LLukas22/scidocs huggingface dataset:
Bridging the Gap between Software Development and Information Security

business units and thus not even practiced in a cohesive, coherent manner. In the worst cases, busy business unit executives trade roving bands of developers like Pokémon cards in a fifth-grade classroom (in an attempt to get ahead). Suffice it to say, none of this is good. The disconnect between security and development has ultimately produced software development efforts that lack any sort of contemporary understanding of technical security risks. Today's complex and highly connected computing environments trigger myriad security concerns, so by blowing off the idea of security entirely, software builders virtually guarantee that their creations will have way too many security weaknesses that could—and should—have been avoided. This article presents some recommendations for solving this problem. Our approach is born out of experience in two diverse fields: software security and information security. Central among our recommendations is the notion of using the knowledge inherent in information security organizations to enhance secure software development efforts. Don't stand so close to me Best practices in software security include a manageable number of simple activities that should be applied throughout any software development process (see Figure 1). These lightweight activities should start at the earliest stages of software development and then continue throughout the development process and into deployment and operations. Although an increasing number of software shops and individual developers are adopting the software security touchpoints we describe here as their own, they often lack the requisite security domain knowledge required to do so. This critical knowledge arises from years of observing system intrusions, dealing with malicious hackers, suffering the consequences of software vulnera-bilities, and so on. Put in this position , even the best-intended development efforts can fail to take into account real-world attacks previously observed on similar application architectures. Although recent books 1,2 are starting to turn this knowledge gap around, the science of attack is a novel one. Information security staff—in particular, incident handlers and vulnerability/patch specialists— have spent years responding to attacks against real systems and thinking about the vulnerabilities that spawned them. In many cases, they've studied software vulnerabili-ties and their resulting attack profiles in minute detail. However, few information security professionals are software developers (at least, on a full-time basis), and their solution sets tend to be limited to reactive techniques such as installing software patches, shoring up firewalls, updating intrusion detection signature databases, and the like. It's very rare to find information security …
International trade standards for commodities and products derived from animals: the need for a system that integrates food safety and animal disease risk management.

A case is made for greater emphasis to be placed on value chain management as an alternative to geographically based disease risk mitigation for trade in commodities and products derived from animals. The geographic approach is dependent upon achievement of freedom in countries or zones from infectious agents that cause so-called transboundary animal diseases, while value chain-based risk management depends upon mitigation of animal disease hazards potentially associated with specific commodities or products irrespective of the locality of production. This commodity-specific approach is founded on the same principles upon which international food safety standards are based, viz. hazard analysis critical control points (HACCP). Broader acceptance of a value chain approach enables animal disease risk management to be combined with food safety management by the integration of commodity-based trade and HACCP methodologies and thereby facilitates 'farm to fork' quality assurance. The latter is increasingly recognized as indispensable to food safety assurance and is therefore a pre-condition to safe trade. The biological principles upon which HACCP and commodity-based trade are based are essentially identical, potentially simplifying sanitary control in contrast to current separate international sanitary standards for food safety and animal disease risks that are difficult to reconcile. A value chain approach would not only enable more effective integration of food safety and animal disease risk management of foodstuffs derived from animals but would also ameliorate adverse environmental and associated socio-economic consequences of current sanitary standards based on the geographic distribution of animal infections. This is especially the case where vast veterinary cordon fencing systems are relied upon to separate livestock and wildlife as is the case in much of southern Africa. A value chain approach would thus be particularly beneficial to under-developed regions of the world such as southern Africa specifically and sub-Saharan Africa more generally where it would reduce incompatibility between attempts to expand and commercialize livestock production and the need to conserve the subcontinent's unparalleled wildlife and wilderness resources.
Exercise training in patients with advanced chronic heart failure (NYHA IIIb) promotes restoration of peripheral vasomotor function, induction of endogenous regeneration, and improvement of left ventricular function.

