gebhart/patrepeval huggingface dataset:
MR brain image classification by multimodal perceptron tree neural network (2002)

We propose a multimodal perceptron tree (MMPT) neural network to segment magnetic resonance (MR) images. The architecture consists of simple networks-neurons, hierarchically connected in a tree structure. The latter is built up during training by the adopted depth-first searching technique augmented with choosing the best hyperplane split of the feature subspace at each tree node. This neural network effectively partitions the feature space into subregions and each terminal subregion is assigned to a class label depending on the data routed to it. As the tree grows, the number of training data for each node decreases, which results in less weight update epochs and decreases the time consumption. The MMPT performance is compared to that of a multilayered perceptron (MLP). The networks are applied to brain MR image segmentation into gray matter/white matter regions.
Security Negotiation for WebNFS (2000)

This document describes a protocol for a WebNFS client [RFC2054] to negotiate the desired security mechanism with a WebNFS server [RFC2055] before the WebNFS client falls back to the MOUNT v3 protocol [RFC1813]. This document is provided so that people can write compatible implementations.
The flexible region of protein L12 from bacterial ribosomes studied by proton nuclear magnetic resonance (1989)

The dimeric protein L7/L12 from bacterial ribosomes has a highly elongated and flexible structure. We have, using 1H NMR methods, analyzed the extent of the flexible region and also the size of the organized structures of the molecule. A number of mutants of the protein as well as monomeric and dimeric forms of the protein and a COOH-terminal fragment have been used for the identification of certain resonances. Thus, residues 37-50 were found to be highly mobile whereas the amino-terminal and COOH-terminal regions are organized into folded domains. The flexibility between the domains and its relation to functional properties of the protein are discussed.
Stability Characterization of a Vaccine Antigen Based on the Respiratory Syncytial Virus Fusion Glycoprotein (2016)

Infection with Respiratory Syncytial Virus (RSV) causes both upper and lower respiratory tract disease in humans, leading to significant morbidity and mortality in both young children and older adults. Currently, there is no licensed vaccine available, and therapeutic options are limited. During the infection process, the type I viral fusion (F) glycoprotein on the surface of the RSV particle rearranges from a metastable prefusion conformation to a highly stable postfusion form. In people naturally infected with RSV, most potent neutralizing antibodies are directed to the prefusion form of the F protein. Therefore, an engineered RSV F protein stabilized in the prefusion conformation (DS-Cav1) is an attractive vaccine candidate. Long-term stability at 4°C or higher is a desirable attribute for a commercial subunit vaccine antigen. To assess the stability of DS-Cav1, we developed assays using D25, an antibody which recognizes the prefusion F-specific antigenic site Ø, and a novel antibody 4D7, which was found to bind antigenic site I on the postfusion form of RSV F. Biophysical analysis indicated that, upon long-term storage at 4°C, DS-Cav1 undergoes a conformational change, adopting alternate structures that concomitantly lose the site Ø epitope and gain the ability to bind 4D7.
S2–02–05: Neuritic alterations and dysfunctions in Alzheimer's disease (2006)

Accumulation of hyperphosphorylated tau protein into neurofibrillary tangles (NFT) in Alzheimer's disease and other tauopathies correlates with neuron loss and cognitive decline; but the relationship of NFT to neuron dysfunction and death in neurodegenerative diseases remains unclear. Recently, a regulatable transgenic mouse line was developed (rTg4510) that expresses human tau with the tauopathy–associated P301L mutation, which can be suppressed with doxycycline. These mice develop progressive behavioral deficits, neuron loss, and tangle formation. We aim to study the relationship of NFT and cell death in the rTg4510 mouse model of tauopathy. In this study in vivo multiphoton microscopy was used to investigate thioflavine S positive tangles, caspase activation, and neuronal morphology using an adeno–associated virus to introduce green fluorescent protein into neurons. We observe thioflavine S positive neurons in the living brain similar to staining of NFT in postmortem human tauopathy cases. A fluorescent indicator of caspase activation applied in vivo shows that both neurons with and without neurofibrillary pathology are positive for activated caspases. Transgene suppression with doxycycline, which halts progression of neuronal loss, also appears to reduce caspase activation in vivo. qPCR analysis of frozen tissue shows an upregulation of caspase 8 in rTg4510 forebrain, which correlates with neuronal loss. While many GFP–filled neuronal processes appear morphologically normal, we observe some axonal varicosities and neurites with torturous trajectories. This study demonstrates for the first time the ability to observe neurofibrillary pathology and dying cells in the intact brain.
The Effect of a Purified Guar Degrading Enzyme on Chick Growth (1982)

