Miracle-dz/UniFAR-FTUs huggingface dataset:
Detecting sex chromosome anomalies and common triploidies in products of conception by array‐based comparative genomic hybridization

In recent years, array‐based comparative genomic hybridization (array CGH) has moved to the forefront of molecular cytogenetics with its ability to rapidly characterize chromosome abnormalities at resolutions much higher than routine chromosome banding. However, array CGH, like all CGH procedures, has heretofore been deemed unable to detect ploidy, a major cause of fetal demise and spontaneous miscarriage.
Renewing the respect for similarity

In psychology, the concept of similarity has traditionally evoked a mixture of respect, stemming from its ubiquity and intuitive appeal, and concern, due to its dependence on the framing of the problem at hand and on its context. We argue for a renewed focus on similarity as an explanatory concept, by surveying established results and new developments in the theory and methods of similarity-preserving associative lookup and dimensionality reduction—critical components of many cognitive functions, as well as of intelligent data management in computer vision. We focus in particular on the growing family of algorithms that support associative memory by performing hashing that respects local similarity, and on the uses of similarity in representing structured objects and scenes. Insofar as these similarity-based ideas and methods are useful in cognitive modeling and in AI applications, they should be included in the core conceptual toolkit of computational neuroscience. In support of this stance, the present paper (1) offers a discussion of conceptual, mathematical, computational, and empirical aspects of similarity, as applied to the problems of visual object and scene representation, recognition, and interpretation, (2) mentions some key computational problems arising in attempts to put similarity to use, along with their possible solutions, (3) briefly states a previously developed similarity-based framework for visual object representation, the Chorus of Prototypes, along with the empirical support it enjoys, (4) presents new mathematical insights into the effectiveness of this framework, derived from its relationship to locality-sensitive hashing (LSH) and to concomitant statistics, (5) introduces a new model, the Chorus of Relational Descriptors (ChoRD), that extends this framework to scene representation and interpretation, (6) describes its implementation and testing, and finally (7) suggests possible directions in which the present research program can be extended in the future.
WHY DO RISK PREMIA VARY OVER TIME? A THEORETICAL INVESTIGATION UNDER HABIT FORMATION

We study the dynamics of risk premia in a model with external habit formation and highlight the significance of “recession predictability”. Although under the specification of Campbell and Cochrane, [Journal of Political Economy 107, 205–251 (1999)] the equity risk premium is countercyclical because increases in risk aversion are reinforced by rising recession risks, this need not be the case more generally. We show analytically that in endowment economies procyclical recession expectations can outweigh countercyclical changes in risk aversion, generating counterfactual risk-premium behavior. However, allowing shocks or habits to be sufficiently persistent, or explicitly accounting for the impact of habits on consumption, suffices to generate countercyclical recession risks and risk premia.
A study of environmental factors in cancer of the larynx

URINC the past five years increasing emD phasis has been placed upon environmental surveys as a means of elucidating the causation and mechanism of cancer development in man. The evidence has centered primarily around retrospective studies in which patients already afflicted with cancer and a suitable comparison group were questioned in respect to multiple lactors considered to have a bearing on the disease. Somcwhat later, prospective studies were undertaken in which a population group apparently free of disease was questioned about environmental factors. Subsequently the death rate was determined to learn whether those exposed to certain factors were more prone LO die from a given disease than were the others. In respect to certain environmental factors, the results of these studies are in close agreement with those of the retrospective studies. Thus it appears that well-conducted and controlled environmental surveys can contribute to our understanding ol the development of some cancers in man. Environmental cancer surveys at present concern cancers of the epidermoid type primarily, because information on epiderrnoid cancer in man, as well as available data on the experimental animal, suggests that it is only rarely that these cancers arise in areas
Change Blindness to Gradual Changes in Facial Expressions

