LLukas22/scidocs huggingface dataset:
Static Analysis of Android Programs

• Our goal is to extend the Julia static analyzer, based on abstract interpretation, to perform formally correct analyses of Android programs. This article is an in depth description of such an extension,of the difficulties that we faced and of the results that we obtained. • We have extended the class analysis of the Julia analyzer, which lies at the heart of many other analyses, by considering some Android key specific features • Classcast, dead code, nullness and termination analysis are done. • Formally correct results in at most 7 min and on standard hardware. • As a language, Android is Java with an extended library for mobile and interactive applications, hence based on an eventdriven architecture. (WRONG)
Impact of package design and materials on reliability for temperature cycling, bend, and drop loading conditions

This paper presents a collection of test data showing how the choice of package design and material can have a different effect on performance depending on the loading conditions. Board level temperature cycling, drop (JESD22-B111), and cyclic bend (JESD22-B113) tests were performed on 0.4 mm ball pitch packages. Factors investigated for this evaluation include mold compound material, mold cap thickness (0.45 vs. 0.7 mm), ball pad finish (NiAu vs. Cu OSP), solder ball composition (SAC305, SAC105, SAC125M, Sn3.5Ag), solder volume (ball vs. bump), package material (RoHS vs Green), and board material (RoHS vs Green). The data presented in this paper indicates that lower silver content solder balls perform better under drop conditions, while temperature cycling reliability suffers as silver content decreases. In addition, mold compound material and thickness, die size, and solder volume have the opposite effect depending on the loading condition. The Green material for test board also showed lower performance than RoHS compliant board material.
Mobile collaborative learning using multicast MANETs

Collaborative learning outside the classroom is vital for many educational disciplines. Three educational scenarios held outdoors are analysed. In the first scenario, students investigate the ancient architecture, archaeological artefacts and historical location at an archaeological site. In the second scenario, students investigate the environmental and natural resource management, endangered species and flora at a national forest. The third scenario describes collaborative game-based learning at outdoors. Multicast Mobile Ad Hoc Networks (MANETs) are employed to support students’ communication and collaboration. Simulation results show the feasibility of multicast MANETs to support students’ communication and collaboration during these three outdoor educational scenarios.
Bayesian Warped Gaussian Processes

Warped Gaussian processes (WGP) [1] model output observations in regression tasks as a parametric nonlinear transformation of a Gaussian process (GP). The use of this nonlinear transformation, which is included as part of the probabilistic model, was shown to enhance performance by providing a better prior model on several data sets. In order to learn its parameters, maximum likelihood was used. In this work we show that it is possible to use a non-parametric nonlinear transformation in WGP and variationally integrate it out. The resulting Bayesian WGP is then able to work in scenarios in which the maximum likelihood WGP failed: Low data regime, data with censored values, classification, etc. We demonstrate the superior performance of Bayesian warped GPs on several real data sets.
Humoral Alloimmunity in Transplantation: Relevance of HLA Epitope Antigenicity and Immunogenicity

HLA mismatching is an important risk factor for antibody-mediated rejection and transplant failure. With the realization HLA antibodies recognize epitopes rather than antigens, it has become apparent that donor-recipient compatibility should be assessed at the epitope level. Recent developments have increased our understanding of the structural basis of HLA antigenicity, i.e., the reactivity with specific antibody and, immunogenicity, i.e., the ability to induce an antibody response. HLAMatchmaker is a computer algorithm that considers each HLA antigen as a series of small configurations of polymorphic residues referred to as eplets as essential components of HLA epitopes. This article addresses the relevance of determining epitope-specificities of HLA antibodies in the identification of acceptable mismatches for sensitized patients considered for transplantation. Permissible mismatching for non-sensitized patients aimed to prevent or reduce HLA antibody responses could consider epitope loads of mismatched antigens and the recently developed non-self-self paradigm of epitope immunogenicity.
Glucagon-like peptide-1 receptor imaging for the localisation of insulinomas: a prospective multicentre imaging study.

BACKGROUND
Small benign insulinomas are hard to localise, leading to difficulties in planning of surgical interventions. We aimed to prospectively assess the insulinoma detection rate of single-photon emission CT in combination with CT (SPECT/CT) with a glucagon-like peptide-1 receptor avid radiotracer, and compare detection rates with conventional CT/MRI techniques.


