LLukas22/scidocs huggingface dataset:
The Ontology of Vaccine Adverse Events (OVAE) and its usage in representing and analyzing adverse events associated with US-licensed human vaccines

BACKGROUND
Licensed human vaccines can induce various adverse events (AE) in vaccinated patients. Due to the involvement of the whole immune system and complex immunological reactions after vaccination, it is difficult to identify the relations among vaccines, adverse events, and human populations in different age groups. Many known vaccine adverse events (VAEs) have been recorded in the package inserts of US-licensed commercial vaccine products. To better represent and analyze VAEs, we developed the Ontology of Vaccine Adverse Events (OVAE) as an extension of the Ontology of Adverse Events (OAE) and the Vaccine Ontology (VO).


RESULTS
Like OAE and VO, OVAE is aligned with the Basic Formal Ontology (BFO). The commercial vaccines and adverse events in OVAE are imported from VO and OAE, respectively. A new population term 'human vaccinee population' is generated and used to define VAE occurrence. An OVAE design pattern is developed to link vaccine, adverse event, vaccinee population, age range, and VAE occurrence. OVAE has been used to represent and classify the adverse events recorded in package insert documents of commercial vaccines licensed by the USA Food and Drug Administration (FDA). OVAE currently includes over 1,300 terms, including 87 distinct types of VAEs associated with 63 human vaccines licensed in the USA. For each vaccine, occurrence rates for every VAE in different age groups have been logically represented in OVAE. SPARQL scripts were developed to query and analyze the OVAE knowledge base data. To demonstrate the usage of OVAE, the top 10 vaccines accompanying with the highest numbers of VAEs and the top 10 VAEs most frequently observed among vaccines were identified and analyzed. Asserted and inferred ontology hierarchies classify VAEs in different levels of AE groups. Different VAE occurrences in different age groups were also analyzed.


CONCLUSIONS
The ontology-based data representation and integration using the FDA-approved information from the vaccine package insert documents enables the identification of adverse events from vaccination in relation to predefined parts of the population (age groups) and certain groups of vaccines. The resulting ontology-based VAE knowledge base classifies vaccine-specific VAEs and supports better VAE understanding and future rational AE prevention and treatment.
Dyson schwinger equations: Connecting small and large length-scales

I illustrate the phenomenological application of Dyson-Schwinger equations to the calculation of meson properties observable at TJNAF. Particular emphasis is given to this framework's ability to unify long-range effects constrained by chiral symmetry with short-range effects prescribed by perturbation theory, and interpolate between them.
SEEKING JUSTICE IN THE WAKE OF TRANSITIONS FOR VICTIMS OF SEXUAL VIOLENCE: A CASE STUDY OF SIERRA LEONE

................................................................................................................... 1 DEDICATION................................................................................................................. II ACKNOWLEDGMENT ...................................................................................................III TABLE OF CONTENTS .................................................................................................IV LIST OF ACRONYMS....................................................................................................V
Axis-Based Virtual Coordinate Assignment Protocol and Delivery-Guaranteed Routing Protocol in Wireless Sensor Networks

In this paper, we propose a method of constructing a virtual coordinate system (ABVCap) in wireless sensor networks where location information is not available. A routing protocol based on ABVCap virtual coordinates is also introduced. Our routing protocol guarantees packet delivery and does not require computing and storing of the global topological features. Using simulations, we evaluate the performance of the proposed routing protocol (ABVCap routing), the greedy routing protocol based on VCap virtual coordinates (VCap routing), the greedy routing protocol based on physical coordinates (Euclidean routing), greedy perimeter stateless routing (GPSR routing), and geometric spanner routing (GSR routing). The simulations show that our method guarantees packet delivery while ensuring moderate routing path length overhead costs.
Bortezomib in combination with conventional chemotherapeutic agents for multiple myeloma compared with bortezomib alone.

BACKGROUND
Recent studies have demonstrated synergy between bortezomib and a number of conventional cytotoxic agents. This study examined whether or not the speed of the response, progression and safety from a combination treatment of bortezomib with common chemotherapeutic drugs is superior to bortezomib monotherapy.


