gebhart/patrepeval huggingface dataset:
Human Protein Data (1998)

Human Protein Data is a unique compilation of data on the most important and best studied human proteins. This two volume set contains a total of about 314 detailed data sheets. The contents corresponds to the up-dated collection of data sheets of Installments 1 to 6 of the loose-leaf edition. The points covered per individual protein far exceed those found in typical protein databases and include biological functions/ physiology/ pathology/ degradation/ genetics/ abnormalities/ half-life/ concentration/isolation method A computer retrievel program on disc permits easy searches trough the complete set of data. In addition to this a list of all contributors with their complete and up-to-date adresses provides the user with a Who is Who of modern protein research. Human Protein Data as an unique and indispensable reference work adds new and valuable dimensions to electronic database searches.
Enhanced pseudo-dynamic receive beamforming using focusing delay error compensation (2014)

Dynamic receive beamforming updates focusing delays for every samples of a scanline, leading to increased hardware complexity. To reduce this, pseudo-dynamic receive beamforming is applied to divide scanlines into windows and each window shares the same focusing delays. However, only one sample in a window is in focus, while the rest are out of focus. This paper presents a method to enhance pseudo-dynamic receive beamforming by using linear least squares approximation of the focusing delay errors for every sample in a window in order to compensate for the delay errors of the out-of-focus samples. The method is preliminarily implemented on a single field-programmable gate array (FPGA) with 500K gates.
Impaired proprioception and osteoarthritis (1997)

The increase in the prevalence of osteoarthritis (OA) with age may be due in part to increased joint load resulting from age-related declines in neuromechanical factors, including joint position sense or proprioception. Several studies have demonstrated that knee proprioception is worse in knee OA patients versus age-matched control subjects. Functional consequences of impaired proprioception may include lower gait velocity, shorter stride length, and slower stair walking time. Some studies have shown that proprioception can be enhanced by wearing an elastic bandage or similar orthoses and by muscle training. A variety of other interventions have been proposed as well. To date studies of proprioception in OA patients have been cross-sectional. Theoretically, impaired proprioception might contribute toward or result from OA. A paradigm depicting directions in the relationship between proprioception impairment and OA is offered. Longitudinal data are badly needed to elucidate cause and effect and to determine the relative importance of impaired proprioception in disease progression. The relationship between sensory input and protective or damaging muscle activity has been minimally evaluated in the setting of OA. In studies of clinical conditions related to OA, experimental effusions had no effect on proprioception. Proprioception was worse in hypermobility syndrome patients versus age-matched controls. Anterior cruciate ligament insufficiency is associated with a decline in proprioception.
Integrated continuous flow polymerase chain reaction and micro‐capillary electrophoresis system with bioaffinity preconcentration (2011)

An integrated and modular DNA analysis system is reported that consists of two modules: (i) A continuous flow polymerase chain reaction (CFPCR) module fabricated in a high T(g) (150°C) polycarbonate substrate in which selected gene fragments were amplified using biotin and fluorescently labeled primers accomplished by continuously shuttling small packets of PCR reagents and template through isothermal zones as opposed to heating and cooling large thermal masses typically performed in batch-type thermal reactors. (ii) μCE (micro-capillary electrophoresis) module fabricated in poly(methylmethacrylate) (PMMA), which utilized a bioaffinity selection and purification bed (2.9 μL) to preconcentrate and purify the PCR products generated from the CFPCR module prior to electrophoretic sorting. Biotin-labeled CFPCR products were hydrostatically pumped through the streptavidin-modified bed, where they were extracted onto the surface of micropillars. The affinity bed was also fabricated in PMMA and was populated with an array of microposts (50 μm width; 100 μm height) yielding a total surface area of ∼117 mm(2). This solid-phase extraction (SPE) process demonstrated high selectivity for biotinylated amplicons and utilized the strong streptavidin/biotin interaction (K(d) = 10(-15) M) to generate high recoveries. The SPE selected CFPCR products were thermally denatured and single-stranded DNA released for injection into a 7-cm-long μCE channel for size-based separations and fluorescence detection. The utility of the system was demonstrated using Alu DNA typing for gender and ethnicity determinations as a model. Compared with the traditional cross-T injection procedure typically used for μCE, the affinity pre-concentration and injection procedure generated signal enhancements of 17- to 40-fold, critical for CFPCR thermal cyclers due to Taylor dispersion associated with their operation.
L-dopa therapy in Parkinson's disease: a critical review of nine years' experience. (1969)

