gebhart/patrepeval huggingface dataset:
Linear and cyclic oligo-&beta;-(1&rarr;6)-D-glucosamines: Synthesis, conformations, and applications for design of a vaccine and oligodentate glycoconjugates (2013)

Poly-&amp;beta;-(1&amp;rarr;6)- N -acetyl-D-glucosamine is an exopolysaccharide secreted by numerous pathogenic bacteria, including Staphylococcus aureus , Escherichia coli , Yersinia pestis , Bordetella pertussis , Acinetobacter baumannii , Burkholderia spp . , and others. A convergent approach was developed for the synthesis of oligosaccharide fragments consisting of 5, 7, 9, and 11 glucosamine or N -acetylglucosamine units and for the preparation of five nona-&amp;beta;-(1&amp;rarr;6)-D-glucosamines with various N -acetylation patterns. Penta- and nona-&amp;beta;‑(1&amp;rarr;6)-D-glucosamines conjugated to protein carriers through a specially developed sulfhydryl linker proved to be highly immunogenic in mice and rabbits and elicited antibodies that mediated opsonic killing of multiple strains of S. aureus (including methicillin-resistant S. aureus , MRSA) and E. coli , and protected against S. aureus skin abscesses and lethal E. coli and B. cenocepacia peritonitis. These findings provide a basis for the construction of a unique semisynthetic vaccine against multiple bacterial targets. Conformational studies by means of special NMR experiments and computer modeling revealed that the oligo-&amp;beta;-(1&amp;rarr;6)-D-glucosamine chain exists mostly in a helix-like conformation, where the terminal monosaccharides are arranged close to each other. Owing to this feature, oligoglucosamines consisting of 2 to 7 residues easily form products of cycloglycosylation. Cyclooligo-&amp;beta;-(1&amp;rarr;6)-D-glucosamines represent a new family of functionalized cyclic oligosaccharides. Owing to their molecular architectonics, these compounds are convenient scaffolds for the design of conjugates with defined valency, symmetry, flexibility, and function.
Design and evaluation of a pulsed-jet chirped-pulse millimeter-wave spectrometer for the 70–102 GHz region (2011)

Chirped-pulse millimeter-wave (CPmmW) spectroscopy is the first broadband (multi-GHz in each shot) Fourier-transform technique for high-resolution survey spectroscopy in the millimeter-wave region. The design is based on chirped-pulse Fourier-transform microwave (CP-FTMW) spectroscopy [G. G. Brown, B. C. Dian, K. O. Douglass, S. M. Geyer, S. T. Shipman, and B. H. Pate, Rev. Sci. Instrum. 79, 053103 (2008)], which is described for frequencies up to 20 GHz. We have built an instrument that covers the 70-102 GHz frequency region and can acquire up to 12 GHz of spectrum in a single shot. Challenges to using chirped-pulse Fourier-transform spectroscopy in the millimeter-wave region include lower achievable sample polarization, shorter Doppler dephasing times, and problems with signal phase stability. However, these challenges have been partially overcome and preliminary tests indicate a significant advantage over existing millimeter-wave spectrometers in the time required to record survey spectra. Further improvement to the sensitivity is expected as more powerful broadband millimeter-wave amplifiers become affordable. The ability to acquire broadband Fourier-transform millimeter-wave spectra enables rapid measurement of survey spectra at sufficiently high resolution to measure diagnostically important electronic properties such as electric and magnetic dipole moments and hyperfine coupling constants. It should also yield accurate relative line strengths across a broadband region. Several example spectra are presented to demonstrate initial applications of the spectrometer.
Fluoride inhibition of yeast enolase: Crystal structure of the enolase–Mg2+–F−–Pi complex at 2.6 Å resolution (1993)

