nils-herrmann/clean_scirepeval huggingface dataset:
A graph-based friend recommendation system using Genetic Algorithm

A social network is composed by communities of individuals or organizations that are connected by a common interest. Online social networking sites like Twitter, Facebook and Orkut are among the most visited sites in the Internet. Presently, there is a great interest in trying to understand the complexities of this type of network from both theoretical and applied point of view. The understanding of these social network graphs is important to improve the current social network systems, and also to develop new applications. Here, we propose a friend recommendation system for social network based on the topology of the network graphs. The topology of network that connects a user to his friends is examined and a local social network called Oro-Aro is used in the experiments. We developed an algorithm that analyses the sub-graph composed by a user and all the others connected people separately by three degree of separation. However, only users separated by two degree of separation are candidates to be suggested as a friend. The algorithm uses the patterns defined by their connections to find those users who have similar behavior as the root user. The recommendation mechanism was developed based on the characterization and analyses of the network formed by the user's friends and friends-of-friends (FOF).
Recent Developments in Radiotherapy.

It is estimated that 470,000 patients receive radiotherapy each year in the United States.1 As many as half of patients with cancer will receive radiotherapy.2 Improvements in diagnosis, therapy, and supportive care have led to increasing numbers of cancer survivors.3 In response, the emphasis of radiation oncology has expanded beyond cure to include reducing side effects, particularly late effects, which may substantially affect a patient’s quality of life. Radiotherapy is used to treat benign and malignant diseases and can be used alone or in combination with chemotherapy, surgery, or both. For primary tumors or metastatic deposits, palliative radiotherapy is often used to reduce pain or mass effect (due to spinal cord compression, brain metastases, or airway obstruction). Therapeutic radiation can be delivered from outside the patient, known as external-beam radiation therapy, or EBRT (see the Glossary in the Supplementary Appendix, available with the full text of this article at NEJM.org), by implanting radioactive sources in cavities or tissues (brachytherapy), or through systemic administration of radiopharmaceutical agents. Multiple technological and biologic advances have fundamentally altered the field of radiation oncology since it was last reviewed in the Journal.4
Quantitative relationship between Kv4.2 mRNA and A-type K+ current in rat striatal cholinergic interneurons during development.

Channel density is a fundamental factor in determining neuronal firing and is primarily regulated during development through transcriptional and translational regulation. In adult rats, striatal cholinergic interneurons have a prominent A-type current and co-express Kv4.1 and Kv4.2 mRNAs. There is evidence that Kv4.2 plays a primary role in producing the current in adult neurons. The contribution of Kv4.2 and Kv4.1 to the A-type current in cholinergic interneurons during development, however, is not known. Here, using patch-clamp recording and semi-quantitative single-cell reverse transcription-polymerase chain reaction (RT-PCR) techniques, we have examined the postnatal development of A-type current and the expression of Kv4.2 and Kv4.1 in rat striatal cholinergic interneurons. A-type current was detectable at birth, and its amplitude was up-regulated with age, reaching a plateau at about 3 wk after birth. At all ages, the current inactivated with two time constants: one ranging from 15 to 27 ms and the other ranging from 99 to 142 ms. Kv4.2 mRNA was detectable at birth, and the expression level increased exponentially with age, reaching a plateau by 3 wk postnatal. In contrast, Kv4.1 mRNA was not detectable during the first week after birth, and the expression level did not show a clear tendency with age. Taken together, our results suggest that Kv4.2 plays an essential role in producing the A-type current in striatal cholinergic interneurons during the entire course of postnatal development.
Emotional distress in infertile women and failure of assisted reproductive technologies: meta-analysis of prospective psychosocial studies

To examine whether pretreatment emotional distress in women is associated with achievement of pregnancy after a cycle of assisted reproductive technology.



Meta-analysis of prospective psychosocial studies.



PubMed, Medline, Embase, PsycINFO, PsychNET, ISI Web of Knowledge, and ISI Web of Science were searched for articles published from 1985 to March 2010 (inclusive). We also undertook a hand search of reference lists and contacted 29 authors. Eligible studies were prospective studies reporting a test of the association between pretreatment emotional distress (anxiety or depression) and pregnancy in women undergoing a single cycle of assisted reproductive technology.  Two authors independently assessed the studies for eligibility and quality (using criteria adapted from the Newcastle-Ottawa quality scale) and extracted data. Authors contributed additional data not included in original publication.



