Miracle-dz/UniFAR-FTUs huggingface dataset:
Deep Sequencing Data Analysis: Challenges and Solutions

Ultra high throughput sequencing, also known as deep sequencing or Next Generation Sequencing (NGS), is revolutionizing the study of human genetics and has immense clinical implications. It has reduced the cost and increased the throughput of genomic sequencing by more than three orders of magnitude in just a few years, a trend which is guaranteed to rapidly accelerate in the near future (Metzker, 2010). Using deep sequencing, for example, it is now possible to discover novel disease causing mutations (Ley et al., 2008) and detect traces of pathogenic microorganisms (Isakov et al., 2011). For the first time, research fields such as personalized medicine for patient treatment are becoming tangible at genomic levels given advances in deep sequencing data integration. The amount of data produced by a single ultra high throughput sequencing run is often tremendous and can reach hundreds of millions of reads in various lengths per experiment (Mardis, 2008). The storage, processing, querying, parsing, analyzing and interpreting of such an incredible amount of data is a significant task that holds many obstacles and challenges (Koboldt et al., 2010). In this chapter we will address some of the possibilities, potentials and questions raised during ultra high throughput sequencing data analysis. We will mainly focus on common pre-analysis concepts and crucial advanced considerations for alignment, assembly and variation detection. Currently, the deep sequencing user is faced with an abundance of deep sequencing data analysis tools, both publicly and commercially available. For each of the aforementioned analysis types, we will point out the various aspects to be considered when choosing a tool, and emphasize the relevant challenges and possible limitations in order to assist the user in picking the most suitable one. Since deep sequencing data analysis is a rapidly evolving field, our focus will be on fundamental concepts of the analysis process and the its challenges, allowing this read to be relevant amid additional published software. Our first part will encompass a brief overview of current leading deep sequencing technologies with special attention to their features, strengths and possible drawbacks in regards to the different preliminary questions that one might ask when using ultra high throughput sequencing. The second part of the chapter introduces pre-analysis processes. These are common quality control and assurance methods that alleviate deep sequencing derived biases and improve the overall results of any down-stream analysis. In the third part of the chapter, we will go over the different aspects of the post-sequencing analysis,
Influence of the Molecular Weight of Bioreducible Oligoethylenimine Conjugates on the Polyplex Transfection Properties

The purpose of the present study was to investigate the influence of molecular weights on the chemical, biophysical, and biological properties of bioreducible oligoethylenimine conjugates. The cationic conjugates were synthesized by polyaddition between branched oligoethylenimine 800 Da (OEI) and the disulfide bond containing N,N′-cystamine bisacrylamide (CBA) linker. A correlation between the copolymer molecular weights and the polyplex transfection properties was found. The OEI–CBA copolymers differing in molecular weights (from 8.6 to 37 kDa) showed good plasmid DNA binding ability resulting in compact 90- to 150-nm-sized polyplexes. Colloidal stability of the polyplexes was lost in reductive environment. A low concentration of dithiothreitol of 5 µM was sufficient to render polyplexes unstable in size. Reducing conditions at physiological salt concentration triggered polyplex dissociation. The bioreducible polymers displayed much lower cytotoxicity (IC50 ∼ 100 μg/mL in cell culture) than branched polyethylenimine 25 kDa (BPEI) and linear polyethylenimine 22 kDa (LPEI). Reporter gene transfection experiments were done with CHO-K1 and B16-F10 cells. The largest (37 kDa) copolymer HC-6-8 demonstrated highest transfection levels among all the bioreducible copolymers, which was comparable with LPEI and much more effective than BPEI.
Pilot and Data Aided Channel Estimation for OFDM systems in Rapidly Time-Varying Channels

In this paper, we propose an efficient estimation technique for time-varying multipath channels by exploiting two dimensional delay-time nature in pilot inserted orthogonal frequency division multiplexing (OFDM) systems. The proposed technique consists of multipath snapshot estimation at periodic channel observation instances over an OFDM block and the linear interpolation of two consecutive multipath snapshots. Two decision-directed data utilizing schemes, data removed and data added correlation schemes, are proposed to enhance the performance of the multipath snapshot estimation.
Physician health and wellness.

