gebhart/patrepeval huggingface dataset:
Nanobodies from camelid mice and llamas neutralize SARS-CoV-2 variants (2021)

Since the start of the COVID-19 pandemic, SARS-CoV-2 has caused millions of deaths worldwide. Although a number of vaccines have been deployed, the continual evolution of the receptor-binding domain (RBD) of the virus has challenged their efficacy. In particular, the emerging variants B.1.1.7, B.1.351 and P.1 (first detected in the UK, South Africa and Brazil, respectively) have compromised the efficacy of sera from patients who have recovered from COVID-19 and immunotherapies that have received emergency use authorization<sup>1-3</sup>. One potential alternative to avert viral escape is the use of camelid VHHs (variable heavy chain domains of heavy chain antibody (also known as nanobodies)), which can recognize epitopes that are often inaccessible to conventional antibodies<sup>4</sup>. Here, we isolate anti-RBD nanobodies from llamas and from mice that we engineered to produce VHHs cloned from alpacas, dromedaries and Bactrian camels. We identified two groups of highly neutralizing nanobodies. Group 1 circumvents antigenic drift by recognizing an RBD region that is highly conserved in coronaviruses but rarely targeted by human antibodies. Group 2 is almost exclusively focused to the RBD-ACE2 interface and does not neutralize SARS-CoV-2 variants that carry E484K or N501Y substitutions. However, nanobodies in group 2 retain full neutralization activity against these variants when expressed as homotrimers, and-to our knowledge-rival the most potent antibodies against SARS-CoV-2 that have been produced to date. These findings suggest that multivalent nanobodies overcome SARS-CoV-2 mutations through two separate mechanisms: enhanced avidity for the ACE2-binding domain and recognition of conserved epitopes that are largely inaccessible to human antibodies. Therefore, although new SARS-CoV-2 mutants will continue to emerge, nanobodies represent promising tools to prevent COVID-19 mortality when vaccines are compromised.
A Pilot Trial of Tumor Lysate-Loaded Dendritic Cells for the Treatment of Metastatic Renal Cell Carcinoma (2003)

Cultured tumor lysate-loaded dendritic cells (TuLy-DC) have been demonstrated in vitro to stimulate potent immune modulations and generate significant antitumor response. We report the results of a pilot trial of TuLy-DC vaccine for patients with metastatic renal cell carcinoma (mRCC). Fourteen mRCC patients underwent nephrectomy to obtain autologous TuLy prepared by subjecting tumor cells to 3 freeze/thaw cycles. Dendritic cells were generated from peripheral blood CD14+ precursors cultured in the presence of GM-CSF, IL-4, and 10% autologous serum. Patients received one vaccination of TuLy alone as an immunologic control, followed by 3 weekly vaccinations of DC-TuLy injected intradermally in the midaxillary region. Peripheral blood lymphocytes were collected before and after weekly vaccines and were assessed for changes in phenotype, cytotoxicity, and cytokine profile. The TuLy-DC vaccine was successfully prepared and administered to 12 patients, whereas 2 patients did not receive vaccine treatment due to declines in postoperative performance status. The vaccines were well tolerated, with only grade 1 toxicities noted. One patient had a partial response to treatment that did not correspond to any significant change in immunologic profile. This pilot trial demonstrated both the safety and feasibility of reliably preparing a DC-based vaccine for mRCC patients. Our data suggest that autologous TuLy-DC vaccines generate only limited clinical response. Further clinical studies are needed to identify the most potent treatment regimen that can consistently mediate an antitumor immune response in vivo.
Dissociation, unfolding and refolding trials of pig kidney 3,4-dihydroxyphenylalanine (dopa) decarboxylase (1993)