Guar gum, a galactomannan, is growth depressing when fed to chicks. As part of the continuing studies on the mode of action of this and other gums in the intestine, a mannanase has been isolated which degrades guar gum. A commercial hemicellulase was separated into several protein fractions by chromatography on DEAE-cellulose. Only one of these proteins effectively reduced the viscosity of a guar gum solution. Activity towards pectin, rye water extract, and barley water extract was not present in the fraction which degraded guar gum but was found in other fractions at lower concentrations. Graded levels of this purified guar-degrading enzyme were incorporated into chick diets having 2% guar gum. This purified enzyme was effective at levels as low as .6 mg protein/kg diet in preventing growth depression caused by the guar gum and thus permitting growth equivalent to controls. Purity of this mannanase was confirmed by chromatography on QAE-Sephadex at pH 6.0 and by slab-gel electrophoresis at pH 8.4.
To cloud or not to cloud: A mobile device perspective on energy consumption of applications (2012)

The cloud computing paradigm enables the work anywhere anytime paradigm by allowing application execution and data storage on remote servers. This is especially useful for mobile computing and communication devices that are constrained in terms of computation power and storage. It is however not clear how preferable cloud-based applications would be for mobile device users. For users of such battery life constrained devices, the most important criteria might be the energy consumed by the applications they run. The goal of this work is to characterize under what scenarios cloud-based applications would be relatively more energy-efficient for users of mobile devices. This work first empirically studies the energy consumption for various types of applications and for multiple classes of devices to make this determination. Subsequently, it presents an analytical model that helps characterize energy consumption of mobile devices under both the cloud and non-cloud application scenarios. Finally, an algorithm GreenSpot is presented that considers application features and energy-performance tradeoffs to determine whether cloud or local execution will be more preferable.
High-pressure phase transformation of silicon nitride (2003)

We provide evidence for a high-pressure phase transformation (HPPT) in the ceramic material silicon nitride. This HPPT is inferred by a high-pressure diamond anvil cell, Raman spectroscopy, scanning/transmission electron microscopy, and optical and acoustic microscope inspection. In the case of silicon nitride, the HPPT involves a ductile or metallike behavior that is observed in severe deformation processes, such as nanoindentation and micromachining. This pressure-induced plasticity is believed to be similar to that found in silicon and germanium with its origin in the high-pressure metallic β-Sn phase formation.
Antigenic variation in<i>Giardia lamblia</i> (2009)

Giardia lamblia undergoes antigenic variation, both in vitro and within the intestines of infected individuals. Variant-specific surface proteins (VSPs) cover the entire surface of the trophozoites and are the main antigens recognized by the host. Only 1 of about 200 VSP genes encoded by the Giardia genome is expressed on the surface of individual Giardia cells at any time; however, VSP antigen switching occurs spontaneously. In the recent year, significant advances in the knowledge of the antigen switching process have been achieved, which strongly suggests that antigenic variation in Giardia is regulated at the post-transcriptional level by a mechanism similar to RNA interference (RNAi). Several enzymes of the RNAi pathway are directly involved in VSP mRNA silencing and/or translational repression. Although several questions remain regarding how individual VSP antigens are selected for expression on the parasite surface, it is clear that an epigenetic mechanism is involved. In this review, we summarize the characteristics of this fascinating mechanism, analyse conflicting information regarding the structure of VSPs as it relates to the host's immune response, and highlight the major issues that need to be resolved to fully understand antigenic variation in this important pathogen.
DeepDynamicHand: A Deep Neural Architecture for Labeling Hand Manipulation Strategies in Video Sources Exploiting Temporal Information (2018)

