Miracle-dz/UniFAR-FTUs huggingface dataset:
Scalable Systems and Algorithms for Genomic Variant Analysis

Author(s): Nothaft, Frank Austin | Advisor(s): Joseph, Anthony D; Patterson, David A | Abstract: With the cost of sequencing a human genome dropping below $1,000, population-scale sequencing has become feasible. With projects that sequence more than 10,000 genomes becoming commonplace, there is a strong need for genome analysis tools that can scale across distributed computing resources while providing reduced analysis cost. Simultaneously, these tools must provide programming interfaces and deployment models that are easily usable by biologists.In this dissertation, we describe the ADAM system for processing large genomic datasets using distributed computing. ADAM provides a decoupled stack-based architecture that can accommodate many data formats, deployment models, and data access patterns. Additionally, ADAM defines schemas that describe common genomic datatypes. ADAM’s schemas and programming models enable the easy integration of disparate genomic datatypes and datasets into a single analysis.To validate the ADAM architecture, we implemented an end-to-end variant calling pipeline using ADAM’s APIs. To perform parallel alignment, we developed the Cannoli tool, which uses ADAM’s APIs to automatically parallelize single node aligners. We then implemented GATK-style alignment refinement as part of ADAM. Finally, we implemented a biallelic genotyping model, and novel reassembly algorithms in the Avocado variant caller. This pipeline provides state-of-the-art SNV calling accuracy, along with high (97%) INDEL calling accuracy. To further validate this pipeline, we reanalyzed 270 samples from the Simons Genome Diversity Dataset.
An intelligent and knowledge‐based overlapping clustering protocol for wireless sensor networks

Overlapping is one of the topics in wireless sensor networks that is considered by researchers in the last decades. An appropriate overlapping management system can prolong network lifetime and decrease network recovery time. This paper proposes an intelligent and knowledge‐based overlapping clustering protocol for wireless sensor networks, called IKOCP. This protocol uses some of the intelligent and knowledge‐based systems to construct a robust overlapping strategy for sensor networks. The overall network is partitioned to several regions by a proposed multicriteria decision‐making controller to monitor both small‐scale and large‐scale areas. Each region is managed by a sink, where the whole network is managed by a base station. The sensor nodes are categorized by various clusters using the low‐energy adaptive clustering hierarchy (LEACH)‐improved protocol in a way that the value of p is defined by a proposed support vector machine–based mechanism. A proposed fuzzy system determines that noncluster heads associate with several clusters in order to manage overlapping conditions over the network. Cluster heads are changed into clusters in a period by a suggested utility function. Since network lifetime should be prolonged and network traffic should be alleviated, a data aggregation mechanism is proposed to transmit only crucial data packets from cluster heads to sinks. Cluster heads apply a weighted criteria matrix to perform an inner‐cluster routing for transmitting data packets to sinks. Simulation results demonstrate that the proposed protocol surpasses the existing methods in terms of the number of alive nodes, network lifetime, average time to recover, dead time of first node, and dead time of last node.
Predictive role of high-density lipoprotein and body mass index in differentiated thyroid carcinoma

Objective: High-density lipoprotein (HDL) and body mass index (BMI) have been implicated in carcinogenesis. However, the significance of HDL and BMI in differentiated thyroid carcinoma (DTC) has not been elucidated. The aim of this study was to assess the roles of HDL and BMI in carcinogenesis and in the prognosis of DTC. Methods: HDL concentrations and BMI values were measured in 155 male patients with DTC and in 65 male patients with benign thyroid nodules. Multivariate logistic regression and Cox regression analyses were performed to evaluate the correlation between variables. Receiver operating characteristic (ROC) curves were constructed to assess the performance of HDL and BMI in the diagnosis of DTC and the prediction of four-year recurrence. Results: HDL (OR, 0.581; 95% CI, 0.371-0.909; p = 0.018) and BMI (OR, 1.174; 95% CI, 1.051-1.130, p = 0.004) were both independent risk factors of DTC. HDL was negatively correlated with distant metastasis (OR, 0.006; 95% CI, 0.000-0.517; p = 0.025), while BMI was significantly correlated with capsule invasion (OR, 1.193; 95% CI, 1.057-1.347; p = 0.004) and multifocality (OR, 1.208; 95% CI, 1.079-1.353; p = 0.001). ROC analysis indicated that HDL could be a good marker for the diagnosis of DTC (AUC, 0.857; 95% CI, 0.805-0.910; p = 0.006) at a cutoff value of 1.37 mmol/L and the prediction of four-year recurrence (AUC, 0.730; 95% CI, 0.585-0.875; p = 0.006) at a cutoff value of 1.14 mmol/L. Multivariate Cox regression analysis showed that a low HDL level (≤ 1.14 mmol/L) was able to predict fouryear recurrence (HR, 0.199; 95% CI, 0.059-0.667; p = 0.009) and a worse outcome. Conclusion: A low HDL level incurs an increased risk of DTC and four-year recurrence, while a high BMI is associated with capsule invasion and multifocality. However, more advanced research is needed in the future to confirm these results.
Determinants of prelacteal feeding practice among postpartum mothers in Debre Markos town, Amhara regional state, Ethiopia, 2016

