Miracle-dz/UniFAR-FTUs huggingface dataset:
Contribution Barriers to Open Source Projects

Contribution barriers are properties of Free/Libre and Open Source Software (FLOSS) projects that may prevent newcomers from contributing. Contribution barriers can be seen as forces that oppose the motivations of newcomers. While there is extensive research on the motivation of FLOSS developers, little is known about contribution barriers. However, a steady influx of new developers is connected to the success of a FLOSS project. The first part of this thesis adds two surveys to the existing research that target contribution barriers and motivations of newcomers. The first exploratory survey provides the indications to formulate research hypotheses for the second main survey with 117 responses from newcomers in the two FLOSS projects Mozilla and GNOME. The results lead to an assessment of the importance of the identified contribution barriers and to a new model of the joining process that allows the identification of subgroups of newcomers affected by specific contribution barriers. The second part of the thesis uses the pattern concept to externalize knowledge about techniques lowering contribution barriers. This includes a complete categorization of the existing work on FLOSS patterns and the first empirical evaluation of these FLOSS patterns and their relationships. The thesis contains six FLOSS patterns that lower specific important contribution barriers identified in the surveys. Wikis are web-based systems that allow its users to modify the wiki's contents. They found on wiki principles with which they minimize contribution barriers. The last part of the thesis explores whether a wiki, whose content is usually natural text, can also be used for software development. Such a Wiki Development Environment (WikiDE) must fulfill the requirements of both an Integrated Development Environment (IDE) and a wiki. The simultaneous compliance of both sets of requirements imposes special challenges. The thesis describes an adapted contribution process supported by an architecture concept that solves these challenges. Two components of a WikiDE are discussed in detail. Each of them helps to lower a contribution barrier. A Proof of Concept (PoC) realization demonstrates the feasibility of the concept.
Efficient admission control for EDF schedulers

We present algorithms for flow admission control at an EDF link scheduler when the flows are characterized by peak rate, average rate and burst size. We show that the algorithms have very low computational complexity and are easily applicable in practice. The complexity can be further decreased by introducing the notion of flex classes. We evaluate the penalty in efficiency that the classes incur to the EDF scheduler. We find that this efficiency degradation can be made arbitrarily small and is acceptable even for a small number of classes.
Long Noncoding RNAs as Novel Biomarkers Have a Promising Future in Cancer Diagnostics

Cancers have a high mortality rate due to lack of suitable specific early diagnosis tumor biomarkers. Emerging evidence is accumulating that lncRNAs (long noncoding RNAs) are involved in tumorigenesis, tumor cells proliferation, invasion, migration, apoptosis, and angiogenesis. Furthermore, extracellular lncRNAs can circulate in body fluids; they can be detected and strongly resist RNases. Many researchers have found that lncRNAs could be good candidates for tumor biomarkers and possessed high specificity, high sensitivity, and noninvasive characteristics. In this review, we summarize the detection methods and possible sources of circulating lncRNAs and outline the biological functions and expression level of the most significant lncRNAs in tissues, cell lines, and body fluids (whole blood, plasma, urine, gastric juice, and saliva) of different kinds of tumors. We evaluate the diagnostic performance of lncRNAs as tumor biomarkers. However, the biological functions and the mechanisms of circulating lncRNAs secretion have not been fully understood. The uniform normalization protocol of sample collection, lncRNAs extraction, endogenous control selection, quality assessment, and quantitative data analysis has not been established. Therefore, we put forward some recommendations that might be investigated in the future if we want to adopt lncRNAs in clinical practice.
Low-rank based compact representation of motion capture data

In this paper, we propose a practical, elegant and effective scheme for compact mocap data representation. Guided by our analysis of the unique properties of mocap data, the input mocap sequence is optimally segmented into a set of subsequences. Then, we project the subsequences onto a pair of computational orthogonal matrices to explore strong low-rank characteristic within and among the subsequences. The experimental results show that the proposed scheme is much more effective for reducing the data size, compared with the existing techniques.
Linking Surface and Sub-Surface Variability in Drake Passage

The Antarctic Circumpolar Current (ACC) is the largest current in the world, with a mean transport of 134 Sv, and it provides a significant barrier to the oceanic transfer of heat from mid-latitudes to polar regions. Infrequent full-depth hydrographic sections have shown large variability in the transport of the ACC and the position of its constituent fronts. The many sources of satellite remote-sensing data, with much more frequent sampling, offer another vista on such variability. The question we address here is how the spatial patterns and modes of variability recorded from satellite data relate to the observations from ships. In this paper, we confine our studies to height and temperature data from sensors that are unaffected by clouds, and thus provide near-complete records along the same. The seasonal variations in temperature are deeper south of 60degS, whereas the interannual variations, associated with meandering fronts, occur further north and are deeper. The variability signal from altimetry lies further north again.
Fused Adaptive Lasso for Spatial and Temporal Quantile Function Estimation