BACKGROUND
Attenuated peripheral perfusion in patients with advanced chronic heart failure (CHF) is partially the result of endothelial dysfunction. This has been causally linked to an impaired endogenous regenerative capacity of circulating progenitor cells (CPC). The aim of this study was to elucidate whether exercise training (ET) affects exercise intolerance and left ventricular (LV) performance in patients with advanced CHF (New York Heart Association class IIIb) and whether this is associated with correction of peripheral vasomotion and induction of endogenous regeneration.


METHODS AND RESULTS
Thirty-seven patients with CHF (LV ejection fraction 24+/-2%) were randomly assigned to 12 weeks of ET or sedentary lifestyle (control). At the beginning of the study and after 12 weeks, maximal oxygen consumption (Vo(2)max) and LV ejection fraction were determined; the number of CD34(+)/KDR(+) CPCs was quantified by flow cytometry and CPC functional capacity was determined by migration assay. Flow-mediated dilation was assessed by ultrasound. Capillary density was measured in skeletal muscle tissue samples. In advanced CHF, ET improved Vo(2)max by +2.7+/-2.2 versus -0.8+/-3.1 mL/min/kg in control (P=0.009) and LV ejection fraction by +9.4+/-6.1 versus -0.8+/-5.2% in control (P<0.001). Flow-mediated dilation improved by +7.43+/-2.28 versus +0.09+/-2.18% in control (P<0.001). ET increased the number of CPC by +83+/-60 versus -6+/-109 cells/mL in control (P=0.014) and their migratory capacity by +224+/-263 versus -12+/-159 CPC/1000 plated CPC in control (P=0.03). Skeletal muscle capillary density increased by +0.22+/-0.10 versus -0.02+/-0.16 capillaries per fiber in control (P<0.001).


CONCLUSIONS
Twelve weeks of ET in patients with advanced CHF is associated with augmented regenerative capacity of CPCs, enhanced flow-mediated dilation suggestive of improvement in endothelial function, skeletal muscle neovascularization, and improved LV function. Clinical Trial Registration- http://www.clinicaltrials.gov. Unique Identifier: NCT00176384.
A new record of Craspedacusta sowerbii, Lankester 1880 (Cnidaria, Limnomedusae) in Northern Italy

A new record of the freshwater jellyfish Craspedacusta sowerbii in Northern Italy is reported. The medusae bloom occurred in a small oligo-mesotrophic artificial lake during July, 2009. At the time of sampling, the medusae were all immature, reached low density and showed feeding preference towards the Daphnia complex of species, the most abundant zooplanktonic species in the lake. Negative feeding selectivity towards small Rotifera was demonstrated. The occasional occurrence of a C. sowerbii bloom in this lake suggests the distribution range of this species may be largely underestimated, and its potential impact on the zooplankton community remains unknown.
Author name disambiguation

Author Name Disambiguation Neil R. Smalheiser and Vetle I. Torvik
Faecal calprotectin in patients with suspected colorectal cancer: a diagnostic accuracy study.

BACKGROUND
NICE guidance exists for the use of faecal calprotectin (FC) when irritable bowel syndrome or inflammatory bowel disease are suspected. Often, however, colorectal cancer is considered within the differential. Should FC have a high diagnostic accuracy for colorectal cancer, it may be applicable as a primary care screening test for all patients with lower gastrointestinal symptoms.


AIM
To determine the negative and positive predictive value (NPV/PPV) of FC in patients referred from primary care with suspected colorectal cancer.


DESIGN AND SETTING
A diagnostic accuracy study conducted at a single secondary care site


METHOD
Consenting patients referred with suspected colorectal cancer within the '2-week wait' pathway provided a stool sample for FC prior to investigation. FC levels were reconciled with end diagnoses: cancer, adenomatous polyps ≥10 mm, and all enteric organic disease.


RESULTS
A total of 654 patients completed the evaluation; median age 69 years, female 56%. The NPV for colorectal cancer was 98.6% and 97.2% when including polyps ≥10 mm. The PPV for all organic enteric disease was 32.7%. The diagnostic yield for cancer based on clinical suspicion was 6.3%. By altering the FC cut-off to fix the NPV at 97.0%, the PPV for cancer increased from 8.7% to 13.3%.


