LLukas22/scidocs huggingface dataset:
Two-dimensional longitudinal strain assessment in the presence of myocardial contrast agents is only feasible with speckle-tracking after microbubble destruction.

BACKGROUND
Longitudinal strain (LS) imaging is an important tool for the quantification of left ventricular function and deformation, but its assessment is challenging in the presence of echocardiographic contrast agents (CAs). The aim of this study was to test the hypothesis that destruction of microbubbles using high mechanical index (MI) could allow the measurement of LS.


METHODS
LS was measured using speckle strain (speckle-tracking LS [STLS]) and Velocity Vector Imaging (VVI) before and after CA administration in 30 consecutive patients. Low MI was used for left ventricular opacification and three-dimensional high MI for microbubble destruction. Four different settings were tested over 60 sec: (1) baseline LS without contrast, (2) LS after CA administration with low MI (0.3), (3) LS after CA administration with high MI (0.9), and (4) LS after microbubble destruction with high MI and three-dimensional imaging.


RESULTS
Baseline feasibility of LS assessment (99.3% and 98.2% with STLS and VVI, respectively) was reduced after CA administration using STLS at low (69%, P < .0001) and high (95.4%, P = .0002) MI as well as with VVI (93.8%, P = .004, and 84.7%, P < .0001, respectively). STLS assessment was feasible with high MI after microbubble destruction (1.7% of uninterpretable segments vs 0.7%, P = .26) but not using VVI (7.2% vs 1.8%, P < .001). Regardless of which microbubbles or image settings were used, VVI was associated with significant variability and overestimation of global LS (for low MI, +4.7%, P < .01; for high MI, +3.3%, P < .001; for high MI after microbubble destruction, +1.3%, P = .04).


CONCLUSIONS
LS assessment is most feasible without contrast. If a CA is necessary, the calculation of LS is feasible using the speckle-tracking method, if three-dimensional imaging is used as a tool for microbubble destruction 1 min after CA administration.
Anatomy of the clitoris.

PURPOSE
We present a comprehensive account of clitoral anatomy, including its component structures, neurovascular supply, relationship to adjacent structures (the urethra, vagina and vestibular glands, and connective tissue supports), histology and immunohistochemistry. We related recent anatomical findings to the historical literature to determine when data on accurate anatomy became available.


MATERIALS AND METHODS
An extensive review of the current and historical literature was done. The studies reviewed included dissection and microdissection, magnetic resonance imaging (MRI), 3-dimensional sectional anatomy reconstruction, histology and immunohistochemical studies.


RESULTS
The clitoris is a multiplanar structure with a broad attachment to the pubic arch and via extensive supporting tissue to the mons pubis and labia. Centrally it is attached to the urethra and vagina. Its components include the erectile bodies (paired bulbs and paired corpora, which are continuous with the crura) and the glans clitoris. The glans is a midline, densely neural, non-erectile structure that is the only external manifestation of the clitoris. All other components are composed of erectile tissue with the composition of the bulbar erectile tissue differing from that of the corpora. The clitoral and perineal neurovascular bundles are large, paired terminations of the pudendal neurovascular bundles. The clitoral neurovascular bundles ascend along the ischiopubic rami to meet each other and pass along the superior surface of the clitoral body supplying the clitoris. The neural trunks pass largely intact into the glans. These nerves are at least 2 mm in diameter even in infancy. The cavernous or autonomic neural anatomy is microscopic and difficult to define consistently. MRI complements dissection studies and clarifies the anatomy. Clitoral pharmacology and histology appears to parallel those of penile tissue, although the clinical impact is vastly different.