The effect of guanidinium chloride (GuCl) on enzyme activity, hydrodynamic volume, circular dichroism, and fluorescence of 3,4-dihydroxyphenylalanine (Dopa) decarboxylase from pig kidney (pkDDC) was studied under equilibrium conditions. Unfolding proceeds in at least three stages. The first transition, occurring between 0 and 1 M GuCl, gives rise to a dimeric inactive species which has lost pyridoxal 5'-phosphate (PLP), and has a high tendency to aggregate, but retains almost all of the native spectroscopic characteristics. The second equilibrium transition, between 1 and 2.2 M GuCl, involves dimer dissociation, with some loss of tertiary and secondary structure. Additionally, gross conformational changes at or near the PLP microenvironment were detected by fluorescence of NaBH4-reduced enzyme. The third step, presumably representing complete unfolding of pkDDC, appears to be complete at 4.5 M GuCl, as indicated by the lack of further substantial changes in any of the signals being studied. Attempts at refolding resulted in the findings that: (1) partial reactivation is observed only starting from enzyme denatured at concentrations below 1.5 M GuCl, and (2) starting from completely denatured protein, the refolding process is apparently reversible down to concentrations of approx. 2 M GuCl. Taken together, this would seem to indicate that the monomer-dimer transition is impaired under the experimental conditions tested. A plausible model is presented for the unfolding/refolding of pkDDC.
Induction (1994)

Many instances of useful reasoning involve the application of generalizations to individual cases. For example, a doctor treating a patient might rely on diagnostic rules such as:
Imaging anisotropic and viscous properties of breast tissue by magnetic resonance‐elastography (2005)

MR-elastography is a new technique for assessing the viscoelastic properties of tissue. One current focus of elastography is the provision of new physical parameters for improving the specificity in breast cancer diagnosis. This analysis describes a technique to extend the reconstruction to anisotropic elastic properties in terms of a so-called transversely isotropic model. Viscosity is treated as being isotropic. The particular model chosen for the anisotropy is appealing because it is capable of describing elastic shear anisotropy of parallel fibers. The dependence of the reconstruction on the particular choice of Poisson's ratio is eliminated by extracting the compressional displacement contribution using the Helmholtz-Hodge decomposition. Results are presented for simulations, a polyvinyl alcohol breast phantom, excised beef muscle, and measurements in two patients with breast lesions (invasive ductal carcinoma and fibroadenoma). The results show enhanced anisotropic and viscous properties inside the lesions and an indication for preferred fiber orientation.
Terabit/sec VCSEL-Based Parallel Optical Module Based on Holey CMOS Transceiver IC (2012)

We report a 24 TX + 24 RX transceiver underpinned by a “holey” CMOS IC. All channels operate at 20 Gb/s (BER &lt;10−12, 7.3 pJ/bit) achieving record aggregate bidirectional bandwidth for parallel transceivers: 0.48 Tb/s.
Lupulin structures revisited (2009)

The crystal structures of lupulin A, C 30 H 46 O 11 , and lupulin D, C 25 H 38 O 8 , should both display the neoclerodane skeleton, but the deposited atomic coordinates of lupulin D correspond to the inverted enantiomer.
Top-down fabrication of vertical silicon nano-rings based on Poisson diffraction (2011)

Vertical Si nano-rings with a uniform thickness of about 100 nm have been fabricated by conventional optical photolithography with a low cost based on Poisson diffraction. Moreover, the roughness of the Si nano-rings can be effectively reduced by sacrificial oxidation. In order to increase the density of the nano-rings, coaxial twin Si nano-rings have been fabricated by the Poisson diffraction method combined with the spacer technique. The thickness of both the inner and outer Si nano-rings is about 60 nm, and the gap between the twin nano-rings is about 100 nm.
Molecular Design and Self‐Assembly of Functional Dendrimers (2007)

This chapter contains sections titled: Introduction Synthesis and Fundamental Properties of Dendrimers Redox-active Dendrimers Light-harvesting Dendrimers Stimuli-responsive Dendrimers Catalytic Dendrimers Self-assembled Dendrimers Conclusions References
INCLUSION REMOVAL IN A TUNDISH BY GAS BUBBLING (2004)