Quantile functions are important in characterizing the entire probability distribution of a random variable, especially when the tail of a skewed distribution is of interest. This article introduces new quantile function estimators for spatial and temporal data with a fused adaptive Lasso penalty to accommodate the dependence in space and time. This method penalizes the difference among neighboring quantiles, hence it is desirable for applications with features ordered in time or space without replicated observations. The theoretical properties are investigated and the performances of the proposed methods are evaluated by simulations. The proposed method is applied to particulate matter (PM) data from the Community Multiscale Air Quality (CMAQ) model to characterize the upper quantiles, which are crucial for studying spatial association between PM concentrations and adverse human health effects.
Protein‐sulfenic acid stabilization and function in enzyme catalysis and gene regulation

Sulfenic acids (R‐SOH) result from the stoichiometric oxidations of thiols with mild oxidants such as H2O2; in solution, however, these derivatives accumulate only transiently due to rapid self‐condensation reactions, further oxidations to the sulfinic and/or sulfonic acids, and reactions with nucleophiles such as R‐SH. In contrast, oxidations of cysteinyl side chains in proteins, where disulfide bond formation can be prevented and where the reactivity of the nascent cysteine‐sulfenic acid (Cys‐SOH) can be controlled, have previously been shown to yield stable active‐site Cys‐SOH derivatives of papain and glyceraldehyde‐3‐phosphate dehydrogenase. More recently, however, functional Cys‐SOH residues have been identified in the native oxidized forms of the FAD‐containing NADH peroxidase and NADH oxidase from Streptococcus faecalis; these two proteins constitute a new class within the flavoprotein disulfide reductase family. In addition, Cys‐SOH derivatives have been suggested to play important roles in redox regulation of the DNA‐binding activities of transcription factors such as Fos and Jun, OxyR, and bovine papillomavirus type 1 E2 protein. Structural inferences for the stabilization of protein‐sulfenic acids, drawn from the refined 2.16‐Å structure of the streptococcal NADH peroxidase, provide a molecular basis for understanding the proposed redox functions of these novel cofactors in both enzyme catalysis and transcriptional regulation. — Claiborne, A. , Miller, H. , Parsonage, D. , Ross, R. P. Protein‐sulfenic acid stabilization and function in enzyme catalysis and gene regulation. FASEB J. 7: 1483‐1490; 1993.
Exploiting web search to generate synonyms for entities

Tasks recognizing named entities such as products, people names, or locations from documents have recently received significant attention in the literature. Many solutions to these tasks assume the existence of reference entity tables. An important challenge that needs to be addressed in the entity extraction task is that of ascertaining whether or not a candidate string approximately matches with a named entity in a given reference table. Prior approaches have relied on string-based similarity which only compare a candidate string and an entity it matches with. In this paper, we exploit web search engines in order to define new similarity functions. We then develop efficient techniques to facilitate approximate matching in the context of our proposed similarity functions. In an extensive experimental evaluation, we demonstrate the accuracy and efficiency of our techniques.
Early Relapse of Follicular Lymphoma After Rituximab Plus Cyclophosphamide, Doxorubicin, Vincristine, and Prednisone Defines Patients at High Risk for Death: An Analysis From the National LymphoCare Study.

PURPOSE Twenty percent of patients with follicular lymphoma (FL) experience progression of disease (POD) within 2 years of initial chemoimmunotherapy. We analyzed data from the National LymphoCare Study to identify whether prognostic FL factors are associated with early POD and whether patients with early POD are at high risk for death. PATIENTS AND METHODS In total, 588 patients with stage 2 to 4 FL received first-line rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP). Two groups were defined: patients with early POD 2 years or less after diagnosis and those without POD within 2 years, the reference group. An independent validation set, 147 patients with FL who received first-line R-CHOP, was analyzed for reproducibility. RESULTS Of 588 patients, 19% (n = 110) had early POD, 71% (n = 420) were in the reference group, 8% (n = 46) were lost to follow-up, and 2% (n = 12) died without POD less than 2 years after diagnosis. Five-year overall survival was lower in the early-POD group than in the reference group (50% v 90%). This trend was maintained after we adjusted for FL International Prognostic Index (hazard ratio, 6.44; 95% CI, 4.33 to 9.58). Results were similar for the validation set (FL International Prognostic Index-adjusted hazard ratio, 19.8). CONCLUSION In patients with FL who received first-line R-CHOP, POD within 2 years after diagnosis was associated with poor outcomes and should be further validated as a standard end point of chemoimmunotherapy trials of untreated FL. This high-risk FL population warrants further study in directed prospective clinical trials.
An Integrative Bioinformatics Framework for Genome-scale Multiple Level Network Reconstruction of Rice

