNA. In contrast, concordant LOH patterns were less frequently observed for microsatellites related to advanced carcinogenesis: only 40% at D3S3050 and 40% at TP53. The significant overlap of loss of heterozygosity supports a monoclonal cell origin and suggests that clonal divergence may occur during tumour progression and differentiation. Divergent patterns of discordant allelic loss of microsatellite markers imply that heterogeneous pathogenetic pathways may exist in the evolution of this enigmatic neoplasm. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
Comparison of the rate of sequence variation in the hypervariable region of E2/NS1 region of hepatitis C virus in normal and hypogammaglobulinemic patients

The hypervariable region (HVR) of the E2/NS1 region of hepatitis C virus (HCV) varies greatly between viral isolates with high rates of genomic change reported during the course of chronic infection. The HVR is thought to encode a structurally unconstrained envelope protein containing several linear B cell epitopes recognized by neutralizing antibody. It has been postulated that amino acid changes in the HVR could result from humoral immune pressure leading to the selection of escape mutants. The aim of this study was to compare the rates of nucleotide and amino acid variation in the HVR of control patients to patients with common variable immunodeficiency (CVID) where the effect of the humoral immune system is reduced. Five controls and four patients with CVID were studied. Serum samples were taken over periods of between 1 and 6 years. HCV was detected by polymerase chain reaction (PCR) with primers derived from conserved flanking regions of the HVR. PCR products were cloned into a plasmid vector and recombinant clones identified by restriction enzyme digestion. Purified DNA from at least three individual clones from each time point was sequenced by the dideoxynucleotide chain‐termination method. Consensus sequences were extracted from the three clones, and the DNA and deduced protein sequences were compared. Control patients had a mean rate of nucleotide change of 6.954 nucleotide substitutions per year, compared with patients with CVID with a rate of 0.415 nucleotide substitutions per year (P < .02). The corresponding rates for amino acid variation were 3.868 amino acid substitutions per year for the control patients compared with 0.185 amino acid substitutions per year for the patients with CVID. These findings suggest that in the absence of humoral immune selective pressure, the frequency of occurrence of genetic variation in the major viral species is reduced. The mutations occur, but in the absence of immune selection remain as minor species. The evolution of viral mutants capable of evading the host's immune system may contribute to the ability of HCV to establish chronic infection.