gebhart/patrepeval huggingface dataset:
Late Neurological Consequences of Zika Virus Infection: Risk Factors and Pharmaceutical Approaches (2019)

Zika virus (ZIKV) infection was historically considered a disease with mild symptoms and no major consequences to human health. However, several long-term, late onset, and chronic neurological complications, both in congenitally-exposed babies and in adult patients, have been reported after ZIKV infection, especially after the 2015 epidemics in the American continent. The development or severity of these conditions cannot be fully predicted, but it is possible that genetic, epigenetic, and environmental factors may contribute to determine ZIKV infection outcomes. This reinforces the importance that individuals exposed to ZIKV are submitted to long-term clinical surveillance and highlights the urgent need for the development of therapeutic approaches to reduce or eliminate the neurological burden of infection. Here, we review the epidemiology of ZIKV-associated neurological complications and the role of factors that may influence disease outcome. Moreover, we discuss experimental and clinical evidence of drugs that have shown promising results in vitro or in vitro against viral replication and and/or ZIKV-induced neurotoxicity.
SecureMLDebugger: A Privacy-Preserving Machine Learning Debugging Tool (2020)

The issue of data privacy is uniquely challenging in machine learning which requires large datasets. Privacypreserving machine learning method based on the concept of model training isolated from data scientists have become a hot topic in recent years. In order to protect data privacy, training data is completely isolated from data scientists. Although this method can protect data privacy, data scientists cannot perceive any training information of data nodes during training, and it is difficult to debug machine learning model. Existing works provide data collection APIs to collect and display metadata during training to help data scientists debug machine learning models. Malicious data scientists can obtain private data through these APIs. In this paper, a novel security machine learning debug tool based non-intrusive metadata collection scheme, called SecureMLDebugger(SMLD), is proposed, which automatically collect, store and manage non-privacy metadata during training without any data collection API. Our tool accelerates users in their machine learning experiment while protecting data privacy. We achieve this by transparently tracing each function call in machine learning code and automatically extracting metadata such as hyperparameters of models, training runs, evaluations and layouts of neural networks. SMLD is integrated with popular frameworks such as scikit-learn and PyTorch, and meets the demands of various privacy-preserving training cases in practical.
Ion dissociation reactions induced in a high‐pressure quadrupole collision cell (1995)

This work concerns a new high-pressure quadrupole collision cell, designed for triple-quadrupole mass spectrometers. This new collision cell operates at pressures up to 10 mTorr, an order of magnitude higher than conventional cells of this type. Previous investigations have concentrated upon the significant increases in transmission efficiency and in resolving power for fragment ions which result from the use of this new design. The present work reports an investigation into the nature of the dissociation reactions which can be induced by collisions in this high-pressure cell. Charge-site-remote fragmentations of a simple precursor ion were chosen as a test case, and were found to be observable at laboratory collision energies lower by a factor of 4-5 than those found previously to be necessary when using conventional low-pressure quadrupole collision cells. It was also shown that the charge-site-remote reactions were accompanied by the mixed-site-fragmentation reactions described by Tuinman and Cook (J. Am. Soc. Mass Spectrom. Vol. 1, p. 85 (1989)). Ionization of collision gas was observed in the case of xenon. Efforts to observe charge-site-remote fragmentations of peptide ions were marginally successful. Highly basic peptides, which have been problematic for sequencing by low-energy tandem mass spectrometry, did not yield useful fragment-ion spectra in the new cell. The fragmentation behaviour of protonated Leu-enkephalin, for which fragmentation pathways have been thoroughly studied previously, suggested that the observed spectra reflected integration of the fragmentation kinetics over a considerably longer time, thus involving many more reaction steps. These combined observations are considered in terms of a qualitative model based on a rapid decrease of ion kinetic energy during passage through the cell, with much longer residence times than for conventional quadrupole cells.
Synergistic activation of NF-κB by nontypeable <i>Haemophilus influenzae</i> and tumor necrosis factor α (2004)

