gebhart/patrepeval huggingface dataset:
Genomes of the human filarial parasites Mansonella perstans and Mansonella ozzardi (2023)

The filarial parasites Mansonella ozzardi and Mansonella perstans , causative agents of mansonellosis, infect hundreds of millions of people worldwide, yet remain among the most understudied of the human filarial pathogens. M. ozzardi is highly prevalent in Latin American countries and Caribbean Islands, while M. perstans is predominantly found in sub-Saharan Africa as well as in a few areas in South America. In addition to the differences in their geographical distribution, the two parasites are transmitted by different insect vectors, as well as exhibit differences in their responses to commonly used anthelminthic drugs. The lack of genome information has hindered investigations into the biology and evolution of Mansonella parasites and understanding the molecular basis of the clinical differences between species. In the current study, high quality genomes of two independent clinical isolates of M. perstans from Cameroon and two M. ozzardi isolates one from Brazil and one from Venezuela are reported. The genomes are approximately 76 Mb in size, encode about 10,000 genes each, and are largely complete based on BUSCO scores of about 90%, similar to other completed filarial genomes. These sequences represent the first genomes from Mansonella parasites and enabled a comparative genomic analysis of the similarities and differences between Mansonella and other filarial parasites. Horizontal DNA transfers (HDT) from mitochondria (nuMTs) as well as transfers from genomes of endosymbiotic Wolbachia bacteria (nuWTs) to the host nuclear genome were identified and analyzed. Sequence comparisons and phylogenetic analysis of known targets of anti-filarial drugs diethylcarbamazine (DEC), ivermectin and mebendazole revealed that all known target genes were present in both species, except for the DEC target encoded by gon-2 gene, which is fragmented in genome assemblies from both M. ozzardi isolates. These new reference genome sequences will provide a valuable resource for further studies on biology, symbiosis, evolution and drug discovery.
SYNTHESIS OF METHYL METHACRYLATE FROM COAL-DERIVED SYNGAS (1999)

Research Triangle Institute (RTI), Eastman Chemical Company, and Bechtel collectively are developing a novel three-step process for the synthesis of methyl methacrylate (MMA) from coal-derived syngas that consists of the steps of synthesis of a propionate, its condensation with formaldehyde to form methacrylic acid (MAA), and esterification of MAA with methanol to produce MMA. The research team has completed the research on the three-step methanol-based route to MMA. Under an extension to the original contract, we are currently evaluating a new DME-based process for MMA. The key research need for DME route is to develop catalysts for DME partial oxidation reactions and DME condensation reactions. During the April-June quarter(04-06/99) the first in-situ formaldehyde generation from DME and condensation with methyl propionate is demonstrated and the results are summarized. The supported niobium catalyst shows better condensation activity, but supported tungsten catalyst has higher formaldehyde selectivity. The project team has also completed a 200-hour long term test of PA-HCHO condensation over 30% Nb{sub 2}O{sub 5}/SiO{sub 2}. Three activity cycles and two regeneration cycles were carried out. 30% Nb{sub 2}O{sub 5}/SiO{sub 2} showed similar MAA yields as 10% Nb{sub 2}O{sub 5}/SiO{sub 2} at 300 C. However, the deactivation appears to be slower with 30% Nb{sub 2}O{sub 5}/SiO{sub 2} than 10% Nb{sub 2}O{sub 5}/SiO{sub 2}. An detailed economic analysis of PA-HCHO condensation process for a 250 million lb/yr MMA plant is currently studied by Bechtel. Using the Amoco data-based azeotropic distillation model as the basis, an ASPEN flow sheet model was constructed to simulate the formaldehyde and propionic acid condensation processing section based on RTI's design data. The RTI MAA effluent azeotropic distillation column was found to be much more difficult to converge. The presence of non-condensible gases along with the byproduct DEK (both of which were not presented in Amoco's data) appear to the culprits.
A Critical Nugget Size Prediction Model for Al–Si-Coated Press Hardened Steel Resistance Spot Welds (2021)

