gebhart/patrepeval huggingface dataset:
789 Generation of a Bicycle NK-TICA™, a novel NK cell engaging molecule to enhance targeted tumor cytotoxicity (2021)

<h3>Background</h3> Natural killer (NK) cells are immune cells that can detect and eliminate tumor cells and bridge innate to adaptive immune responses. Tumor specific activation of NK cells is thus an area of active investigation in immune oncology, but to date has relied on complex biologic modalities (e.g., antibodies, fusion proteins, or cell therapies), each of which has inherent disadvantages in this application. Thus, alternative approaches are warranted. Bicycle® are small (ca. 1.5 kDa), chemically synthetic, structurally constrained peptides discovered via phage display and optimized using structure-driven design and medicinal chemistry approaches. We have now applied this technology to identify Bicycles that bind specifically to the key activating receptors, NKp46 and CD16a. When chemically coupled to tumor antigen binding Bicycles this results in highly potent, antigen-dependent receptor activation and NK cell activation. We term this new class of fully synthetic molecules Bicycle® natural killer- tumor-targeted immune cell agonists (NK-TICAs™) and we will describe their discovery and evaluation in this presentation. <h3>Methods</h3> Using our unique phage display screening platform, we have identified high affinity, selective binders to NKp46 and CD16a. By conjugating the Bicycle® NK cell-engaging binders to a model tumor antigen EphA2-binding Bicycle®, we have developed a bifunctional Bicycle NK-TICA™ molecule. In in vitro functional assays, we evaluated the ability of the Bicycle NK-TICAs™ to induce NK cell activation as well as cell-mediated cytotoxicity and cytokine production in NK-tumor co-culture assays. <h3>Results</h3> We have developed a novel modular compound with high affinity and selectivity to NK cell receptors with specific tumor targeting capability. We demonstrate potent, selective binding of our Bicycles to receptor-expressing cells and the capability of the bifunctional molecule to induce NK cell function. With Bicycle9s novel NK-TICA™ compound, we demonstrate engagement of NK cells, specific activation and function of NK cells, and enhanced EphA2-expressing tumor cytotoxicity, in a dose dependent manner. <h3>Conclusions</h3> Bicycle NK-TICAs™ are novel therapeutic agents capable of enhancing the landscape of immune oncology. We hypothesize that utilization of Bicycle NK-TICA™ as a multifunctional immune cell engager will promote modulation of NK cells, and infiltration and anti-tumor activity of NK cells in solid tumors. The data presented here provide initial proof of concept for application of the Bicycle technology to drive NK cell-mediated tumor immunity.
Acoustic Radiation Force: A Review of Four Mechanisms for Biomedical Applications (2021)

Radiation force is a universal phenomenon in any wave motion where the wave energy produces a static or transient force on the propagation medium. The theory of acoustic radiation force (ARF) dates back to the early 19th century. In recent years, there has been an increasing interest in the biomedical applications of ARF. Following a brief history of ARF, this article describes a concise theory of ARF under four physical mechanisms of radiation force generation in tissue-like media. These mechanisms are primarily based on the dissipation of acoustic energy of propagating waves, the reflection of the incident wave, gradients of the compressional wave speeds, and the spatial variations of energy density in standing acoustic waves. Examples describing some of the practical applications of ARF under each mechanism are presented. This article concludes with a discussion on selected ideas for potential future applications of ARF in biomedicine.
The hidden potential of small synthetic molecules and peptides as affinity ligands for bioseparations (2013)