AbstractAbstractThe probabilities of inclusion removal from liquid steel by collision and attachment to rising gas bubbles have been analyzed. A simple mathematical model of inclusion removal by gas bubbling in a tundish has been developed. It was found that maintaining bubble size in the range of 0.5 to 3 mm should enhance inclusion removal efficiency. Increasing the bubbly volume fraction in the tundish and the tundish residence time can be used to improve the inclusion removal efficiency by gas bubbling. However, the formation of small bubbles in a tundish may be problematic as bubble size is affected by the high wetting angles typical of liquid metal contact with bubble orifice materials.On a analysé la probabilité de l'enlèvement d'inclusions de l'acier liquide par collision et attachement à des bulles ascendantes de gaz. On a développé un modèle mathématique simple de l'enlèvement d'inclusions par barbotage de gaz dans un panier de coulée. On a trouvé que le maintien de la taille de bulle dans la plage de 0.5 à 3 mm devrait accroître le rendement de l'enlèvement d'inclusions. On peut utiliser l'augmentation de la fraction volumique de bulles dans le panier de coulée et son temps de résidence pour améliorer le rendement de l'enlèvement d'inclusions par barbotage de gaz. Cependant, la formation de petites bulles dans un panier de coulée peut être un problème car la taille des bulles est affectée par les angles mouillants élevés typiques du contact du métal liquide avec les matériaux d'orifice de bulle.
Enhancing Vibration Robustness and Noise in Automotive Gyroscope with Large Drive Motion and Levered Sense Mode (2019)

The work presents a new geometry of amplitude-modulated in-plane and out-of-plane gyroscopes for improved vibration rejection in automotive applications. To this purpose, the design embeds a levered sense mode, enables to reach drive displacements as large as 13 μm and allows complete electromechanical quadrature compensation. Under the effect of 10 g (gravity units) peak-to-peak vibrations, the sensors demonstrate 10- to 100-fold improved vibration rejection compared to previous yaw-rate geometries, holding similar characteristics for pitch-rate sensing. At the same time, noise and stability performance are 2-fold better than best-in-class automotive gyroscopes.
Metals in select beers commercially available in the US: Unmonitored sources of concerning exposure (2018)

Stemming from the need to inform US consumers about the potential health hazards originating from regulatory deficiencies and an inadequate capacity to conduct the complete screening of beverage products entering the US, this study aimed to answer two questions: (1) how do concerning metal concentrations of beers imported to the US market compare to those in US produced beers; and (2) do imported and domestic beers exhibit concerning metal concentrations below the existing US primary drinking water standards. To address this aim: (1) beers manufactured worldwide, which were commercially available on the US market were obtained; (2) the concentration of concerning metals in the beers was analyzed; and (3) data were examined and correlated to explore any US maximum contaminant level (MCL) exceedances and determine whether geographic or grain-related trends exist. The results showed that there are no significant differences between the concerning metal concentrations of imported vs. domestic beers in the US market. Some specific heavy metals, like arsenic, are present in both imported and domestic beers in concentrations that exceed the national primary drinking water standards MCLs. Although water quality may be a factor contributing to the elevated concentrations of concerning metals in beers, it is more likely that the grain ingredients are greater contributors to the observed trends.
Communication Models for Distributed Acoustic Sensing for Telemetry (2017)

Distributed acoustic sensing (DAS) works as an efficient tool for monitoring acoustic signals in adverse environments, such as those commonly found in geophysical explorations, oil & gas, and military applications. DAS employs fiber-optic cables in order to record the acoustic wave impinging on them. These sensors can be several kilometers long, and its distributed capacity allows the acoustic wave to be measured with an adjustable space-frequency resolution. Recent DAS advances have shown that this technology is a formidable tool for implementing communication/telemetry systems in hostile environments. Notwithstanding the increasing practical interest in this technology, communication and signal processing communities have not concentrated proper efforts on addressing the myriad of challenges this technology raises. This paper bridges this gap by describing the basic signal model of a DAS system in a style compatible with the common background of these communities. It first derives, in an ideal setup, the relation between pressure signal and acquired baseband electric signals. The pressure signal is assumed to be a consequence of acoustic activity, whereas, the electric signals are obtained through the use of photodiodes which sense pressure-modulated light signals. The consequences of using long-pulse signals are also studied considering a simple continuous model for the reflections at different spatial regions of the fiber, called Rayleigh backscattering phenomenon. This paper includes results that compare the theoretical proposals with practical signals acquired in controlled experiments.
Dynamics of Natural Killer Cells Cytotoxicity in Microwell Arrays with Connecting Channels (2017)

