LLukas22/scidocs huggingface dataset:
Ontology-centered syndromic surveillance for bioterrorism

In recent years, public health surveillance has become a priority, driven by concerns of possible bioterrorist attacks and disease outbreaks. Authorities argue that syndromic surveillance, or the monitoring of prediagnostic health-related data for early detection of nascent outbreaks, is crucial to preventing massive illness and death. Syndromic surveillance could prevent widespread illness and death, but public-health analysts face many technical barriers. To meet syndromic surveillance's complex operational and research needs, and as part of DARPA'S national biosurveillance technology program, we've developed BioSTORM (the biological spatio-temporal outbreak reasoning module). BioSTORM is an experimental end-to-end computational framework that integrates disparate data sources and deploys various analytic problem solvers to support public health analysts in interpreting surveillance data and identifying disease outbreaks. BioSTORM can help them by supporting ontology-based data integration and problem-solver deployment.
Which Noun Phrases Denote Which Concepts?

Resolving polysemy and synonymy is required for high-quality information extraction. We present ConceptResolver, a component for the Never-Ending Language Learner (NELL) (Carlson et al., 2010) that handles both phenomena by identifying the latent concepts that noun phrases refer to. ConceptResolver performs both word sense induction and synonym resolution on relations extracted from text using an ontology and a small amount of labeled data. Domain knowledge (the ontology) guides concept creation by defining a set of possible semantic types for concepts. Word sense induction is performed by inferring a set of semantic types for each noun phrase. Synonym detection exploits redundant information to train several domain-specific synonym classifiers in a semi-supervised fashion. When ConceptResolver is run on NELL’s knowledge base, 87% of the word senses it creates correspond to real-world concepts, and 85% of noun phrases that it suggests refer to the same concept are indeed synonyms.
A two-site, population-based study of barriers to cataract surgery in rural china.

PURPOSE
China has among the lowest cataract surgical rates in Asia. This study was conducted to identify barriers to cataract surgery in rural China.


METHODS
All subjects having undergone cataract surgery and persons with presenting visual acuity <or=6/60 (in Yangjiang) or <or=6/18 (in Handan) in >or=1 eye due to nonsurgically treated cataract were identified in two population-based studies in southern (Yangjiang) and northern (Handan) China. The subjects were administered a questionnaire assessing attitudes in four areas constituting potential barriers to surgery: knowledge about cataract, perceptions of local surgical quality, transportation and cost, and available resources.


RESULTS
Interviews were completed on 71% to 86% of eligible subjects in both sites. Interviewed subjects did not differ significantly from nonrespondents with regard to age, sex, and presenting acuity in the better-seeing eye. A total of 214 (80.4%) nonsurgical and 131 (76.6%) surgical participants were interviewed, with a mean age of 71.8 +/- 8.0 and 73.7 +/- 7.4 years, respectively (P > 0.1). Among the nonsurgical subjects, 67.8% were blind (presenting vision, <or=6/60) in >or=1 eye due to cataract, whereas among the surgical participants, 25.2% remained blind in the eye that had undergone surgical removal of the cataract. In a multivariate analysis adjusted for age, sex, and site, increased knowledge and higher estimates of the quality of surgery were associated with having had surgery, whereas cost and transportation scores were not.


CONCLUSIONS
Lack of knowledge about cataract and concerns about the quality of local services appear to be the principal barriers to cataract surgery in rural China.
Catheter ablation of atrial fibrillation via superior approach in patients with interruption of the inferior vena cava.

BACKGROUND
Percutaneous transcatheter ablation of atrial fibrillation (AF) in patients with interruption of inferior vena cava (IVC) has not been reported in the literature.


OBJECTIVE
The purpose of this article was to demonstrate the safety and feasibility of the superior approach via the right internal jugular vein in performing catheter ablation of AF.


METHODS
We performed AF ablation in 3 patients (mean age: 51.7 +/- 18.5 years, 2 paroxysmal AF and 1 persistent AF) with complete interruption of IVC. Transseptal puncture was performed via the right internal jugular vein with a long sheath and manually curved Brockenbrough needle to facilitate the tip downward to the FO. Three-dimensional (3D) mapping was performed in 2 patients. Electrical isolation of each pulmonary vein (PV) was confirmed by a circular mapping catheter. Bidirectional block at the RA isthmus was achieved in 1 patient with clinically documented typical atrial flutter.