While extensively used as drugs, small synthetic molecules have not yet been widely applied in the industry as affinity ligands for the purification of biopharmaceuticals. Yet, a substantial amount of published research indicates that synthetic ligands, such as triazine scaffolds, amino acids, and peptides show a great deal of promise for becoming the next generation affinity ligands for bioseparations. In this review, we present a comprehensive account on small synthetic ligands, from triazine dyes to the most recent polycyclic peptide ligands, selected for targeting high-value biopharmaceuticals, such as immunoglobulins, blood factors and therapeutic enzymes. These ligands could play a significant role in improving downstream processing and helping the bioprocessing industry overcome the urgent issues of costs and availability posed by growing economies on the global pharmaceutical market.
ChemInform Abstract: Synthesis and Pharmacological Profile of a Series of 2,5‐Substituted‐N,N‐dimethyltryptamine Derivatives (I) as Novel Antagonists for the Vascular 5‐HT1B‐Like Receptor. (2000)

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.
Chemocavity: Specific Concavity in Protein Reserved for the Binding of Biologically Functional Small Molecules (2008)

The idea that there should be a specific site on a protein for a particular functional small molecule is widespread. It is, however, usually not so easy to understand what characteristics of the site determine the binding ability of the functional small molecule. We have focused on the concurrence rate of the 20 standard amino acids at such binding sites. In order to correlate the concurrence rate and the specific binding site, we have analyzed high-quality X-ray structures of complexes between proteins and small molecules. A novel index characterizing the binding site based on the concurrency rate has been introduced. Using this index we have identified that there is a specific concavity designated as a chemocavity where a specific group of small molecules, i.e., canonical molecular group, is highly inclined to be bound. This study has demonstrated that a chemocavity is reserved for a specific canonical molecular group, and the prevalent idea has been confirmed.
Dynamic M2M device attachment and redirection in virtual home gateway environments (2016)

Virtualized access to M2M (Machine-to-Machine) devices can offer to operators various benefits in terms of hardware and management costs. However, it is often impeded by the inability to efficiently handle the traffic from the devices towards servers that are appropriate to serve as virtual hosts for the given devices. In this paper we present a solution which can be applied in a virtual Home Gateway environment and is based on (i) encoding information about the device and its virtualization technology into TCP/IP packet headers, (ii) selecting virtual hosts based on their compatibility to certain virtualization technologies, and (iii) using Software-defined Networking to make this virtual host selection at the network level in a dynamic manner. Compared to the main alternatives, which are based either on Deep Packet Inspection or on homogeneous servers, our solution is the only one that combines a tailored and non-costly server infrastructure with low networking complexity.
ChemInform Abstract: Synthesis of 4‐Oxo‐4,7‐dihydrofuro[2,3‐b]pyridine‐5‐carboxamides with Broad‐Spectrum Human Herpesvirus Polymerase Inhibition. (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 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.
Mitochondrial DNA as a Biomarker for Acute Central Serous Chorioretinopathy: A Case-Control Study (2022)

We showed serum mtDNA and HMGB1 level elevation and its relation to the clinical activities of CSC, indicating that serum mtDNA and HMGB1 could serve as biomarkers for the acute phase of the disease. The use of these biomarkers makes it possible to predict disease onset and determine disease severity.
PMUs performance testing and evaluation in China (2014)

Phasor measurement units (PMU) are taking an increasingly important role in power system dynamic security monitoring and control. However, traditional Discrete Fourier Transforms (DFT) used by PMUs cannot obtain accurate phasor measurements during frequency excursion and transient events, being limited by its static phasor model. Therefore, the performance of PMUs under both static and dynamic conditions is fundamental. In this paper, the averaging effect of DFT is explored, which results in the measurement errors of PMUs under dynamic conditions. Then, a PMU testing system is introduced. With that, a centralized test aiming to improve the performance of M-class PMUs in China is accomplished by evaluating the PMUs from seven manufactures in China under static and dynamic conditions. The testing results show that the PMUs under test can satisfy most requirements in the standard by improving their algorithms. The testing data is analyzed to demonstrate the correctness of the theoretical derivation of the averaging effect of DFT.
29 Si MAS NMR Study of Dicalcium Silicate: The Structural Influence of Sulfate and Alumina Stabilizers (1995)

