nils-herrmann/clean_scirepeval huggingface dataset:
Improving sensitivity of linear regression based cell type specific differential expression deconvolution with per gene vs. global significance threshold
Venue: BMC Bioinformatics

BackgroundThe goal of many human disease oriented studies is to detect molecular mechanisms different between healthy controls and patients. Yet, commonly used gene expression measurements from blood samples suffer from variability of cell composition. This variability hinders the detection of differentially expressed genes and is often ignored. Combined with cell counts, heterogeneous gene expression may provide deeper insights into the gene expression differences on the cell type specific level.Published computational methods use linear regression to estimate cell type specific differential expression, and a global cutoff to judge significance, such as False Discovery Rate (FDR) Yet, they do not consider many artifacts hidden in high dimensional gene expression data that may negatively affect linear regression. In this paper we quantify the parameter space affecting the performance of linear regression (sensitivity of cell type specific differential expression detection) on a per gene basis.ResultsWe evaluated the effect of sample sizes, cell type specific proportion variability, and mean squared error on sensitivity of cell type specific differential expression detection using linear regression. Each parameter affected variability of cell type specific expression estimates and, subsequently, the sensitivity of differential expression detection. We provide the R package, LRCDE, which performs linear regression based cell type specific differential expression (deconvolution) detection on a gene by gene basis. Accounting for variability around cell type specific gene expression estimates, it computes per gene t statistics of differential detection, p values, t statistic based sensitivity, group specific mean squared error, and several gene specific diagnostic metrics.ConclusionsThe sensitivity of linear regression based cell type specific differential expression detection differed for each gene as a function of mean squared error, per group sample sizes, and variability of the proportions of target cell (cell type being analyzed) We demonstrate that LRCDE, which uses Welch's t test to compare per gene cell type specific gene expression estimates, is more sensitive in detecting cell type specific differential expression at a 0.05 missed by the global false discovery rate threshold FDR 0.3.
Enumerateblood an R package to estimate the cellular composition of whole blood from Affymetrix Gene ST gene expression profiles
Venue: BMC Genomics

BackgroundMeasuring genome wide changes in transcript abundance in circulating peripheral whole blood is a useful way to study disease pathobiology and may help elucidate the molecular mechanisms of disease, or discovery of useful disease biomarkers. The sensitivity and interpretability of analyses carried out in this complex tissue, however, are significantly affected by its dynamic cellular heterogeneity. It is therefore desirable to quantify this heterogeneity, either to account for it or to better model interactions that may be present between the abundance of certain transcripts, specific cell types and the indication under study. Accurate enumeration of the many component cell types that make up peripheral whole blood can further complicate the sample collection process, however, and result in additional costs. Many approaches have been developed to infer the composition of a sample from high dimensional transcriptomic and, more recently, epigenetic data. These approaches rely on the availability of isolated expression profiles for the cell types to be enumerated. These profiles are platform specific, suitable datasets are rare, and generating them is expensive. No such dataset exists on the Affymetrix Gene ST platform.ResultsWe present 'Enumerateblood' a freely available and open source R package that exposes a multi response Gaussian model capable of accurately predicting the composition of peripheral whole blood samples from Affymetrix Gene ST expression profiles, outperforming other current methods when applied to Gene ST data.Conclusions'Enumerateblood' significantly improves our ability to study disease pathobiology from whole blood gene expression assayed on the popular Affymetrix Gene ST platform by allowing a more complete study of the various components of this complex tissue without the need for additional data collection. Future use of the model may allow for novel insights to be generated from the ~400 Affymetrix Gene ST blood gene expression datasets currently available on the Gene Expression Omnibus (GEO) website.
Emerging Issues in Diagnosis, Biology, and Inhibitor Risk in Mild Hemophilia A.
Venue: Seminars in thrombosis and hemostasis

Mild hemophilia A (MHA) is an X linked bleeding disorder defined by factor VIII (FVIII) levels between 5 and 40 U/dL. Diagnosis occurs later in life compared with severe or moderate disease. Although bleeding episodes are especially posttraumatic, their unexpected occurrence may be potentially life threatening if diagnosis is missed or delayed. Desmopressin is the treatment of choice for MHA since it is cheap and safe, but a significant proportion of cases do not attain FVIII postinfusion greater than 50 U/dL, which is considered a safe level for major surgery. Thus, replacement therapy may be needed and is usually successful in MHA, but recent data indicate that this can be associated with the occurrence of inhibitors against FVIII, as for severe hemophilia A. However, in contrast to severe or moderate hemophilia A, patients with MHA have a lifelong risk of inhibitor formation. Inhibitors may change the clinical phenotype dramatically, as the inhibitor frequently cross reacts with the patient's endogenous FVIII, reducing the endogenous FVIII plasma levels below 1 U/dL. Specific F8 missense mutations predispose to inhibitor development. Inhibitors are frequently provoked by intensive treatment with therapeutic FVIII concentrates (more than 5 consecutive exposure days) Bleeding in inhibitor patients may be treated with desmopressin, high doses of FVIII concentrate or FVIII bypassing agents. Many inhibitors disappear over time when no FVIII concentrate is administered. However, this does not imply that a patient is tolerant and an anamnestic reaction may occur when treatment with FVIII concentrate is again necessary. To eradicate, an inhibitor different strategies may be used: watchful waiting, immunosuppression, or immune tolerance induction regimen.
Ambient Backscatter Communication Systems: Detection and Performance Analysis
Venue: IEEE Transactions on Communications

