gebhart/patrepeval huggingface dataset:
The effect of nonionic surfactant structure on hemolysis (1993)

The hemolytic properties of polyoxyethylene‐type nonionic surfactants were investigated in the concentration range of 0.1–5.0 wt/vol%. The effects of hydrophiliclipophilic balance, molecular weight, chemical structure and solubilizing ability of the nonionic surfactants in hemolysis are discussed. Bulky surfactants with three or four alkyl chains in their molecules, which show low solubilizing ability of lipids, were the least likely to induce hemolysis. Morphological observations of erythrocytes by video‐enhanced microscopy showed that linear surfactants induce the formation of spherocytes and cause hemolysis, whereas bulky surfactants induce only morphological changes from discocytes to spheroechinocytes.
Nineteen Baculovirus Open Reading Frames, Including LEF-12, Support Late Gene Expression (1998)

A set of 18 plasmid subclones of the Autographa californica nuclear polyhedrosis virus genome, each containing an identified late expression factor gene (lef), supports expression from a late viral promoter in transient expression assays in the SF-21 cell line derived from Spodoptera frugiperda. We have constructed a further set of plasmids in which each lef open reading frame (ORF) is controlled by the Drosophila melanogaster heat shock protein 70 (hsp70) promoter and epitope tagged. Failure of this set of plasmids to support transient late gene expression, and the inability of the p47 ORF to replace the p47-containing plasmid supplied in the lef plasmid library, led to the identification of a 19th late expression factor gene (lef-12) located adjacent to the p47 gene. The sequence of lef-12 is predicted to encode a protein of 21 kDa with no homology to any previously identified protein. The set of 19 hsp70-controlled lef ORFs (HSEpiHis lef library) supports transient expression from a late viral promoter. lef-12 did not affect expression from an early baculovirus promoter. In TN-368 cells, which are also permissive for virus replication, lef-12 provided a stimulatory effect but did not appear to be essential.
Filtration of Beauveria bassiana with high-yield chitosanase and its activity of hydrolyzing chitosan (1999)

Two high chitosanase producing mutant srains mutagenized by UV were obtained. The experimental results indicated that the highest-yield mutant^s chitosanase activity in the fermentation liquid was 0.2U/ml and 8 times higher than the original strain. Some certain kinds of chitosan oligosaccharides were obtained.
Therapeutic Angiogenesis: Controlled Delivery of Angiogenic Factors (2012)

Therapeutic angiogenesis aims at treating ischemic diseases by generating new blood vessels from existing vasculature. It relies on delivery of exogenous factors to stimulate neovasculature formation. Current strategies using genes, proteins and cells have demonstrated efficacy in animal models. However, clinical translation of any of the three approaches has proved to be challenging for various reasons. Administration of angiogenic factors is generally considered safe, according to accumulated trials, and offers off-the-shelf availability. However, many hurdles must be overcome before therapeutic angiogenesis can become a true human therapy. This article will highlight protein-based therapeutic angiogenesis, concisely review recent progress and examine critical challenges. We will discuss growth factors that have been widely utilized in promoting angiogenesis and compare their targets and functions. Lastly, since bolus injection of free proteins usually result in poor outcomes, we will focus on controlled release of proteins.
Surface Finishing of Selective Laser Sintering Parts with Robot (1998)

Compared with conventional subtractive manufacturing technologies, RP has great benefits in shortening the design-manufacture cycle time of a product. Even ifmechanical properties are not considered, most RP products still cannot be directly used in applications until the requirements for overall surface quality are satisfied. To improve the overall surface quality of Selective Laser Sintering parts, a robotic finishing system has been developed as a part of an ongoing research project. A finishing tool is held by a robot and moved according to programmed paths generated from the original CAD model data. This paper describes the experimental system in detail and shows that the surface roughness, dimensional accuracy, and geometrical accuracy can be improved.
Metalloproteinases in degenerative aortic disease (1991)

