Miracle-dz/UniFAR-FTUs huggingface dataset:
Coalescent: an open-science framework for importance sampling in coalescent theory

Background. In coalescent theory, computer programs often use importance sampling to calculate likelihoods and other statistical quantities. An importance sampling scheme can exploit human intuition to improve statistical efficiency of computations, but unfortunately, in the absence of general computer frameworks on importance sampling, researchers often struggle to translate new sampling schemes computationally or benchmark against different schemes, in a manner that is reliable and maintainable. Moreover, most studies use computer programs lacking a convenient user interface or the flexibility to meet the current demands of open science. In particular, current computer frameworks can only evaluate the efficiency of a single importance sampling scheme or compare the efficiencies of different schemes in an ad hoc manner. Results. We have designed a general framework (http://coalescent.sourceforge.net; language: Java; License: GPLv3) for importance sampling that computes likelihoods under the standard neutral coalescent model of a single, well-mixed population of constant size over time following infinite sites model of mutation. The framework models the necessary core concepts, comes integrated with several data sets of varying size, implements the standard competing proposals, and integrates tightly with our previous framework for calculating exact probabilities. For a given dataset, it computes the likelihood and provides the maximum likelihood estimate of the mutation parameter. Well-known benchmarks in the coalescent literature validate the accuracy of the framework. The framework provides an intuitive user interface with minimal clutter. For performance, the framework switches automatically to modern multicore hardware, if available. It runs on three major platforms (Windows, Mac and Linux). Extensive tests and coverage make the framework reliable and maintainable. Conclusions. In coalescent theory, many studies of computational efficiency consider only effective sample size. Here, we evaluate proposals in the coalescent literature, to discover that the order of efficiency among the three importance sampling schemes changes when one considers running time as well as effective sample size. We also describe a computational technique called “just-in-time delegation” available to improve the trade-off between running time and precision by constructing improved importance sampling schemes from existing ones. Thus, our systems approach is a potential solution to the “28 programs problem” highlighted by Felsenstein, because it provides the flexibility to include or exclude various features of similar coalescent models or importance sampling schemes.
Cavity‐filling dolomite speleothems and submarine cements in the Ediacaran Dengying microbialites, South China: Responses to high‐frequency sea‐level fluctuations in an ‘aragonite–dolomite sea’

Speleothems, mostly composed of calcium carbonate, are widely present in modern karst‐originated caves, but have rarely been reported in palaeokarst systems. This study presents a novel type of dolomite speleothem and subsequent submarine dolomite cement, which are widely present in the upper Ediacaran Dengying Formation in the upper Yangtze area. These precipitated materials occur in the cavity system that cuts across several peritidal cycles. The interconnected cavity networks with irregular shapes, embayed walls, internal breccias on cavity floor and their preferential development in the shallower cycle tops (for example, tepee‐deformed beds) suggest that they were initially generated by subaerial dissolution. As the earliest infills, the hemispherical protrusions, icicle‐like pendants and ground‐up columns show similar morphological features and occurrence patterns to the cave popcorn, stalactites and stalagmites, respectively. Thus, these earliest infills are speleothems resulting from associated meteoric precipitation during subaerial exposure. The isopachous growth pattern of subsequent more extensive fibrous dolomite cements points to a submarine diagenetic environment in which they were precipitated. Microscopically, the micritic to micro‐crystalline dolomite, acicular dolomite in speleothems and the subsequent fibrous dolomite share similar crystal fabrics to metastable precursors (for example, Mg‐calcite). Meanwhile, the carbon‐oxygen isotope compositions of the speleothem and fibrous dolomite, although partly altered by burial diagenesis, share a large overlap with host rock and coeval marine carbonates all over the Yangtze Platform. For these reasons, these speleothems and fibrous cements are considered to have been initially precipitated as metastable carbonate precursors in meteoric and submarine environments, respectively, and stabilized during submarine mimetic dolomitization. The cyclic occurrence of cavity systems filled with speleothems and submarine cements reflects periodic subaerial exposure and marine flooding of broad tidal flat in the upper Yangtze area, driven by high‐frequency sea‐level fluctuations. Furthermore, the Neoproterozoic seawater chemistry that favoured early dolomitization of carbonate precursor mineralogies was an advantage for the preservation of fabrics from metastable precursor minerals.
Predictors of breast cancer among women in a northern state of Malaysia: a matched case-control study.

