LLukas22/scidocs huggingface dataset:
Using Model-Driven Engineering for Managing Safety Evidence: Challenges, Vision and Experience

Certification is a major prerequisite for most safety-critical systems before they can be put into operation. During certification, system suppliers often have to present a coherent body of evidence demonstrating that the developed systems are safe for operation. Regardless of the certification approach taken (process-based or product-based), collection of proper evidence at the proper stage ofdevelopment is critical  for successful certification. Currently,system suppliers and certification bodies alike are facing various challenges in relation to safety evidence collection. Notably, they find it hard to interpret the evidence requirements imposed by the safety standards within the domain of application; little support exists for recording, querying, and reporting evidence in a structured manner; and there is a general absence of guidelines on how the collected evidence supports the safety objectives. This paper states our position on how safety evidence should be characterized and managed. Specifically, we propose the application of Model-Driven Engineering as an enabler for performing the various tasks related to safety evidence management. We outline our current work on the specification of safety evidence requirements, upfront planning of evidence collection activities, tailoring of evidence information to domain-specific needs, and storage of evidence information. Based on this work, we identify a number of challenges that need further investigation and provide a future research agenda for managing safety evidence for software safety certification.
Long-term clinical follow-up of the multicentre, randomized study to test immunosuppressive therapy with oral prednisone for the prevention of restenosis after percutaneous coronary interventions: Cortisone plus BMS or DES veRsus BMS alone to EliminAte Restenosis (CEREA-DES).

AIMS
To analyse the clinical outcome at 4 years in patients with coronary artery disease treated with bare metal stents (BMS) vs. BMS and oral prednisone, or drug-eluting stents (DES), all assuming similar adjunctive medical treatment.


METHODS AND RESULTS
Five Italian hospitals enrolled 375 non-diabetic, ischaemic patients without contraindications to dual anti-platelet treatment or corticosteroid therapy in a randomized controlled study. The primary endpoint was the event-free survival of cardiovascular death, myocardial infarction, and recurrence of ischaemia needing repeated target vessel revascularization at 1 year, and this was significantly lower in the BMS group (80.8%) compared with the prednisone (88.0%) and DES group (88.8%, P = 0.04 and 0.006, respectively). The long-term analysis of the primary endpoint was a pre-specified aim of the trial, and was performed at 1447 days (median, IQ range = 1210-1641). Patients receiving BMS alone had significantly lower event-free survival (75.3%) compared with 84.1% in the prednisone group (HR: 0.447; 95% CI: 0.25-0.80, P = 0.007) and 80.6% in DES patients (HR: 0.519; 95% CI: 0.29-0.93, P = 0.03). Prednisone-treated patients did not develop new treatment-related clinical problems. Drug-eluting stents patients suffered more very late stent thrombosis as a cause of spontaneous myocardial infarction. The need for target vessel revascularization remained lower in the prednisone and DES groups (13.6 and 15.2%, respectively), compared with BMS (23.2%).


CONCLUSIONS
The clinical benefits of prednisone compared with BMS only persisted almost unchanged at 4 years. Drug-eluting stents performed better than BMS at long-term, although the advantages observed at 1 year were in part attenuated because of the occurrence of very late stent thrombosis and late revascularizations. Clinical Trial NCT 00369356.
Deixis and Conjunction in Multimodal Systems

In order to realize their full potential, multimodal interfaces need to support not just input from multiple modes, but single comnmnds optinmlly distributed across the available input modes. A multimodal language processing architecture is needed to integrate semantic content from the different modes. Johnston 1998a proposes a modular approach to multimodal language processing in which spoken language parsing is completed before lnultimodal parsing. In this paper, I will demonstrate the difficulties this approach faces as the spoken language parsing component is expanded to provide a compositional analysis of deictic expressions. I propose an alternative architecture in which spoken and multimodal parsing are tightly interleaved. This architecture greatly simplifies the spoken language parsing grm-nmar and enables predictive information fiom spoken language parsing to drive the application of multimodal parsing and gesture combination rules. I also propose a treatment of deictic numeral expressions that supports the broad range of pen gesture combinations that can be used to refer to collections of objects in the interface.
Outcome of surgically resected thymic carcinoma: a multicenter experience.

