gebhart/patrepeval huggingface dataset:
Synthesis towards microcystins and related toxins (1996)

H. Y. Kim, K. Stein and P. L. Toogood, Chem. Commun., 1996, 1683 DOI: 10.1039/CC9960001683
Coordination of Growth Rate, Cell Cycle, Stress Response, and Metabolic Activity in Yeast (2007)

We studied the relationship between growth rate and genome-wide gene expression, cell cycle progression, and glucose metabolism in 36 steady-state continuous cultures limited by one of six different nutrients (glucose, ammonium, sulfate, phosphate, uracil, or leucine). The expression of more than one quarter of all yeast genes is linearly correlated with growth rate, independent of the limiting nutrient. The subset of negatively growth-correlated genes is most enriched for peroxisomal functions, whereas positively correlated genes mainly encode ribosomal functions. Many (not all) genes associated with stress response are strongly correlated with growth rate, as are genes that are periodically expressed under conditions of metabolic cycling. We confirmed a linear relationship between growth rate and the fraction of the cell population in the G0/G1 cell cycle phase, independent of limiting nutrient. Cultures limited by auxotrophic requirements wasted excess glucose, whereas those limited on phosphate, sulfate, or ammonia did not; this phenomenon (reminiscent of the "Warburg effect" in cancer cells) was confirmed in batch cultures. Using an aggregate of gene expression values, we predict (in both continuous and batch cultures) an "instantaneous growth rate." This concept is useful in interpreting the system-level connections among growth rate, metabolism, stress, and the cell cycle.
Supplementary Table 1 from Telomerase Peptide Vaccination in NSCLC: A Phase II Trial in Stage III Patients Vaccinated after Chemoradiotherapy and an 8-Year Update on a Phase I/II Trial (2023)

&lt;p&gt;PDF file - 17KB&lt;/p&gt;
Learning Unified Embedding for Apparel Recognition (2017)

In apparel recognition, specialized models (e.g. models trained for a particular vertical like dresses) can significantly outperform general models (i.e. models that cover a wide range of verticals). Therefore, deep neural network models are often trained separately for different verticals. However, using specialized models for different verticals is not scalable and expensive to deploy. This paper addresses the problem of learning one unified embedding model for multiple object verticals (e.g. all apparel classes) without sacrificing accuracy. The problem is tackled from two aspects: training data and training difficulty. On the training data aspect, we figure out that for a single model trained with triplet loss, there is an accuracy sweet spot in terms of how many verticals are trained together. To ease the training difficulty, a novel learning scheme is proposed by using the output from specialized models as learning targets so that L2 loss can be used instead of triplet loss. This new loss makes the training easier and make it possible for more efficient use of the feature space. The end result is a unified model which can achieve the same retrieval accuracy as a number of separate specialized models, while having the model complexity as one. The effectiveness of our approach is shown in experiments.
Bromodomain Proteins Contribute to Maintenance of Bloodstream Form Stage Identity in the African Trypanosome (2015)

Trypanosoma brucei, the causative agent of African sleeping sickness, is transmitted to its mammalian host by the tsetse. In the fly, the parasite's surface is covered with invariant procyclin, while in the mammal it resides extracellularly in its bloodstream form (BF) and is densely covered with highly immunogenic Variant Surface Glycoprotein (VSG). In the BF, the parasite varies this highly immunogenic surface VSG using a repertoire of ~2500 distinct VSG genes. Recent reports in mammalian systems point to a role for histone acetyl-lysine recognizing bromodomain proteins in the maintenance of stem cell fate, leading us to hypothesize that bromodomain proteins may maintain the BF cell fate in trypanosomes. Using small-molecule inhibitors and genetic mutants for individual bromodomain proteins, we performed RNA-seq experiments that revealed changes in the transcriptome similar to those seen in cells differentiating from the BF to the insect stage. This was recapitulated at the protein level by the appearance of insect-stage proteins on the cell surface. Furthermore, bromodomain inhibition disrupts two major BF-specific immune evasion mechanisms that trypanosomes harness to evade mammalian host antibody responses. First, monoallelic expression of the antigenically varied VSG is disrupted. Second, rapid internalization of antibodies bound to VSG on the surface of the trypanosome is blocked. Thus, our studies reveal a role for trypanosome bromodomain proteins in maintaining bloodstream stage identity and immune evasion. Importantly, bromodomain inhibition leads to a decrease in virulence in a mouse model of infection, establishing these proteins as potential therapeutic drug targets for trypanosomiasis. Our 1.25Å resolution crystal structure of a trypanosome bromodomain in complex with I-BET151 reveals a novel binding mode of the inhibitor, which serves as a promising starting point for rational drug design.
<title>MPEG-4 playback of multimedia objects searchable by their description</title> (2000)

