gebhart/patrepeval huggingface dataset:
Atomic Force Microscopy Studies of Human Recombinant Bone Morphogenetic Protein OP-1 (2002)

Journal Article Atomic Force Microscopy Studies of Human Recombinant Bone Morphogenetic Protein OP-1 Get access L M Siperko, L M Siperko Department of Biochemistry and Molecular Pathology, Northeastern Ohio Universities College of Medicine, Rootstown, OH 44272 Search for other works by this author on: Oxford Academic Google Scholar S Chubinskaya, S Chubinskaya Department of Biochemistry and Section of Rheumatology, Rush Medical College, Chicago, IL 60612 Search for other works by this author on: Oxford Academic Google Scholar D Rueger, D Rueger Biotech, Hopkinton, MA 01748 Search for other works by this author on: Oxford Academic Google Scholar W J Landis W J Landis Department of Biochemistry and Molecular Pathology, Northeastern Ohio Universities College of Medicine, Rootstown, OH 44272 Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 8, Issue S02, 1 August 2002, Pages 778–779, https://doi.org/10.1017/S1431927602106696 Published: 01 August 2002
Characteristics of the binding of a bacterial expansin (BsEXLX1) to microcrystalline cellulose (2012)

Plant expansin proteins induce plant cell wall extension and have the ability to extend and disrupt cellulose. In addition, these proteins show synergistic activity with cellulases during cellulose hydrolysis. BsEXLX1 originating from Bacillus subtilis is a structural homolog of a β-expansin produced by Zea mays (ZmEXPB1). The Langmuir isotherm for binding of BsEXLX1 to microcrystalline cellulose (i.e., Avicel) revealed that the equilibrium binding constant of BsEXLX1 to Avicel was similar to those of other Type A surface-binding carbohydrate-binding modules (CBMs) to microcrystalline cellulose, and the maximum number of binding sites on Avicel for BsEXLX1 was also comparable to those on microcrystalline cellulose for other Type A CBMs. BsEXLX1 did not bind to cellooligosaccharides, which is consistent with the typical binding behavior of Type A CBMs. The preferential binding pattern of a plant expansin, ZmEXPB1, to xylan, compared to cellulose was not exhibited by BsEXLX1. In addition, the binding capacities of cellulose and xylan for BsEXLX1 were much lower than those for CtCBD3.
Data from Predictors of Survival in Never-Smokers with Non–Small Cell Lung Cancer: A Large-Scale, Two-Phase Genetic Study (2023)

&lt;div&gt;Abstract&lt;p&gt;&lt;b&gt;Purpose:&lt;/b&gt; Lung cancer in never-smokers (LCINS) is increasingly recognized as a distinct disease from that in ever-smokers owing to substantial differences in etiology, clinical characteristics, and prognosis. Therefore, we aimed to identify prognostic markers specific for LCINS.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Experimental Design:&lt;/b&gt; First, 11,930 single-nucleotide polymorphisms (SNP) in 904 inflammation-related genes were genotyped, and their associations with overall survival in 411 patients with LCINS at MD Anderson Cancer Center were analyzed. Next, validation of the top 27 SNPs in 311 patients with LCINS at Mayo Clinic was conducted.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Results:&lt;/b&gt; Three SNPs (&lt;i&gt;IL17RA&lt;/i&gt;:rs879576, &lt;i&gt;BMP&lt;/i&gt;8A:rs698141, and &lt;i&gt;STY:&lt;/i&gt;rs290229) were validated (&lt;i&gt;P&lt;/i&gt; &lt; 0.05), and two SNPs (&lt;i&gt;CD74&lt;/i&gt;:rs1056400 and &lt;i&gt;CD38:&lt;/i&gt;rs10805347) reached borderline significance (&lt;i&gt;P&lt;/i&gt; = 0.08) in the Mayo Clinic population. We validated a survival-tree created in the MD Anderson population exploring gene–gene interactions in the Mayo Clinic population. This survival-tree stratified patients into subsets with significantly different risks of death: patients with the rs1056400_&lt;i&gt;GG&lt;/i&gt;/rs698141_&lt;i&gt;GA&lt;/i&gt; + &lt;i&gt;AA&lt;/i&gt; genotype had significantly higher risk of death in both MD Anderson (HR:2.32, 95%CI: 1.58–3.41) and Mayo (HR:1.97, 95%CI: 1.11–3.50) populations compared with those with the rs1056400_&lt;i&gt;GG&lt;/i&gt;/rs698141_&lt;i&gt;GG&lt;/i&gt; or rs1056400_&lt;i&gt;GA&lt;/i&gt; + &lt;i&gt;AA&lt;/i&gt; genotype. We evaluated these five SNPs in 996 ever-smokers from MD Anderson and found no significant associations.&lt;/p&gt;&lt;p&gt;&lt;b&gt;Conclusions:&lt;/b&gt; Our study provides strong evidence that inflammation-related genetic variations can affect clinical outcomes in LCINS, which may lead to significant biologic insight into these outcomes. &lt;i&gt;Clin Cancer Res; 18(21); 5983–91. ©2012 AACR&lt;/i&gt;.&lt;/p&gt;&lt;/div&gt;
Stereochemical inversion as a route to improved biophysical properties of therapeutic peptides exemplified by glucagon (2018)

