gebhart/patrepeval huggingface dataset:
SARS-CoV-2 S2P spike ages through distinct states with altered immunogenicity (2021)

The SARS-CoV-2 spike is the primary target of virus-neutralizing antibodies and critical to the development of effective vaccines against COVID-19. Here, we demonstrate that the prefusion-stabilized two-proline "S2P" spike-widely employed for laboratory work and clinical studies-unfolds when stored at 4 °C, physiological pH, as observed by electron microscopy (EM) and differential scanning calorimetry, but that its trimeric, native-like conformation can be reacquired by low pH treatment. When stored for approximately 1 week, this unfolding does not significantly alter antigenic characteristics; however, longer storage diminishes antibody binding, and month-old spike elicits virtually no neutralization in mice despite inducing high ELISA-binding titers. Cryo-EM structures reveal the folded fraction of spike to decrease with aging; however, its structure remains largely similar, although with varying mobility of the receptor-binding domain. Thus, the SARS-CoV-2 spike is susceptible to unfolding, which affects immunogenicity, highlighting the need to monitor its integrity.
Figure S5 from A Novel Engineered Small Protein for Positron Emission Tomography Imaging of Human Programmed Death Ligand-1: Validation in Mouse Models and Human Cancer Tissues (2023)

Figure S5 from A Novel Engineered Small Protein for Positron Emission Tomography Imaging of Human Programmed Death Ligand-1: Validation in Mouse Models and Human Cancer Tissues
Multiple Model Fitting by Evolutionary Dynamics (2014)

We propose a novel multiple model fitting method based on outlier insensitive evolutionary dynamics, fulfilling several important requirements. Our method automatically identifies a unspecified number of models and is robust to noise and outliers in the data. Furthermore, we are able to handle overlapping models, by allowing that data points are assigned to more than one model. This is implicitly handled during model fitting and not as a post-processing step. Gross outliers are directly identified, by letting some points unassigned. We also introduce a technique, considering nearest neighbor analysis, to significantly reduce computation time, while maintaining model fitting accuracy. We show experiments on real-world and synthetic data, achieving accurate model fitting results also demonstrating an application of plane fitting on a consumer hardware providing RGB-D video streams.
Neoplastic stem cells: A novel therapeutic target in clinical oncology (2006)

Cancer is among the leading causes of morbidity and mortality in the Western world. Despite recent advances, most therapeutic approaches fail to eradicate the entire neoplastic clone. The remaining cells often develop metastasis and/or recurrences and therefore may represent attractive targets of therapy. A new exciting concept in this regard suggests that each neoplasm represents a heterogeneous population of cells that pertain to long-term tumor growth both in vivo in the natural host and in experimental animals. This concept postulates the existence of small fractions of 'tumor stem cells' that exhibit a capacity for self-renewal and unlimited growth and therefore are distinct from their progeny. Based on these hypotheses, the targeting of neoplastic stem cells is considered indispensable for eradication of the entire clone and for the development of curative treatment approaches. However, tumor stem cells often may be quiescent cells and may express a different profile of targets compared with 'more mature' tumor cells. Therefore, current efforts have attempted to characterize target expression profiles in cancer stem cells in various malignancies. In the this review, the authors have provided a brief summary of the current knowledge of neoplastic stem cells and the application of respective concepts in translational oncology with the ultimate objective of improving anticancer therapy.
The influence of mechanical rubbing on the field-effect mobility in polyhexylthiophene (2003)

This paper reports on improvements of the field-effect mobility in regioregular head-to-tail coupled poly(3-hexylthiophene) based transistors by mechanically induced alignment of polymer chains in the active layer. It is demonstrated that mechanical rubbing perpendicular to the source drain contacts can increase the field-effect mobility up to 800% whereas rubbing parallel to the source drain contacts results in a reduced mobility. The polymer alignment is thereby deduced from optically polarized transmission spectroscopy on polymer-coated quartz glass substrates and is shown to directly correlate with the electrical behavior of a bottom-gate field-effect transistor. The influence of layer thickness on rubbing is investigated and it is shown that annealing after mechanical rubbing at high temperature can further increase the alignment. Differences between thick drop-cast and thin spin-coated films are explained in terms of different solvent evaporation rates, allowing the material to order to a different degree. This interpretation is deduced from characteristic optical and electrical features of the differently prepared poly(3-hexylthiophene) films.
Designers want proofs - but show me the money (2005)

