LLukas22/scidocs huggingface dataset:
A Template for Scatter Search and Path Relinking

Scatter search and its generalized form called path relinking are evolutionary methods that have recently been shown to yield promising outcomes for solving combinatorial and nonlinear optimization problems. Based on formulations originally proposed in the 1960s for combining decision rules and problem constraints, these methods use strategies for combining solution vectors that have proved effective for scheduling, routing, financial product design, neural network training, optimizing simulation and a variety of other problem areas. These approaches can be implemented in multiple ways, and offer numerous alternatives for exploiting their basic ideas. We identify a template for scatter search and path relinking methods that provides a convenient and "user friendly" basis for their implementation. The overall design can be summarized by a small number of key steps, leading to versions of scatter search and path relinking that are fully specified upon providing a handful of subroutines. Illustrative forms of these subroutines are described that make it possible to create methods for a wide range of optimization problems. Highlights of these components include new diversification generators for zero-one and permutation problems (extended by a mapping-byobjective technique that handles additional classes of problems), together with processes to avoid generating or incorporating duplicate solutions at various stages (related to the avoidance of cycling in tabu search) and a new method for creating improved solutions. *** UPDATED AND EXTENDED: February 1998 *** Previous version appeared in Lecture Notes in Computer Science, 1363, J.K. Hao, E. Lutton, E. Ronald, M. Schoenauer, D. Snyers (Eds.), 13-54, 1997. This research was supported in part by the Air Force Office of Scientific Research Grant #F49620-97-1-0271.
New onset vasomotor symptoms but not musculoskeletal symptoms associate with clinical outcomes on extended adjuvant letrozole - Analyses from NCIC CTG MA.17.

PURPOSE
New onset symptoms on adjuvant aromatase inhibitors for hormone receptor positive early breast cancer may associate with clinical outcomes. We performed this exploratory analysis of the association of new onset musculoskeletal (MSK) and vasomotor (VM) symptoms with clinical outcomes in the NCIC CTG MA.17 trial 5 years of extended adjuvant endocrine therapy with letrozole after tamoxifen.


METHODS
Symptoms were collected at baseline, 1, 6, and every 12 months on study. Multivariate Cox Models adjusting for age, nodal status, duration of tamoxifen and prior chemotherapy were used to compare disease-free survival (DFS), distant disease-free survival (DDFS), and overall survival (OS) based on data collected before, and after, the unblinding between women with VM or MSK symptoms and those without.


RESULTS
Data post-unblinding showed new VM symptoms on extended letrozole significantly improved DFS and DDFS when occurring 1 month (DFS HR 0.52, 95% CI, 0.28-0.96; p = 0.04; DDFS HR 0.49, 95% CI, 0.24-0.99; p = 0.046) and 6 months (DFS HR 0.43, 95% CI, 0.24-0.78; p = 0.006; DDFS HR 0.44, 95% CI, 0.22-0.85; p = 0.02) after treatment initiation. Those with new VM symptoms at 12 months also had a significantly better DFS (HR 0.47, 95% CI 0.26, 0.84; P = 0.01) and a trend in improved DDFS. Only a trend to improved OS was found for those with VM symptoms 6 month after treatment. No significant improvement was found for those with new MSK symptoms at any time point or for any endpoint.


CONCLUSIONS
New onset VM symptoms with extended letrozole may be useful in predicting treatment benefit.
Brushless doubly-fed induction machine with rotating power electronic converter for wind power applications

This paper introduces, simulates and analyzes a new topology of a brushless doubly-fed induction machine with rotating power electronic converter for wind power applications. Topology consists of two machines, one is the main machine which is directly connected to the grid while the second machine is the auxiliary machine which handles the slip power. The rotor of the two machines are connected via a power electronic converter which is mounted on the shaft and rotates with it. The steady state equivalent circuit of the two machine configuration is developed and analyzed. It is shown through simulations that the stator terminals of the machine can be operated at a unity power factor for variable speed range. Furthermore, it is shown that the presented system operates at a high efficiency at rated load and unity power factor.
Maritime inventory routing with multiple products: A case study from the cement industry