Fourteen studies with 3583 infertile women undergoing a cycle of fertility treatment were included in the meta-analysis. The effect size used was the standardised mean difference (adjusted for small sample size) in pretreatment anxiety or depression (priority on anxiety where both measured) between women who achieved a pregnancy (defined as a positive pregnancy test, positive fetal heart scan, or live birth) and those who did not. Pretreatment emotional distress was not associated with treatment outcome after a cycle of assisted reproductive technology (standardised mean difference -0.04, 95% confidence interval -0.11 to 0.03 (fixed effects model); heterogeneity I²=14%, P=0.30). Subgroup analyses according to previous experience of assisted reproductive technology, composition of the not pregnant group, and timing of the emotional assessment were not significant. The effect size did not vary according to study quality, but a significant subgroup analysis on timing of the pregnancy test, a contour enhanced funnel plot, and Egger's test indicated the presence of moderate publication bias.



The findings of this meta-analysis should reassure women and doctors that emotional distress caused by fertility problems or other life events co-occurring with treatment will not compromise the chance of becoming pregnant.
How not to get scar(r)ed: pointers to the correct diagnosis in patients with suspected primary cicatricial alopecia.

Primary cicatricial alopecias (PCAs) are a rare, but important, group of disorders that cause irreversible damage to hair follicles resulting in scarring and permanent hair loss. They may also signify an underlying systemic disease. Thus, it is of paramount importance that clinicians who manage patients with hair loss are able to diagnose these disorders accurately. Unfortunately, PCAs are notoriously difficult conditions to diagnose and treat. The aim of this review is to present a rational and pragmatic guide to help clinicians in the professional assessment, investigation and diagnosis of patients with PCA. Illustrating typical clinical and histopathological presentations of key PCA entities we show how dermatoscopy can be profitably used for clinical diagnosis. Further, we advocate the search for loss of follicular ostia as a clinical hallmark of PCA, and suggest pragmatic strategies that allow rapid formulation of a working diagnosis.
Context-Aware Elevator Scheduling

Research on context-aware systems is usually user- centric and thus focussed on the context of a specific user to serve his or her needs in an optimized way. In this paper, we want to apply core concepts developed in research on context-awareness in a system-centric way, namely to elevator systems. We show with three different examples that the performance of an elevator system can be significantly improved if the elevator control has access to contextual knowledge. The first example demonstrates that an appropriate elevator group scheduling algorithm can be chosen and adjusted to the current and near-future passenger traffic situation. The second example incorporates a second predominant technology used in many ubiquitous computing environments, namely RFID tags, to predict the passengers destination. The third example shows that adaptation to a specific emergency situation can further increase the transportation capacity of an elevator system which is ultimately important to save as many lifes as possible in an emergency. Evidence for the increased efficiency is provided by using a comprehensive simulation of a diverse set of scheduling algorithms and scenarios.
Memories of bug fixes

The change history of a software project contains a rich collection of code changes that record previous development experience. Changes that fix bugs are especially interesting, since they record both the old buggy code and the new fixed code. This paper presents a bug finding algorithm using bug fix memories: a project-specific bug and fix knowledge base developed by analyzing the history of bug fixes. A bug finding tool, BugMem, implements the algorithm. The approach is different from bug finding tools based on theorem proving or static model checking such as Bandera, ESC/Java, FindBugs, JLint, and PMD. Since these tools use pre-defined common bug patterns to find bugs, they do not aim to identify project-specific bugs. Bug fix memories use a learning process, so the bug patterns are project-specific, and project-specific bugs can be detected. The algorithm and tool are assessed by evaluating if real bugs and fixes in project histories can be found in the bug fix memories. Analysis of five open source projects shows that, for these projects, 19.3%-40.3% of bugs appear repeatedly in the memories, and 7.9%-15.5% of bug and fix pairs are found in memories. The results demonstrate that project-specific bug fix patterns occur frequently enough to be useful as a bug detection technique. Furthermore, for the bug and fix pairs, it is possible to both detect the bug and provide a strong suggestion for the fix. However, there is also a high false positive rate, with 20.8%-32.5% of non-bug containing changes also having patterns found in the memories. A comparison of BugMem with a bug finding tool, PMD, shows that the bug sets identified by both tools are mostly exclusive, indicating that BugMem complements other bug finding tools.
Liposomes as carriers of hydrophilic small molecule drugs: strategies to enhance encapsulation and delivery.

