gebhart/patrepeval huggingface dataset:
Easy‐to‐Attach/Detach Solubilizing‐Tag‐Aided Chemical Synthesis of an Aggregative Capsid Protein (2018)

Abstract A solubilizing Trt‐K 10 tag was developed for the effective chemical preparation of peptides/proteins with low solubility. The Trt‐K 10 tag comprises a hydrophilic oligo‐Lys sequence and a trityl anchor, and can be selectively introduced to a side chain thiol of Cys of deprotected peptides/proteins with a trityl alcohol‐type introducing reagent Trt(OH)‐K 10 under acidic conditions. Significantly, the ligation product in the reaction mixture of a thiol‐additive‐free native chemical ligation can be modified directly in a one‐pot manner to facilitate the isolation of the product by high‐performance liquid chromatography. Finally, the Trt‐K 10 tag can be readily removed with a standard trifluoroacetic acid cocktail. Using this easy‐to‐attach/detach tag‐aided method, a hepatitis B virus capsid protein that is usually difficult to handle was synthesized successfully.
Building Domain-Specific Search Engines with Machine Learning Techniques (1999)

Domain-specific search engines are growing in popularity because they offer increased accuracy and extra functionality not possible with the general, Web-wide search engines. For example, www.campsearch.com allows complex queries by age-group, size, location and cost over summer camps. Unfortunately these domain-specific search engines are difficult and timeconsuming to maintain. This paper proposes the use of machine learning techniques to greatly automate the creation and maintenance of domain-specific search engines. We describe new research in reinforcement learning, information extraction and text classification that enables efficient spidering, identifying informative text segments, and populating topic hierarchies. Using these techniques, we have built a demonstration system: a search engine for computer science research papers. It already contains over 50,000 papers and is publicly available at www.cora.justresearch.com. 1 Introduction As the amount of information on the Wor...
High temporal resolution functional MRI with partial separability model (2015)

Even though the hemodynamic response is a slow phenomenon, high temporal resolution in functional fMRI can enable better differentiation between the signal of interest and physiological noise or increase the statistical power of functional studies. To increase the temporal resolution, several methods have been developed to decrease the repetition time, TR, such as simultaneous multi-slice imaging and MR encephalography approaches. In this work, a method using a fast acquisition and a partial separability model is presented to achieve a multi-slice fMRI protocol at a temporal resolution of 75 ms. The method is demonstrated on a visual block task.
An optimum thickness indicator for evaporating metals on Schottky barrier solar cells (1978)

The thickness of the barrier metal on a Schottky solar cell is very critical to the conversion efficiency. Precise control of the optimum thickness can be achieved by monitoring the first derivative of the photocurrent during deposition. A true DC differentiator with fast response time for a very slowly varying field can be made by using sample-and-hold circuits.
The Neurospora crassa Genome: Cosmid Libraries Sorted by Chromosome (2001)

A Neurospora crassa cosmid library of 12,000 clones (at least nine genome equivalents) has been created using an improved cosmid vector pLorist6Xh, which contains a bacteriophage lambda origin of replication for low-copy-number replication in bacteria and the hygromycin phosphotransferase marker for direct selection in fungi. The electrophoretic karyotype of the seven chromosomes comprising the 42.9-Mb N. crassa genome was resolved using two translocation strains. Using gel-purified chromosomal DNAs as probes against the new cosmid library and the commonly used medium-copy-number pMOcosX N. crassa cosmid library in two independent screenings, the cosmids were assigned to chromosomes. Assignments of cosmids to linkage groups on the basis of the genetic map vs. the electrophoretic karyotype are 93 +/- 3% concordant. The size of each chromosome-specific subcollection of cosmids was found to be linearly proportional to the size of the particular chromosome. Sequencing of an entire cosmid containing the qa gene cluster indicated a gene density of 1 gene per 4 kbp; by extrapolation, 11,000 genes would be expected to be present in the N. crassa genome. By hybridizing 79 nonoverlapping cosmids with an average insert size of 34 kbp against cDNA arrays, the density of previously characterized expressed sequence tags (ESTs) was found to be slightly <1 per cosmid (i.e., 1 per 40 kbp), and most cosmids, on average, contained an identified N. crassa gene sequence as a starting point for gene identification.
Functional and binding studies of the roles of prothrombin and beta 2- glycoprotein I in the expression of lupus anticoagulant activity (1994)