In this paper, from the standpoint of their potential for multimedia applications/services we examine key new elements of the MPEG-4 standard as well as concepts leading to the ongoing work for the MPEG-7 standard. We first examine generic requirements common to several practical future multimedia applications/services. We then identify and examine key new features of the MPEG-4 standard such as, image/video objects, facial animation, advanced sound, integration with the web, multi-user worlds and Java control. Next, we briefly review the goal, requirements and progress in the ongoing work on the MPEG-7 standard. We then discuss the player we intend to use which integrates a number of key features of MPEG-4 and search and retrieval concepts similar to that of MPEG-7 standard, as well as how to create content for the player. Next, we discuss an example multimedia application that we have developed. Finally, we summarize the key highlights of the paper.
[Bone metabolism in aromatase-knockout mice]. (2003)

Aromatase is the sole enzyme which converts androgen into estrogen. We have reported that aromatase-knockout (ArKO) mice showed bone loss by increased bone resorption not only in female but also in male mice, suggesting essential roles of estrogen in bone metabolism in both sexes. When ArKO mice were orchidectomized (ORX) to induce a double deficiency of estrogen and androgen, ORX/ArKO mice showed severe osteopenia. In females, estrogen is major sex steroid for bone turnover. However, estrogen and androgen may play distinct roles in bone turnover of male mice before and after reaching sexual maturity.
Solid state quantum yield determination of a novel base photogenerator (1991)

The photoefficiency of a new class of base photogenerating materials, based on the photoremoval of the α,α-dimethyl-3,5-dimethoxybenzyloxycarbonyl (Ddz) group from masked amine-type bases, was investigated. The solid state quantum yield for the photogeneration of cyclohexylamine from its corresponding Ddz carbamate was evaluated at 280 nm using a number of quantitative IR methods. A value of 0.10 was found using the optimal method involving a comparison of the intensities of a strong IR reference band solely associated with the polymer matrix with the decreasing carbonyl absorption of the Ddz substrate. Comparable quantum yields were also found by using an intense band associated with the Ddz-masked amine, thus indicating the overall applicability and reliability of the method provided that careful choice of the reference band was made. The value of the quantum efficiency for the photodeprotection of Ddz-masked amines is sufficiently high for practical applications requiring the use of photogenerated base.
Multisociety Consensus Quality Improvement Guidelines for Intraarterial Catheter-directed Treatment of Acute Ischemic Stroke, from the American Society of Neuroradiology, Canadian Interventional Radiology Association, Cardiovascular and Interventional Radiological Society of Europe, Society for Cardiovascular Angiography and Interventions, Society of Interventional Radiology, Society of NeuroInterventional Surgery, European Society of Minimally Invasive Neurological Therapy, and Society of Vascular and Interventional Neurology. (2013)

Quality improvement guidelines are provided for endovascular acute ischemic stroke revascularization procedures.
Effects of a Vegetarian Diet on Cardiometabolic Risk Factors, Gut Microbiota, and Plasma Metabolome in Subjects With Ischemic Heart Disease: A Randomized, Crossover Study (2020)