OBJECTIVE
Thymic carcinoma (TC) is a rare and invasive mediastinal tumor, with poor prognosis. Most of the previous published papers are single-institution based, reporting small series of patient, sometimes including palliative resection. This study collected patients with TC treated in 5 high-volume Italian Thoracic Surgery Institutions.


METHODS
A multicenter retrospective study of patients operated for TC between 2000 and 2011 was conducted. Exclusion criteria were: Neuroendocrine thymic neoplasms, debulking/palliative resection and tumor biopsy. Cause specific survival (CSS) was the primary endpoint.


RESULTS
Four hundred and seventy-eight patients underwent surgery for thymic malignancies: 40 of them (8.4%) had TC. Eleven (27.5%) received induction chemotherapy because of their radiological invasiveness. A complete resection (R0) was achieved in 36 (90%; 9/11 submitted to induction chemotherapy). Adjuvant radio/chemotherapy was offered to 37 patients, according to the type of surgical resection and tumor invasiveness. Three, 5 and 10-year survival rates were 79%, 75% and 58%. Recurrences developed in 10 patients. R0 resection (p<0.0003) and absence of tumor recurrences (p=0.03) resulted significant prognostic factors at univariate analysis. Independent CSS predictor was the achievement of a complete resection (p<0.05).


CONCLUSIONS
TC is a rare and invasive mediastinal tumor. A multimodal approach is indicated especially in TC invasive forms. The achievement of a complete surgical resection is fundamental to improve survival.
Sirolimus-eluting stent or paclitaxel-eluting stent vs balloon angioplasty for prevention of recurrences in patients with coronary in-stent restenosis: a randomized controlled trial.

CONTEXT
In patients with de novo coronary lesions, drug-eluting stents have drastically reduced restenosis risk compared with bare metal stents and conventional balloon angioplasty. It is less clear whether drug-eluting stents are superior to conventional balloon angioplasty for the treatment of patients with in-stent restenosis.


OBJECTIVES
To assess if drug-eluting stents are a more effective treatment of in-stent restenosis than conventional balloon angioplasty, and to assess the relative merits of 2 drug-eluting stents, a sirolimus-eluting stent and a paclitaxel-eluting stent.


DESIGN, SETTING, AND PARTICIPANTS
Randomized, open-label, active-controlled trial conducted among 300 patients with angiographically significant in-stent restenosis in 2 tertiary German centers from June 1, 2003, to October 20, 2003.


INTERVENTIONS
After pretreatment with 600 mg of clopidogrel for at least 2 hours before intervention, all patients were randomly assigned to 1 of 3 treatment groups: sirolimus stent, paclitaxel stent, or balloon angioplasty (100 patients in each group).


MAIN OUTCOME MEASURES
Primary end point: angiographic restenosis (diameter stenosis > or =50%) at 6-month follow-up angiography based on "in-segment" analysis. Primary analysis was comparison between stent groups and balloon angioplasty groups; a secondary analysis compared sirolimus and paclitaxel stents.


RESULTS
Follow-up angiography was performed in 275 (92%) of 300 patients. The incidence of angiographic restenosis was 44.6% (41/92) in the balloon angioplasty group, 14.3% (13/91) in the sirolimus stent group (P<.001 vs balloon angioplasty), and 21.7% (20/92) in the paclitaxel stent group (P = .001 vs balloon angioplasty). When compared with balloon angioplasty, receiving a sirolimus stent had a relative risk (RR) of angiographic restenosis of 0.32 (95% confidence interval [CI], 0.18-0.56); a paclitaxel stent had an RR of 0.49 (95% CI, 0.31-0.76). The incidence of target vessel revascularization was 33.0% (33/100) in the balloon angioplasty group, 8.0% (8/100) in the sirolimus stent group (P<.001 vs balloon angioplasty), and 19.0% (19/100) in the paclitaxel stent group (P = .02 vs balloon angioplasty). The secondary analysis showed a trend toward a lower rate of angiographic restenosis (P = .19) and a significantly lower rate of target vessel revascularization (P = .02) among sirolimus stent patients compared with paclitaxel stent patients.


