Miracle-dz/UniFAR-FTUs huggingface dataset:
Reconciling disagreement over climate–conflict results in Africa

Significance Whether climatic changes affect civil conflicts has been the subject of intense academic debate. Much of this controversy originates from a highly cited dispute between a previous PNAS paper—which finds that civil war incidence in sub-Saharan Africa is associated with increasing local temperature—and a subsequent rebuke of this result, also published in PNAS. We reexamine this apparent disagreement by comparing the statistical models from the two papers using formal tests. When we implement the correct statistical procedure, we find that the evidence presented in the second paper is actually consistent with that of the first. We conclude that the original grounds for the dispute over whether the climate–conflict relationship exists were erroneous. A recent study by Burke et al. [Burke M, Miguel E, Satyanath S, Dykema J, Lobell D (2009) Proc Natl Acad Sci USA 106(49):20670–20674] reports statistical evidence that the likelihood of civil wars in African countries was elevated in hotter years. A following study by Buhaug [Buhaug H (2010) Proc Natl Acad Sci USA 107(38):16477–16482] reports that a reexamination of the evidence overturns Burke et al.’s findings when alternative statistical models and alternative measures of conflict are used. We show that the conclusion by Buhaug is based on absent or incorrect statistical tests, both in model selection and in the comparison of results with Burke et al. When we implement the correct tests, we find there is no evidence presented in Buhaug that rejects the original results of Burke et al.
Tellurite Resistance and Reduction by a Paenibacillus Sp. Isolated from Heavy Metal‐Contaminated Sediment

A gram‐positive bacterium (designated as strain TeW) that is highly resistant to tellurite was isolated from sediment. The bacterium can grow in the presence of up to 2,000 μmol/L of potassium tellurite (K2TeO3). Reduction of K2TeO3 to tellurium was indicated by the blackening of the growth medium. No lag in growth was observed when cells unexposed to tellurite were transferred to the growth medium containing K2TeO3, indicating that resistance to tellurite was not inducible. Up to 50 and 90% of the metalloid oxyanion tellurite (Te⅔−) was removed from the medium by strain TeW during growth in nonstatic (shaking) and static (without shaking) conditions, respectively. The bacterium was identified as a Paenibacillus sp. according to its morphology, physiology, and 16S rDNA sequence homology.
Analysis of the rat liver gap junction protein : clarification of anomalies in its molecular size

The major gap junction polypeptide in most tissues has an apparent molecular mass of 27 kDa with a 47 kDa dimer present in junction-enriched fractions. However, a 54 kDa protein recognized by gap junction-specific antibodies has been reported and a complementary DNA (cDNA) sequence for both human and rat liver gap junctions codes for a 32 kDa protein. In this paper we show that these are all forms of the same gap junction protein that can be observed on SDS–polyacrylamide gels simply by varying the concentration of acrylamide in the gels. A 64 kDa dimer is also obtainable. Antibodies to the gap junction protein or to a synthetic peptide constructed to match the rat liver gap junction amino-terminal sequence recognize all of these forms. Under some conditions a 54 kDa dimer is ‘preferred’, explaining the presence of this species in whole tissue homogenate Western blots. These results clarify several controversies and indicate that the protein forming the gap junction channel probably undergoes no major post-translational modification as the cDNA sequence codes for a protein of molecular mass 32 kDa and this protein species and its 64 kDa dimer are demonstrable on SDS–polyacrylamide gels under appropriate conditions.
COALA: A Tool for Inter-document Coreference Resolution Evaluation

A significant obstacle to scientific progress in machine reading is an objective evaluation method. Precision and recall, while for the most part quantitative, are often measured with respect to some “gold standard” or “ground truth” – itself typically a human annotated corpus. For more complex tasks, such as interdocument coreference resolution, or open ended tasks such as machine reading, relying on a ground truth is often (if not always) impractical. Yet a data-driven approach still requires techniques for evaluation. To address this, we present here a new approach to evaluation of linguistic analysis implemented in a tool we have developed called COALA. The approach basically requires establishing a baseline system that produces some results, and evaluations are performed by incrementally changing that system and comparing the results manually. In order to reduce the load on the human evaluator, our tool implements basically an intelligent and task-specific “diff” between the two results, allowing the evaluator to focus only on the changes and evaluate
Cytotoxic T lymphocytes specific for self tumor immunoglobulin express T cell receptor delta chain

