gebhart/patrepeval huggingface dataset:
Expression of P. falciparum var Genes Involves Exchange of the Histone Variant H2A.Z at the Promoter (2011)

Plasmodium falciparum employs antigenic variation to evade the human immune response by switching the expression of different variant surface antigens encoded by the var gene family. Epigenetic mechanisms including histone modifications and sub-nuclear compartmentalization contribute to transcriptional regulation in the malaria parasite, in particular to control antigenic variation. Another mechanism of epigenetic control is the exchange of canonical histones with alternative variants to generate functionally specialized chromatin domains. Here we demonstrate that the alternative histone PfH2A.Z is associated with the epigenetic regulation of var genes. In many eukaryotic organisms the histone variant H2A.Z mediates an open chromatin structure at promoters and facilitates diverse levels of regulation, including transcriptional activation. Throughout the asexual, intraerythrocytic lifecycle of P. falciparum we found that the P. falciparum ortholog of H2A.Z (PfH2A.Z) colocalizes with histone modifications that are characteristic of transcriptionally-permissive euchromatin, but not with markers of heterochromatin. Consistent with this finding, antibodies to PfH2A.Z co-precipitate the permissive modification H3K4me3. By chromatin-immunoprecipitation we show that PfH2A.Z is enriched in nucleosomes around the transcription start site (TSS) in both transcriptionally active and silent stage-specific genes. In var genes, however, PfH2A.Z is enriched at the TSS only during active transcription in ring stage parasites. Thus, in contrast to other genes, temporal var gene regulation involves histone variant exchange at promoter nucleosomes. Sir2 histone deacetylases are important for var gene silencing and their yeast ortholog antagonises H2A.Z function in subtelomeric yeast genes. In immature P. falciparum parasites lacking Sir2A or Sir2B high var transcription levels correlate with enrichment of PfH2A.Z at the TSS. As Sir2A knock out parasites mature the var genes are silenced, but PfH2A.Z remains enriched at the TSS of var genes; in contrast, PfH2A.Z is lost from the TSS of de-repressed var genes in mature Sir2B knock out parasites. This result indicates that PfH2A.Z occupancy at the active var promoter is antagonized by PfSir2A during the intraerythrocytic life cycle. We conclude that PfH2A.Z contributes to the nucleosome architecture at promoters and is regulated dynamically in active var genes.
Proton Exchange Membranes by Irradiation Induced Grafting of Styrene Onto FEP and ETFE: Influences of the Crosslinker N,N-Methylene-bis-acrylamide (2002)

Energy generation using polymer electrolyte fuel cells has gained increased interest due to limited oil resources. At present perfluoro sulfonic acid membranes like Nafion are the most popular and hence have been comprehensively characterized according to their water incorporation and diffusion, proton and gas diffusion as well as their thermal stability. Perfluoro sulfonic acid membranes are expensive. For this reason the development of cheaper membranes with equivalent or improved properties is necessary.
Methodical software-supported, multi-target optimization and redesign of a gear wheel for additive manufacturing (2020)

Additive manufacturing gives new freedom to part design by enabling the manufacturing of complex structures. Mastering this degree of freedom poses challenges for product developers with experience from conventional manufacturing. In order to meet this challenge in a structured manner, a practical method is presented in which creative idea development is combined with software-based design optimization. First, optimization goals are defined. Then a baseline design is developed through a creative ideation process. Variants are derived from the baseline design, evaluated according to simulation results and selected. The method is illustrated by the development of a lightweight and function-integrated gear wheel.
The Oncogenic BRAF Kinase Inhibitor PLX4032/RG7204 Does Not Affect the Viability or Function of Human Lymphocytes across a Wide Range of Concentrations (2010)

The preserved viability and function of lymphocytes exposed to high concentrations of PLX4032 suggest that this agent could be a potential candidate for combining with immunotherapy strategies for the treatment of patients with BRAF(V600)(E) mutant melanoma.
Emissive Pt(ii) complexes bearing both cyclometalated ligand and 2-pyridyl hexafluoropropoxide ancillary chelate (2008)