Change blindness - our inability to detect changes in a stimulus - occurs even when the change takes place gradually, without disruption (Simons, Franconeri, & Reimer, 2000). Such gradual changes are more difficult to detect than changes that involve a disruption. In this experiment, we extend previous findings to the domain of facial expressions of emotions occurring in the context of a realistic scene. Even with changes occurring in central, highly relevant stimuli such as faces, gradual changes still produced high levels of change blindness: Detection rates were three times lower for gradual changes than for displays involving disruption, with only 15% of the observers perceiving the gradual change within a single trial. However, despite this high rate of change blindness, changes on faces were significantly better detected than colour changes occurring on non facial objects in the same scene.
NT-proANP and BNP in Renovascular and in Severe and Mild Essential Hypertension

Background/Aims: The plasma concentrations of atrial natriuretic peptide (ANP) and brain natriuretic peptide (BNP) become increased in hypertension. However, it is unknown what is the effect of the etiology and the severity of hypertension on the plasma concentrations of ANP and BNP. Methods: We examined plasma levels of ANP (measured as N-terminal fragment of proatrial natriuretic peptide; NT-proANP) and BNP in patients having sustained hypertension of different etiology and severity: in patients with renovascular hypertension (RVHT, n = 12), severe essential hypertension (SEHT, n = 37), and mild essential hypertension (MEHT, n = 29). In addition, we studied the diagnostic value of NT-proANP and BNP to discriminate patients with RVHT from patients with essential hypertension. Results: The plasma concentrations of NT-proANP and BNP were higher in the RVHT group (593 ± 80 and 25.0 ± 9.3 pmol/l, respectively) than in the SEHT group (320 ± 33 and 4.7 + 0.6 pmol/l, respectively; p < 0.001 for both), in spite of the similar blood pressure level, and also higher than in the MEHT group (356 ± 30 and 7.0 ± 1.0 pmol/l; p = 0.004 and p = 0.006, respectively). There was no difference in natriuretic peptide levels between the SEHT and MEHT groups. Plasma NT-proANP and BNP correlated positively with aging and serum creatinine concentration and inversely with left ventricular diastolic filling. In addition, NT-proANP correlated positively with systolic blood pressure and BNP with left ventricular mass index. The areas under receiver operating characteristic curves for plasma NT-proANP and BNP to discriminate RVHT patients from patients with essential hypertension were 0.793 and 0.782, respectively. The best cutoff value was 530 pmol/l for NT-proANP, giving a sensitivity of 67% with a specificity of 86%. The cutoff value of 9.8 pmol/l for BNP resulted in a sensitivity of 58% and a specificity of 90%. Conclusions: Patients with RVHT have higher plasma levels of NT-proANP and BNP than patients with essential hypertension. In addition to the etiology of hypertension, also left ventricular characteristics are important determinants of NT-proANP and BNP concentrations in hypertension. Due to the low sensitivity, NT-proANP and BNP are not suitable as screening tools for RVHT.
Test Re-Test Reliability and Validity of Different Visual Acuity and Stereoacuity Charts Used in Preschool Children.

BACKGROUND Preschool vision screenings are cost effective ways to detect children with vision impairments. The use of any vision tests in children must be age appropriate, testable, repeatable and valid. AIM To compare the test re-test reliability, sensitivity and specificity of different visual acuity and stereo acuity charts used in preschool children. MATERIALS AND METHODS Monocular visual acuity of 90 subjects (180 eyes) of age 36 to 71 months was assessed with HOTV, Lea and E-chart in a preschool located in a semi urban area, Manipal, Karnataka. After the vision assessment, stereo acuity was recorded using Frisby and Titmus stereo charts followed by comprehensive eye examination. Repeated measurements of visual acuity and stereo acuity were done one week after the initial assessment. RESULTS Mean age of children was 53± 10 months with equal gender distribution. Intra class correlation (ICC) of Lea, HOTV, E-chart, Frisby and Titmus charts were 0.96, 0.99, 0.92, 1.0 and 1.0 respectively. The area under receiver operating curve (ROC) for Lea and E-chart was 0.892 and 0.776. HOTV was considered as the gold standard as it showed the least difference on repeated measurements. The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of E-chart was 99, 15, 45, 94 and 21.8 percent, and Lea was 93, 56, 59 and 92 percent. The sensitivity, specificity, PPV and NPV of Frisby was 75, 27, 9, 92 percent were as of Titmus was 75, 13, 8 and 85 percent respectively. CONCLUSION HOTV chart can be used as the gold standard for measuring visual acuity of pre-schoolers in a semi urban area. Lea chart can be used in the absence of HOTV chart. Frisby and Titmus charts are good screening tools, but with poor diagnostic criteria.
Comparison of transposed brachiobasilic fistulas to upper arm grafts and brachiocephalic fistulas.