BACKGROUND Impaired physician health can have a direct impact on patient health care and safety. In the past, problems of alcoholism and substance abuse among physicians have received more attention than other conditions-usually in the form of discipline. While patient safety is paramount, the medical profession may be more successful in achieving the required standards by fostering a culture committed to health and wellness as well as supporting impaired physicians. OBJECTIVE To develop ethical guidelines regarding physician health and wellness. METHODS The American Medical Association's (AMA's) Council on Ethical and Judicial Affairs developed recommendations based on the AMA's Code of Medical Ethics, an analysis of relevant Medline-indexed articles, and comments from experts. The report's recommendations were adopted as policy of the Association in December 2003. RESULTS Individually, physicians can promote their personal health and wellness through healthy living habits, including having a personal physician. The medical profession can foster health and wellness if its members are taught to identify colleagues in need of assistance and initiate appropriate methods of intervention, including referrals to physician health programs. CONCLUSIONS Physicians whose health or wellness is compromised should seek appropriate help and engage in honest self-assessment of their ability to practice. The medical profession should provide an environment that helps to maintain and restore health and wellness. Physicians need to ensure that impaired colleagues promptly modify or cease practice until they can resume professional patient care. In addition, physicians may be required to report impaired colleagues who continue to practice despite reasonable offers of assistance.
Older people's experiences of acute hospitalisation: an investigation of how occupations are affected.

BACKGROUND/AIM Few qualitative studies have investigated older people's experiences of hospital admission and none has done so from an occupational perspective. The purpose of this study was to examine older people's experience of acute hospitalisation. METHODS In-depth semi-structured interviews were conducted with six participants recruited from the Alfred hospital, Melbourne, Victoria. Data were analysed using Colaizzi's (1978) approach to phenomenological analysis. RESULTS Five themes describing older people's experience of acute hospitalisation emerged from the analysis: (i) not part of 'normal life'; (ii) undesirable, but for the good of my health; (iii) understanding my condition and abilities; (iv) subject to approval; and (v) getting back into life. The importance of the individual's occupational narrative emerged as a central theme in understanding the older person's experience of acute hospitalisation. CONCLUSIONS Occupational therapists have a unique contribution to make in encouraging meaningful occupation on hospital wards. Identifying the manner by which occupational therapists can most effectively implement the assessment of occupational performance in the acute care setting should constitute a research priority for future investigations.
Inflammatory biomarkers and the prediction of coronary events among people at intermediate risk: the EPIC-Norfolk prospective population study

Objective: To evaluate the role of the inflammatory biomarkers C-reactive protein (CRP), myeloperoxidase, paraoxonase, secretory phospholipase A2 group IIA (sPLA2), lipoprotein-associated phospholipase A2, fibrinogen, macrophage chemoattractant protein-1 and adiponectin, in predicting the risk of coronary heart disease (CHD) among people estimated to be at intermediate risk according to the Framingham Risk Score (FRS). Design: Prospective case–control study nested in EPIC-Norfolk cohort. Setting: Norfolk, UK. Patients: Apparently healthy men and women aged 45–79 years. Main outcome measures: Risk of future coronary artery disease. Results: For participants predicted to be at intermediate risk by the FRS, the highest c statistics were observed for FRS plus CRP (0.61, 95% CI 0.57 to 0.65) and for FRS plus sPLA2 (0.56, 95% CI 0.52 to 0.6). Net correct reclassification of cases and controls for each marker was assessed for people across the entire risk spectrum and again for people at intermediate risk only. The largest differences were observed for CRP, 12.0% net reclassification improvement in the entire risk spectrum and 28.4% net reclassification improvement in the intermediate-risk group and for sPLA2, the net reclassification improvement was 6.4% in the entire risk spectrum and 16.3% in the intermediate-risk group. Conclusions: The discriminatory potential of inflammatory biomarkers was substantially different when analysed across the entire risk spectrum compared with the subgroup of people at intermediate risk.
INNOVATION, PUBLIC POLICY AND PUBLIC SERVICES DELIVERY IN THE UK. THE WORD THAT WOULD BE KING?

This paper explores the dialogue about innovation in public services currently found within public policy and creates an interaction between research and practice about its strengths and limitations. It argues that this dialogue is a flawed one, often both at odds with the existing evidence and lacking a holistic understanding of the nature of innovation and its distinctive policy and managerial challenges. It therefore synthesizes existing research to challenge current public policy thinking about the role and determinants of innovation in public services. It concludes by offering five lessons towards effective policy-making and implementation that would provide a more sophisticated and evidence-based approach to the encouragement and sustenance of public service innovation – and four key areas for further research.
IP Security (IPsec) and Internet Key Exchange (IKE) Document Roadmap

Over the past few years, the number of RFCs that define and use IPsec and IKE has greatly proliferated. This is complicated by the fact that these RFCs originate from numerous IETF working groups: the original IPsec WG, its various spin-offs, and other WGs that use IPsec and/or IKE to protect their protocols' traffic. This document is a snapshot of IPsec- and IKE-related RFCs. It includes a brief description of each RFC, along with background information explaining the motivation and context of IPsec's outgrowths and extensions. It obsoletes the previous IPsec Document Roadmap [RFC2411].
N-(2,3-Dimethylphenyl)-4-hydroxy-2-methyl-2H-1,2-benzothiazine-3-carboxamide 1,1-dioxide