RESULTS
In all patients, AF ablation after transseptal puncture via the superior approach was successfully performed without complications. Selective PV isolation of arrhythmogenic PV was done in 1 patient, and circumferential bilateral antral ablations were done in 2 patients. In 1 patient with persistent AF, linear ablations of left atrial roof and perimitral and RA isthmus were done after electrical isolation of all PVs. At a mean follow-up of 18.7 +/- 15.5 months, arrhythmias were free without any antiarrhythmic drugs in all patients.


CONCLUSION
AF ablation via the superior approach is a safe and feasible alternative technique when a femoral venous approach is not available.
Silibinin is a potent antiviral agent in patients with chronic hepatitis C not responding to pegylated interferon/ribavirin therapy.

BACKGROUND & AIMS
Oral Silibinin (SIL) is widely used for treatment of hepatitis C, but its efficacy is unclear. Substantially higher doses can be administered intravenously (IV).


METHODS
Pedigreed nonresponders to full-dose pegylated (Peg)-interferon/ribavirin (PegIFN/RBV) were studied. First, 16 patients received 10 mg/kg/day SIL IV (Legalon Sil; Madaus, Köln, Germany) for 7 days. In a subsequent dose-finding study, 20 patients received 5, 10, 15, or 20 mg/kg/day SIL for 14 days. In both protocols, PegIFN alpha-2a/RBV were started on day 8. Viral load was determined daily.


RESULTS
Unexpectedly, in the first study, HCV-RNA declined on IV SIL by 1.32 +/- 0.55 log (mean +/- SD), P < .001 but increased again in spite of PegIFN/RBV after the infusion period. The viral load decrease was dose dependent (log drop after 7 days SIL: 0.55 +/- 0.5 [5 mg/kg, n = 3], 1.41 +/- 0.59 [10 mg/kg, n = 19], 2.11 +/- 1.34 [15 mg/kg, n = 5], and 3.02 +/- 1.01 [20 mg/kg, n = 9]; P < .001), decreased further after 7 days combined SIL/PegIFN/RBV (1.63 +/- 0.78 [5 mg/kg, n = 3], 4.16 +/- 1.28 [10 mg/kg, n = 3], 3.69 +/- 1.29 [15 mg/kg, n = 5], and 4.85 +/- 0.89 [20 mg/kg, n = 9]; P < .001), and became undetectable in 7 patients on 15 or 20 mg/kg SIL, at week 12. Beside mild gastrointestinal symptoms, IV SIL monotherapy was well tolerated.


CONCLUSIONS
IV SIL is well tolerated and shows a substantial antiviral effect against HCV in nonresponders.
Mining data streams: a review

The recent advances in hardware and software have enabled the capture of different measurements of data in a wide range of fields. These measurements are generated continuously and in a very high fluctuating data rates. Examples include sensor networks, web logs, and computer network traffic. The storage, querying and mining of such data sets are highly computationally challenging tasks. Mining data streams is concerned with extracting knowledge structures represented in models and patterns in non stopping streams of information. The research in data stream mining has gained a high attraction due to the importance of its applications and the increasing generation of streaming information. Applications of data stream analysis can vary from critical scientific and astronomical applications to important business and financial ones. Algorithms, systems and frameworks that address streaming challenges have been developed over the past three years. In this review paper, we present the state-of-the-art in this growing vital field.
Spinal prostaglandin E receptors of the EP2 subtype and the glycine receptor α3 subunit, which mediate central inflammatory hyperalgesia, do not contribute to pain after peripheral nerve injury or formalin injection