Abstract For the automotive industry, it is important to predict the fracture mode of resistance spot-welded joints. Traditional 4t0.5 (where t is the sheet thickness) criterion for the transition from interfacial fracture (IF) to button pullout fracture (BPF) mode is not applicable for press hardened steel, press-hardened steel (PHS), welds. This study aims to investigate the effect of Al–Si coating and critical heat affected zone (CHAZ) location on the lap-shear fracture mode transition mechanism of Al–Si-coated PHS welds. It was found that in-situ tempering pulse after the welding stage could change the relative location of the CHAZ and weld nugget, which in turn, had a significant effect upon the fracture mode transition. Thus, a new analytical model was built to predict the critical nugget size for Al–Si-coated PHS, wherein the Al–Si coating and the CHAZ location are considered as critical factors for predicting the fracture mode transition of PHS spot welds and are incorporated into this model. A reasonable correlation of the model to experimental data was achieved.
Molecular Mechanism of ISC Iron–Sulfur Cluster Biogenesis Revealed by High-Resolution Native Mass Spectrometry (2020)

Iron-sulfur (Fe-S) clusters are ubiquitous protein cofactors that are required for many important biological processes including oxidative respiration, nitrogen fixation, and photosynthesis. Biosynthetic pathways assemble Fe-S clusters with different iron-to-sulfur stoichiometries and distribute these clusters to appropriate apoproteins. In the ISC pathway, the pyridoxal 5'-phosphate-dependent cysteine desulfurase enzyme IscS provides sulfur to the scaffold protein IscU, which templates the Fe-S cluster assembly. Despite their functional importance, mechanistic details for cluster synthesis have remained elusive. Recent advances in native mass spectrometry (MS) have allowed proteins to be preserved in native-like structures and support applications in the investigation of protein structure, dynamics, ligand interactions, and the identification of protein-associated intermediates. Here, we prepared samples under anaerobic conditions and then applied native MS to investigate the molecular mechanism for Fe-S cluster synthesis. This approach was validated by the high agreement between native MS and traditional visible circular dichroism spectroscopic assays. Time-dependent native MS experiments revealed potential iron- and sulfur-based intermediates that decay as the [2Fe-2S] cluster signal developed. Additional experiments establish that (i) Zn(II) binding stabilizes IscU and protects the cysteine residues from oxidation, weakens the interactions between IscU and IscS, and inhibits Fe-S cluster biosynthesis; and (ii) Fe(II) ions bind to the IscU active site cysteine residues and another lower affinity binding site and promote the intermolecular sulfur transfer reaction from IscS to IscU. Overall, these results support an iron-first model for Fe-S cluster synthesis and highlight the power of native MS in defining protein-associated intermediates and elucidating mechanistic details of enzymatic processes.
Secreted Proteins from Mycobacterium tuberculosis Gain Access to the Cytosolic MHC Class-I Antigen-Processing Pathway (2006)

CD8+ T cells play an important role in the host response to infection with Mycobacterium tuberculosis (Mtb). Mtb resides in an arrested phagosome that is phenotypically similar to an early endosome. The mechanisms by which Mtb-derived Ags gain access to the HLA-I-processing pathway are incompletely characterized. Studies with CD8+ T cell lines have suggested that Mtb Ags gain access to the HLA-I pathway in an alternate vacuolar pathway that is both brefeldin A (BFA) and TAP independent. To define the requirements of entry of Ag into the HLA-I pathway, we have used human CD8+ T cell clones specific for the secreted Mtb Ag CFP10. Human monocyte-derived dendritic cells were pulsed with CFP10 expressed in a recombinant adenovirus, surface adsorbed to microspheres, or in its native form by Mtb. When delivered by adenovirus, processing and presentation of CFP10 were blocked by both BFA and the proteasomal blocker lactacystin. In contrast, processing of CFP10 adsorbed to the surface of microspheres was not affected by either of these Ag-processing inhibitors. BFA, lactacystin, and TAP inhibition blocked the recognition of Mtb-infected dendritic cells, suggesting that processing was via a cytosolic pathway for this secreted protein Ag. We conclude that secreted proteins from Mtb can be processed in a BFA- and proteasome-dependent manner, consistent with egress of Ag into the cytosol and subsequent loading of proteasomally derived peptides.
Realization of Minimum and Maximum Gate Function in Ta2O5-based Memristive Devices (2016)