Abstract Peptides and small proteins are attractive therapeutic candidates due to their inherent selectivity and limited off-target effects. Unfortunately, their potential is often hindered by unfavorable physicochemical properties. This is particularly true in the case of glucagon, a peptide indispensable in the treatment of life-threatening hypoglycemia. Glucagon displays extremely low solubility in physiological buffers and suffers chemical degradation when the pH is adjusted in either direction. Here we systematically examine site-specific stereochemical inversion as a means to enhance aqueous solubility and stability, yet not diminish bio-potency or pharmacodynamics. We report several analogs that maintain full biological activity with substantially increased aqueous solubility, and resistance to fibrillation. We conclude that d -amino acids offer an attractive option for biophysical optimization of therapeutic peptides.
Highly diastereoselective aldol reactions of chiral methyl ketones (1993)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTHighly diastereoselective aldol reactions of chiral methyl ketonesBharat R. Lagu, Heidi M. Crane, and Dennis C. LiottaCite this: J. Org. Chem. 1993, 58, 16, 4191–4193Publication Date (Print):July 1, 1993Publication History Published online1 May 2002Published inissue 1 July 1993https://doi.org/10.1021/jo00068a006RIGHTS & PERMISSIONSArticle Views257Altmetric-Citations23LEARN 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 (310 KB) Get e-AlertsSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Inside polyMOFs: layered structures in polymer-based metal–organic frameworks (2020)

In this report, we explore the internal structural features of polyMOFs consisting of equal mass ratios of metal-coordinating poly(benzenedicarboxylic acid) blocks and non-coordinating poly(ethylene glycol) (PEG) blocks. The studies reveal alternating lamellae of metal-rich, crystalline regions and metal-deficient non-crystalline polymer, which span the length of hundreds of nanometers. Polymers consisting of random PEG blocks, PEG end-blocks, or non-coordinating poly(cyclooctadiene) (COD) show similar alternation of metal-rich and metal-deficient regions, indicating a universal self-assembly mechanism. A variety of techniques were employed to interrogate the internal structure of the polyMOFs, including transmission electron microscopy (TEM), scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and small-angle synchrotron X-ray scattering (SAXS). Independent of the copolymer architecture or composition, the internal structure of the polyMOF crystals showed similar lamellar self-assembly at single-nanometer length scales.
Multi-antenna interference management for coded caching (2020)

A multi-antenna broadcast channel scenario is considered where a base station delivers contents to cache-enabled user terminals. A joint design of coded caching (CC) and multigroup multicast beamforming is proposed to benefit from spatial multiplexing gain, improved interference management and the global CC gain, simultaneously. The developed general content delivery strategies utilize the multiantenna multicasting opportunities provided by the CC technique while optimally balancing the detrimental impact of both noise and inter-stream interference from coded messages transmitted in parallel. Flexible resource allocation schemes for CC are introduced where the multicast beamformer design and the receiver complexity are controlled by varying the size of the subset of users served during a given time interval, and the overlap among the multicast messages transmitted in parallel, indicated by parameters α and β, respectively. Degrees of freedom (DoF) analysis is provided showing that the DoF only depends on α while it is independent of β. The proposed schemes are shown to provide the same degrees-of-freedom at high signal-to-noise ratio (SNR) as the state-of-art methods and, in general, to perform significantly better, especially in the finite SNR regime, than several baseline schemes.
Sequential Feeding of Glucose and Valerate in a Fed-Batch Culture of Ralstonia eutropha for Production of Poly(hydroxybutyrate-co-hydroxyvalerate) with High 3-Hydroxyvalerate Fraction (2004)