The last 10 years have seen great activity in the investigation of cerebral catecholamines, particular attention having been paid to dopamine. The low dopamine content in the basal ganglia and in the urine of patients with Parkinson's disease led to the logical use of the precursor DOPA in the treatment of this disorder. Between 1961 and 1966, both the oral and the intravenous routes were utilized and some effects were noted upon akinesia and rigidity. The doses then used were low and the results remained somewhat controversial. When higher oral levels of L-dopa were introduced, the beneficial action of L-dopa upon parkinsonian symptoms and signs was proved beyond doubt, but there came to light a number of troublesome side effects, the worst of which were hypotension and a variety of abnormal involuntary movements. Recently, new approaches to the therapy have been tried and the sum total of these observations is to challenge our peace of mind regarding a seemingly logical chain of events. We are convinced that such second thoughts will eventually result in better and safer methods of treating this too frequent and disabling neurological disorder.
The kSORT Assay to Detect Renal Transplant Patients at High Risk for Acute Rejection: Results of the Multicenter AART Study (2014)

The kSORT blood QPCR assay is a noninvasive tool to detect high risk of AR of renal transplants. Please see later in the article for the Editors' Summary.
Quark flavor mixing and its physical implications (1980)

This is a very fast developing field and the amount of literature on the subject is vast. It is impossible not to miss quoting some papers. I intend to inform you of the scope of the developments on the subject of flavor mixing, especially the Kobayashi‐Maskawa model, since the Tokyo conference in 1978.
Quake: quality-aware detection and correction of sequencing errors (2010)

We introduce Quake, a program to detect and correct errors in DNA sequencing reads. Using a maximum likelihood approach incorporating quality values and nucleotide specific miscall rates, Quake achieves the highest accuracy on realistically simulated reads. We further demonstrate substantial improvements in de novo assembly and SNP detection after using Quake. Quake can be used for any size project, including more than one billion human reads, and is freely available as open source software from http://www.cbcb.umd.edu/software/quake.
<i>N</i>-Heterocyclic Carbene Catalyzed Ring Expansion of 4-Formyl-β-lactams:  Synthesis of Succinimide Derivatives (2007)

N-heterocyclic carbene (NHC) has been employed as an efficient catalyst for ring expansion of 4-formyl-beta-lactams, allowing the facile synthesis of succinimide derivatives. This organocatalytic process features readily availability of the catalyst, low catalyst loading, and mild reaction conditions.
Extracellular potentials from active myelinated fibers inside insulated and noninsulated peripheral nerve (1998)

A model is presented that calculates the single-fiber extracellular field and action potential (ap) of an active myelinated nerve fiber placed centrally or eccentrically inside a nerve with a cylindrical geometry, representing essentially a one-fascicle nerve. This one-fascicle nerve has the dimensions and conductivities of the rat peroneal nerve branch. The results show a wide variety of wave shapes to be measured, depending on the position of the intraneural electrode with respect to the fiber axis and to the nodes of Ranvier and depending on the presence of an isolating cuff around the nerve. Action potential shapes may range from the "classical" quasi-biphasic one, to more triphasic, or even more complicated in the case of a short insulating cuff being present around the nerve. In the latter case, when measured bipolarly, ap-wave shapes become almost monophasic.
<i>In situ</i>X-ray analysis of protein crystals in low-birefringent and X-ray transmissive plastic microchannels (2008)

