gebhart/patrepeval huggingface dataset:
Structural prediction of antibody‐APRIL complexes by computational docking constrained by antigen saturation mutagenesis library data (2019)

IgA nephropathy (IgAN) is the most prevalent cause of primary glomerular disease worldwide, and the cytokine A PRoliferation-Inducing Ligand (APRIL) is emerging as a key player in IgAN pathogenesis and disease progression. For a panel of anti-human APRIL antibodies with known antagonistic activity, we sought to define their structural mode of engagement to understand molecular mechanisms of action and aid rational antibody engineering. Reliable computational prediction of antibody-antigen complexes remains challenging, and experimental methods such as X-ray co-crystallography and cryoEM have considerable technical, resource, and throughput barriers. To overcome these limitations, we implemented an integrated and accessible experimental-computational workflow to more accurately predict structures of antibody-APRIL complexes. Specifically, a yeast surface display library encoding site-saturation mutagenized surface positions of APRIL was screened against a panel of anti-APRIL antibodies to rapidly obtain a comprehensive biochemical profile of mutational impact on binding for each antibody. The experimentally derived mutational profile data were used as quantitative constraints in a computational docking workflow optimized for antibodies, resulting in robust structural models of antibody-antigen complexes. The model results were confirmed by solving the cocrystal structure of one antibody-APRIL complex, which revealed strong agreement with our model. The models were used to rationally select and engineer one antibody for cross-species APRIL binding, which quite often aids further testing in relevant animal models. Collectively, we demonstrate a rapid, integrated computational-experimental approach to robustly predict antibody-antigen structures information, which can aid rational antibody engineering and provide insights into molecular mechanisms of action.
A new voice activity detection method using maximized Sub-band SNR (2010)

This paper presents a novel voice activity detection (VAD) method using Maximum Values of Sub-band SNR (MVSS) as the detection feature. The proposed new feature MVSS has different distributions between speech and non-speech signal, which is helpful for separating the speech signal from heavy noise. An adaptive threshold is applied to improve VAD accuracies and track the noisy signal rapidly without complex computation. Experimental results show that the proposed method achieves better performance than the conventional ETSI AMR VADs under the NOISEX-92 database.
Medullasin activity in granulocytes of patients with multiple sclerosis (1984)

Medullasin activity in mature granulocytes was measured in the blood of 22 patients with multiple sclerosis (definite type, 16; probable type, 6). The activity was elevated in every patient in relapse; it decreased to nearly normal levels at the beginning of improvement and further decreased to normal levels with remission. Serial determinations of the level of medullasin activity in 3 patients revealed that activity increased several days before the onset of acute exacerbation. Medullasin activity level in mature granulocytes obtained from patients with neurological diseases other than multiple sclerosis was largely within the normal range, except in 2 patients with spinocerebellar degeneration. Measurement of medullasin activity in mature granulocytes may become useful in both diagnosis and evaluation of multiple sclerosis.
<i>Fgf8</i> is mutated in zebrafish <i>acerebellar</i> (<i>ace</i>) mutants and is required for maintenance of midbrain-hindbrain boundary development and somitogenesisy (1998)

We describe the isolation of zebrafish Fgf8 and its expression during gastrulation, somitogenesis, fin bud and early brain development. By demonstrating genetic linkage and by analysing the structure of the Fgf8 gene, we show that acerebellar is a zebrafish Fgf8 mutation that may inactivate Fgf8 function. Homozygous acerebellar embryos lack a cerebellum and the midbrain-hindbrain boundary organizer. Fgf8 function is required to maintain, but not initiate, expression of Pax2.1 and other marker genes in this area. We show that Fgf8 and Pax2.1 are activated in adjacent domains that only later become overlapping, and activation of Fgf8 occurs normally in no isthmus embryos that are mutant for Pax2.1. These findings suggest that multiple signaling pathways are independently activated in the midbrain-hindbrain boundary primordium during gastrulation, and that Fgf8 functions later during somitogenesis to polarize the midbrain. Fgf8 is also expressed in a dorsoventral gradient during gastrulation and ectopically expressed Fgf8 can dorsalize embryos. Nevertheless, acerebellar mutants show only mild dorsoventral patterning defects. Also, in spite of the prominent role suggested for Fgf8 in limb development, the pectoral fins are largely unaffected in the mutants. Fgf8 is therefore required in development of several important signaling centers in the zebrafish embryo, but may be redundant or dispensable for others.
[Characteristics of virus growth factor (VGF) encoded by vaccinia virus Tian Tan strain]. (1997)