Nontypeable Haemophilus influenzae (NTHi) is an important human pathogen causing otitis media in children and exacerbation of chronic obstructive pulmonary disease in adults. Like most other bacterial infections, NTHi infections are also characterized by inflammation, which is mainly mediated by cytokines and chemokines such as tumor necrosis factor alpha (TNF-alpha). Among a variety of transcription regulators, NF-kappaB has been shown to play a critical role in regulating the expression of large numbers of genes encoding inflammatory mediators. In review of the current studies on NF-kappaB regulation, most of them have focused on investigating how NF-kappaB is activated by a single inducer at a time. However, in bacteria-induced inflammation in vivo, multiple inducers including both exogenous and endogenous mediators are present simultaneously. A key issue that has yet to be addressed is whether the exogenous inducers such as NTHi and the endogenous factors such as TNF-alpha activate NF-kappaB in a synergistic manner. We show that NTHi and TNF-alpha, when present together, synergistically induce NF-kappaB activation via two distinct signaling pathways: NF-kappaB translocation-dependent and -independent pathways. The NF-kappaB translocation-dependent pathway involves NF-kappaB-inducing kinase-IkappaB kinase beta/gamma-dependent phosphorylation and degradation of IkappaBalpha, whereas the NF-kappaB translocation-independent pathway involves mitogen-activated protein kinase (MAPK)/extracellular signal-regulated kinase kinase kinase 1-dependent activation of MAPK kinase 3/6-p38 MAPK pathway. In addition, the same signaling pathways are also involved in synergistic induction of TNF-alpha, IL-1beta, and IL-8. These studies should deepen our understanding of the molecular mechanisms underlying the combinatorial regulation of inflammation and lead to development of therapeutic strategies for NTHi-induced infections.
Fast color-transfer-based image fusion method for merging infrared and visible images (2010)

We present a computationally efficient color image fusion algorithm for merging infrared and visible images. At the core of the proposed method is the color transfer technique based on the linear <i>YC<sub>B</sub>C<sub>R</sub></i> space. The method directly uses the grayscale fused image and the difference signals of the input images to construct the source YCBCR components, then uses the statistical color transfer technique to form a color fused image that takes the target image's color characteristics. Two different strategies, which respectively employ the pixel averaging fusion scheme and the multiresolution fusion scheme as the grayscale image fusion solution, are proposed to fulfill different user needs. The simple strategy using the pixel averaging fusion scheme answers to a need of easy implementation and speed of use. And the complex strategy using the multiresolution fusion scheme answers to the high quality need of the fused products. In addition, we also describe some useful theories about color-transfer-based image fusion. Experimental results show that the proposed color image fusion algorithm can effectively produce a natural appearing "daytime-like" color fused image, and even using the pixel averaging fusion scheme to implement the grayscale fusion can also provide a pleasing result.
Detection of virus mRNA within infected host cells using an isothermal nucleic acid amplification assay: marine cyanophage gene expression within Synechococcus sp (2007)

The SMART assay is based on isothermal nucleic acid amplification, allowing the detection of specific sequences of DNA or RNA. It was shown to be suitable for differentiating between virus-infected and non-infected host cultures and for the detection of virus gene expression: the first reported use of this technology for such applications.
Metallic Phase with Long-Range Orientational Order and No Translational Symmetry (1984)

We have observed a metallic solid (Al-14-at.%-Mn) with long-range orientational order, but with icosahedral point group symmetry, which is inconsistent with lattice translations. Its diffraction spots are as sharp as those of crystals but cannot be indexed to any Bravais lattice. The solid is metastable and forms from the melt by a first-order transition.
An Efficient Method for the N-Bromosuccinimide Catalyzed Synthesis of Indolyl-Nitroalkanes (2009)

An efficient and practical method for the synthesis of indolyl-nitroalkane derivatives catalyzed by N-bromosuccinimide is described. The generality of this method was demonstrated by synthesizing an array of diverse 3-substituted indole derivatives by the reaction of different beta-nitrostyrenes with various substituted indoles. Simple reaction conditions accompanied by good yields of indolyl-nitroalkanes are the merits of this methodology.
Support Vector Data Description for image categorization from Internet images (2008)