Several important properties of poly(3-hydroxybutyric-co-3-hydroxyvaleric acids) (P(3HB-co-3HV) depend mainly on the HV unit fraction of the copolymer. Sequential and simultaneous feeding of glucose and valerate were employed to produce P(3HB-co-3HV) in a fed-batch culture of Ralstonia eutropha, and the effects of feeding models on the cell growth, 3HV unit fraction, and copolymer productivity have been investigated. The sequential feeding of glucose and then valerate resulted in a cell density of 110.2 g/L, 3HV unit fraction of 62.7 mol %, and copolymer productivity of 0.56 g/(L.h), while the latter simultaneous feeding strategy never achieved the 3HV fraction of P(3HB-co-3HV) higher than 50%. A nuclear magnetic resonance study confirmed that the production of random copolymer P(3HB-co-3HV) with high 3HV unit fraction was possible even with sequential feeding of glucose and valerate.
Targeting Mycolic Acid Transport by Indole-2-carboxamides for the Treatment of Mycobacterium abscessus Infections (2017)

Mycobacterium abscessus is a fast-growing, multidrug-resistant organism that has emerged as a clinically significant pathogen in cystic fibrosis (CF) patients. The intrinsic resistance of M. abscessus to most commonly available antibiotics seriously restricts chemotherapeutic options. Herein, we report the potent activity of a series of indolecarboxamides against M. abscessus. The lead compounds, 6 and 12, exhibited strong activity in vitro against a wide panel of M. abscessus isolates and in infected macrophages. High resistance levels to the indolecarboxamides appear to be associated with an A309P mutation in the mycolic acid transporter MmpL3. Biochemical analyses demonstrated that while de novo mycolic acid synthesis remained unaffected, the indolecarboxamides strongly inhibited the transport of trehalose monomycolate, resulting in the loss of trehalose dimycolate production and abrogating mycolylation of arabinogalactan. Our data introduce a hereto unexploited chemical structure class active against M. abscessus infections with promising translational development possibilities for the treatment of CF patients.
Interpolative frame-erasure concealment of moving-average prediction coding parameters in ITU-T Recommendation G.718 (2008)

An interpolative concealment algorithm for parameters encoded using interframe prediction is presented. A lost parameter is concealed using information received correctly in the next frame. In the presented algorithm, a lost parameter is determined by minimising the sum of distances between the parameters decoded in the previous and current frames and the parameters decoded in the current and subsequent frames. The algorithm was applied to concealment algorithms for the immittance spectral frequency and fixed codebook gain parameters of the ITU-T Recommendation G.722.2 decoder. The effectiveness of the algorithm was confirmed in a random frame erasure condition. The algorithm was adopted as a part of the G.722.2-interoperable mode of the new ITU-T Recommendation G.718 approved in June 2008.
Bisulfite ion-catalyzed transamination of cytosine residues with .alpha.,.omega.-alkanediamines: The effect of chain length on the reaction kinetics (1993)

Pseudo-first-order rate constants for the bisulfite ion-catalyzed transamination of cytidine with 1,2-ethanediamine, 1,3-propanediamine, 1,4-butanediamine, and 1,6-hexanediamine have been determined. Hydrolytic deamination has been shown to compete with transamination under acidic conditions, but is of minor importance at pH > 5.3 when the total concentration of diamine is greater than 0.2 mol dm-3. The dependence of the transamination rate on pH and the concentration of diamine and bisulfite ion indicates that the major reaction involves nucleophilic attack of the diamine monocation on the N3 protonated bisulfite adduct of cytidine. The effect of the chain length of the diamine on the rate of transamination is discussed, and the results are compared with those obtained by reacting single-stranded DNA with the same diamines and labeling the transaminated product with a europium chelate.
ChemInform Abstract: Diastereoselective Synthesis of 2,3,5‐Trisubstituted Tetrahydrofurans via Cyclofunctionalization Reactions. Evidence of Stereoelectronic Effects. (2002)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Diagnostic criteria for retained products of conception—A scoping review (2021)