Vaccinia virus growth factor (VGF) is encoded by an early gene located near the border between the terminal inverted repeats and the internal unique region of the viral genome. It has been suggested that secreted VGF may serve to stimulate the metabolism of neighboring uninfected cells, thereby increasing the capacity of these cells to support viral replication. In this study, we cloned and sequenced the VGF gene of vaccinia virus strain Tian Tap. The analytical results indicated that VGF of strain Tian Tan possessed the core sequences of Epidermal growth factor superfamily, and more closely related to that of strain WR than to those of other orthopoxvirus strains. Overall deduced amino acid divergence of 4.3% was observed between Tian Tan and WR VGF protein, while divergences ranged from 10% to 20% compared to other orthopoxviruses strains. Most of the amino acid substitutions were found within signal peptide and transmembrane regions, but were not present in secreted ligand domain. It was striking that the amino acid sequence deduced from the ORF TB22L which located within the right terminal region of genome was identical to VGF protein amino acids 67-140, suggesting that ORF TB22L may be derived from the seconed copy of VGF gene of strain Tian Tan.
1101 Determination of friction coefficient of an oil film under ultra high pressures with a bouncing ball tester (2008)

A bouncing ball tester was manufactured aiming at measurements of shear stress of a lubricant film under a higher pressure than 2GPa. The principle of the measurements is that the normal load and the tangential load were simultaneously determined with the Multi element piezo-electric sensor. Experiments were conducted as a parameter of the impact angle under a room temperature. The coefficient of friction measured for two lubricants with the bouncing ball tester agreed with the curve based on the coefficient of traction determined with the disk on roller type EHL tester.
Performance evaluation of object detection algorithms (2003)

The continuous development of object detection algorithms is ushering in the need for evaluation tools to quantify algorithm performance. In this paper a set of seven metrics are proposed for quantifying different aspects of a detection algorithm's performance. The strengths and weaknesses of these metrics are described. They are implemented in the Video Performance Evaluation Resource (ViPER) system and will be used to evaluate algorithms for detecting text, faces, moving people and vehicles. Results for running two previous text-detection algorithms on a common data set are presented.
District Heating in Sweden – Achievements and challenges (2010)

The Swedish district heating sector has achieved a strong position with a market share of 60% during 2008 in the heat market for buildings in the residential and service sectors. This position has been reached during the last 30 years without major use of combined heat and power (CHP) plants. The district heat has instead been generated from a basket of waste incineration, industrial surplus heat, biomass, and some fossil CHP. But during the recent years, the fossil CHP has been replaced by biomass CHP. The specific carbon dioxide emissions are now more than 80% lower than in other European cities and towns using natural gas and fuel oil to heat buildings. This paper gives a short overview of the development of the Swedish district heating sector with respect to market position, the CHP situation, the carbon dioxide emissions, and the additional social cost for district heating.
900 mW continuous wave operation of AlInGaP tapered lasers and superluminescent diodes at 640 nm (2004)

900 mW of continuous-wave power has been achieved in AlInGaP tapered lasers at 640 nm. Good beam quality and high device efficiency are obtained. Superluminescent diodes show strongly increased spectral width while retaining the good beam properties.
Analyse mehrachsiger Eigenspannungsverteilungen im intermediären Werkstoffbereich zwischen Oberfläche und Volumen mittels energiedispersiver Röntgenbeugung (2003)

