gebhart/patrepeval huggingface dataset:
Testing for Shift-Contagion Vulnerability Among MENA Stock Markets During the Turkish Financial Crisis (2018)

This paper is an empirical study that seeks to determine whether any of the Middle East and North Africa (MENA) stock markets are vulnerable to financial contagion in the wake of the 2001 Turkish crisis. We test the nonlinearity of the mechanisms spreading shocks, estimated with a model of long-term interdependence. Our results provide evidence of a high level of interdependence between MENA stock markets. However, we find that, with the exception of the contamination of Israel’s stock market, there is no longer evidence of shift-contagion in the transmission of financial shocks across MENA stock markets.
Broadly Neutralizing Antibody Responses in a Large Longitudinal Sub-Saharan HIV Primary Infection Cohort (2016)

Broadly neutralizing antibodies (bnAbs) are thought to be a critical component of a protective HIV vaccine. However, designing vaccines immunogens able to elicit bnAbs has proven unsuccessful to date. Understanding the correlates and immunological mechanisms leading to the development of bnAb responses during natural HIV infection is thus critical to the design of a protective vaccine. The IAVI Protocol C program investigates a large longitudinal cohort of primary HIV-1 infection in Eastern and South Africa. Development of neutralization was evaluated in 439 donors using a 6 cross-clade pseudo-virus panel predictive of neutralization breadth on larger panels. About 15% of individuals developed bnAb responses, essentially between year 2 and year 4 of infection. Statistical analyses revealed no influence of gender, age or geographical origin on the development of neutralization breadth. However, cross-clade neutralization strongly correlated with high viral load as well as with low CD4 T cell counts, subtype-C infection and HLA-A*03(-) genotype. A correlation with high overall plasma IgG levels and anti-Env IgG binding titers was also found. The latter appeared not associated with higher affinity, suggesting a greater diversity of the anti-Env responses in broad neutralizers. Broadly neutralizing activity targeting glycan-dependent epitopes, largely the N332-glycan epitope region, was detected in nearly half of the broad neutralizers while CD4bs and gp41-MPER bnAb responses were only detected in very few individuals. Together the findings suggest that both viral and host factors are critical for the development of bnAbs and that the HIV Env N332-glycan supersite may be a favorable target for vaccine design.
Productivity and economic implications of various silvicultural thinning regimes in Tasmanian regrowth eucalypt forests (2004)

Thinning of native eucalypt forests is employed in the densest even-aged regrowth stands. A series of simulated regimes involving different combinations of thinnings at ages of approximately 17, 32 and 47 years were applied to assessment data from high quality, young stands using growth and economic models. The objective was to evaluate the regimes on the basis of their ability to maximise sawlog volume and to determine their economic implications. Net Present Value (NPV) was calculated for each regime discounted back to the time of pre-commercial thinning (PCT) intervention using real discount rates of 5% and 10%. Regimes which ranked highest in terms of NPV did not rank highest in terms of sawlog volume, and vice versa. Sawlog yields in all thinned regimes exceeded those in the unthinned stands over a 65-year rotation, and consisted of larger sawlogs. A regime involving PCT plus one commercial thinning produced more sawlog volume at age 65 years than an unthinned regime at age 80 years. All regimes involving one or more commercial thinnings resulted in higher NPVs than allowing these stands to grow on without intervention until rotation ages of up to 80 years. The preferred thinning regime will vary according to the primary management objective.
Transglutaminase crosslinked gelatin as a tissue engineering scaffold (2007)

