gebhart/patrepeval huggingface dataset:
A-CNN: Annularly Convolutional Neural Networks on Point Clouds (2019)

Analyzing the geometric and semantic properties of 3D point clouds through the deep networks is still challenging due to the irregularity and sparsity of samplings of their geometric structures. This paper presents a new method to define and compute convolution directly on 3D point clouds by the proposed annular convolution. This new convolution operator can better capture the local neighborhood geometry of each point by specifying the (regular and dilated) ring-shaped structures and directions in the computation. It can adapt to the geometric variability and scalability at the signal processing level. We apply it to the developed hierarchical neural networks for object classification, part segmentation, and semantic segmentation in large-scale scenes. The extensive experiments and comparisons demonstrate that our approach outperforms the state-of-the-art methods on a variety of standard benchmark datasets (e.g., ModelNet10, ModelNet40, ShapeNet-part, S3DIS, and ScanNet).
Clostridium difficile Vaccine and Serum Immunoglobulin G Antibody Response to Toxin A (2003)

There is a strong association between serum antibody responses to toxin A and protection against Clostridium difficile diarrhea. A parenteral C. difficile toxoid vaccine induced very-high-level responses to anti-toxin A immunoglobulin G (IgG) in the sera of healthy volunteers. After vaccination, the concentrations of anti-toxin A IgG in the sera of all 30 recipients exceeded the concentrations that were associated with protection in previous clinical studies. Furthermore, the median concentration of serum anti-toxin A IgG in the test group was 50-fold higher than the previous threshold. These findings support the feasibility of using a vaccine to protect high-risk individuals against C. difficile-associated diarrhea and colitis.
New Convex Grating Types Manufactured by Electron Beam Lithography (1998)

The advantages of spectrometer forms utilizing concentric surfaces have been recognized for some time. 1,2 In order to realize these advantages in practice, a reliable and flexible method of generating gratings on curved substrates is needed. Concave gratings are commonly manufactured using both ruling and holographic techniques. However, it is difficult to produce well-blazed curved gratings. 3,4,5 These difficulties are exacerbated in concentric spectrometer designs in which the grating must typically cover an arc that is greater than the blaze angle itself.
Metabolism of 3-(p-chlorophenyl)pyrrolidine. Structural effects in conversion of a prototype .gamma.-aminobutyric acid prodrug to lactam and .gamma.-aminobutyric acid type metabolites (1989)

By use of rat liver or brain homogenate supernatants containing microsomes and/or mitochondria, it was found that the prototype GABAergic prodrug [3-(p-chlorophenyl)pyrrolidine (1)] underwent a series of alpha-oxidation transformations to a pair of amino acid metabolites and a pair of lactam metabolites [4-amino-3-(p-chlorophenyl)butanoic acid, baclofen (5); 4-amino-2-(p-chlorophenyl)butanoic acid (10); 4-(chlorophenyl)pyrrolidin-2-one and 3-(p-chlorophenyl)pyrrolidine-2-one (11)]. With the liver homogenates, the formation of the lactam metabolites was approximately 2 orders of magnitude greater than that of the amino acid metabolites, while with the brain homogenates, the amino acid and lactam pathways were of similar magnitude. For either tissue, for both the lactam and the amino acid series, attack at the less sterically hindered 5-position of the pyrrolidine ring was greater than the attack at the 2-position (5 greater than 10 and 6 greater than 11) with the exception of the liver homogenate mitochondrial fraction (6 less than 11). The parenteral administration of the prodrug 1 was found to give detectable brain levels of 5 as well as activity in an isoniazid-induced (GABA-inhibited) convulsion model.
A mathematical model for the distribution balance of extraction processes from waste batteries (2011)

金属 Cd 抽取的实验在油 phase/aqueous 被执行三次阶段(记帐)= 1 并且 pH 2.2 由使用 1.3 mol/L di (2-ethylhexyl ) 磷的酸(DEHPA ) 作为代理人，与 99.5% 的抽取率。金属公司抽取的实验在记帐 = 被做三次 0.5 并且 pH 4.7 由把 0.4 mol/L Cyanex 272 用作代理人，与 99.2% 的抽取率。由使用平衡数据和巨大的计算在抽取系统之中分析并且预言相互作用，这份报纸为上述二个抽取环的平衡集中象他们的参数值一样提出了实验模型的多项式。
Treatment of Sickle Cell Anemia Mouse Model with iPS Cells Generated from Autologous Skin (2007)

