gebhart/patrepeval huggingface dataset:
Long-Term Persistence of Infection in Chimpanzees Inoculated with an Infectious Hepatitis C Virus Clone Is Associated with a Decrease in the Viral Amino Acid Substitution Rate and Low Levels of Heterogeneity (2004)

Two chimpanzees, 1535 and 1536, became persistently infected following inoculation with RNA transcripts from cDNA clones of hepatitis C virus (HCV). Analysis of the HCV genomes from both animals showed an accumulation of amino acid substitutions over time. The appearance of substitutions in the envelope genes was associated with increased antienvelope antibody titers. However, extensive mutations were not incorporated into hypervariable region 1 (HVR1). A comparison of the nonsynonymous substitution rate/synonymous substitution rate was made at various time points to analyze selective pressure. The highest level of selective pressure occurred during the acute phase and decreased as the infection continued. The nonsynonymous substitution rate was initially higher than the synonymous substitution rate but decreased over time from 3.3 x 10(-3) (chimpanzee 1535) and 3.2 x 10(-3) (chimpanzee 1536) substitutions/site/year at week 26 to 1.4 x 10(-3) (chimpanzee 1535) and 1.7 x 10(-3) (chimpanzee 1536) at week 216, while the synonymous substitution rate remained steady at approximately 1 x 10(-3) substitutions/site/year. Analysis of PCR products using single-stranded conformational polymorphism indicated a low level of heterogeneity in the viral genome. The results of these studies confirm that the persistence of infection is not solely due to changes in HVR1 or heterogeneity and that the majority of variants observed in natural infections could not arise simply through mutation during the time period most humans and chimpanzees are observed. These data also indicate that immune pressure and selection continue throughout the chronic phase.
Programming events in the regulation of cell proliferation and death. (1993)

In developing new and more successful therapies for preventing and treating cancer, it is critical to understand what normally regulates cell proliferation and cell death and what are the specific dysfunctions associated with these regulations in individual cancers. Here we review the programmed series of molecular, cellular, and biochemical events required for a cell's entrance and progression through the proliferative vs death processes as a starting point for such approaches to new therapies.
Costimulation of CD4+ and CD8+ T cells through CD26: The ADA-binding epitope is not essential for complete signaling (1995)

It was previously shown that CD26 (DPP IV, EC 3.4.14.5) is a binding site for adenosine deaminase (ADA, EC 3.5.4.4) on T cells and that costimulation by some anti-CD26 monoclonal antibodies (mAbs) and anti-CD3 induces CD4+ T cell proliferation. The CD26 epitopes involved in costimulation, the precise sequence of the events preceding proliferation, and the response of CD8+ compared with CD4+ T cells to CD26 were not extensively studied. We therefore compared the effects of the novel TA5.9 anti-CD26 mAb, recognizing an ADA-binding epitope, and the clearly distinct anti-Ta1 reference anti-CD26 mAb for their costimulatory properties in various T cell subsets. Both purified CD4+ and CD8+ T cells proliferated upon costimulation with anti-CD3 and either anti-CD26 mAb, but anti-TA5.9 mAb induced a more potent response than anti-Ta1. Either anti-CD26 mAb, together with anti-CD3, caused a similar sequential up-regulation of CD69, CD25 (IL-2R alpha), and CD71 (transferrin receptor) expression on CD4+ and CD8+ T cells. The activation markers appeared faster on the CD45R0+ than on the CD45R0- subsets. After costimulation, CD4+ T cell cultures contained significant amounts of the Th1 cytokines IL-2, interferon-gamma (IFN-gamma), and tumor necrosis factor-alpha (TNF-alpha). In CD8+ T cell cultures relatively more IFN-gamma and TNF-alpha but almost no IL-2 was measured after triggering of CD3 and CD26. Our data demonstrate that the recognition of the ADA-binding epitope is not a prerequisite for the costimulatory capacity of anti-CD26 mAbs. Both CD4+ and CD8+ T cells and their CD45R0- and CD45R0+ subsets are sensitive to various aspects of activation via CD26, but the magnitude and/or kinetics differ according to the anti-CD26 used and the T cell subset studied.
Assessing Antigen Structural Integrity through Glycosylation Analysis of the SARS-CoV-2 Viral Spike (2021)