METHODS
In our prospective imaging study, we enrolled adults aged 25-81 years at centres in Germany, Switzerland, and the UK. Eligible patients had proven clinical and biochemical endogenous hyperinsulinaemic hypoglycaemia and no evidence for metastatic disease on conventional imaging. CT/MRI imaging was done at referring centres according to standard protocols. At three tertiary nuclear medicine centres, we used whole body planar images and SPECT/CT of the abdomen up to 168 h after injection of (111)In-[Lys40(Ahx-DTPA-(111)In)NH2]-exendin-4 ((111)In-DTPA-exendin-4) to identify insulinomas. Consenting patients underwent surgery and imaging findings were confirmed histologically.


FINDINGS
Between Oct 1, 2008, and Dec 31, 2011, we recruited 30 patients. All patients underwent (111)In-DTPA-exendin-4 imaging, 25 patients underwent surgery (with histological analysis), and 27 patients were assessed with CT/MRI. (111)In-DTPA-exendin-4 SPECT/CT correctly detected 19 insulinomas and four additional positive lesions (two islet-cell hyperplasia and two uncharacterised lesions) resulting in a positive predictive value of 83% (95% CI 62-94). One true negative (islet-cell hyperplasia) and one false negative (malignant insulinoma) result was identified in separate patients by (111)In-DTPA-exendin-4 SPECT/CT. Seven patients (23%) were referred to surgery on the basis of (111)In-DTPA-exendin-4 imaging alone. For 23 assessable patients, (111)In-DTPA-exendin-4 SPECT/CT had a higher sensitivity (95% [95% CI 74-100]) than did CT/MRI (47% [27-68]; p=0.011).


INTERPRETATION
(111)In-DTPA-exendin-4 SPECT/CT could provide a good second-line imaging strategy for patients with negative results on initial imaging with CT/MRI.


FUNDING
Oncosuisse, the Swiss National Science Foundation, and UK Department of Health.
Hindman's theorem: an ultrafilter argument in second order arithmetic

Hindman's Theorem is a prototypical example of a combinatorial theorem with a proof that uses the topology of the ultrafilters. We show how the methods of this proof, including topological arguments about ultrafilters, can be translated into second order arithmetic.
Convergence of finite volume monotone schemes for scalar conservation laws on bounded domains

This paper is devoted to the study of the finite volume methods used in the discretization of conservation laws defined on bounded domains. General assumptions are made on the data: the initial condition and the boundary condition are supposed to bemeasurable bounded functions.Using a generalized notion of solution to the continuous problem (namely the notion of entropy process solution, see [9]) and a uniqueness result on this solution, we prove that the numerical solution converges to the entropyweak solution of the continuous problem inLploc for every p ∈ [ 1,+∞). This also yields a new proof of the existence of an entropy weak solution.
Graph Cut Algorithms in Vision , Graphics and Machine Learning An Integrative Paper

This integrative paper studies graph-cut and network flow algorithms on graphs and compares its applications towards solving diverse problems in Computer Vision, Computer Graphics and Machine Learning. The following three papers form the core of this comparative study. • ’An Experimental Comparison of Min-Cut/MaxFlow Algorithms for Energy Minimization in Vision’ by Boykov et.al.[1] reformulates a variety of problems in computer vision namely image restoration, stereo and segmentation into energy minimization problems and solves them using graph-cut algorithms. • ’Graph Cut Textures: Image and Video Synthesis Using Graph Cuts’ by Kwatra et. al. [4] proposes a new algorithm for image and video texture synthesis in the area of Computer Graphics. At the core of their method is a graph-cut technique for computing optimal seams across multiple image patches which are to be blended and merged together to generate the syn-
Inequality aversion and voting on redistribution☆

Some people have a concern for a fair distribution of incomes while others do not. Does such a concern matter for majority voting on redistribution? Fairness preferences are relevant for redistribution outcomes only if fair-minded voters are pivotal. Pivotality, in turn, depends on the structure of income classes. We experimentally study voting on redistribution between two income classes and show that the effect of inequality aversion is asymmetric. Inequality aversion is more likely to matter if the "rich" are in majority. With a "poor" majority, we find that redistribution outcomes look as if all voters were exclusively motivated by self-interest.
Clinical utility of HIV-1 genotyping and expert advice: the Havana trial.