It has recently been demonstrated that mouse and human fibroblasts can be reprogrammed into an embryonic stem cell-like state by introducing combinations of four transcription factors. However, the therapeutic potential of such induced pluripotent stem (iPS) cells remained undefined. By using a humanized sickle cell anemia mouse model, we show that mice can be rescued after transplantation with hematopoietic progenitors obtained in vitro from autologous iPS cells. This was achieved after correction of the human sickle hemoglobin allele by gene-specific targeting. Our results provide proof of principle for using transcription factor-induced reprogramming combined with gene and cell therapy for disease treatment in mice. The problems associated with using retroviruses and oncogenes for reprogramming need to be resolved before iPS cells can be considered for human therapy.
Of Two Make One: The Biosynthesis of Phenazines (2009)

Five easy steps: Phenazines are redox-active bacterial secondary metabolites that possess broad-specificity antibiotic activity and can also play an important role as virulence factors in infectious disease. Their biosynthesis from two molecules of chorismic acid is catalyzed by enzymes encoded in the conserved phz operon.
Abstract B18: A simple method to prepare oligonucleotide-conjugated antibodies for multiplex protein detection (2016)

Abstract With rapid advances in nucleic acid detection technologies, genomics studies are being conducted in highly multiplexed formats. However, multiplex analysis is still a daunting task in the proteomics field; it would be of great interest to use genomics tools for protein detection. One way to accomplish this is to use oligonucleotide-conjugated antibodies to bind to specific protein targets, and to monitor conjugated-oligonucleotide levels rather than to measure protein levels directly. In this report we describe a simple method for preparing oligonucleotide-conjugated antibodies and discuss this method’s application in oligo extension reaction (OER) for multiplex protein detection. Conjugation is based on strain-promoted alkyne-azide cycloaddition (the Cu-free click reaction), in which the antibody is activated with a dibenzocyclooctyne (DBCO) moiety and linked covalently with an azide-modified oligonucleotide. The reaction condition and purification process were optimized to achieve maximum yield and best performance in the functional test. The OER assay employs a pair of antibody binders (two antibodies, each conjugated with its own oligonucleotide) developed for each protein target. The two oligonucleotides contain a six-base complementary region at their 3′ prime ends to allow annealing and extension by DNA synthesis enzymes to form a DNA template. The template is then detected by qPCR on the Biomark HD system. Distinct oligonucleotide sequences are assigned to different antibody binders to enable multiplex protein detection. When tested using recombinant proteins, some antibody binders, such as those specific to CSTB, MET, EpCAM and CASP3, had an estimated limit of detection (LOD) of about 0.06 pg/mL and a dynamic range of ≥5 logs. These antibody binders were used in multiplex protein detection in single cells using the C1™ system. The results in individual cells showed the expression of similar protein levels for CSTB and CASP3, but highly varied protein levels for EpCAM, CCNB1 and MUC1. This simple method for the preparation of oligonucleotide-conjugated antibodies is essential for the development of affordable multiplex protein assays, which has the potential to accelerate proteomics research. Citation Format: Haibiao Gong, Ilona Holcomb, Aik Ooi, Xiaohui Wang, Daniel Majonis, Marc Unger, Ramesh Ramakrishnan. A simple method to prepare oligonucleotide-conjugated antibodies for multiplex protein detection. [abstract]. In: Proceedings of the Fourth AACR International Conference on Frontiers in Basic Cancer Research; 2015 Oct 23-26; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2016;76(3 Suppl):Abstract nr B18.
Diagnosis of Renal Vascular Disease with MR Angiography (1999)

