LLukas22/scidocs huggingface dataset:
A new open-source software developed for numerical simulations using discrete modeling methods

The purpose of this work is to present the development of an open–source software based on a discrete description of matter applied to study the behavior of geomaterials. This software uses Object Oriented Programming techniques, and its methodology design uses three different methods, which are the Discrete Element Method (DEM) [10, 11], the Finite Element Method (FEM) [27, 31] and the Lattice Geometrical Method (LGM) [17–20]. These methods are implemented within a single object–oriented framework in C++ using OOP design patterns. The bulk of the original work consisted mainly of finding common objects which will work for these different modeling methods without changing a single line of the C++ code. With this approach it is possible to add new numerical models by only plugging– in the corresponding formulas. The advantages of the resulting YADE framework are the following: (1) generic design provides great flexibility when adding new scientific simulation code, (2) numerous simulation methods can be coupled within the same framework like for example DEM/FEM and (3) with the open–source philosophy, the community of users collaborate and improve the software. The YADE framework is a new emerging software, which can be downloaded at the http://yade.wikia.com webpage.
A survey of approaches and challenges in 3D and multi-modal 3D + 2D face recognition

This survey focuses on recognition performed by matching models of the three-dimensional shape of the face, either alone or in combination with matching corresponding two-dimensional intensity images. Research trends to date are summarized, and challenges confronting the development of more accurate three-dimensional face recognition are identified. These challenges include the need for better sensors, improved recognition algorithms, and more rigorous experimental methodology. 2005 Elsevier Inc. All rights reserved.
Querying the Semantic Web with Corese Search Engine

This paper presents an ontology-based approach for web querying, using semantic metadata. We propose a query language based on ontologies and emphasize its ability to express approximate queries, useful for an efficient information retrieval on the web. We present the Corese search engine dedicated to RDF(S) metadata and illustrate it through several real-world applications.
A role for Streptococcus pneumoniae in virus-associated pneumonia

Here we show, in a double-blind, randomized, placebo-controlled trial in 37,107 fully immunized infants in Soweto, South Africa, that a 9-valent pneumococcal conjugate vaccine, PncCV, prevents 31% (95% confidence interval = 15–43%) of pneumonias associated with any of seven respiratory viruses in children in hospital. These data suggest that the pneumococcus has a major role in the development of pneumonia associated with these viruses and that viruses contribute to the pathogenesis of bacterial pneumonia.NOTE: In the version of this article originally published online, the species name was misspelled Streptococcus pnemoniae in the title of the article. The name should be Streptococcus pneumoniae. This error has been corrected for the HTML and print versions of the article.
Two-year follow-up of patients with septic shock presenting with low HDL: the effect upon acute kidney injury, death and estimated glomerular filtration rate.

BACKGROUND
Sepsis is associated with decreased levels of high-density lipoprotein (HDL) cholesterol. HDL has anti-inflammatory properties, and the use of Apo A-I mimetic peptides is associated with renal function improvement in animal models of sepsis. However, it is not known whether decreased HDL level results in impaired renal function in human sepsis. We investigated whether low levels of HDL conferred an increased risk of sepsis-associated acute kidney injury (AKI) or long-term decreased estimated glomerular filtration rate (eGFR) after sepsis.


METHODS
HDL concentration (mg dL-1 ) was measured in plasma samples from 180 patients with septic shock at admission to the Emergency Department (ED). We divided the patients using median HDL as a cut-off value and assessed the frequency of sepsis-associated AKI and long-term decreased eGFR after sepsis. Univariate and multivariate analyses were performed.


RESULTS
Patients with low HDL had a significantly greater frequency of KDIGO 2 or 3 sepsis-associated AKI [39/90 (43.3%) vs. 12/90 (13.3%), P < 0.001] and decreased long-term eGFR [24/58 (41.4%) vs. 11/57 (19.3%), P = 0.018] compared to those with high HDL. The adjusted OR for sepsis-associated AKI and decreased eGFR after sepsis in the lower HDL group was 2.80 (95% CI 1.08-7.25, P = 0.033) and 5.45 (95% CI 1.57-18.93, P = 0.008), respectively.