Im Mittelpunkt der vorliegenden Arbeit steht die Analyse von Eigenspannungsgradienten in vielkristallinen Werkstoffen mittels energiedispersiver Röntgenbeugung in Reflexionsgeometrie. Ziel ist es, mehrachsige Eigenspannungstiefenverteilungen im intermediären Bereich zwischen der Werkstoffoberfläche und dem Volumen zu ermitteln, einem Bereich, der mit den konventionellen Röntgenbeugungsverfahren nicht mehr zu erfassen ist. Dafür werden winkeldispersiv arbeitende Messverfahren auf den energiedispersiven Fall übertragen und weiterentwickelt sowie bestehende energiedispersive Verfahren hinsichtlich ihrer Eignung untersucht. Zunächst werden die Unterschiede, die sich zwischen winkeldispersiv und energiedispersiv arbeitenden Verfahren ergeben, sowie die sich daraus für energiedispersive Verfahren ergebenden Anforderungen an die Messgeometrie, die zu einer Optimierung der Eindringtiefe führen, dargestellt. Für verschiedene Messgeometrien, unterschiedlichen Messverfahren entsprechend, werden die Interferenzlinienverschiebungen durch den Beugungsprozess für einen vorgegebenen dreiachsigen Eigenspannungszustand simuliert und die Auswirkung auf die verschiedenen Analysemethoden untersucht. Sie zeigen die Vorzüge der energiedispersiv durchgeführten Streuvektoranalyse gegenüber den anderen Verfahren. Anhand von experimentellen Untersuchungen, die sowohl im Labor als auch am Synchrotron durchgeführt wurden, wird das hohe Potential der energiedispersiven Eigenspannungsanalyse für den intermediären Bereich dargestellt. Vergleichende Messungen zeigen eine gute Übereinstimmung der energiedispersiv ermittelten Eigenspannungstiefenprofile mit den konventionell winkeldispersiv ermittelten Eigenspannungstiefenprofilen im oberflächennahen Bereich. Der Hauptanwendungsbereich der energiedispersiven Methoden zur Eigenspannungsanalyse in Reflexion wird zukünftig in der prozessbegleitenden Analytik liegen, da viele Prozesse, die zum mechanischen Versagen von Bauteilen führen, z.B. Rissbildung, im intermediären Bereich ihren Ursprung haben.
Detection and Prediction of the Performance Deterioration of a Turbofan Engine (2003)

Many airlines nowadays demand payment for their engine maintenance costs on an hourly-utilization basis. Thus engine manufacturers have become more focused on performancedeterioration modelling and prognostics capability in order to achieve greater confidence in their cash-flow projections. Hence a method for predicting the performance deterioration of civil aeroengines has been devised. The main aims are to achieve significant benefits in mission scheduling and maintenance planning, as well as to reduce both fuel consumption and the costs of maintenance servicing. An example concerning performancedeterioration prognosis is studied.
Primary structure of the porin protein of Haemophilus influenzae type b determined by nucleotide sequence analysis (1989)

Sequencing techniques for single- and double-stranded DNA were used to determine the nucleotide sequence of the gene encoding P2, the major outer membrane (porin) protein of Haemophilus influenzae type b (Hib). The open reading frame encoding the P2 protein comprised 361 amino acid codons. Comparison of the inferred amino acid sequence with data obtained by amino acid sequencing of the N terminus of the mature or fully processed P2 protein revealed that this protein has a signal peptide composed of 20 amino acids. N-terminal amino acid sequencing of tryptic peptides derived from purified P2 allowed direct identification of 158 of the 341 amino acids in the fully processed P2 protein; there was 100% correlation between these amino acid sequences and that inferred from the nucleotide sequence. The amino acid sequence of Hib P2 protein had 23 to 25% homology with the sequence of the OmpF porin of Escherichia coli and with that of the Neisseria gonorrhoeae porin P.IA. Codon usage in the Hib P2 gene was significantly different from that observed for a gene encoding a porin of E. coli. DNA hybridization studies indicated that there is a single copy of the P2 gene in the Hib chromosome. The availability of the nucleotide and amino acid sequences for the Hib P2 protein will facilitate investigation of the antigenic characteristics and structure-function relationship of this porin.
A motif in the C-terminal domain of ϕC31 integrase controls the directionality of recombination (2008)