Plastic microchannel crystallization template designs made from inexpensive cyclic olefin copolymers have been shown to be low-birefringent, X-ray transmissive and compatible with microfluidic fabrication in restricted geometry. The model proteins thaumatin, lysozyme and bacteriorhodopsin demonstrated the feasibility of conducting counter-diffusion equilibration within the new plastic configuration. Crystals of each of these proteins were directly evaluated in situ using synchrotron radiation and their diffraction quality was evaluated without invasive manipulation or cryofreezing. Protein crystals able to produce complete X-ray data sets were used to calculate electron-density maps for structure determination. Fluidic crystallization in the plastic platform was also coupled with a commercialized automated imager and an in situ X-ray scanner that allowed optical and X-ray inspection of crystallization hits. The results demonstrate the feasibility of rapid nanovolume counter-diffusion crystallization experiments without the need for additional instrumentation.
Peculiarities of Starch Cationization with Glycidyltrimethylammonium Chloride (2006)

Abstract Cationic starch derivatives containing quaternary ammonium groups with high degree of substitution are prepared by reaction of starch with glycidyltrimethylammonium chloride (GTAC) in different reaction media. In aqueous solutions of GTAC along with conventional hydrolysis of epoxy groups, their interaction with chloride ions also takes place. This resulted in formation of hydroxyl ions which accelerate both the hydrolysis of GTAC epoxy groups and can act as the internal catalyst in the reaction of GTAC with starch. Therefore, even in the absence of the external catalyst, cationic starch with a high degree of substitution can be obtained. The autocatalytic reaction of GTAC with starch proceeds more rapidly at higher temperatures but with lower reaction efficiency. Both in the absence of the external catalyst and in the case when sodium alkali is used as a catalyst the reaction of starch with GTAC proceeds only when a particular quantity of “free” water is present in the system. When the NaOH as catalyst is used the reaction efficiency is about 90%. The yield of starch cationization reaction decreases when the quantity of “free” water is twice or thrice higher than required for starch modification to begin.
Real-Time Camera Tracking and 3D Reconstruction Using Signed Distance Functions (2013)

The ability to quickly acquire 3D models is an essential capability needed in many disciplines including robotics, computer vision, geodesy, and architecture. In this paper we present a novel method for real-time camera tracking and 3D reconstruction of static indoor environments using an RGB-D sensor. We show that by representing the geometry with a signed distance function (SDF), the camera pose can be efficiently estimated by directly minimizing the error of the depth images on the SDF. As the SDF contains the distances to the surface for each voxel, the pose optimization can be carried out extremely fast. By iteratively estimating the camera poses and integrating the RGB-D data in the voxel grid, a detailed reconstruction of an indoor environment can be achieved. We present reconstructions of several rooms using a hand-held sensor and from onboard an autonomous quadrocopter. Our extensive evaluation on publicly available benchmark data shows that our approach is more accurate and robust than the iterated closest point algorithm (ICP) used by KinectFusion, and yields often a comparable accuracy at much higher speed to feature-based bundle adjustment methods such as RGB-D SLAM for up to medium-sized scenes.
Multi arm snake-like robot kinematics (2013)

The next step in minimally invasive surgery is the further reduction of incisions by surgery through natural orifices (NOTES) or one single artificial incision (Single-Port). However, physicians pointed out, that those procedures are only possible if new technologies will increase the dexterity of the instruments inside of the body. Especially the missing ability to manipulate tissue from two sides (triangulation), needs to be obtained. This article is about the development of different kinematics for a Multi Arm Snake-Like Robot to manipulate flexible endoscopic instruments at the tip of a flexible endoscope. By using Selective Laser Sintering (SLS) it is feasible to create various shapes and designs, custom made for different patients. We are using flexure hinges and compliant mechanisms to create defined movements in serial kinematic structures. In the experiments, the relation between different structures and the influence of the inserted flexible endoscopic instrument are compared. The proposed kinematics are able to manipulate flexible endoscopic instruments. That proves that SLS structures get more advances towards a use for a flexible Single-Port Multi Arm Snake-Like Robot.
Ridiculously Fast Shot Boundary Detection with Fully Convolutional Neural Networks (2018)