Gelatin is one of the most commonly used biomaterials for creating cellular scaffolds due to its innocuous nature. In order to create stable gelatin hydrogels at physiological temperatures (37 degrees C), chemical crosslinking agents such as glutaraldehyde are typically used. To circumvent potential problems with residual amounts of these crosslinkers in vivo and create scaffolds that are both physiologically robust and biocompatible, a microbial transglutaminase (mTG) was used in this study to enzymatically crosslink gelatin solutions. HEK293 cells encapsulated in mTG-crosslinked gelatin proliferated at a rate of 0.03 day(-1). When released via proteolytic degradation with trypsin, the cells were able to recolonize tissue culture flasks, suggesting that cells for therapeutic purposes could be delivered in vivo using an mTG-crosslinked gelatin construct. Upon submersion in a saline solution at 37 degrees C, the mTG-crosslinked gelatin exhibited no mass loss, within experimental error, indicating that the material is thermally stable. The proteolytic degradation rate of mTG-crosslinked gelatin at RT was slightly faster than that of thermally-cooled (physically-crosslinked) gelatin. Thermally-cooled gelatin that was subsequently crosslinked with mTG resulted in hydrogels that were more resistant to proteolysis. Degradation rates were found to be tunable with gelatin content, an attribute that may be useful for either long-time cell encapsulation or time-released regenerative cell delivery. Further investigation showed that proteolytic degradation was controlled by surface erosion.
Cross-Domain Collaborative Learning via Discriminative Nonparametric Bayesian Model (2017)

Cross-domain data analysis has been becoming more and more important, and can be effectively adopted for many applications. However, it is difficult to propose a unified cross-domain collaborative learning framework for cross-domain analysis in social multimedia, because cross-domain data have multidomain, multimodal, sparse, and supervised properties. In this paper, we propose a generic cross-domain collaborative learning (CDCL) framework via a discriminative nonparametric Bayesian dictionary learning model for cross-domain data analysis. Compared with existing cross-domain learning methods, our proposed model mainly has four advantages: First, to address the domain discrepancy, we utilize the shared domain priors among multiple domains to make them share a common feature space. Second, to exploit the multimodal property, we use the shared modality priors to model the relationship between different modalities. Third, to deal with the sparse property of media data in one domain, our goal is to learn a shared dictionary to bridge different domains and complement each other. Finally, to make use of the supervised property, we exploit class label information to learn the shared discriminative dictionary, and utilize a latent probability vector to select different dictionary elements for representation of each class. Therefore, the proposed model can investigate the superiorities of different sources to supplement and improve each other effectively. In experiments, we have evaluated our model for two important applications including cross-platform event recognition and cross-network video recommendation. The experimental results have showed the effectiveness of our CDCL model for cross-domain analysis.
Stereocontrolled Synthesis of 1,4‐Dicarbonyl Compounds by Photochemical Organocatalytic Acyl Radical Addition to Enals (2018)

We report a visible-light-mediated organocatalytic strategy for the enantioselective acyl radical conjugate addition to enals, leading to valuable 1,4-dicarbonyl compounds. The process capitalizes upon the excited-state reactivity of 4-acyl-1,4-dihydropyridines that, upon visible-light absorption, can trigger the generation of acyl radicals. By means of a chiral amine catalyst, iminium ion activation of enals ensures a stereoselective radical trap. We also demonstrate how the combination of this acylation process with a second catalyst-controlled bond-forming event allows to selectively access the full matrix of all possible stereoisomers of the resulting 2,3-substituted 1,4-dicarbonyl products.
Functional outcomes after gamma knife thalamotomy for essential tremor and MS-related tremor (2000)

Twelve patients with a median age of 75 years underwent gamma knife thalamotomy for essential tremor (ET) (n = 9) or MS-related tremor (n = 3). All 11 evaluable patients noted improvement in action tremor. Six of eight ET patients had complete tremor arrest, and the violent action tremor in all three patients with MS was improved. One patient developed transient arm weakness. Stereotactic radiosurgery for ET and MS-related tremor is safe and effective for patients who may be poor candidates for other procedures.
Haplotyping as perfect phylogeny (2002)

