gebhart/patrepeval huggingface dataset:
PointGrid: A Deep Network for 3D Shape Understanding (2018)

Volumetric grid is widely used for 3D deep learning due to its regularity. However the use of relatively lower order local approximation functions such as piece-wise constant function (occupancy grid) or piece-wise linear function (distance field) to approximate 3D shape means that it needs a very high-resolution grid to represent finer geometry details, which could be memory and computationally inefficient. In this work, we propose the PointGrid, a 3D convolutional network that incorporates a constant number of points within each grid cell thus allowing the network to learn higher order local approximation functions that could better represent the local geometry shape details. With experiments on popular shape recognition benchmarks, PointGrid demonstrates state-of-the-art performance over existing deep learning methods on both classification and segmentation.
Targeted mutation of Ncam to produce a secreted molecule results in a dominant embryonic lethality. (1996)

The neural cell adhesion molecule (NCAM) is a membrane-associated member of the immunoglobulin superfamily capable of both homophilic and heterophilic binding. To investigate the significance of this binding, a gene targeting strategy in embryonic stem (ES) cells was used to replace the membrane-associated forms of NCAM with a soluble, secreted form of its extracellular domain. Although the heterozygous mutant ES cells were able to generate low coat color chimeric mice, only the wild-type allele was transmitted, suggesting the possibility of dominant lethality. Analysis of chimeric embryos with high level of ES cell contribution revealed severe growth retardation and morphological defects by E8.5-E9.5. The second allele was also targeted, and embryos derived almost entirely from the homozygous mutant ES cells exhibited the same lethal phenotype as observed with heterozygous chimeras. Together, these results indicate that dominant lethality associated with the secreted NCAM does not require the presence of membrane-associated NCAM. Furthermore, the data indicate that potent bioactive cues or signals can be generated by NCAM.
HOMOLOGOUS SERUM JAUNDICE AND ITS RELATION TO METHODS OF PLASMA STORAGE (1950)

The infective agent responsible for homologous serum jaundice or serum hepatitis is thought to be a virus. It is transmitted by transfusion or inoculation in man by human products, particularly by blood, plasma or serum, but it has not been successfully transmitted to other species. The disease has been produced in human volunteers by as little as 0.1 cc. of infected plasma. 1 For this reason, one donor who is a carrier of the disease can infect an entire pool of plasma. It has been recommended that the donor population of pooled plasma not exceed five and that plasma be used only as an emergency measure. As a consequence, plasma is not used as extensively as before. This hazard of pooled plasma must be overcome if it is to be stockpiled and used for civilian defense. The purpose of this report is twofold: first, to call attention to the fact
Delayed cutaneous hypersensitivity to autologous tumor cells in colorectal cancer patients immunized with an autologous tumor cell: Bacillus Calmette-Guérin vaccine. (1984)

The principles and procedures of active specific immunotherapy developed from studies with the inbred guinea pig hepatocarcinoma model were used as the basis of a randomized, controlled prospective trial of active specific immunotherapy of colorectal cancer patients. The goal was to determine whether colorectal cancer patients treated with vaccines made of autologous tumor cells plus Bacillus Calmette-Guérin as adjuvant would have an increased reaction to their autologous tumor cells as measured by delayed-type cutaneous hypersensitivity (DCH) responses. Our results demonstrate that the active specific immunotherapy significantly increased the DCH responses to autologous tumor cells in 16 of 24 patients (67%). The DCH response of immunized patients to autologous normal mucosa, used as a normal tissue control, did not increase significantly. Furthermore, no significant DCH responses against autologous tumor or mucosa cells were detected in a group of nonimmunized control patients. The induced DCH responses were not correlated with other factors, such as the presence of bacteria in the cell preparation or the protein concentration of the cell preparations. The qualitative and quantitative differences in DCH responses to tumor cells and to normal mucosa cells suggest that the immunizations are targeted mainly to tumor-associated antigens with tissue-associated antigens playing a secondary role.
Computer-aided gene design (1992)