Natural killer (NK) cells serve an important role in immune system by recognizing and killing the potentially malignant cells without antigen sensitization, and could be promising in cancer therapy. We have designed and fabricated microwell arrays with microchannel connections in polydimethylsiloxane (PDMS) substrates to study the interaction dynamics of NK-92MI cells with MCF7 breast cancer cells using time-lapse imaging by fluorescence microscopy for 15 h. Although cell seeding density was the same, NK cell cytotoxicity was found to be higher in larger microwells, which is manifested as increased target death ratio from 13.7 ± 3.1 to 46.3 ± 3.3% and shorter triggering time of first target lysis from 502 ± 49 to 391 ± 63 min in 150 μm × 150 μm microwells comparing to 50 μm × 50 μm wells in 15 h. Mirochannel connection between adjacent microwells of the same size increased the overall target death ratio by >10%, while connection between microwells of different sizes led to significantly increased target death ratio and delayed first target lysis in smaller microwells. Our findings reveal unique cell interaction dynamics, such as initiation and stimulation, of NK cell cytotoxicity in a confined microenvironment, which is different from population-based study, and the results could lead to a better understanding of the dynamics of NK cell cytotoxicity.
X-Ray Imaging of the Filling of “T” Shaped Microchannel Using a MEDIPIX2 Pixel Detector (2004)

Fluid flows in “T” or “Y” shaped structures of microchannels are studied in order to develop modeling approaches as well as adapted measurement techniques. The applications of these structures are numerous and concern in particular biology and chemical engineering for which the integration of microchannels in lab-on-chip and/or microreactor is an important challenge. Our works concern the development of a measurement technique for the study of the filling of a “T” shaped microchannel structure by a liquid. In the studied channels, the experimental constraints are strong. Indeed, the space steps involved within the phenomena are very much reduced and vary from 1 to 10 μm. Moreover, the dynamics of the flow implies a high acquisition frequency, ranging from 10 to 100 Hz. Our technological choice is based on the measurement of the attenuation of an X-ray beam in the matter. The main advantage of this non-intrusive technique is that it can be implemented even in media opaque to visible light. Also, that X-ray techniques can theoretically reach a better space resolution than optical ones. The measurement technique is quantitative and a 3D measurement is achievable by tomography. These methods are validated for problems located at centimetric space steps and high acquisition frequencies, [1], [2]. The objective of this work is to match the microfluidics field requirement (space steps and attenuation contrast), while preserving high time frequencies. Our experimental bench consists of a X-ray generator, that makes possible to obtain high enlargements of the observed object whit a reduced blur in the image. The image is obtained by a pixel detector called Medipix2. This detector is under development within a European collaboration which gathers 16 partners around the CERN, the CEA being a partner. The main assets of this detector are its high space resolution, its operational photon counting mode and its high acquisition frequency. The presented works constitute a very first implementation and validation of the proposed technique for the microfluidics field. Experimental results are obtained and presented. They allow a measurement of the filling conditions of the “T” shape structure of microchannels. The orientations and research perspectives to improve the obtained results by the technique could be evaluated accurately and important basis of our work are now established and quantified for the future.
Quantifying Glomerular Permeability of Fluorescent Macromolecules Using 2-Photon Microscopy in Munich Wistar Rats (2013)

