nils-herrmann/clean_scirepeval huggingface dataset:
Graph guided joint prediction of class label and clinical scores for the Alzheimer's disease
Venue: Brain Structure and Function
Year: 2015

AbstractAccurate diagnosis of Alzheimer's disease and its prodromal stage, i.e. mild cognitive impairment, is very important for early treatment. Over the last decade, various machine learning methods have been proposed to predict disease status and clinical scores from brain images. It is worth noting that many features extracted from brain images are correlated significantly. In this case, feature selection combined with the additional correlation information among features can effectively improve classification/regression performance. Typically, the correlation information among features can be modeled by the connectivity of an undirected graph, where each node represents one feature and each edge indicates that the two involved features are correlated significantly. In this paper, we propose a new graph guided multi task learning method incorporating this undirected graph information to predict multiple response variables (i.e. class label and clinical scores) jointly. Specifically, based on the sparse undirected feature graph, we utilize a new latent group Lasso penalty to encourage the correlated features to be selected together. Furthermore, this new penalty also encourages the intrinsic correlated tasks to share a common feature subset. To validate our method, we have performed many numerical studies using simulated datasets and the Alzheimer's Disease Neuroimaging Initiative dataset. Compared with the other methods, our proposed method has very promising performance.
ORAI1 mutations abolishing store operated Ca2+ entry cause anhidrotic ectodermal dysplasia with immunodeficiency
Venue: The Journal of allergy and clinical immunology
Year: 2018

Store operated Ca2+ entry (SOCE) through Ca2+ release activated Ca2+ channels is an essential signaling pathway in many cell types. Ca2+ release activated Ca2+ channels are formed by ORAI1, ORAI2, and ORAI3 proteins and activated by stromal interaction molecule (STIM) 1 and STIM2. Mutations in the ORAI1 and STIM1 genes that abolish SOCE cause a combined immunodeficiency (CID) syndrome that is accompanied by autoimmunity and nonimmunologic symptoms.  We performed molecular and immunologic analysis of patients with CID, anhidrosis, and ectodermal dysplasia of unknown etiology.  We performed DNA sequencing of the ORAI1 gene, modeling of mutations on ORAI1 crystal structure, analysis of ORAI1 mRNA and protein expression, SOCE measurements, immunologic analysis of peripheral blood lymphocyte populations by using flow cytometry, and histologic and ultrastructural analysis of patient tissues.  We identified 3 novel autosomal recessive mutations in ORAI1 in unrelated kindreds with CID, autoimmunity, ectodermal dysplasia with anhidrosis, and muscular dysplasia. The patients were homozygous for p.V181SfsX8, p.L194P, and p.G98R mutations in the ORAI1 gene that suppressed ORAI1 protein expression and SOCE in the patients' lymphocytes and fibroblasts. In addition to impaired T cell cytokine production, ORAI1 mutations were associated with strongly reduced numbers of invariant natural killer T and regulatory T (Treg) cells and altered composition of &ggr;&dgr; T cell and natural killer cell subsets.  ORAI1 null mutations are associated with reduced numbers of invariant natural killer T and Treg cells that likely contribute to the patients' immunodeficiency and autoimmunity. ORAI1 deficient patients have dental enamel defects and anhidrosis, representing a new form of anhidrotic ectodermal dysplasia with immunodeficiency that is distinct from previously reported patients with anhidrotic ectodermal dysplasia with immunodeficiency caused by mutations in the nuclear factor &kgr;B signaling pathway (IKBKG and NFKBIA)
The Impact of Institutional Power on Higher Degree Research Supervision: Implications for the Quality of Doctoral Outcomes
Venue: Universal Journal of Educational Research
Year: 2019

This paper examines the impact of power in the supervision process as experienced by the PhD students, the institutional influence upon this, and implications for the quality of the doctoral outcome. This research paper is based on findings of a larger, recently completed PhD with the aim to develop a participant driven theory of the lived experience of being a PhD student. This was done by analyzing the reported experiences of 23 PhD students in various disciplines and stages of their PhD studying at Australian Universities over a period of 12 months. Participants were given the freedom to choose and prioritize the experiences to report on and how they reported on them. Core to the supervision findings was the issue of power and how institutional influences distort the power relationship between the supervisor and the supervisee. Adopting French and Raven's (1959) Bases of Social Power, the institutional power sources that play on the PhD candidate are enacted through 'actors' in the institutional process including the supervisor who are presented. The findings support the need for institutions to systematically review their practices to meet their duty of care to their PhD students to provide high quality HDR supervision and improve doctoral outcomes. This research addresses a gap in contemporary supervision literature by addressing the impact of institutional power and institutional practices on the academic supervisor and how these play out in the utilization of power on and over the PhD student and the doctoral outcome.
Mixed integer programming approaches for the tree $t^$t* spanner problem
Venue: Optim. Lett.
Year: 2019