Understanding how metabolic reactions translate the genome of an organism into its phenotype is a grand challenge in biology. Genome-wide association studies (GWAS) statistically connect genotypes to phenotypes, without any recourse to known molecular interactions, whereas a molecular mechanistic description ties gene function to phenotype through gene regulatory networks (GRNs), protein-protein interactions (PPIs) and molecular pathways. Integration of different regulatory information levels of an organism is expected to provide a good way for mapping genotypes to phenotypes. However, the lack of curated metabolic model of rice is blocking the exploration of genome-scale multi-level network reconstruction. Here, we have merged GRNs, PPIs and genome-scale metabolic networks (GSMNs) approaches into a single framework for rice via omics’ regulatory information reconstruction and integration. Firstly, we reconstructed a genome-scale metabolic model, containing 4,462 function genes, 2,986 metabolites involved in 3,316 reactions, and compartmentalized into ten subcellular locations. Furthermore, 90,358 pairs of protein-protein interactions, 662,936 pairs of gene regulations and 1,763 microRNA-target interactions were integrated into the metabolic model. Eventually, a database was developped for systematically storing and retrieving the genome-scale multi-level network of rice. This provides a reference for understanding genotype-phenotype relationship of rice, and for analysis of its molecular regulatory network.
Improvements in the efficient composition of applications built using a component-based programming environment

Summary form only given. The efficient development of composite applications is discussed with the focus being on the use of software components to package the user code that is used to build the composite applications. Because of the complex nature of scientific applications, using software components in a plug-and-play style is not so simple. The design of the software components (or user tasks) and the frameworks used to integrate them into a composite application need to support a great deal of flexibility. This is needed to allow efficient experimentation in the development of the application. Additionally, frameworks need to assist the application developer beyond just ensuring interface compatibility. Matching the internal behavior of two user tasks that are coupled in a composite application is equally important. While a completely automatic behavioral analysis may never be a reality, frameworks can include sub-systems that provide the user with insight as to the compatibility of the integration of a task into a composite application. The goal of the research program is to address the above issues by applying several relatively new techniques to explore the design of components, frameworks, and the associated programming styles. Metadata is being used extensively to describe various elements of an application and a framework and software tools are being developed that use this metadata to augment the execution of the user tasks. Aspect-oriented programming concepts are being used to support better modularity and portability in the design of components and composite applications. Behavioral analysis techniques are being used to further enhance portability by including knowledge about the use of an task in its metadata.
A Self-Organizing Fuzzy Neural Network Based on a Growing-and-Pruning Algorithm

A novel growing-and-pruning (GP) approach is proposed, which optimizes the structure of a fuzzy neural network (FNN). This GP-FNN is based on radial basis function neurons, which have center and width vectors. The structure-learning phase and the parameter-training phase are performed concurrently. The structure-learning approach relies on the sensitivity analysis of the output. A set of fuzzy rules can be inserted or reduced during the learning process. The parameter-training algorithm is implemented using a supervised gradient decent method. The convergence of the GP-FNN-learning process is also discussed in this paper. The proposed method effectively generates a fuzzy neural model with a highly accurate and compact structure. Simulation results demonstrate that the proposed GP-FNN has a self-organizing ability, which can determine the structure and parameters of the FNN automatically. The algorithm performs better than some other existing self-organizing FNN algorithms.
Semantic and inferencing abilities in children with communication disorders.

BACKGROUND Semantic and inferencing abilities have not been fully examined in children with communication difficulties. AIMS To investigate the inferential and semantic abilities of children with communication difficulties using newly designed tasks. METHODS & PROCEDURES Children with different types of communication disorder were compared with each other and with three groups of typically developing children: those of the same chronological age and two groups of younger children. In total, 25 children aged 11 years with specific language impairment and 22 children, also 11 years of age, with primary pragmatic difficulties were recruited. Typically developing groups aged 11 (n=35; age-match), and those aged 9 (n=40) and 7 (n=37; language similar) also participated as comparisons. OUTCOMES & RESULTS For Semantic Choices, children with specific language impairment performed significantly more poorly than 9- and 11-year-olds, whilst the pragmatic difficulties group scored significantly lower than all the typically developing groups. Borderline differences between specific language impairment and pragmatic difficulties groups were found. For inferencing, children with communication impairments performed significantly below the 11-year-old peers, but not poorer than 9- and 7-year-olds, suggesting that this skill is in line with language ability. Six children in the pragmatic difficulties group who met diagnosis for autism performed more poorly than the other two clinical groups on both tasks, but not statistically significantly so. CONCLUSIONS Both tasks were more difficult for those with communication impairments compared with peers. Semantic but not inferencing abilities showed a non-significant trend for differences between the two clinical groups and children with pragmatic difficulties performed more poorly than all typically developing groups. The tasks may relate to each other in varying ways according to type of communication difficulty.
Determinants of white-coat syndrome assessed by ambulatory blood pressure or self-measured home blood pressure