In the crystal structure of the title compound, C18H18N2O4S, the thiazine ring adopts a distorted half-chair conformation. 1,2-Benzothiazines of this kind have a wide range of biological activities and are mainly used as medicines in the treatment of inflammation and rheumatoid arthritis. The enolic H atom is involved in an intramolecular O—H⋯O hydrogen bond, forming a six-membered ring. The molecules arrange themselves into centrosymmetric dimers by means of intermolecular N—H⋯O hydrogen bonds. A weak intermolcular C—H⋯O interaction is also present.
Applications of Economic and Pricing Models for Resource Management in 5G Wireless Networks: A Survey

This paper presents a comprehensive literature review on applications of economic and pricing theory for resource management in the evolving fifth generation (5G) wireless networks. The 5G wireless networks are envisioned to overcome existing limitations of cellular networks in terms of data rate, capacity, latency, energy efficiency, spectrum efficiency, coverage, reliability, and cost per information transfer. To achieve the goals, the 5G systems will adopt emerging technologies such as massive multiple-input multiple-output, mmWave communications, and dense heterogeneous networks. However, 5G involves multiple entities and stakeholders that may have different objectives, e.g., high data rate, low latency, utility maximization, and revenue/profit maximization. This poses a number of challenges to resource management designs of 5G. While the traditional solutions may neither efficient nor applicable, economic and pricing models have been recently developed and adopted as useful tools to achieve the objectives. In this paper, we review economic and pricing approaches proposed to address resource management issues in the 5G wireless networks including user association, spectrum allocation, and interference and power management. Furthermore, we present applications of economic and pricing models for wireless caching and mobile data offloading. Finally, we highlight important challenges, open issues and future research directions of applying economic and pricing models to the 5G wireless networks.
Saline groundwater management and optimal cropping pattern

ABSTRACT In areas having scarce canal water and poor quality groundwater, an opportunity exists to use the two sources conjunctively for irngation water supply. However, the use of saline water, either in isolation or by mixing with canal water, threatens soil salinization, unless steps are taken to protect the salt balance in the root zone. A deterministic linear programming model has been developed, incorporating both leaching requirements and the salinity response function of crops, to find the optimal cropping pattern and optimum use of saline groundwater. The model was applied to a canal command area.
Categorical versus continuous risk factors and the calculation of potential impact fractions

Background The potential impact fraction is a measure of effect that calculates the proportional change in disease risk after a change in the exposure of a related risk factor. Potential impact fractions are increasingly used to calculate attributable fractions when the lowest exposure is non-zero. Methods Risk-factor exposure can be expressed as a categorical or a continuous variable. For a categorical risk factor, a change in risk-factor exposure can be expressed as a change in the proportion of the population in each category (‘proportions shift’). For a continuous risk factor, the change is expressed as a change in its parameters (‘distribution shift’). A third method (‘RR shift’) takes elements of both the categorical and the continuous approach. We compare the three calculation methods using hypothetical data on BMI and an intervention that affects the obese category. Results The ‘proportion shift’ calculation produces non-linear artefacts and is best avoided. The ‘RR shift’ and ‘distribution shift’ calculation require the estimation of an RR function to describe excess risk, but perform much better. Conclusion The ‘proportion shift’ calculation is best avoided. The ‘RR shift’ and ‘distribution shift’ calculation produce virtually the same results. For evaluating high-risk strategies, the ‘RR shift’ calculation is the simplest and therefore preferred. The ‘distribution shift’ is best suited for evaluating population strategies.
The Effects of Party Campaign Spending Under Proportional Representation: Evidence from Germany

Most of the literature investigating the effects of campaign spending on electoral outcomes focuses on individual candidates in majoritarian systems. This paper contributes to the literature on the effectiveness of party campaign spending on party vote shares under systems of proportional representation. German data are used to test several hypotheses derived from a simple election contest model. The results are mixed and only partially support the hypothesis of a positive effect of campaign spending on a party's vote share.
Key genes of the sex pheromone biosynthesis pathway in female moths are required for pheromone quality and possibly mediate olfactory plasticity in conspecific male moths in Spodoptera litura