CONCLUSION
FC has a high NPV for colorectal cancer and significant polyps in patients with suspected cancer. In total, 27.8% of patients had a normal FC and could safely have been spared a '2-week wait' referral. The addition of FC testing into the current symptom-based assessment has the potential to increase colorectal cancer detection rate yet be clinically and cost effective.
Exploiting Wearable Goniometer Technology for Motion Sensing Gloves

This paper presents an innovative wearable kinesthetic glove realized with knitted piezoresistive fabric (KPF) sensor technology. The glove is conceived to capture hand movement and gesture by using KPF in a double-layer configuration working as angular sensors (electrogoniometers). The sensing glove prototype is endowed by three KPF goniometers, used to track flexion and extension movement of metacarpophalangeal joint of thumb, index, and middle fingers. The glove is devoted to the continuous monitoring of patients during their daily-life activities, in particular for stroke survivors during their rehabilitation. The prototype performances have been evaluated in comparison with an optical tracking system considered as a gold standard both for relieving static and dynamic posture and gesture of the hand. The introduced prototype has shown very interesting figures of merit. The angular error, evaluated through the standard Bland Altman analysis, has been estimated in ${\bf \pm 3^\circ}$ which is slightly less accurate than commercial electrogoniometers. Moreover, a new conceptual prototype design, preliminary evaluated within this study, is presented and discussed in order to solve actual limitations in terms of number and type of sensor connections, avoiding mechanical constraints given by metallic inextensible wires and improving user comfort.
Doctors’ views of disulfiram and their response to relapse in alcohol-dependent patients, Free State, 2009

BACKGROUND
Disulfiram is the oldest and best known drug to prevent relapse after detoxification from alcohol. Effective use of the drug is dependent on stringent monitoring and high levels of external motivation. Doctors' perceptions about the drug have not been investigated extensively.


AIM
We investigated the perceptions and practices of doctors involved in relapse prevention in alcoholics with regard to disulfiram and their response to relapse.


SETTING
The study population consisted of 60 doctors from the Free State Province, involved in the follow-up of alcoholics across various work settings.


METHODS
A cross-sectional descriptive study design was used, and data collection involved the use of a questionnaire and semi-structured interviews. Quantitative results are presented in figures and percentages to provide a background for the qualitative findings that are clustered in themes.


RESULTS
A quarter of participants did not prescribe disulfiram, another quarter prescribed disulfiram routinely after detoxification, and half of them prescribed it for selected cases only. Subject to affordability, selection of disulfiram was mainly determined by the perceived level of the patient's motivation. External motivation sometimes took the form of threats of bodily harm or death caused by drinking. Some participants regarded relapse as confirmation of poor motivation and even a valid reason for terminating the doctor-patient relationship.


CONCLUSION
Doctors perceive disulfiram as a psychological tool to induce motivation through creating fear of drinking. Failure and success are perceived as related to the level of motivation. These perceptions could be unfair as biological factors in inter-patient variability in response are ignored.
Effects of Dietary n-3 Fatty Acids on Hepatic and Peripheral Insulin Sensitivity in Insulin-Resistant Humans

OBJECTIVE
Dietary n-3 polyunsaturated fatty acids, including eicosapentaenoic acid (EPA) and docosahexaenoic acid (DHA), prevent insulin resistance and stimulate mitochondrial biogenesis in rodents, but the findings of translational studies in humans are thus far ambiguous. The aim of this study was to evaluate the influence of EPA and DHA on insulin sensitivity, insulin secretion, and muscle mitochondrial function in insulin-resistant, nondiabetic humans using a robust study design and gold-standard measurements.


RESEARCH DESIGN AND METHODS
Thirty-one insulin-resistant adults received 3.9 g/day EPA+DHA or placebo for 6 months in a randomized double-blind study. Hyperinsulinemic-euglycemic clamp with somatostatin was used to assess hepatic and peripheral insulin sensitivity. Postprandial glucose disposal and insulin secretion were measured after a meal. Measurements were performed at baseline and after 6 months of treatment. Abdominal fat distribution was evaluated by MRI. Muscle oxidative capacity was measured in isolated mitochondria using high-resolution respirometry and noninvasively by magnetic resonance spectroscopy.