CTL are thought to play a role in the elimination of transformed cells in vivo. The effectiveness of such CTL is in part dependent on recognition of tumor specific antigens. Among the best characterized tumor-specific antigens are the unique or idiotypic determinants on the Ig of B cell lymphomas. Here we describe the generation and properties of human CTL specific for the idiotype on autologous B cell tumors. These cells are CD3+,CD4-,CD8- and express the delta chain of the TCR. Such cells may prove useful in tumor-specific adoptive therapy.
Detecting Patching of Executables without System Calls

Popular software applications (e.g. web browsers) are targeted by malicious organizations which develop potentially unwanted programs (PUPs). If such a PUP executes on benign user devices, it is able to manipulate the process memory of popular applications, their locally stored resources or their environment in a profitable way for the attacker and in detriment to benign end-users. We describe the implementation of a tamper detection mechanism based on code self-checksumming, able to detect static and dynamic patching of executables, performed by PUPs or other attackers. As opposed to other works based on code self-checksumming, our approach can also checksum instructions which contain absolute addresses affected by relocation, without using calls to external libraries. We implemented this solution for the x86 ISA and evaluated the performance impact and effectiveness. The results indicate that the run-time overhead of self-checksumming grows proportionally with the level of protection, which can be specified as input to our implementation. We have applied our implementation on the Chromium web-browser and observed that the overhead is practically unobservable for the end-user.
The Effects of Acidic Fluoride Solutions on Early Enamel Erosion in vivo

Acidic fluoride solutions may reduce dental erosion. The aim of this study was to compare the effect of different acidic fluoride solutions on enamel dissolution using an established in vivo model. When possible 4 anterior teeth (255 teeth in a total of 67 subjects) were isolated and exposed to 0.01 M citric acid. The acid was collected in test tubes before (etch I) and 5 min after (etch II) application of test fluoride preparations. Acidic fluoride solutions (pH range 1.5–2.9), i.e. SnF2, TiF4 and hydrogen fluoride (HF) (all approx. 0.1 M F), HF (0.027, 0.055, 0.082 M F) and neutral NaF solution (0.1 M F) as control were applied to the labial surfaces of the teeth for 1 min (6 ml/min). Enamel dissolution was examined by chemical analysis of calcium content in the citric acid etch solutions using atom absorption spectrometry. The change in calcium concentration (ΔCa) and the percentage of mean calcium reduction were calculated from the difference in calcium loss between etch I and etch II. Statistical analysis was carried out using the Wilcoxon signed rank test and Kruskal-Wallis tests with Dunn’s multiple comparison. Results showed a mean ΔCa of 0.671 mg/l (SD 0.625) for SnF2, and ranged from 0.233 mg/l (SD 0.248) for the weakest HF solution to 0.373 mg/l (SD 0.310) for the strongest HF solution. This represented a 67% reduction in enamel dissolution for SnF2 and a 40–76% reduction for the HF solutions. No reduction was observed for TiF4 or NaF. The types of metal, pH and fluoride concentration are all important for the in vivo effect.
Perineal template interstitial brachytherapy salvage for recurrent endometrial adenocarcinoma metastatic to the vagina.