BackgroundGender, age, smoking, race, and body mass index have been reported to determine the ambulatory white-coat effect (WCE) and white-coat hypertension (WCH). MethodsBaseline conventional, day-time ambulatory and self-measured home blood pressure measurements from the THOP trial were used to study the effect of gender, age, body mass index, smoking habits and treatment status on the white-coat syndrome as assessed by ambulatory monitoring or self-measurement. ResultsThe mean systolic/diastolic WCE was 9.1/6.7 mmHg if based on ambulatory blood pressure and 12.2/8.7 mmHg if based on self-measured blood pressure. The ambulatory WCE was significantly higher in women, in older subjects (65+), in obese subjects, in non-smokers and in patients on antihypertensive drug treatment. The self-measured WCE was significantly higher in women and in non-smokers. Ambulatory WCH was present in 6.6% of the untreated patients and 14.2% had self-measured WCH. The proportion of ambulatory WCH was significantly higher in obese subjects; the proportion of self-measured WCH did not differ by gender, age, body mass index, or smoking habits. ConclusionsThe ambulatory white-coat syndrome was determined by gender, age, body mass index, smoking habits, and treatment status. The self-measured white-coat syndrome was greater than the ambulatory white-coat syndrome but depended less on the determinants under study.
Call-by-name Gradual Type Theory

We present gradual type theory, a logic and type theory for call-by-name gradual typing. We define the central constructions of gradual typing (the dynamic type, type casts and type error) in a novel way, by universal properties relative to new judgments for gradual type and term dynamism, which were developed in blame calculi and to state the "gradual guarantee" theorem of gradual typing. Combined with the ordinary extensionality ($\eta$) principles that type theory provides, we show that most of the standard operational behavior of casts is uniquely determined by the gradual guarantee. This provides a semantic justification for the definitions of casts, and shows that non-standard definitions of casts must violate these principles. Our type theory is the internal language of a certain class of preorder categories called equipments. We give a general construction of an equipment interpreting gradual type theory from a 2-category representing non-gradual types and programs, which is a semantic analogue of Findler and Felleisen's definitions of contracts, and use it to build some concrete domain-theoretic models of gradual typing.
A Longitudinal, End-to-End View of the DNSSEC Ecosystem

The Domain Name System's Security Extensions (DNSSEC) allow clients and resolvers to verify that DNS responses have not been forged or modified inflight. DNSSEC uses a public key infrastructure (PKI) to achieve this integrity, without which users can be subject to a wide range of attacks. However, DNSSEC can operate only if each of the principals in its PKI properly performs its management tasks: authoritative name servers must generate and publish their keys and signatures correctly, child zones that support DNSSEC must be correctly signed with their parent's keys, and resolvers must actually validate the chain of signatures. This paper performs the first large-scale, longitudinal measurement study into how well DNSSEC's PKI is managed. We use data from all DNSSEC-enabled subdomains under the . com, . org, and . net TLDs over a period of 21 months to analyze DNSSEC deployment and management by domains; we supplement this with active measurements of more than 59K DNS resolvers worldwide to evaluate resolver-side validation. Our investigation reveals pervasive mismanagement of the DNSSEC infrastructure. For example, we found that 31% of domains that support DNSSEC fail to publish all relevant records required for validation; 39% of the domains use insufficiently strong key-signing keys; and although 82% of resolvers in our study request DNSSEC records, only 12% of them actually attempt to validate them. These results highlight systemic problems, which motivate improved automation and auditing of DNSSEC management.
Understanding White Matter Disease: Imaging-Pathological Correlations in Vascular Cognitive Impairment

Most strokes are covert and observed incidentally on brain scans, but their presence increases risk of overt stroke and dementia. Amyloid angiopathy, associated with Alzheimer Disease (AD) causes stroke, and when even small strokes coexist with AD, they lower the threshold for dementia. Diffuse ischemic white matter disease impairs executive functioning, information processing speed, and gait. Neuroimaging techniques, such as tissue segmentation, Diffusion Tensor Imaging, MR Spectroscopy, functional MRI and amyloid PET, probe microstructural integrity, molecular biology, and activation patterns, providing new insights into brain-behavior relationships. MR-pathological studies of periventricular hyperintensity (leukoaraiosis) in aging and dementia reveal arteriolar tortuosity, reduced vessel density, and occlusive venous collagenosis which causes venous insufficiency and vasogenic edema. Activated microglia, oligodendroglial apoptosis, clasmatodendritic astrocytosis, and upregulated hypoxia-markers are seen on immunohistochemistry. Further research is needed to understand and treat this chronic subcortical vascular disease, which is epidemic in our aging population.