RESULTS
Compared with placebo, EPA+DHA did not alter peripheral insulin sensitivity, postprandial glucose disposal, or insulin secretion. Hepatic insulin sensitivity, determined from the suppression of endogenous glucose production by insulin, exhibited a small but significant improvement with EPA+DHA compared with placebo. Muscle mitochondrial function was unchanged by EPA+DHA or placebo.


CONCLUSIONS
This study demonstrates that dietary EPA+DHA does not improve peripheral glucose disposal, insulin secretion, or skeletal muscle mitochondrial function in insulin-resistant nondiabetic humans. There was a modest improvement in hepatic insulin sensitivity with EPA+DHA, but this was not associated with any improvements in clinically meaningful outcomes.
Metabolic Engineering of Bacteria

Metabolic glycoengineering is a technique introduced in the early 90s of the last century by Reutter et al.. It utilises the ability of cells to metabolically convert sugar derivatives with bioorthogonal side chains like azides or alkynes and by that incorporation into several glyco structures. Afterwards, the carbohydrates can be labelled to study their distribution, dynamics and roles in different biological processes. So far many studies were performed on mammal cell lines as well as in small animals. Very recently, bacterial glyco-structures were targeted by glycoengineering, showing promising results in infection prevention by reducing pathogen adhesion towards human epithelial cells. Introduction Bacteria were among the first life forms to appear on earth, and are present in most habitats on the planet, e. g., they live in symbiosis with plants and animals. Compared to human cells there are ten times as many bacterial cells in our body. Most of them are harmless or even beneficial. But some species are pathogenic and cause infectious diseases with more than 1.2 million deaths each year [1]. Those infections include cholera, syphilis, anthrax, leprosy, and bubonic plague as well as respiratory infections like tuberculosis. 1 This article is part of the Proceedings of the Beilstein Glyco-Bioinformatics Symposium 2013. www.proceedings.beilstein-symposia.org Discovering the Subtleties of Sugars June 10 – 14, 2013, Potsdam, Germany
Improving Word Representations via Global Context and Multiple Word Prototypes

Unsupervised word representations are very useful in NLP tasks both as inputs to learning algorithms and as extra word features in NLP systems. However, most of these models are built with only local context and one representation per word. This is problematic because words are often polysemous and global context can also provide useful information for learning word meanings. We present a new neural network architecture which 1) learns word embeddings that better capture the semantics of words by incorporating both local and global document context, and 2) accounts for homonymy and polysemy by learning multiple embeddings per word. We introduce a new dataset with human judgments on pairs of words in sentential context, and evaluate our model on it, showing that our model outperforms competitive baselines and other neural language models. 1
Longevity of implantable cardioverter-defibrillators for cardiac resynchronization therapy in current clinical practice: an analysis according to influencing factors, device generation, and manufacturer

AIMS
Device replacement at the time of battery depletion of implantable cardioverter-defibrillators (ICDs) may carry a considerable risk of complications and engenders costs for healthcare systems. Therefore, ICD device longevity is extremely important both from a clinical and economic standpoint. Cardiac resynchronization therapy defibrillators (CRT-D) battery longevity is shorter than ICDs. We determined the rate of replacements for battery depletion and we identified possible determinants of early depletion in a series of patients who had undergone implantation of CRT-D devices.