METHODS
Fifty-seven patients with relapsed, refractory multiple myeloma (MM) who had received at least two cycles of treatment including bortezomib were enrolled in this study. The median age was 56 (35-79) years and 49.1% were male. Thirty-two patients were treated with bortezomib alone and 25 were treated with chemotherapeutic agents that were given in combination with bortezomib. The monoclonal immunoglobulin (mIg) or free light chain (FLC) concentrations were determined in the sera before and after two cycles of bortezomib treatment. The adverse events were assessed and graded according to the NCI Common Toxicity Criteria (version 2.0).


RESULTS
Thirty-one of the 57 patients (54.4%) attained an early objective response (EOR) after the second bortezomib treatment, defined as a >/=50% decrease in the serum mIg or FLC concentration. Improvements in the response were observed when common chemotherapeutic agents were added to bortezomib monotherapy. In patients who received bortezomib combined with chemotherapeutic agents, 19 out of 25 patients (76%) showed an EOR, whereas 12 out of 32 patients (37.5%) given bortezomib monotherapy achieved an EOR after the second cycle of bortezomib treatment (P = 0.004); the median decrease from the baseline in the paraprotein level was 74.6 +/- 5.9 and 39.7 +/- 4.2%, respectively (P = 0.003). A statistically significant elevation of serum lactic dehydrogenase (P = 0.007) and alkaline phosphatase (P = 0.027) from baseline within two cycles of bortezomib treatment was observed in responding patients. With the combination treatment, peripheral neuropathy of >/=Grade II occurred in 12 out of 25 patients (48%) compared with 12 of 32 (37.5%) in those given bortezomib alone (P = 0.589). The median time to progression of disease was similar in the two groups (359 +/- 43.5 versus 365 +/- 103.5, P = 0.688). The multivariate Cox regression model showed that a high serum albumin and low beta2-microglobulin are favorable factors for the progression-free survival following bortezomib treatment.


CONCLUSIONS
Bortezomib in combination with common chemotherapeutic agents is more active in the treatment of relapsed, refractory MM than with bortezomib alone. However, more effective post-bortezomib treatment is needed to reduce the rate of disease progression particularly in patients with high tumor burden.
Supporting Systematic Reviews Using Text Mining

In this paper, we describe how we are using text mining solutions used to enhance the production of systematic reviews. This collaborative project also serves as a proof of concept and as a testbed for deriving requirements for the development of more generally applicable text mining tools and services.
Cognitive Therapy and Recovery from Acute Psychosis : a Controlled Trial

Background. The appiioa@onof cogni@vetherapy (Cl) to psychosis is currently being de veloped in the UK.This paper reportsa trialof CTin acute psychosis with the objective of hasteningthe resolutionof positivesymptomsandreducingresidualsymptoms. Method. 0f117 patients wkh acute non-affective psychosis, 69 satisfied inclusion critena and 40 proceeded to stratified randomisation. The experimental intervention involvingk@dividual and group CTwas compared with a group receiving matched hours Oftherapist input providing structured activities and informalsupport routine pharmacotherapy was provided by clinicians blindto group allocation.Patientswere monitoredweeldy using self-reportand mentalstate assessments during admission and over the subsequent nine months. Results. Both groups showed a decline in positive symptoms but this was more marked uithe CTgroup (P<O.0O1).At 9 months 5%of the CTgroup,v.56%of the controlgroup,showed moderateorsevere residualsymptoms. Conclusion. CTappears to be a potent adjunctto pharmacotherapyand standardcare for acute psychosis. Issues concerning internaland external validityof the studyand opportunities for further research are discussed.
A Dyad Theory of Hydrodynamics and Electrodynamics

The dyadic calculus is developed in a form suitable for the description of physical relations in curved space. The 4-space equations of hydrodynamics and electrodynamics are constructed using this dyadic calculus. As a demonstration of the relationship between gravity and electrodynamics a time varying metric is shown to generate electromagnetic radiation.
Sequence Data Mining Techniques and Applications