0377-2217/$ see front matter 2010 Elsevier B.V. A doi:10.1016/j.ejor.2010.08.023 ⇑ Corresponding author. Tel.: +47 73593602; fax: + E-mail address: Marielle.Christiansen@iot.ntnu.no This paper considers a maritime inventory routing problem faced by a major cement producer. A heterogeneous fleet of bulk ships transport multiple non-mixable cement products from producing factories to regional silo stations along the coast of Norway. Inventory constraints are present both at the factories and the silos, and there are upper and lower limits for all inventories. The ship fleet capacity is limited, and in peak periods the demand for cement products at the silos exceeds the fleet capacity. In addition, constraints regarding the capacity of the ships’ cargo holds, the depth of the ports and the fact that different cement products cannot be mixed must be taken into consideration. A construction heuristic embedded in a genetic algorithmic framework is developed. The approach adopted is used to solve real instances of the problem within reasonable solution time and with good quality solutions. 2010 Elsevier B.V. All rights reserved.
‘Going private’: a qualitative comparison of medical specialists’ job satisfaction in the public and private sectors of South Africa

UNLABELLED



BACKGROUND
There is a highly inequitable distribution of health workers between public and private sectors in South Africa, partly due to within-country migration trends. This article elaborates what South African medical specialists find satisfying about working in the public and private sectors, at present, and how to better incentivize retention in the public sector.


METHODS
Seventy-four qualitative interviews were conducted - among specialists and key informants - based in one public and one private urban hospital in South Africa. Interviews were coded to determine common job satisfaction factors, both financial and non-financial in nature. This served as background to a broader study on the impacts of specialist 'dual practice', that is, moonlighting. All qualitative specialist respondents were engaged in dual practice, generally working in both public and private sectors. Respondents were thus able to compare what was satisfying about these sectors, having experience of both.


RESULTS
Results demonstrate that although there are strong financial incentives for specialists to migrate from the public to the private sector, public work can be attractive in some ways. For example, the public hospital sector generally provides more of a team environment, more academic opportunities, and greater opportunities to feel 'needed' and 'relevant'. However, public specialists suffer under poor resource availability, lack of trust for the Department of Health, and poor perceived career opportunities. These non-financial issues of public sector dissatisfaction appeared just as important, if not more important, than wage disparities.


CONCLUSIONS
The results are useful for understanding both what brings specialists to migrate to the private sector, and what keeps some working in the public sector. Policy recommendations center around boosting public sector resources and building trust of the public sector through including health workers more in decision-making, inter alia. These interventions may be more cost-effective for retention than wage increases, and imply that it is not necessarily just a matter of putting more money into the public sector to increase retention.
Perceptions of effective and ineffective nurse-physician communication in hospitals.

PROBLEM
Nurse-physician communication affects patient safety. Such communication has been well studied using a variety of survey and observational methods; however, missing from the literature is an investigation of what constitutes effective and ineffective interprofessional communication from the perspective of the professionals involved. The purpose of this study was to explore nurse and physician perceptions of effective and ineffective communication between the two professions.


METHODS
Using focus group methodology, we asked nurses and physicians with at least 5 years' acute care hospital experience to reflect on effective and ineffective interprofessional communication and to provide examples. Three focus groups were held with 6 participants each (total sample 18). Sessions were audio recorded and transcribed verbatim. Transcripts were coded into categories of effective and ineffective communication.


FINDINGS
The following themes were found. For effective communication: clarity and precision of message that relies on verification, collaborative problem solving, calm and supportive demeanor under stress, maintenance of mutual respect, and authentic understanding of the unique role. For ineffective communication: making someone less than, dependence on electronic systems, and linguistic and cultural barriers.


CONCLUSION
These themes may be useful in designing learning activities to promote effective interprofessional communication.
Umbilical pilonidal sinus: a new treatment technique of sinus excision with umbilical preservation.