BACKGROUND Breast cancer has been increased in South East Asia countries, but there are limited data for breast cancer risk factors in these countries. To clarify the risk for breast cancer among the Malaysian women, a matched case-control study was conducted. METHOD Between October 2009 and April 2010, a survey was prospectively conducted among women admitted to clinics of Penang General Hospital for examination and/or treatment by using a questionnaire. Therefore, characteristics of patients diagnosed with breast cancer (n=150) were compared with control cases (n=150) admitted to hospital for non-neoplastic, non-hormone related diseases. RESULTS Family history of a distant relative with breast cancer (OR=2.84), history of first-degree relatives with breast cancer (OR=2.95), history of benign breast disease (OR=2.43), menstrual irregularity (OR=4.24), and use of oral contraceptive pills (OCP) (OR=2.15) were found to be significant risk factors for breast cancer in our population. Furthermore, education more than 11 years (OR=0.40), breastfeeding (OR=0.50), being employed (OR=0.45) and practicing low fat diet (OR=0.53) were strongly protective against breast cancer development. CONCLUSION The results emphasize the importance of conducting a series of awareness campaigns that highlights the protective role of longer breastfeeding period against breast cancer and the negative relationships between OCP use and high fat diet with this disease.
Mining exception-handling rules as sequence association rules

Programming languages such as Java and C++ provide exception-handling constructs to handle exception conditions. Applications are expected to handle these exception conditions and take necessary recovery actions such as releasing opened database connections. However, exception-handling rules that describe these necessary recovery actions are often not available in practice. To address this issue, we develop a novel approach that mines exception-handling rules as sequence association rules of the form “(FC1<inf>c</inf><sup>1</sup>…FC<inf>c</inf><sup>n</sup>) ∧ FC<inf>a</inf> ⇒ (FC<inf>e</inf><sup>1</sup>…FC<inf>e</inf><sup>m</sup>)”. This rule describes that function call FCa should be followed by a sequence of function calls (FC<inf>e</inf><sup>1</sup>…FC<inf>e</inf><sup>m</sup>) when FC<inf>a</inf> is preceded by a sequence of function calls (FC<inf>e</inf><sup>1</sup>…FC<inf>c</inf><sup>n</sup>). Such form of rules is required to characterize common exception-handling rules. We show the usefulness of these mined rules by applying them on five real-world applications (including 285 KLOC) to detect violations in our evaluation. Our empirical results show that our approach mines 294 real exception-handling rules in these five applications and also detects 160 defects, where 87 defects are new defects that are not found by a previous related approach.
Effect of Micronutrient and Probiotic Fortified Yogurt on Immune-Function of Anti-Retroviral Therapy Naive HIV Patients

Background: Micronutrient supplementation has been shown to reduce the progression of HIV but does not have an effect on the intestinal barrier or the intestinal microbiota of HIV patients. Studies have suggested that probiotics could potentially complement micronutrients in preserving the immune-function of HIV patients. Objective: Assess the impact of micronutrient supplemented probiotic yogurt on the immune function of HIV patients. Design:We performed a randomized, double blind, controlled trial with CD4 count as primary outcome among HIV patients naïve to anti-retroviral treatment. Secondary outcomes included hematological parameters, incidence of diarrhea and clinical symptoms. A total of 112 HIV patients were randomized to receive a micronutrient fortified yogurt with (n = 55) or without additional probiotic Lactobacillus rhamnosus GR-1 (n = 57) for four weeks. Results:An average decline in CD4 count of −70 cells/μL (95% CI: −154 to −15) was observed in the micronutrient, probiotic group versus a decrease of −63 cells/μL (95% CI: −157 to −30) in the micronutrient control group (p = 0.9). Additional probiotic supplementation was well tolerated and not associated with adverse events. No difference between groups was detected in incidence of diarrhea or clinical symptoms. An improvement of hemoglobin levels was observed for all subjects, based upon a mean difference from baseline of 1.4 g/L (SD = 6) (p = 0.02). Conclusion:The addition of probiotics to a micronutrient fortified yogurt was well tolerated by HIV patients but was not associated with a further increase in CD4 count after one month.
Analysis of the Wikipedia Category Graph for NLP Applications