A computer program, which runs on MS-DOS personal computers, is described that assists in the design of synthetic genes coding for proteins. The goal of the program is the design of a gene which (i) contains as many unique restriction sites as possible and (ii) uses a specific codon usage. The gene designed according to the criteria above is (i) suitable for 'modular mutagenesis' experiments and (ii) optimized for expression. The program 'reverse-translates' protein sequences into degenerated DNA sequences, generates a map of potential restriction sites and locates sequence positions where unique restriction sites can be accommodated. The nucleic acid sequence is then 'refined' according to a specific codon usage to remove any degeneration. Unique restriction sites, if potentially present, can be 'forced' into the degenerated nucleic acid sequence by using 'priority codes' assigned to different restriction sequences.
DNA Vaccines Employing Intracellular Targeting Strategies and a Strategy to Prolong Dendritic Cell Life Generate a Higher Number of CD8 + Memory T Cells and Better Long-Term Antitumor Effects Compared with a DNA Prime–Vaccinia Boost Regimen (2005)

We have previously shown that intradermal coadministration of DNA encoding Bcl-x(L), an antiapoptotic protein, with DNA encoding E7 antigen linked to the sorting signal of the lysosome-associated membrane protein type 1 (Sig/E7/LAMP-1) prolongs dendritic cell life and enhances antigen presentation through the MHC class I and II pathways. In the current study, we compared this approach with a conventional DNA prime-vaccinia boost protocol on the basis of their ability to generate antigen-specific CD8(+) memory T cells and longterm antitumor effects against an E7-expressing tumor. Mice primed and boosted with Sig/E7/LAMP-1 DNA mixed with Bcl-x(L) DNA generated significantly higher numbers of E7-specific CD8(+) memory T cells and a better long-term protective antitumor effect compared with mice primed with Sig/E7/LAMP-1 DNA and boosted with Sig/E7/LAMP-1 vaccinia (Vac-Sig/E7/LAMP-1). Furthermore, coadministration of Sig/E7 /LAMP-1 DNA mixed with Bcl-x(L) DNA also generated higher avidity E7-specific CD8(+) T cells than did vaccination with Sig/E7/LAMP-1 DNA followed by a Vac-Sig/E7/LAMP-1 booster. Our results indicate that coadministration of a DNA vaccine employing intracellular targeting strategies and a DNA encoding antiapoptotic proteins may potentially generate a higher number of memory CD8(+) T cells and better long-term protective antitumor effects compared with the conventional DNA prime-vaccinia boost regimen.
Single-Chain Fv/Folate Conjugates Mediate Efficient Lysis of Folate-Receptor-Positive Tumor Cells (1997)

Bispecific antibodies that bind to a tumor antigen and the T cell receptor (TCR) redirect cytotoxic T lymphocytes (CTL) to lyse tumor cells which have escaped normal immune recognition mechanisms. One well-characterized tumor antigen, the folate receptor (FR), is expressed on most ovarian carcinomas and some types of brain cancer. Recently, it was shown that conjugates of folate and anti-TCR antibodies are extremely potent bispecific agents that target tumor cells expressing the high-affinity folate receptor, but not normal cells expressing only the reduced folate carrier protein. In this paper, it is shown that the size of these conjugates can be reduced to the smallest bispecific agent yet described (30 kDa) by attaching folate to a single-chain antibody, scFv, of the anti-TCR antibody KJ16. The scFv/folate conjugates are as effective as IgG/folate conjugates in mediating lysis of FR4 tumor cells by CTL. The optimal folate density was in the range of 5-15 folate molecules per scFv or IgG molecule, which yielded half-maximal lysis values (EC50) of approximately 40 pM (1.2 ng/mL for scFv). Finally, the scFv/folate conjugates could efficiently target tumor cells even in the presence of free folic acid at concentrations that are normally found in serum. Compared to conventional bispecific antibodies, the small size of scFv/folate conjugates may prove advantageous in the ability to penetrate tumors and in reduced immunogenicity.
An IPv6 Routing Header for Source Routes with the Routing Protocol for Low-Power and Lossy Networks (RPL) (2012)