There is wide variation in the way RPOC are assessed, and the criteria used to define RPOC following induced abortion and early pregnancy loss; ultrasonographic measurement of endometrial thickness, with a cut-off of 15 mm or more 2 weeks after primary treatment is the most widely used diagnostic approach. A meta-analysis on diagnostic accuracy of endometrial thickness of 15 mm or more did not lead to solid results. These findings can be a first step to develop a workable standard of establishing RPOC after induced abortion or early pregnancy loss.
- Coatings for minimally processed fruits and vegetables (2011)

Before dealing with coatings, this chapter rst addresses the basic physiology and quality issues of fresh-cut fruit and vegetables, the better to appreciate the coatings devised to improve quality of these products.
Aggression and Misogyny Detection using BERT: A Multi-Task Approach (2020)

In recent times, the focus of the NLP community has increased towards offensive language, aggression, and hate-speech detection.This paper presents our system for TRAC-2 shared task on “Aggression Identification” (sub-task A) and “Misogynistic Aggression Identification” (sub-task B). The data for this shared task is provided in three different languages - English, Hindi, and Bengali. Each data instance is annotated into one of the three aggression classes - Not Aggressive, Covertly Aggressive, Overtly Aggressive, as well as one of the two misogyny classes - Gendered and Non-Gendered. We propose an end-to-end neural model using attention on top of BERT that incorporates a multi-task learning paradigm to address both the sub-tasks simultaneously. Our team, “na14”, scored 0.8579 weighted F1-measure on the English sub-task B and secured 3rd rank out of 15 teams for the task. The code and the model weights are publicly available at https://github.com/NiloofarSafi/TRAC-2. Keywords: Aggression, Misogyny, Abusive Language, Hate-Speech Detection, BERT, NLP, Neural Networks, Social Media
A high-power ultrafast laser source with 300 MHz repetition rate for trapped-ion quantum logic (2011)

We implement a mode-locked UV laser source at 300 MHz repetition rate for use in fast quantum logic gates with trapped ions. The architecture allows scaling of repetition rate into the GHz range.
"Through-arc" process monitoring: techniques for control of automated gas metal arc welding (2003)

Improved sensors are needed to enable automatic GMAW to accommodate a greater range of disturbing inputs. A low-cost, non-intrusive sensing technique, known as through-arc sensing, involves collecting and analyzing welding current and voltage signals. Through-arc sensing can be used to detect various GMAW quality indicators. It is shown that through-arc sensing can detect arc-start quality, steady-state arc stability, and the mode of metal transfer. Furthermore, the technique shows promise for detecting the onset of GMAW process disturbances including variations in tip-to-work distance, insufficient shielding gas coverage, electrode feeding problems, joint fit-up problems, and contact tip wear. Additional work is needed to refine and implement these techniques into a production-worthy system.
Single and Combined Effects of Growth Hormone and Testosterone Administration on Measures of Body Composition, Physical Performance, Mood, Sexual Function, Bone Turnover, and Muscle Gene Expression in Healthy Older Men (2002)