Shot boundary detection (SBD) is an important component of many video analysis tasks, such as action recognition' video indexing, summarization and editing. Previous work typically used a combination of low-level features like color histograms, in conjunction with simple models such as SVMs to predict shot changes. Instead, we propose to learn shot detection end-to-end, from pixels to final shot boundaries. For training such a model, we rely on our insight that all shot boundaries are generated. Thus, we create a dataset with one million frames and automatically generated transitions such as cuts, dissolves and fades. In order to efficiently analyze hours of videos, we propose a Convolutional Neural Network (CNN) which is fully convolutional in time, thus allowing to use a large temporal context without the need to repeatedly processing frames. With this architecture our method obtains state-of-the-art results on the RAI dataset, while running at an unprecedented speed of more than 120x real-time.
Protoporphyrin-IX: Some Useful Substituent Manipulations (1987)

Various substituent manipulations of the side chains in commercially available hemin (3) and its metal-free derivative, protoporphyrin-IX (4), are described, which illustrate the usefulness of these starting materials for preparation of a large number of theoretically, chemically, biologically, and spectroscopically useful porphyrins and hemes. © 1987.
Amino-derivatives of the sesquiterpene lactone class of natural products as prodrugs (2012)

The medicinal chemistry of amino-derivatives of the sesquiterpene lactones is described, beginning with synthetic development, moving into pharmacological applications, and finishing with clinical translation.
Very Simple BICM-ID Using Repetition Code and Extended Mapping with Doped Accumulator (2011)

This paper proposes very simple bit-interleaved coded modulation with iterative detection (BICM-ID) as a spectrally efficient signal transmission scheme, where irregular repetition code and extended mapping with rate-1 doped accumulator (ACC) are combined to achieve a clear turbo-cliff. Doped ACC is used for close matching of the demapper and decoder’s extrinsic information transfer curves. Although the proposed BICM-ID system is very simple, it can achieve excellent performances and completely eliminate bit-error-rate floor. An exemplifying result for extended non-Gray mapped 4-quadrature amplitude modulation symbol shows that with 0.916 bits/channel use, turbo-cliff happens at 1.27 dB away from the Shannon limit.
Did United States v. Hayashi Fail to Provide a Safe Harbor for Marine Mammals Under the Marine Mammal Protection Act (1997)

This note focuses on one such instance where a court erred in interpreting a key term in the MMPA. In United States v. Hayashi, the Ninth Circuit, sitting en bane, found that a fisherman who shot at porpoises to deter them from his catch did not commit a "taking" under the MMPA. The court held that to constitute a criminal "taking" under the MMPA, harassment of a marine mammal must entail direct and serious disruptions of normal mammal behavior. This decision may result in further exploitation and suffering of marine mammals.
Increased Exopolysaccharide Production in <i>Lactococcus lactis</i> due to Increased Levels of Expression of the NIZO B40 <i>eps</i> Gene Cluster (2003)

Exopolysaccharides (EPS) play an important role in the rheology and texture of fermented food products. This is the first report demonstrating that homologous overexpression of a complete eps gene cluster in Lactococcus lactis leads to increased EPS production levels. A ninefold-elevated EPS plasmid copy number led to an almost threefold increase in the eps expression level, resulting in an almost fourfold increase in the NIZO B40 EPS production level. It was previously reported that increased EPS precursor levels did not influence NIZO B40 EPS production levels. However, the present results indicate that the maximal NIZO B40 EPS production level is limited by the activity level of the expression products of the eps gene cluster rather than by the level of EPS precursors.
Prediction of Drag Reduction in Supersonic and Hypersonic Flows with Counterflow Jets (2002)