BACKGROUND Renewed interest in transposed brachiobasilic fistulas has occurred since the release of the National Kidney Foundation-Dialysis Outcomes Quality Initiative (NKF-DOQI) guidelines because it is an alternative method to achieve an upper arm fistula in patients who cannot achieve a functional brachiocephalic fistula. The objective of this study was to compare outcomes among transposed brachiobasilic fistulas, upper arm grafts, and brachiocephalic fistulas. METHODS A cohort of patients with upper arm accesses was retrospectively identified. Access outcomes were determined from medical records and contact with physicians, dialysis providers, and patients. Primary outcome was thrombosis-free survival. Secondary outcomes were primary failure, time to use, risk of catheter-related bacteremia, need for intervention, incidence of access-related complications, cumulative, and functional patency. Group differences in age, sex, race, diabetes, peripheral vascular disease, and number of previous accesses were adjusted for in the analysis where appropriate. RESULTS Transposed brachiobasilic fistulas, upper arm grafts, and brachiocephalic fistulas were compared in 59, 82, and 56 patients, respectively. Compared with transposed brachiobasilic fistulas, upper arm grafts were more likely to thrombose with an adjusted relative risk (RR) of 2.6 (95% CI, 1.3 to 5.3) excluding primary failures and 1.6 (95% CI, 1.0 to 2.7) when accounting for the lower risk of primary failure for grafts. Transposed brachiobasilic fistulas also required less intervention (0.7 vs. 2.4 per access-year, P < 0.01) and were less likely to become infected (0 vs. 13%, P < 0.05) than grafts. Mature brachiocephalic fistulas were less likely to fail (RR 0.3, 95% CI, 0.1 to 1.0) and showed a trend for less thrombosis (RR 0.3, 0.1 to 1.1) than mature brachiobasilic fistulas. There was no significant difference in cumulative patency (failure-free survival) among the three types of access if primary failure was included at the median follow-up of 594 days. Transposed brachiobasilic fistulas provided catheter-free access one month sooner than brachiocephalic fistulas and one month later than upper arm grafts. CONCLUSIONS Transposed brachiobasilic fistulas provide cumulative patency equivalent to upper arm grafts and brachiocephalic fistulas. They are less likely to thrombose and become infected than upper arm grafts. Compared with brachiocephalic fistula, they are more likely to mature but are at increased risk of thrombosis after maturation. Transposed brachiobasilic fistulas should be considered before placing an upper arm graft for patients that cannot achieve a functional brachiocephalic fistula.
Nicotinic acetylcholine receptor is internalized via a Rac-dependent, dynamin-independent endocytic pathway

Endocytosis of the nicotinic acetylcholine receptor (AChR) is a proposed major mechanism of neuromodulation at neuromuscular junctions and in the pathology of synapses in the central nervous system. We show that binding of the competitive antagonist α-bungarotoxin (αBTX) or antibody-mediated cross-linking induces the internalization of cell surface AChR to late endosomes when expressed heterologously in Chinese hamster ovary cells or endogenously in C2C12 myocytes. Internalization occurs via sequestration of AChR–αBTX complexes in narrow, tubular, surface-connected compartments, which are indicated by differential surface accessibility of fluorescently tagged αBTX–AChR complexes to small and large molecules and real-time total internal reflection fluorescence imaging. Internalization occurs in the absence of clathrin, caveolin, or dynamin but requires actin polymerization. αBTX binding triggers c-Src phosphorylation and subsequently activates the Rho guanosine triphosphatase Rac1. Consequently, inhibition of c-Src kinase activity, Rac1 activity, or actin polymerization inhibits internalization via this unusual endocytic mechanism. This pathway may regulate AChR levels at ligand-gated synapses and in pathological conditions such as the autoimmune disease myasthenia gravis.
DAPK1 as an independent prognostic marker in liver cancer