CONCLUSION
Low HDL levels during sepsis are associated with increased risk of sepsis-associated AKI, and/or subsequent decreased eGFR. These results suggest that HDL may be involved and/or may be a marker of kidney injury during and after sepsis.
Measuring the National Impact of Coastal and Ocean Management

The National Oceanic and Atmospheric Administration is developing a National Coastal Management Performance Measurement System to assess the national impact of the state coastal management programs and National Estuarine Research Reserves developed under the Coastal Zone Management Act.
RIOT : One OS to Rule Them All in the IoT

The Internet of Things (IoT) embodies a wide spectrum of machines ranging from sensors powered by 8-bits microcontrollers, to devices powered by processors roughly equivalent to those found in entry-level smartphones. Neither traditional operating systems (OS) currently running on internet hosts, nor typical OS for sensor networks are capable to fulfill all at once the diverse requirements of such a wide range of devices. Hence, in order to avoid redundant developments and maintenance costs of IoT products, a novel, unifying type of OS is needed. The following analyzes requirements such an OS should fulfill, and introduces RIOT, a new OS satisfying these demands. Key-words: Network, internet, things, objects, IoT, routing, OS, energy, efficient, operating system, protocol, IPv6, wireless, radio, constrained, embedded RIOT: One OS to Rule Them All in the IoT 3
International Financial Liberalization and Economic Growth

This paper pulls together existing theory and evidence to assess whether international financial liberalization, by improving the functioning of domestic financial markets and banks, accelerates economic growth. The analysis suggests that the answer is yes. First, liberalizing restrictions on international portfolio flows tends to enhance stock market liquidity. In turn, enhanced stock market liquidity accelerates economic growth primarily by boosting productivity growth. Second, allowing greater foreign bank presence tends to enhance the efficiency of the domestic banking system. In turn, better-developed banks spur economic growth primarily by accelerating productivity growth. Thus, international financial integration can promote economic development by encouraging improvements in the domestic financial system. *Levine: Finance Department, Carlson School of Management, University of Minnesota, 321 19 Avenue South, Minneapolis, MN 55455. Tel: 612-624-9551, Fax: 612-626-1335, E-mail: rlevine@csom.umn.edu. I thank, without implicating, Maria Carkovic and two anonymous referees for very helpful comments. JEL Classification Numbers: F3, G2, O4 Abbreviations: GDP, TFP Number of Figures: 0 Number of Tables: 2 Date: September 5, 2000 Address of Contact Author: Ross Levine, Finance Department, Carlson School of Management, University of Minnesota, 321 19 Avenue South, Minneapolis, MN 55455. Tel: 612-624-9551, Fax: 612-626-1335, E-mail: rlevine@csom.umn.edu.
Feature Detection and Tracking with Constrained Local Models

We present an efficient and robust model matching method which uses a joint shape and texture appearance model to generate a set of region template detectors. The model is fitted to an unseen image in an iterative manner by generating templates using the joint model and the current parameter estimates, correlating the templates with the target image to generate response images and optimising the shape parameters so as to maximise the sum of responses. The appearance model is similar to that used in the AAM [1]. However in our approach the appearance model is used to generate likely feature templates, instead of trying to approximate the image pixels directly. We show that when applied to human faces, our Constrained Local Model (CLM) algorithm is more robust and more accurate than the original AAM search method, which relies on the image reconstruction error to update the model parameters. We demonstrate improved localisation accuracy on two publicly available face data sets and improved tracking on a challenging set of in-car face sequences.
Diagnostic performance of collagen IV and laminin for the prediction of fibrosis and cirrhosis in chronic hepatitis C patients: a multicenter study.

BACKGROUND/AIM
To date, liver biopsy has been the gold standard used for the assessment of liver fibrosis in patients with chronic hepatitis C. Our aim was to evaluate the diagnostic performance of a panel of simple blood markers of liver fibrosis and the development a novel score to replace liver biopsy.


PATIENTS AND METHODS
Liver biochemical profile including transaminases, bilirubin, alkaline phosphatase, and albumin, in addition to platelet count, was evaluated using standard methods in 305 chronic hepatitis C patients. Serum type IV collagen and laminin were assayed using the ELISA technique. Liver biopsies were performed. Statistical analyses were carried out by logistic regression and receiver operating characteristic curves to assess and compare the diagnostic accuracy of blood markers. A stepwise combination algorithm was developed and validated in 317 additional patients.