The effect on β‐C 2 S of two stabilizing agents, calcium sulfate and alumina, has been investigated using high‐resolution 29 Si solid state NMR spectroscopy. Syntheses were achieved via the gel route, wet or dry processes. Room‐temperature NMR spectra characteristics were analyzed as a function of the sintering temperature. The incorporation of Al 3+ and S 6+ ions, which finds expression in a noticeable line broadening, is shown to be effective above 1200°C. The 29 Si chemical shift is unchanged upon doping, suggesting a mean SiO 4 tetrahedra geometry identical to that in pure β‐C 2 S. General trends on the structure adopted by C 2 S upon Al 3+ and S 6+ doping are also discussed.
Automation of Cloud Node Installation for Testing and Scalable Provisioning (2017)

Motivated by the lack of automated provisioning and testing tools for physical systems in modern cloud infrastructures, we developed a toolset to automate the installation of a commercial platform virtualization software: the IBM PowerVM NovaLink software. This toolset automates numerous manual installation steps and post-installation tests. The toolset uses Python programs to prepare the target system and to generate installation-configuration files through interaction with a web-interface of the POWER firmware. Expect scripts are used to drive the rest of the installation via interactions through a remote text console. With different scenarios of applying this automation toolset, we demonstrate its use in driving regression testing for the development of the NovaLink installer in a DevOps environment. Furthermore, we discuss its use in provisioning a large number of IBM POWER systems to be ready for cloud management software.
An alternative information web for visually impaired users in developing countries (2008)

Websites in World Wide Web are primarily meant for visual consumption. Moreover, the wide variety of visual controls available make it harder to interpret the websites with screen readers. This problem of accessing information and services on the web escalates even further for visually impaired in developing regions since most are either semi-literate/illiterate or cannot afford computers and high-end phones with screen reading capability.In this paper, we present an alternate platform -- the World Wide Telecom Web (WWTW). WWTW is already being successfully deployed as a network of VoiceSites that can be created and accessed by a voice interaction over an ordinary phone. WWTW presents a whole new set of opportunities for delivering information and services to the visually impaired. We present a preliminary user study that leads us towards the belief that the Telecom Web can be the mainstream Web for blind users.
Effects of Introduction of InGaN Quantum Structures on Structural and Optical Properties of InGaN Nanocolumns (2017)

We systematically investigate and compare the structural and optical properties of InGaN nanocolumns (NCs) and InGaN/GaN single quantum structures (SQSs) fabricated on top of GaN NCs as functions of the GaN column diameter. Each InGaN/GaN SQS comprises an In‐rich InGaN single quantum dot at the center of a semipolar Ga‐rich InGaN single quantum well. The InGaN NCs and InGaN/GaN SQSs qualitatively exhibit similar optical properties. However, the specific diameters at which the photoluminescence spectra change from single‐peak emission patterns to double‐peak patterns are different. Based on scanning transmission electron microscopy observations of the InGaN layers formed on the GaN NCs with different growth times, a model for the growth of InGaN on GaN NCs is proposed and the origin of the difference in the specific diameters is elucidated. Finally, when QSs are introduced to the InGaN‐based NCs, the radiative recombination probability increases while the nonradiative and surface recombination probabilities decrease, thus leading to high emission efficiency.
Trehalose Improves Human Fibroblast Deficits in a New CHIP-Mutation Related Ataxia (2014)