Redox-based resistive switching devices (ReRAM) are considered key enablers for future non-volatile memory and logic applications. Functionally enhanced ReRAM devices could enable new hardware concepts, e.g. logic-in-memory or neuromorphic applications. In this work, we demonstrate the implementation of ReRAM-based fuzzy logic gates using Ta2O5 devices to enable analogous Minimum and Maximum operations. The realized gates consist of two anti-serially connected ReRAM cells offering two inputs and one output. The cells offer an endurance up to 10(6) cycles. By means of exemplary input signals, each gate functionality is verified and signal constraints are highlighted. This realization could improve the efficiency of analogous processing tasks such as sorting networks in the future.
Age-related presence of spermatogonia in patients with Klinefelter syndrome: a systematic review and meta-analysis (2019)

While azoospermia is a common finding in the KS patient population, many patients are positive for spermatogonia. Recent advances in SSC in vitro propagation, transplantation and differentiation open new avenues for these patients for fertility preservation. This would offer a new subset of KS patients a chance of biological paternity. Data surrounding the hormonal profiles of KS patients and their relation to fertility should be interpreted with caution as a paucity of adequately powered data exists. Future work is needed to clarify the utility of FSH, LH, testosterone and inhibin B as biomarkers for successful retrieval of spermatogonia.
Fast Thermal Switching of Wideband Optical Delay Line With No Long-Term Transient (2011)

We present results for a broad bandwidth continuously tunable optical delay line based on the balanced side-coupled integrated space sequence of resonators scheme. A tunable delay of up to 345 ps is obtained without distortion of the optical signal. Fast thermal switching speed under 10 μs is achieved without any measurable long-term transient by utilizing a novel balanced thermal tuning scheme.
Photoactivated cross-linking of proteins within the erythrocyte membrane core. (1976)

We describe the reactions of three lipophilic, photoactivated cross-linking reagents, 1,5-diazidonapthalene, 4,4'-diazidobiphenyl, and the reversible 4,4'-dithiobisphenylazide, with erythrocyte membranes. Cross-linking occurs only upon photoactivation. At pH 7 to 8, only spectrin components are cross-linked by these reagents. At pH 5.0 to 5.5 several additional membrane proteins including the major "integral" membrane proteins are also cross-linked, despite equivalent binding of the cross-linkers at neutral and acid pH. The cross-linking rates of various membrane proteins at pH 5.0 to 5.5 depend distinctly upon duration of photoactivation. Bidimensional electrophoresis of membrane proteins after cross-linking with the reversible cross-linker, 4,4'-dithiobisphenylazide, has allowed for the identification of homopolymeric products of cross-linking (e.g. dimers and tetramers of Band 3) and heterocomplexes (spectrin plus other membrane proteins). The data suggest that at reduced pH, cross-linking can proceed not only at the membrane surface but also in the membrane core.
Extensor Quadriga: Pathomechanics and Treatment (2004)

The extensor tendons to the index, long, ring and small fingers are motored by the common extensor digitorum communis muscle body. Effective function of this muscle can only occur if the gliding amplitude of each of its four extensor tendons is normal. As a corollary, limitation of the excursion of any of the individual tendons by adhesions at a fracture or tendon repair site, a fixed flexion contracture at the metacarpophalangeal joint, or by rupture, attenuation or laceration of a saggital band or juncturae tendinum, will result in reduction of the excursion of the adjacent extensor tendons. This pathological state has been termed the extensor quadriga because of its similarities to the analogous pathology affecting the flexor digitorum profundus system. Improper management of this clinical entity may lead to an abnormal pathomechanical kinematic chain imbalance. Early identification and treatment is critical to address this entity appropriately.
Optimization of Ground-via Patterns for via Transitions by Minimizing Loop Inductance (2023)