Enolase in the presence of its physiological cofactor Mg2+ is inhibited by fluoride and phosphate ions in a strongly cooperative manner (Nowak, T, Maurer, P. Biochemistry 20:6901, 1981). The structure of the quaternary complex yeast enolase-Mg(2+)-F(-)-Pi has been determined by X-ray diffraction and refined to an R = 16.9% for those data with F/sigma (F) > or = 3 to 2.6 A resolution with a good geometry of the model. The movable loops of Pro-35-Ala-45, Val-153-Phe-169, and Asp-255-Asn-266 are in the closed conformation found previously in the precatalytic substrate-enzyme complex. Calculations of molecular electrostatic potential show that this conformation stabilizes binding of negatively charged ligands at the Mg2+ ion more strongly than the open conformation observed in the native enolase. This closed conformation is complementary to the transition state, which also has a negatively charged ion, hydroxide, at Mg2+. The synergism of inhibition by F- and Pi most probably is due to the requirement of Pi for the closed conformation. It is possible that other Mg(2+)-dependent enzymes that have OH- ions bound to the metal ion in the transition state also will be inhibited by fluoride ions.
Some calculations on the range and straggling of protons (1939)

Thesis (B.S.)--Massachusetts Institute of Technology, Dept. of Physics, 1939.
The High Mobility Group (HMG) Proteins (2018)

The discovery and subsequent initial characterization of the group of chromosomal proteins called the high mobility group (HMG) proteins has created considerable interest because of the suggestion that they may be associated with active genes. The groundwork of good protein chemistry in terms of fractionation, isolation, characterization, and structure laid the foundation for the subsequent functional work. The trout protein H6 has considerable sequence homologies with calf HMG17, including a proline-rich region, but being smaller H6 has a number of deletions. Two of these proteins, HMG19A and 19B, resemble HMG14 and 17 in their amino acid compositions and a third, HMG18, resembles histones H1 and H5, but further characterization of these proteins is required before we can classify them with confidence in the low molecular weight HMG group. Most of the amino acid sequence of calf HMG1 has been published together with that of the unfractionated HMG2.
Autolabeling 3D Objects with Differentiable Rendering of SDF Shape\n Priors (2019)

We present an automatic annotation pipeline to recover 9D cuboids and 3D\nshapes from pre-trained off-the-shelf 2D detectors and sparse LIDAR data. Our\nautolabeling method solves an ill-posed inverse problem by considering learned\nshape priors and optimizing geometric and physical parameters. To address this\nchallenging problem, we apply a novel differentiable shape renderer to signed\ndistance fields (SDF), leveraged together with normalized object coordinate\nspaces (NOCS). Initially trained on synthetic data to predict shape and\ncoordinates, our method uses these predictions for projective and geometric\nalignment over real samples. Moreover, we also propose a curriculum learning\nstrategy, iteratively retraining on samples of increasing difficulty in\nsubsequent self-improving annotation rounds. Our experiments on the KITTI3D\ndataset show that we can recover a substantial amount of accurate cuboids, and\nthat these autolabels can be used to train 3D vehicle detectors with\nstate-of-the-art results.\n
Silicon MEMS Thermocatalytic Gas Sensor in Miniature Surface Mounted Device Form (2021)

A reduced size thermocatalytic gas sensor was developed for the detection of methane over the 20% of the explosive concentration. The sensor chip is formed from two membranes with a 150 µm diameter heated area in their centers and covered with highly dispersed nano-sized catalyst and inert reference, respectively. The power dissipation of the chip is well below 70 mW at the 530 °C maximum operation temperature. The chip is mounted in a novel surface mounted metal-ceramic sensor package in the form-factor of SOT-89. The sensitivity of the device is 10 mV/v%, whereas the response and recovery times without the additional carbon filter over the chip are &lt;500 ms and &lt;2 s, respectively. The tests have shown the reliability of the new design concerning the hotplate stability and massive encapsulation, but the high degradation rate of the catalyst coupled with its modest chemical power limits the use of the sensor only in pulsed mode of operation. The optimized pulsed mode reduces the average power consumption below 2 mW.
A Virosome‐Mimotope Approach to Synthetic Vaccine Design and Optimization: Synthesis, Conformation, and Immune Recognition of a Potential Malaria‐Vaccine Candidate (2003)