1. Atherosclerosis and aneurysm of the abdominal aorta are associated with thinning of the medial connective tissue. We have investigated the presence of the connective-tissue-degrading metalloproteinases in homogenates prepared from atherosclerotic, aneurysmal and control aortic media. 2. Gelatinase activity was much increased in homogenates from atherosclerotic and aneurysmal aorta [10.9 +/- 1.8 and 13.3 +/- 3.3 micrograms of gelatin hydrolysed h-1 (mg of protein)-1 respectively]. This gelatinase activity was highest at the luminal aspect of the aortic media, where the activity increased three- to five-fold after the destruction of alpha 2-macroglobulin. Zymograms demonstrated the principal gelatinase in atherosclerotic aorta to have a molecular mass of about 92 kDa, whereas in aneurysmal aorta there was a spectrum of gelatinase activity from 92 to 55 kDa. 3. Collagenase and stromelysin (proteoglycanase) could be detected by immunoblotting in homogenates of aneurysmal aorta, but rarely in atherosclerotic aorta and never in control aorta. Collagenase and stromelysin activities were low, but increased two- to three-fold after the destruction of tissue inhibitor of metalloproteinases. Collagenase and stromelysin activities were highest at the adventitial aspect of aneurysmal media. 4. The secretion of gelatinase by inflammatory cells at the intima of diseased aorta could have a pathological role in establishing atherosclerotic plaques and medial thinning. Secretion of collagenase, gelatinase and stromelysin from the adventitia could accelerate connective tissue degradation in the media of aneurysmal aorta.
The axr2-1 mutation of Arabidopsis thaliana is a gain-of-function mutation that disrupts an early step in auxin response. (1994)

The dominant axr2-1 mutation of Arabidopsis thaliana confers resistance to the plant hormones auxin, ethylene, and abscisic acid. In addition, axr2-1 has pleiotropic effects on plant morphology which include gravitropic defects in roots, hypocotyls and inflorescences of axr2-1 plants. Two genetic screens were conducted to isolate new mutations at the AXR2 locus. First, axr2-1 pollen was gamma-irradiated, crossed onto wild-type plants, and the M1 progeny screened for loss of the axr2-1 phenotype. Large deletions of the axr2-1 region on chromosome 3 resulted; however, none of these deletions appeared to be heritable. In the second, M2 seed obtained from axr2-1 gl-1 plants was screened for reversion of the axr2-1 phenotype. One revertant line, axr2-r3, has a distinctive phenotype caused by a second mutation at the axr2 locus. To learn more about the nature of the axr2-1 mutation, the effects of varying the ratio of wild-type to mutant copies of the AXR2 gene were examined by comparing plants of the following genotypes: +/+, +/+/+, axr2-1/axr2-1, axr2-1/+ and axr2-1/+/+. Additionally, accumulation of transcripts from the auxin-inducible SAUR-AC1 gene was examined to determine the response of wild-type and mutant plants to auxin. Wild-type seedlings and mature plants accumulate transcripts with auxin treatment. In contrast, axr2-1 tissue does not accumulate SAUR-AC1 transcripts in response to auxin. Taken together, these results indicate that axr2-1 is a neomorphic or hypermorphic mutation that disrupts an early step in an auxin response pathway.
An Efficient Pilot Design Scheme for Sparse Channel Estimation in OFDM Systems (2013)

This paper investigates the pilot placement problem for sparse channel estimation in orthogonal frequency division multiplexing (OFDM) systems. Prompted by the success of the compressed sensing technique in recovering sparse signals from undersampled measurements, compressed sensing has been successfully applied for pilot-aided sparse channel estimation in OFDM systems to reduce the transmitted overhead. However, the selection of pilot tones significantly affects channel estimation performance. Seeking optimal pilot placement for sparse channel estimation, in the sense of minimum mean-square error of the channel estimation, through an exhaustive search of all possible pilot placements is extremely computationally intensive. To reduce the computational complexity and simultaneously maximize the accuracy of sparse channel estimation, cross-entropy optimization is introduced to determine the optimal pilot placement. Computer simulation results demonstrate that the pilot index sequences obtained using the proposed method performed better compared with those obtained using the conventional equispaced scheme and the random search method.
The foetal origins of the metabolic syndrome - a South African perspective : review article (2002)