This thesis shows that designers definitely do want proofs. The first author saw ample evidence of that at Motorola, where he managed a verification CAD group, and at Synopsys, where he was involved in verification tools, customers, and in verification projects with our DesignWare component groups. Our talk will discuss some success we had with our DesignWare team.
Versatile Preparation of Silica Nanocapsules for Biomedical Applications (2020)

Abstract Core–shell nanocapsules are receiving increasing interest for drug delivery applications. Silica nanocapsules have been the focus of intensive studies due to their biocompatibility, versatile silica chemistry, and tunable porosity. However, a versatile one‐step preparation of silica nanocapsules with well‐defined core–shell structure, tunable size, flexible interior loading, and tailored shell composition, permeability, and surface functionalization for site‐specific drug release and therapeutic tracking remains a challenge. Herein, an interfacially confined sol–gel process in miniemulsion for the one‐step versatile preparation of functional silica nanocapsules is developed. Uniform nanocapsules with diameters from 60 to 400 nm are obtained and a large variety of hydrophobic liquids are encapsulated in the core. When solvents with low boiling point are loaded, subsequent solvent evaporation converts the initially hydrophobic cavity into an aqueous environment. Stimuli‐responsive permeability of nanocapsules is programmed by introducing disulfide or tetrasulfide bonds in the shell. Selective and sustained release of dexamethasone in response to glutathione tripeptide for over 10 d is achieved. Fluorescence labeling of the silica shell and magnetic loading in the internal cavity enable therapeutic tracking of nanocapsules by fluorescence and electron microscopies. Thus, silica nanocapsules represent a promising theranostic nanoplatform for targeted drug delivery applications.
Syntheses of new benzoxazole derivatives (2011)

Abstract 2‐(Arylidene)cyanomethylbenzoxazoles have been prepared in water from benzoxazole‐2‐ylacetonitriles. Using multi‐component reactions, a variety of heterocycles containing benzoxazole and nitrile functionality has been prepared. J. Heterocyclic Chem., (2011).
Hypoxia-activated anticancer drugs (2005)

AbstractWhilst hypoxia is increasingly recognised as a limiting factor in the successful treatment of solid tumours by conventional radiotherapy and chemotherapy, its unique occurrence in such tumours is also viewed as offering the possibility of selective chemotherapy. Prodrugs designed to be selectively activated in hypoxic tissue by oxygen-sensitive reductases have been a common design motif for some time, and include such chemical classes as quinones, nitro-aromatics, aliphatic and heteroaromatic N-oxides, and transition metal complexes. This review discusses the mechanistic aspects of the activation of such prodrugs and the key overall properties needed. Prominent among the latter properties are efficient extravascular diffusion of the prodrug to the tumour, and back-diffusion of the activated drug (effector) in the tumour. The appropriate design of clinical trials for these prodrugs is also important. Exciting new mechanisms for prodrug research include activation by therapeutic radiation and the use of hypoxia-selective gene therapy vectors, such as Clostridia.Keywords:: cancer chemotherapydrug designdrug diffusionhypoxiahypoxia-activated prodrug
Material ITQ-45, su procedimiento de obtención y su uso (2012)

En la presente invención, se presenta un material&#13;\ncristalino microporoso y su procedimiento de&#13;\npreparación, que tiene una composición:&#13;\nXXP3 : ZZ02 : Y Y02&#13;\nen la que X es un elemento trivalente tal como Al, B,&#13;\nFe, In, Ga, Cr, o mezclas de éstos, donde (y+z)/x&#13;\npuede tomar valores entre 9 e infinito; Z corresponde&#13;\na un elemento tetravalente seleccionado entre Si y Ge&#13;\no mezclas de ellos; Y corresponde a corresponde a&#13;\nun elemento tetravalente tal como Ti, Sn, Zr, V o&#13;\nmezclas de ellos, donde z/y puede tomar valores&#13;\nentre 10 e infinito.&#13;\nA1
Cleaved high molecular weight kininogen binds directly to the integrin CD11b/CD18 (Mac-1) and blocks adhesion to fibrinogen and ICAM-1 (2000)