Renal magnetic resonance (MR) angiography allows accurate evaluation of patients suspected to have renal artery stenosis without the risks associated with nephrotoxic contrast agents, ionizing radiation, or arterial catheterization. Other applications of renal MR angiography are mapping the vascular anatomy for planning renal revascularization, planning repair of abdominal aortic aneurysms, assessing renal bypass grafts and renal transplant anastomoses, and evaluating vascular involvement by renal tumors. A variety of pulse sequences provide complementary information about kidney morphology, arterial anatomy, blood flow, and renal function and excretion. Three-dimensional gadolinium-enhanced MR angiography can be combined with several other sequences to produce a comprehensive approach to renal MR angiography. This comprehensive approach is designed to allow hemodynamic characterization of renal artery stenosis with a single MR imaging examination that can be easily completed in 1 hour. Three-dimensional gadolinium-enhanced MR angiography demonstrates the renal arteries along with the abdominal aorta, iliac arteries, and mesenteric arteries in a 20-30-second acquisition that can be performed during breath holding. Numerous projections are reconstructed from a single three-dimensional volume of data acquired with a single injection of contrast material to obtain perpendicular and optimized views of each renal artery.
GaAs/GaAlAs curved rib waveguides (1982)

Curved dielectric optical waveguides suffer from radiation loss due to bending. To minimize the bending loss and reduce the radius of curvature, it is necessary to fabricate guides which provide strong optical confinement. This paper gives a brief review of curved waveguide analysis and presents some experimentally measured loss values for GaAs/GaAlAs curved rib waveguides. The rib waveguides, fabricated using ion beam milling, have a large rib height and are tightly guided structures. When corrected for reflection losses and input coupling efficiency, a minimum loss of approximately 3 dB has been achieved for a multimode 90° curved guide with a radius of curvature of 300 μm, and 8.5 dB for a single-mode curved guide with a radius of curvature of 400 μm. It is believed that most of this residual loss is not radiation loss due to bending, but rather scattering loss due to rib wall imperfections.
IL-11 regulates macrophage effector function through the inhibition of nuclear factor-kappaB (1997)

Recombinant human IL-11 (rhIL-11) is an anti-inflammatory cytokine that can reduce the production of inflammatory mediators such as TNF-alpha, IL-1beta, IL-12, IL-6, and nitric oxide. Inhibition of proinflammatory cytokine production from activated macrophages was associated with a reduction in the levels of LPS-induced TNF-alpha, IL-1beta, IL-6, and IL-12 p40 mRNA. Analysis of rhIL-11 effects on transcription factors that activate proinflammatory cytokines demonstrated that the level of LPS-induced NF-kappaB binding activity in the nucleus of rhIL-11-treated peritoneal macrophages was significantly reduced. The block to NF-kappaB nuclear translocation correlated with the ability of rhIL-11 to maintain or increase protein levels of the inhibitors of NF-kappaB, IkappaB-alpha, and IkappaB-beta following LPS treatment. Furthermore, rhIL-11-treatment of LPS macrophages resulted in significant elevation of IkappaB-alpha and IkappaB-beta mRNA levels. These results suggest that the anti-inflammatory activity of rhIL-11 is mediated in part by inhibition of NF-kappaB-dependent transcriptional activation. Furthermore, these studies demonstrate for the first time the regulation of IkappaB-beta by an anti-inflammatory cytokine. Given the finding that inappropriate activation of NF-kappaB contributes to multiple inflammatory conditions, the ability of rhIL-11 to inhibit the binding activity of this pleiotropic transcription factor indicates that rhIL-11 has therapeutic potential in a wide range of diseases.
HNS: Speech modification based on a harmonic+noise model (1993)

HNS (harmonic plus noise synthesis), an analysis/modification/synthesis model based on a harmonic plus noise representation of the speech signal, is presented. Significant improvements over previous work on the subject are proposed at both the analysis and the synthesis stages: a model of harmonically related sinusoids with linearly varying complex amplitudes for the representation of the deterministic part of the signal; a joint time-domain and frequency-domain representations of the stochastic part of the signal; and a pitch-synchronous PSOLA (pitch-synchronized overlap-add)-like synthesis scheme. Informal listening-tests demonstrate the effectiveness of this approach for time-scale modifications.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Oligonucleotide Conjugates for Therapeutic Applications (2013)

Insufficient pharmacokinetic properties and poor cellular uptake are the main hurdles for successful therapeutic development of oligonucleotide agents. The covalent attachment of various ligands designed to influence the biodistribution and cellular uptake or for targeting specific tissues is an attractive possibility to advance therapeutic applications and to expand development options. In contrast to advanced formulations, which often consist of multiple reagents and are sensitive to a variety of preparation conditions, oligonucleotide conjugates are defined molecules, enabling structure-based analytics and quality control techniques. This review gives an overview of current developments of oligonucleotide conjugates for therapeutic applications. Attached ligands comprise peptides, proteins, carbohydrates, aptamers and small molecules, including cholesterol, tocopherol and folic acid. Important linkage types and conjugation methods are summarized. The distinct ligands directly influence biochemical parameters, uptake mechanisms and pharmacokinetic properties.
From famine to feast: the role of methylglyoxal production in Escherichia coli (1998)