OBJECTIVE
To determine whether HIV-1 genotyping and expert advice add additional short-term virologic benefit in guiding antiretroviral changes in HIV+ drug-experienced patients.


DESIGN
A two factorial (genotyping and expert advice), randomized, open label, multi-center trial. The patients were stratified according to the number of treatment failures.


PATIENTS AND METHODS
HIV-1 infected patients on stable antiretroviral therapy who presented virological failure were included into the study. Genotypic testing was performed by using TrueGene HIV Genotyping kit and the results were interpreted by a software package (RetroGram, version 1.0). An expert advisory committee suggested the new therapeutic approach based on clinical information alone or on clinical information plus HIV-1 genotyping results. Plasma HIV-1 RNA load, CD4+ cell count and adverse events were recorded at baseline and every 12 weeks.


RESULTS
A total of 326 patients were included. The baseline CD4+ cell count and plasma HIV-1 RNA were 387 (+/- 224) x 10(6) cells/l and 4 (+/- 1) log(10) respectively. The proportion of patients with plasma HIV-1 RNA < 400 copies/ml at 24 weeks differed between genotyping and no genotyping arms (48.5 and 36.2%, P < 0.05). Factors associated with a higher probability of plasma HIV-1 RNA < 400 copies/ml were HIV-1 genotyping [odds ratio (OR), 1.7; 95% confidence interval (CI), 1.1-2.8; P = 0.016] and the expert advice in patients failing to a second-line antiretroviral therapy (OR, 3.2; 95% CI, 1.2-8.3; P = 0.016).


CONCLUSIONS
HIV-1 genotyping interpreted by a software package improves the virological outcome when it is added to the clinical information as a basis for decisions on changing antiretroviral therapy. The expert advice also showed virologic benefit in the second failure group.
Noninvasive Mechanical Ventilation Improves Breathing-Swallowing Interaction of Ventilator Dependent Neuromuscular Patients: A Prospective Crossover Study

BACKGROUND
Respiratory involvement in neuromuscular disorders may contribute to impaired breathing-swallowing interactions, swallowing disorders and malnutrition. We investigated whether the use of non-invasive ventilation (NIV) controlled by the patient could improve swallowing performances in a population of neuromuscular patients requiring daytime NIV.


METHODS
Ten neuromuscular patients with severe respiratory failure requiring extensive NIV use were studied while swallowing without and with NIV (while ventilated with a modified ventilator allowing the patient to withhold ventilation as desired). Breathing-swallowing interactions were investigated by chin electromyography, cervical piezoelectric sensor, nasal flow recording and inductive plethysmography. Two water-bolus sizes (5 and 10ml) and a textured yogurt bolus were tested in a random order.


RESULTS
NIV use significantly improved swallowing fragmentation (defined as the number of respiratory interruption of the swallowing of a single bolus) (p = 0.003) and breathing-swallowing synchronization (with a significant increase of swallows followed by an expiration) (p <0.0001). Patient exhibited piecemeal swallowing which was not influenced by NIV use (p = 0.07). NIV use also significantly reduced dyspnea during swallowing (p = 0.04) while preserving swallowing comfort, regardless of bolus type.


CONCLUSION
The use of patient controlled NIV improves swallowing parameters in patients with severe neuromuscular respiratory failure requiring daytime NIV, without impairing swallowing comfort.


TRIAL REGISTRATION
ClinicalTrials.gov NCT01519388.
Dimensions of meaning in the occupations of daily life.

BACKGROUND
According to the existential philosophers, meaning, purpose and choice are necessary for quality of life. Qualitative researchers exploring the perspectives of people who have experienced health crises have also identified the need for meaning, purpose and choice following life disruptions. Although espousing the importance of meaning in occupation, occupational therapy theory has been primarily preoccupied with purposeful occupations and thus appears inadequate to address issues of meaning within people's lives.