Inflammation, peripheral nerve injury and chemical irritants can cause central sensitization in pain pathways. Prostaglandins produced in the CNS induce central sensitization during inflammation mainly by relieving nociceptive neurons from glycinergic inhibition. We have recently identified spinal prostaglandin E receptors of the EP2 subtype (EP2 receptors) and the glycine receptor alpha3 subunit (GlyR alpha3) as signal transduction elements involved in the generation of central inflammatory hyperalgesia. It is however still unknown to what extent inhibition of glycine receptors by PGE2 contributes to neuropathic or chemically induced pain. To address this question, we have analyzed mice deficient in the EP2 receptor (EP2-/- mice) or in the GlyR alpha3 subunit (GlyR alpha3-/- mice) using the chronic constriction injury (CCI) model of neuropathic pain and the formalin test. We found that EP2-/- mice and GlyR alpha3-/- mice develop thermal and mechanical hyperalgesia in the CCI model indistinguishable from that seen in wild-type mice. In the formalin test, EP2-/- mice, but not GlyR alpha3-/- mice, exhibited reduced nocifensive behavior. The lack of a phenotype in GlyR alpha3-/- mice together with the absence of a facilitating effect of intrathecal PGE2 on formalin-induced nociception in wild-type mice suggests that peripheral rather than spinal EP2 receptors are involved. These results indicate that inhibition of glycinergic neurotransmission by EP2 receptor activation does not contribute to pain following peripheral nerve injury or chemical irritation with formalin. Our results thus provide further evidence that inflammatory hyperalgesia and neuropathic pain involve different mechanisms of central sensitization.
Treatment of abdominal compartment syndrome in severe acute pancreatitis patients with traditional Chinese medicine.

AIM
To investigate the therapeutic effect of traditional Chinese traditional medicines Da Cheng Qi Decoction (Timely-Purging and Yin-Preserving Decoction) and Glauber's salt combined with conservative measures on abdominal compartment syndrome (ACS) in severe acute pancreatitis (SAP) patients.


METHODS
Eighty consecutive SAP patients, admitted for routine non-operative conservative treatment, were randomly divided into study group and control group (40 patients in each group). Patients in the study group received Da Cheng Qi Decoction enema for 2 h and external use of Glauber's salt, once a day for 7 d. Patients in the control group received normal saline (NS) enema. Routine non-operative conservative treatments included non-per os nutrition (NPON), gastrointestinal decompression, life support, total parenteral nutrition (TPN), continuous peripancreatic vascular pharmaceutical infusion and drug therapy. Intra-cystic pressure (ICP) of the two groups was measured during treatment. The effectiveness and outcomes of treatment were observed and APACHE II scores were applied in analysis.


RESULTS
On days 4 and 5 of treatment, the ICP was lower in the study group than in the control group (P < 0.05). On days 3-5 of treatment, acute physiology and chronic health evaluation II (APACHE II) scores for the study and control groups were significantly different (P < 0.05). Both the effectiveness and outcome of the treatment with Da Cheng Qi Decoction on abdominalgia, burbulence relief time, ascites quantity, cyst formation rate and hospitalization time were quite different between the two groups (P < 0.05). The mortality rate for the two groups had no significant difference.


CONCLUSION
Da Cheng Qi Decoction enema and external use of Glauber's salt combined with routine non-operative conservative treatment can decrease the intra-abdominal pressure (IAP) of SAP patients and have preventive and therapeutic effects on abdominal compartment syndrome of SAP.
Financial portfolio management through the goal programming model: Current state-of-the-art

Since Markowitz (1952) formulated the portfolio selection problem, many researchers have developed models aggregating simultaneously several conflicting attributes such as: the return on investment, risk and liquidity. The portfolio manager generally seeks the best combination of stocks/assets that meets his/ her investment objectives. The Goal Programming (GP) model is widely applied to finance and portfolio management. The aim of this paper is to present the different variants of the GP model that have been applied to the financial portfolio selection problem from the 1970s to nowadays. 2013 Elsevier B.V. All rights reserved.
Addressing Scheme for IOT Network Using IPV 6 T

Abstract—The goal of this paper is to present an addressing scheme that allows for assigning a unique IPv6 address to each node in the Internet of Things (IoT) network. This scheme guarantees uniqueness by extracting the clock skew of each communication device and converting it into an IPv6 address. Simulation analysis confirms that the presented scheme provides reductions in terms of energy consumption, communication overhead and response time as compared to four studied addressing schemes Strong DAD, LEADS, SIPA and CLOSA.
A randomized double-blind multi-center trial of hydrogen water for Parkinson's disease: protocol and baseline characteristics.

BACKGROUND
Our previous randomized double-blind study showed that drinking hydrogen (H2) water for 48 weeks significantly improved the total Unified Parkinson's Disease Rating Scale (UPDRS) score of Parkinson's disease (PD) patients treated with levodopa. We aim to confirm this result using a randomized double-blind placebo-controlled multi-center trial.