Via is a commonly-used interconnect structure for vertically connecting signal traces or power or ground planes in packages and boards. As the speed of data transfer increases, the electrical properties of via structure becomes more and more important for getting better signal quality. Modeling a via structure typically involves complex computation. In this article, authors use partial element method to model the structure as coupled inductor array. It firstly proves that the loop inductance of a single-ended via transition is minimized through perturbation analysis. On the other hand, the differential-mode loop inductance of a via pair surrounded by 2, 4, 6, and 8 ground vias respectively is also derived. The full-wave simulation results all show good agreement with the ones predicted by formulae. Thus, with these formula, the optimization of ground via placement could be quickly found.
On the capacity of MIMO broadcast channels with reduced feedback by antenna selection (2008)

In this paper we analyze the performance of random beamforming schemes in a multi-user Gaussian broadcast channel utilizing SINR feedback. For generality, the receivers are allowed to have multiple receive antennas. The first scheme analyzed allows each receiver to feed back the largest SINR it observes for each transmit beam. The distribution function of the maximum SINR is derived and is noted to differ from previous work. In an effort to further reduce feedback, a scheme where each user feeds back the maximum SINR observed over its receive antennas and transmit beams. Using the Frechet bounds and properties of chi-squared random variables, the throughput of this system is bounded and empirically shown to approach the performance of the previous scheme as the number of users increases.
Artificial Neural Networks as Feature Extractors in Continuous Evolutionary Optimization (2021)

Recent years have seen the advancement of data-driven paradigms in population-based and evolutionary optimization. This reflects on one hand the mere abundance of available data, but on the other hand also progresses in the refinement of previously available machine learning methods. Surprisingly, deep pattern recognition methods emerging from the studies of neural networks have only been sparingly applied. This comes unexpected, as the complex data generated by evolutionary search algorithms can be considered tedious and intractable for manual analysis with mere practical intuitions. In this work, we therefore explore opportunities to employ deep networks to directly learn problem characteristics of continuous optimization problems. Particularly, with data obtained during initial runs of an optimization algorithm. We find that a graph neural network, trained upon a graph representation of continuous search spaces, shows in comparison to more traditional approaches higher validation accuracy and retrieves characteristics within the latent space which are better at distinguishing different continuous optimization problems. We hope that our study can pave the way towards new approaches which allow us to learn problem-dependent algorithm components and recall these from predictions of inputs generated during the run-time of an optimization algorithm.
Isotropic (2016)

In the past, aggregation and self-assembly have been associated principally with micellar and colloidal systems of molecules; however, with the advent of supramolecular chemistry, molecular self-assembly has been opened to a much wider understanding that has facilitated access to a variety of different shapes and sizes, along with the construction of new and fascinating molecular topologies. This document aims at defining more than 150 terms related to aggregation and self-assembly in the particular case of macromolecules. The list is restricted to the most commonly encountered terms.
Transcatheter mitral valve replacement with a novel self-expandable prosthesis (2017)

CardiAQ valve placement is safe using a transapical or transseptal approach. Following valve replacement, there was a marked functional improvement in survivors. Transcatheter mitral valve replacement is a promising therapy for mitral regurgitation in a selected patient population.
Transcriptional and functional motifs defining renal function revealed by single-nucleus RNA sequencing (2022)

Recent advances in single-cell sequencing provide a unique opportunity to gain novel insights into the diversity, lineage, and functions of cell types constituting a tissue/organ. Here, we performed a single-nucleus study of the adult <i>Drosophila</i> renal system, consisting of Malpighian tubules and nephrocytes, which shares similarities with the mammalian kidney. We identified 11 distinct clusters representing renal stem cells, stellate cells, regionally specific principal cells, garland nephrocyte cells, and pericardial nephrocytes. Characterization of the transcription factors specific to each cluster identified <i>fruitless</i> (<i>fru</i>) as playing a role in stem cell regeneration and <i>Hepatocyte nuclear factor 4</i> (<i>Hnf4</i>) in regulating glycogen and triglyceride metabolism. In addition, we identified a number of genes, including <i>Rho guanine nucleotide exchange factor at 64C</i> (<i>RhoGEF64c</i>), <i>Frequenin 2</i> (<i>Frq2</i>), <i>Prip</i>, and <i>CG1093</i> that are involved in regulating the unusual star shape of stellate cells. Importantly, the single-nucleus dataset allows visualization of the expression at the organ level of genes involved in ion transport and junctional permeability, providing a systems-level view of the organization and physiological roles of the tubules. Finally, a cross-species analysis allowed us to match the fly kidney cell types to mouse kidney cell types and planarian protonephridia, knowledge that will help the generation of kidney disease models. Altogether, our study provides a comprehensive resource for studying the fly kidney.
Sixteenth Biannual Report of the Cochrane Haematological Malignancies Group: Focus on Non-Hodgkin's Lymphoma (2014)