Kidney diseases involving urinary loss of large essential macromolecules, such as serum albumin, have long been thought to be caused by alterations in the permeability barrier comprised of podocytes, vascular endothelial cells, and a basement membrane working in unison. Data from our laboratory using intravital 2-photon microscopy revealed a more permeable glomerular filtration barrier (GFB) than previously thought under physiologic conditions, with retrieval of filtered albumin occurring in an early subset of cells called proximal tubule cells (PTC)(1,2,3). Previous techniques used to study renal filtration and establishing the characteristic of the filtration barrier involved micropuncture of the lumen of these early tubular segments with sampling of the fluid content and analysis(4). These studies determined albumin concentration in the luminal fluid to be virtually non-existent; corresponding closely to what is normally detected in the urine. However, characterization of dextran polymers with defined sizes by this technique revealed those of a size similar to serum albumin had higher levels in the tubular lumen and urine; suggesting increased permeability(5). Herein is a detailed outline of the technique used to directly visualize and quantify glomerular fluorescent albumin permeability in vivo. This method allows for detection of filtered albumin across the filtration barrier into Bowman's space (the initial chamber of urinary filtration); and also allows quantification of albumin reabsorption by proximal tubules and visualization of subsequent albumin transcytosis(6). The absence of fluorescent albumin along later tubular segments en route to the bladder highlights the efficiency of the retrieval pathway in the earlier proximal tubule segments. Moreover, when this technique was applied to determine permeability of dextrans having a similar size to albumin virtually identical permeability values were reported(2). These observations directly support the need to expand the focus of many proteinuric renal diseases to included alterations in proximal tubule cell reclamation.
Matrix Completion and Extrapolation via Kernel Regression (2019)

Matrix completion and extrapolation (MCEX) are dealt with here over reproducing kernel Hilbert spaces (RKHSs) in order to account for prior information present in the available data. Aiming at a fast and low-complexity solver, the task is formulated as one of kernel ridge regression. The resultant MCEX algorithm can also afford online implementation, while the class of kernel functions also encompasses several existing approaches to MC with prior information. Numerical tests on synthetic and real datasets show that the novel approach is faster than widespread methods such as alternating least-squares (ALS) or stochastic gradient descent (SGD), and that the recovery error is reduced, especially when dealing with noisy data.
Scalable and distributed submodular maximization with matroid constraints (2015)

Submodular maximization enables efficient approximation of machine learning, networking, and language processing problems. Typically, these problems have been shown to have matroid constraints, which generalize matching and partition conditions. Developing scalable, distributed submodular optimization algorithms that guarantee the same performance as centralized techniques has been an active area of research. In this paper, we address the problem of developing scalable distributed algorithms for submodular maximization with a matroid constraint. Our key step is to construct an auxiliary function from the submodular objective function, and develop distributed exchange-based algorithms for optimizing the auxiliary function. We first introduce a distributed algorithm for maximizing a submodular function with a matroid constraint. We then develop an algorithm for maximizing time-varying submodular functions under partition matroid constraints, which arises in sensor placement and data caching. We prove that both algorithms provide (1-1/e) optimality bounds, and hence achieve the same guarantees as the best centralized algorithms.
A new method for interpreting changes in arbitrary engineering quantities by using optic fibre (2015)

A new monitoring method is proposed, which is designed for reading and interpreting changes in general engineering quantities such as deformation, subtle movement of soil particles, alteration of underground water level etc. The key feature in the method lies in the use of plastic optic fibre used to read changes in general engineering quantities occurring in geo-materials, by measuring light intensity affected by these phenomena. In this method, two plastic optical fibres, both having diameter of 1 mm, are used to read local disturbance or deformation at a point in granular material, such as sand, soil, or broken rocks. As light is sent into the first fibre and reaches its end, it leaves the fibre and hits surfaces of nearby particles. Part of the reflected light then gets into the second fibre, which can be digitally recorded by using photo diode. The paper introduces the fundamental mechanism of how the system works, shows several examples in which the proposed method is tested to interpret turbidity of muddy water, collapse behaviour of a model slope, liquefaction and so on. The results show the use of light for reading various behaviours is promising as a new monitoring scheme for rock engineering projects.
The Synthesis of Deoxygalactostatin and 2,6-Imino-heptitol Derivatives via Stannane Mediated Hydroxymethylation of 5-Azido-1,4-lactones (1998)

Deoxygalactostatin, homogalactonojirimycin derivatives and other 2,6-imino-heptitols are accessed via the nucleophilic addition of a hydroxymethyl anion equivalent to 5-azido-1,4-lactones to afford 6-azido-lactols. Subsequent hydrogenation induces intramolecular reductive amination to produce the desired piperidine ring systems.