We present functional and binding data relevant to the reported roles for prothrombin and beta 2-glycoprotein I (beta 2GPI) in the expression of lupus anticoagulant activity. In a purified system containing human prothrombin, Xa, Va, and a rate-limiting concentration of phosphatidylserine (PS)/phosphatidylcholine (PC) vesicles, the preliminary incubation of vesicles with protein A separated IgG preparations from 10 lupus anticoagulant plasmas, calcium, and prothrombin enhanced the inhibitory effect of all IgG preparations upon thrombin generation. Experiments in a purified factor X activation system provided supporting data that a similar preliminary incubation with prothrombin enhanced the inhibitory effect of many of the IgG preparations upon factor X activation. However, we could not obtain unequivocal evidence that prothrombin was an obligatory cofactor for lupus anticoagulant IgG to inhibit procoagulant phospholipid function, because lupus anticoagulant IgG separated by protein A chromatography contained traces of prothrombin. The binding of many IgG preparations to immobilized PS was enhanced by prothrombin when calcium ions were present. beta 2GPI enhanced binding of many of the IgG preparations to immobilized PS both in the presence and absence of calcium, yet beta 2GPI failed to enhance the ability of the IgG preparations to inhibit phospholipid function in purified prothrombin and factor X assays. Moreover, the IgG preparations prolonged the dilute Russell's viper venom time (dRVVT) of beta 2GPI-depleted normal plasma. Nine of 10 IgG preparations bound to prothrombin on Western blots in the absence of calcium and phospholipid, whereas no preparation bound to beta 2GPI. Passage of five citrated lupus anticoagulant plasmas through a prothrombin affinity column in the absence of added calcium and phospholipid removed most of the activity prolonging the dRVVT of normal plasma, and IgG in the pass-through plasma no longer bound to PS in the presence of prothrombin and calcium ions. IgG in prothrombin column eluates had strikingly enhanced specific lupus anticoagulant activity and also specific PS binding activity in the presence of prothrombin and calcium ions. Thus, lupus anticoagulant plasmas were shown to contain IgG binding to prothrombin, in the absence of calcium ions and phospholipid, which could also, in the presence of calcium ions and prothrombin, bind to PS and express lupus anticoagulant activity.
Federated Learning of User Authentication Models (2020)

Machine learning-based User Authentication (UA) models have been widely deployed in smart devices. UA models are trained to map input data of different users to highly separable embedding vectors, which are then used to accept or reject new inputs at test time. Training UA models requires having direct access to the raw inputs and embedding vectors of users, both of which are privacy-sensitive information. In this paper, we propose Federated User Authentication (FedUA), a framework for privacy-preserving training of UA models. FedUA adopts federated learning framework to enable a group of users to jointly train a model without sharing the raw inputs. It also allows users to generate their embeddings as random binary vectors, so that, unlike the existing approach of constructing the spread out embeddings by the server, the embedding vectors are kept private as well. We show our method is privacy-preserving, scalable with number of users, and allows new users to be added to training without changing the output layer. Our experimental results on the VoxCeleb dataset for speaker verification shows our method reliably rejects data of unseen users at very high true positive rates.
Supplementary Figure 4 from Constitutive HER2 Signaling Promotes Breast Cancer Metastasis through Cellular Senescence (2023)

&lt;p&gt;PDF file - 136K, Expression of p95HER2 leads to senescence in MCF7 cell xenografts&lt;/p&gt;
Early development of an identified serotonergic neuron inHelisoma trivolvis embryos: Serotonin expression, de-expression, and uptake (1998)