A new series of mono-cyclometalated Pt(II) complexes 1-4 with chelating 2-pyridyl hexafluoropropoxide as the ancillary ligand were synthesized. Single crystal X-ray diffraction studies were examined, giving evidence for the occurrence of pi pi stacking between the cyclometalated ligands, but a lack of intermolecular Pt ... Pt interaction. Among these complexes, the benzo[h]quinoline analogue 2a shows the greatest degree of pi pi stacking, which is also confirmed by the observation of additional, large Stokes shifted emission attributed to the aggregated counterparts in solid thin film. All these Pt(II) complexes are highly emissive in solid state, whereas except for 4-phenylquinazoline analogues 4a and 4b, complexes 1-3 in solution are subject to dominant radiationless deactivation induced, in part, by the solvent collision to the square planar Pt(II) framework. Electroluminescent OLEDs employing 2-phenylpyridine analogue 1b as the dopants were fabricated, rendering satisfactory performance data suited for future improvement.
Using Fluorescent Post‐Labeling To Probe the Subcellular Localization of DNA‐Targeted Platinum Anticancer Agents (2013)

Das Grüne in der Zelle: Eine Postmarkierungsmethode wurde entwickelt, um ein DNA-targetierendes Platin-Agens in Krebszellen durch konfokale Fluoreszenzmikroskopie sichtbar zu machen. Die Markierung erfolgt durch Umsetzung eines azidfunktionalisierten Platin-Acridin-Tumortherapeutikums mit einem alkinmodifizierten AlexaFluor-488-Farbstoff (grüner Stern, siehe Schema). Das Platin-Agens ist in den Nukleoli von NCI-H460-Krebszellen lokalisiert. As a service to our authors and readers, this journal provides supporting information supplied by the authors. Such materials are peer reviewed and may be re-organized for online delivery, but are not copy-edited or typeset. Technical support issues arising from supporting information (other than missing files) should be addressed to the authors. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Science and technology of rubber (1995)

A.N. Gent, Rubber Elasticity: Basic Concepts and Behavior. R.P. Quirk and M.M. Morton, Polymerization. G. Ver Strate and D.J. Lohse, Structure Characterization in the Science and Technology of Elastomers. B. Erman and J.E. Mark, The Molecular Basis of Rubberlike Elasticity. O. Kramer, S. Hvidt, and J.D. Ferry, Dynamic Mechanical Properties. J.L. White, Rheological Behavior of Processing of Unvulcanized Rubber. A.Y. Coran, Vulcanization. A.I. Medalia and G. Kraus, Reinforcement of Elastomers by Particulate Fillers. W.W. Barbin and M.B. Rodgers, The Science of Rubber Compounding. A.N. Gent, Strength of Elastomers. A.F. Halasa, J.M. Massie, and R.J. Ceresa, The Chemical Modification of Polymers. P.J. Corish, Elastomer Blends. B.P. Grady and S.L. Cooper, Thermoplastic Elastomers. F.J. Kovac and M.B. Rodgers, Tire Engineering. Chapter References. Subject Index.
Predictive Integrators with Thermal Noise Cancellation (2023)

This paper proposes a simple thermal noise cancellation technique to effectively reduce the output noise in predictive integrators. By combining a low-gain two-stage amplifier and a small auxiliary noise-cancelling capacitor, the output noise is highly attenuated. Simulation results for a classic Nagaraj-Ki predictive integrator, considering real MOS switches, demonstrate that the output thermal noise can be reduced up to 87%.
How Proteins Adapt: Lessons from Directed Evolution (2009)

Applying artificial selection to create new proteins has allowed us to explore fundamental processes of molecular evolution. These "directed evolution" experiments have shown that proteins can readily adapt to new functions or environments via simple adaptive walks involving small numbers of mutations. With the entire "fossil record" available for detailed study, these experiments have provided new insight into adaptive mechanisms and the effects of mutation and recombination. Directed evolution has also shown how mutations that are functionally neutral can set the stage for further adaptation. Watching adaptation in real time helps one to appreciate the power of the evolutionary design algorithm.
The CMU Statistical Language Modeling Toolkit and its use in the 1994 ARPA CSR Evaluation (2018)