Under general anesthesia, careful inspection revealed a 3-mm ulcerated site in the depth of the umbilicus from which bits of hair protruded. A vertical skin incision through the umbilicus skirting one side of the sinuses was made. Diathermy cutting was used to minimize bleeding and ensure visibility of the lesion. There were several strands of hair projecting through three sinus openings (Figure 1). These communicated with a single subcutaneous tract that reached the sheath in the midline but did not branch laterally. All three openings and the tract were completely excised using a probe as a guide (Figure 2), approaching the tract superiorly, inferiorly, and laterally deep to the umbilicus, excluding the umbilical cicatrix and thus preserving it. The skin was closed primarily with subcuticular polypropylene, and the patient was given a course of antibiotics. He recovered uneventfully, had the sutures removed 10 days postoperatively, and has had no recurrence at 2 years.
Retrieval, reuse, revision and retention in case-based reasoning

Case-based reasoning (CBR) is an approach to problem solving that emphasizes the role of prior experience during future problem solving (i.e., new problems are solved by reusing and if necessary adapting the solutions to similar problems that were solved in the past). It has enjoyed considerable success in a wide variety of problem solving tasks and domains. Following a brief overview of the traditional problem-solving cycle in CBR, we examine the cognitive science foundations of CBR and its relationship to analogical reasoning. We then review a representative selection of CBR research in the past few decades on aspects of retrieval, reuse, revision, and retention. 2 R. LÓPEZ DE MÁNTARAS ET AL.
Security Policies and Security Models

We assune that the reader is familiar with the ubiquity of information in the modern world and is sympathetic with the need for restricting rights to read, add, modify, or delete information in specific contexts. This need is particularly acute for systems having computers as significant components.
Myotonia fluctuans. A third type of muscle sodium channel disease.

OBJECTIVES
To define a new type of dominant myotonic muscle disorder and to identify the gene lesion.


DESIGN
Case series, clinical examination and electromyography, measurements of grip force and relaxation time, and DNA analysis to probe for mutation in the gene for the skeletal muscle sodium channel.


SETTING
Outpatient clinic and home.


PATIENTS
Three families studied; all together, 17 affected and nine unaffected individuals.


RESULTS
The findings in these three families confirm the existence of myotonia fluctuans as we described it previously in another family. Myotonia (prolongation of relaxation time) developed 20 to 40 minutes after exercise. Potassium caused generalized myotonia. Cooling had no major effect on muscle function. Three families had a common mutation in exon 22 and one family had a mutation in exon 14 of the gene for the sodium channel alpha subunit.


CONCLUSIONS
Myotonia fluctuans is a disorder of the muscle sodium channel. There are at present two other distinct clinical muscle disorders associated with mutations in the sodium channel: hyperkalemic periodic paralysis and paramyotonia congenita. The findings in the present report indicate that myotonia fluctuans belongs to a third type of sodium channel disorder. Further work is needed to understand the complex genotype-phenotype correlations in sodium channel disorders.
Evaluation of Potential Pharmacokinetic Drug-Drug Interaction between Armodafinil and Aripiprazole in Healthy Adults.

INTRODUCTION
Armodafinil, a moderate inducer of cytochrome P450 (CYP) 3A4, has been studied as adjunctive therapy to maintenance medications for major depressive episodes associated with bipolar I disorder. We evaluated the effect of daily dosing with armodafinil on the pharmacokinetics and safety of the CYP3A4 substrate aripiprazole, an atypical antipsychotic used to treat bipolar I disorder.


METHODS
Healthy adults received 15 mg aripiprazole alone and after armodafinil (250 mg/day) pretreatment. Pharmacokinetic parameters were derived from plasma concentrations of aripiprazole and its active metabolite, dehydro-aripiprazole, obtained over 16 days after each aripiprazole administration. Steady-state pharmacokinetics of armodafinil and its 2 circulating metabolites was assessed.