Humans are capable of complex manipulation interactions with the environment, relying on the intrinsic adaptability and compliance of their hands. Recently, soft robotic manipulation has attempted to reproduce such an extraordinary behavior, through the design of deformable yet robust end-effectors. To this goal, the investigation of human behavior has become crucial to correctly inform technological developments of robotic hands that can successfully exploit environmental constraint as humans actually do. Among the different tools robotics can leverage on to achieve this objective, deep learning has emerged as a promising approach for the study and then the implementation of neuro-scientific observations on the artificial side. However, current approaches tend to neglect the dynamic nature of hand pose recognition problems, limiting the effectiveness of these techniques in identifying sequences of manipulation primitives underpinning action generation, e.g., during purposeful interaction with the environment. In this work, we propose a vision-based supervised Hand Pose Recognition method which, for the first time, takes into account temporal information to identify meaningful sequences of actions in grasping and manipulation tasks. More specifically, we apply Deep Neural Networks to automatically learn features from hand posture images that consist of frames extracted from grasping and manipulation task videos with objects and external environmental constraints. For training purposes, videos are divided into intervals, each associated to a specific action by a human supervisor. The proposed algorithm combines a Convolutional Neural Network to detect the hand within each video frame and a Recurrent Neural Network to predict the hand action in the current frame, while taking into consideration the history of actions performed in the previous frames. Experimental validation has been performed on two datasets of dynamic hand-centric strategies, where subjects regularly interact with objects and environment. Proposed architecture achieved a very good classification accuracy on both datasets, reaching performance up to 94%, and outperforming state of the art techniques. The outcomes of this study can be successfully applied to robotics, e.g., for planning and control of soft anthropomorphic manipulators.
A collision avoidance model based on the Lobula giant movement detector (LGMD) neuron of the locust (2004)

In insects, we can find very complex and compact neural structures that are task specific. These neural structures allow them to perform complex tasks such as visual navigation, including obstacle avoidance, landing, self-stabilization, etc. Obstacle avoidance is fundamental for successful navigation, and it can be combined with more systems to make up more complex behaviors. In this paper, we present a model for collision avoidance based on the Lobula giant movement detector (LGMD) cell of the locust. This is a wide-field visual neuron that responds to looming stimuli and that can trigger avoidance reactions whenever a rapidly approaching object is detected. Here, we present result based on both an offline study of the model and its application to a flying robot.
<title>Quick-disconnect harness system for helmet-mounted displays</title> (1992)

We have designed a pilot's harness-mounted, high voltage quick-disconnect connectors with 62 pins, to transmit voltages up to 13.5 kV and video signals with 70 MHz bandwidth, for a binocular helmet-mounted display system. It connects and disconnects with power off, and disconnects 'hot' without pilot intervention and without producing external sparks or exposing hot embers to the explosive cockpit environment. We have implemented a procedure in which the high voltage pins disconnect inside a hermetically-sealed unit before the physical separation of the connector. The 'hot' separation triggers a crowbar circuit in the high voltage power supplies for additional protection. Conductor locations and shields are designed to reduce capacitance in the circuit and avoid crosstalk among adjacent circuits. The quick- disconnect connector and wiring harness are human-engineered to ensure pilot safety and mobility. The connector backshell is equipped with two hybrid video amplifiers to improve the clarity of the video signals. Shielded wires and coaxial cables are molded as a multi-layered ribbon for maximum flexibility between the pilot's harness and helmet. Stiff cabling is provided between the quick-disconnect connector and the aircraft console to control behavior during seat ejection. The components of the system have been successfully tested for safety, performance, ergonomic considerations, and reliability.
Compact mass axis alignment device with piezoelements for optical fibers (1992)