High molecular weight kininogen (HK) and its cleaved form (HKa) have been shown to bind to neutrophils. Based on studies using monoclonal antibodies (mAbs), we postulated that CD11b/CD18 (Mac-1) might be the receptor on the neutrophils for binding to HK/HKa. However, the direct interaction of HK/HKa and Mac-1 had not been demonstrated. We therefore transfected HEK 293 cells with human Mac-1. Cell binding assays using fluorescein isothiocyanate-labeled HKa showed increased binding to the Mac-1 transfected cells compared with the control transfected cells. The binding was specific because unlabeled HKa, Mac-1–specific antibody, and fibrinogen can inhibit the binding of biotin-HKa to Mac-1 transfected cells. HKa bound to Mac-1 transfected cells (20 000 molecules/cell) with a Kd = 62 nmol/L. To demonstrate directly the formation of a complex between HKa and Mac-1, we examined the interaction of HKa and purified Mac-1 in a cell-free system using an IAsys resonant mirror optical biosensor. The association and dissociation rate constants (kon and koff, respectively) were determined, and they yielded a dissociation constant (Kd) of 3.2×10−9mol/L. The functional significance of direct interaction of HKa to Mac-1 was investigated by examining the effect of HKa on cellular adhesion to fibrinogen and intercellular adhesion molecule-1 (ICAM-1), molecules abundant in the injured vessel wall. HKa blocked the adhesion of Mac-1 transfected cells to fibrinogen and ICAM-1 in a dose-dependent manner. Thus, HKa may interrupt Mac-1–mediated cell–extracellular matrix and cell–cell adhesive interactions and may therefore influence the recruitment of circulating neutrophils/monocytes to sites of vessel injury.
Photonically Enabled Metasurfaces for 5G (2020)

An optically reconfigurable metasurface is proposed for use as an antenna radiator at 28 GHz. The metasurface is transmittive and is fed through a horn antenna connected to a multi-core-fibre link, significantly reducing the losses compared to a mm-wave feed. In the proposed system, radiated beams will be photonically controlled using a spatial light modulator, thus not requiring the use of optical fibers. For optical reconfigurability the switching component will be based on silicon instead of photodiodes and varactors, eliminating the need for an active biasing network.
Outage probability of multi-cellular MIMO systems in Rayleigh fading (2004)

We analyze the performance of multi-cellular MIMO systems in Rayleigh fading. Consistent with practical scenarios, we assume two types of interference: intracell interference from users within the same cell as the desired user and intercell interference from users in other cells. We derive a compact closed form expression for the outage probability of such a system in the form of finite sums. The expression is easily computable and allows for a simpler and faster study of various MIMO configurations. An interesting outcome of the analysis is that using multiple antennas on the receiver side results in better performance since transmit diversity does not combat interference from same cell users.
Are fMRI event-related response constant in time? A model selection answer (2006)

An accurate estimation of the hemodynamic response function (HRF) in functional magnetic resonance imaging (fMRI) is crucial for a precise spatial and temporal estimate of the underlying neuronal processes. Recent works have proposed non-parametric estimation of the HRF under the hypotheses of linearity and stationarity in time. Biological literature suggests, however, that response magnitude may vary with attention or ongoing activity. We therefore test a more flexible model that allows for the variation of the magnitude of the HRF with time in a maximum likelihood framework. Under this model, the magnitude of the HRF evoked by a single event may vary across occurrences of the same type of event. This model is tested against a simpler model with a fixed magnitude using information theory. We develop a standard EM algorithm to identify the event magnitudes and the HRF. We test this hypothesis on a series of 32 regions (4 ROIS on eight subjects) of interest and find that the more flexible model is better than the usual model in most cases. The important implications for the analysis of fMRI time series for event-related neuroimaging experiments are discussed.
Imaging of the Elbow: Muscle and Tendon Injuries (2010)