In Low-Power and Lossy Networks (LLNs), memory constraints on routers
may limit them to maintaining, at most, a few routes. In some
configurations, it is necessary to use these memory-constrained
routers to deliver datagrams to nodes within the LLN. The Routing
Protocol for Low-Power and Lossy Networks (RPL) can be used in some
deployments to store most, if not all, routes on one (e.g., the
Directed Acyclic Graph (DAG) root) or a few routers and forward the
IPv6 datagram using a source routing technique to avoid large routing
tables on memory-constrained routers. This document specifies a new
IPv6 Routing header type for delivering datagrams within a RPL routing
domain. [STANDARDS-TRACK]
Early Intrathecal Production of Interleukin-6 Predicts the Size of Brain Lesion in Stroke (1995)

Our study demonstrates an intrathecal production of IL-6 and IL-1 beta in patients with stroke, supporting the notion of localized inflammatory response to acute brain lesion. In addition, the significant correlation between early intrathecal production of IL-6 and the subsequent size of the brain lesion can be used as a prognostic tool, predicting the size of the brain damage before it is possible to accurately visualize it with radiological methods.
Setting time and sealing ability of alpha-tricalcium phosphate cement containing titanic oxide. (1998)

We developed a new type of calcium phosphate cement for clinical use in endodontics as a root canal sealer or pulp cupping agent. The solid phase of the sealer is composed of 70% of alpha-tricalcium phosphate (alpha-TCP) and 30% of titanic oxide (TiO2), and the liquid phase is 37% citric acid, 5% tannic acid and 58% distilled water. TiO2 was added to control setting time and handling of the cement. We used commercially available calcium phosphate root canal sealer as a control. ISO standards specify that new endodontic products should be examined thoroughly before clinical use. It is important to carry out in vitro cytotoxicity and in vivo histocompatibility tests. We first did in vitro test of setting time and root canal sealing ability of the cement. We found that this developed calcium phosphate cement had an appropriate setting time and excellent sealing ability as a root canal sealer, and concluded that it was suitable for clinical use as a root canal sealer.
Stress-induced transcription of the clusterin/apoJ gene (1997)

Clusterin/apoJ is an intriguing gene frequently isolated by differential screening in laboratories from different areas of molecular biology, since it is overexpressed in numerous cases of degenerative diseases such as Alzheimer's disease and scrapie. While the dramatic increase of clusterin expression in injured tissues is well established, the molecular basis of the gene induction remains unclear. In this study, we have focused our attention on the only DNA region strictly conserved between clusterin gene proximal promoters from different vertebrate classes. We show that this 14-bp DNA element is specifically recognized by the HSF1 transcription factor and can mediate heat-shock-induced transcription in transient expression assays. Conversely, the avian clusterin proximal promoter, point-mutated at the level of this element, no longer transmits heat-shock activation. These findings provide a possible explanation for the high sensitivity of clusterin expression to environmental changes and allow the classification of clusterin as an extracellular version of heat-shock protein.
Toward Efficient Trajectory Planning: The Path-Velocity Decomposition (1986)

We present a novel approach to solving the trajectory plan ning problem (TPP) in time-varying environments. The es sence of our approach lies in a heuristic but natural decom position of TPP into two subproblems: (1) planning a path to avoid collision with static obstacles and (2) planning the velocity along the path to avoid collision with moving obsta cles. We call thefirst subproblem the path planning problem (PPP) and the second the velocity planning problem (VPP). Thus, our decomposition is summarized by the equation TPP =&gt; PPP + VPP. The symbol =&gt; indicates that the de composition holds under certain assumptions, e.g., when obstacles are moving independently of ( i.e., not tracking ) the robot. Furthermore, we pose the VPP in path-time space, where time is explicitly represented as an extra dimension, and reduce it to a graph search in this space. In fact, VPP is transformed to a two-dimensional PPP in path-time space with some additional constraints. Algorithms are then pre sented to solve the VPP with different optimality criteria: minimum length in path-time space, and minimum time.
Hierarchical structural control of visual properties in self-assembled photonic-plasmonic pigments (2014)