Severe acute respiratory syndrome coronavirus 2 is the causative pathogen of the COVID-19 pandemic which as of March 29, 2021, has claimed 2 776 175 lives worldwide. Vaccine development efforts focus on the viral trimeric spike glycoprotein as the main target of the humoral immune response. Viral spikes carry glycans that facilitate immune evasion by shielding specific protein epitopes from antibody neutralization, and antigen efficacy is influenced by spike glycoprotein production in vivo. Therefore, immunogen integrity is important for glycoprotein-based vaccine candidates. Here, we show how site-specific glycosylation differs between virus-derived spikes, wild-type, non-stabilized spikes expressed from a plasmid with a CMV promoter and tPA signal sequence, and commonly used recombinant, engineered spike glycoproteins. Furthermore, we show that their distinctive cellular secretion pathways result in different protein glycosylation and secretion patterns, including shedding of spike monomeric subunits for the non-stabilized wild-type spike tested, which may have implications for the resulting immune response and vaccine design.
Breath Formate Is a Marker of Airway S-Nitrosothiol Depletion in Severe Asthma (2010)

We conclude that EBC formate concentration is significantly higher in the breath of children with asthma than in those without asthma. In addition, amongst asthmatics, formate is elevated in the breath of those with severe asthma compared to those with mild-to-moderate asthma. We suggest that this difference is related to asthma pathology and may be a product of increased catabolism of endogenous S-nitrosothiols.
Combining renewable gum rosin and lignin: Towards hydrophobic polymer composites by controlled polymerization (2011)

Abstract Rosin polymer–grafted lignin composites were prepared via “grafting from” atom transfer radical polymerization (ATRP) with the aid of 2‐bromoisobutyryl ester‐modified lignin as macroinitiators. Three different monomers derived from dehydroabietic acid (DA) were used for execution of grafting from ATRP, while DA was separately attached onto lignin by a simple esterification reaction. Kinetic studies indicated controlled and “living” characteristics of all monomer polymerizations. Thermal studies indicated that rosin polymer–grafted lignin composites exhibited glass transition temperatures in a broad temperature range from ∼20 to 100°C. The grafting of both DA and rosin polymers significantly enhanced hydrophobicity of lignin. Static contact angle measurement of water droplets showed ∼90° for all these rosin modified lignin composites. X‐ray photoelectron spectroscopy demonstrated that the surface of rosin–lignin composites was dominated with chemical compositions originating from the hydrocarbon rich rosin moiety. The impartation of hydrophobicity of rosin into lignin provided excellent water resistance of this class of renewable polymers, as all rosin‐modified lignin composites showed water uptake below 1.0 wt %. © 2011 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2011
A 230mV-950mV 2.8Tbps/W Unified SHA256/SM3 Secure Hashing Hardware Accelerator in 14nm Tri-Gate CMOS (2018)

A unified SHA256/SM3 secure hashing hardware accelerator for cross-geo authentication is fabricated in 14nm tri-gate CMOS, with a throughput of 9.5/8.3Gbps respectively measured at 0.75V, 25°C. Message digest pre-addition, with mode-multiplexed digest/scheduler completion adders and distributed final hash computation reduces critical path delay by 14% and accelerator area by 48%, resulting in a compact layout of 5992μm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> . 2/4-way parallel message scheduler enables 0.5/0.25× frequency scaling at iso-hash throughput enabling 35/62% scheduler power reduction. Robust sub-threshold voltage operation down to 230mV enables a peak energy-efficiency of 2.8Tbps/W measured at 300mV.
ChemInform Abstract: STEREOCHEMIE 38. MITT. FLUORIERTE STEROIDE 7. MITT. GERUESTUMLAGERUNG VON CHOLESTERIN (1971)

Abstract Die Addition von HF bei ‐60°C an Cholesterin (I), die zu den epimeren Fluorhydrinen (II) führt, wird von einer Gerüstumlagerung begleitet.
Automated anterior chamber angle localization and glaucoma type classification in OCT images (2013)