RESULTS
The Fibrosis Discriminant Score (FDS) was developed combining collagen, laminin, aspartate aminotransferase/platelet ratio index, and albumin. FDS produced an area under receiver operating characteristic curve of 0.831 for significant fibrosis, 0.791 for advanced fibrosis, and 0.881 for cirrhosis. The FDS was correctly classified in 82% of patients with significant fibrosis with 79% sensitivity and 88% specificity at cut-off 0.66 or more. Similar results were obtained in a validation study in which, of 317 patients, liver biopsy could have been avoided in 81%.


CONCLUSION
A simple fibrosis index can be useful to select hepatitis C virus-infected patients with a very low risk of significant fibrosis in whom the protocol of liver biopsies may be avoided.
Bioactivity of phenolic acids: metabolites versus parent compounds: a review.

Phenolic acids are present in our diet in different foods, for example mushrooms. Due to their bioactive properties, phenolic acids are extensively studied and there is evidence of their role in disease prevention. Nevertheless, in vivo, these compounds are metabolized and circulate in the organism as glucuronated, sulphated and methylated metabolites, displaying higher or lower bioactivities. To clarify the importance of the metabolism of phenolic acids, knowledge about the bioactivity of metabolites is extremely important. In this review, chemical features, biosynthesis and bioavailability of phenolic acids are discussed, as well as the chemical and enzymatic synthesis of their metabolites. Finally, metabolite bioactive properties are compared with that of the corresponding parental compounds.
Perinatal risks of untreated depression during pregnancy.

OBJECTIVE
To review the literature on the perinatal risks involved in untreated depression during pregnancy.


METHOD
We searched Medline and medical texts for all studies pertaining to this area up to the end of April 2003. Key phrases entered were depression and pregnancy, depression and pregnancy outcome, and depression and untreated pregnancy. We did not include bipolar depression.


RESULTS
While there is wide variability in reported effects, untreated depression during pregnancy appears to carry substantial perinatal risks. These may be direct risks to the fetus and infant or risks secondary to unhealthy maternal behaviours arising from the depression. Recent human data suggest that untreated postpartum depression, not treatment with antidepressants in pregnancy, results in adverse perinatal outcome.


CONCLUSION
The biological dysregulation caused by gestational depression has not received appropriate attention: most studies focus on the potential but unproven risks of psychotropic medication. No in-depth discussion of the role of psychotherapy is available. Because they are not aware of the potentially catastrophic outcome of untreated maternal depression, this imbalance may lead women suffering from depression to fear teratogenic effects and refuse treatment.
Continuous time mean variance asset allocation: A time-consistent strategy

We develop a numerical scheme for determining the optimal asset allocation strategy for time-consistent, continuous time, mean variance optimization. Any type of constraint can be applied to the investment policy. The optimal policies for time-consistent and pre-commitment strategies are compared. When realistic constraints are applied, the efficient frontiers for the precommitment and time-consistent strategies are similar, but the optimal investment strategies are quite different.
Occipital nerve stimulation in fibromyalgia: a double-blind placebo-controlled pilot study with a six-month follow-up.

OBJECTIVE
The goal of this study is to evaluate the effectiveness of occipital nerve stimulation (ONS) as a surgical treatment for fibromyalgia in a placebo-controlled design.


MATERIALS AND METHODS
Eleven patients were selected based on the American College of Rheumatology-90 criteria and implanted with an occipital nerve trial-lead stimulator. Baseline scores for pain, mood, and fatigue were acquired, and patients were randomized in a ten-week double-blinded crossover design with placebo and effective subsensory threshold stimulation (no paresthesias). After finalizing the trial, nine patients were implanted permanently; evaluation was performed prior to surgery and at six months after surgery for pain, fatigue, and mood of the number of trigger points and overall morbidity.


RESULTS
Significant results were found during the trial for a decrease in pain intensity (39.74%) on visual analogue scale (VAS; p < 0.001) and pain catastrophizing scale (PCS) during effective stimulation. A total of 9/11 patients responded to trial treatment; however, in two patients, this might be a placebo effect, recognizable due to the study design. Six months after permanent implantation, pain intensity remained decreased (44.01%) on VAS (p < 0.05). Besides the VAS, significant changes were noted for PCS, fatigue (modified fatigue impact scale), the number of trigger points, and overall morbidity (fibromyalgia impact questionnaire). There were no serious adverse events.