Ninety sex pheromone biosynthesis genes in Spodoptera litura were identified in transcriptome data and were investigated and classified into the following five groups: fatty acid synthase, beta oxidase, fatty acyl‐coenzyme A (CoA) reductase, desaturase and acetyl‐CoA acetyltransferase. Fourteen female‐specific genes were identified through semi‐quantitative PCR, and 15 additional genes had expression levels that were 3‐ to 10‐fold higher in females than in males. The majority of the genes had higher expression levels in the sex pheromone glands. Injection of double‐stranded RNA (dsRNA) against nine selected genes showed that down‐regulation of Desaturase 3 (Des3), Des5 or fatty acyl coenzyme A reductase 17 (FAR17) significantly changed the ratio of the four sex pheromone components (Z,E) ‐9,11‐tetradecadienyl acetate (Z9E11‐14:Ac), (Z,E)‐9,12‐Tetradecadienyl acetate(Z9E12–14:Ac), (Z)‐9‐tetradecenyl acetate (Z9‐14:Ac), (E)‐11‐Tetradecenyl acetate(E11–14:Ac). These key genes were differentially expressed in female moths collected from different geographical regions. Furthermore, field bioassays demonstrated geographical variation in the olfactory profile of male moths in response to the different sex pheromone mixtures, which therefore indicates that a significant variation in the sex pheromone components exists in the natural population. Our results suggest that a change in the expression of these key genes, Des3, Des5 and FAR17, in the sex pheromone biosynthesis pathway could change the ratio of the sex pheromone components. We surmise that the differential expression levels of the key genes of the sex pheromone biosynthesis pathway may lead to differential ratios of the sex pheromones in the field. Our field trapping experiment suggested that the change of the ratio of the sex pheromone components may have been adapted by the olfactory system and possibly mediate olfactory plasticity in conspecific male moths.
A New Streaming Media Network Architecture Based on the Fusion of P2P and CDN

A new streaming media network-architecture based on the fusion of P2P and CDN is proposed in this paper. It uses P2P network as the backbone, selects nodes of high-performance, high-bandwidth, and stable online time as CDN edge servers, and provides non-P2P users with streaming media services under the schedule of the load-balancing servers. Since P2P has the inherent drawback of flow disorder, an optimized idea of P4P has been introduced into P2P network in this architecture to make the flow ordered. Theoretical analysis and experimental results show that this architecture has optimized P2P network with higher transmission efficiency, lower bandwidth utilization of the backbone network and lower cost and fewer resources to provide streaming media services as higher network scalability and quality as possible. Compared to the current existing "P2P+CDN" network architecture, it has lower expansion cost and higher scalability as well as robustness.
DIPLOMO: the tool for a new type of evolutionary analysis

A package of computer programs called DIPLOMO (DIstance PLOt MOnitor) has been developed for making pairwise comparisons of different estimates of the distances between a set of taxa by plotting them against each other in a simple scatter plot. Taxa with similar relative distance characteristics are thereby grouped graphically. Groupings of different taxa may be directly identified, and the distance characteristics of chosen groups visualised and compared using devices to give them different colours or symbols. The program is particularly useful for detecting and analysing subtle trends in gene sequence evolution. This is done by comparing different components of change, for example synonymous versus non-synonymous nucleotide changes, transversions versus transitions and changes in different genes of the same set of taxa, etc. The program has a wide range of other uses, for example comparing different methods of sequence analysis, assessing which components of genetic change correlate best with phenotypic change or with geographical separation. This paper describes the DIPLOMO package, and illustrates typical DIPLOMO analyses using lentivirus gene sequence data.
Measuring value progress in outsourcing organizations

Purpose – The purpose of this paper is to develop and validate a scale for measuring value progress in outsourcing organizations. The scale is also intended to capture the differences in the nature of progress between different categories of outsourcing organizations.Design/methodology/approach – The procedure for developing measures suggested by Churchill was adopted. The balanced scorecard framework has been used to generate items. Data were collected from 693 employees in 49 outsourcing organizations in India (specifically, those categorized as knowledge process outsourcing (KPO) and business process outsourcing (BPO)) and the scale reliability and validity was tested using content validity, exploratory and confirmatory factor analysis, and co‐efficient alpha scores. Confirmatory fit indices have been used to establish validity and unidimensionality of the measures.Findings – The study statistically establishes a tool to measure progress of outsourcing organizations. The findings reveal that some organ.
The Roles that Forecast Surprise and Forecast Error Play in Determining Management Forecast Precision

SYNOPSIS: Studying the determinants of management forecast precision is important because a better understanding of the factors affecting management’s choice of forecast precision can provide investors and other users with cues about the characteristics of the information contained in the forecasts. In addition, as regulators assess the regulation of voluntary management disclosures, they need to better understand how managers choose among forecast precision disclosure alternatives. Using 16,872 management earnings forecasts collected from 1995 through 2004, we provide strong evidence that forecast precision is negatively associated with the magnitude of the forecast surprise and that this negative association is stronger when the forecast is bad news than when it is good news. We also find that forecast precision is negatively associated with the absolute magnitude of the forecast error that proxies for the forecast uncertainty that managers face when they issue forecasts, and that the negative associati.