To identify glaucoma type with OCT (optical coherence tomography) images, we present an image processing and machine learning based framework to localize and classify anterior chamber angle (ACA) accurately and efficiently. In digital OCT photographs, our method automatically localizes the ACA region, which is the primary structural image cue for clinically identifying glaucoma type. Next, visual features are extracted from this region to classify the angle as open angle (OA) or angle-closure (AC). This proposed method has three major contributions that differ from existing methods. First, the ACA localization from OCT images is fully automated and efficient for different ACA configurations. Second, it can directly classify ACA as OA/AC based on only visual features, which is different from previous work for ACA measurement that relies on clinical features. Third, it demonstrates that higher dimensional visual features outperform low dimensional clinical features in terms of angle closure classification accuracy. From tests on a clinical dataset comprising of 2048 images, the proposed method only requires 0.26s per image. The framework achieves a 0.921 ± 0.036 AUC (area under curve) value and 84.0% ± 5.7% balanced accuracy at a 85% specificity, which outperforms existing methods based on clinical features.
Passive location estimation using TOA measurements (2011)

Ultra-wideband (UWB) radios offer highly accurate ranging, i.e., measurement of signal travel time. This is important for positioning (localization), in particular in indoor environments, where GPS is not available. This paper considers UWB-based positioning of passive objects, where one transmitter and multiple, distributed, receivers are employed. We consider the case where the transmitter and receivers can be synchronized, so that time-of-arrival (TOA) instead of time-difference-of-arrival (TDOA) information can be utilized. Assuming Gaussian errors for the range estimates, we propose a novel, Two-Step, Expectation Maximization (TSEM) based algorithm for the localization of the passive object. This algorithm achieves the Cramer-Rao Lower Bound (CRLB) of TOA algorithms. Simulation results show that the error variance of TSEM is much lower (often 30 dB) than that of the existing, TDOA-based, algorithms.
Optical Simulation for Designing a PPG Signal Patch (2019)

Abstract Designing an optical patch for photoplethysmogram (PPG) signal considers the optical simulation of the patch on the skin. The skin model for the optical simulation consists of epidermis, a dermis, a subcutaneous fat, and a blood vessel, while the model of the patch includes an organic light emitting diode (OLED) and an organic photodiode (OPD). Each model of skin layers is implemented using bulk and scattering of the optical parameter. In order to model the AC/DC of PPG signal, the blood vessel of the optical model uses the diameter of 2 mm and 2.2 mm. The simulation conducted by sweeping the distance of OPD model apart of OLED in knowing the optimal distance between OLED and OPD. The simulation of the different shape of patches is conducted to know the optimum shape of the patch. The 8-shaped patch has the optimum value of the AC/DC signal which is 0.0045.
Defeating Cancers’ Adaptive Defensive Strategies Using Thermal Therapies: Examining Cancer’s Therapeutic Resistance, Ablative, and Computational Modeling Strategies as a means for Improving Therapeutic Outcome (2018)

This review lays out the various molecular adaptive mechanisms-the hallmarks of cancer-responsible for therapeutic resistance, on one hand, and how various ablative therapies, including both heating- and freezing-based strategies, overcome many of cancer's defenses, on the other hand, thereby enhancing the potential for curative approaches for various cancers.
20(S)-protopanaxadiol regio-selectively targets androgen receptor: anticancer effects in castration-resistant prostate tumors (2018)

We have explored the effects of 20(S)-protopanaxadiol (aPPD), a naturally derived ginsenoside, against androgen receptor (AR) positive castration resistant prostate cancer (CRPC) xenograft tumors and have examined its interactions with AR. <i>In silico</i> docking studies for aPPD binding to AR, alongside transactivation bioassays and <i>in vivo</i> efficacy studies were carried out in the castration-resistant C4-2 xenograft model. Immunohistochemical (IHC) and Western blot analyses followed by evaluation of AR, apoptotic, cell cycle and proliferative markers in excised tumors was performed. The growth of established CRPC tumors was inhibited by 53% with aPPD and a corresponding decrease in serum PSA was seen compared to controls. The IHC data revealed that Ki-67 was significantly lower for aPPD treated tumors and was associated with elevated p21 and cleaved caspase-3 expression, compared to vehicle treatment. Furthermore, aPPD decreased AR protein expression in xenograft tumors, while significantly upregulating p27 and Bax protein levels. <i>In vitro</i> data supporting this suggests that aPPD binds to and significantly inhibits the N-terminal or the DNA binding domains of AR. The AR androgen binding site docking score for androgen (dihydrotestosterone) was -11.1, while that of aPPD was -7.1. The novel findings described herein indicate aPPD potently inhibits PCa <i>in vivo</i> partly via inhibition of a site on the AR N-terminal domain. This manifested as cell cycle arrest and concurrent induction of apoptosis via an increase in Bax, cleaved-caspase-3, p27 and p21 expression.
Calculation of the efficiency of ultraviolet screeners in plastics (1987)