Ein optimiertes cyclisches Peptidmimetikum (siehe Abbildung) der NPNA-Wiederholungseinheit im Circumsporozoit(CS)-Protein von P. falciparum wurde hergestellt. Wenn es dem Immunsystem auf human verträglichen virusähnlichen Partikeln (Virosomen) zugeführt wird, induziert das Mimetikum effektiv die Ausschüttung Sporozoit-bindender Antikörper. Dieser Virosom-Mimotop(Virotop)-Ansatz könnte für Design und Prüfung neuer synthetischer Impfstoffe von Bedeutung sein.
A statistical model for synthesis of bandgap graded nanostructure (2018)

Bandgap graded nanostructure has lots of potential applications in fields such as multicolor display, nanoscale light source and photovoltaic devices. Thus, their productivity improvement has always been a critical problem. Here we proposed a statistic model to describe the bandgap graded CdSSe nanostructure growth process, which would enable the prediction and control of the yield. The model investigated the relation between the productivity of CdSSe nanostructure and the vapor-liquid-solid (VLS) growth conditions, including temperature, pressure and distance from the heating zoom. The model would help to reduce the uncertainty in nanostructure growth process and realize robust synthesis of bandgap graded nanostructure.
AN EVALUATION OF RETRIEVAL EFFECTIVENESS FOR A FULL-TEXT DOCulwvT-l?ETl?lEviiL SYSTEM (1985)

Document retrieval is the problem of finding stored documents that contain useful information. There exist a set of documents on a range of topics, written by different authors, at different times, and at varying levels of depth, detail, clarity, and precision, and a set of individuals who, at different times and for different reasons, search for recorded information that may be contained in some of the documents in this set. In each instance in which an individual seeks information, he or she will find some documents of the set useful and other documents not useful; the documents found useful are, we say, relevant; the others, not relevant. How should a collection of documents be organized so that a person can find all and only the relevant items? One answer is automatic full-text retrieval, which on its surface is disarmingly simple: Store the full text of all documents in the collection on a computer so that every character of every word in every sentence of every document can be located by the machine. Then, when a person wants information from that stored collection, the computer is instructed to search for all documents containing certain specified words and word combinations, which the user has specified. Two elements make the idea of automatic full-text retrieval even more attractive. On the one hand, digital technology continues to provide computers that are larger, faster, cheaper, more reliable, and easier to use; and, on the other hand, full-text retrieval avoids the
Unilateral thalamic deep brain stimulation for refractory essential tremor and Parkinson's disease tremor (1998)

Thalamic DBS is a safe and effective treatment of ET and the tremor of PD. In PD, its use should be limited to patients in whom high-amplitude tremor results directly in significant functional disability.
Catalytic nanoparticles for carbon nanotube growth synthesized by through thin film femtosecond laser ablation (2014)

The synthesis of metal nanoparticles by femtosecond laser vaporization of nm-thickness metal films is explored with the goal of comparing the salient features of femtosecond-based through thin film laser ablation (TTFA) to that of ns TTFA, and testing the feasibility of direct synthesis of clean nanoparticle alloys to explore the synthesis of carbon nanotubes by chemical vapor deposition. It is demonstrated that evaporated metal films are cleanly removed from quartz substrates using the technique, producing a highly forward-directed plume of nanoparticles (angle of divergence of ~2.5&deg;) which were cleanly deposited onto different supports for analysis. TEM showed the nanoparticles were spherical with diameters that ranged from a few nm to hundreds of nm in a bimodal fashion. Unlike ns-TTFA, it was found that raising the pressure had no effect on the intensity of the smaller mode within the distribution, suggesting that nanoparticle formation by gas phase condensation was not at play under the present conditions. Close examination of size distributions from a 20 and 10nm Pt film revealed an 80nm downshift in the position of the large mode within the distribution, suggesting film thickness may provide a route to controlling the modal distribution of nanoparticles produced by this method. Lastly, particles sourced by a Fe/Mo bilayer film were found to be effective in growing single wall carbon nanotubes by atmospheric chemical vapor deposition, indicating sufficiently small and catalytically active particles were produced.
New Approach for K-mean and K-medoids Algorithm (2012)