The Carnegie Mellon Statistical Language Modeling (CMU SLM) Toolkit is a set of Unix software tools designed to facilitate language modeling work in the research community. The package, including source code, is freely available for research purposes. As of December 1994, the toolkit is in active use by 23 research groups in 8 countries. It was recently used to process the 2.5 GB NAB corpus for the ARPA CSR community. In this paper, I ﬁrst discuss the design principles and features of the toolkit. Then, I describe the composition of the NAB corpus, and report on the ngram statistics, standard vocabulary and language models created using the SLM tools.
Moral Issues of Human-Non-Human Primate Neural Grafting (2005)

The scientific, ethical, and policy issues raised by research involving the engraftment of human neural stem cells into the brains of nonhuman primates are explored by an interdisciplinary working group in this [Policy Forum][1]. The authors consider the possibility that this research might alter the cognitive capacities of recipient great apes and monkeys, with potential significance for their moral status.

 [1]: http://www.sciencemag.org/cgi/content/full/309/5733/385
Benzo[b]naphthyridines (2006)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF.
Measures of quantum computing speedup (2013)

We introduce the concept of strong quantum speedup. We prove that approximating the ground-state energy of an instance of the time-independent Schr\"odinger equation, with $d$ degrees of freedom and large $d$, enjoys strong exponential quantum speedup. It can be easily solved on a quantum computer. Some researchers in discrete complexity theory believe that quantum computation is not effective for eigenvalue problems. One of our goals in this paper is to explain this dissonance.
Phenolic Compounds in Particles of Mainstream Waterpipe Smoke (2012)

The large quantities of phenols and phenol derivatives in waterpipe smoke add to the growing evidence that habitual waterpipe use may increase the risk of cancer and cardiovascular diseases.
Shuffling across rounds: A lightweight strategy to counter side-channel attacks (2016)

Side-channel attacks are a potent threat to the security of devices implementing cryptographic algorithms. Designing lightweight countermeasures against side-channel analysis that can run on resource constrained devices is a major challenge. One such lightweight countermeasure is shuffling, in which the designer randomly permutes the order of execution of potentially vulnerable operations. State of the art shuffling countermeasures advocate shuffling a set of independent operations in a single round of a cryptographic algorithm, but are often found to be insufficient as standalone countermeasures. In this paper, we propose a two-round version of the shuffling countermeasure, and test its security when applied to a serialized implementation of AES-128 using Test Vector Leakage Assessment (TVLA). Our results show that the required number of traces to break AES-128 implemented using our proposed countermeasure is significantly larger than the implementations using simple one-round shuffling. Furthermore, the new shuffling method has significantly lower overhead of around 1.3 times, as compared to other side-channel countermeasures such as masking that have an overhead of approximately two times.
Is the outcome from acute respiratory distress syndrome improving? (1996)

Mortality rates of the acute respiratory distress syndrome have been high since the syndrome was first described in 1967. The survival rate approximates 40% in all major series. Approximately 90% of all deaths in patients with acute respiratory distress syndrome occur within 2 to 3 weeks after the onset of the syndrome. The major determinant of outcome in acute respiratory distress syndrome is the failure of other vital organ systems. In the past two decades, although we have increased our knowledge about some of the pathophysiological aspects of acute respiratory distress syndrome, improvements in supportive care in ICUs reportedly have not led to an increase in the very low survival rates. Differences in patient selection, severity of underlying disease, patient age, and predisposition for acute respiratory distress syndrome may in fact explain the differences in mortality rates reported in most patient series. Recently, there is some evidence showing that the survival rate is increasing in centers with expertise in the management of acute respiratory distress syndrome.
Expression and Cleavage of Middle East Respiratory Syndrome Coronavirus nsp3-4 Polyprotein Induce the Formation of Double-Membrane Vesicles That Mimic Those Associated with Coronaviral RNA Replication (2017)