Calculation of the effect of light absorbers (UV screeners) on the photochemistry of polymers shows that a critical factor in reducing the rate of photodegradation is the thickness of the actual degraded layer. When the degradation is confined to a zone within a few microns of the exposed surface, the efficiency of light absorption as a stabilization mechanism is greatly reduced. The relative absorptivity of the base resin and pigment loadings are calculated to have a minor effect on stabilization efficiency for polymers having thin layers of degradation.
Plasma metabolomic biomarker panel to distinguish patients with amyotrophic lateral sclerosis from disease mimics (2014)

Our objective was to identify plasma biomarkers of ALS that can aid in distinguishing patients with ALS from those with disease mimics. In this multi-center study, plasma samples were collected from 172 patients recently diagnosed with ALS, 50 healthy controls, and 73 neurological disease mimics. Samples were analyzed using metabolomics. Using all identified biochemicals detected in > 50% of all samples in the metabolomics analysis, samples were classified as ALS or mimic with 65% sensitivity and 81% specificity by LASSO analysis (AUC of 0.76). A subset panel of 32 candidate biomarkers classified these diagnosis groups with a specificity of 90%/sensitivity 58% (AUC of 0.81). Creatinine was lower in subjects with lower revised ALS Functional Rating Scale (ALSFRS-R) scores. In conclusion, ALS can be distinguished from neurological disease mimics by global biochemical profiling of plasma samples. Our analysis identified ALS versus mimics with relatively high sensitivity. We identified a subset of 32 metabolites that identify patients with ALS with a high specificity. Interestingly, lower creatinine correlates significantly with a lower ALSFRS-R score. Finally, molecules previously reported to be important in disease pathophysiology, such as urate, are included in our metabolite panel.
ChemInform Abstract: Phosphoramidite Ligands (2013)

Abstract Review: 173 refs.
Beneficial Effects of (pGlu-Gln)-CCK-8 on Energy Intake and Metabolism in High Fat Fed Mice are Associated with Alterations of Hypothalamic Gene Expression (2013)

Cholecystokinin (CCK) is a gastrointestinal hormone with potential therapeutic promise for obesity-diabetes. The present study examined the effects of twice daily administration of the N-terminally modified stable CCK-8 analogue, (pGlu-Gln)-CCK-8, on metabolic control and hypothalamic gene expression in high fat fed mice. Sub-chronic twice daily injection of (pGlu-Gln)-CCK-8 for 16 days significantly decreased body weight (p<0.05), energy intake (p<0.01), circulating blood glucose (p<0.001), and plasma insulin (p<0.001) compared to high fat controls. Furthermore, (pGlu-Gln)-CCK-8 markedly improved glucose tolerance (p<0.05) and insulin sensitivity (p<0.05). Assessment of hypothalamic gene expression on day 16 revealed significantly elevated NPY (p<0.05) and reduced POMC (p<0.05) and MC4R (p<0.05) mRNA expression in (pGlu-Gln)-CCK-8 treated mice. High fat feeding or (pGlu-Gln)-CCK-8 treatment had no significant effects on hypothalamic gene expression of receptors for leptin, CCK₁ and GLP-1. These studies underscore the potential of (pGlu-Gln)-CCK-8 for the treatment of obesity-diabetes and suggest modulation of NPY and melanocortin related pathways may be involved in the observed beneficial effects.
Binuclear Copper(I) Macrocycles Synthesized via the Weak-Link Approach (2004)

The weak-link approach has been employed to synthesize a series of bimetallic Cu(I) macrocycles in high yield. Addition of phosphinoalkylether or -thioether ligands to [Cu(MeCN)4]PF6 produces "condensed" intermediates, [mu-(1,4-(PPh2CH2CH2X)2Y)2Cu2][PF6]2 (X = S, O; Y = C6H4, C6F4), containing strong P-Cu bonds and weaker O-Cu or S-Cu bonds. The weak bonds of these intermediates can be cleaved through ligand substitution reactions to generate macrocyclic structures, [mu-(1,4-(PPh2CH2CH2X)2Y)2(Z)nCu2][PF6]2 (X = S, O; Y = C6H4, C6F4; Z = pyridine, acetonitrile, diimines, isocyanide) in nearly quantitative yields. The incorporation of tetrahedral Cu(I) metal centers into these macrocycles provides a pathway to complexes that differ from analogous d8 square planar macrocycles generated via this approach in their increased air stability, small molecule reactivity, and ability to form multiple structural isomers. Solid-state structures, as determined by single-crystal X-ray diffraction studies, are presented for condensed intermediates and an open macrocycle
Properties and applications of precision oligomer materials; where organic and polymer chemistry join forces (2021)