The developing world is experiencing a rise in the prevalence of obesity, diabetes and cardiovascular disease to such an extent that it is often described as an epidemic. The most common explanation advanced for this phenomenon is the so-called epidemiological transition, with the biological basis of the thrifty genotype. The thrifty genotype theory suggests that genes derived from times of deprivation may result in adaptations that have adverse effects in times of plenty. However, a divergent theory is the so-called foetal origins of chronic disease which ascribes the epidemic, in part, to an adverse intrauterine environment. There is compelling evidence, based on large numbers of epidemiological studies conducted in both developing and developed countries, that small size at birth in full-term pregnancies is linked with the subsequent development of the major features of the metabolic syndrome, namely glucose intolerance, increased blood pressure, dyslipidaemia and increased mortality from cardiovascular disease.
An adapted Severity of Dependence Scale is valid for the detection of medication overuse: the Akershus study of chronic headache (2010)

The SDS is valid for detecting medication overuse and dependency like behaviour amongst people with chronic headache. The adapted version may be used to identify chronic headache patients who may benefit from detoxification.
Amphiphilic Model Conetworks of Polyisobutylene Methacrylate and 2-(Dimethylamino)ethyl Methacrylate Prepared by the Combination of Quasiliving Carbocationic and Group Transfer Polymerizations (2007)

A series of amphiphilic polymer conetworks (APCN) of the hydrophobic polyisobutylene methacrylate macromonomer (PIBMA) and the ionizable hydrophilic 2-(dimethylamino)ethyl methacrylate (DMAEMA) were synthesized by combining, for the first time, two controlled polymerization methods, quasiliving carbocationic polymerization (QLCCP) and group transfer polymerization (GTP). First, isobutylene (IB) was polymerized by QLCCP, and the resulting IB 7-mer (PIB) was modified to yield PIBMA with exact chain end-functionality of 1.0. Subsequently, PIBMA was successfully polymerized sequentially by GTP with DMAEMA (comonomer) and ethylene glycol dimethacrylate (EGDMA, cross-linker) using a bifunctional GTP initiator, 1,4-bis(methoxytrimethylsiloxymethylene)cyclohexane. Amphiphilic conetworks with linear segments of well-defined molecular weights (model conetworks) and a randomly cross-linked conetwork with linear segments characterized by a broad size distribution between the cross-links were prepared. Four of the model conetworks were based on poly(PIBMA-b-DMAEMA-b-PIBMA) triblock copolymers and two were based on poly(DMAEMA-b-PIBMA-b-DMAEMA) triblock copolymers of different degrees of polymerization (DP). Another conetwork was prepared from statistical copolymer chains. For comparison, four more networks, two of them based on DMAEMA homopolymers and two others based on copolymers of DMAEMA and methyl methacrylate, were also synthesized in the course of this study. Gel permeation chromatography and 1H NMR analyses indicated that the precursors to all the networks had the desired molecular weights and compositions. The degrees of swelling (DS) of the conetworks in tetrahydrofuran, n-hexane, and acidic water depended on the DP and the composition of the polymer chains between the EGDMA cross-links, while the DSs in neutral water were very low and almost constant because of the low degree of ionization of DMAEMA units in the conetworks in this solvent. These results show that the swelling behavior of the DMAEMA-PIBMA and DMAEMA-MMA conetworks can be controlled by the length and the composition of the chains between the cross-links, by the solvent polarity and the pH in a broad range.
Structural insights into peptide bond formation (2002)

The large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-RNA fragments of tRNA. We have refined at 3-A resolution the structures of both A and P site substrate and product analogues, as well as an intermediate analogue, bound to the Haloarcula marismortui 50S ribosomal subunit. A P site substrate, CCA-Phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the P site. The CCA portions of these analogues are bound identically by either the A or P loop of the 23S rRNA. Combining the separate P and A site substrate complexes into one model reveals interactions that may occur when both are present simultaneously. The alpha-NH(2) group of an aminoacylated fragment in the A site forms one hydrogen bond with the N3 of A2486 (2451) and may form a second hydrogen bond either with the 2' OH of the A-76 ribose in the P site or with the 2' OH of A2486 (2451). These interactions position the alpha amino group adjacent to the carbonyl carbon of esterified P site substrate in an orientation suitable for a nucleophilic attack.
Calcitonin Gene-Related Peptide In Vivo Positive Inotropy Is Attributable to Regional Sympatho-Stimulation and Is Blunted in Congestive Heart Failure (2005)