We present a simple one-pot co-assembly method for the synthesis of hierarchically structured pigment particles consisting of silica inverse-opal bricks that are doped with plasmonic absorbers. We study the interplay between the plasmonic and photonic resonances and their effect on the visual appearance of macroscopic collections of photonic bricks that are distributed in randomized orientations. Manipulating the pore geometry tunes the wavelength- and angle-dependence of the scattering profile, which can be engineered to produce angle-dependent Bragg resonances that can either enhance or contrast with the color produced by the plasmonic absorber. By controlling the overall dimensions of the photonic bricks and their aspect ratios, their preferential alignment can either be encouraged or suppressed. This causes the Bragg resonance to appear either as uniform color travel in the former case or as sparse iridescent sparkle in the latter case. By manipulating the surface chemistry of these photonic bricks, which introduces a fourth length-scale (molecular) of independent tuning into our design, we can further engineer interactions between liquids and the pores. This allows the structural color to be maintained in oil-based formulations, and enables the creation of dynamic liquid-responsive images from the pigment.
Active Probing Approach for Fault Localization in Computer Networks (2006)

Active probing is an active network monitoring technique that has potential for developing effective solutions for fault localization. In this paper we use active probing to present an approach to develop tools for performing fault localization. We discuss various design issues involved and propose architecture for building such a tool. We describe an algorithm for probe set selection for problem detection and present simulation results to show its effectiveness. We demonstrate through analysis and experiments that active probing has the potential to greatly reduce the probe traffic and the fault diagnosis time.
UBIQUITIN AND THE CONTROL OF PROTEIN FATE IN THE SECRETORY AND ENDOCYTIC PATHWAYS (1998)

The modification of proteins by chains of ubiquitin has long been known to mediate targeting of cytosolic and nuclear proteins for degradation by proteasomes. In this article, we discuss recent developments that reveal the involvement of ubiquitin in the degradation of proteins retained within the endoplasmic reticulum (ER) and in the internalization of plasma membrane proteins. Both luminal and transmembrane proteins retained in the ER are now known to be retrotranslocated into the cytosol in a process that involves ER chaperones and components of the protein import machinery. Once exposed to the cytosolic milieu, retro-translocated proteins are degraded by the proteasome, in most cases following polyubiquitination. There is growing evidence that both the ubiquitin-conjugating machinery and proteasomes may be associated with the cytosolic face of the ER membrane and that they could be functionally coupled to the process of retrotranslocation. The ubiquitination of plasma membrane proteins, on the other hand, mediates internalization of the proteins, which in most cases is followed by lysosomal/vacuolar degradation. There is, however, a well-documented case of a plasma membrane protein (the c-Met receptor) for which ubiquitination results in proteasomal degradation. These recent findings imply that ubiquitin plays more diverse roles in the regulation of the fate of cellular proteins than originally anticipated.
Observation of Recording Pole Instability in Perpendicular Recording (2006)

Down- and cross-track distributions of medium magnetization are determined by the recording pole field profile and the switching dynamics. Earlier studies of the write pole footprint in perpendicular magnetic recording revealed asymmetrical media saturation caused by magnetic pole nonuniformity. In this paper, we report variable footprint shapes indicating recording pole instability. We extend our spin-stand "footprint" measurements to also evaluate recording pole instability
Fundamentals of Carrier Transport (2000)

Fundamentals of Carrier Transport is an accessible introduction to the behaviour of charged carriers in semiconductors and semiconductor devices. It is written specifically for engineers and students without an extensive background in quantum mechanics and solid-state physics. This second edition contains many new and updated sections, including a completely new chapter on transport in ultrasmall devices. The author begins by covering a range of essential physical principles. He then goes on to cover both low- and high-field transport, scattering, transport in devices, and transport in mesoscopic systems. The use of Monte Carlo simulation methods is explained in detail. Many homework exercises are provided and there are a variety of worked examples. The book will be of great interest to graduate students of electrical engineering and applied physics. It will also be invaluable to practising engineers working on semiconductor device research and development.
Acute cAMP Stimulation in Leydig Cells: Rapid Accumulation of a Protein Similar to That Detected in Adrenal Cortex and Corpus Luteum (1986)