CONCLUSIONS
Our data strongly suggest that ONS is beneficial in the treatment of fibromyalgia. The beneficial effects are stable at six months after permanent implantation. Subsensory threshold stimulation is feasible in designing a placebo-controlled trial.
Variants within the immunoregulatory CBLB gene are associated with multiple sclerosis

A genome-wide association scan of ∼6.6 million genotyped or imputed variants in 882 Sardinian individuals with multiple sclerosis (cases) and 872 controls suggested association of CBLB gene variants with disease, which was confirmed in 1,775 cases and 2,005 controls (rs9657904, overall P = 1.60 × 10−10, OR = 1.40). CBLB encodes a negative regulator of adaptive immune responses, and mice lacking the ortholog are prone to experimental autoimmune encephalomyelitis, the animal model of multiple sclerosis.
The psychology of career theory – a new perspective?

Seeks to argue that recent developments in psychology have invalidated some theories of career development. Following a detailed explanation of the perspectives put forward by Bronfenbrenner and Plomin six frequently invoked career theories are considered. It is concluded that three are based on the now invalidated psychological assumptions and three are compatible with current psychology.
Cognitive function and oxidative stress after carotid endarterectomy: comparison of propofol to sevoflurane anesthesia.

OBJECTIVE
To examine the antioxidant role of propofol in ischemia-reperfusion during carotid endarterectomy (CEA) and its influence on cognitive dysfunction after CEA.


DESIGN
A randomized prospective study.


SETTING
Single-center study in a university hospital.


PARTICIPANTS
Forty-four patients.


INTERVENTIONS
Patients underwent elective CEA under general anesthesia with either sevoflurane (group S, n = 21) or propofol (group P, n = 23).


MEASUREMENTS AND MAIN RESULTS
Cognitive function was assessed with the Mini-Mental State Examination (MMSE) before CEA, 1 hour after CEA, and 24 hours after CEA. Blood samples from the radial artery and the internal jugular vein were drawn before carotid clamping and 5 minutes following unclamping, and peripheral blood was obtained 24 hours postoperatively. Samples were analyzed for lactate, S100B, and P-selectin concentrations and for the antioxidative markers malondialdehyde/low-density lipoprotein ratio and nitrate + nitrite concentrations. Compared with group S, patients in group P exhibited a greater increase in their MMSE values 24 hours postoperatively. Patients who had their MMSE performance reduced at 24 hours also were significantly fewer in group P (13% v 43% in group S, p<0.05). Significantly lower levels of lactate and S100B were observed in arterial and jugular vein samples in group P. In addition, the jugular vein-arterial differences of malondialdehyde-to-low-density lipoprotein ratio and nitrates + nitrites concentrations were lower during propofol anesthesia.


CONCLUSIONS
Propofol seemed to improve cognitive performance after CEA. This improvement was associated with decreased indices of ischemic cerebral damage and seemed to be due to antioxidative effect in the ischemic cerebral circulation.
Depigmented and polymerised house dust mite allergoid: allergen content, induction of IgG4 and clinical response.

BACKGROUND
Polymerised allergenic extracts (allergoids) are commonly used in allergen immunotherapy. Clinical efficacy and safety of these extracts have been demonstrated. Recently, allergen sequences have been identified by mass spectrometry in depigmented and polymerised (Dpg-Pol) extracts. The objectives of this study were to investigate the presence of allergens in Dpg-Pol extracts of house dust mite and to analyze the immunological changes induced by these extracts in asthmatic patients enrolled in a double-blind, placebo-controlled study.


METHODS
Dpg-Pol extracts were manufactured and vaccines with a composition of 50% Dermatophagoides pteronyssinus and 50% D. farinae (100 HEPL/ml) were prepared. Allergen composition was analyzed by mass spectrometry. Patients with asthma and rhinoconjunctivitis were treated in a 1-year, double-blind, placebo-controlled, parallel-group study with 6 up-dosing and monthly maintenance injections. Specific IgE and IgG4 titres to D. pteronyssinus, Der p 1 and Der p 2 were measured in patients' sera using the CAP system and direct ELISA experiments.