PURPOSE To evaluate the use of interstitial brachytherapy salvage of recurrent endometrial adenocarcinoma metastatic to the vagina. METHODS From September 1989 to February 1995, 15 patients with locally recurrent endometrial adenocarcinoma were treated with perineal template interstitial irradiation with low-dose-rate brachytherapy 192Ir/137Cs. Five of the 7 previously unirradiated patients received pelvic external beam radiation therapy (EBRT) of 45-50 Gy, with standard fractionation followed by an interstitial brachytherapy boost dose of 30 Gy (range 25 to 35 Gy). The other 2 patients received only brachytherapy of 40 Gy (palliative) and 50 Gy. Eight previously irradiated patients received only brachytherapy of 50 to 55 Gy. RESULTS After a median follow-up of 47 months (range 14-81), the actuarial local control rate was 66.6%. The local control rate for patients treated with interstitial irradiation only was 64.3% and the local control rate for patients treated with interstitial irradiation + EBRT was 100%. Distant metastases occurred in 30.7% of the patients. Actuarial overall and disease-specific 5-year survival were 42.3 and 67.5%, respectively. Toxicity has been minimal, with 6 patients complaining of vaginal/rectal (RTOG) grade 1-3 complications (5 patients grade 1-2, 1 patient grade 3). CONCLUSIONS These results suggest that perineal template interstitial irradiation (if possible with supplementary EBRT) is an effective alternative to radical or exenterative pelvic surgery for locally recurrent endometrial cancer. Excellent survival and local control rates can be achieved with low morbidity, especially if EBRT is added.
Consistency and Fluctuations For Stochastic Gradient Langevin Dynamics

Applying standard Markov chain Monte Carlo (MCMC) algorithms to large data sets is computationally expensive. Both the calculation of the acceptance probability and the creation of informed proposals usually require an iteration through the whole data set. The recently proposed stochastic gradient Langevin dynamics (SGLD) method circumvents this problem by generating proposals which are only based on a subset of the data, by skipping the accept-reject step and by using decreasing step-sizes sequence (δm)m≥0. We provide in this article a rigorous mathematical framework for analysing this algorithm. We prove that, under verifiable assumptions, the algorithm is consistent, satisfies a central limit theorem (CLT) and its asymptotic bias-variance decomposition can be characterized by an explicit functional of the step-sizes sequence (δm)m≥0. We leverage this analysis to give practical recommendations for the notoriously difficult tuning of this algorithm: it is asymptotically optimal to use a step-size sequence of the type δm = m-1/3, leading to an algorithm whose mean squared error (MSE) decreases at rate O(m-1/3).
The Geriatric Depression Scale (GDS)

WHY: Depression is common in late life, affecting nearly 5 million of the 31 million Americans aged 65 and older with clinically significant depressive symptoms reaching 13% in older adults aged 80 and older (Blazer, 2009). Major depression is reported in 8-16% of community dwelling older adults, 5-10% of older medical outpatients seeing a primary care provider, 10-12% of medical-surgical hospitalized older adults with 23% more experiencing significant depressive symptoms (Blazer, 2009). Recognition in long-term care facilities is poor and not consistent amongst studies (Blazer, 2009).
Noninvasive feature-based detection of delayed gastric emptying in humans using neural networks

Radioscintigraphy is currently the gold standard for gastric emptying test which involves radiation exposure and is considerably expensive. The authors present a feature-based detection approach using neural networks for the noninvasive diagnosis of delayed gastric emptying from the cutaneous electrogastrogram (EGG). Simultaneous recordings of the EGG and scintigraphic gastric emptying test were made in 152 patients with symptoms suggestive of delayed gastric emptying. Spectral analyses were performed to derive EGG parameters which were used as the input of the neural network. The result of scintigraphic gastric emptying was used as the gold standard for the training and testing of the neural network. A correct classification of 85% (a specificity of 89% and a sensitivity of 82%) was achieved using the proposed method.
Synthetic Lethal Screening with Small-Molecule Inhibitors Provides a Pathway to Rational Combination Therapies for Melanoma