Ambient backscatter technology that utilizes the ambient radio frequency signals to enable the communications of battery free devices has attracted much attention recently. In this paper, we study the problem of signal detection for an ambient backscatter communication system that adopts the differential encoding to eliminate the necessity of channel estimation. Specifically, we formulate a new transmission model, design the data detection algorithm, and derive two closed form detection thresholds. One threshold is used to approximately achieve the minimum sum bit error rate (BER) while the other yields balanced error probabilities for "0" bit and "1" bit. The corresponding BER expressions are derived to fully characterize the detection performance. In addition, the lower and the upper bounds of BER at high signal to noise ratio regions are also examined to simplify a performance analysis. Simulation results are then provided to corroborate the theoretical studies.
The Save KPK Movement: A Framing Analysis of Coverage in Indonesian News Media Surrounding the KPK and Police Dispute

Previous studies focusing on protest and social movement mostly concern identifying marginalization strategies that the media used to delegitimize the movement. This study attempted to examine how Indonesian mainstream media framed the Save KPK movement which emerged as a result of the dispute between the KPK and the Police. This study viewed these two institutions as collective and competing actors that represent certain interests and pursue the legality of their actions. In particular, this study proposed a typology of five framing devices used in the coverage of the Save KPK movement and explored the occurrence of framing strategies and the overall tone of the news coverage of the movement. A total of 246 articles on the Save KPK Movement was derived from the two most influential elite newspapers in Indonesia: the Kompas and the Media Indonesia. The Media Indonesia had 138 articles, while the Kompas published 108 articles. The results show that conflict, morality, and responsibility are the three framing devices mostly used in media coverage of the Save KPK movement. Further, the results demonstrated that the social movement organizations seem to be successful in the process of diagnostic, prognostic, and motivational framing. The results of this study provide more insight concerning framing strategies and media contents could be applied to be effective in shaping public opinion. In particular, the results highlight the positive side of the social movement organizations and their actions could strengthen the support of the public for the consequences of that target group.
Frequency domain ultrasound waveform tomography breast attenuation imaging
Venue: SPIE Medical Imaging

Ultrasound waveform tomography techniques have shown promising results for the visualization and characterization of breast disease. By using frequency domain waveform tomography techniques and a gradient descent algorithm, we have previously reconstructed the sound speed distributions of breasts of varying densities with different types of breast disease including benign and malignant lesions. By allowing the sound speed to have an imaginary component, we can model the intrinsic attenuation of a medium. We can similarly recover the imaginary component of the velocity and thus the attenuation. In this paper, we will briefly review ultrasound waveform tomography techniques, discuss attenuation and its relations to the imaginary component of the sound speed, and provide both numerical and ex vivo examples of waveform tomography attenuation reconstructions.
Mammary gland segmentation using intensity correction for brightness attenuation in breast ultrasound image
Venue: 2016 IEEE International Conference on Imaging Systems and Techniques (IST)

This paper presents a method of segmenting mammary gland tissue for breast ultrasound images. In order to improve the quality of diagnoses for breast ultrasound screening, Computer Aided Detection (CADe) systems have been developed by a number of researchers. However, such systems suffer in terms of making many false positives for non mammary gland tissue where no cancer exists. Accordingly, it is necessary to accurately determine the area of mammary gland tissue within ultrasound images for CADe systems. In this study, we propose a method of segmenting mammary gland tissue from ultrasound images for breasts. Within ultrasound images, brightness is attenuated as ultrasound waves move from the ultrasound probe to internal tissue. Accordingly, we correct intensity (brightness) using zero phase component analysis (ZCA) whitening in order to reduce such brightness attenuation. Moreover, we apply a Conditional Random Field (CRF) which can render as smooth the region boundary of ultrasound images. The results of an experiment, conducted with five target patients to verify the effectiveness of the proposed methods, demonstrate that the method is capable of segmenting mammary gland tissue from breast ultrasound images.
Coital Urinary Incontinence Induced by Impairment of the Dorsal Nerve of the Clitoris in Rats.
Venue: The Journal of urology