Background A vegetarian diet (VD) may reduce future cardiovascular risk in patients with ischemic heart disease. Methods and Results A randomized crossover study was conducted in subjects with ischemic heart disease, assigned to 4-week intervention periods of isocaloric VD and meat diet (MD) with individually designed diet plans, separated by a 4-week washout period. The primary outcome was difference in oxidized low-density lipoprotein cholesterol (LDL-C) between diets. Secondary outcomes were differences in cardiometabolic risk factors, quality of life, gut microbiota, fecal short-chain and branched-chain fatty acids, and plasma metabolome. Of 150 eligible patients, 31 (21%) agreed to participate, and 27 (87%) participants completed the study. Mean oxidized LDL-C (-2.73 U/L), total cholesterol (-5.03 mg/dL), LDL-C (-3.87 mg/dL), and body weight (-0.67 kg) were significantly lower with the VD than with the MD. Differences between VD and MD were observed in the relative abundance of several microbe genera within the families Ruminococcaceae, Lachnospiraceae, and Akkermansiaceae. Plasma metabolites, including l-carnitine, acylcarnitine metabolites, and phospholipids, differed in subjects consuming VD and MD. The effect on oxidized LDL-C in response to the VD was associated with a baseline gut microbiota composition dominated by several genera of Ruminococcaceae. Conclusions The VD in conjunction with optimal medical therapy reduced levels of oxidized LDL-C, improved cardiometabolic risk factors, and altered the relative abundance of gut microbes and plasma metabolites in patients with ischemic heart disease. Our results suggest that composition of the gut microbiota at baseline may be related to the reduction of oxidized LDL-C observed with the VD. Registration URL: https://www.clini​caltr​ials.gov; Unique identifier: NCT02942628.
Finite-element analysis of 1-3 composite transducers (1991)

The vibrational and electromechanical characteristics of a wide range of 1-3 composite structures, comprising ceramic pillars aligned within a polymer phase, are considered using finite-element analysis. The influence of pillar geometry, ceramic volume fraction, and pillar orientation is described in terms of overall transduction efficiency. It is shown that the finite-element method provides a versatile means of analysis and the results obtained permit a set of useful design guidelines to be developed. In general, a small pillar aspect ratio and a relatively high volume fraction provides the most satisfactory performance, in terms of electromechanical efficiency and uniformity of thickness dilation.
A Network Coding Approach to Network Monitoring (Invited Paper) (2005)

Network Monitoring is a challenging problem that has received a lot of attention in the Internet community, particularly in the context of overlay networks. Independently, recent advances in Network Coding have shown that it is possible to increase network capacity and better share the available resources by allowing intermediate nodes to perform processing operations, in addition to just forwarding packets. In this work, we propose the use of Network Coding techniques to improve Network Monitoring. As a specific application, we use our approach for the well-known problem of network tomography, and in particular for inferring link loss rates from end-to-end measurements. We demonstrate that our approach can decrease the bandwidth used by probes, improve the accuracy of estimation, and decrease the complexity of selecting paths or trees to send probes. Overall, we argue that the use of Network Coding techniques shows great promise for improving several aspects of monitoring in overlay networks.
Simulation-Based Performance Comparison of VANETs Backbone Formation Algorithms (2008)

Mobile ad hoc networks (MANETs) are gaining increased interest as the technology that potentially will make the nowadays illusion of mobile computing a tangible reality. vehicular ad-hoc networks (VANETs) are the special kind of MANETs that aims at providing communications among vehicles on the roads. The connected dominating set (CDS), a.k.a. virtual backbone or spine, has been proposed to facilitate routing, broadcasting, and establishing a dynamic infrastructure for distributed location databases in VANETs. Minimizing the CDS cardinality simplifies the VANETpsilas abstracted topology and allows for using shorter routes. Since, it is NP-complete to find the minimum size CDS (MCDS), approximation algorithms and heuristics are used to tackle this problem. It has been reported that localized CDS creation algorithms run fast and generate light signaling overhead. Some theoretical performance analysis of these algorithms is presented in the literature; however, this analysis has not been validated across any physical or at least simulation-based measures. Moreover, the cost of maintaining the CDS in the presence of topology changes is an important cost that is overlooked most of the time. In this paper, a simulation-based comparison between the performance of these algorithms is conducted using the ns2 network simulator. Moreover, the effect of mobility rate and network size on the performance of each algorithm is investigated.
Flexibility of spectral efficiency by means of power-efficient multidimensional constellations (2014)

Power-efficient modulation formats are a key technology for optical transport networks. Recently, flexibility of spectral efficiency for efficient utilization of available bandwidth has become a central issue as well. In this contribution, we show that the demand for both flexibility and power efficiency can be fulfilled simultaneously using multidimensional constellations.
The optimization of conditions for the production of acid-hydrolysed winged bean and soybean proteins with reduction of 3-monochloropropane-1,2-diol (3-MCPD) (2004)