The next high-priority phase of human genomics will involve the development of a full Haplotype Map of the human genome [12]. It will be used in large-scale screens of populations to associate specific haplotypes with specific complex genetic-influenced diseases. A prototype Haplotype Mapping strategy is presently being finalized by an NIH working-group. The biological key to that strategy is the surprising fact that genomic DNA can be partitioned into long where genetic recombination has been rare, leading to strikingly fewer distinct haplotypes in the population than previously expected [12, 6, 21, 7].In this paper we explore the algorithmic implications of the key (and now realistic) in long blocks observation, for the problem of inferring haplotypes in populations. We observe that the no-recombination assumption is very powerful. This assumption, along with the standard population-genetic assumption of infinite sites [23, 14] imposes severe combinatorial constraints on the permitted solutions to the haplotype inference problem, leading to an efficient deterministic algorithm to deduce all features of the permitted haplotype solution(s) that can be known with certainty. The technical key is to view haplotype data as disguised information about paths in an unknown tree, and the haplotype deduction problem as a problem of reconstructing the tree from that path information. This formulation allows us to exploit deep theorems and algorithms from graph and matroid theory to efficiently find one permitted solution to the haplotype problem; it gives a simple test to determine if it is the unique solution; if not, we can implicitly represent the set of all permitted solutions so that each can be efficiently created.
Person versus process praise and criticism: Implications for contingent self-worth and coping. (1999)

Conventional wisdom suggests that praising a child as a whole or praising his or her traits is beneficial. Two studies tested the hypothesis that both criticism and praise that conveyed person or trait judgments could send a message of contingent worth and undermine subsequent coping. In Study 1, 67 children (ages 5-6 years) role-played tasks involving a setback and received 1 of 3 forms of criticism after each task: person, outcome, or process criticism. In Study 2, 64 children role-played successful tasks and received either person, outcome, or process praise. In both studies, self-assessments, affect, and persistence were measured on a subsequent task involving a setback. Results indicated that children displayed significantly more "helpless" responses (including self-blame) on all dependent measures after person criticism or praise than after process criticism or praise. Thus person feedback, even when positive, can create vulnerability and a sense of contingent self-worth.
The CD24 Protein Inducible Expression System Is an Ideal Tool to Explore the Potential of CD24 as an Oncogene and a Target for Immunotherapy in Vitro and in Vivo (2011)

CD24 is a cell surface, heavily glycosylated glycosylphosphatidylinositol-anchored mucin-like protein that is overexpressed in various human malignancies. To accurately analyze CD24 function and dissect its biological role in a defined genetic background, it is critical to tightly regulate its expression and be able to turn it on/off in a restricted environment and at a specific time. The tetracycline-induced expression system is most promising as it exhibits such regulation, lack of pleiotropic effects, and high and rapid induction levels. To evaluate the oncogenic and immunotherapeutic potential of CD24 by applying the Tet-On system, the human CD24 gene was cloned downstream to two tetracycline operator sequences, resulting in pCDNA4/TO-CD24, which was then transfected into tetracycline (Tet) repressor-expressing cells (293T-REx), allowing tight on/off regulation, thereby resulting in a very low background or leaky CD24 expression. Selected clones were chosen for further studies and characterized in vitro and in vivo, and several treatment modalities were examined. In addition, the role of CD24 in promoting cell proliferation and tumor growth was studied. The tetracycline-dependent system was successfully implemented. Tetracycline treatment induced CD24 expression in a dose- and time-dependent fashion, which was abrogated following treatment with anti-CD24 monoclonal antibodies (mAbs). CD24-induced expression led to an increased proliferation rate that was inhibited by mAb treatment. In vivo, significantly larger tumors were developed in tetracycline-fed mice. The CD24 Tet-On system is a good model to unravel the role and underlying CD24 pathogenesis in vivo. This valuable tool allows the successful study of novel treatment options, whose effectiveness depends on the CD24 expression level. This set of experiments supports CD24 oncogenic properties.
Microstructure and magnetic properties of iron-based rare-earth magnets (1986)