CONCLUSIONS
Typical textbook descriptions of the clitoris lack detail and include inaccuracies. It is impossible to convey clitoral anatomy in a single diagram showing only 1 plane, as is typically provided in textbooks, which reveal it as a flat structure. MRI provides a multiplanar representation of clitoral anatomy in the live state, which is a major advantage, and complements dissection materials. The work of Kobelt in the early 19th century provides a most comprehensive and accurate description of clitoral anatomy, and modern study provides objective images and few novel findings. The bulbs appear to be part of the clitoris. They are spongy in character and in continuity with the other parts of the clitoris. The distal urethra and vagina are intimately related structures, although they are not erectile in character. They form a tissue cluster with the clitoris. This cluster appears to be the locus of female sexual function and orgasm.
The OCRopus open source OCR system

OCRopus is a new, open source OCR system emphasizing modularity, easy extensibility, and reuse, aimed at both the research community and large scale commercial document conversions. This paper describes the current status of the system, its general architecture, as well as the major algorithms currently being used for layout analysis and text line recognition.
THE SIMILARITY OF XML-BASED DOCUMENTS IN FINDING THE LEGAL INFORMATION

In this paper, we propose to integrate semantic similarity assessment in an edit distance algorithm, seeking to amend similarity judgments when comparing XML-based legal documents[3].
Perinatal probiotic supplementation in the prevention of allergy related disease: 6 year follow up of a randomised controlled trial

BACKGROUND
Perinatal probiotics supplementation has been shown to be effective in the primary prevention of atopic dermatitis (AD) in early childhood, although the long term effects of probiotics on AD and other allergic diseases is less certain. We have previously reported a significant reduction in the cumulative incidence of AD at 2 years after maternal probiotic supplementation. In this study we present the effects of perinatal probiotics given to women from a general population on allergy related diseases in their offspring at 6 years.


METHODS
Four hundred and fifteen pregnant women were randomised to receive probiotic or placebo milk in a double-blinded trial from 36 week gestation until 3 months postpartum. Probiotic milk contained Lactobacillus rhamnosos GG, L. acidophilus La-5 and Bifidobacterium animalis subsp. lactis Bb-12. At 6 years, children were re-assessed for AD, atopic sensitisation, asthma and allergic rhinoconjunctivitis (ARC).


RESULTS
At 6 years, 81 and 82 children were assessed for AD in the probiotic and placebo groups, respectively. In a multiple imputation analysis, there was as trend towards a lower cumulative incidence of AD in the probiotic group compared to the placebo group (OR 0.64, 95 % CI 0.39-1.07, p = 0.086; NNT = 10). This finding was statistically significantly in the complete case analysis (OR 0.48, 95 % CI 0.25-0.92, p = 0.027, NNT = 6). The prevalence of asthma and atopic sensitisation, and the cumulative incidence of ARC were not significantly affected by the probiotic regime at 6 years of age.


CONCLUSIONS
Maternal probiotic ingestion alone may be sufficient for long term reduction in the cumulative incidence of AD, but not other allergy related diseases.


TRIAL REGISTRATION
ClinicalTrials.gov identifier: NCT00159523.
Gene expression inference with deep learning

MOTIVATION
Large-scale gene expression profiling has been widely used to characterize cellular states in response to various disease conditions, genetic perturbations, etc. Although the cost of whole-genome expression profiles has been dropping steadily, generating a compendium of expression profiling over thousands of samples is still very expensive. Recognizing that gene expressions are often highly correlated, researchers from the NIH LINCS program have developed a cost-effective strategy of profiling only ∼1000 carefully selected landmark genes and relying on computational methods to infer the expression of remaining target genes. However, the computational approach adopted by the LINCS program is currently based on linear regression (LR), limiting its accuracy since it does not capture complex nonlinear relationship between expressions of genes.


RESULTS
We present a deep learning method (abbreviated as D-GEX) to infer the expression of target genes from the expression of landmark genes. We used the microarray-based Gene Expression Omnibus dataset, consisting of 111K expression profiles, to train our model and compare its performance to those from other methods. In terms of mean absolute error averaged across all genes, deep learning significantly outperforms LR with 15.33% relative improvement. A gene-wise comparative analysis shows that deep learning achieves lower error than LR in 99.97% of the target genes. We also tested the performance of our learned model on an independent RNA-Seq-based GTEx dataset, which consists of 2921 expression profiles. Deep learning still outperforms LR with 6.57% relative improvement, and achieves lower error in 81.31% of the target genes.