Bacteriophage C31 encodes an integrase, which acts on the phage and host attachment sites, attP and attB, to form an integrated prophage flanked by attL and attR. In the absence of accessory factors, C31 integrase cannot catalyse attL x attR recombination to excise the prophage. To understand the mechanism of directionality, mutant integrases were characterized that were active in excision. A hyperactive integrase, Int E449K, gained the ability to catalyse attL x attR, attL x attL and attR x attR recombination whilst retaining the ability to recombine attP x attB. A catalytically defective derivative of this mutant, Int S12A, E449K, could form stable complexes with attP/attB, attL/attR, attL/attL and attR/attR under conditions where Int S12A only complexed with attP/attB. Further analysis of the Int E449K-attL/attR synaptic events revealed a preference for one of the two predicted synapse structures with different orientations of the attL/attR sites. Several amino acid substitutions conferring hyperactivity, including E449K, were localized to one face of a predicted coiled-coil motif in the C-terminal domain. This work shows that a motif in the C-terminal domain of C31 integrase controls the formation of the synaptic interface in both integration and excision, possibly through a direct role in protein-protein interactions.
Mini-Ckpts (2016)

Concern is growing in the high-performance computing (HPC) community on the reliability of future extreme-scale systems. Current efforts have focused on application fault-tolerance rather than the operating system (OS), despite the fact that recent studies have suggested that failures in OS memory may be more likely. The OS is critical to a system's correct and efficient operation of the node and processes it governs---and the parallel nature of HPC applications means any single node failure generally forces all processes of this application to terminate due to tight communication in HPC. Therefore, the OS itself must be capable of tolerating failures in a robust system. In this work, we introduce mini-ckpts, a framework which enables application survival despite the occurrence of a fatal OS failure or crash. mini-ckpts achieves this tolerance by ensuring that the critical data describing a process is preserved in persistent memory prior to the failure. Following the failure, the OS is rejuvenated via a warm reboot and the application continues execution effectively making the failure and restart transparent. The mini-ckpts rejuvenation and recovery process is measured to take between three to six seconds and has a failure-free overhead of between 3-5% for a number of key HPC workloads. In contrast to current fault-tolerance methods, this work ensures that the operating and runtime systems can continue in the presence of faults. This is a much finer-grained and dynamic method of fault-tolerance than the current coarse-grained application-centric methods. Handling faults at this level has the potential to greatly reduce overheads and enables mitigation of additional faults.
Decreasing effect of fluoride content in Antarctic krill (<i>Euphausia superba</i>) by chemical treatments (2013)

Summary Decreasing effects of fluoride contents in Antarctic krill ( Euphausia superba ) as affected by chemical treatments with and without heating were investigated. The used chemicals were Na OH , Na 2 CO 3 , Na 2 SO 3 , citric acid, acetic acid, phosphoric acid, HC l, ethanol, lysine, aminoguanidine, arginine, carnitine, betaine, and creatine. Fluoride contents per dry weight were 788 ± 10 mg kg −1 in the whole body of krill ( WBK ) and 294 ± 4 mg kg −1 in the peeled krill meat ( PKM ) respectively. When WBK was treated with chemicals with and without heating or thawed, fluoride was not decreased. On the other hand, when the PKM was treated with chemicals without heating was remarkably decreased to less than 100 mg kg −1 , which is the criteria recommended by FDA . Particularly, the treatment of betaine without heating showed the best reduction effect of 30 ± 6 mg kg −1 , followed by carnitine (38 ± 17 mg kg −1 ), acetic acid (52 ± 1 mg kg −1 ), phosphoric acid (67 ± 2 mg kg −1 ) and hydrochloric acid (68 ± 1 mg kg −1 ).
Stream-join revisited in the context of epoch-based SQL continuous query (2012)

The current generation of stream processing systems is in general built separately from the query engine thus lacks the expressive power of SQL and causes significant overhead in data access and movement. This situation has motivated us to leverage the query engine for stream processing.
The Oxidation Potential of the System Potassium Ferrocyanide–Potassium Ferricyanide at Various Ionic Strengths (1935)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe Oxidation Potential of the System Potassium Ferrocyanide–Potassium Ferricyanide at Various Ionic StrengthsI. M. KolthoffI. M. KolthoffMore by I. M. Kolthoff and William J. TomsicekWilliam J. TomsicekMore by William J. TomsicekCite this: J. Phys. Chem. 1935, 39, 7, 945–954Publication Date (Print):July 1, 1935Publication History Published online1 May 2002Published inissue 1 July 1935https://doi.org/10.1021/j150367a004RIGHTS & PERMISSIONSArticle Views3524Altmetric-Citations165LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InReddit PDF (519 KB) Get e-Alerts
General Approach to Glycosidase Inhibitors. Enantioselective Synthesis of Deoxymannojirimycin and Swainsonine (2005)