The magnetic properties of various commercial Fe-Nd-B magnets have been measured and compared with their microstructure and magnetic domain structure. The coercivity is found to be strongly dependent on both the applied field and temperature. Remanent magnetization curves indicate two possible domain wall pinning mechanisms. The microstructure of all magnets studied is very similar showing the predominant Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">14</inf> Nd <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</inf> B grain in coexistence with some Nd-rich phases and the tetragonal Fe <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> NdB <inf xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4</inf> phase. The higher coercivities observed in Neo30H are attributed to the presence of a small amount of Dy in this magnet leading to higher anisotropy fields.
Structure, chromosomal assignment, and deduced amino acid sequence of a human gene for mast cell chymase (1991)

A gene encoding human chymase was cloned and sequenced. The protein-coding exons reveal a preproenzyme with a 19-amino acid signal peptide, an acidic 2-amino acid propeptide, and a 226-amino acid catalytic domain. The mature enzyme is predicted to be cationic (net charge of +13) and to be modified by N-glycosylation at two sites. The amino acid sequence is identical to the 35 residues of NH2-terminal amino acid sequence reported for human skin chymase and is identical to 29 of 31 residues of NH2-terminal and internal amino acid sequence reported for human heart chymase. The full predicted sequence of the catalytic domain reveals a high level of sequence identity to dog mast cell chymase (83%) and a lower level of identity to the sequences of rodent chymases (58-62%). In the phase and placement of introns, the organization of this human chymase gene is similar to that of several other granule-associated leukocyte serine proteases, including rat chymase II, lymphocyte granzymes, and neutrophil cathespin G and elastase. However, the gene organization differs from that of mast cell tryptase, providing additional evidence that the major mast cell serine proteases are separated by substantial evolutionary distance. Amplification of chymase gene-specific fragments from hamster/human hybrid cell line DNA suggests localization of the chymase gene to human chromosome 14. High stringency hybridization of chymase DNA to a human genomic DNA blot suggests the possibility of more than one human chymase gene. Evidence that the chymase gene is expressed in human tissues was obtained by the amplification of chymase-specific DNA from skin and placental cDNA libraries.
Cyber Security Issues in Connected Vehicle of Intelligent Transport System (2016)

Background/Objectives: Requirement for security and safety with interest and growth to C-ITS application is increased. It is needed to security threat issue and risk consideration in the connected vehicle environment. Methods/Statistical Analysis: For efficient communication assistance of connected vehicle, the understanding and access of WAVE mode such as CCH, SCH for multi channel and WSMP specification are preferred in control, communication and signal processing for cooperative intelligence transport system. In security risk assessment and debugging, it is applied to reviewing of source code, analysis and evaluating of compliance, fuzzing and conducting of vulnerability. Findings: Main objectives of this article are to see risk issue and cyber threats in connected vehicle of ITS. Understanding for issues of risk assessment such as debugging, fuzzing, real time application, evaluating of compliance, connectivity and computational performance are required. Also for build up security of ITS it should be established guideline of ITS security factors such as PKI, security architecture, cost and interoperable solution. Application/Improvements: The risk assessment and cyber threats are basically emphasized guideline of ITS security and safety in terms of cyber security procedure and security considerations.Keywords: Intelligence Traffic Security, Standard, Traffic, Vehicle Communication
Exact schema theory for GP and variable-length GAs with homologous crossover (2001)

In this paper we present a new exact schema theory for genetic programming and variable-length genetic algorithms which is applicable to the general class of homologous crossovers. These are a group of operators, including GP one-point crossover and GP uniform crossover, where the offspring are created preserving the position of the genetic material taken from the parents. The theory is based on the concepts of GP crossover masks and GP recombination distributions (both introduced here for the first time), as well as the notions of hyperschema and node reference systems introduced in other recent research. This theory generalises and refines previous work in GP and GA theory.
Topical cromolyn (disodium cromoglycate) solution in the treatment of young children with atopic dermatitis (1990)