In this paper, we discuss two graphs in Wikipedia (i) the article graph, and (ii) the category graph. We perform a graphtheoretic analysis of the category graph, and show that it is a scale-free, small world graph like other well-known lexical semantic networks. We substantiate our findings by transferring semantic relatedness algorithms defined on WordNet to the Wikipedia category graph. To assess the usefulness of the category graph as an NLP resource, we analyze its coverage and the performance of the transferred semantic relatedness algorithms.
Stochastic Power Control for Time-Varying Long-Term Fading Wireless Networks

A new time-varying (TV) long-term fading (LTF) channel model which captures both the space and time variations of wireless systems is developed. The proposed TV LTF model is based on a stochastic differential equation driven by Brownian motion. This model is more realistic than the static models usually encountered in the literature. It allows viewing the wireless channel as a dynamical system, thus enabling well-developed tools of adaptive and nonadaptive estimation and identification techniques to be applied to this class of problems. In contrast with the traditional models, the statistics of the proposed model are shown to be TV, but converge in steady state to their static counterparts. Moreover, optimal power control algorithms (PCAs) based on the new model are proposed. A centralized PCA is shown to reduce to a simple linear programming problem if predictable power control strategies (PPCS) are used. In addition, an iterative distributed stochastic PCA is used to solve for the optimization problem using stochastic approximations. The latter solely requires each mobile to know its received signal-to-interference ratio. Generalizations of the power control problem based on convex optimization techniques are provided if PPCS are not assumed. Numerical results show that there are potentially large gains to be achieved by using TV stochastic models, and the distributed stochastic PCA provides better power stability and consumption than the distributed deterministic PCA.
Development of a predictive model to identify inpatients at risk of re-admission within 30 days of discharge (PARR-30)

Objectives To develop an algorithm for identifying inpatients at high risk of re-admission to a National Health Service (NHS) hospital in England within 30 days of discharge using information that can either be obtained from hospital information systems or from the patient and their notes. Design Multivariate statistical analysis of routinely collected hospital episode statistics (HES) data using logistic regression to build the predictive model. The model's performance was calculated using bootstrapping. Setting HES data covering all NHS hospital admissions in England. Participants The NHS patients were admitted to hospital between April 2008 and March 2009 (10% sample of all admissions, n=576 868). Main outcome measures Area under the receiver operating characteristic curve for the algorithm, together with its positive predictive value and sensitivity for a range of risk score thresholds. Results The algorithm produces a ‘risk score’ ranging (0–1) for each admitted patient, and the percentage of patients with a re-admission within 30 days and the mean re-admission costs of all patients are provided for 20 risk bands. At a risk score threshold of 0.5, the positive predictive value (ie, percentage of inpatients identified as high risk who were subsequently re-admitted within 30 days) was 59.2% (95% CI 58.0% to 60.5%); representing 5.4% (95% CI 5.2% to 5.6%) of all inpatients who would be re-admitted within 30 days (sensitivity). The area under the receiver operating characteristic curve was 0.70 (95% CI 0.69 to 0.70). Conclusions We have developed a method of identifying inpatients at high risk of unplanned re-admission to NHS hospitals within 30 days of discharge. Though the models had a low sensitivity, we show how to identify subgroups of patients that contain a high proportion of patients who will be re-admitted within 30 days. Additional work is necessary to validate the model in practice.
A novel electric energy management strategy applied in hybrid PV system