METHODS
Changes in the total UPDRS scores from baseline to the 8(th), 24(th), 48(th), and 72(nd) weeks, and after the 8(th) week, will be evaluated. The primary endpoint of the efficacy of this treatment in PD is the change in the total UPDRS score from baseline to the 72(nd) week. The changes in UPDRS part II, UPDRS part III, each UPDRS score, PD Questionnaire-39 (PDQ-39), and the modified Hoehn and Yahr stage at these same time-points, as well as the duration until the protocol is finished because additional levodopa is required or until the disease progresses, will also be analyzed. Adverse events and screening laboratory studies will also be examined. Participants in the hydrogen water group will drink 1000 mL/day of H2 water, and those in the placebo water group will drink normal water. One-hundred-and-seventy-eight participants with PD (88 women, 90 men; mean age: 64.2 [SD 9.2] years, total UPDRS: 23.7 [11.8], with levodopa medication: 154 participants, without levodopa medication: 24 participants; daily levodopa dose: 344.1 [202.8] mg, total levodopa equivalent dose: 592.0 [317.6] mg) were enrolled in 14 hospitals and were randomized.


DISCUSSION
This study will confirm whether H2 water can improve PD symptoms.


TRIAL REGISTRATION
UMIN000010014 (February, 13, 2013).
Evaluation of response to fractionated radioimmunotherapy with 90Y-epratuzumab in non-Hodgkin's lymphoma by 18F-fluorodeoxyglucose positron emission tomography.

BACKGROUND
The study aimed to evaluate FDG-PET imaging for early prediction of response to radioimmunotherapy in patients with non-Hodgkin's lymphoma.


DESIGN AND METHODS
Twenty-seven patients from a large ongoing, multicenter, phase I/II trial of fractionated radioimmunotherapy using anti-CD22 (90)Y-epratuzumab underwent FDG-PET imaging. They also underwent assessment by conventional diagnostic methods that included chemotherapy at baseline and six weeks post-radioimmunotherapy, and every three months until progression. Responses evaluated from conventional methods were classified using International Workshop Response Criteria as complete response, unconfirmed CR, partial response, stable disease, or progression of disease. FDG-PET images were evaluated visually and were classified as complete response, partial response or progression of disease. The gold standard was histology and follow-up.


RESULTS
A total of 81 paired imaging studies were obtained post-radioimmunotherapy (including 3 patients after retreatment) and evaluated as complete response (n=34), partial response (n=24) or progression of disease (n=23) by FDG-PET, and complete response (n=12), unconfirmed complete response (n=31), partial response (n=15), stable disease (n=8) or progression of disease (n=15) by conventional methods. Of the 31 responses evaluated as unconfirmed complete response by conventional methods, 20 (65%) were classified as negative for disease (complete response) by PET while the other 11 (35%) were positive for disease (7 partial response and 4 progression of disease). Among 22 assessable PET images acquired at six weeks post-radioimmunotherapy, the mean time-to-progression was 15.6 months when PET was negative for disease (complete response), compared with 5.4 months when PET was positive (partial response or progression of disease) (p=0.008). Sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of PET six weeks after radioimmunotherapy were 86%, 63%, 80%, 71% and 77% respectively, compared with 36%, 87%, 83%, 44% and 55% respectively using conventional methods.


CONCLUSIONS
A positive assessment of disease by PET acquired six weeks after radioimmunotherapy corresponded with a shorter time to progression.
Impact factors: use and abuse.