A double-blind, randomized-group comparative trial was conducted to assess the therapeutic effect of cromolyn solution on atopic dermatitis in young children (less than 3 yr old). Topically applied cromolyn solution was found to be very effective, improving dermatitis, itching and sleep disturbance, with no untoward effects.
RosENet: Improving Binding Affinity Prediction by Leveraging Molecular Mechanics Energies with an Ensemble of 3D Convolutional Neural Networks (2020)

The worldwide increase and proliferation of drug resistant microbes, coupled with the lag in new drug development, represents a major threat to human health. In order to reduce the time and cost for exploring the chemical search space, drug discovery increasingly relies on computational biology approaches. One key step in these approaches is the need for the rapid and accurate prediction of the binding affinity for potential leads. Here, we present RosENet (<b>Ros</b>etta <b>E</b>nergy Neural <b>Net</b>works), an ensemble of three-dimensional (3D) Convolutional Neural Networks (CNNs), which combines voxelized molecular mechanics energies and molecular descriptors for predicting the absolute binding affinity of protein-ligand complexes. By leveraging the physicochemical properties captured by the molecular force field, our ensemble model achieved a Root Mean Square Error (RMSE) of 1.24 on the PDBBind v2016 core set. We also explored some limitations and the robustness of the PDBBind data set and our approach on nearly 500 structures, including structures determined by Nuclear Magnetic Resonance and virtual screening experiments. Our study demonstrated that molecular mechanics energies can be voxelized and used to help improve the predictive power of the CNNs. In the future, our framework can be extended to features extracted from other biophysical and biochemical models, such as molecular dynamics simulations.
Systematic evaluation of supervised classifiers for fecal microbiota-based prediction of colorectal cancer (2017)

Predicting colorectal cancer (CRC) based on fecal microbiota presents a promising method for non-invasive screening of CRC, but the optimization of classification models remains an unaddressed question. The purpose of this study was to systematically evaluate the effectiveness of different supervised machine-learning models in predicting CRC in two independent eastern and western populations. The structures of intestinal microflora in feces in Chinese population (N = 141) were determined by 454 FLX pyrosequencing, and different supervised classifiers were employed to predict CRC based on fecal microbiota operational taxonomic unit (OTUs). As a result, Bayes Net and Random Forest displayed higher accuracies than other algorithms in both populations, although Bayes Net was found with a lower false negative rate than that of Random Forest. Gut microbiota-based prediction was more accurate than the standard fecal occult blood test (FOBT), and the combination of both approaches further improved the prediction accuracy. Moreover, when unclassified OTUs were used as input, the BayesDMNB text algorithm achieved higher accuracy in the Chinese population (AUC=0.994). Taken together, our results suggest that Bayes Net classification model combined with unclassified OTUs may present an accurate method for predicting CRC based on the compositions of gut microbiota.
Electrohydrodynamic deformation and interaction of drop pairs (1998)

The motion of two drops in a uniform electric field is considered using the leaky dielectric model. The drops are assumed to have no native charge and a dielectrophoretic effect favours translation of the drops toward one another. However, circulatory flows that stem from electrohydrodynamic stresses may either act with or against this dielectrophoretic effect. Consequently, both prolate and oblate drop deformations may be generated and significant deformation occurs near drop contact owing to enhancement of the local electric field. For sufficiently widely spaced drops, electrohydrodynamic flows dominate direct electrical interactions so drops may be pushed apart, though closely spaced drops almost always move together as a result of the electrical interaction or deformation.
Logarithmic Online Regret Bounds for Undiscounted Reinforcement Learning (2007)

We present a learning algorithm for undiscounted reinforcement learning.Our interest lies in bounds for the algorithm's online performance after some finite number of steps.In the spirit of similar methods already successfully applied for the exploration-exploitation tradeoff in multi-armed bandit problems, we use upper confidence bounds to show that our UCRL algorithm achieves logarithmic online regret in the number of steps taken with respect to an optimal policy.