In early-stage embryos of Helisoma trivolvis, a bilateral pair of identified neurons (ENC1) express serotonin and project primary descending neurites that ramify in the pedal region of the embryo prior to the formation of central ganglia. Pharmacological studies suggest that serotonin released from ENC1 acts in an autoregulatory pathway to regulate its own neurite branching and in a paracrine or synaptic pathway to regulate the activity of pedal ciliary cells. In the present study, several key features of early ENC1 development were characterized as a necessary foundation for further experimental studies on the mechanisms underlying ENC1 development and its physiological role during embryogenesis. ENC1 morphology was determined by confocal microscopy of serotonin-immunostained embryos and by differential-interference contrast (DIC) microscopy of live embryos. The soma was located at an anteriolateral superficial position and contained several distinguishing features, including a large spherical nucleus with prominent central nucleolus, large granules in the apical cytoplasm, a broad apical dendrite ending in a sensory-like structure at the embryonic surface, and a ventral neurite. ENC1 first expressed serotonin immunoreactivity around stage E13, followed immediately by the appearance of an immunoreactive neurite (stage E14). Both the intensity of immunoreactivity and primary neurite length were consistently greater in the right ENC1 at early stages. Serotonin uptake, as indicated by 5,7-dihydroxytryptamine-induced fluorescence, first occurred between stages E18 and E25. At later stages of embryogenesis (after stage E65), serotonin immunoreactivity disappeared, whereas serotonin uptake and normal cell morphology were retained.
Integrating A Deep Learning-based Plane Detector in Mobile AR Systems for Improvement of Plane Detection (2022)

With the increasing interest in Augmented Reality (AR) technology and the enhancement of mobile device capability, mobile AR systems become very popular. In mobile AR systems, plane detection, which plays a major role in determining the location of virtual objects, often shows insufficient performance. We address this limitation in mobile AR systems by adopting a Machine Learning (ML)-based plane detector. We specifically develop a hybrid plane detection pipeline in which an ML-based plane detector and the point cloud information obtained by a mobile device are fused, showing its robust performance in plane detection for various environment conditions.
Transverse Explosive Shock-Wave Compression of Nd2Fe14B High-Energy Hard Ferromagnets: Induced Magnetic Phase Transition (2006)

Investigations of the magnetic phase state of Nd2Fe14B high‐energy hard ferromagnets under the action of an explosive shock wave traveling across the magnetization vector, M, have been performed. We demonstrate that the transverse shock‐wave compression of an Nd2Fe14B hard ferromagnet with pressure at the shock wave front of P = 22.3 GPa causes a hard ferromagnet — to — weak magnet phase transition. Due to this phase transition, the magnetostatic energy stored for an indefinite period of time in the Nd2Fe14B ferromagnet is released within a short time interval and can be transformed into pulsed primary power. Based on this effect we have developed a new type of ultracompact (volumes from 9 to 50 cm3) autonomous explosive‐driven source of primary power that is capable of powering a magnetic flux compression generator with current up to 4 kA, and of charging high‐voltage Arkadiev‐Marx type generator capacitor banks.
In favour of the vesicular hypothesis: neurochemical evidence that vesamicol (AH5183) inhibits stimulation‐evoked release of acetylcholine from neuromuscular junction (1989)