Recent data show that extracellular signals are transmitted through a network of proteins rather than hierarchical signaling pathways, suggesting that the inhibition of a single component of a canonical pathway is insufficient for the treatment of cancer. The biologic outcome of signaling through a network is inherently more robust and resistant to inhibition of a single network component. In this study, we conducted a functional chemical genetic screen to identify novel interactions between signaling inhibitors that would not be predicted on the basis of our current understanding of signaling networks. We screened over 300 drug combinations in nine melanoma cell lines and have identified pairs of compounds that show synergistic cytotoxicity. The synergistic cytotoxicities identified did not correlate with the known RAS and BRAF mutational status of the melanoma cell lines. Among the most robust results was synergy between sorafenib, a multikinase inhibitor with activity against RAF, and diclofenac, a nonsteroidal anti-inflammatory drug (NSAID). Drug substitution experiments using the NSAIDs celecoxib and ibuprofen or the MAP–ERK kinase inhibitor PD325901 and the RAF inhibitor RAF265 suggest that inhibition of COX and mitogen-activated protein kinase signaling are targets for the synergistic cytotoxicity of sorafenib and diclofenac. Cotreatment with sorafenib and diclofenac interrupts a positive feedback signaling loop involving extracellular signal–regulated kinase, cellular phospholipase A2, and COX. Genome-wide expression profiling shows synergy-specific downregulation of survival-related genes. This study has uncovered novel functional drug combinations and suggests that the underlying signaling networks that control responses to targeted agents can vary substantially, depending on unexplored components of the cell genotype. Mol Cancer Ther; 11(11); 2505–15. ©2012 AACR.
A survey of client-side Web threats and counter-threat measures

The increasing frequency and malevolence of online security threats require that we consider new approaches to this problem. The existing literature focuses on the Web security problem from the server-side perspective. In contrast, we explore it from the client-side, considering the major types of threats. After a short threat summary, we discuss related research and existing countermeasures. We then examine intuitive human-oriented trust models and posit a flexible, multilayer framework to facilitate automated client-side decision making. The proposed suggestions are not intrusive and do not require advanced technical knowledge from end users. Copyright © 2011 John Wiley & Sons, Ltd. (Improving Web security for end users is technically possible by deploying known countermeasures to prevent execution of untrusted mobile code. Additionally, trust algebra provides a basis for defining a Web site avoidance policy based on a crowd-sourced Web site ratings. The primary hurdle to improving Web security rests with standardized, real-world implementations of these concepts both in the Internet and in browser software.)
Whole-Body Intensive Rehabilitation Is Feasible and Effective in Chronic Stroke Survivors: A Retrospective Data Analysis

Abstract Purpose: Upper extremity (UE) intensive repetitive training, locomotor training, and functional strength training, delivered in isolation, promote neural plasticity and functional recovery after stroke. However, the effectiveness of a comprehensive whole-body approach combining these interventions has not been thoroughly investigated. The purpose of this retrospective data analysis was to evaluate the efficacy and feasibility of intensive, comprehensive rehabilitation for a heterogeneous population of chronic stroke survivors in a community clinic setting. Method: Whole-body intensive rehabilitation (3–6 hours/day, 4–5 days/week, ≥2 weeks) consisted of locomotor, balance, and transfer training; progressive resistive strengthening exercise; and repetitive task-specific UE practice. Outcome measures were collected from all patients participating in the program between March 2003 and January 2008 who were diagnosed with a stroke ≥12 months prior to treatment initiation (N = 35). Results: Significant improvements in function were observed as measured by the Fugl-Meyer Assessment, Wolf Motor Function Test (WMFT), Box and Block test, Berg Balance Scale, Timed Up & Go Test (TUG), and 6-minute walk test. Conclusion: Whole-body intensive rehabilitation is an effective and feasible approach to promote recovery in chronic stroke survivors with moderate to severe deficits. Further research is necessary to confirm these results in a more controlled environment.
Signal transduction through the fibronectin receptor induces collagenase and stromelysin gene expression