Abstract Response Surface Methodology (RSM) was used to establish the optimum time and temperature for production of acid-hydrolysed winged bean protein (aHWBP) and acid-hydrolysed soybean protein (aHSBP). Seven hours of hydrolysis at 125 °C was the optimum condition for producing aHWBP, whereas it was 5 h of hydrolysis at 125 °C for production of aHSBP. Although aHWBP and aHSBP produced using these conditions had favourable sensory qualities, they were found to have up to 25 mg kg−1 of 3-monochloropropane-1,2-diol (3-MCPD). This exceeds the maximum level permissible in Commission Regulation (EC) No 466/2001. However, additional alkaline thermal treatment at pH 8.5 for 2 h at 100 °C effectively reduced the 3-MCPD contents of aHWBP and aHSBP to undetectable levels. aHWBP has a distinctive flavour, which is different from that of aHSBP. The former has higher mean scores for meaty and vegetable attributes but lower mean scores for soy, umami and beany attributes than the latter.
Roles of insulin-like growth factor II in cardiomyoblast apoptosis and in hypertensive rat heart with abdominal aorta ligation (2006)

Although IGF-II activating the IGF-II receptor signaling pathway has been found to stimulate cardiomyocyte hypertrophy, the role of IGF-II in cardiac cell apoptosis remains unclear. This study aimed to identify the roles of IGF-II and/or IGF-II receptors (IGF-II/IIR) in cardiomyoblast apoptosis and in hypertensive rat hearts with abdominal aorta ligation. Cultured rat heart-derived H9c2 cardiomyoblasts and excised hearts from Sprague-Dawley rats with 0- to 20-day complete abdominal aorta ligation, a model of ANG II elevation and hypertension, were used. IGF-II/IIR expression, caspase activity, DNA fragmentation, and apoptotic cells were measured by RT-PCR, Western blot, agarose gel electrophoresis, and TUNEL assay following various combinations of ANG II, IGF-II/IIR antibody, CsA (calcineurin inhibitor), SP-600125 (JNK inhibitor), SB-203580 (p38 inhibitor), U-0126 (MEK inhibitor), or Staurosporine (PKC inhibitor) in H9c2 cells. ANG II-induced DNA fragmentation and TUNEL-positive cells were blocked by IGF-II/IIR antibodies and antisense IGF-II, but not by IGF-II sense. IGF-II-induced apoptosis was blocked by IGF-IIR antibody and CsA. The increased gene expressions of IGF-II and -IIR induced by ANG II were reversed by U-0126 and Sp600125, respectively. Caspase 8 activities induced by ANG II were attenuated by U-0126, SP-600125, and CsA. DNA fragmentation induced by ANG II was totally blocked by SP-600125, and CsA and was attenuated by U-0126. In rats with 0- to 20-day complete abdominal aorta ligation, the increases in IGF-II/IIR levels in the left ventricle were accompanied by hypertension as well as increases in caspase 9 activities and TUNEL-positive cardiac myocytes. ANG II-induced apoptosis was reversed by IGF-II/IIR blockade and coexisted with increased transactivation of IGF-II and -IIR, which are mediated by ERK and JNK pathways, respectively, both of which further contributed to cardiomyoblast apoptosis via calcineurin signaling. The increased cardiac IGF-II, IGF-IIR, caspase 9, and cellular apoptosis were also found in hypertensive rats with abdominal aorta ligation.
PROPHYLACTIC ADMINISTRATION OF ANTIBIOTICS COMPROMISES RETICULOENDOTHELIAL SYSTEM FUNCTION AND EXACERBATES SHOCK MORTALITY IN RATS (1980)

The effects of short-term (3 days) administration of three different antimicrobial agents (i.e., kanamycin, cephalothin and polymyxin B) on reticuloendothelial system (RES) phagocytic function and mortality after bowel ischaemic shock was studied in intact rats. All three antibiotics significantly depressed RES phagocytic function and exacerbated mortality after shock. The degree of antibiotic-induced inhibition of RES function seemed to parallel the antimicrobial effects on shock mortality; the greater the degree of RES inhibition, the greater the degree of exacerbation of shock mortality. In view of such findings, caution should be exercised in administering antibiotics prophylactically to patients and animals.
Sea of dual mode polymer pillar I/O interconnections for gigascale integration (2003)