Addition of cAMP (as the dibutyryl compound) to a primary culture of mouse Leydig cells caused the accumulation of a protein, i(b), with the same dependence on cAMP concentration as the increase in testosterone synthesis. Stimulation of both protein i(b) and testosterone production were inhibited by cycloheximide. Additionally, cAMP caused repression of synthesis of another protein, p(b), with the same approximate molecular weight (28,000 daltons) as i(b), but more basic isoelectric point. This behavior resembles an event which has been documented in the adrenal cortex (Krueger, R.J., and Orme-Johnson, N.R., J. Biol. Chem., 258, 10159-10167, 1983) and corpus luteum (Pon, L.A., and Orme-Johnson, N.R., J. Biol. Chem., 261, 6594-6599, 1986). The discovery of these proteins in a third steroid-producing cell type and the close correlation between conditions causing increased steroid synthesis and increased i(b) production is further indication that protein i(b) may be an intermediary in peptide hormone or cAMP control of steroid hormone biosynthesis.
Rational design of potent domain antibody inhibitors of amyloid fibril assembly (2012)

Antibodies hold significant potential for inhibiting toxic protein aggregation associated with conformational disorders such as Alzheimer's and Huntington's diseases. However, near-stoichiometric antibody concentrations are typically required to completely inhibit protein aggregation. We posited that the molecular interactions mediating amyloid fibril formation could be harnessed to generate antibodies with potent antiaggregation. Here we report that grafting small amyloidogenic peptides (6-10 residues) into the complementarity-determining regions of a single-domain (V(H)) antibody yields potent domain antibody inhibitors of amyloid formation. Grafted AMyloid-Motif AntiBODIES (gammabodies) presenting hydrophobic peptides from Aβ (Alzheimer's disease), α-Synuclein (Parkinson's disease), and islet amyloid polypeptide (type 2 diabetes) inhibit fibril assembly of each corresponding polypeptide at low substoichiometric concentrations (1:10 gammabody:monomer molar ratio). In contrast, sequence- and conformation-specific antibodies that were obtained via immunization are unable to prevent fibrillization at the same substoichiometric concentrations. Gammabodies prevent amyloid formation by converting monomers and/or fibrillar intermediates into small complexes that are unstructured and benign. We expect that our antibody design approach--which eliminates the need for immunization or screening to identify sequence-specific domain antibody inhibitors--can be readily extended to generate potent aggregation inhibitors of other amyloidogenic polypeptides linked to human disease.
Facile Total Synthesis of Benzo[b]furan Natural Product XH-14 (2009)

Abstract An efficient and practical total synthesis of benzo[b]furan natural product XH-14 is demonstrated in nine steps from vanillin. Introduction of iodide substituents in the reaction including optimization of the reaction sequences is essential for the successful synthesis of XH-14. Sonogashira coupling with iodobenzene, iodine-induced cyclization, Wittig reaction, and formylation are critical in the high-yield total synthesis of XH-14.
Code completion with statistical language models (2014)

We address the problem of synthesizing code completions for programs using APIs. Given a program with holes, we synthesize completions for holes with the most likely sequences of method calls.
Reactive oxygen species facilitate the in vitro and in vivo lipopolysaccharide-induced release of tumor necrosis factor. (1989)

Secretion of TNF from mouse peritoneal macrophages exposed to LPS in vitro was enhanced in the presence of H2O2 or sodium periodate. Neither of these agents induced release of TNF in the absence of LPS. Both iron chelators and free radical scavengers inhibited this enhanced secretion of TNF, implying the involvement of free radicals via a Fenton-type reaction. Oxidant stress, in the form of alloxan or divicine, also enhanced serum levels of TNF in mice made sensitive to LPS by low-level infection with malaria, and then given i.v. LPS. Pretreatment with the iron chelator, desferal, or the free radical scavenger, BHA, inhibited TNF release in these animals. Less TNF was also detected in mice given desferal before LPS in the absence of exogenous radical generator. These results could have implications for understanding the details of the MLR, the adherence of neutrophils to the walls of pulmonary vessels in free radical-induced lung pathology, and the side effects of bleomycin.