The enzyme methylglyoxal synthase (MGS) was partially purified from Escherichia coli extracts, and the amino-terminal sequence of candidate proteins was determined, based on the native protein being a tetramer of about 69 kDa. Database analysis identified an open reading frame in the E. coli genome, YccG, corresponding to a protein of 16.9 kDa. When amplified and expressed from a controlled promoter, it yielded extracts that contained high levels of MGS activity. MGS expressed from the trc promoter accumulated to approximately 20% of total cell protein, representing approximately 900-fold enhanced expression. This caused no detriment during growth on glucose, and the level of methylglyoxal (MG) in the medium rose to only 0.08 mM. High-level expression of MGS severely compromised growth on xylose, arabinose and glycerol. A mutant lacking MGS was constructed, and it grew normally on a range of carbon sources and on low-phosphate medium. However, the mutant failed to produce MG during growth on xylose in the presence of cAMP, and growth was inhibited.
Supramolecular polymers at work (2004)

Sophisticated polymeric materials with ‘responsive’ properties are beginning to reach the market. The use of reversible, noncovalent interactions is a recurring design principle for responsive materials. Now, recently developed hydrogen-bonding units allow this design principle to be taken to its extreme. Supramolecular polymers, where hydrogen bonds are the only force keeping the monomers together, form materials whose (mechanical) properties respond strongly to a change in temperature or solvent. In this review, we describe the developments that have led to hydrogen-bonded supramolecular polymers and discuss the use of these materials in advanced applications.
Simultaneous measurement of strain and temperature based on polarization loss properties of arc-induced long-period gratings (2004)

A new sensing configuration is proposed for simultaneous measurement of strain and temperature that relies on a single long period grating written by the electric arc technique. The underlying principle is the azimuthal asymmetry induced by the electric arc fabrication technique, which results in a device with polarization dependent insertion loss sensitive to both temperature and strain. With the proposed configuration, resolutions of &plusmn;2.8&deg;C/&radic;Hz and &plusmn;13.9&mu;&epsilon;/&radic;Hz are obtained for temperature and strain measurements, respectively.
Human CD100, a novel leukocyte semaphorin that promotes B-cell aggregation and differentiation. (1996)

Herein we describe the molecular characterization of the human leukocyte activation antigen CD100 and identify it as the first semaphorin, to our knowledge, in the immune system. Semaphorins have recently been described as neuronal chemorepellants that direct pioneering neurons during nervous system development. In this study we demonstrate that CD100 induces B cells to aggregate and improves their viability in vitro. We show that CD100 modifies CD40-CD40L B-cell signaling by augmenting B-cell aggregation and survival and down-regulating CD23 expression. Thus, these results suggest that semaphorins as exemplified by CD100 also play a functional role in the immune system.
The effect of carp EGG-mRNA on the transformation of goldfish tail. (1977)

Poly A attached mRNA was prepared from carp's mature ovarian eggs. When injected into fertilized eggs from different strains of goldfish, it mediated tail transformation from the double to single. The frequency varied according to the strain of goldfish. This discovery provides new information not only supporting but also expanding the previous report that crucian egg-mRNA mediated tail transformation in goldfish.
5‐Hydroxytryptamine increases excitability of CA1 hippocampal pyramidal cells (1992)