The Sea of Polymer Pillars offers highly compliant electrical, optical, and RF wafer-level I/O interconnects at an I/O density larger than 10/sup 5//cm/sup 2/. Dual mode I/O pillars function simultaneously as both electrical and optical interconnects to offer circuit/system designers essentially unlimited I/O bandwidth at potentially the lowest cost.
Coherent summation of laser beams from a GaAlAs array using binary phase holograms (1986)

GaAs lasers are generally limited to output powers of a few tens of milliwatts due to catastrophic facet damage which occurs at high power levels. We have developed a holographic method of laser beam addition capable of producing large optical powers from the coherent sum of many modular laser sources. The coherent addition of six GaAlAs lasers from a monolithic array has been demonstrated. This method is applicable to a wide variety of laser types and is readily extendable to 2-D arrays of lasers.
Ecophysiological studies on arthropods from Spitsbergen (1983)

The cold-hardiness, high temperature tolerance and metabolic activity of summer specimens of staphylinid beetles (Atheta graminicola), collembolans (Onichiurus groenlandicw), spiders (Erigone arcrica), and prostigmatid mites (Molgus linoralb) from Spitsbergen were investigated. The animals displayed coldhardiness and haemolymph melting points within the normal ranges for summer insects from temperate regions, but were less tolerant to high temperatures. Haemolymph from spiders and from one species of collembolans (lsoroma sp.) was found to contain thermal hysteresis factors. The beetles. collembolans. and mites were found to have oxygen consumption rates above the values of their relatives in other climatic zones, whereas the spiders had values within the range of temperate arachnoids. The study supports the view that polar arthropods have activation energy values lower than those of temperate animals.
Development of fast response MR-fluid actuator (2003)

Magnetorheological (MR) fluids are materials that change their rheological behavior by an applied magnetic field. We have developed MR-fluid actuator. In this paper, we investigate the dynamic characteristics of the MR-fluid actuator and aim to improve the response. The transient magnetic analysis is examined in consideration of the eddy current. Finally, we realize a much faster MR-fluid actuator.
Facilitating the Commercialization of University Innovation: The Carolina Express License Agreement (2010)

As the United States recovers from the most severe recession since the 1930s, efforts to boost economic growth assume paramount importance. This means not only finding ways to spur rapid job creation but also advancing the country’s capacity for innovation. One way to do this is to encourage academic research enterprises to facilitate the transfer and spillover of scientific and technological research into commercial application. In particular, the research laboratories of our nation’s universities are unparalleled sources of dynamic new spin-off and startup companies. These fledgling enterprises in turn have the potential to become high-growth firms. Recent Kauffman Foundation research demonstrates that top-performing new companies are a fertile source of new jobs.In this paper, we examine an innovative new set of practices associated with the commercialization of university research developed and implemented at the University of North Carolina at Chapel Hill. New standard licensing agreements support and expedite firm formation as an outcome of university-based intellectual property. A committee chaired by one of this paper’s authors developed the licensing agreement. The committee included entrepreneurial UNC faculty members with experience in firm birthing, colleagues from the Office of Technology Development (OTD), venture capitalists from the firm Intersouth Partners, and attorneys from a number of firms that have represented UNC startups. The outcome of these discussions produced the Carolina Express License Agreement.
Recent developments in the production of human therapeutic proteins in eukaryotic algae (2005)

Antibody-based therapeutics have had great success over the last few years, and continue to be one of the fastest growing sectors of drug development. The efficacy and specificity of antibody-based drugs makes them ideal candidates for new drug development, but the specificity of these drugs comes from their complexity, and this complexity makes antibodies very expensive to produce. To address this problem, the authors have developed a system for the expression of recombinant proteins using the unicellular eukaryotic green algae, Chlamydomonas reinhardtii. As proof of concept, the authors have engineered microalgae to produce several forms of a human IgA antibody directed against herpes simplex virus. The expression of human monoclonal antibodies in C. reinhardtii offers an attractive alternative to traditional mammalian-based expression systems, as both the plastid and nuclear genomes are easily and quickly transformed, and the production of proteins in algae has an inherently low cost of capitalisation and production.