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Miglitol attenuates non‐alcoholic steatohepatitis in diabetic patients

Postprandial hyperglycemia is frequently accompanied by non‐alcoholic fatty liver disease (NAFLD) and steatohepatitis (NASH). Although α‐glucosidase inhibitors (αGIs) can slow glucose absorption from the intestine and suppress the surge of circulating glucose concentration after meals, it remains unclear whether αGIs are also beneficial for NASH. The aim of this prospective study was to examine the efficacy and safety of miglitol, a typical αGI, for NASH.
Non-resolvinganemia with gastrointestinal stromal tumors - Case report

Prevalence of non-communicable diseases are higher among the Sri Lankan society.Alarge roportion were carcinomas of different systems. The demographic transition has a pivotal role for this diseases burden. Gastrointestinal stromal tumors (GIST) are among rare clinical entity. At present private health sector in Sri Lanka is capable of detecting these neoplasms. This report presents probably the first case of Jejunal gastrointestinal stromal tumor operated recently in a 56-year-old female patient, in private hospital. The diagnosis, treatment, outcome, as well as literature review of the pathological identification, sites of origin and prognosis as presented as follows.
Developmental Trajectories of Attention in Typically Developing Chinese Children: A Four-Wave Longitudinal Study

ABSTRACT We conducted a 4-year longitudinal study to investigate trajectories of attention in a sample of 145 Chinese children. The Test of Everyday Attention was administered and latent growth modeling was used to capture developmental trajectories. We found that children’s selective attention showed a linear increase, whereas attentional control and sustained attention increased rapidly then slowed down over 4 years. There was no significant correlation between the slopes of growth model for any subsystems. Girls showed higher initial levels of selective attention than boys, but no difference in growth rate. These findings support different developmental patterns in the attention network systems.
The Impact of Global Sensitivities and Design Measures in Model-Based Optimal Experimental Design

In the field of chemical engineering, mathematical models have been proven to be an indispensable tool for process analysis, process design, and condition monitoring. To gain the most benefit from model-based approaches, the implemented mathematical models have to be based on sound principles, and they need to be calibrated to the process under study with suitable model parameter estimates. Often, the model parameters identified by experimental data, however, pose severe uncertainties leading to incorrect or biased inferences. This applies in particular in the field of pharmaceutical manufacturing, where usually the measurement data are limited in quantity and quality when analyzing novel active pharmaceutical ingredients. Optimally designed experiments, in turn, aim to increase the quality of the gathered data in the most efficient way. Any improvement in data quality results in more precise parameter estimates and more reliable model candidates. The applied methods for parameter sensitivity analyses and design criteria are crucial for the effectiveness of the optimal experimental design. In this work, different design measures based on global parameter sensitivities are critically compared with state-of-the-art concepts that follow simplifying linearization principles. The efficient implementation of the proposed sensitivity measures is explicitly addressed to be applicable to complex chemical engineering problems of practical relevance. As a case study, the homogeneous synthesis of 3,4-dihydro-1H-1-benzazepine-2,5-dione, a scaffold for the preparation of various protein kinase inhibitors, is analyzed followed by a more complex model of biochemical reactions. In both studies, the model-based optimal experimental design benefits from global parameter sensitivities combined with proper design measures.
Jasmonic Acid Inhibits Auxin-Induced Lateral Rooting Independently of the CORONATINE INSENSITIVE1 Receptor1

JA preferentially inhibits auxin-induced lateral rooting via stabilization of Aux/IAA repressors. Plant root systems are indispensable for water uptake, nutrient acquisition, and anchoring plants in the soil. Previous studies using auxin inhibitors definitively established that auxin plays a central role regulating root growth and development. Most auxin inhibitors affect all auxin signaling at the same time, which obscures an understanding of individual events. Here, we report that jasmonic acid (JA) functions as a lateral root (LR)-preferential auxin inhibitor in Arabidopsis (Arabidopsis thaliana) in a manner that is independent of the JA receptor, CORONATINE INSENSITIVE1 (COI1). Treatment of wild-type Arabidopsis with either (−)-JA or (+)-JA reduced primary root length and LR number; the reduction of LR number was also observed in coi1 mutants. Treatment of seedlings with (−)-JA or (+)-JA suppressed auxin-inducible genes related to LR formation, diminished accumulation of the auxin reporter DR5::GUS, and inhibited auxin-dependent DII-VENUS degradation. A structural mimic of (−)-JA and (+)-coronafacic acid also inhibited LR formation and stabilized DII-VENUS protein. COI1-independent activity was retained in the double mutant of transport inhibitor response1 and auxin signaling f-box protein2 (tir1 afb2) but reduced in the afb5 single mutant. These results reveal JAs and (+)-coronafacic acid to be selective counter-auxins, a finding that could lead to new approaches for studying the mechanisms of LR formation.
Group Communication Treatment for Individuals with PPA and Their Partners