In this work we investigate the role of CHIP in a new CHIP-mutation related ataxia and the therapeutic potential of trehalose. The patient's fibroblasts with a new form of hereditary ataxia, related to STUB1 gene (CHIP) mutations, and three age and sex-matched controls were treated with epoxomicin and trehalose. The effects on cell death, protein misfolding and proteostasis were evaluated. Recent studies have revealed that mutations in STUB-1 gene lead to a growing list of molecular defects as deregulation of protein quality, inhibition of proteasome, cell death, decreased autophagy and alteration in CHIP and HSP70 levels. In this CHIP-mutant patient fibroblasts the inhibition of proteasome with epoxomicin induced severe pathophysiological age-associated changes, cell death and protein ubiquitination. Additionally, treatment with epoxomicin produced a dose-dependent increase in the number of cleaved caspase-3 positive cells. However, co-treatment with trehalose, a disaccharide of glucose present in a wide variety of organisms and known as a autophagy enhancer, reduced these pathological events. Trehalose application also increased CHIP and HSP70 expression and GSH free radical levels. Furthermore, trehalose augmented macro and chaperone mediated autophagy (CMA), rising the levels of LC3, LAMP2, CD63 and increasing the expression of Beclin-1 and Atg5-Atg12. Trehalose treatment in addition increased the percentage of immunoreactive cells to HSC70 and LAMP2 and reduced the autophagic substrate, p62. Although this is an individual case based on only one patient and the statistical comparisons are not valid between controls and patient, the low variability among controls and the obvious differences with this patient allow us to conclude that trehalose, through its autophagy activation capacity, anti-aggregation properties, anti-oxidative effects and lack of toxicity, could be very promising for the treatment of CHIP-mutation related ataxia, and possibly a wide spectrum of neurodegenerative disorders related to protein disconformation.
Detailed genetic and physical mapping of tumor suppressor loci on chromosome 3p in ovarian cancer. (1999)

Hemizygosity and homozygosity mapping studies show that many common sporadic cancers including lung, breast, kidney, cervical, ovarian, and head and neck cancer display deletions on the short arm of chromosome 3. For ovarian cancer, monochromosomal transfer suppression studies have identified three candidate regions for chromosome 3p ovarian cancer tumor suppressor genes (OCTSGs). To accurately map OCTSG candidate regions, we analyzed 70 ovarian tumors for loss of heterozygosity (LOH) at 20 loci on chromosome 3p that were selected to target those regions proposed to contain tumor suppressor genes for common sporadic cancers. All samples were informative for at least five markers. In 33 (52%) tumors without microsatellite instability, LOH was observed for at least one 3p marker. Analysis of 27 ovarian tumors demonstrating both loss and retention of 3p markers enabled us to define four nonoverlapping minimal deletion regions (OCLOHRs): (a) OCLOHR-1 mapped distal to D3S3591 at 3p25-26; (b) OCLOHR-2 mapped between D3S1317 and D3S1259 at 3p24-25; (c) OCLOHR-3 mapped between D3S1300 and D3S1284, an area that includes the FHIT locus at 3p14.2; and (d) OCLOHR-4 mapped between D3S1284 and D3S1274 at 3p12-13, a region known to contain overlapping homozygous deletions in lung and breast tumor cell lines. However, microsatellite markers from the chromosome 3p21.3 interval homozygously deleted in lung cancer cell lines did not identify a distinct OCLOHR. The frequency and extent of 3p LOH correlated with tumor stage such that LOH at two or more OCLOHRs was present in 53% (16 of 30) of stage III tumors but only 26% (5 of 19) of stage I/II tumors (P = 0.08). To determine the relationship between the OCLOHRs and the three candidate ovarian cancer suppression regions (OCSRs) identified previously by monochromosome transfer studies, we performed detailed genetic and physical mapping studies to define the extent of the three candidate OCSRs and to establish YAC contigs covering each region. OCSR-A at 3p25-26 and OCSR-B at 3p24 were shown to overlap with OCLOHR-1 and OCLOHR-2, respectively, providing further evidence for OCTSGs in these regions. We also show that OCSR-C overlaps with a locus at 3p21.3 previously implicated in lung and breast cancer.
An arm exoskeleton system for teleoperation and virtual environments applications (2002)