1. The effects of optical isomers of vesamicol (2-(4-phenylpiperidino) cyclohexanol), an inhibitor of acetylcholine (ACh) storage, on stimulation-evoked release of [3H]-acetylcholine [( 3H]-ACh) from the neuromuscular junction have been studied in the region of the mouse hemidiaphragm which contains the motor endplates, and which can easily be loaded with [3H]-choline. This method made it possible to detect exclusively the Cao-dependent release of [3H]-ACh in response to stimulation, and therefore to test the vesicular hypothesis. 2. (-)-Vesamicol was approximately 20 times more potent than (+)-vesamicol in reducing stimulation-evoked release of [3H]-ACh. 3. 4-Aminopyridine, a potassium channel blocker, enhanced the release of ACh in response to stimulation, but failed to increase release from hemidiaphragm which had been pretreated with (-)-vesamicol. 4. The fact that (-)-vesamicol inhibited the release of [3H]-ACh in response to electrical stimulation only when it was administered prior to the loading of the tissue with [3H]-choline, and had no effect when the stores had already been filled with labelled [3H]-ACh indicates that the stimulation-evoked release of [3H]-ACh is of vesicular origin and (-)-vesamicol has no effect on the release process. This is the first neurochemical evidence for the vesicular origin of stimulation-evoked release of ACh from the neuromuscular junction.
Polymer alloys based on poly(2,6-dimethyl-1,4-phenylene ether) and poly(styrene-co-acrylonitrile) using poly(styrene-b-(ethylene-co-butylene)-b-methyl methacrylate) triblock copolymers as compatibilizers (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTPolymer alloys based on poly(2,6-dimethyl-1,4-phenylene ether) and poly(styrene-co-acrylonitrile) using poly(styrene-b-(ethylene-co-butylene)-b-methyl methacrylate) triblock copolymers as compatibilizersClemens Auschra and Reimund StadlerCite this: Macromolecules 1993, 26, 24, 6364–6377Publication Date (Print):November 1, 1993Publication History Published online1 May 2002Published inissue 1 November 1993https://pubs.acs.org/doi/10.1021/ma00076a011https://doi.org/10.1021/ma00076a011research-articleACS PublicationsRequest reuse permissionsArticle Views469Altmetric-Citations83LEARN 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 InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Bigenomic transcriptional regulation of all thirteen cytochrome c oxidase subunit genes by specificity protein 1 (2013)

Cytochrome c oxidase (COX) is one of only four known bigenomic proteins, with three mitochondria-encoded subunits and 10 nucleus-encoded ones derived from nine different chromosomes. The mechanism of regulating this multi-subunit, bigenomic enzyme is not fully understood. We hypothesize that specificity protein 1 (Sp1) functionally regulates the 10 nucleus-encoded COX subunit genes directly and the three mitochondrial COX subunit genes indirectly by regulating mitochondrial transcription factors A and B (TFAM, TFB1M and TFB2M) in neurons. By means of in silico analysis, electrophoretic mobility shift and supershift assays, chromatin immunoprecipitation, RNA interference and over-expression experiments, the present study documents that Sp1 is a critical regulator of all 13 COX subunit genes in neurons. This regulation is intimately associated with neuronal activity. Silencing of Sp1 prevented the upregulation of all COX subunits by KCl, and over-expressing Sp1 rescued all COX subunits from being downregulated by tetrodotoxin. Thus, Sp1 and our previously described nuclear respiratory factors 1 and 2 are the three key regulators of all 13 COX subunit genes in neurons. The binding sites for Sp1 on all 10 nucleus-encoded COX subunits, TFAM, TFB1M and TFB2M are highly conserved among mice, rats and humans.
Modulation of Bambusuril Anion Affinity in Water (2017)

Neutral and negatively charged anion receptors functioning in pure water are rare in supramolecular chemistry. Moreover, studies on adjusting the affinity of such receptors toward anions in water are absent from the literature. Two new bambusurils, 1 a and 2 a, were prepared to demonstrate that the affinity of bambusurils towards anions can be altered by the length of carboxyalkyl groups attached to the macrocycles. The stability of the bambusuril complexes was further controlled by the pH value. The crystal structure of bambusuril 1 a was described, in which two carboxyalkyl arms fold into the macrocycle cavity, thus forming the intramolecular self-inclusion complex.
Systematic approach to process parameter optimization for laser powder bed fusion of low-alloy steel based on melting modes (2023)