Training a classifier for object category recognition using images on the Internet is an attractive approach due to its scalability. However, a big challenge in this approach is that it is difficult to automatically obtain sets of negative samples that are guaranteed to be free of positive samples. In this paper we propose to address this challenge with a Support Vector Data Description (SVDD) classifier. An SVDD classifier does not need negative images in training. It computes a hypersphere around the potentially good images in the feature space and uses this boundary to distinguish images of target visual category from outliers. Evaluation on standard test sets shows that we are able to achieve competitive classification performance using the contaminated training images from the Internet without the need for large datasets of negative examples.
A statistical approach to the inverse problem of aquifer hydrology: 1. Theory (1979)

A new statistically based approach to the problem of estimating spatially varying aquifer transmissivities on the basis of steady state water level data is presented. The method involves solving a family of generalized nonlinear regression problems and then selecting one particular solution from this family by means of a comparative analysis of residuals. A linearized error analysis of the solution is included. This analysis allows one to estimate the covariance of the transmissivity estimates as well as the square error of the estimates of hydraulic head. In addition to the explicitly statistical orientation of the method, it has an additional feature of permitting the user to incorporate a priori information about the transmissivities. This information may be based on actual field data such as pumping tests, or on statistical data accumulated from similar aquifers elsewhere in the world. A highly efficient explicit numerical scheme for solving the inverse problem in an approximate manner when errors in water level data are sufficiently small is also described. When these errors are large, the explicit scheme may still be useful for obtaining a rapid initial idea about the approximate location of the optimum solution. Paper 1 presents the theory and illustrates it by a theoretical example. The purpose of this example is to demonstrate the effectiveness of our method in dealing with noisy data obtained from a known model. Application of the method to real data will be described in paper 2.
An Organic Molecule with Asymmetric Structure Exhibiting Aggregation‐Induced Emission, Delayed Fluorescence, and Mechanoluminescence (2014)

Compounds displaying delayed fluorescence (DF), from severe concentration quenching, have limited applications as nondoped organic light-emitting diodes and material sciences. As a nondoped fluorescent emitter, aggregation-induced emission (AIE) materials show high emission efficiency in their aggregated states. Reported herein is an AIE-active, DF compound in which the molecular interaction is modulated, thereby promoting triplet harvesting in the solid state with a high photoluminescence quantum yield of 93.3%, which is the highest quantum yield, to the best of our knowledge, for long-lifetime emitters. Simultaneously, the compound with asymmetric molecular structure exhibited strong mechanoluminescence (ML) without pretreatment in the solid state, thus exploiting a design and synthetic strategy to integrate the features of DF, AIE, and ML into one compound.
SOLUTION GROWTH OF INTERMETALLIC SINGLE CRYSTALS: A BEGINNER'S GUIDE (2009)

Progress in experimental solid state physics, as well as in related disciplines, is often hampered by limited access to single crystals of novel materials. This lack of single crystalline samples constrains researchers to study or measure materials that are available rather than the materials that are most relevant to the questions at hand. The extreme example of this is the allegorical Ph.D. student who has to measure the one crystal that the advisor has on hand, regardless of the physical question to be probed. As part of the second Euroschool on complex metals I presented lectures on the design, discovery, growth and characterization of novel intermetallic compounds. In this paper I will focus on the basics of solution growth of novel compounds.
Genetic Analysis of <i>Pseudomonas aeruginosa</i> Isolates from the Sputa of Australian Adult Cystic Fibrosis Patients (2002)