In the presence of spiperone to block the 5-HT1A-mediated inhibition of pyramidal cell activity, 5-hydroxytryptamine (serotonin, 5-HT) produces a rapid transient increase in amplitude of the extracellularly recorded population spike from area CA1 of the hippocampus. Intracellular recording techniques in area CA1 of rat hippocampal slices were used to identify the ionic mechanism and to characterize the 5-HT receptor mediating this excitatory response to 5-HT. Most of the experiments were conducted in the presence of spiperone to block the 5HT1A hyperpolarization. Since spiperone also has high affinity for 5-HT2 receptors, any response mediated by 5-HT2 receptors would also be blocked. Bath perfusion of the slice with 5-HT increased the rectification of pyramidal cells in the subthreshold region, increased the resistance, and increased the amplitude of subthreshold excitatory postsynaptic potentials (EPSPs) to initiate spike firing. The 5-HT2,1C-selective agonist DOI mimicked this effect of 5-HT, and the 5-HT2,1C antagonist ketanserin (1 microM) blocked the effect of DOI. There was no change in the amplitude of the slow afterhyperpolarization (sAHP) or the amplitude of evoked inhibitory postsynaptic potentials (IPSPs). The increase in rectification and EPSP amplitude by 5-HT occurred even in the presence of the 5-HT4-selective antagonist BRL 24924 to prevent the decrease in amplitude of the sAHP by 5-HT. We conclude that 5-HT produces a fast excitatory response by increasing subthreshold conductance in CA1 hippocampal pyramidal cells. The identity of the receptor mediating this response was not conclusively identified, but resembled the 5-HT1C receptor.
SURFACE MODIFICATION ISSUES FOR ORTHOPAEDIC IMPLANT BEARING SURFACES (1992)

ABSTRACT In total joint replacement, generally a polished metal surface articulates against an ultra high molecular weight polyethylene (UHMWPE) counter bearing surface. Metals used include 316L stainless steel, Co-Cr-Mo alloy, and Ti-6AI-4V alloy (particularly with a hardened N+ ion implanted surface). Minimizing friction and UHMWPE wear is of prime concern for long-term performance. Additionally, it is desirable to minimize metal ion release which results from constant removal and reformation of passive surface oxides and oxyhydroxides during articulation. Long term effects from the presence of potentially toxic or carcinogenic ions of Cr, Co, Mo, Ni, V, and Al are not well known. Inert ceramic bearing surfaces eliminate this issue and are also resistant to potential three-body wear from bone cement debris or potential stray porous metal coating material. However ceramic (Al2O3 and ZrO2) materials are only available for total hip replacement. For total knee replacement, ft is too difficult and expensive to manufacture a monolithic ceramic knee surface, thus various surface coating methods are being investigated. These methods include plasma sprayed Al2O3 and ZrO2, TiN and amorphous diamond like coatings via PVD/CVD methods, and in-sKu oxidation. In other cases, the existing metal surfaces are simply hardened using methods such as N+ ion implantation and oxygen or nitrogen diffusion hardening. This paper reviews the limitations of existing total joint systems and the effectiveness of various surface modification methods of orthopaedic implant bearing surfaces on friction, abrasion, UHMWPE wear, and metal ion release.
Saccharomyces cerevisiae elongation factor 2. Genetic cloning, characterization of expression, and G-domain modeling. (1992)

The elongation factor 2 (EF-2) genes of the yeast Saccharomyces cerevisiae have been cloned and characterized with the ultimate goal of gaining a better understanding of the mechanism and control of protein synthesis. Two genes (EFT1 and EFT2) were isolated by screening a bacteriophage lambda yeast genomic DNA library with an oligonucleotide probe complementary to the domain of EF-2 that contains diphthamide, the unique posttranslationally modified histidine that is specifically ADP-ribosylated by diphtheria toxin. Although EFT1 and EFT2 are located on separate chromosomes, the DNA sequences of the two genes differ at only four positions out of 2526 base pairs, and the predicted protein sequences are identical. Genetic deletion of each gene revealed that at least one functional copy of either EFT gene is required for cell viability. Messenger RNA levels of yeast EF-2 parallel cellular growth and peak in mid-log phase cultures. The EF-2 protein sequence is strikingly conserved through evolution. Yeast EF-2 is 66% identical to, and shares over 85% homology with, human EF-2. In addition, yeast and mammalian EF-2 share identical sequences at two critical functional sites: (i) the domain containing the histidine residue that is modified to diphthamide and (ii) the threonine residue that is specifically phosphorylated in vivo in mammalian cells by calmodulin-dependent protein kinase III, also known as EF-2 kinase. Furthermore, yeast EF-2 also contains the Glu-X-X-Arg-X-Ile-Thr-Ile "effector" sequence motif that is conserved among all known elongation factors, and its GTP-binding domain exhibits strong homology to the G-domain of Escherichia coli elongation factor Tu (EF-Tu) and other G-protein family members. Based upon these observations, we have modeled the G-domain of the deduced EF-2 protein sequence to the solved crystallographic structure for EF-Tu.