A compact mass axis alignment device with piezoelements which can independently align individual optical fibers is proposed. Axis alignment experiments were performed with the fabricated device. The authors describe the construction of the mass axis alignment device. Experimental results of axis alignment with the fabricated device are reported. Splice loss reduction through the use of the proposed device is outlined. The estimated splicing loss that occurs when using the proposed device is 0.063 dB for 1.55- mu m DSF.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Designer Amphiphilic Short Peptides Enhance Thermal Stability of Isolated Photosystem-I (2010)

Stability of membrane protein is crucial during protein purification and crystallization as well as in the fabrication of protein-based devices. Several recent studies have examined how various surfactants can stabilize membrane proteins out of their native membrane environment. However, there is still no single surfactant that can be universally employed for all membrane proteins. Because of the lack of knowledge on the interaction between surfactants and membrane proteins, the choice of a surfactant for a specific membrane protein remains purely empirical. Here we report that a group of short amphiphilic peptides improve the thermal stability of the multi-domain protein complex photosystem-I (PS-I) in aqueous solution and that the peptide surfactants have obvious advantages over other commonly used alkyl chain based surfactants. Of all the short peptides studied, Ac-I(5)K(2)-CONH(2) (I(5)K(2)) showed the best stabilizing effect by enhancing the melting temperature of PS-I from 48.0 degrees C to 53.0 degrees C at concentration of 0.65 mM and extending the half life of isolated PS-I significantly. AFM experiments showed that PS-I/I(5)K(2)/Triton X-100 formed large and stable vesicles and thus provide interfacial environment mimicking that of native membranes, which may partly explain why I(5)K(2) enhanced the thermal stability of PS-I. Hydrophobic and hydrophilic group length of I(x)K(y) had an important influence on the stabilization of PS-I. Our results showed that longer hydrophobic group was more effective in stabilizing PS-I. These simple short peptides therefore exhibit significant potential for applications in membrane protein studies.
Gains and Amplifications of <i>c-myc, EGFR</i>, and <i>20.q13</i> Loci in the No Dysplasia–Dysplasia–Adenocarcinoma Sequence of Barrett's Esophagus (2008)

The progression of Barrett's esophagus to esophageal adenocarcinoma is often characterized by the accumulation of genetic abnormalities. The goal was to evaluate the copy number alterations of several oncogene loci, including 7p12 [epidermal growth factor receptor (EGFR)], 8q24 (c-myc), and 20q13 in the sequence of no dysplasia-dysplasia-adenocarcinoma of Barrett's esophagus. Fluorescence in situ hybridization with DNA probes for the centromeric region of chromosome 7 and the locus-specific regions of 7p12 (EGFR), 8q24 (c-myc), and 20q13 was applied on 99 brush cytology specimens of patients with Barrett's esophagus with different stages of dysplasia or esophageal adenocarcinoma. Gains (3-4 copies) of chromosome 17, 8q24 (c-myc), and 20q.13 loci were found in the low frequencies in nondysplastic Barrett's esophagus. Their frequencies increased with the stage of dysplasia and reached a high incidence in esophageal adenocarcinoma. Amplification (>4 copies) of at least 1 of the loci was observed in 14% of high-grade dysplasia and increased to 50% in esophageal adenocarcinoma (P = 0.015). The most frequently amplified locus was c-myc (18%), followed by 20q13 (13%) and EGFR (11%) in the high-grade dysplasia/esophageal adenocarcinoma cases. High amplification levels (>10 copies) of the loci were more frequent in esophageal adenocarcinoma (72%) compared with high-grade dysplasia (20%; P = 0.049). Amplifications of the c-myc, EGFR, and 20q12 loci may serve as diagnostic markers to identify patients with Barrett's esophagus with high-grade dysplasia or esophageal adenocarcinoma. Gains of the loci might be of value as prognostic markers because they are already present in nondysplasia cases and may precede the later event of the amplification as observed in high-grade dysplasia and esophageal adenocarcinoma.
Copper-zinc superoxide dismutase of Caulobacter crescentus: cloning, sequencing, and mapping of the gene and periplasmic location of the enzyme (1990)