Genetic investigations were carried out with 50 phenotypically selected strains of Pseudomonas aeruginosa from 18 patients attending an Australian cystic fibrosis (CF) center. The isolates were analyzed by restriction fragment length polymorphism (RFLP) analysis by pulsed-field gel electrophoresis (PFGE). Phylogenetic analysis of the macrorestriction patterns showed rates of genetic similarity ranging from 76 to 100%; 24 (48%) of the strains from 11 patients had greater than 90% similarity. A dominant strain emerged: 15 isolates from seven patients had identical PFGE patterns, and 4 other isolates were very closely related. The 50 isolates were grouped into 21 pulsotypes on the basis of visual delineation of a three-band difference. Ten of the 18 (56%) patients were infected with clonal or subclonal strains. Sequence analysis of PCR products derived from the mucA gene showed 20 mutations, with the number of mutations in individual isolates ranging from 1 to 4; 19 of these changes are reported here for the first time. Potentially functional changes were found in 22 (44%) isolates. Eight changes (five transversions and three single base deletions) led to premature stop codons, providing support for the presence of mucA mutations as one pathway to mucoidy. There was a trend toward an association between the dominant strain and lack of potentially functional mucA mutations (P = 0.09 by the chi(2) test) but no relationship between genotype and phenotype. This is the first study of genetic variation in P. aeruginosa isolates from adult Australian CF patients. The findings highlight the need for further investigations on the transmissibility of P. aeruginosa in CF patients.
Criterion-referenced Assessment and the Development of Knowledge and Understanding (1995)

The paper argues that no criterion-referenced assessment system can achieve both reliability and validity at one and the same time. It shows that the reasons for this are conceptual, and hence that empirical research into the'problem' is a waste of money and effort. Considerable discussion is devoted to ideas of knowledge and understanding, and to proper educational objectives pertaining to these. Much reference is made to the current National Curriculum context in the United Kingdom, and conclusions are drawn for appropriate educational policy in this area.
Performance Evaluation of Transmission Technique Utilizing Linear Combination Diversity in MIMO Spatial Multiplexing Systems (2008)

In this paper, we evaluate BER (bit error rate) performance and diversity gain when employing a transmission technique utilizing LC (Linear Combination) diversity using 2 time slots with QPSK channels in 2×2 MIMO (Multiple-Input Multiple-Output) spatial multiplexing systems by comparing it with the upper and lower bound on BER. This evaluation shows that this transmission technique realizes high diversity gain and high transmission rate in LOS (line-of-sight) and NLOS (non line-of-sight) environments.
Characterization of Homocysteine γ-Lyase from Submerged and Solid Cultures of Aspergillus fumigatus ASH (JX006238) (2013)

Among 25 isolates, Aspergillus fumigatus ASH (JX006238) was identified as a potent producer of homocysteine gamma- lyase. The nutritional requirements to maximize the enzyme yield were optimized under submerged (SF) and solid-state fermentation (SSF) conditions, resulting in a 5.2- and 2.3-fold increase, respectively, after the last purification step. The enzyme exhibited a single homogenous band of 50 kDa on SDS-PAGE, along with an optimum pH of 7.8 and pH stability range of 6.5 to 7.8. It also showed a pI of 5.0, as detected by pH precipitation with no glycosyl residues. The highest enzyme activity was obtained at 37-40 degrees C, with a Tm value of 70.1 degrees C. The enzyme showed clear catalytic and thermal stability below 40 degrees C, with T1/2 values of 18.1, 9.9, 5.9, 3.3, and 1.9 h at 30 degrees C, 35 degrees C, 40 degrees C, 50 degrees C, and 60 degrees C, respectively. Additionally, the enzyme Kr values were 0.002, 0.054, 0.097, 0.184, and 0.341 S-1 at 30 degrees C, 35 degrees C, 40 degrees C, 50 degrees C, and 60 degrees C, respectively. The enzyme displayed a strong affinity to homocysteine, followed by methionine and cysteine when compared with non-S amino acids, confirming its potency against homocysteinuriarelated diseases, and as an anti-cardiovascular agent and a specific biosensor for homocysteinuria. The enzyme showed its maximum affinity for homocysteine (Km 2.46 mM, Kcat 1.39 × 10(-3) s(-1)), methionine (Km 4.1 mM, Kcat 0.97 × 10(-3) s(-1)), and cysteine (Km 4.9 m M, Kcat 0.77 × 10(-3) s(-1)). The enzyme was also strongly inhibited by hydroxylamine and DDT, confirming its pyridoxal 5'-phosphate (PLP) identity, yet not inhibited by EDTA. In vivo, using Swiss Albino mice, the enzyme showed no detectable negative effects on platelet aggregation, the RBC number, aspartate aminotransferase, alanine aminotransferase, or creatinine titer when compared with negative controls.
Dictating Pt-Based Electrocatalyst Performance in Polymer Electrolyte Fuel Cells, from Formulation to Application (2019)