Although hydrophilic small molecule drugs are widely used in the clinic, their rapid clearance, suboptimal biodistribution, low intracellular absorption and toxicity can limit their therapeutic efficacy. These drawbacks can potentially be overcome by loading the drug into delivery systems, particularly liposomes; however, low encapsulation efficiency usually results. Many strategies are available to improve both the drug encapsulation efficiency and delivery to the target site to reduce side effects. For encapsulation, passive and active strategies are available. Passive strategies encompass the proper selection of the composition of the formulation, zeta potential, particle size and preparation method. Moreover, many weak acids and bases, such as doxorubicin, can be actively loaded with high efficiency. It is highly desirable that once the drug is encapsulated, it should be released preferentially at the target site, resulting in an optimal therapeutic effect devoid of side effects. For this purpose, targeted and triggered delivery approaches are available. The rapidly increasing knowledge of the many overexpressed biochemical makers in pathological sites, reviewed herein, has enabled the development of liposomes decorated with ligands for cell-surface receptors and active delivery. Furthermore, many liposomal formulations have been designed to actively release their content in response to specific stimuli, such as a pH decrease, heat, external alternating magnetic field, ultrasound or light. More than half a century after the discovery of liposomes, some hydrophilic small molecule drugs loaded in liposomes with high encapsulation efficiency are available on the market. However, targeted liposomes or formulations able to deliver the drug after a stimulus are not yet a reality in the clinic and are still awaited.
Cross-layer detection of malicious websites

Web threats pose the most significant cyber threat. Websites have been developed or manipulated by attackers for use as attack tools. Existing malicious website detection techniques can be classified into the categories of static and dynamic detection approaches, which respectively aim to detect malicious websites by analyzing web contents, and analyzing run-time behaviors using honeypots. However, existing malicious website detection approaches have technical and computational limitations to detect sophisticated attacks and analyze massive collected data. The main objective of this research is to minimize the limitations of malicious website detection. This paper presents a novel cross-layer malicious website detection approach which analyzes network-layer traffic and application-layer website contents simultaneously. Detailed data collection and performance evaluation methods are also presented. Evaluation based on data collected during 37 days shows that the computing time of the cross-layer detection is 50 times faster than the dynamic approach while detection can be almost as effective as the dynamic approach. Experimental results indicate that the cross-layer detection outperforms existing malicious website detection techniques.
A supermatrix analysis of genomic, morphological, and paleontological data from crown Cetacea

Cetacea (dolphins, porpoises, and whales) is a clade of aquatic species that includes the most massive, deepest diving, and largest brained mammals. Understanding the temporal pattern of diversification in the group as well as the evolution of cetacean anatomy and behavior requires a robust and well-resolved phylogenetic hypothesis. Although a large body of molecular data has accumulated over the past 20 years, DNA sequences of cetaceans have not been directly integrated with the rich, cetacean fossil record to reconcile discrepancies among molecular and morphological characters. We combined new nuclear DNA sequences, including segments of six genes (~2800 basepairs) from the functionally extinct Yangtze River dolphin, with an expanded morphological matrix and published genomic data. Diverse analyses of these data resolved the relationships of 74 taxa that represent all extant families and 11 extinct families of Cetacea. The resulting supermatrix (61,155 characters) and its sub-partitions were analyzed using parsimony methods. Bayesian and maximum likelihood (ML) searches were conducted on the molecular partition, and a molecular scaffold obtained from these searches was used to constrain a parsimony search of the morphological partition. Based on analysis of the supermatrix and model-based analyses of the molecular partition, we found overwhelming support for 15 extant clades. When extinct taxa are included, we recovered trees that are significantly correlated with the fossil record. These trees were used to reconstruct the timing of cetacean diversification and the evolution of characters shared by "river dolphins," a non-monophyletic set of species according to all of our phylogenetic analyses. The parsimony analysis of the supermatrix and the analysis of morphology constrained to fit the ML/Bayesian molecular tree yielded broadly congruent phylogenetic hypotheses. In trees from both analyses, all Oligocene taxa included in our study fell outside crown Mysticeti and crown Odontoceti, suggesting that these two clades radiated in the late Oligocene or later, contra some recent molecular clock studies. Our trees also imply that many character states shared by river dolphins evolved in their oceanic ancestors, contradicting the hypothesis that these characters are convergent adaptations to fluvial habitats.
The science on front-of-package food labels.

The U.S. Food and Drug Administration and Institute of Medicine are currently investigating front-of-package (FOP) food labelling systems to provide science-based guidance to the food industry. The present paper reviews the literature on FOP labelling and supermarket shelf-labelling systems published or under review by February 2011 to inform current investigations and identify areas of future research.



A structured search was undertaken of research studies on consumer use, understanding of, preference for, perception of and behaviours relating to FOP/shelf labelling published between January 2004 and February 2011.



Twenty-eight studies from a structured search met inclusion criteria. Reviewed studies examined consumer preferences, understanding and use of different labelling systems as well as label impact on purchasing patterns and industry product reformulation.