The tree $t^$t* spanner problem is an NP hard problem, which is concerned with finding a spanning tree in a given undirected weighted graph, such that for each pair of nodes the ratio of the shortest distance in the spanning tree and the shortest distance in the given graph is bounded by t. The goal is to find a spanning tree, which gives the minimal t. This problem is associated with many network design applications, but in particular, in the context of architecture of distributed systems. We introduce mixed integer programming formulations for the tree $t^$t* spanner problem, and present a branch and cut solution approach based on these formulations. The branch and cut is enhanced with an initialization procedure and a primal heuristic. A computational study is done to assess the effectiveness of our proposed algorithmic strategies. To the best of our knowledge, this is the first time that an exact approach is proposed for this problem.
A Survey of Role Mining
Venue: ACM Comput. Surv.
Year: 2016

Role Based Access Control (RBAC) is the most widely used model for advanced access control deployed in diverse enterprises of all sizes. RBAC critically depends on defining roles, which are a functional intermediate between users and permissions. Thus, for RBAC to be effective, an appropriate set of roles needs to be identified. Since many organizations already have user permission assignments defined in some form, it makes sense to identify roles from this existing information. This process, known as role mining, is one of the critical steps for successful RBAC adoption in any enterprise. In recent years, numerous role mining techniques have been developed, which take into account the characteristics of the core RBAC model, as well as its various extended features. In this article, we comprehensively study and classify the basic problem of role mining along with its several variants and the corresponding solution strategies. Categorization is done on the basis of the nature of the target RBAC system, the objective of role mining, and the type of solution. We then discuss the limitations of existing work and identify new areas of research that can lead to further enrichment of this field.
Accelerating pharmaceutical structure guided drug design: a successful model.
Venue: Drug discovery today
Year: 2019

The impact and value of structure based drug design to pharmaceutical discovery across the industry are now undeniable, with many break through therapies on the market that are structure based in nature. Enabling the structural research is the Industrial Macromolecular Crystallography Association Collaborative Access Team (IMCA CAT) formed over 25 years ago as a world class research facility at the synchrotron at Argonne National Laboratory. What makes IMCA CAT unique is the strategy of the founding consortium to comprehensively provide for the evolving needs of industry in one facility. This includes year round high quality data, capabilities that match target portfolios, throughput and capacity that are never limiting, and unfailing security. Here, we illuminate the unique capabilities offered by IMCA CAT and instruct how all industrial organizations can access this facility.
Interference in Large Wireless Networks
Venue: Found. Trends Netw.
Year: 2009

Since interference is the main performance limiting factor in most wireless networks, it is crucial to characterize the interference statistics. The two main determinants of the interference are the network geometry (spatial distribution of concurrently transmitting nodes) and the path loss law (signal attenuation with distance) For certain classes of node distributions, most notably Poisson point processes, and attenuation laws, closed form results are available, for both the interference itself as well as the signal to interference ratios, which determine the network performance. This monograph presents an overview of these results and gives an introduction to the analytical techniques used in their derivation. The node distribution models range from lattices to homogeneous and clustered Poisson models to general motion invariant ones. The analysis of the more general models requires the use of Palm theory, in particular conditional probability generating functionals, which are briefly introduced in the appendix.
Diastereoselective synthesis of C3 quaternary indolenines using a,b unsaturated N aryl ketonitrones and activated alkynes.
Venue: Angewandte Chemie
Year: 2012

Indole containing structures are ubiquitous in natural products, medicinal compounds, and organic materials. Given their biomedical importance, synthetic methods towards these structural motifs remain relevant even after decades of innovations. However, despite all the efforts toward the efficient construction of C3 quaternary indole derivatives, significant challenges remain. These challenges are found in the forms of spirooxindole, pyrroloindoline, furoindoline, and other indole containing polycycles, which exist in a large number of alkaloids, such as physovenine, physostigmine, minfiensine, citrinadin B, communesin B, aspidophylline A, and mitraphylline (Scheme 1) Many of the
Author Reply: Toward a Multilevel Mechanistic Explanation of Complex Regularities Between Environment and Emotional Components
Year: 2014

In reply to the commentaries of Clay Warner (2014) Gendolla (2014) Nesse (2014) Shweder (2014) and Zachar (2014) I repeat the essential features of appraisal theories of the second flavor: They take emotional components (and not specific emotions) as the phenomenon to be explained, and they strive for a multilevel mechanistic explanation that leaves room for complex and dynamical processes or mechanisms. Every mechanistic explanation starts with an accurate description of regularities between inputs and outputs. Regularities do not preclude context dependent variety, because there is no limit to the number of input factors that can influence the output, and back.
The Interactive Relationship between Regional Trade Integration and Foreign Direct Investment
Year: 2017