We have investigated the effects of ligation of the fibronectin receptor (FnR) on gene expression in rabbit synovial fibroblasts. Monoclonal antibodies to the FnR that block initial adhesion of fibroblasts to fibronectin induced the expression of genes encoding the secreted extracellular matrix-degrading metalloproteinases collagenase and stromelysin. That induction was a direct consequence of interaction with the FnR was shown by the accumulation of mRNA for stromelysin and collagenase. Monoclonal antibodies to several other membrane glycoprotein receptors had no effect on metalloproteinase gene expression. Less than 2 h of treatment of the fibroblasts with anti-FnR in solution was sufficient to trigger the change in gene expression, and induction was blocked by dexamethasone. Unlike other inducers of metalloproteinase expression, including phorbol diesters and growth factors, addition of the anti-FnR in solution to cells adherent to serum-derived adhesion proteins or collagen produced no detectable change in cell shape or actin microfilament organization. Inductive effects were potentiated by cross-linking of the ligand. Fab fragments of anti-FnR were ineffective unless cross-linked or immobilized on the substrate. Adhesion of fibroblasts to native fibronectin did not induce metallo-proteinases. However, adhesion to covalently immobilized peptides containing the arg-gly-asp sequence that were derived from fibronectin, varying in size from hexapeptides up to 120 kD, induced collagenase and stromelysin gene expression. This suggests that degradation products of fibronectin are the natural inductive ligands for the FnR. These data demonstrate that signals leading to changes in gene expression are transduced by the FnR, a member of the integrin family of extracellular matrix receptors. The signaling of changes in gene expression by the FnR is distinct from signaling involving cell shape and actin cytoarchitecture. At least two distinct signals are generated: the binding of fibronectin-derived fragments and adhesion- blocking antibodies to the FnR triggers events different from those triggered by binding of the native fibronectin ligand. Because the genes regulated by this integrin are for enzymes that degrade the extracellular matrix, these results suggest that information transduced by the binding of various ligands to integrins may orchestrate the expression of genes regulating cell behavior in the extracellular environment.
Lego4TOSCA: Composable Building Blocks for Cloud Applications

The Topology and Orchestration Specification for Cloud Applications (TOSCA) enables the description, provisioning, and management of complex cloud applications in a portable way. TOSCA, therefore, provides a comprehensive yet complex set of mechanisms that may hinder users from unleashing its power due to misusing or neglecting parts of those mechanisms. TOSCA has just been standardized and, although it seems to be highly adopted in industry, there is a lack of systematic research of its features and capabilities. In this work we discuss the design of basic building blocks for cloud applications, called node types, and show how they can benefit from a deep integration with TOSCA. We developed a generic architecture for the realization of TOSCA node types, show an implementation of this architecture and validate it based on a sample cloud application. Our work gives an insight into the capabilities of TOSCA with respect to enable the creation of portable cloud services based on a set of composable building blocks.
Analyzing User Patterns to Derive Design Guidelines for Job Seeking and Recruiting Website

More and more competitive websites are targeting online job seeking and recruiting. In this paper, we discuss user pattern in an online job seeking website in Switzerland, by analyzing user profiles and actions. Then based on our findings, we derive design guidelines to improve both the interface usability and the efficiency of the embedded jobs/candidates recommender system. Keywords-patterns; job seeking; recruiting; Web design; recommender system;
Polynomial wavelet regression for images with irregular boundaries

In this paper, we focus on denoising images for which observations are equally spaced except around the boundaries which are irregular. Such images are very common in many fields, for example in geophysics. The advantages of adding a low-order polynomial term when implementing a wavelet regression for such images are presented. Besides removing the classical restriction of having a dyadic of number of observations, this strategy reduces the bias at the edges without significantly increasing the risk. In addition, this method is simple to implement, fast and efficient. Its utility is illustrated with simulation studies and a real example.
TAP-independent, beta 2-microglobulin-dependent surface expression of functional mouse CD1.1

CD1 molecules consist of beta 2-microglobulin (beta 2m) noncovalently complexed to a non-major histocompatibility complex (MHC)-encoded monomorphic integral membrane protein homologous to MHC class I alpha chains. Little is known about the requirements for cell surface expression and T cell recognition of CD1. We inserted the mouse CD1.1 gene into vaccinia virus to create a recombinant virus expressing CD1.1 under the control of a viral promoter. Using this recombinant virus to infect normal or mutant cell lines, we found that the expression of molecules reactive with the CD1.1-specific monoclonal antibody 3C11 requires the expression of beta 2m but was not affected by the absence of the MHC-encoded peptide transporter (TAP). Consistent with these results, IL-2 production by the mCD1.1-specific T cell hybridoma DN32.D3 was induced by thymocytes from normal mice or mice with a homozygous deletion of the TAP1 gene, but not by thymocytes from mice with a homozygous deletion of the beta 2m gene. These results indicate that expression of functional mCD1.1 occurs in a beta 2m-dependent, TAP- independent manner.