K-means and K-medoids clustering algorithms are widely used for many practical applications. Original k-mean and kmedoids algorithms select initial centroids and medoids randomly that affect the quality of the resulting clusters and sometimes it generates unstable and empty clusters which are meaningless. The original k-means and k-mediods algorithm is computationally expensive and requires time proportional to the product of the number of data items, number of clusters and the number of iterations. The new approach for the k mean algorithm eliminates the deficiency of exiting k mean. It first calculates the initial centroids k as per requirements of users and then gives better, effective and stable cluster. It also takes less execution time because it elimi nates unnecessary distance computation by using previous iteration. The new approach for k-medoids selects initial k medoids systematically based on initial centroids. It generates stable clusters to improve accuracy.
Repair, Evaluation, Maintenance, and Rehabilitation Research Program. Underwater Stilling Basin Repair Techniques Using Precast or Prefabricated Elements (1991)

The purpose of this study was to investigate methods of repairing stilling basins of hydraulic structures underwater, thereby eliminating costly dewatering operations, and to develop a plan to evaluate products or concepts. The effort focused on methods using precast concrete or prefabricated steel panels. This report reviews underwater repairs of the Old River Low Sill Control Structure, Upper St. Anthony Falls Lock, and Kinzua Dam. An overview of the required underwater construction tasks is presented (preplanning, mobilization, surface preparation, installation of field anchors and panel supports, installation of panels, concrete placement, and inspection). Construction methods for underwater repairs are discussed, including the use of divers, wall enclosures, caissons, cofferdams, above-water platforms, and submersibles. Panel design factors considered are abrasion resistance, uplift forces, joints, and weight. Other panels considerations include shapes, joints, bond, and supports. It is feasible to relay on divers in underwater repair projects, because most stilling basins have low-water depths of 40 ft or less. Steel panels or composite steel-concrete panels are preferred to concrete panels because of the abrasion resistance of steel. Design details become important to assure that the steel panels remain serviceable under vibration and uplift forces from high- velocity water flow and impact from rocks in turbulent flow.
LoOkie - it feels like being there (2011)

In this paper, we describe an interaction design process and the challenges encountered during the development of LoOkie, a social mobile application, which enables members to request and receive live videos or pictures of desired locations from people who are present at the scene. The paper describes, from a human-computer interaction perspective, the development of the application from the birth of the idea through the design process encountered up to the point of the launch of the application for Beta at the beginning of 2011.
Cardiac Troponin and Outcome in Acute Heart Failure (2008)

In patients with acute decompensated heart failure, a positive cardiac troponin test is associated with higher in-hospital mortality, independently of other predictive variables. (ClinicalTrials.gov number, NCT00366639 [ClinicalTrials.gov].).
Chronic Relapsing Experimental Allergic Encephalomyelitis (1980)

The immunohistochemical staining of immunoglobulins (Ig), complement (C3), and fibrinogen in chronic relapsing experimental allergic encephalomyelitis lesions showed different staining patterns in the acute vs the chronic stage of the disease. In the acute stage, Ig, C3, and fibrinogen were present in the perivascular tissue of the brain and the spinal cord. In hyperacute-type lesions, the binding of Ig and C3 to the parenchyma was especially pronounced. The chronic stage of the disease was characterized by Ig-containing cells and Ig binding to white matter in actively demyelinating lesions. Linear or granular deposits of immunoglobulin and complement, reminiscent of those described in immune complex disease, were found in the choroid plexus.
Control Over Noisy Forward and Reverse Channels (2010)