The control of exploratory and manipulative procedures in teleoperation and virtual environments requires the availability of adequate advanced interfaces capable not only of recording the movements of the human hands and arms, but also of replicating sensations of contact and collisions. In this paper the problem of replicating external forces acting against the remote/virtual arm is addressed. The design of an arm exoskeleton system developed in the authors' laboratory is presented. The exoskeleton consists of a 7 DOF actuated and sensorized mechanical structure wrapping up completely the human arm and directly supported by the shoulders and the trunk of the human operator. Emphasis is given to the implemented control procedures and to the description of the transputer-based control architecture.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
The reconstruction and use of Roman weaponry in the second century BC (2000)

The color Doppler twinkling artifact manifests as a rapidly changing mixture of red and blue colors behind strongly reflective structures. The twinkling artifact occurs behind diseased cardiac valves, although the phenomenon is not well described. This study sought to determine the presence of the color Doppler twinkling artifact in calcified cardiac valves in vitro using soft tissue radiography for reference. Seventeen specimens of diseased cardiac valves from patients undergoing valve replacement surgery were studied. The overall sensitivity and specificity for the detection of calcifications using the presence of the twinkling artifact were 66.7% and 81.8%, respectively. If valves with only microcalcifications or smooth calcifications were eliminated from the analysis, all (100%) of the three valves with irregular macrocalcifications exhibited the twinkling artifact. It is important to recognize this artifact because it may lead to misdiagnosis of vascular flow in echocardiography.
“What If We Get Sick?”: Spanish Adaptation and Validation of the Fear of Illness and Virus Evaluation Scale in a Non-clinical Sample Exposed to the COVID-19 Pandemic (2021)

Distinct sources of stress have emerged during the COVID-19 pandemic. Particularly, fear is expected to generate significant psychological burden on individuals and influence on either unsafe behavior that may hinder recovery efforts or virus-mitigating behaviors. However, little is known about the properties of measures to capture them in research and clinical settings. To resolve this gap, we evaluated the psychometric properties of a novel measure of fear of illness and viruses and tested its predictive value for future development of distress. We extracted a random sample of 450 Chilean adult participants from a large cross-sectional survey panel and invited to participate in this intensive longitudinal study for 35 days. Of these, 163 ended up enrolling in the study after the demanding nature of the measurement schedule was clearly explained to them. For this final sample, we calculated different Confirmatory Factor Analyses (CFA) to evaluate the preliminary proposed structure for the instrument. Complementarily, we conducted a content analysis of the items to qualitatively extract its latent structure, which was also subject to empirical test via CFA. Results indicated that the original structure did not fit the data well; however, the new proposed structure based on the content analysis did. Overall, the modified instrument showed good reliability through all subscales both by its internal consistency with Cronbach's alphas ranging from 0.814 to 0.913, and with test-retest correlations ranging from 0.715 to 0.804. Regarding its convergent validity, individuals who scored higher in fears tended to also score higher in depressive and posttraumatic stress symptoms at baseline. Furthermore, higher fears at baseline predicted a higher score in posttraumatic stress symptomatology 7 days later. These results provide evidence for the validity, reliability, and predictive performance of the scale. As the scale is free and multidimensional potentially not circumscribed to COVID-19, it might work as a step toward understanding the psychological impact of current and future pandemics, or further life-threatening health situations of similar characteristics. Limitations, practical implications, and future directions for research are discussed.
Highlights on interesting findings of High Modulus Asphalt Concrete (HMAC/EME) for cold regions in cooperative research project (2020)

This paper presents a methodology to support growth and implementation of a new asphalt mix, such as high modulus asphalt concretes (HMAC) for cold regions. This requires laboratory studies (fatigue, E* and sensitivity) and elaboration of trial sections with several steps. Even though that different fatigue test methods were used in this project (tension-compression and 2 points bending), similar Wohler’s law parameters were obtained with referring to a discriminant failure criterion. Overall, the laboratory investigation shows good to excellent thermomechanical properties of HMAC tested as regards stiffness, fatigue, low temperature, and rutting resistances. Moreover, the ongoing sensitivity study shows that HMAC mixes make with bitumen and filler dosage fluctuations in accordance to regulation are not more sensitive than usual HMA.