RESULTS
Sequences from the major allergens Der p 1 and Der p 2 and from other allergens were identified in native and Dpg-Pol extracts. There was a statistically significant increase in specific IgG4, a decrease in the ratio of IgE/IgG4 to D. pteronyssinus and a significant increase in specific IgG4 to Der p 1 and Der p 2 in the patients allotted to active treatment.


CONCLUSIONS
The detection of allergen sequences suggests preservation of major and minor allergens in Dpg-Pol allergoids from house dust mites. Efficacy in asthma treatment and the increase in specific IgG4 seem to be associated with the presence of major allergens in Dpg-Pol allergen extracts.
Different fever definitions and the rate of fever and neutropenia diagnosed in children with cancer: a retrospective two-center cohort study.

BACKGROUND
The definition of fever, and thus fever and neutropenia (FN), varies between different pediatric oncology centers. Higher temperature limit should reduce FN rates, but may increase rates of FN with complications by delaying therapy. This study determined if different fever definitions are associated with different FN rates.


PROCEDURE
Two pediatric oncology centers had used three fever definitions in 2004-2011: ear temperature ≥38.5 °C persisting ≥2 hours (low definition); axillary temperature ≥38.5 °C ≥ 2 hours or ≥39.0 °C once (middle); and ear temperature ≥39.0 °C once (high). Clinical information was retrospectively extracted from charts. FN rates were compared using mixed Poisson regression.


RESULTS
In 521 pediatric patients with cancer, 783 FN were recorded during 6,009 months cumulative chemotherapy exposure time (501 years; rate, 0.13/month [95% CI, 0.12-0.14]), 124 of them with bacteremia (16%; 0.021/month [0.017-0.025]). In univariate analysis, the high versus low fever definition was associated with a lower FN rate (0.10/month [0.08-0.11] vs. 0.15/month [0.13-0.16]; rate ratio, 0.66 [0.45-0.97]; P = 0.036), the middle definition was intermediate (0.13/month [0.11-0.15]). This difference was not confirmed in multivariate analysis (rate ratio, 0.94 [0.67-1.33]; P = 0.74). The high versus low definition was not associated with an increased rate of FN with bacteremia (multivariate rate ratio, 1.39 [0.53-3.62]; P = 0.50).


CONCLUSION
A higher fever definition was not associated with a lower FN rate, nor with an increased rate of FN with bacteremia. These may be false negative findings due to methodological limitations. These questions, with their potential impact on health-related quality of life, and on costs, need to be assessed in prospective studies.
Vernakalant hydrochloride for rapid conversion of atrial fibrillation: a phase 3, randomized, placebo-controlled trial.

BACKGROUND
The present study assessed the efficacy and safety of vernakalant hydrochloride (RSD1235), a novel compound, for the conversion of atrial fibrillation (AF).


METHODS AND RESULTS
Patients were randomized in a 2:1 ratio to receive vernakalant or placebo and were stratified by AF duration of 3 hours to 7 days (short duration) and 8 to 45 days (long duration). A first infusion of placebo or vernakalant (3 mg/kg) was given for 10 minutes, followed by a second infusion of placebo or vernakalant (2 mg/kg) 15 minutes later if AF was not terminated. The primary end point was conversion of AF to sinus rhythm for at least 1 minute within 90 minutes of the start of drug infusion in the short-duration AF group. A total of 336 patients were randomized and received treatment (short duration, n=220; long duration, n=116). Of the 145 vernakalant patients, 75 (51.7%) in the short-duration AF group converted to sinus rhythm (median time, 11 minutes) compared with 3 of the 75 placebo patients (4.0%; P<0.001). Overall, in the short- and long-duration AF groups, 83 of the 221 vernakalant patients (37.6%) experienced termination of AF compared with 3 of the 115 placebo patients (2.6%; P<0.001). Transient dysgeusia and sneezing were the most common side effects in vernakalant-treated patients. Four vernakalant-related serious adverse events (hypotension [2 events], complete atrioventricular block, and cardiogenic shock) occurred in 3 patients.


CONCLUSIONS
Vernakalant demonstrated rapid conversion of short-duration AF and was well tolerated.