The death-associated protein kinase 1 (DAPK1) can act as an oncogene or a tumor suppressor gene depending on the cellular context as well as external stimuli. Our study aims to investigate the prognostic significance of DAPK1 in liver cancer in both mRNA and protein levels. The mRNA expression of DAPK1 was extracted from the Gene Expression Omnibus database in three independent liver cancer datasets while protein expression of DAPK1 was detected by immunohistochemistry in our Chinese liver cancer patient cohort. The associations between DAPK1 expression and clinical characteristics were tested. DAPK1 mRNA expression was down-regulated in liver cancer. Low levels of DAPK1 mRNA were associated with shorter survival in a liver cancer patient cohort (n = 115; p = 0.041), while negative staining of DAPK1 protein was significantly correlated with shorter time to progression (p = 0.002) and overall survival (p = 0.02). DAPK1 was an independent prognostic marker for both time to progression and overall survival by multivariate analysis. Liver cancer with the b-catenin mutation has a lower DAPK1 expression, suggesting that DAPK1 may be regulated under the b-catenin pathway. In addition, we also identified genes that are co-regulated with DAPK1. DAPK1 expression was positively correlated with IRF2, IL7R, PCOLCE and ZBTB16, and negatively correlated with SLC16A3 in both liver cancer datasets. Among these genes, PCOLCE and ZBTB16 were significantly down-regulated, while SLC16A3 was significantly upregulated in liver cancer. By using connectivity mapping of these co-regulated genes, we have identified amcinonide and sulpiride as potential small molecules that could potentially reverse DAPK1/PCOLCE/ZBTB16/SLC16A3 expression. Our study demonstrated for the first time that both DAPK1 mRNA and protein expression levels are important prognostic markers in liver cancer, and have identified genes that may contribute to DAPK1-mediated liver carcinogenesis.
Incidence and mortality of the leading cancer types in Puerto Rico: 1987-2004.

BACKGROUND Cancer remains one of the leading causes of morbidity and mortality worldwide and is the second cause of death in Puerto Rico (PR). This article describes the incidence and the mortality from cancer in PR for the period of 1987 to 2004. METHODS We analyzed data from the PR Central Cancer Registry and the PR Demographic Registry from 1987-2004, for the leading cancer types in men and women in PR. Age-adjusted incidence and mortality rates were estimated by sex, municipality, health region and primary site and were age-standardized to the 2000 PR population. RESULTS Incidence rates for overall cancer remained constant in men and increased in women (APC = 0.6%, p < 0.05), while mortality rates decreased (APC = -1.0%) for both sexes. A significant increase was observed in the cancer incidence rates for colorectal cancer in men, while in women, an increase in breast, colorectal, and corpus and uterus cancer was observed. Mortality rates decreased for most of the major cancers types in both sexes, except for colorectal cancer in men which showed a significant increase (p < 0.05). CONCLUSION The most important cancer types in PR (prostate, breast, colorectal, and lung) for both incidence and mortality are susceptible to primary prevention (eliminating or reducing risk factors) or to secondary prevention (early diagnosis) strategies. Our results are essential for the development of cancer prevention and control strategies in the Island.
Coupon replication systems