METHODS AND RESULTS
We retrieved data on 1726 consecutive CRT-D systems implanted from January 2008 to March 2010 in nine centres. Five years after a successful CRT-D implantation procedure, 46% of devices were replaced due to battery depletion. The time to device replacement for battery depletion differed considerably among currently available CRT-D systems from different manufacturers, with rates of batteries still in service at 5 years ranging from 52 to 88% (log-rank test, P < 0.001). Left ventricular lead output and unipolar pacing configuration were independent determinants of early depletion [hazard ratio (HR): 1.96; 95% 95% confidence interval (CI): 1.57-2.46; P < 0.001 and HR: 1.58, 95% CI: 1.25-2.01; P < 0.001, respectively]. The implantation of a recent-generation device (HR: 0.57; 95% CI: 0.45-0.72; P < 0.001), the battery chemistry and the CRT-D manufacturer (HR: 0.64; 95% CI: 0.47-0.89; P = 0.008) were additional factors associated with replacement for battery depletion.


CONCLUSION
The device longevity at 5 years was 54%. High left ventricular lead output and unipolar pacing configuration were associated with early battery depletion, while recent-generation CRT-Ds displayed better longevity. Significant differences emerged among currently available CRT-D systems from different manufacturers.
Two-Year Trajectory of Fall Risk in People With Parkinson Disease: A Latent Class Analysis.

OBJECTIVE
To examine fall risk trajectories occurring naturally in a sample of individuals with early to middle stage Parkinson disease (PD).


DESIGN
Latent class analysis, specifically growth mixture modeling (GMM), of longitudinal fall risk trajectories.


SETTING
Assessments were conducted at 1 of 4 universities.


PARTICIPANTS
Community-dwelling participants with PD of a longitudinal cohort study who attended at least 2 of 5 assessments over a 2-year follow-up period (N=230).


INTERVENTIONS
Not applicable.


MAIN OUTCOME MEASURES
Fall risk trajectory (low, medium, or high risk) and stability of fall risk trajectory (stable or fluctuating). Fall risk was determined at 6 monthly intervals using a simple clinical tool based on fall history, freezing of gait, and gait speed.


RESULTS
The GMM optimally grouped participants into 3 fall risk trajectories that closely mirrored baseline fall risk status (P=.001). The high fall risk trajectory was most common (42.6%) and included participants with longer and more severe disease and with higher postural instability and gait disability (PIGD) scores than the low and medium fall risk trajectories (P<.001). Fluctuating fall risk (posterior probability <0.8 of belonging to any trajectory) was found in only 22.6% of the sample, most commonly among individuals who were transitioning to PIGD predominance.


CONCLUSIONS
Regardless of their baseline characteristics, most participants had clear and stable fall risk trajectories over 2 years. Further investigation is required to determine whether interventions to improve gait and balance may improve fall risk trajectories in people with PD.
Application of a level set method for simulation of droplet collisions

A level set technique for interface tracking is presented, both for the continuum surface force formulation and the ghost fluid method approach. A projection method is used to solve incompressible Navier– Stokes equations that are coupled to a transport equation for the level set function, defined as the algebraic distance to interface. Results are presented for head-on droplet collisions in coalescence and reflexive regimes with a 2D axi-symmetric code, and for an off-center droplet collision in a separation regime for a large impact parameter with 3D code. Simulations provided realistic and various droplet collision behaviors and they correspond to experimental observations. 2005 Elsevier Ltd. All rights reserved.
MODELING OF MACHINED SURFACE ROUGHNESS AND OPTIMIZATION OF CUTTING PARAMETERS IN FACE MILLING

The surface quality is one of the most specified customer requirements and the major indicator of surface quality on machined parts is surface roughness. The surface roughness is mainly a result of various controllable or uncontrollable process parameters and it is harder to attain and track than physical dimensions are. A considerable number of studies have researched the effects of the cutting speed, feed, depth of cut, nose radius and other factors on the surface roughness. In recent studies 1, 2, 3 the effects of some factors on surface roughness has been evaluated and models has been developed. A central task in science and engineering practice is to develop models that give a satisfactory description of physical systems being observed. The goal of this study is to obtain a mathematical model that relates the surface roughness to three cutting parameters in face milling, precisely to the cutting speed, feed rate and depth of cut. In this work two different approaches have been used in order to get the mathematical models. The first approach is a design of experiment (DOE) together with an analysis of variance (ANOVA) and regression analysis (RA). The second approach is modeling by means of artificial neural networks (ANNs).