RESULTS
Of 36 subjects enrolled, 24 were evaluable for pharmacokinetic analysis. Armodafinil reduced systemic exposure to aripiprazole (Cmax, - 8%; AUC0-∞, -34%) and dehydro-aripiprazole, which is both formed and eliminated in part via CYP3A4 (Cmax, - 10%; AUC0-∞, - 32%). Adverse events were generally consistent with known safety profiles of each agent.


DISCUSSION
Systemic exposure to aripiprazole and dehydro-aripiprazole was moderately reduced following armodafinil pretreatment. The combination was generally well tolerated under the conditions studied.
Psychological barriers for living kidney donation: how to inform the potential donors?

BACKGROUND
This is the first large-scale interview study carried out in patients and potential donors who seem unwilling or unable to pursue living kidney donation. By investigating these groups, we explored whether further expansion of the living kidney donation program is feasible.


METHODS
We interviewed 91 patients on the waiting list for a kidney transplant who did not pursue living kidney donation and their potential donors (n=53). We also included a comparison group. All respondents underwent an in-depth interview by a psychologist about topics that could influence their willingness to pursue living kidney donation.


RESULTS
A total of 78% of the patients on the waiting list were willing to accept the offer of a living donor. The main reason for not pursuing living kidney donation was reluctance to discuss the issue with the potential donors. This was also found in the comparison group. Both groups indicated that if there was no donor offer, they tended to interpret this as a refusal to donate. This interpretation not always holds: more than one third (19 of 53) of the potential donors were open to consider themselves as a potential donor. On the other hand, a comparably sized group of potential donors (21 of 53) was reluctant about donation. The main reason for donor reluctance was fear for their health after donation.


CONCLUSION
The majority of patients on the waiting list are willing to accept a living kidney donor, but adopt an awaiting attitude towards their potential donors. Offering those patients professional assistance should be considered.
Association between plasma concentrations of certolizumab pegol and endoscopic outcomes of patients with Crohn's disease.

BACKGROUND & AIMS
Monitoring plasma concentrations of anti-tumor necrosis factor agents could optimize treatment of patients with Crohn's Disease (CD). In a post hoc analysis of data from a clinical trial, we compared the relationship between plasma concentrations of certolizumab pegol (CZP) and endoscopic and clinical responses and remission with CZP therapy in patients with moderate to severe ileocolonic CD.


METHODS
We analyzed data from the Endoscopic Mucosal Improvement in Patients with Active CD Treated with CZP trial, from 89 adult patients with active endoscopic CD (ulceration in ≥ 2 intestinal segments and CD Endoscopic Index of Severity [CDEIS] scores of ≥ 8 points). Patients received subcutaneous CZP (400 mg) at weeks 0, 2, and 4 and then every 4 weeks until week 52. Endoscopic evaluations were performed at weeks 0, 10, and 54. Blood samples were collected to measure CZP plasma concentrations at weeks 8 and 54. CZP quartiles at weeks 8 (n = 80) and 54 (n = 45) were correlated with endoscopic response (>5-point decrease in CDEIS from baseline) and remission (CDEIS, <6) at weeks 10 and 54, respectively.


RESULTS
Higher concentrations of CZP at week 8 were associated with endoscopic response (P = .0016) and remission (P = .0302) at week 10 (n = 45). At week 54, the rates of endoscopic remission correlated with plasma concentrations of CZP (P = .0206). There was a significant inverse relationship between plasma concentrations of CZP and baseline levels of C-reactive protein and body weight (P = .0014 and P = .0373, respectively).