Abstract In the metal additive manufacturing (AM) process of laser powder bed fusion (LPBF), there are a limited number of materials suitable for producing parts with high density and desired mechanical properties. To establish novel materials, it is essential to determine optimized process parameters in order to overcome process-related challenges and mitigate defects such as lack of fusion, keyholing, and balling. Scaling laws based on thermophysical properties and process parameters can be used to transfer knowledge from other materials or LPBF systems. In this work, a scaling law is used to adjust process parameters for single-track experiments over a wide range, which are laser power P L (100–1000 W), scan speed v s (300–2500 mm/s), and laser spot size d s (0.08–0.25 mm). Compared to existing studies, the parameter range is thus extended towards large laser spot sizes and high laser powers. The scaling law used is based on the calculation of the normalized enthalpy $$\frac{\Delta H}{{h}_{s}}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mfrac> <mml:mrow> <mml:mi>Δ</mml:mi> <mml:mi>H</mml:mi> </mml:mrow> <mml:msub> <mml:mi>h</mml:mi> <mml:mi>s</mml:mi> </mml:msub> </mml:mfrac> </mml:math> . The ratio of the deposited energy density $$\Delta$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:mi>Δ</mml:mi> </mml:math> H and the melting enthalpy h s correlates with the dimensions of the melt pool. According to the aspect ratio $${\delta }_{\mathrm{c}}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"> <mml:msub> <mml:mi>δ</mml:mi> <mml:mi>c</mml:mi> </mml:msub> </mml:math> of the melt pool of each single track, the respective melting mode—conduction, transition, and keyhole mode—was identified. The process parameters of the single tracks in transition mode were used to optimize the density of the LPBF specimens with varying hatch distance h d (0.06–0.12 mm), resulting in specimens with a relative density of &gt; 99.8%. The proposed methodology can accelerate the process parameter finding for new alloys and avoid process-related defects. Graphical Abstract
Computer-assisted Structural Design of Industrial Woven Fabrics Part I: Need, Scope, Background, and System Architecture (1994)

This is the first of a three-part series describing an attempt to develop a comprehensive computational framework for aiding the engineering design of woven industrial fabrics. The work has two major aims. The first is to develop a generalized knowledge-based CAD system for use in fabric design. A detailed analytic phase will then follow, which will comprise a set of computational models for the simulation of fabric behavior under external stimuli which will be used for the predictive estimation of some important properties. Accordingly, the second focus of this work is to develop an analysis of the uniaxial/biaxial load-deformation behavior of a plain woven fabric. Part I provides the rationale for choosing this domain of industrial fabric design, and discusses the characteristics and the limitations of current design procedures. It examines the requirements for a computer-based system intended to provide decision-making support for a generic design task. There is a short review of such CAD systems within the textiles domain and also in other areas of science/engineering. Finally, this paper concludes by describing the components of this fabric design (ie, ‘FABCAD’) system, its architecture and functional model. Parts II and III will deal with details of how the two research goals have been accomplished.
Longitudinal dynamics of Streptococcus pneumoniae carriage and SARS-CoV-2 infection in households with children (2023)

ABSTRACT Background To characterize interferences between Streptococcus pneumoniae and SARS-CoV-2 we investigated the longitudinal patterns of viral infection and pneumococcal carriage in households infected with SARS-CoV-2. Methods SARS-CoV-2 and pneumococcus were detected with quantitative molecular methods in saliva from members of eighty participating households. Samples were collected between October 2020 and January 2021 from n=197 adults and n=118 children of which n=176 adults and n=98 children had a complete set of ten samples collected within 42 days since enrolment. Time-dependent Cox models were used to evaluate the associations between SARS-CoV-2 and pneumococcal carriage. Results In the entire cohort, cumulative pneumococcal carriage and SARS-CoV-2 infection rates were 58% and 65%, respectively. Pneumococcal abundances were associated with an increased risk of SARS-CoV-2 infection (HR 1.14, 95% CI, 1.01 – 1.29, P =0.04) and delayed clearance of SARS-CoV-2 infection (HR 0.90, 95% CI, 0.82 – 0.99, P =0.03). Elevated viral loads were observed among pneumococcal carriers and individuals with high overall bacterial 16S abundances, however, there were no longitudinal differences in viral loads in linear mixed-effects models. Individuals with high 16S abundances displayed delayed viral clearance (HR 0.65, 95% CI 0.55 – 0.78, P &lt;0.0001). Conclusions Although we found insufficient evidence for a strong impact of SARS-CoV-2 infection on pneumococcal carriage. Results from the current study suggest that pneumococcal carriers may have an increased risk of SARS-CoV-2 infection and high pneumococcal abundances and 16S abundances may be associated with elevated viral loads and delayed clearance of SARS-CoV-2 infection.