We examined the effects of GH and/or testosterone (T) administration on body composition, performance, mood, sexual function, bone turnover, and muscle-gene expression in healthy older men. Ten men [mean (SEM) age, 68 (2.5) yr; height, 171.5 (2.4) cm; and weight, 80 (3.0) kg] completed each of the following 1-month, double-blind interventions after a baseline (B) study in randomized order with an intervening 3-month washout: transdermal T patch (5.0 mg/daily); recombinant human GH (6.25 micro g/kg sc daily); and combined hormones (GHT). ANOVA with repeated measures was used to evaluate interventional effects. Integrated serum GH concentrations [mean (SEM)] were elevated comparably by GH and GHT: [B = 363 (55), GH = 1107 (120), T = 459 (131), and GHT = 1189 (46) micro g/liter.min; P < 0.0001]. Serum IGF-I concentrations also increased commensurately after GH and GHT: [B = 168 (14), GH = 285 (16), T = 192 (25), and GHT = 294 (25) micro g/liter; P < 0.0001]. GHT administration increased total estradiol: [B = 110 (20), GH = 106 (13), T = 129 (13), and GHT = 153 (17) pmol/liter; P < 0.02], and both T and GHT elevated free T: [B = 12 (2.1), GH = 11 (1.5), T = 22 (2.8), and GHT = 24 (2.5) pg/ml; P < 0.0001]. No significant changes occurred in strength, flexibility, percentage body fat, or sexual function and mood. However, fat-free mass increased under combined GHT exposure: [B = 55 (1.3), GH = 56 (1.1), T = 55 (1.5), GHT = 57 (1.7) kg; P < 0.03]. Balance improved in response to GH intervention (P < 0.05), as did 30-m walk time during T and GHT interventions [B = 6.6 (0.3), GH = 6.2 (0.7), T = 5.9 (0.3), GHT = 5.5 (0.3) sec; P = 0.04] and stair climb time for all three interventions [B = 32.2 (1.4), GH = 29.8 (1.2), T = 30.5 (1.4), and GHT = 29.9 (1.2) sec (P = 0.0034), wherein the effects of GH, T, and GHT were different from that of B]. Muscle IGF-I gene expression increased by 1.9-fold during GH administration and by 2.3-fold during GHT administration (P < 0.05, compared with B). Myostatin and androgen receptor gene expression were not affected. Serum osteocalcin increased in response to the GH and GHT interventions: [B = 4.8 (0.52), GH = 5.7 (0.54), T = 4.7 (0.33), and GHT = 5.5 (0.39); P <0.009]. There were no significant adverse events during 30 patient-months of intervention. We conclude that 1 month of GH and/or T administration improves certain measures of balance and physical performance in older men and increases muscle IGF-I gene expression.
A Microfluidic System for the Continuous Recycling of Unmodified Homogeneous Palladium Catalysts through Liquid/Liquid Phase Separation (2013)

A parting of the waves: A prototype microflow system for the continuous recycling of homogeneous catalysts through liquid/liquid phase separation was developed and its effectiveness demonstrated in a challenging palladium-catalyzed hydroxylation reaction. The unmodified catalyst is recycled under standard reaction conditions by using a combination of chemical and engineering methods.
Third-Party Hardware IP Assurance against Trojans through Supervised Learning and Post-processing (2021)

System-on-chip (SoC) developers increasingly rely on pre-verified hardware intellectual property (IP) blocks acquired from untrusted third-party vendors. These IPs might contain hidden malicious functionalities or hardware Trojans to compromise the security of the fabricated SoCs. Recently, supervised machine learning (ML) techniques have shown promising capability in identifying nets of potential Trojans in third party IPs (3PIPs). However, they bring several major challenges. First, they do not guide us to an optimal choice of features that reliably covers diverse classes of Trojans. Second, they require multiple Trojan-free/trusted designs to insert known Trojans and generate a trained model. Even if a set of trusted designs are available for training, the suspect IP could be inherently very different from the set of trusted designs, which may negatively impact the verification outcome. Third, these techniques only identify a set of suspect Trojan nets that require manual intervention to understand the potential threat. In this paper, we present VIPR, a systematic machine learning (ML) based trust verification solution for 3PIPs that eliminates the need for trusted designs for training. We present a comprehensive framework, associated algorithms, and a tool flow for obtaining an optimal set of features, training a targeted machine learning model, detecting suspect nets, and identifying Trojan circuitry from the suspect nets. We evaluate the framework on several Trust-Hub Trojan benchmarks and provide a comparative analysis of detection performance across different trained models, selection of features, and post-processing techniques. The proposed post-processing algorithms reduce false positives by up to 92.85%.
Updated processing of Control Flags for BGP VPLS (2019)

This document updates the meaning of the Control Flags field in the
Layer2 Info Extended Community used for BGP-VPLS NLRI as defined in
RFC4761. This document updates RFC4761.