CONCLUSIONS
In patients with in-stent restenosis, a strategy based on sirolimus- or paclitaxel-eluting stents is superior to conventional balloon angioplasty for the prevention of recurrent restenosis. Sirolimus-eluting stents may be superior to paclitaxel-eluting stents for treatment of this disorder.
Genital and cutaneous human papillomavirus (HPV) types in relation to conjunctival squamous cell neoplasia: A case-control study in Uganda

We investigated the role of infection with genital and cutaneous human papillomavirus types (HPV) in the aetiology of ocular surface squamous neoplasia (which includes both conjunctival intraepithelial neoplasia (CIN) and carcinoma) using data and biological material collected as part of a case-control study in Uganda. Among 81 cases, the prevalence of genital and cutaneous HPV types in tumour tissue did not differ significantly by histological grade of the lesion. The prevalence of genital HPV types did not differ significantly between cases and controls (both 38%; Odds ratio [OR] 1.0, 95% confidence interval [CI] 0.4–2.7, p = 1.0). The prevalence of cutaneous HPV types was 22% (18/81) among cases and 3% (1/29) among controls (OR 8.0, 95% CI 1.0–169, p = 0.04). We find no evidence of an association between genital HPV types and ocular surface squamous neoplasia. The prevalence of cutaneous HPV was significantly higher among cases as compared to controls. Although consistent with results from two other case-control studies, the relatively low prevalence of cutaneous HPV types among cases (which does not differ by histological grade of tumour) indicates that there remains considerable uncertainty about a role for cutaneous HPV in the aetiology of this tumour.
Two-dimensional packing problems: A survey

We consider problems requiring to allocate a set of rectangular items to larger rectangular standardized units by minimizing the waste. In two-dimensional bin packing problems these units are finite rectangles, and the objective is to pack all the items into the minimum number of units, while in two-dimensional strip packing problems there is a single standardized unit of given width, and the objective is to pack all the items within the minimum height. We discuss mathematical models, and survey lower bounds, classical approximation algorithms, recent heuristic and metaheuristic methods and exact enumerative approaches. The relevant special cases where the items have to be packed into rows forming levels are also discussed in detail. 2002 Elsevier Science B.V. All rights reserved.
Lateral Meniscus Posterior Root and Meniscofemoral Ligaments as Stabilizing Structures in the ACL-Deficient Knee: A Biomechanical Study

BACKGROUND
The biomechanical effects of lateral meniscal posterior root tears with and without meniscofemoral ligament (MFL) tears in anterior cruciate ligament (ACL)-deficient knees have not been studied in detail.


PURPOSE
To determine the biomechanical effects of the lateral meniscus (LM) posterior root tear in ACL-intact and ACL-deficient knees. In addition, the biomechanical effects of disrupting the MFLs in ACL-deficient knees with meniscal root tears were evaluated.


STUDY DESIGN
Controlled laboratory study.


METHODS
Ten paired cadaveric knees were mounted in a 6-degrees-of-freedom robot for testing and divided into 2 groups. The sectioning order for group 1 was (1) ACL, (2) LM posterior root, and (3) MFLs, and the order for group 2 was (1) LM posterior root, (2) ACL, and (3) MFLs. For each cutting state, displacements and rotations of the tibia were measured and compared with the intact state after a simulated pivot-shift test (5-N·m internal rotation torque combined with a 10-N·m valgus torque) at 0°, 20°, 30°, 60°, and 90° of knee flexion; an anterior translation load (88 N) at 0°, 30°, 60°, and 90° of knee flexion; and internal rotation (5 N·m) at 0°, 30°, 60°, 75°, and 90°.


RESULTS
Cutting the LM root and MFLs significantly increased anterior tibial translation (ATT) during a pivot-shift test at 20° and 30° when compared with the ACL-cut state (both Ps < .05). During a 5-N·m internal rotation torque, cutting the LM root in ACL-intact knees significantly increased internal rotation by between 0.7° ± 0.3° and 1.3° ± 0.9° (all Ps < .05) except at 0° (P = .136). When the ACL + LM root cut state was compared with the ACL-cut state, the increase in internal rotation was significant at greater flexion angles of 75° and 90° (both Ps < .05) but not between 0°and 60° (all Ps > .2). For an anterior translation load, cutting the LM root in ACL-deficient knees significantly increased ATT only at 30° (P = .007).


CONCLUSION
The LM posterior root was a significant stabilizer of the knee for ATT during a pivot-shift test at lower flexion angles and internal rotation at higher flexion angles.