Computational fluid dynamics solutions of the flowfield of a truncated cone-cylinder with and without counterflow jets have been obtained for the short penetration mode (SPM) and long penetration mode (LPM) of the freestream-counterflow jet interaction flowfield. For the case without the counterflow jet, the comparison of the normalized surface pressures showed very good agreement with experimental data. For the case with the SPM jet, the predicted surface pressures did not compare as well with the experimental data upstream of the expansion corner, while aft of the expansion corner, the comparison of the solution and the data is seen to give much better agreement. The difference in the prediction and the data could be due to the transient character of the jet penetration modes, possible effects of the plasma physics that are not accounted for here, or even the less likely effect of flow turbulence, etc. For the LPM jet computations, one-dimensional isentropic relations were used to derived the jet exit conditions in order to obtain the LPM solutions. The solution for the jet exit Mach number of 3 shows a jet penetration several times longer than that of the SPM, and therefore much weaker bow shock, with an attendant reduction in wave drag. The LPM jet is, in essence, seen to be a pencil of fluid, with much higher dynamic pressure, embedded in the oncoming supersonic or hypersonic freestream. The methodology for determining the conditions for the LPM jet could enable a practical approach for the design and application of counterflow LPM jets for the reduction of wave drag and heat flux, thus significantly enhancing the aerodynamic characteristics and aerothermal performance of supersonic and hypersonic vehicles. The solutions show that the qualitative flow structure is very well captured. The obtained results, therefore, suggest that counterflowing jets are viable candidate technology concepts that can be employed to give significant reductions in wave drag, heat flux, and other attendant aerodynamic benefits.
The effect of metformin on measurements of insulin sensitivity and β cell response in 18 horses and ponies with insulin resistance (2008)

Metformin may be indicated as a treatment for IR in equids. Further studies are required to define appropriate selection of subjects warranting therapy, dosing schedule and pharmacokinetics.
New "light" for one-world approach toward safe and effective control of animal diseases and insect vectors from leishmaniac perspectives (2016)

Light is known to excite photosensitizers (PS) to produce cytotoxic reactive oxygen species (ROS) in the presence of oxygen. This modality is attractive for designing control measures against animal diseases and pests. Many PS have a proven safety record. Also, the ROS cytotoxicity selects no resistant mutants, unlike other drugs and pesticides. Photodynamic therapy (PDT) refers to the use of PS as light activable tumoricides, microbicides and pesticides in medicine and agriculture.Here we describe "photodynamic vaccination" (PDV) that uses PDT-inactivation of parasites, i.e. Leishmania as whole-cell vaccines against leishmaniasis, and as a universal carrier to deliver transgenic add-on vaccines against other infectious and malignant diseases. The efficacy of Leishmania for vaccine delivery makes use of their inherent attributes to parasitize antigen (vaccine)-presenting cells. Inactivation of Leishmania by PDT provides safety for their use. This is accomplished in two different ways: (i) chemical engineering of PS to enhance their uptake, e.g. Si-phthalocyanines; and (ii) transgenic approach to render Leishmania inducible for porphyrinogenesis. Three different schemes of Leishmania-based PDV are presented diagrammatically to depict the cellular events resulting in cell-mediated immunity, as seen experimentally against leishmaniasis and Leishmania-delivered antigen in vitro and in vivo. Safety versus efficacy evaluations are under way for PDT-inactivated Leishmania, including those further processed to facilitate their storage and transport. Leishmania transfected to express cancer and viral vaccine candidates are being prepared accordingly for experimental trials.We have begun to examine PS-mediated photodynamic insecticides (PDI). Mosquito cells take up rose bengal/cyanosine, rendering them light-sensitive to undergo disintegration in vitro, thereby providing a cellular basis for the larvicidal activity seen by the same treatments. Ineffectiveness of phthalocyanines and porphyrins for PDI underscores its requirement for different PS. Differential uptake of PS by insect versus other cells to account for this difference is under study.The ongoing work is patterned after the one-world approach by enlisting the participation of experts in medicinal chemistry, cell/molecular biology, immunology, parasitology, entomology, cancer research, tropical medicine and veterinary medicine. The availability of multidisciplinary expertise is indispensable for implementation of the necessary studies to move the project toward product development.