Many interesting real-life mining applications rely on modeling data as sequences of discrete multi-attribute records. Mining models for network intrusion detection view data as sequences of TCP/IP packets. Text information extraction systems model the input text as a sequence of words and delimiters. Customer data mining applications profile buying habits of customers as a sequence of items purchased. In computational biology, DNA, RNA and protein data are all best modeled as sequences. Classifying, clustering and characterizing such sequence data presents interesting issues in feature engineering, discretization and pattern discovery. In this seminar we will review techniques ranging from item set counting, MDL-based discretization and Markov modeling to perform various supervised and unsupervised pattern discovery tasks on sequences. We will present case studies from network intrusion detection and DNA sequence mining to illustrate these techniques. Sunita Sarawagi researches in the fields of databases, data mining, machine learning and data warehousing. She is a member of the faculty at IIT Bombay. Prior to that she was a research staff member at IBM Almaden Research Center. She got her PhD in databases from the University of California at Berkeley. Proceedings of the 19th International Conference on Data Engineering (ICDE’03) 1063-6382/03 $ 17.00 © 2003 IEEE
Joint image denoising using adaptive principal component analysis and self-similarity

The nonlocal means (NLM) has attracted enormous interest in image denoising problem in recent years. In this paper, we propose an efficient joint denoising algorithm based on adaptive principal component analysis (PCA) and self-similarity that improves the predictability of pixel intensities in reconstructed images. The proposed algorithm consists of two successive steps without iteration: the low-rank approximation based on parallel analysis, and the collaborative filtering. First, for a pixel and its nearest neighbors, the training samples in a local search window are selected to form the similar patch group by the block matching method. Next, it is factorized by singular value decomposition (SVD), whose left and right orthogonal basis denote local and nonlocal image features, respectively. The adaptive PCA automatically chooses the local signal subspace dimensionality of the noisy similar patch group in the SVD domain by the refined parallel analysis with Monte Carlo simulation. Thus, image features can be well preserved after dimensionality reduction, and simultaneously the noise is almost eliminated. Then, after the inverse SVD transform, the denoised image is reconstructed from the aggregate filtered patches by the weighted average method. Finally, the collaborative Wiener filtering is used to further remove the noise. The experimental results validate its generality and effectiveness in a wide range of the noisy images. The proposed algorithm not only produces very promising denoising results that outperforms the state-of-the-art methods in most cases, but also adapts to a variety of noise levels. † Corresponding Author. Tel: +86-10-82529641; fax: +86-10-82529207. E-mail address: guozongming@pku.edu.cn Preprint submitted to Information Sciences August 5, 2013
Collagen plug vascular closure devices and reduced risk of bleeding with bivalirudin versus heparin plus abciximab in patients undergoing percutaneous coronary intervention for non st-segment elevation myocardial infarction.

INTRODUCTION
In ISAR-REACT-4 (abciximab and heparin vs. bivalirudin for non-ST-elevation myocardial infarction [NSTEMI]), bivalirudin reduced the risk of bleeding after percutaneous coronary intervention (PCI) compared with unfractionated heparin plus abciximab (UFH + abciximab). Vascular closure devices (VCDs) may also prevent bleeding complications, and thus attenuate the benefit of bivalirudin. This analysis examined whether there exists an interaction on bleeding between VCDs and bivalirudin versus UFH + abciximab after PCI.


METHODS
Patients with NSTEMI were randomly assigned to either receive UFH + abciximab or bivalirudin for PCI. The use of a VCD after femoral access was left to the operator's discretion. The effect of randomized treatment in patients who received a VCD was compared to that in patients with manual compression of the femoral access site. The primary end-point of this analysis was the 30-day incidence of ISAR-REACT-4 major bleeding.


RESULTS
A total of 1,711 patients were enrolled in this analysis. Among the 365 (21.3%) patients receiving a VCD, 188 (51.5%) were treated with UFH + abciximab and 177 (48.5%) with bivalirudin. ISAR- REACT-4 major bleeding was higher with UFH + abciximab than with bivalirudin, independent of whether a VCD was used (4.8% vs. 2.3% with VCD and 4.6% vs. 2.7% without VCD, Pint = 0.76). There were also no interactions between randomized treatment and VCDs with respect to any of the ischemic end-points or net clinical outcome (Pint > 0.56).