Elbow injuries can be divided into lateral, medial, anterior, and posterior compartments. Each compartment has specific anatomical landmarks and muscle-tendon units that are injured in a specific location and pattern related to the mechanism of injury. Magnetic resonance imaging provides superior soft tissue visualization and assessment of these injuries. Muscle and tendon injuries that occur in each of the four compartments vary in accordance to their population and associated activities. These injuries range from tendinopathy to complete tears that may be a result of repetitive microtrauma, an acute traumatic event, or a combination of the two. Common pathomechanisms of these injuries are discussed including basic treatment options. The treatment options also vary in accordance to the compartment involved and the severity of the injury. The treatment options range from conservative measures such as observation with activity modification to operative measures including debridement and repair.
114 Role of Vaccine-induced V2 Antibodies in Protection From HIV Infection of Recipients in the RV144 Clinical Vaccine Trial (2012)

Objective Determine the role of V2 antibodies (Abs) in protecting vaccinees from HIV infection after immunization with ALVAC/HIV and clade E and B recombinant gp120 (RV144 vaccine regimen). ELISA reactivity to a V1V2-gp70 fusion protein and a cyclic V2 peptide was assessed using coded plasma specimens from RV144 participants. Results showed that Ab responses were divided into tertiles (low, medium and high). Vaccinees with a high level of Abs to V1V2-gp70 had a lower rate of HIV infection than did those with a low level of Abs. Multivariate logistic regression analysis showed an estimated 71% reduction in the infecton rate for vaccinees with high vs vaccinees with low Ab responses to V1V2-gp70 (P = 0.02). Similarly, compared to the entire placebo group that was HIV- at 26 weeks, the estimated Vaccine Efficacy (VE) was 3% (P = 0.91) for subjects with a low V1V2 Ab response, while the estimated VE was 58% (P = 0.02) for vaccinees with high V1V2 Abs. The Abs measured by this assay appear to be specific for V2 because no V1 Abs were detected, and epitope mapping data suggest that the epitope recognized by vaccinees' Abs target the mid-loop region of V2. There was no statistically significant correlation between infection rate and Abs reactive with a cyclic V2 peptide containing the entire V2 loop of the clade E A244 strain. In the primary case control analysis the Ab response to V1V2-gp70 was statistically significantly inversely correlated with infection. While secondary analyses suggest that other immunologic responses (including Abs to other epitopes and cellular responses) may also play a role in protection, the data most strongly support the hypothesis that V2 Abs are important for protection.
InGaAs Membrane Waveguide: A Promising Platform for Monolithic Integrated Mid-Infrared Optical Gas Sensor (2020)

Mid-infrared (mid-IR) absorption spectroscopy based on integrated photonic circuits has shown great promise in trace-gas sensing applications in which the mid-IR radiation directly interacts with the targeted analyte. In this paper, considering monolithic integrated circuits with quantum cascade lasers (QCLs) and quantum cascade detectors (QCDs), the InGaAs-InP platform is chosen to fabricate passive waveguide gas sensing devices. Fully suspended InGaAs waveguide devices with holey photonic crystal waveguides (HPCWs) and subwavelength grating cladding waveguides (SWWs) are designed and fabricated for mid-infrared sensing at λ = 6.15 μm in the low-index contrast InGaAs-InP platform. We experimentally detect 5 ppm ammonia with a 1 mm long suspended HPCW and separately with a 3 mm long suspended SWW, with propagation losses of 39.1 and 4.1 dB/cm, respectively. Furthermore, based on the Beer-Lambert infrared absorption law and the experimental results of discrete components, we estimated the minimum detectable gas concentration of 84 ppb from a QCL/QCD integrated SWW sensor. To the best of our knowledge, this is the first demonstration of suspended InGaAs membrane waveguides in the InGaAs-InP platform at such a long wavelength with gas sensing results. Also, this result emphasizes the advantage of SWWs to reduce the total transmission loss and the size of the fully integrated device's footprint by virtue of its low propagation loss and TM mode compatibility in comparison to HPCWs. This study enables the possibility of monolithic integration of quantum cascade devices with TM polarized characteristics and passive waveguide sensing devices for on-chip mid-IR absorption spectroscopy.
QUALITY OF LIFE (QOL) FIVE YEARS AFTER ANTERIOR CRUCIATE LIGAMENT (ACL) RECONSTRUCTION (2011)