AVAILABILITY AND IMPLEMENTATION
D-GEX is available at https://github.com/uci-cbcl/D-GEX CONTACT: xhx@ics.uci.edu


SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Effect of topical capsaicin on the cutaneous reactions and itching to histamine in atopic eczema compared to healthy skin

Capsaicin (trans-8-methyl-N-vanillyl-6-nonenamide) is thought to produce analgesic and possibly also antipruritic effects when applied topically. Capsaicin 0.05% was applied three times daily over a 5-day period to the same infrascapular region. The effects of the pretreatment upon the pruritogenic and wheal and flare reactions to subsequent histamine iontophoresis (20 mC) were evaluated on the following day. The antipruritic effects of the pretreatment were compared with the effects of placebo pretreatment and no pretreatment. Wheal and flare areas were evaluated planimetrically. Itch or pain were rated every minute over a 24-min period. The areas of alloknesis, i.e. the induction of perifocal itch sensation by usually nonitching (e.g. mechanical) stimuli, were also evaluated. In control subjects, but not in atopic eczema (AE) patients, capsaicin pretreatment significantly reduced the flare area. Compared with control subjects, AE patients showed a lack of alloknesis or significantly smaller areas of alloknesis in pretreated and nonpretreated skin. In control subjects, capsaicin pretreatment significantly reduced itch sensations compared with nonpretreated skin, whereas in AE patients no differences were seen. Itch sensations in capsaicin-pretreated skin were significantly lower in control subjects than in AE patients. We conclude that capsaicin does effectively suppress histamine-induced itching in healthy skin but has less effect in AE. The diminished itch sensations and the absence of alloknesis in atopic individuals indicate that histamine is not the key factor in itching in AE.
Countering self-radicalisation

RSIS Commentaries are intended to provide timely and, where appropriate, policy relevant background and analysis of contemporary developments. The views of the authors are their own and do not represent the official position of the S.Rajaratnam School of International Studies, NTU. These commentaries may be reproduced electronically or in print with prior permission from RSIS. Due recognition must be given to the author or authors and RSIS. Please email: RSISPublication@ntu.edu.sg or call 6790 6982 to speak to the Editor RSIS Commentaries, Yang Razali Kassim.
Modelling and simulation of distributed generation system using HOMER software

A microgrid is an integrated form of Distributed Energy Resources (DERs) which are connected together to serve electrical power to the selected consumers or can exchange power with the existing utility grid under stand alone or grid connected mode. Distributed generators can provide high reliability by providing on-site generation. As a result of this many hybrid systems came in existence like PV cells, fuel cells, micro turbines, wind, diesel and small hydro systems. The distributed generation system having Photo Voltaic (PV), wind turbine and diesel generator is simulated and analyzed. This paper gives simulation results of PV-Wind-Diesel hybrid system. HOMER (Hybrid Optimization Models for Energy Resources) power optimization software by NREL (National Renewable Energy Laboratory) is used to simulate and analyze the PV-Wind-Diesel hybrid system.
Effects of running, static stretching and practice jumps on explosive force production and jumping performance.

AIM
The interaction between running, stretching and practice jumps during warm-up for jumping tests has not been investigated. The purpose of the present study was to compare the effects of running, static stretching of the leg extensors and practice jumps on explosive force production and jumping performance.


METHODS
Sixteen volunteers (13 male and 3 female) participated in five different warm-ups in a randomised order prior to the performance of two jumping tests. The warm-ups were control, 4 min run, static stretch, run + stretch, and run + stretch + practice jumps. After a 2 min rest, a concentric jump and a drop jump were performed, which yielded 6 variables expressing fast force production and jumping performance of the leg extensor muscles (concentric jump height, peak force, rate of force developed, drop jump height, contact time and height/time).