The findings indicate that the Multiple Traffic Light system has most consistently helped consumers identify healthier products; however, additional research on different labelling systems' abilities to influence consumer behaviour is needed.
Next-generation psychiatric assessment: Using smartphone sensors to monitor behavior and mental health.

Optimal mental health care is dependent upon sensitive and early detection of mental health problems. We have introduced a state-of-the-art method for the current study for remote behavioral monitoring that transports assessment out of the clinic and into the environments in which individuals negotiate their daily lives. The objective of this study was to examine whether the information captured with multimodal smartphone sensors can serve as behavioral markers for one's mental health. We hypothesized that (a) unobtrusively collected smartphone sensor data would be associated with individuals' daily levels of stress, and (b) sensor data would be associated with changes in depression, stress, and subjective loneliness over time.



A total of 47 young adults (age range: 19-30 years) were recruited for the study. Individuals were enrolled as a single cohort and participated in the study over a 10-week period. Participants were provided with smartphones embedded with a range of sensors and software that enabled continuous tracking of their geospatial activity (using the Global Positioning System and wireless fidelity), kinesthetic activity (using multiaxial accelerometers), sleep duration (modeled using device-usage data, accelerometer inferences, ambient sound features, and ambient light levels), and time spent proximal to human speech (i.e., speech duration using microphone and speech detection algorithms). Participants completed daily ratings of stress, as well as pre- and postmeasures of depression (Patient Health Questionnaire-9; Spitzer, Kroenke, & Williams, 1999), stress (Perceived Stress Scale; Cohen et al., 1983), and loneliness (Revised UCLA Loneliness Scale; Russell, Peplau, & Cutrona, 1980).



Mixed-effects linear modeling showed that sensor-derived geospatial activity (p < .05), sleep duration (p < .05), and variability in geospatial activity (p < .05), were associated with daily stress levels. Penalized functional regression showed associations between changes in depression and sensor-derived speech duration (p < .05), geospatial activity (p < .05), and sleep duration (p < .05). Changes in loneliness were associated with sensor-derived kinesthetic activity (p < .01).



Smartphones can be harnessed as instruments for unobtrusive monitoring of several behavioral indicators of mental health. Creative leveraging of smartphone sensing could provide novel opportunities for close-to-invisible psychiatric assessment at a scale and efficiency that far exceeds what is currently feasible with existing assessment technologies.
Expectation and purpose: understanding users' mental models of mobile app privacy through crowdsourcing

Smartphone security research has produced many useful tools to analyze the privacy-related behaviors of mobile apps. However, these automated tools cannot assess people's perceptions of whether a given action is legitimate, or how that action makes them feel with respect to privacy. For example, automated tools might detect that a blackjack game and a map app both use one's location information, but people would likely view the map's use of that data as more legitimate than the game. Our work introduces a new model for privacy, namely privacy as expectations. We report on the results of using crowdsourcing to capture users' expectations of what sensitive resources mobile apps use. We also report on a new privacy summary interface that prioritizes and highlights places where mobile apps break people's expectations. We conclude with a discussion of implications for employing crowdsourcing as a privacy evaluation technique.
Practical guidelines for evaluation of loose anagen hair syndrome.

To better categorize the epidemiologic profile, clinical features, and disease associations of loose anagen hair syndrome (LAHS) compared with other forms of childhood alopecia.



Retrospective survey.



Academic pediatric dermatology practice.  Three hundred seventy-four patients with alopecia referred from July 1, 1997, to June 31, 2007.



Epidemiologic data for all forms of alopecia were ascertained, such as sex, age at onset, age at the time of evaluation, and clinical diagnosis. Patients with LAHS were further studied by the recording of family history, disease associations, hair-pull test or biopsy results, hair color, laboratory test result abnormalities, initial treatment, and involvement of eyelashes, eyebrows, and nails.



Approximately 10% of all children with alopecia had LAHS. The mean age (95% confidence interval) at onset differed between patients with LAHS (2.8 [1.2-4.3] years) vs patients without LAHS (7.1 [6.6-7.7] years) (P < .001), with 3 years being the most common age at onset for patients with LAHS. All but 1 of 37 patients with LAHS were female. The most common symptom reported was thin, sparse hair. Family histories were significant for LAHS (n = 1) and for alopecia areata (n = 3). In 32 of 33 patients, trichograms showed typical loose anagen hairs. Two children had underlying genetic syndromes. No associated laboratory test result abnormalities were noted among patients who underwent testing.



Loose anagen hair syndrome is a common nonscarring alopecia in young girls with a history of sparse or fine hair. Before ordering extensive blood testing in young girls with diffusely thin hair, it is important to perform a hair-pull test, as a trichogram can be instrumental in the confirmation of a diagnosis of LAHS.