This sixteenth biannual report of the Cochrane Haematological Malignancies Group highlights recently published randomized controlled trials (RCTs) in the field of hemato-oncology, with special focus on non-Hodgkin's lymphoma. The report covers the publication period June 2012 to July 2013. Trials are selected regarding their methodology and implication for clinical practice. Studies were identified by electronic search of MEDLINE using a broad search filter that covers all topics in hemato-oncology combined with a highly sensitive search filter for randomized trials (Cochrane Handbook for Systematic Reviews of Interventions). Four RCTs are presented in detail, followed by two further RCTs of high importance in a short version. The report is finalized with an overview of new and updated Cochrane Reviews.
COVID-19 Testing R&D (Final Report) (2021)

Eleven Labs within the US Department of Energy (DOE), National Virtual Biotechnology Laboratory (NVBL), came together as a team to address significant R&D gaps in COVID-19 testing. Beginning in March 2020, the NVBL COVID Testing Team developed an R&D agenda, worked with DOE and other agencies to set priorities, and collaborated to deliver timely results. Priority was given to quick implementation as well as development of novel capabilities for immediate and evolving pandemic needs without placing additional burden on operational performers. Priority elements capitalized on DOE National Laboratory strengths and expertise. The Team delivered: testing and evaluation that enabled decisions on testing options, forwardleaning approaches to prepare for future scale-up needs, and models and experiments that supported prioritization of diagnostic and therapeutic candidates.
Prostasin Serine Protease as a Breast Cancer Invasion Marker and a Metastasis Suppressor (2006)

Abstract : This project had one Specific Aim after the peer and programmatic reviews, to evaluate prostasin, a glycosylphosphatidylinositol (GPI)-anchored extracellular serine protease as a potential metastasis suppressor of breast cancer in nude mice models. Two types of breast cancer metastasis, experimental and spontaneous, were to be used with the cell lines MDA-MB-231 and MDA-MB-435, respectively. We have found that prostasin must be activated by another membrane serine protease, matriptase before becoming functionally active as a proteolytic enzyme. The activating enzyme matriptase, however, is not expressed by either of the two model cell lines, an essential factor previously unrecognized, as well as an underlying reason for our previous inconsistent findings concerning prostasin s impact on breast cancer cell metastasis. In future research on membrane serine proteases in breast cancer cell biology, the newly recognized proteolytic cascade should be addressed with consideration of all of its current and potentially new member proteases.
Studies on the Primary Structure and the Replication Mechanism of Bacteriophage RNA (1969)

The RNA of the bacteriophage MS2 carries the genetic information for the synthesis of at least three viral proteins. Furthermore it is specifically recognized and replicated via a complementary strand by a viral RNA polymerase (Haruna, Nozu, Ohtaka, and Spiegelman, 1963; Fiers, Verplancke, and Van Styvendaele, 1967). In addition, it forms a complex with the homologous coat protein (Sugiyama, Hebert, and Hartman, 1967; Hohn, 1969). These processes involve highly specific interactions, which can only be understood in detail if more insight into the structure of the viral RNA is achieved.
Renewable Energy Operation and Conversion Schemes: A Summary of Discussions During the Seminar on Renewable Energy Systems (2010)

A short summary of some speeches given during Seminar on Renewable Energy system (SERENE) is presented. The contributions have been mainly focused on power electronics for photovoltaic (PV) and sea wave energies, pointing out some aspects related to efficiency, reliability, and grid integration. Finally, main issues concerning fuel cell (FC) systems as generators based on hydrogen as a low environmental impact energy vector are presented.