Introduction: The International Knee Documentation Committee (IKDC) recommends use of the IKDC score to document subjective, objective and functional ACL outcome. To further improve knowledge concerning patient QOL after ACL reconstruction, an additional specific QOL questionnaire was developed. Using a combination of univariate and multivariate analysis the patient factors and surgical factors that influenced QOL 5- years after ACL reconstruction were determined. Materials: 500 patients operated on for arthroscopic ACL reconstruction at our institution between 1997 and 2001 were prospectively enrolled. Patient psychosocial profile, sport expectations, knee exam, type of graft, associated lesion, type of anesthesia, complications, IKDC, KT 2000 at 6 moths, 1 year and 2 years were recorded. At five years, patients were asked to complete a 5-subscale validated QOL questionnaire for ACL deficiency. A multivariate analysis was performed to identify the factors influencing 5-year QOL. Results: 203 patients completed the 5-years QOL questionnaire. Responders did not statistically differ from non responders. Patient subjective factors such as: patient expectations, pre-operative symptoms, work-school concerns, recreations concerns, social and psycho-social concerns were significantly (p Discussion: In this large prospective study, most of the factors influencing the 5-year QOL results after ACL reconstruction were related to patient expectations, psycho-social, symptoms and work-sport concerns. The presence of a meniscus tear and greater KT 2000 laxity also contributed to poorer 5-year QOL results.
Comparison of Amino Acid Helix Propensities (s-values) in Different Experimental Systems (1993)

Three years ago, work started on measuring the α-helix propensities of the amino acids in different short peptide systems (1 - 8). As in earlier experiments with synthetic polypeptides (9,10), the helix propensity of an amino acid is taken as its s-value, where s is the propagation parameter of the Zimm-Bragg theory of α-helix formation (11). Although the results found with short peptides are still preliminary, the helix propensities are evidently different from those measured earlier with random-sequence polypeptides by the "host-guest" technique (9,10). The rank order of helix propensities in the different peptide systems is similar; however, one consistent set of s-values has not been produced. Here we compare the results of these substitution experiments and comment on possible reasons for the disagreements. Experimental Systems for Measurement of Helix Propensities The major differences between the short peptide and host-guest systems are in the sizes of the molecules studied
Multidisciplinary assessment of the Abbott BinaxNOW SARS-CoV-2 point-of-care antigen test in the context of emerging viral variants and self-administration (2021)

While there has been significant progress in the development of rapid COVID-19 diagnostics, as the pandemic unfolds, new challenges have emerged, including whether these technologies can reliably detect the more infectious variants of concern and be viably deployed in non-clinical settings as "self-tests". Multidisciplinary evaluation of the Abbott BinaxNOW COVID-19 Ag Card (BinaxNOW, a widely used rapid antigen test, included limit of detection, variant detection, test performance across different age-groups, and usability with self/caregiver-administration. While BinaxNOW detected the highly infectious variants, B.1.1.7 (Alpha) first identified in the UK, B.1.351 (Beta) first identified in South Africa, P.1 (Gamma) first identified in Brazil, B.1.617.2 (Delta) first identified in India and B.1.2, a non-VOC, test sensitivity decreased with decreasing viral loads. Moreover, BinaxNOW sensitivity trended lower when devices were performed by patients/caregivers themselves compared to trained clinical staff, despite universally high usability assessments following self/caregiver-administration among different age groups. Overall, these data indicate that while BinaxNOW accurately detects the new viral variants, as rapid COVID-19 tests enter the home, their already lower sensitivities compared to RT-PCR may decrease even more due to user error.
Lightweight CMP Profile (2020)

The goal of this document is to facilitate interoperability and
automation by profiling the Certificate Management Protocol (CMP)
version 2 and the related Certificate Request Message Format (CRMF)
version 2 and the HTTP Transfer for the Certificate Management
Protocol. It specifies a subset of CMP and CRMF focusing on typical
uses cases relevant for managing certificates of devices in many
industrial and IoT scenarios. To limit the overhead of certificate
management for more constrained devices only the most crucial types of
transactions are specified as mandatory. To foster interoperability
also in more complex scenarios, other types of transactions are
specified as recommended or optional.