Abstract Primary progressive aphasia (PPA) is a neurodegenerative syndrome characterized by insidious language deterioration. This young-onset disorder leaves adults with reduced communication skills for participation in social activities. There is limited evidence regarding group treatment for individuals with PPA, though the principles of chronic aphasia groups can be applied to this clinical population. We developed a PPA group treatment model incorporating compensatory strategies from augmentative and alternative communication (AAC), communication partner training from aphasia rehabilitation, and systematic instruction from dementia management. Six modules were designed and delivered to people with PPA and their communication partners in a university clinic setting over a 6-week period. Treatment was provided by graduate clinicians with supervision from a certified speech–language pathologist and faculty member. Primary treatment goals were to provide education about PPA symptoms and progression; to increase practice and use of multimodal communication by people with PPA; and to establish an environment where people with PPA and their partners could connect for training and support. We present pre/post comparisons and satisfaction data provided by five individuals with PPA and their partners in the group. Results suggest that group training is an effective service delivery model. Participants reported gains in both knowledge about PPA and in using many different modalities to communicate. The new compensatory strategies learned provide tools for maintenance and improvement of language use. Participants saw increased confidence and participation in daily activities, and highlighted the value of the PPA group for individuals with this relatively rare condition and their family members.
Union Dissolution and Migration

BACKGROUND While there is a limited body of research regarding residential mobility and migration following union dissolution, there is a particular dearth of studies that go into detail about the factors that shape how union dissolution may result in long-distance migration. OBJECTIVE This research isolates and identifies the processes that influence inter-state migration in the period immediately following the dissolution of a marital union. METHODS Multilevel logit models of the probability of inter-state migration following the dissolution of marital unions are estimated using data drawn from the 1975 through 2011 US Panel Study of Income Dynamics (PSID). RESULTS The results provide support for a gendered model of family migration, indicate that separated parents are less likely to migrate than ex-partners without children, and suggest that the migration decisions of former partners may remain linked through their children even after the end of their union. CONCLUSIONS These results indicate that the migration of separated parents is constrained by the need for parents with joint or shared children to remain in close geographic proximity to each other. Since both the number of children living with separated parents and the number of those parents with joint or shared custody are increasing, it is likely that this plays some role in the long-term decline in US migration rates.
Waveguide Tuning Stub with Internal Choke

We present working principles, circuit analyses, electromagnetic simulation, and experiments in 2.45-GHz band of a noncontacting waveguide tuning stub structure that incorporates a microwave choke inside the stub. The main advantages of such an internal choke compared to traditional external chokes built in the body surrounding the stub are a substantially lower radiation leakage, smaller overall radius, and the possibility of using air as the choke dielectric.
Continuous leakage–resilient IBE in cloud computing

Cloud computing is an efficient tool in which cloud storage shares plenty of encrypted data with other data owners. In existing cloud computing scenarios, it may suffer from some new attacks like side channel attacks. Therefore, we are eager to introduce a new cryptographic scheme that can resist these new attacks. In this work, we exploit a new technique to build leakage‐resilient identity‐based encryption and use the stronger existing partial leakage model, such as continual leakage model. More specifically, our proposal is based on the underlying decisional bilinear Diffie‐Hellman assumption, but proven adaptively secure against adaptive chosen ciphertext attack in the standard model. Above all, a continuous leakage–resilient IBE scheme with adaptive security meets cloud computing with stronger security.
de Meaning of temperature in different thermostatistical ensembles

Depending on the exact experimental conditions, the thermodynamic properties of physical systems can be related to one or more thermostatistical ensembles. Here, we survey the notion of thermodynamic temperature in different statistical ensembles, focusing in particular on subtleties that arise when ensembles become non-equivalent. The ‘mother’ of all ensembles, the microcanonical ensemble, uses entropy and internal energy (the most fundamental, dynamically conserved quantity) to derive temperature as a secondary thermodynamic variable. Over the past century, some confusion has been caused by the fact that several competing microcanonical entropy definitions are used in the literature, most commonly the volume and surface entropies introduced by Gibbs. It can be proved, however, that only the volume entropy satisfies exactly the traditional form of the laws of thermodynamics for a broad class of physical systems, including all standard classical Hamiltonian systems, regardless of their size. This mathematically rigorous fact implies that negative ‘absolute’ temperatures and Carnot efficiencies more than 1 are not achievable within a standard thermodynamical framework. As an important offspring of microcanonical thermostatistics, we shall briefly consider the
Epitaxial Growth of Aligned Semiconductor Nanowire Metamaterials for Photonic Applications