CONCLUSIONS
In patients undergoing PCI for NSTEMI, the reduction of major bleeding by bivalirudin compared with UFH + abciximab was not affected whether a VCD was used.
Team Performance Management Emerald Article : Building trust and collaboration in a virtual team

Organizations are increasing their reliance on virtual relationships in structuring operations for a global environment. Like all teams, virtual teams require a solid foundation of mutual trust and collaboration, if they are to function effectively. Identifying and applying appropriate team building strategies for a virtual environment will not only enhance organizational effectiveness but will also impact positively on the quality of working life for virtual team members.
Choice functions and abstract convex geometries

Abstract A main aim of this paper is to make connections between two well – but up to now independently – developed theories, the theory of choice functions and the theory of closure operators. It is shown that the classes of ordinally rationalizable and path independent choice functions are related to the classes of distributive and anti-exchange closures.
Weekly combination of topotecan and gemcitabine in early recurrent ovarian cancer patients: a French multicenter phase II study.

OBJECTIVES
The aim of this phase II study was to assess the benefits of a weekly administration of topotecan and gemcitabine in patients with ovarian carcinoma having relapsed after platinum/taxane-based first-line chemotherapy.


METHODS
Seventy-seven patients with progression of disease </=12 months after first-line chemotherapy were enrolled to receive topotecan (2.5 mg/m(2)) and gemcitabine (1000 mg/m(2)) on days 1, 8 and 15 (q 28 d). Primary endpoint was the response rate. Stabilization rate and symptom improvement were also assessed.


RESULTS
All patients received the combination and 66 were evaluable (>/=2 cycles administered). The only major severe toxicity was neutropenia grades 3 (17%) and 4 (6%). Approximately 60% of the patients received the complete schedule of treatment, dose interruptions/delays being mainly due to moderate thrombocytopenia or neutropenia. The objective response rate was 14%, the values for patients having relapsed within 6 (n=30) and 6-12 (n=36) months being 7% and 20%, respectively. Median durations of response were 4.9 and 6.4 months and clinical benefit rates including stabilizations reached 63% and 69% in patients having relapsed within 6 or 6-12 months, respectively. Corresponding median overall survival was 7.5 and 15.6 months. Symptoms and pain were reduced in 64% and 39% of the patients concerned, respectively.


CONCLUSION
In early relapse ovarian cancer, weekly combination of gemcitabine and topotecan has a modest objective response rate. However, a high proportion of patients experienced stable disease and symptom control leading to acceptable quality of life.
UHF RFID TAG CHARACTERIZATION : OVERVIEW AND STATE-OFTHE-ART

In this paper, we present an overview of UHF RFID tag performance characterization. We review the link budget of RFID system, explain different tag performance characteristics, and describe various testing methods. We also review state-of-the art test systems present on the market today.
A facile microwave-induced synthesis of titanium pyrophosphate nanocrystals

Abstract Titanium pyrophosphate (TiP 2 O 7 ) nanocrystals are synthesized using a facile microwave (MW) heating method, in which titanium hydroxide (TH) and H 3 PO 4 (85%) are used as Ti and P sources without surfactant or template assistance. X-ray diffraction results suggest that pure cubic-structured TiP 2 O 7 could be obtained via MW irradiation at 800 W for 5 min. Scanning electron microscope and transmission electron microscope photographs show that the grain sizes of the samples range from 20 nm to 100 nm and vary with the irradiation time. The effects of different sample preparation conditions on the experimental result are also discussed. The band gap energy of as-synthesized TiP 2 O 7 is determined to be 3.8 eV by UV diffuse reflectance spectral analysis. Luminescence spectral analysis shows that nanocrystal TiP 2 O 7 shows white-light emission at 300 nm.
Radon in homes and risk of lung cancer: collaborative analysis of individual data from 13 European case-control studies.