RESULTS
Generally the stretching warm-up produced the lowest values and the run or run + stretch + jumps warm-ups produced the highest values of explosive force production. There were no significant differences (p<0.05) between the control and run + stretch warm-ups, whereas the run yielded significantly better scores than the run + stretch warm-up for drop jump height (3.2%), concentric jump height (3.4%) and peak concentric force (2.7%) and rate of force developed (15.4%).


CONCLUSION
The results indicated that submaximum running and practice jumps had a positive effect whereas static stretching had a negative influence on explosive force and jumping performance. It was suggested that an alternative for static stretching should be considered in warm-ups prior to power activities.
Effectiveness and cost-effectiveness of web-based treatment for phobic outpatients on a waiting list for psychotherapy: protocol of a randomised controlled trial

BACKGROUND
Phobic disorders are highly prevalent and constitute a considerable burden for patients and society. As patients wait for face-to-face psychotherapy for phobic disorders in outpatient clinics, this time can be used for guided self-help interventions. The aim of this study is to investigate a five week internet-based guided self-help programme of exposure therapy in terms of clinical effectiveness and impact on speed of recovery in psychiatric outpatients, as well as the cost-effectiveness of this pre-treatment waiting list intervention.


METHODS/DESIGN
A randomised controlled trial will be conducted among 244 Dutch adult patients recruited from waiting lists of outpatient clinics for face-to-face psychotherapy for phobic disorders. Patients suffering from at least one DSM-IV classified phobic disorder (social phobia, agoraphobia or specific phobia) are randomly allocated (at a 1:1 ratio) to either a five-week internet-based guided self-help program followed by face-to-face psychotherapy, or a control group followed by face-to-face psychotherapy. Waiting list status and duration are unchanged and actual need for further treatment is evaluated prior to face-to-face psychotherapy. Clinical and economic self-assessment measurements take place at baseline, post-test (five weeks after baseline) and at 3, 6, 9 and 12 months after baseline.


DISCUSSION
Offering pre-treatment internet-based guided self-help efficiently uses time otherwise lost on a waiting list and may increase patient satisfaction. Patients are expected to need fewer face-to-face sessions, reducing total treatment cost and increasing speed of recovery. Internet-delivered treatment for phobias may be a valuable addition to psychotherapy as demand for outpatient treatment increases while budgets decrease.


TRIAL REGISTRATION
Netherlands Trial Register NTR2233.
KIT pathway alterations in mucosal melanomas of the vulva and other sites.

PURPOSE
A significant proportion of mucosal melanomas contain alterations in KIT. The aim of this study was to characterize the pattern of KIT, NRAS, and BRAF mutations in mucosal melanomas at specific sites and to assess activation of the KIT downstream RAF/MEK/extracellular signal-regulated kinase (ERK) and phosphoinositide 3-kinase (PI3K)/AKT pathways in mucosal melanoma specimens.


EXPERIMENTAL DESIGN
Seventy-one primary mucosal melanomas from various sites were studied. Mutation analysis was done by DNA sequencing. Expression of KIT, phosphorylated (p)-ERK, and p-AKT was evaluated by immunohistochemistry.


RESULTS
KIT mutations were detected in 35% (8 of 23) of vulvar, 9% (2 of 22) of anorectal, 7% (1 of 14) of nasal cavity, and 20% (1 of 5) of penile melanomas. No KIT mutations were found in 7 vaginal melanomas. The difference in KIT mutation frequency between vulvar and nonvulvar cases was statistically significant (P = 0.014). The overall frequencies of NRAS and BRAF mutations were 10% and 6%, respectively. Notably, vaginal melanomas showed a NRAS mutation rate of 43%. KIT gene amplification (≥4 copies), as assessed by quantitative real-time PCR, was observed in 19% of cases. KIT expression was associated with KIT mutation status (P < 0.001) and was more common in vulvar than nonvulvar tumors (P = 0.016). Expression of p-ERK and p-AKT was observed in 42% and 59% of tumors, respectively, and occurred irrespective of KIT/NRAS/BRAF mutation status. NRAS mutation was associated with worse overall survival in univariate analysis.