We determined the effect of chronic bilateral neurectomy of the dorsal nerve of the clitoris on urinary parameters and sexual behavior of conscious female rats.  A total of 18 anesthetized virgin female Wistar rats were used in this study, including 11 that underwent bilateral neurectomy of the dorsal nerve of the clitoris and 7 that underwent sham surgery. Urinary parameters were determined in awake animals preoperatively, and 3 and 10 days postoperatively. Sexual behavior was tested 14 days postoperatively to determine whether the females expelled urine during sexual encounters. After male ejaculation the females were anesthetized with urethane to record external urethral sphincter electromyogram activity in response to clitoris, perigenital skin and vaginal stimulation. Neurectomy was corroborated anatomically.  Sham surgery did not significantly modify urinary parameter values. However, bilateral neurectomy of the dorsal nerve of the clitoris significantly increased voiding frequency and voiding duration (p <0.05) It did not significantly affect the flow rate, voided volume or voiding interval. Of females that underwent bilateral neurectomy of the dorsal nerve of the clitoris 67% expelled urine just after male ejaculation.  These results suggest that the pudendal nerve is an important neural pathway in the convergence and crosstalk of female urogenital neural circuits, and genital deafferentation may be a causal factor of coital urinary incontinence. Rats with bilateral transection of the dorsal nerve of the clitoris may serve as an animal model of coital incontinence.
Should the Clitoris become a Vestigial Organ by Personal Psychological Clitoridectomy? A Critical Examination of the Literature

Should the Clitoris become a Vestigial Organ by Personal 'Psychological Clitoridectomy' A Critical Examination of the Literature An extensive series of papers by Brody and co workers using questionnaires have correlated penile vaginal intercourse (PVI) and clitoral stimulation with various female functions and malfunctions. A major claim is that only PVI 'competently performed and sensitively experienced' leading to orgasm is 'associated with, and in some cases, causes processes associated with better psychological and physical functioning' Clitoral stimulation to orgasm per se or to facilitate orgasm even during PVI, however, is not beneficial to women's, psychological, interpersonal or behavioural health and can lead to 'noxious consequences' Recently, as correlations are no guarantee of causation, independent studies have not confirmed some of their claims.
The Scary World of Online News? Internet News Exposure and Public Attitudes Toward Crime and Justice

A substantial body of literature indicates that certain forms of media consumption may increase anxiety about crime and support for social controls. However, few studies have examined whether Internet news consumption is positively associated with such attitudes. The void is significant given the public's increasing use of online news sources. This study addresses this research gap.MethodsWe draw on data from four national surveys conducted between 2007 and 2013, which collectively include interviews with more than 13,000 Americans. Using OLS and logistic regression, we assess the relationships between exposure to traditional and online media and perceptions of victimization risk, support for punitive crime policies, and views about police powers.ResultsConsistent with prior work, we find positive relationships between exposure to traditional forms of media television news and crime programming and anxiety about victimization and support for harsh crime policies. In contrast, Internet news exposure is generally not associated with anxieties about crime or support for getting tough on criminals. However, there is evidence of an interactive relationship between political ideology and Internet news exposure.ConclusionsThe results provide little support for cultivation theory in the context of Internet news consumption. We discuss the import of our findings, and suggest new lines of research to explore the correlates and the effects of exposure to online news sources.
The internet and racial hate crime: offline spillovers from online access

This research note reports on an empirical investigation of the effect of the Internet on racial hate crimes in the United States from the period 2001 2008. We find evidence that, on average, broadband availability increases racial hate crimes. We also document that the Internet's impact on these hate crimes is not uniform in that the positive effect is stronger in areas with higher levels of racism, which we identify as those with more segregation and a higher proportion of racially charged search terms, but not significant in areas with lower levels of racism. We analyze in depth whether Internet access will enhance hate group operations but find no support for the idea that this mechanism is driving the result. In contrast, we find that online access is increasing the incidence of racial hate crimes executed by lone wolf perpetrators. Several other mechanisms that could be driving the results are described. Overall, our results shed light on one of the many offline societal challenges from increased online access.
Development of sensor surfaces using poly (N vinylformamide) for sensitive detection of 2,4,6 trinitrotoluene by displacement method on a surface plasmon resonance sensor

To detect 2,4,6 trinitrotoluene (TNT) using a displacement method over a surface plasmon resonance immunosensor, we developed sensor surfaces modified with a poly (N vinylformamideco vinylamine) which was synthesized from a monomer, N vinylformamide, and was hydrolyzed to produce amine groups, and TNT analogs. Poly (N vinylformamide co vinylamine) that reacted with succinic acid was used as a matrix of a sensor surface for increasing the number of antibody binding sites. 2,4 Dinitrophenyl glycine, 3 nitrophenyl acetic acid, and 4 nitrophenyl acetic acid were immobilized on the polymer modified sensor surfaces. We evaluated the suppression ability of the sensor surface for nonspecific adsorption and determined the limit of detection (LOD) for TNT. As a result, a sensor chip suppressed nonspecific adsorption for 1 mg/mL bovine serum albumin and lysozyme. TNT was measured by the displacement method, and the LOD achieved over a 3 nitrophenyl acetic acid modified sensor chip was 0.9 ng/mL (ppb)
Creating Marketing Strategies for Development of the Wine Tourism