A novel class of optical metamaterials is presented consisting of high densities of aligned gallium phosphide (GaP) nanowires fabricated using metal‐organic vapor phase‐epitaxy. Starting from a gold island film as a catalyst for nanowire growth, a sequential combination of vapor–liquid–solid and lateral growth modes is employed to obtain a continuous tunability of the nanowire volume fraction from 7% to over 35%. By choosing different crystallographic orientations of the GaP substrate, metamaterials are designed with different nanowire orientations. The anisotropy of the nanowire building blocks results in strong optical birefringence. Polarization interferometry demonstrates a very large polarization extinction contrast of 4 × 103 combined with a sharp angular resonance which holds promise for optical sensing. Nanowire metamaterials may find applications in photonics, optoelectronics, non‐linear and quantum optics, microfluidics, bio‐, and gas sensing.
Predictors of Poor Tuberculosis Treatment Outcome at Arba Minch General Hospital, Southern Ethiopia: A Case-Control Study

Introduction: Tuberculosis (TB) is a major public health problem throughout the world. About a third of the world’s population is estimated to be infected with TB and hence at risk of developing active disease. Ethiopia ranks seventh among the world's 22 countries with a high burden of TB. This study was aimed at assessing the predictors of poor TB treatment outcome at Arba Minch General Hospital (AMGH), Southern Ethiopia.Methods: A case-control study comprising simple random sampling was conducted from Jan to Feb 2014. Cases were patients registered as treatment failures, defaulted or died during TB treatment follow up; and controls were patients registered as cured or completed the treatment in the period of 1st Jan 2009-30th Dec 2013 in AMGH. A prepared standard checklist adapted from WHO was used to assess the predictors of poor treatment outcome. A chi-square test and a paired T-test were used to compare categorical and continuous variables in cases and controls, respectively. Multivariable logistic regression was used in the final model.Results: The case group was composed of 224 patients with poor treatment outcome while the control group was composed of 448 patients with successful outcome. Male sex (Adjusted Odds Ratio (AOR)=1.6; 95%CI: 1.1-2.3), age >35 years (AOR=2.4; 95%CI:1.6-3.4), rural residence (AOR=1.5; 95%CI:1.0-2.2), retreatment category (AOR=3.3; 95%CI:1.3-8.4), smear negative Pulmonary TB (AOR=2.4; 95%CI:1.4-4.1), Extra-pulmonary TB (AOR=2.5; 95%CI:1.3-4.6), HIV positives (AOR=2.4; 95%CI:1.6-3.5) and TB treated (unknown HIV status) in the year before 2011 (AOR=2.5; 95%CI:1.3-5.1) were found predictors of poor TB treatment outcome.Conclusion: Male sex, rural residence, older age, previous treatment, smear negative PTB and EPTB, HIV coinfection, unknown HIV status but treated for TB before 2011 were found significant risk factors for developing poor treatment outcome. Targeted measures should be considered to reduce the proportion of poor outcome among highrisk groups.
Effect of the silica content of diatom prey on the production, decompositionand sinking of fecal pellets of the copepod Calanus sinicus

Abstract. The effects of changing the amount of silica in the cell wall of diatom prey, on the production, decomposition rate and sinking velocity of fecal pellets of the calanoid copepod, Calanus sinicus, were examined. Using different light intensities to control the growth of the diatom Thalassiosira weissflogii also led to the accumulation of different amounts of biogenic silica. Copepods were then fed either low ( ∼ 1600 cells L−1) or high ( ∼ 8000 cells L−1) concentrations of this diatom. Copepods fed a high concentration of diatoms with high-silica content exhibited a lower grazing rate and lower fecal pellet production rate than those fed a high concentration of diatoms with low-silica content. However, there was no difference in either the grazing or fecal pellet production rates at low prey concentrations with high- or low-silica content. The size of the fecal pellets produced was only affected by the prey concentration, and not by the silica content of prey. In addition, the degradation rate of the fecal pellets was much higher for copepods fed a low-silica diet than for those fed a high-silica diet. Significantly lower densities and sinking rates only occurred in the fecal pellets of copepods fed a low-silica diet and a low prey concentration. Calculating the L ratio (the ratio of degradation rate : sinking rate) for each group indicated that the fecal pellets produced by copepods fed highly silicified diatoms are likely to transport both biogenic silica and organic carbon to the deep layer, whereas those produced following the consumption of low-silica diatoms are likely to decompose in the mixing layer.