Motivated by the study of peer-to-peer file swarming systems à la BitTorrent, we introduce a probabilistic model of coupon replication systems. These systems consist of users aiming to complete a collection of distinct coupons. Users enter the system with an initial coupon provided by a bootstrap server, acquire other coupons from other users, and leave once they complete their coupon collection. For open systems, with exogenous user arrivals, we derive stability condition for a layered scenario, where encounters are between users holding the same number of coupons. We also consider a system where encounters are between users chosen uniformly at random from the whole population. We show that sojourn time in both systems is asymptotically optimal as the number of coupon types becomes large. We also consider closed systems with no exogenous user arrivals. In a special scenario where users have only one missing coupon, we evaluate the size of the population ultimately remaining in the system, as the initial number of users Ngoes to infinity. We show that this size decreases geometrically with the number of coupons K. In particular, when the ratio K/log(N) is above a critical threshold, we prove that this number of leftovers is of order log(log(N)). These results suggest that, under the assumption that the bootstrap server is not a bottleneck, the performance does not depend critically on either altruistic user behavior or on load-balancing strategies such as rarest first.
Classification of learning disabilities: An evidence-based evaluation.

The purpose of this paper is to review research on the classification of learning disabilities (LD). We begin by briefly reviewing the nature of classification research. Then we discuss the evolution of definitions of LD, making explicit the classification hypotheses from which these definitions derive. An extensive review of the evidence for these hypotheses will be provided for the three components of classification implicit in the federal definition of LD: discrepancy, heterogeneity, and exclusion. We will show that classification hypotheses involving discrepancy and exclusion as embedded in federal (and state) policy have at best weak validity, often representing inaccurate and outdated assumptions about LD. There is evidence for heterogeneity of LD, but some reorganization of the types of LD identified in the federal definition may be necessary. Throughout the paper we identify alternative approaches to classification and identification, including weaknesses in any psychometric approach to the identification of LD. We suggest that classifications based on inclusionary definitions that specify attributes of different forms of LD are more desirable than current exclusionary definitions. Inclusionary definitions permit a focus on identification procedures that are intervention oriented as well as a focus on prevention, both of which are desirable and could contribute to improved results in remediating LD.
Accurate BER Analysis of QPSK Modulated Asynchronous DS-CDMA Systems Communicating over Rayleigh Channels

The accurate average BER calculation of an asynchronous DS-CDMA system using random spreading sequences is studied in Rayleigh fading channels. An accurate closed-form expression is derived for the conditional characteristic function of the multiple access interference. An accurate BER expression is provided, which only requires a single numerical integration. Our numerical simulation results verify its accuracy, and also demonstrate the relative inaccuracy of the Gaussian approximation
HBV infection in untreated HIV-infected adults in Maputo, Mozambique

Background HIV/ HBV coinfected patients are at high risk of developing chronic HBV infection, liver cirrhosis and hepatocellular carcinoma. In Mozambique, where HIV prevalence is one of the highest in the world, HIV-infected patients are scarcely characterized in terms of HBV coinfection and 3TC-resistance mutations profile. Methods To characterize ART-naïve HIV-infected adults, with and without HBV coinfection, a cross-sectional study was conducted between May and November 2012 in two health centers from Maputo city, Mozambique. Subjects were consecutively enrolled in the study and, then, tested for hepatitis B surface antigen (HBsAg). Moreover, CD4+ T cells count, HBV DNA in plasma, HBV genotyping and 3TC-resistance mutations profile of HBV were assessed in HIV/HBV coinfected patients. Results In total, 518 patients were enrolled in the study. The median age was 33 years old and 66.8% were women. The median CD4+ T cells count was 361 cells/mm3 and 47 (9.1%) were coinfected with HBV. Out of 46 coinfected patients, 24 (55.2%) had HBV DNA ≥ 20 - < 20 000 and 12 (26.1%) had HBV-DNA ≥20 000. APRI > 2.0 was reported in 4.3% of coinfected and 1.7% of monoinfected patients (p = 0.228), while FIB-4 > 3.25 was reported in 4.4% of coinfected and 1.3% of monoinfected patients (p = 0.112). Genotype A was the most frequent, identified in 25/27 (92.6%) patients, whereas genotype E was present in 2/27 (7.4%) patients. No patient had 3TC-resistance mutations. Conclusions This study showed that HBV coinfection was prevalent among ART-naïve HIV-infected adults in Mozambique. Overall, these data highlight the importance of screening HBV coinfection as an integrated measure of HIV routine care to improve health conditions and treatment of HIV/HBV coinfected patients.