CONCLUSIONS
Results show that KIT mutations are more common in vulvar melanomas than other types of mucosal melanomas and that both the RAF/MEK/ERK and PI3K/AKT pathways are activated in mucosal melanoma specimens.
Voice and silence: Why groups take credit for acts of terror

Terrorism is designed to draw attention to particular issues and causes. Yet, the incidence of credit-taking (announcing one’s responsibility for acts of terror) varies even though anonymity can undermine the clarity of the intended messages. This article offers an explanation of the variation in credit-taking that emphasizes how the competitive context in which groups operate shapes terrorists groups’ need to cultivate support for their activities. Increasing numbers of terrorist organizations make it difficult for the supporters of terrorism to reward the perpetrators of particular attacks with their backing. Since such support is critical to the proper functioning of terrorist organizations, groups use claims of responsibility to distinguish themselves from those that had no hand in the violence. Consequently, variation in the probability of credit-taking fluctuates as a function of the number of active terrorist groups in a given theater of operations. This argument is contrasted with theories that suggest credit-taking is influenced by: the ideological mix of terrorist organizations; the willingness of governments to respond to terrorism using military force; state sponsorship; the depth of communal grievances; and the use of suicide attacks. The results, based on an analysis of transnational terrorism events conducted in the Israeli theater of operations between 1968 and 2004, suggest that competitive context is a consistently strong predictor of credit-taking. By implication, the results point to the utility of counter-terrorism strategies that interfere with the transmission of information between terrorist organizations and their supporters.
Understanding Cancer Mutations by Genome Editing

Ali, M. A. 2014. Understanding Cancer Mutations by Genome Editing. Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Medicine 1054. 37 pp. Uppsala: Acta Universitatis Upsaliensis. ISBN 978-91-554-9106-2. Mutational analyses of cancer genomes have identified novel candidate cancer genes with hitherto unknown function in cancer. To enable phenotyping of mutations in such genes, we have developed a scalable technology for gene knock-in and knock-out in human somatic cells based on recombination-mediated construct generation and a computational tool to design gene targeting constructs. Using this technology, we have generated somatic cell knock-outs of the putative cancer genes ZBED6 and DIP2C in human colorectal cancer cells. In ZBED6 cells complete loss of functional ZBED6 was validated and loss of ZBED6 induced the expression of IGF2. Whole transcriptome and ChIP-seq analyses revealed relative enrichment of ZBED6 binding sites at upregulated genes as compared to downregulated genes. The functional annotation of differentially expressed genes revealed enrichment of genes related to cell cycle and cell proliferation and the transcriptional modulator ZBED6 affected the cell growth and cell cycle of human colorectal cancer cells. In DIP2Ccells, transcriptome sequencing revealed 780 differentially expressed genes as compared to their parental cells including the tumour suppressor gene CDKN2A. The DIP2C regulated genes belonged to several cancer related processes such as angiogenesis, cell structure and motility. The DIP2Ccells were enlarged and grew slower than their parental cells. To be able to directly compare the phenotypes of mutant KRAS and BRAF in colorectal cancers, we have introduced a KRAS allele in RKO BRAF cells. The expression of the mutant KRAS allele was confirmed and anchorage independent growth was restored in KRAS cells. The differentially expressed genes both in BRAF and KRAS mutant cells included ERBB, TGFB and histone modification pathways. Together, the isogenic model systems presented here can provide insights to known and novel cancer pathways and can be used for drug discovery.
Metaheuristics in large-scale global continues optimization: A survey

Metaheuristic algorithms are extensively recognized as effective approaches for solving high-dimensional optimization problems. These algorithms provide effective tools with important applications in business, engineering, economics, and science. This paper surveys state-of-the-art metaheuristic algorithms and their current applications in the field of large-scale global optimization. The paper mainly covers the fundamental algorithmic frameworks such as decomposition and non-decomposition methods. More than 200 papers are carefully reviewed to prepare the current comprehensive survey. 2014 Published by Elsevier Inc.