E conomic integration among countries has continued to deepen over the past decade. This is especially visible at the regional level, with the escalation of Regional Integration Agreements (RIAs) ranging from Free Trade Areas (FTAs) to Customs Unions (CUs) Nowadays, many developing countries have entered a new regional integration agreement with developed and developing countries. Since international trade and Foreign Direct Investment (FDI) are generally recognized as the two main channels of economic integration, the common question is whether international trade and FDI act as complements or substitutes. This paper tries to examine the interaction between trade integration and FDI in Iran, and provide an empirical assessment of the complementarity or substituting relationship between trade and FDI. We consider Iran bilateral trade as integration variable, with selected countries in EU, ASEAN+3, ECO and D8, by using 2SLS estimators within the period 1994 2014. Results indicate that the bilateral manufacturing export and foreign direct investment have a significant direct relationship with each other in Iran. Also, economic similarities with ECO and D8 have higher effect on both export and FDI.
Employee Management System at Municipal Corporation, Hinganghat
Year: 2016

The aim of this system is to handle the database administration in municipal corporations. This report describes the development of two applications (Client Server) and a database. The server application will perform the link function between the client and the database source. We integrate the data from all departments. Employee Information Management System provides a simple interface for maintenance of employee information. The creation and management of accurate, up to date information regarding employees is taken care. Employee information system deals with all kind of employee details, service related record, leave record, salary statement, attendance maintaining record and other resource related details too. It tracks all the details of an employee from the day one to the end of the service which can be used for all reporting purpose, tracking of attendance, progress in the service, completed service, years, task or any other assignment details embedded in the employee's website.  Database; Client; Server.
Chemical and microbial remediation of hexavalent chromium from contaminated soil and mining/metallurgical solid waste: a review.
Venue: Journal of hazardous materials
Year: 2013

Chromium is a highly toxic non essential metal for microorganisms and plants, and its occurrence is rare in nature. Lower to higher chromium containing effluents and solid wastes released by activities such as mining, metal plating, wood preservation, ink manufacture, dyes, pigments, glass and ceramics, tanning and textile industries, and corrosion inhibitors in cooling water, induce pollution and may cause major health hazards. Besides, natural processes (weathering and biochemical) also contribute to the mobility of chromium which enters in to the soil affecting the plant growth and metabolic functions of the living species. Generally, chemical processes are used for Cr remediation. However, with the inference derived from the diverse Cr resistance mechanism displayed by microorganisms and the plants including biosorption, diminished accumulation, precipitation, reduction of Cr(VI) to Cr(III) and chromate efflux, bioremediation is emerging as a potential tool to address the problem of Cr(VI) pollution. This review focuses on the chemistry of chromium, its use, and toxicity and mobility in soil, while assessing its concentration in effluents/wastes which becomes the source of pollution. In order to conserve the environment and resources, the chemical/biological remediation processes for Cr(VI) and their efficiency have been summarised in some detail. The interaction of chromium with various microbial/bacterial strains isolated and their reduction capacity towards Cr(VI) are also discussed.
A Unique One Time Password Table Sequence Pattern Authentication: Application to Bicol University Union of Federated Faculty Association, Inc. (BUUFFAI) eVoting System
Venue: ArXiv
Year: 2017

Electronic Voting System (EVS) is a type of voting program that deals primarily with the selection, the casting of votes with embedded security mechanism that detects errors, and the tamper proof election of results done through the use of an electronic system. It can include optical scan, specialized voting kiosks and Internet voting approach. Most organizations have difficulties when it comes to voting and the Bicol University Union of Federated Faculty Association Incorporated (BUUFFAI) is not an exception. Some of the problems involved include convenience, cost, geographical location of the polling precinct, and voting turnouts. This study extends the scope of the current BUUFFAI eVoting system to address such issues and to eliminate inconvenience both to the faculty voters and the facilitators. This voting scheme used an algorithmic OTP scheme based on table sequence pattern schedule that randomly generates an XY coordinate unique to voters that will be sent to voter registered email address. This study addressed the security requirements and maintained election procedures with confidentiality, integrity and availability.
Von der Gesundheitsokonomie zur Gesundheitswirtschaft
Venue: Perspektiven der Wirtschaftspolitik
Year: 2019