This paper presents a hybrid PV system operated in accordance with an electric energy management strategy for public lighting equipments in apartment buildings. We attempt to alternate PV with grid-connected power systems to avoid the occurrences of islanding, safe protection and the low reliability of power supply in standalone PV system through implementing the electric energy management strategy presented herein. The power conversion devices included in the proposed system contain buck-boost, push-pull, full-bridge inverter, switches and high-efficient digital signal controller as means of achieving MPPT, power charging and power system switching. A 100W experimental prototype of hybrid PV system was built in the lab. Experimental results are shown to verify the effectiveness of proposed energy management strategy.
Educational Level Signals Unobserved Abilities of People with High Functioning Autism Spectrum Disorders

The effect of educational level on employment of people with high functioning autism spectrum disorders (HFASD) was examined. If education augments natural abilities to accomplish tasks in people with HFASD, then those with more education would have comparative advantages in both obtaining and retaining jobs. In contrast, if education did not augment natural abilities and only signaled unobservable abilities, one would expect an advantage only in obtaining a job, but not in retention. 22 people with HFASD replied to questionnaires regarding their history of education and employment. Those with job experience had higher educational levels than those with no job experience, but educational level was not significantly different between groups with and without more than one year of job experience. Educational level seems to be associated with abilities, but probably the unobserved abilities underlie both educational attainment and employment history.
Ultrastructure and antigenicity of the unique cell wall pimple of the Candida opaque phenotype

Cells of Candida albicans WO-1 switch frequently and reversibly between two colony-forming phenotypes, white and opaque. In the white form, budding cells appear similar to those of most other strains of C. albicans, but in the opaque form, budding cells are larger, are bean shaped, and possess pimples on the wall. These pimples exhibit a unique and complex morphology. With scanning electron microscopy, a central pit can be discerned, and in many cases, a bleb can be observed emerging from the pimple center. With transmission electron microscopy, channels are evident in some pimples and vesicles are apparent under the pimple in the cytoplasm, in the actual wall of the pimple, or emerging from the tip of the pimple. A large vacuole predominates in the opaque-cell cytoplasm. This vacuole is usually filled with spaghettilike membranous material and in a minority of cases is filled with vesicles, many of which exhibit a relatively uniform size. An antiserum to opaque cells recognizes three opaque-cell-specific antigens with molecular masses of approximately 14.5, 21, and 31 kilodaltons (kDa). Absorption with nonpermeabilized opaque cells demonstrated that only the 14.5-kDa antigen is on the cell surface; indirect immunogold labeling demonstrated that it is localized in or on the pimple. The possibility is suggested that the vacuole of opaque cells is the origin of membrane-bound vesicles which traverse the wall through specialized pimple structures and emerge from the pimple with an intact outer double membrane, a unique phenomenon in yeast cells. The opaque-cell-specific 14.5-kDa antigen either is in the pimple channel or is a component of the emerging vesicle. The functions of the unique opaque-cell pimple and emerging vesicle are not known.
First prenatal diagnosis of defects in the HsPDX1 gene encoding protein X, an additional lipoyl‐containing subunit of the human pyruvate dehydrogenase complex

We have previously reported a genetic study of a neonatal lactic acidosis linked to a pyruvate dehydrogenase complex deficiency due to the absence of the protein X subunit. This rare autosomal recessive disorder is associated with specific deletions in this polypeptide which is encoded by the HsPDX1 gene, located on chromosome 11p1.3. The pathology of the patient was considered to arise from a large homozygous deletion (78del85) found at the 5′ end of the HsPDX1 coding sequence. Her heterozygous mother underwent prenatal diagnosis during a subsequent pregnancy. Chorionic villus samples were used for three independent studies: (1) normal levels of the protein X component of the PDH complex were detected by immunoblotting; (2) RT‐PCR analysis showed no deletion at the 5′ end of the cDNA but the presence of a distinct heterozygous deletion (965del59) at its 3′ end inherited from the father; (3) haplotype analysis revealed the presence of the father's mutated allele and the mother's normal allele. It was concluded that the fetus was heterozygous for this separate 3′ deletion, so, it was likely to be not affected. This study permitted us to characterize more precisely the genetic abnormalities of the HsPDX1 cDNA occurring in each family's member. Copyright © 1999 John Wiley & Sons, Ltd.
Do CSF total tau, phosphorylated tau, and β-amyloid 42 help to predict progression of mild cognitive impairment to Alzheimer's disease? A systematic review and meta-analysis of the literature