The impact factor is only one of three standardized measures created by the Institute of Scientific Information (ISI), which can be used to measure the way a journal receives citations to its articles over time. The build-up of citations tends to follow a curve like that of Figure 1. Citations to articles published in a given year rise sharply to a peak between two and six years after publication. From this peak citations decline exponentially. The citation curve of any journal can be described by the relative size of the curve (in terms of area under the line), the extent to which the peak of the curve is close to the origin and the rate of decline of the curve. These characteristics form the basis of the ISI indicators impact factor, immediacy index and cited half-life . The impact factor is a measure of the relative size of the citation curve in years 2 and 3. It is calculated by dividing the number of current citations a journal receives to articles published in the two previous years by the number of articles published in those same years. So, for example, the 1999 impact factor is the citations in 1999 to articles published in 1997 and 1998 divided by the number of articles published in 1997 and 1998. The number that results can be thought of as the average number of citations the average article receives per annum in the two years after the publication year. The immediacy index gives a measure of the skewness of the curve, that is, the extent to which the peak of the curve lies near the origin of the graph. It is calculated by dividing the citations a journal receives in the current year by the number of articles it publishes in that year, i.e., the 1999 immediacy index is the average number of citations in 1999 to articles published in 1999. The number that results can be thought of as the initial gradient of the citation curve, a measure of how quickly items in that journal get cited upon publication. The cited half-life is a measure of the rate of decline of the citation curve. It is the number of years that the number of current citations takes to decline to 50% of its initial value; the cited half-life is 6 years in the example given in (Figure 1). It is a measure of how long articles in a journal continue to be cited after publication.
Documenting aspect-oriented PHP (AOPHP)

This paper describes the process for documenting programs using Aspect-Oriented PHP through AOPHPdoc. We discuss some of the problems involved in documenting Aspect-Oriented programs, solutions to these problems, and the creation of documentation with AOPHPdoc. A survey of programmers found no preference for Javadoc-styled documentation over the colored-coded AOPHP documentation.
On the vacuum Cherenkov radiation in noncommutative electrodynamics and the elusive effects of Lorentz violation

We show that in the framework of noncommutative classical electrodynamics Cherenkov radiation is permitted in vacuum and we explicitly compute its spectrum at first order in the noncommutative parameter. We discuss the phenomenological impact of the merge of this new analysis with the old results of the substantial modification to the spectrum of the synchrotron radiation obtained in Castorina P., Iorio A. and Zappala D., Phys. Rev. D 69 (2004) 065008. We propose to consider the pulsars' radiation spectrum—due to its very strong magnetic field—to investigate these Lorentz violating effects in astrophysical phenomena.
Search Methodologies: Introductory Tutorials in Optimization and Decision Support Techniques

1. INTRODUCTION The biological immune system is a robust, complex, adaptive system that defends the body from foreign pathogens. It is able to categorize all cells (or molecules) within the body as self-cells or non-self cells. It does this with the help of a distributed task force that has the intelligence to take action from a local and also a global perspective using its network of chemical
Phase I study of cediranib in combination with oxaliplatin and infusional 5-Fluorouracil in patients with advanced colorectal cancer.

PURPOSE
Cediranib is a potent oral inhibitor of the tyrosine kinase activity associated with all subtypes of vascular endothelial growth factor receptor. Purposes of this study were to determine the recommended phase II dose of cediranib in combination with standard doses of modified FOLFOX-6 (mFOLFOX-6), and the tolerability, safety, pharmacokinetics, and antitumor activity of this combination in patients with untreated metastatic colorectal cancer.


EXPERIMENTAL DESIGN
Cediranib was administered daily orally at a starting dose of 30 mg and escalated to 45 mg daily, and mFOLFOX-6 was repeated every 14 days. Pharmacokinetic studies were done for oxaliplatin, 5-fluorouracil, and cediranib. Response was assessed by Response Evaluation Criteria in Solid Tumors every four cycles.


RESULTS
Sixteen patients received 150 cycles of treatment (median, 6; range, 1-20 cycles). Of 9 patients enrolled at the 30-mg dose level, 1 patient experienced grade 3 diarrhea during cycle 1. No dose-limiting toxicity was observed in 7 patients at the 45-mg dose level. Common grade 3 toxicities related to cediranib included hypertension, diarrhea, fatigue, and anorexia. Of 14 patients evaluable for response, there were 6 partial responses (42.9%; 95% confidence interval, 17.7-71.1%) and 6 stable disease. The median progression-free survival was 9.3 months. There were no pharmacokinetic interactions between cediranib and 5-fluorouracil or free plasma intact oxaliplatin.


CONCLUSIONS
Toxicities of this combination were manageable and consistent with previous studies. The recommended phase II dose is cediranib at 30 mg daily continuously in combination with standard doses of mFOLFOX-6. Cediranib and mFOLFOX-6 has promising antitumor activity and this combination warrants further investigation.