Zusammenfassung Die Gesundheitsokonomie hat sich als Studienfach und Forschungsgebiet uber die vergangenen rund 40 Jahre entwickelt. In diesem Uberblicksartikel arbeitet Klaus Dirk Henke die Ursachen heraus, verdeutlicht Besonderheiten und zieht einen Vergleich zu anderen Studienfachern. Nach diesem fachspezifischen Abschnitt folgt ein Uberblick zur qualitativen und quantitativen Erfassung der Gesundheitswirtschaft sowie zu ihrem wirtschaftlichen und gesellschaftlichen Nutzen als eigenstandige Wachstumsbranche mit ihren Starken und Schwachen. Zudem enthalt der Beitrag einen Exkurs zur Uber und Fehlversorgung in deutschen Krankenhausern. Dieser Zusammenhang von Okonomie und Medizin steht thematisch zwischen der Gesundheitsokonomie als Studienfach auf der einen Seite und der Gesundheitswirtschaft als Wirtschafts und Industriezweig auf der anderen.
Ultrahigh superelastic damping at the nano scale: A robust phenomenon to improve smart MEMS devices
Venue: Acta Materialia
Year: 2019

Micro and nano pillars of Copper based shape memory alloys (SMAs) with feature sizes between about 2 mm and 250 nm are known to exhibit ultra high mechanical damping due to the nucleation and motion of stress induced martensite interfaces during superelastic straining. While this behavior could be extremely useful to protect micro electro mechanical systems (MEMS) against vibrations in aggressive environments, a fundamental question must yet be answered in order to envisage further applications, namely, whether this damping is reproducible and stable over long times and many cycles, or whether the damping is a signal of accumulating damage that could compromise long term usage. In the present paper this crucial question is answered; we show that micropillar arrays of Cu Al Ni SMAs exhibit a completely recoverable and reproducible superelastic response, with an ultra high damping loss factor e 0.1, or even higher for sub micrometer pillars, e 0.2, even after thousands of cycles >5000) and after long times spanning more than four years. Furthermore, the first high frequency tests on such nanoscale SMAs show that their superelastic response is very fast and relevant to ultra high damping even at frequencies as high as 1000 Hz. This paves the way for the design of micro/nano dampers, based on SMAs, to improve the reliability of MEMS in noisy environments.
Ingress of NaCl in concrete with alkali reactive aggregate: effect on silicon solubility
Year: 2016

Enhanced damage due to the alkali silica reaction (ASR) in concrete exposed to deicing salt (NaCl) is usually attributed to binding of chloride ions in the hydration products of cement. To balance charge, OH ions are released into the concrete pore solution which increases alkalinity. However, during NaCl ingress a decrease in the OH concentration of the concrete pore solution due to potassium leaching would reduce SiO2 solubility and therefore ASR damage. The present work combines expansion measurements with pore solution analysis by ICP OES and XRD measurements on concretes and hydrated cement pastes. Solubility equilibria calculations were performed with the hydrogeochemical simulation program PHREEQC. The investigations show that the OH concentration of the pore solution is mainly lowered by potassium leaching during NaCl ingress. The OH concentration also decreases owing to the formation of Friedel's salt from ettringite which is associated with the release of sulphate. Although the OH concentration with NaCl is lower, ASR damage is intensified and the silicon concentration in the pore solution is higher. Higher silicon solubility is explained by the higher total alkali concentration which increases surface silicate solubility, the formation of an aqueous complex NaHSiO30 and a higher ionic strength. These effects promote the sensitivity of silicate minerals to ASR, the formation of alkali silica gel and finally ASR damage.
Comparative transcriptomic evidence for Tween80 enhanced biodegradation of phenanthrene by Sphingomonas sp. GY2B.
Venue: The Science of the total environment
Year: 2017

Previous study of the effects of surfactants on the biodegradation of phenanthrene focused on investigating alterations of the cell characteristics of Sphingomonas sp. GY2B. However, genes regulation associated with biodegradation and biological processes in response to the presence of surfactants, remains unclear. In this study, comparative transcriptome analysis was conducted to observe the gene expression of GY2B during phenanthrene biodegradation in the presence and absence of Tween80. A diverse set of genes was regulated by Tween80, leading to increased biodegradation of phenanthrene by GY2B: (i) Tween80 increased expression of genes related to H+ transport in the plasma membrane to provide a driving force (i.e. ATP) for accelerating transmembrane transport of phenanthrene with increasing Tween80 concentrations, thereby enhancing the uptake and degradation of phenanthrene by GY2B; (ii) Tween80 (1 and 8 CMC) promoted intracellular biodegradation of phenanthrene by stimulating expression of genes encoding dioxygenases and monooxygenase, increasing expression of genes involved in intracellular metabolic processes (e.g. TCA cycle) and (iii) Tween80 likely increased GY2B vitality and growth by inducing expression of genes associated with ABC transporters and protein transport, regulating genes involved in other biological processes (e.g. transcription, translation)