The search for biomarkers as a diagnostic aid to the identification of patients in pre-dementia stages is a fast growing research area. In view of the low specificity attained with the clinically based diagnostic criteria, including those for mild cognitive impairment (MCI), biomarker information will add precision to the incipient dementia diagnostic work-up, particularly Alzheimer's disease (AD). We present a systematic review of the literature and meta-analysis of the most relevant publications about the role of CSF biomarkers in the identification of patients with probable Alzheimer's disease at pre-dementia stages. A total of 16 studies were included in the systematic review, five of which were suitable for meta-analysis. We compared the standard mean differences (SMD) of β-amyloid 42 (Aβ42), total tau (T-tau) and phosphorylated tau (P-tau) for 130, 169 and 123 patients with MCI who converted to AD (MCI-AD) and 142, 157 and 130 controls, respectively. We conclude that when a clinical diagnosis of MCI is made at baseline assessment, low CSF levels of Aβ42 (SMD: −1.57, CI95% [−2.30 to −0.84], P<0.001), along with high T-tau (SMD: 1.52, CI95% [1.25 to 1.79], P<0.001), and high P-tau (SMD: 1.75, CI95% [0.99 to 2.51], P<0.001), help to predict the conversion to Alzheimer's disease as compared to controls subjects.
Non-Small Cell Lung Cancer Cyclooxygenase-2-dependent Regulation of Cytokine Balance in Lymphocytes and Macrophages : Up-Regulation of Interleukin 10 and Down-Regulation of Interleukin 12 Production 1

Tumor-derived prostaglandin }â€¢'. , i ]'(.! â€¢,,i modifies cytokine balance and inhibits host immunity. We hypothesized that a high level of PGE2 pro duction by lung tumor cells is dependent on tumor cyclooxygenase (COX)-2 expression. We found that PGE2 production by A549 non-small cell lung cancer (NSCLC) cells was elevated up to 50-fold in response to interleukin (IL)-lÃŸ. Reversal of IL-lÃŸ-induced ! '(,! , production in A549 cells was achieved by specific pharmacological or antisense oligonucleotide inhibition of COX-2 activity or expression. In contrast, specific COX-1 inhibition was not effective. Consistent with these findings, II -1/! induced COX-2 mRNA expression and protein production in A549 cells. Specific inhibition of COX-2 abrogated the capacity of IL-lÃŸ-stimulated A549 cells to induce II -10 in lymphocytes and macrophages. Further more, specific inhibition of A549 COX-2 reversed the tumor-derived PGE2-dependent inhibition of macrophage I1-I2 production when whole blood was cultured in tumor supernatants. Our results indicate that lung tumor-derived I'<;i . plays a pivotal role in promoting lymphocyte and macrophage II III induction while simultaneously inhibiting macrophage 11-12 production. Immunohistochemistry of human NSCLC tissues ob tained from lung cancer resection specimens revealed cytoplasmic staining for COX-2 within tumor cells. This is the first description of functional COX-2 expression by NSCLC cells and the definition of a pathway whereby tumor COX-2 expression and a high level of PGE2 production mediate profound alteration in cytokine balance in the lung cancer mi-
An in-vivo lateral ankle ligament strain behavior assessment technique for potential use in robot-assisted therapy

Ankle sprains are very common, especially in sports activities. Accurate assessment of ankle ligament strain behavior is crucial in understanding ankle function and optimizing ankle rehabilitation programs. This study proposed an in-vivo lateral ankle ligament strain assessment technique for potential use in robot-assisted therapy. It consists of two phases: real-time identification of ankle joint and subtalar joint orientations and simulation of lateral ankle ligament strain behavior. A healthy participant conducted robot-assisted rehabilitation exercises and the results compared to a kinematic model. The model was found to be realistic, leading to the conclusion that this method may be appropriate for determining lateral ankle ligament strain in robot-assisted therapy.