[reaction: see text] Deoxymannojirimycin (2) and swainsonine (4) have been synthesized from each enantiomer of the same bicyclic carbamate precursor 7. The key intermediate was prepared by a simple and efficient three-step synthesis involving RCM of the diene 8, which in turn is easily accessible in any configuration from enantiomerically enriched 2,3-epoxy-4-penten-1-ol 9.
The Reference Path Tracer (2021)

The addition of ray tracing to a real-time renderer makes it possible to create beautiful dynamic effects-such as soft shadows, reflections, refractions, indirect illumination, and even caustics-that were previously not possible. Substantial tuning and optimization are required for these effects to run in real time without artifacts, and this process is simplified when the real-time rendering engine can progressively generate a "known-correct" reference image to compare against. In this chapter, we walk through the steps to implement a simple, but sufficiently featured, path tracer to serve as such a reference.
Monolayer-Protected Clusters with Fluorescent Dansyl Ligands (2000)

Monolayer-protected Au cluster (MPC) molecules with mixed monolayers of alkanethiolate and ω-carboxylalkanethiolate ligands were functionalized with the fluorescent label dansyl cadaverine. The emission intensity per MPC-attached dansyl group varies with (a) the number of dansyl sites per MPC (i.e., loading, 4 to 24), (b) with the linker chainlength between Au core and dansyl site, and (c) with chainlengths of alkanethiolates in the surrounding MPC monolayer coating. Emission intensity per MPC-attached dansyl group increases with loading and with the length of core−dansyl linker chains when the surrounding alkanethiolate monolayers have chain lengths equal to or greater than the linker. These results are interpreted in terms of distance-dependent energy transfer from the excited dansyl label to the metal-like MPC core and various steric constraints on thermal fluctuations of linker chains that influence the distance of approach of the label to the core. Correction for self-absorption by the highly colored MPC solution was necessary. Emission intensities of MPC-attached dansyl labels are lower than those from equivalent concentrations of dansyl units and MPCs as unattached cosolutes.
Results of International Space Station Vehicle Materials Exposed on Misse-7b (2013)

Materials samples were exposed to the low Earth orbit (LEO) environment as part of the MISSE-7B flight experiment for 18 months. Optical properties, thickness/mass loss, surface elemental analysis, visual and microscopic analysis for surface change are some of the techniques employed in this investigation. Where possible, the MISSE-7B results are compared to analyses from other LEO experiments. ISS materials currently flying on MISSE-8 are also discussed.
Influence of site and size of the area at risk in acute ischemic mitral regurgitation (1992)

Background In order to examine the influence of ischemic zone site and size on mitral regurgitation, we performed transesophageal two-dimensional echo and color flow Doppler in nine closed-chest anesthetized dogs. Methods The left anterior descending (LAD) and left circumflex (LCX) coronary arteries were each occluded for 3 minutes in random order, with 60 minutes of reperfusion between the two occlusions. Areas at risk were 25.7% ± 7.1% and 30.9% ± 8.1% of the left ventricle for LAD and LCX occlusions, respectively (P is not significant), as assessed by postmortem staining of the perfusion bed. Results The size of the temporally averaged mitral regurgitant color flow area was larger after LCX and LAD occlusion (1.1 ± 2.6 cm2 versus 0.5 ± 0.2 cm2; P<0.05). These differences could not be explained by differences in left atrial or ventricular dimensions or pressures. Linear regression analysis failed to reveal a significant relation between the size of the area at risk and color flow area for either LAD or LCX occlusion. Conclusions Thus, in this canine model of coronary occlusion, the magnitude of acute mitral regurgitation is dependent on the ischemic zone site but not on the size of the ischemic area at risk.
Is carpal tunnel release under-utilized in veterans with spinal cord injury? (2011)

CTS appears to be under-diagnosed and under-treated in veterans with SCI.