PURPOSE
This paper proposes that the fundamental orientation of occupational therapy should be the contributions that occupation makes to meaning in people's lives, furthering the suggestion that occupation might be viewed as comprising dimensions of meaning: doing, being, belonging and becoming. Drawing upon perspectives and research from philosophers, social scientists and occupational therapists, this paper will argue for a renewed understanding of occupation in terms of dimensions of meaning rather than as divisible activities of self-care, productivity and leisure.


PRACTICE IMPLICATIONS
Focusing on meaningful, rather than purposeful occupations more closely aligns the profession with its espoused aspiration to enable the enhancement of quality of life.
Boswellia frereana suppresses HGF-mediated breast cancer cell invasion and migration through inhibition of c-Met signalling

Hepatocyte growth factor (HGF) plays a pivotal role in breast cancer cell motility, invasion and angiogenesis. These pro-metastatic events are triggered through HGF coupling and activation of the c-Met receptor. Reports have demonstrated that HGF/c-Met signalling plays an important part in breast cancer progression and that their expression is linked to poor patient outcome. In the present study, we investigated the anti-metastatic potential of an extract from traditional Somalian frankincense, Boswellia frereana, on human breast cancer cells. In addition, we also examined the effect of this Boswellia frereana extract (BFE) upon HGF-mediated stimulation of the c-Met receptor. Two triple negative human breast cancer cell lines, BT549 and MDA-MB-231, were utilised in the study to examine the effect of BFE on tumour cell proliferation, migration, matrix-adhesion, angiogenesis and invasion. Cell migration was investigated using a Cell IQ time-lapsed motion analysis system; while tumour cell–matrix adhesion, angiogenesis and invasion were assessed through Matrigel-based in vitro assays. Breast cancer cell growth and spheroid formation was examined through proliferation assay and 3D non-scaffold cell culture techniques. Western Blotting was employed to determine the phosphorylation status of the c-Met receptor tyrosine kinase following BFE treatment and subsequent HGF stimulation. Following HGF treatment, the breast cancer cells displayed a significant increase in migration, matrix adhesion, vessel/tubule formation, invasion and c-Met activation. HGF did not appear to have any bearing on the proliferation rate or spheroid formation of these breast cancer cells. The addition of the BFE extract quenched the HGF-enhanced migratory, angiogenic and invasive potential of these cells. Further study revealed that BFE inhibited c-Met receptor tyrosine kinase phosphorylation within these breast cancer cells. Our findings reveal that BFE was able to significantly suppress the influence of HGF in breast cancer cell motility and invasion in vitro, through the ability of BFE to reduce HGF/c-Met signalling events. Therefore, these results indicate that BFE could play a novel role in the treatment of breast cancer.
From organic waste to biodiesel : Black soldier fly , Hermetia illucens , makes it feasible

Biodiesel is a renewable and environmentally friendly liquid fuel. However, the feedstock, predominantly crop oil, is a limited and expensive food resource which prevents large scale application of biodiesel. Development of non-food feedstocks are therefore, needed to fully utilize biodiesel’s potential. In this study, the larvae of a high fat containing insect, black soldier fly (Hermetia illucens) (BSFL), was evaluated for biodiesel production. Specifically, the BSFL was grown on organic wastes for 10 days and used for crude fat extraction by petroleum ether. The extracted crude fat was then converted into biodiesel by acid-catalyzed (1% H2SO4) esterification and alkaline-catalyzed (0.8% NaOH) transesterification, resulting in 35.5 g, 57.8 g and 91.4 g of biodiesel being produced from 1000 BSFL growing on 1 kg of cattle manure, pig manure and chicken manure, respectively. The major ester components of the resulting biodiesel were lauric acid methyl ester (35.5%), oleinic acid methyl ester (23.6%) and palmitic acid methyl ester (14.8%). Fuel properties of the BSFL fat-based biodiesel, such as density (885 kg/m), viscosity (5.8 mm/s), ester content (97.2%), flash point (123 C), and cetane number (53) were comparable to those of rapeseed-oil-based biodiesel. These results demonstrated that the organic waste-grown BSFL could be a feasible non-food feedstock for biodiesel production. 2010 Elsevier Ltd. All rights reserved.
Effects of non-steroidal anti-inflammatory drug treatments on cognitive decline vary by phase of pre-clinical Alzheimer disease: findings from the randomized controlled Alzheimer's Disease Anti-inflammatory Prevention Trial.