OBJECTIVE
To determine the risk of lung cancer associated with exposure at home to the radioactive disintegration products of naturally occurring radon gas.


DESIGN
Collaborative analysis of individual data from 13 case-control studies of residential radon and lung cancer.


SETTING
Nine European countries.


SUBJECTS
7148 cases of lung cancer and 14,208 controls.


MAIN OUTCOME MEASURES
Relative risks of lung cancer and radon gas concentrations in homes inhabited during the previous 5-34 years measured in becquerels (radon disintegrations per second) per cubic metre (Bq/m3) of household air.


RESULTS
The mean measured radon concentration in homes of people in the control group was 97 Bq/m3, with 11% measuring > 200 and 4% measuring > 400 Bq/m3. For cases of lung cancer the mean concentration was 104 Bq/m3. The risk of lung cancer increased by 8.4% (95% confidence interval 3.0% to 15.8%) per 100 Bq/m3 increase in measured radon (P = 0.0007). This corresponds to an increase of 16% (5% to 31%) per 100 Bq/m3 increase in usual radon--that is, after correction for the dilution caused by random uncertainties in measuring radon concentrations. The dose-response relation seemed to be linear with no threshold and remained significant (P = 0.04) in analyses limited to individuals from homes with measured radon < 200 Bq/m3. The proportionate excess risk did not differ significantly with study, age, sex, or smoking. In the absence of other causes of death, the absolute risks of lung cancer by age 75 years at usual radon concentrations of 0, 100, and 400 Bq/m3 would be about 0.4%, 0.5%, and 0.7%, respectively, for lifelong non-smokers, and about 25 times greater (10%, 12%, and 16%) for cigarette smokers.


CONCLUSIONS
Collectively, though not separately, these studies show appreciable hazards from residential radon, particularly for smokers and recent ex-smokers, and indicate that it is responsible for about 2% of all deaths from cancer in Europe.
Joint segmentation and named entity recognition using dual decomposition in Chinese discharge summaries.

OBJECTIVE
In this paper, we focus on three aspects: (1) to annotate a set of standard corpus in Chinese discharge summaries; (2) to perform word segmentation and named entity recognition in the above corpus; (3) to build a joint model that performs word segmentation and named entity recognition.


DESIGN
Two independent systems of word segmentation and named entity recognition were built based on conditional random field models. In the field of natural language processing, while most approaches use a single model to predict outputs, many works have proved that performance of many tasks can be improved by exploiting combined techniques. Therefore, in this paper, we proposed a joint model using dual decomposition to perform both the two tasks in order to exploit correlations between the two tasks. Three sets of features were designed to demonstrate the advantage of the joint model we proposed, compared with independent models, incremental models and a joint model trained on combined labels.


MEASUREMENTS
Micro-averaged precision (P), recall (R), and F-measure (F) were used to evaluate results.


RESULTS
The gold standard corpus is created using 336 Chinese discharge summaries of 71 355 words. The framework using dual decomposition achieved 0.2% improvement for segmentation and 1% improvement for recognition, compared with each of the two tasks alone.


CONCLUSIONS
The joint model is efficient and effective in both segmentation and recognition compared with the two individual tasks. The model achieved encouraging results, demonstrating the feasibility of the two tasks.
The heat treatment effect on the structure and mechanical properties of electrodeposited nano grain size Ni–W alloy coatings

Abstract The Ni–W alloy coatings with tungsten content from 32.5 to 61.2 wt.% were prepared in this study by electro-deposition. Experimental results show that the grain size of Ni–W coatings evaluated by XRD decreased with increasing tungsten content in coatings, however, the micro-hardness increased with increasing tungsten content. As-deposited Ni–61.2 wt.%W coating has amorphous-like structure and the grain size is around 1.5 nm, after annealing at 500 °C, the hardness of the coating is promoted to 1293 Hv owing to formation of Ni 4 W and NW precipitates. In addition, the heat-treated Ni–W coatings show a better wear resistance than the as-plated Ni–W coatings.