In situ electrochemical diagnostics designed to probe ionomer interactions with platinum and carbon were applied to relate ionomer coverage and conformation, gleaned from anion adsorption data, with O<sub>2</sub> transport resistance for low-loaded (0.05 mg<sub>Pt</sub> cm<sup>-2</sup>) platinum-supported Vulcan carbon (Pt/Vu)-based electrodes in a polymer electrolyte fuel cell. Coupling the in situ diagnostic data with ex situ characterization of catalyst inks and electrode structures, the effect of ink composition is explained by both ink-level interactions that dictate the electrode microstructure during fabrication and the resulting local ionomer distribution near catalyst sites. Electrochemical techniques (CO displacement and ac impedance) show that catalyst inks with higher water content increase ionomer (sulfonate) interactions with Pt sites without significantly affecting ionomer coverage on the carbon support. Surprisingly, the higher anion adsorption is shown to have a minor impact on specific activity, while exhibiting a complex relationship with oxygen transport. Ex situ characterization of ionomer suspensions and catalyst/ionomer inks indicates that the lower ionomer coverage can be correlated with the formation of large ionomer aggregates and weaker ionomer/catalyst interactions in low-water content inks. These larger ionomer aggregates resulted in increased local oxygen transport resistance, namely, through the ionomer film, and reduced performance at high current density. In the water-rich inks, the ionomer aggregate size decreases, while stronger ionomer/Pt interactions are observed. The reduced ionomer aggregation improves transport resistance through the ionomer film, while the increased adsorption leads to the emergence of resistance at the ionomer/Pt interface. Overall, the high current density performance is shown to be a nonmonotonic function of ink water content, scaling with the local gas (H<sub>2</sub>, O<sub>2</sub>) transport resistance resulting from pore, thin film, and interfacial phenomena.
Transcriptional and post-transcriptional mechanisms of BAFF-receptor dysregulation in human B lineage malignancies  (2010)

Together, circulating BAFF and dominant receptor BAFF-R homeostatically regulate the humoral immune system. Consistently aberrant BAFF-R expression in leukemic cells reveals an intimate connection of these cells' malignant physiology to the BAFF/BAFF-R axis and also provides an additional survival mechanism to the expressing cells. In this study, we used primary cells and cell lines to interrogate the mechanisms underlying aberrant BAFF-R expression in precursor B acute lymphoblastic leukemia (precursor B-ALL) and mature B chronic lymphocytic leukemia (CLL). Here we demonstrate the aberrant expression of BAFF-R in precursor B-ALL cell lines and reveal that these cells acquire BAFF-R expression through premature transcriptional activation of the BAFF-R promoter in coordination with regulatory transcription factor c-Rel. Investigations using primary CLL cells provide a crucial counterpoint through their paucity of BAFF-R relative to their benign mature B cell counterparts, which we establish as functionally significant in its depletion of the CLL cells' BAFF-binding capacity. Furthermore, BAFF-R downregulation in CLL patients is revealed here to be restricted to the malignant compartment and mediated post-transcriptionally in order to compensate for the consistently unchanged levels of transcription factor c-Rel and BAFF-R mRNA. Finally, we present evidence that CLL cells retain endogenous mechanisms of BAFF-R regulatory control despite active receptor dysregulation.