Betacoronaviruses, such as Middle East respiratory syndrome coronavirus (MERS-CoV), are important pathogens causing potentially lethal infections in humans and animals. Coronavirus RNA synthesis is thought to be associated with replication organelles (ROs) consisting of modified endoplasmic reticulum (ER) membranes. These are transformed into double-membrane vesicles (DMVs) containing viral double-stranded RNA and into other membranous elements such as convoluted membranes, together forming a reticulovesicular network. Previous evidence suggested that the nonstructural proteins (nsp's) 3, 4, and 6 of the severe acute respiratory syndrome coronavirus (SARS-CoV), which contain transmembrane domains, would all be required for DMV formation. We have now expressed MERS-CoV replicase self-cleaving polyprotein fragments encompassing nsp3-4 or nsp3-6, as well as coexpressed nsp3 and nsp4 of either MERS-CoV or SARS-CoV, to characterize the membrane structures induced. Using electron tomography, we demonstrate that for both MERS-CoV and SARS-CoV coexpression of nsp3 and nsp4 is required and sufficient to induce DMVs. Coexpression of MERS-CoV nsp3 and nsp4 either as individual proteins or as a self-cleaving nsp3-4 precursor resulted in very similar DMVs, and in both setups we observed proliferation of zippered ER that appeared to wrap into nascent DMVs. Moreover, when inactivating nsp3-4 polyprotein cleavage by mutagenesis, we established that cleavage of the nsp3/nsp4 junction is essential for MERS-CoV DMV formation. Addition of the third MERS-CoV transmembrane protein, nsp6, did not noticeably affect DMV formation. These findings provide important insight into the biogenesis of coronavirus DMVs, establish strong similarities with other nidoviruses (specifically, the arteriviruses), and highlight possible general principles in viral DMV formation.<b>IMPORTANCE</b> The RNA replication of positive stranded RNA viruses of eukaryotes is thought to take place at cytoplasmic membranous replication organelles (ROs). Double-membrane vesicles are a prominent type of viral ROs. They are induced by coronaviruses, such as SARS-CoV and MERS-CoV, as well as by a number of other important pathogens, yet little is known about their biogenesis. In this study, we explored the viral protein requirements for the formation of MERS-CoV- and SARS-CoV-induced DMVs and established that coexpression of two of the three transmembrane subunits of the coronavirus replicase polyprotein, nonstructural proteins (nsp's) 3 and 4, is required and sufficient to induce DMV formation. Moreover, release of nsp3 and nsp4 from the polyprotein by proteolytic maturation is essential for this process. These findings provide a strong basis for further research on the biogenesis and functionality of coronavirus ROs and may point to more general principles of viral DMV formation.
Neutralization of B-Cell Activating Factor (BAFF) by Belimumab Reinforces Small Molecule Inhibitor Treatment in Chronic Lymphocytic Leukemia (2020)

The introduction of idelalisib, ibrutinib and venetoclax for treatment of chronic lymphocytic leukemia (CLL) has greatly improved long term survival of patients. However, many patients do not achieve complete remission and suffer from development of resistance upon treatment with these small molecule inhibitors. Here we report that the TNF family member B-cell activating factor (BAFF) mediates resistance of CLL cells to idelalisib, ibrutinib and venetoclax by sustaining survival and preventing apoptosis of the malignant B cells as revealed by analysis of cellular ATP levels and mitochondrial membrane integrity as well as caspase activation, respectively. As BAFF also plays a prominent role in autoimmune diseases, the BAFF-neutralizing antibody belimumab was developed and approved for treatment of systemic lupus erythematosus (SLE). When we employed belimumab in the context of CLL treatment with idelalisib, ibrutinib and venetoclax, BAFF neutralization was found to significantly increase the sensitivity of the leukemic cells to all three small molecule inhibitors. Notably, BAFF neutralization proved to be beneficial independently of clinical stage according to Binet and Rai or IgVH mutational status. Our results identify drug repurposing of belimumab for neutralization of BAFF to complement small molecule inhibitor treatment as a promising therapeutic approach in CLL that is presently undergoing clinical evaluation.
Data from Sarcoma Eradication by Doxorubicin and Targeted TNF Relies upon CD8<sup>+</sup> T-cell Recognition of a Retroviral Antigen (2023)