We consider the problem of remotely controlling a continuous-time linear time-invariant system driven by Brownian motion process, when communication takes place over noisy memoryless discrete- or continuous-alphabet channels. What makes this class of remote control problems different from most of the previously studied models is the presence of noise in both the forward channel (connecting sensors to the controller) and the reverse channel (connecting the controller to the plant). For stability of the closed-loop system, we look for the existence of an invariant distribution for the state, for which we show that it is necessary that the entire control space and the state space be encoded, and that the reverse channel be at least as reliable as the forward channel. We obtain necessary conditions and sufficient conditions on the channels and the controllers for stabilizability. Using properties of the underlying sampled Markov chain, we show that under variable-length coding and some realistic channel conditions, stability can be achieved over discrete-alphabet channels even if the entire state and control spaces are to be encoded and the number of bits that can be transmitted per unit time is strictly bounded. For control over continuous-alphabet channels, however, a variable rate scheme is not necessary. We also show that memoryless policies are rate-efficient for Gaussian channels.
Assessment of Generative Adversarial Networks Model for Synthetic Optical Coherence Tomography Images of Retinal Disorders (2020)

The medical image synthesis based on GANs is promising in humans and machines to fulfill clinical tasks.
Dimensional anchors (1999)

We introduce a graphic primitive, called a dimensional anchor (DA), which facilitates the creation of new visualizations and provides insight into the analysis of information visualizations. The DA represents an attempt to provide a unified framework or model for a variety of visualizations, including Parallel Coordinates, scatter plot matrices, Radviz, Survey Plots and Circle Segments A dimensional anchor is constructed by assigning values to parameters associated with various geometric graphic elements that encode the basics of the above visualizations. We define a visualization vector space in which all of the above visualizations and many new ones are represented by vectors. These encodings make it possible to perform a Grand Tour traveling from Parallel Coordinates to Survey Plot, and visiting many other visualizations in between
Cross comparison of nitrogen sources, sinks and transport within river basins: the Italian Nitrogen Network initiative (INN) (2014)

Nitrogen deficit or excess within ecosystems imply different problems. The shortage of this key nutrient strongly affects agricultural productions while its abundance ("too much of a good thing") determines water&#13;\neutrophication and associated setbacks. At the beginning of 2014 a national initiative was launched to researchers dealing with nitrogen, including limnologists, ecologists, biologists, agronomists and&#13;\nhydrogeologists. The initiative (INN, Italian Nitrogen Network) consists in sharing a common methodology to evaluate the nitrogen budget at the watershed level. Specific meetings were organized to share and discuss a common method for data collection and budget calculation. Most necessary data can be free downloaded&#13;\nfrom national statistical databases and have the municipality resolution. They include agricultural productions in terms of surfaces, typologies and amounts of farmed animals. All input data are converted&#13;\ninto nitrogen units by means of site-specific, appropriate coefficients. An inventory of input (associated to manure, synthetic fertilizers deposition, biological fixation) and output terms (crop uptake, ammonia volatilization, denitrification in soils) is produced and a net budget is calculated across the agricultural lands.&#13;\nAs for most Italian rivers water flows and hydrochemical data at the closing sections are available, N export from each basin can be computed and compared to the budget. This, together with detailed knowledge of&#13;\naccessory information (e.g. population density, land use, slopes, presence of wetlands, soil permeability) allows to infer about the system capacity to metabolize N loads and its relevance in planning appropriate management actions. At present some budgets are already available (Oglio, Mincio, Volano, Agogna, Parma, Secchia, Adda, Panaro), while others are in progress (Adige, Reno, Tevere, Scrivia, Alento, Lambro, Olona, Ticino, Enza, Crostolo, Arborea Plain, Venice Lagoon Basin). We present here the initiative, the aims, material and methods, the investigated watersheds and the perspectives
Experimental investigation of a two-layer shearing instability in a cylindrical Couette cell (1996)

A new experiment is presented to investigate interfacial instability between two immiscible liquids with different viscosity. Two density-matched fluids are confined between the walls of a concentric cylinder Couette cell that is aligned parallel to gravity. The resulting interface is parallel to the walls of the Couette cell and gravity. At sufficiently fast rotation rates, interfacial waves form with amplitudes that vary azimuthally and with crests parallel to gravity. Experiments and detailed results on the behavior of the system including a phase map and video stills are presented as a function of depth ratio and rotation rate. Both two-dimensional periodic wave trains and localized waves are observed. The experimental wavelength of the two-dimensional waves agree with the predictions of the Orr–Sommerfeld equation.