Although widely found in the cytoplasm of eucaryotes, the copper-zinc form of superoxide dismutase (CuZnSOD) has been identified in only a small number of bacterial species. One species is the freshwater bacterium Caulobacter crescentus, which also contains an SOD with iron as the metal cofactor (FeSOD). To investigate the function of this CuZnSOD and its structural relationship to the eucaryotic CuZnSODs, the gene encoding CuZnSOD (sodC) of C. crescentus CB15 was cloned and sequenced. By hybridization to pulsed-field electrophoresis gels, sodC was mapped near cysE in the C. crescentus chromosome. Through analysis of spheroplasts, the two SODs of C. crescentus were shown to be differently localized, CuZnSOD in the periplasm and FeSOD in the cytoplasm. In its natural habitat, C. crescentus is frequently associated with blue-green algae (cyanobacteria). The oxygen evolved by these photosynthetic algae may create an extracellular oxidative stress against which the periplasmic CuZnSOD may defend more effectively than the cytoplasmic FeSOD. Amino acid sequence alignments of C. crescentus CuZnSOD with eucaryotic CuZnSODs and with CuZnSOD of Photobacterium leiognathi (the only other bacterium from which CuZnSOD has been isolated and sequenced) suggest similar supersecondary structures for bacterial and eucaryotic CuZnSODs but reveal four novel substitutions in C. crescentus CuZnSOD: a phenylalanine critical to intrasubunit hydrophobic bonding replaced by alanine, a histidine ligand of zinc replaced by aspartate, and substitutions of two other previously invariant residues that stabilize zinc or both copper and zinc. These amino acid substitutions in C. crescentus CuZnSOD may have implications for its catalysis and stability.
Molecular imaging of T4 phage in mammalian tissues and cells (2014)

Advances in phage therapy encourage scientific interest in interactions of phages with human and animal organisms. This has created a need for developing tools that facilitate studies of phage circulation and deposition in tissues and cells. Here we propose a new green fluorescent protein (GFP)-based method for T4 phage molecular imaging in living systems. The method employs decoration of a phage capsid with GFP fused to the N-terminus of Hoc protein by in vivo phage display. Fluorescent phages were positively assessed as regards their applicability for detection inside living mammalian cells (by phagocytosis) and tissues (filtering and retention by lymph nodes and spleen). Molecular imaging provides innovative techniques that have brought substantial progress in life sciences. We propose it as a useful tool for studies of phage biology.
[Myocardial protection by retrograde cardioplegic perfusion through the right atrium]. (1990)

Three types of cardioplegic delivery with ink into the isolated canine hearts were compared: (1) antegrade aortic root perfusion (AARP), (2) retrograde coronary sinus perfusion (RCSP) and (3) retrograde right atrium perfusion (RRAP). Ink was not distributed in the area distal to the coronary occlusion by AARP but well distribution in the same area by RCSP or RRAP. The right ventricular wall and ventricular septum were poorly perfused by RCSP but well perfused by RRAP. During cardiopulmonary bypass, RRAP created a fairly rapid cardiac arrest and satisfactory myocardial cooling. During Perfusion, the right heart was somewhat dilated but all the 10 canine hearts rebeat well. The left and right ventricular ejection fraction showed no significant change after bypass. No marked myocardial ultrastructural injury was found in left and right ventricles at the end of 90 minutes' ischemia. 4 patient, 1 of whom had 162 minutes' aortic cross-clamping received RRAP in operations on ascending aorta or coronary arteries and the myocardial protect ion was satisfactory. No complication was found pertaining to RRAP.
Phase Frequency Detector With Minimal Blind Zone for Fast Frequency Acquisition (2010)

Blind zone in a phase-frequency detector (PFD) reduces the input detection range and aggravates cycle slips. This brief analyzes the blind zone in latch-based PFDs and proposes a technique that removes the blind zone caused by the precharge time of the internal nodes. With the proposed technique, the PFD achieves a small blind zone close to the limit imposed by process-voltage-temperature variations. The comparison between the proposed design and previous works is presented. Fabricated in a 130-nm CMOS technology, the measured blind zone is 61 ps, which is smaller than that of the existing topologies by almost 100 ps.