Calcitonin gene-related peptide (CGRP) is a nonadrenergic/noncholinergic (NANC) peptide with vasodilatative/inotropic action that may benefit the failing heart. However, precise mechanisms for its in vivo inotropic action remain unclear. To assess this, dogs with normal or failing (sustained tachypacing) hearts were instrumented for pressure-dimension analysis. In control hearts, CGRP (20 pmol/kg per minute) enhanced cardiac contractility (eg, +33+/-4.2% in end-systolic elastance) and lowered afterload (-14.2+/-2% in systemic resistance, both P<0.001). The inotropic response was markedly blunted by heart failure (+6.5+/-2%; P<0.001 versus control), whereas arterial dilation remained unaltered (-19.3+/-5%). CGRP-positive inotropy was not attributable to reflex activation because similar changes were observed in the presence of a ganglionic blocker. However, it was fully prevented by the beta-receptor antagonist (timolol), identifying a dominant role of sympatho-stimulatory signaling. In control hearts, myocardial interstitial norepinephrine assessed by microdialysis almost doubled in response to CGRP infusion, whereas systemic plasma levels were unchanged. In addition, CGRP receptors were not observed in ventricular myocardium but were prominent in coronary arteries and the stellate ganglia. Ventricular myocytes isolated from normal and failing hearts displayed no inotropic response to CGRP, further supporting indirect sympatho-stimulation as the primary in vivo mechanism. In contrast, the peripheral vasodilatative capacity of CGRP was similar in femoral vascular rings from normal and failing hearts in dogs. Thus, CGRP-mediated positive inotropy is load-independent but indirect and attributable to myocardial sympathetic activation rather than receptor-coupled stimulation in canine hearts. This mechanism is suppressed in heart failure, so that afterload reduction accounts for CGRP-enhanced function in this setting.
Click Chemistry and Radiochemistry: The First 10 Years (2016)

The advent of click chemistry has had a profound influence on almost all branches of chemical science. This is particularly true of radiochemistry and the synthesis of agents for positron emission tomography (PET), single photon emission computed tomography (SPECT), and targeted radiotherapy. The selectivity, ease, rapidity, and modularity of click ligations make them nearly ideally suited for the construction of radiotracers, a process that often involves working with biomolecules in aqueous conditions with inexorably decaying radioisotopes. In the following pages, our goal is to provide a broad overview of the first 10 years of research at the intersection of click chemistry and radiochemistry. The discussion will focus on four areas that we believe underscore the critical advantages provided by click chemistry: (i) the use of prosthetic groups for radiolabeling reactions, (ii) the creation of coordination scaffolds for radiometals, (iii) the site-specific radiolabeling of proteins and peptides, and (iv) the development of strategies for in vivo pretargeting. Particular emphasis will be placed on the four most prevalent click reactions-the Cu-catalyzed azide-alkyne cycloaddition (CuAAC), the strain-promoted azide-alkyne cycloaddition (SPAAC), the inverse electron demand Diels-Alder reaction (IEDDA), and the Staudinger ligation-although less well-known click ligations will be discussed as well. Ultimately, it is our hope that this review will not only serve to educate readers but will also act as a springboard, inspiring synthetic chemists and radiochemists alike to harness click chemistry in even more innovative and ambitious ways as we embark upon the second decade of this fruitful collaboration.
Origins of mRNA identity: Capping enzymes bind to the phosphorylated C-terminal domain of RNA polymerase II (1997)

Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans the biological, physical, and social sciences.
ChemInform Abstract: Synthesis of 4,5‐Diarylimidazoline‐2‐thiones and Their Photoconversion to Bis(4,5‐diarylimidazol‐2‐yl) Sulfides. (1990)

Abstract The imidazoles (III) and (VII) are prepared via an improved route.
Adenoviral and adeno-associated viral transfer of genes to the peripheral nervous system (2000)

Targeted expression of foreign genes to the peripheral nervous system is interesting for many applications, including gene therapy of neuromuscular diseases, neuroanatomical studies, and elucidation of mechanisms of axonal flow. Here we describe a microneurosurgical technique for injection of replication-defective viral vectors into dorsal root ganglia (DRG). Adenovirus- and adeno-associated virus-based vectors with transcriptional competence for DRG neurons led to expression of the gene of interest throughout the first neuron of the sensory system, from the distal portions of the respective sensory nerve to the ipsilateral nucleus gracilis and cuneatus, which contains the synapses to the spinothalamic tracts. Use of Rag-1 ablated mice, which lack all B and T lymphocytes, allowed for sustained expression for periods exceeding 100 days. In immunocompetent mice, long-term (52 days) expression was achieved with similar efficiency by using adeno-associated viral vectors. DRG injection was vastly superior to intraneural injection into the sciatic nerve, which mainly transduced Schwann cells in the vicinity of the site of inoculation site but only inefficiently transduced nerve fibers, whereas i.m. injection did not lead to any significant expression of the reporter gene in nerve fibers. The versatile and efficient transduction of genes of interest should enable a wide variety of functional studies of peripheral nervous system pathophysiology.
A high performance FPGA-based accelerator for large-scale convolutional neural networks (2016)

In recent years, convolutional neural networks (CNNs) based machine learning algorithms have been widely applied in computer vision applications. However, for large-scale CNNs, the computation-intensive, memory-intensive and resource-consuming features have brought many challenges to CNN implementations. This work proposes an end-to-end FPGA-based CNN accelerator with all the layers mapped on one chip so that different layers can work concurrently in a pipelined structure to increase the throughput. A methodology which can find the optimized parallelism strategy for each layer is proposed to achieve high throughput and high resource utilization. In addition, a batch-based computing method is implemented and applied on fully connected layers (FC layers) to increase the memory bandwidth utilization due to the memory-intensive feature. Further, by applying two different computing patterns on FC layers, the required on-chip buffers can be reduced significantly. As a case study, a state-of-the-art large-scale CNN, AlexNet, is implemented on Xilinx VC709. It can achieve a peak performance of 565.94 GOP/s and 391 FPS under 156MHz clock frequency which outperforms previous approaches.
Estimating Performance of a Ray-Tracing ASIC Design (2006)

Recursive ray tracing is a powerful rendering technique used to compute realistic images by simulating the global light transport in a scene. Algorithmic improvements and FPGA-based hardware implementations of ray tracing have demonstrated realtime performance but hardware that achieves performance levels comparable to commodity rasterization graphics chips is still not available. This paper describes the architecture and ASIC implementations of the DRPU design (dynamic ray processing unit) that closes this performance gap. The DRPU supports fully programmable shading and most kinds of dynamic scenes and thus provides similar capabilities as current GPUs. It achieves high efficiency due to SIMD processing of floating point vectors, massive multithreading, synchronous execution of packets of threads, and careful management of caches for scene data. To support dynamic scenes B-KD trees are used as spatial index structures that are processed by a custom traversal and intersection unit and modified by an update processor on scene changes. The DRPU architecture is specified as a high-level structural description in a functional language and mapped to both FPGA and ASIC implementations. Our FPGA prototype clocked at 66 MHz achieves higher ray tracing performance than CPU-based ray tracers even on a modern multi-GHz CPU. We provide performance results for two 130 nm ASIC versions and estimate what performance would be using a 90 nm CMOS process. For a 90nm version with a 196 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> die we conservatively estimate clock rates of 400 MHz and ray tracing performance of 80 to 290 fps at 1024times768 resolution in our test scenes. This estimated performance is 70 times faster than what is achievable with standard multi-GHz desktop CPUs