OBJECTIVE
We examined the effects of non-steroidal anti-inflammatory drugs on cognitive decline as a function of phase of pre-clinical Alzheimer disease.


METHODS
Given recent findings that cognitive decline accelerates as clinical diagnosis is approached, we used rate of decline as a proxy for phase of pre-clinical Alzheimer disease. We fit growth mixture models of Modified Mini-Mental State (3MS) Examination trajectories with data from 2388 participants in the Alzheimer's Disease Anti-inflammatory Prevention Trial and included class-specific effects of naproxen and celecoxib.


RESULTS
We identified three classes: "no decline", "slow decline", and "fast decline", and examined the effects of celecoxib and naproxen on linear slope and rate of change by class. Inclusion of quadratic terms improved fit of the model (-2 log likelihood difference: 369.23; p < 0.001) but resulted in reversal of effects over time. Over 4 years, participants in the slow-decline class on placebo typically lost 6.6 3MS points, whereas those on naproxen lost 3.1 points (p-value for difference: 0.19). Participants in the fast-decline class on placebo typically lost 11.2 points, but those on celecoxib first declined and then gained points (p-value for difference from placebo: 0.04), whereas those on naproxen showed a typical decline of 24.9 points (p-value for difference from placebo: <0.0001).


CONCLUSIONS
Our results appeared statistically robust but provided some unexpected contrasts in effects of different treatments at different times. Naproxen may attenuate cognitive decline in slow decliners while accelerating decline in fast decliners. Celecoxib appeared to have similar effects at first but then attenuated change in fast decliners.
Rules of intersensory integration in spatial scene analysis and speechreading

Audiovisual interactions observed in the ventriloquism and McGurk illusions were compared, using the same materials. The ventriloquism effect was estimated through a discordance detection task and the McGurk illusion through an identification task. The stimuli were visually displayed on a screen located in front of the participants’ head and acoustically delivered through one of nine hidden loudspeakers located from straight ahead (0°) to 80° (20° steps) left and right. The speaker’s face was either upright or inverted. The ventriloquism effect was affected by the degree of spatial separation, but unaffected by upright vs. inverted presentation of the face, or by the congruency of the stimuli. The McGurk illusion was of the same size whatever the loudspeaker location but was reduced by face inversion. The differences in the spatial and cognitive rules that govern both interactions are discussed in terms of specific functionality of the underlying mechanisms.
Seven-point checklist of dermoscopy revisited.

BACKGROUND
Most dermoscopic algorithms to diagnose melanoma were established more than 10 years ago and have been tested primarily on clear-cut melanomas and excised melanocytic naevi.


OBJECTIVES
To assess the diagnostic performance of pattern analysis and seven-point checklist on lesions that reflect the current clinical setting, compared with a revised seven-point checklist with a lower threshold for excision.


METHODS
Eight experienced dermatologists viewed dermoscopic images of 100 excised melanomas, 100 excised naevi and 100 monitored naevi. Each lesion was evaluated by pattern analysis and scored as naevus, melanoma or lesion to be excised. Images were then evaluated using the seven-point criteria, with both standard and revised thresholds for excision.


RESULTS
Pooled data using the pattern analysis algorithm showed that 82% of melanomas and 87·5% of monitored naevi were correctly scored as lesion to be excised and benign naevus, respectively. Using the standard and revised thresholds for the seven-point checklist, excision was recommended for 77·9% and 87·8% of the lesions in the melanoma set, respectively. The standard threshold produced 'no excision' recommendations for 85·6% of the monitored naevi, compared with 74·5% using the revised threshold. Pattern analysis, standard seven-point and revised seven-point algorithms resulted in recommendations of 'excision' for 63·6%, 60·3% and 72·0% of the excised naevi, respectively.


CONCLUSIONS
The diagnostic approach to naevi and melanoma should be adapted to the current clinical setting, in which patients may present with early-stage melanomas and multiple atypical naevi. To increase sensitivity, a revised seven-point checklist with a lower threshold for excision should be used.