CONCLUSIONS
Endoscopic response and remission are associated with higher plasma concentrations of CZP in patients with moderate to severe ileocolonic CD. These results support the need to consider the pharmacokinetics of anti-tumor necrosis factor agents and therapeutic drug monitoring to optimize treatment. Clinicaltrials.gov Number, NCT00297648.
Optimizing ecology-friendly drawing of plans of buildings by means of grammatical evolution

This is an electronic version of the paper presented at the International Industrial Simulation Conference (ISC 2006), held in Palermo (Italy)
POPISK: T-cell reactivity prediction using support vector machines and string kernels

Accurate prediction of peptide immunogenicity and characterization of relation between peptide sequences and peptide immunogenicity will be greatly helpful for vaccine designs and understanding of the immune system. In contrast to the prediction of antigen processing and presentation pathway, the prediction of subsequent T-cell reactivity is a much harder topic. Previous studies of identifying T-cell receptor (TCR) recognition positions were based on small-scale analyses using only a few peptides and concluded different recognition positions such as positions 4, 6 and 8 of peptides with length 9. Large-scale analyses are necessary to better characterize the effect of peptide sequence variations on T-cell reactivity and design predictors of a peptide's T-cell reactivity (and thus immunogenicity). The identification and characterization of important positions influencing T-cell reactivity will provide insights into the underlying mechanism of immunogenicity. This work establishes a large dataset by collecting immunogenicity data from three major immunology databases. In order to consider the effect of MHC restriction, peptides are classified by their associated MHC alleles. Subsequently, a computational method (named POPISK) using support vector machine with a weighted degree string kernel is proposed to predict T-cell reactivity and identify important recognition positions. POPISK yields a mean 10-fold cross-validation accuracy of 68% in predicting T-cell reactivity of HLA-A2-binding peptides. POPISK is capable of predicting immunogenicity with scores that can also correctly predict the change in T-cell reactivity related to point mutations in epitopes reported in previous studies using crystal structures. Thorough analyses of the prediction results identify the important positions 4, 6, 8 and 9, and yield insights into the molecular basis for TCR recognition. Finally, we relate this finding to physicochemical properties and structural features of the MHC-peptide-TCR interaction. A computational method POPISK is proposed to predict immunogenicity with scores which are useful for predicting immunogenicity changes made by single-residue modifications. The web server of POPISK is freely available at http://iclab.life.nctu.edu.tw/POPISK .
Prevalence of hip dislocation among children with cerebral palsy in regions with and without a surveillance programme: a cross sectional study in Sweden and Norway

BACKGROUND
Hip dislocation is a serious complication among children with cerebral palsy (CP). The aim of this study was to compare the prevalence of hip dislocation among children with CP in an area providing regular care with an area providing hip surveillance services.


METHODS
This is a cross-sectional study in seven Norwegian counties providing regular care and one Swedish healthcare region where a hip surveillance programme was introduced in 1994. Data were provided by the Norwegian Cerebral Palsy Register and the CP Register in Southern Sweden. Children born 1996 - 2003 with moderate to severe CP, defined as Gross Motor Classification System (GMFCS) levels III - V, were included. In all, 119 Norwegian and 136 Swedish children fulfilled the criteria. In Norway, data on hip operations and radiographs of the hips were collected from medical records, while these data are collected routinely in the Swedish register. The hip migration percentage was measured on the recent radiographs. Hip dislocation was defined as a migration percent of 100%.


RESULTS
The proportion of children at GMFCS levels III - V was 34% in the Norwegian and 38% in the Swedish population. In the Norwegian population, hip dislocation was diagnosed in 18 children (15.1%; CI: 9.8 - 22.6) compared with only one child (0.7%; 95% CI: 0.01 - 4.0) in Southern Sweden (p = < 0.001). Hip surgery was performed in 53 (44.5%) of the Norwegian children and in 43 (32%) of the Swedish children (p = 0.03). The total number of hip operations was 65 in Norway and 63 in Sweden. Norwegian children were first operated at a mean age of 7.6 years (SD: 2.9) compared with 5.7 years (SD: 2.3) in Sweden (p = 0.001).


CONCLUSIONS
The surveillance programme reduced the number of hip dislocations and the proportion of children undergoing hip surgery was lower. However, with the surveillance programme the first operation was performed at a younger age. Our results strongly support the effectiveness of a specifically designed follow-up programme for the prevention of hip dislocation in children with CP.