&lt;div&gt;Abstract&lt;p&gt;Antibody–cytokine complexes may offer new tools to treat cancer. Here, we show how TNF-linked antibodies, which recognize tumor-selective splice isoforms of fibronectin (F8-TNF), can be exploited to eradicate sarcomas in immunocompetent mice. We treated mice bearing WEHI-164 fibrosarcoma with a combination of F8-TNF and doxorubicin, curing the majority of treated animals (29/37). Notably, cured mice were resistant to rechallenge not only by WEHI-164 cells but also heterologous C51 or CT26 colorectal tumor cells in a CD8&lt;sup&gt;+&lt;/sup&gt; T-cell–dependent process. Mechanistic analyses revealed that each tumor cell line presented AH1, a common endogenous retroviral peptide. Numbers of AH1-specific CD8&lt;sup&gt;+&lt;/sup&gt; T cells exhibiting cytotoxic capacity were increased by F8-TNF plus doxorubicin treatment, arguing that cognate CD8&lt;sup&gt;+&lt;/sup&gt; T cells contributed to tumor eradication. Sequence analysis of T-cell receptors of CD8&lt;sup&gt;+&lt;/sup&gt; T cells revealed the presence of H-2L&lt;sup&gt;d&lt;/sup&gt;/AH1-specific T cells and an expansion of sequence diversity in treated mice. Overall, our findings provide evidence that retroviral genes contribute to tumoral immunosurveillance in a process that can be generally boosted by F8-TNF and doxorubicin treatment. &lt;i&gt;Cancer Res; 77(13); 3644–54. ©2017 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Theoretical studies of current transport in interband tunnel structures using the effective bond orbital model (2002)

A model has been developed that incorporates realistic band structure calculations to describe carrier transport in interband tunnel structures based on the InAs/GaSb/AlSb material system. The light-hole, heavy-hole, and split-off valence bands, and the lowest conduction band, have been incorporated using the effective bond orbital model. The results of the present calculations are compared with those obtained using a two-band model in which only the lowest conduction band and the light-hole valence band have been included. It is found that heavy-hole states can introduce substantial hole-mixing effects in device structures containing GaSb valence-band quantum wells, and could have a significant influence on the current-voltage characteristics of interband devices. >
A novel, simple and sensitive ligand affinity capture method for detecting molecular interactions by MALDI mass spectrometry (2008)

A simple and sensitive ligand affinity capture method (LAC) was developed to detect biotinylated biomolecules bound to a biotin-avidin base by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI ToF MS). Glass slides covered with a metal film for MALDI MS applications were treated with amino-silane and derivatized with biotin followed by binding of avidin. Washing buffers with high ionic strength increased the specificity of the subsequent binding of biotinylated biomolecules to the avidin layer. A combined thin layer-dried droplet method using alpha-cyano-4-hydroxycinnamic acid (CHCA) in acetone or ethyl acetate resulted in the most intense ions of biotinylated polymyxin B, whereas the matrix conditions did not influence the detection of angiotensin II. Addition of biotinylated biomolecules in the low femtomole to low picomole range resulted in sufficient ion intensity for detection by the LAC method. The LAC concept was extended by binding of biotinylated lipopolysaccharide to the biotin-avidin base followed by preferential capture and specific detection of the binding antagonist polymyxin B.
Multi-Connectivity for Multicast Video Streaming in Cellular Networks (Extended Abstract) (2023)

In video streaming applications especially during live streaming events (such as the Super Bowl), video traffic can account for a significant portion of network traffic and can lead to severe network congestion. During such events, multicast transmission can be used to avoid network congestion since the same video content is being streamed to multiple users simultaneously. However, providing seamless connectivity to cellular users in multicast streaming remains an open problem. To address this issue, this paper explores the potential of using multi-connectivity (MC) in wireless multicast streaming. Our results reveal that MC significantly improves the performance of multicast services, especially for cell edge users who often suffer from poor channel conditions. We prove that optimal resource allocation in MC multicast streaming is an NP-hard problem. Therefore, we propose a greedy approximation algorithm for this problem with an approximation factor of $(1-1/e)$. We also prove that no other polynomial-time algorithm can provide a better approximation.
Electrical Constants and Relative Capabilities of Bundled-Conductor Transmission Lines (1964)

The electrical characteristics of bundled-conductor transmission lines are analyzed in terms of the transmission capability of bundled-conductor versus single-conductor lines. The results of the analysis are presented in the form of several graphs as well as extensive tabulations of bundled-conductor transmission line constants (inductive and capacitive reactances, surge impedances, and surge impedance factors) as a function of conductor size, bundled-conductor or intragroup spacing, number of conductors per phase, and phase separation. The range of analysis is such that transmission voltage classes between 69 kv and 700 kv are considered.