Abstract Precise oligomeric materials constitute a growing area of research with implications for various applications as well as fundamental studies. Notably, this field of science which can be termed macro‐organic chemistry, draws inspiration from both traditional polymer chemistry and organic synthesis, combining the molecular precision of organic chemistry with the materials properties of macromolecules. Discrete oligomers enable access to unprecedented materials properties, for example, in self‐assembled structures, crystallization, or optical properties. The degree of control over oligomer structures resembles many biological systems and enables the design of materials with tailored properties and the development of fundamental structure–property relationships. This Review highlights recent developments in macro‐organic chemistry from synthetic concepts to materials properties, with a focus on self‐assembly and molecular recognition. Finally, an outlook for future research directions is provided.
Intracisternal urocortin inhibits vagally stimulated gastric motility in rats: role of CRF2 (2002)

On page 238 of the above paper the structure of astressin 2 -B was incorrectly described as: cyclo(31 34)[D-Phe 11 ,His 12 ,Nle 17 ,C d MeLeu 13,39 ,Glu 31 ,Lys 34 ]-Ac-Sauvagine (8 40)
Locating Anchors in WSN Using a Wearable IMU-Camera (2014)

Localization in a wireless sensor network (WSN) becomes important for many modern applications, like landslide detection, precision agriculture, health care, and so forth. The more precise the position of an anchor node is, the more accurate the localization of a sensor node can be measured. Since the Global Positioning System (GPS) device cannot work properly indoor, some existing localization methods configure anchor nodes in a manual fashion. However, neither applying GPS modules nor manually configuring anchor nodes is suitable for a WSN and especially artificial errors of manual configuration may be propagated and affect the results of localization. In this paper, we propose an alternative method to estimate anchor node locations in an indoor environment. We collect the Received Signal Strength Indicator (RSSI) data from the anchor node when human is walking around them. Meanwhile, we use a wearable IMU-camera device to assist the moving trajectory estimation. We implement a monocular Visual Odometry with a human walking model to estimate moving trajectories. An Unscented Kalman Filter (UKF) is used to estimate the anchor node location by fusing the RSSI data and moving trajectory. The experiment results show that the proposed method has lower estimation error when locating anchors.
Predicting gene essentiality in Caenorhabditis elegans by feature engineering and machine-learning (2020)

Defining genes that are essential for life has major implications for understanding critical biological processes and mechanisms. Although essential genes have been identified and characterised experimentally using functional genomic tools, it is challenging to predict with confidence such genes from molecular and phenomic data sets using computational methods. Using extensive data sets available for the model organism <i>Caenorhabditis elegans</i>, we constructed here a machine-learning (ML)-based workflow for the prediction of essential genes on a genome-wide scale. We identified strong predictors for such genes and showed that trained ML models consistently achieve highly-accurate classifications. Complementary analyses revealed an association between essential genes and chromosomal location. Our findings reveal that essential genes in <i>C. elegans</i> tend to be located in or near the centre of autosomal chromosomes; are positively correlated with low single nucleotide polymorphim (SNP) densities and epigenetic markers in promoter regions; are involved in protein and nucleotide processing; are transcribed in most cells; are enriched in reproductive tissues or are targets for small RNAs bound to the argonaut CSR-1. Based on these results, we hypothesise an interplay between epigenetic markers and small RNA pathways in the germline, with transcription-based memory; this hypothesis warrants testing. From a technical perspective, further work is needed to evaluate whether the present ML-based approach will be applicable to other metazoans (including <i>Drosophila melanogaster</i>) for which comprehensive data sets (i.e. genomic, transcriptomic, proteomic, variomic, epigenetic and phenomic) are available.
New Nonlinear Tolerant Phase Modulation Based OTDM Scheme with Low Insertion Loss for 80Gb/s Transmission (2002)

We propose an OTDM technique that exhibits 3 dB less insertion loss and 1.6 dB higher tolerance to non-linear effects compared to conventional OTDM transmitter it is compact and flexible in design of duty ratio