CLINICAL RELEVANCE
Increased knee anterior translation and rotatory instability due to posterior lateral meniscal root disruption may contribute to increased loads on an ACL reconstruction graft. It is recommended that lateral meniscal root tears be repaired at the same time as an ACL reconstruction to prevent possible ACL graft overload.
Synchrony of Clinical and Laboratory Surveillance for Influenza in Hong Kong

BACKGROUND
Consultation rates of influenza-like illness (ILI) in an outpatient setting have been regarded as a good indicator of influenza virus activity in the community. As ILI-like symptoms may be caused by etiologies other than influenza, and influenza virus activity in the tropics and subtropics is less predictable than in temperate regions, the correlation between of ILI and influenza virus activity in tropical and subtropical regions is less well defined.


METHODOLOGY AND PRINCIPAL FINDINGS
In this study, we used wavelet analysis to investigate the relationship between seasonality of influenza virus activity and consultation rates of ILI reported separately by General Out-patient Clinics (GOPC) and General Practitioners (GP). During the periods 1998-2000 and 2002-2003, influenza virus activity exhibited both annual and semiannual cycles, with one peak in the winter and another in late spring or early summer. But during 2001 and 2004-2006, only annual cycles could be clearly identified. ILI consultation rates in both GOPC and GP settings share a similar non-stationary seasonal pattern. We found high coherence between ILI in GOPC and influenza virus activity for the annual cycle, but this was only significant (p<0.05) during the periods 1998-1999 and 2002-2006. For the semiannual cycle high coherence (p<0.05) was also found significant during the period 1998-1999 and year 2003 when two peaks of influenza were evident. Similarly, ILI in GP setting is also associated with influenza virus activity for both the annual and semiannual cycles. On average, oscillation of ILI in GP and of ILI in GOPC preceded influenza virus isolation by approximately four and two weeks, respectively.


CONCLUSIONS
Our findings suggest that consultation rates of ILI precede the oscillations of laboratory surveillance by at least two weeks and can be used as a predictor for influenza epidemics in Hong Kong. The validity of our model for other tropical regions needs to be explored.
The Monadic Second-order Logic of Graphs VI: On Several Representations of Graphs by Relational Structures

Page 117: Email is courcell@labri.u-bordeaux.fr. Page 120, line 4: “... larger than that of T.“. Page 121, line 6: “... so that A can be of the form . ..“. Page 122, first line of the proof: “... (VX.(X E Xi *$i (x))} . ..“. Page 130, line 8 and page 133, line 1: read v instead of v. Page 131, line 3 of Remark 3.4: < instead of d . Page 133, lines 1,3,4 of the proof: replace “only” by “the one” (3 times). Page 134, last line: read “... m = k2 + 1.“. Page 135, line 7: The link mark is (S) not (5). Page 138, 5 lines before Proposition 6.1: read und (Bp) instead of und(Bf ). Page 142, line before Proposition 6.6: “... the unique one in . . . “.
Reflex Torque Response to Movement of the Spastic Elbow: Theoretical Analyses and Implications for Quantification of Spasticity

A parametric model of the human reflex torque response to a large-amplitude, constant angular velocity elbow extension was developed in order to help quantify spasticity in hemiparetic stroke patients, and to better understand its pathophysiology. The model accounted for the routinely observed leveling of torque (i.e., a plateau) at a mean angular increment of 51°±10° s.d. (n=98) after the initial rise. This torque “plateau” was observed in all eight subjects, and in 98 of 125 trials across 25 experimental sessions. The occurrence of this plateau cannot be explained by decreases in elbow flexor moment arms during elbow extension. Rather, the plateau is attributable to a consistent leveling in muscle activation as confirmed both qualitatively from recordings of rectified, smoothed electromyograph (EMG) activity, and quantitatively using an EMG coefficient model. A parametric model was developed in which the pattern of muscle activation in the stretch reflex response of elbow flexors was described as a cumulative normal distribution with respect to joint angle. Two activation functions, one related to biceps and the other to brachioradialis/brachialis, were incorporated into the model in order to account for observations of a bimodal angular stiffness profile. The resulting model yielded biologically plausible parameters of the stretch reflex response which may prove useful for quantifying spasticity. In addition, the model parameters had clear pathophysiological analogs, which may help us understand the nature of the stretch reflex response in spastic muscles. © 1999 Biomedical Engineering Society. PAC99: 8719Rr, 8719Xx, 8719St, 8719Nn, 8719Ff, 8710+e
Capturing community search expertise for personalized web search using snippet-indexes