The development of the wine tourism every day is meaningful on a global level. This fact makes the paper to draw attention on the creation of marketing strategies in order to increase the visibility of our country worldwide. Today to gain the trust and the loyalty of the consumers is very difficult; it should be accessed new, specific spaces as well as new ways of a presentation of the tourism products. This paper outlines the creation of effective strategies to achieve competitive advantage in the global wine tourism market. In the paper are set out the conditions and prospects of the wine tourism of Republic of Macedonia through proper analysis. Based on the presented results measures are proposed to create a successful strategy for the development of the wine tourism, which will improve the competitive position.
A Hybrid Decision Making Model for Maintenance Prioritization in Health Care Systems

Clinical engineering departments have to establish and continuously regulate a Medical Equipment Management Program (MEMP) to ensure a high reliability and safety of their critical medical devices. Asset criticality assessment is an essential element of reliability centered maintenance and risk based maintenance, especially when enormous various devices exist and the worst failure consequences are not evident. This paper presents a new risk based prioritization framework for maintenance decisions. We propose a Multi Expert Multi Criteria decision making (MEMC) model to classify medical devices according to their criticality and we describe how obtained scores are used to set up guidelines for appropriate maintenance strategies.
Active Learning Strategies and Instructor Presence in An Online Research Methods Course: Can we Decrease Anxiety and Enhance Knowledge?

Research methods courses elicit more anxiety than usual for graduate social work students, and the online environment may pose an even greater challenge as the personal interaction between instructor and student is reduced or absent. It is therefore incumbent on research instructors to creatively engage students, reduce anxiety, and foster learning. There is a dearth of evidence, particularly regarding online education, explicating specific teaching strategies. This exploratory study sought to provide some answers. First semester MSW students were invited to participate in a voluntary, anonymous, online survey at the end of a research methods course to determine which online teaching strategies were most effective in decreasing anxiety and increasing perception of knowledge. Strategies used in the class include asynchronous activities such as discussion questions, PowerPoint lectures, and email and telephone contact with instructors in addition to synchronous class sessions. Three tactics were rated by the 43 respondents as being most helpful for both decreasing anxiety and enhancing the perception of knowledge: personal contact with the instructor either via email, phone, and/or online meetings; the instructor's synchronous class sessions; and active learning strategies employed during the synchronous class sessions. Implications for teaching and future research are discussed.
Overview of the Macedonian Policy Analysis Model (MAKPAM)

This paper describes the Macedonian Policy Analysis Model (MAKPAM) which is used at the National Bank of the Republic of Macedonia (NBRM) for medium term macroeconomic forecasting and policy analysis. The MAKPAM is a medium scale, New Keynesian gap model that incorporates the key characteristics of the Macedonian economy: a small open economy with a fixed exchange rate regime. This model outlines the transmission mechanism of the monetary policy in the Macedonian economy, and it helps to quantify the reaction of the economy to various shocks. Since 2008, the MAKPAM model has gradually become an important block of the macroeconomic forecasting system of the NBRM. The model is therefore an important analytic tool for supporting the monetary policy decision making of the NBRM.
Eunomos, a legal document and knowledge management system for the Web to provide relevant, reliable and up to date information on the law
Venue: Artificial Intelligence and Law

This paper describes the Eunomos software, an advanced legal document and knowledge management system, based on legislative XML and ontologies. We describe the challenges of legal research in an increasingly complex, multi level and multi lingual world and how the Eunomos software helps users cut through the information overload to get the legal information they need in an organized and structured way and keep track of the state of the relevant law on any given topic. Using NLP tools to semi automate the lower skill tasks makes this ambitious project a realistic commercial prospect as it helps keep costs down while at the same time allowing greater coverage. We describe the core system from workflow and technical perspectives, and discuss applications of the system for various user groups.
Robotics and law: Key legal and regulatory implications of the robotics age (Part I of II)
Venue: Comput. Law Secur. Rev.

In the previous edition of this special series on robotics and law, we explored some of the legal, regulatory and ethical implications of robotic systems and applications. We continue on that theme in this edition, focusing on specific types of robotic systems (medical device robots and nanorobotics) and core legal and regulatory issues, including intellectual property, employment and cyber security. In exploring these areas, our objective remains to start a dialogue about how our existing legal frameworks might need to adapt and change to meet the demands of the robotics age. We then conclude this special series with our views on the future of robotics law and the development of legal practice in this area.