We describe and evaluate an approach to capturing and re-using search expertise within a community of like minded searchers, such as the employees of a company or organisation. Within knowledge based industries, search expertise - the ability to quickly and accurately locate information according to a specific information need - is an important corporate asset and in our approach we attempt to capture this knowledge by mining the title and snippet texts of results that have been selected by community members in response to their queries. Our assumption is that the snippet text of a result must play a role in helping users to judge the initial relevance of that result and that the snippet terms of selected results must contain especially informative terms about the goals and preferences of the searchers. In other words, results are selected because the user recognises certain combinations of terms in their snippets which are related to their information needs. Our approach seeks to build a community-based snippet index that reflects the evolving interests of a group of searchers. This index is then used to re-rank the results returned by some underlying search engine by boosting the ranking of key results that have been frequently selected for similar queries by community members in the past.
Mathematical Foundations of Computer Science

Problem 2. (20 points) Let X, Y, Z be any three nonempty sets and let g : Y → Z be any function. Define the function, Lg : Y X → Z , (Lg, as a reminder that we compose with g on the left), by Lg(f) = g ◦ f, for every function, f : X → Y . (a) Prove that if Y = Z and g = idY , then LidY (f) = f, for all f : X → Y . Let T be another nonempty set and let h : Z → T be any function. Prove that Lh◦g = Lh ◦ Lg. (b) Use (a) to prove that if g is injective, then Lg : Y X → Z is also injective and if g is surjective, then Lg : Y X → Z is also surjective.
Domestication, Genomics and the Future for Banana

BACKGROUND
Cultivated bananas and plantains are giant herbaceous plants within the genus Musa. They are both sterile and parthenocarpic so the fruit develops without seed. The cultivated hybrids and species are mostly triploid (2n = 3x = 33; a few are diploid or tetraploid), and most have been propagated from mutants found in the wild. With a production of 100 million tons annually, banana is a staple food across the Asian, African and American tropics, with the 15 % that is exported being important to many economies.


SCOPE
There are well over a thousand domesticated Musa cultivars and their genetic diversity is high, indicating multiple origins from different wild hybrids between two principle ancestral species. However, the difficulty of genetics and sterility of the crop has meant that the development of new varieties through hybridization, mutation or transformation was not very successful in the 20th century. Knowledge of structural and functional genomics and genes, reproductive physiology, cytogenetics, and comparative genomics with rice, Arabidopsis and other model species has increased our understanding of Musa and its diversity enormously.


CONCLUSIONS
There are major challenges to banana production from virulent diseases, abiotic stresses and new demands for sustainability, quality, transport and yield. Within the genepool of cultivars and wild species there are genetic resistances to many stresses. Genomic approaches are now rapidly advancing in Musa and have the prospect of helping enable banana to maintain and increase its importance as a staple food and cash crop through integration of genetical, evolutionary and structural data, allowing targeted breeding, transformation and efficient use of Musa biodiversity in the future.
CS229 Titanic – Machine Learning From Disaster

In this project, we see how we can use machine-learning techniques to predict survivors of the Titanic. With a dataset of 891 individuals containing features like sex, age, and class, we attempt to predict the survivors of a small test group of 418. In particular, compare different machine learning techniques like Naïve Bayes, SVM, and decision tree analysis.
3D Knowledge-Based Segmentation Using Pose-Invariant Higher-Order Graphs

Segmentation is a fundamental problem in medical image analysis. The use of prior knowledge is often considered to address the ill-posedness of the process. Such a process consists in bringing all training examples in the same reference pose, and then building statistics. During inference, pose parameters are usually estimated first, and then one seeks a compromise between data-attraction and model-fitness with the prior model. In this paper, we propose a novel higher-order Markov Random Field (MRF) model to encode pose-invariant priors and perform 3D segmentation of challenging data. The approach encodes data support in the singleton terms that are obtained using machine learning, and prior constraints in the higher-order terms. A dual-decomposition-based inference method is used to recover the optimal solution. Promising results on challenging data involving segmentation of tissue classes of the human skeletal muscle demonstrate the potentials of the method.