gebhart/patrepeval huggingface dataset:
Highly selective synthesis of 1,3-oleoyl-2-palmitoylglycerol by lipase catalysis (1999)

1,3-Oleoyl-2-palmitoylglycerol (OPO), an important structured triglyceride in infant nutrition, was synthesized by a two-step process in high yields and purity using sn1,3-regiospecific lipases. In the first step, tripalmitin (TP) was subjected to an alcoholysis reaction in an organic solvent catalyzed by sn1,3-regiospecific lipases yielding the corresponding 2-monopalmitin (2-MP). The 2-MP was isolated in up to 85% yield and >95% purity by crystallization and esterified in the second step with oleic acid using the same lipases to form the structured triglyceride OPO in up to 78% yield containing 96% palmitic acid in the sn2-position. Water activity, solvent, as well as carrier for lipase immobilization strongly influenced the yield and purity of products in both steps. The best results were achieved with lipases from Rhizomucor miehei and Rhizopus delemar immobilized on EP 100 and equilibrated to a water activity of 0.43. Special emphasis was given to develop this process in solvents that are allowed to be used in foodstuffs and to perform the second step in a solvent-free system.
<title>Time-of-flight range imaging with a custom solid state image sensor</title> (1999)

A complete range camera system, working with the time-of- flight principle, is introduced. This ranging system uses modulated LEDs as active illumination source and a new lock-in CCD sensor as demodulator and detector. It requires no mechanically scanning parts because every pixel of the sensor contains a lock-in amplifier, enabling both intensity and range measurement for all pixels in parallel. Two such lock-in imagers are realized in 2.0 micrometer CMOS/CCD technology, (1) a line sensor with 108 pixels and an optical fill factor of 100% and (2) a 64 X 25 pixel image sensor with 20% fill factor. The basics of time-of-flight ranging are introduced with a detailed description of the elements necessary. Shot noise limitation to ranging resolution is deduced and confirmed by simulation. An optical power budget is offered giving the relation between the number of photons in a pixel depending on the light source, the observed object, and several camera parameters. With the described lab setup, non- cooperative targets can be measured over a distance of several meters with a resolution of some centimeters.
Mass-spectrometric analysis of naturally processed peptides recognized by ovarian tumor-associated CD8(+) CTL (1997)

Antigens recognized by cytotoxic T cells (CTL) are expressed as peptides presented by MHC class I molecules. To isolate peptides from the MHC molecule HLA-A2.1 and identify epitopes that define the activity profile of ovarian CD8(+) CTL, peptides were separated by reverse-phase high-pressure liquid chromatography (HPLC), and analyzed by electrospray ionization-tandem mass spectrometry (ES-MS). HLA-A2.1-bound peptides were extracted from the ovarian tumor line SKOV3 transfected with the HLA-A2.1 (clone 1E4) and C1R.A2 cells transfected with HCA-A2.1 and HER-2 (clone HER-2.J) by immunoaffinity chromatography. At least five peaks of distinct retention times (termed 1, 2A, 2B, 2C, and 3) were recognized by an ovarian HER-2(high) (HER-2(hi)) tumor-associated HLA-A2(+), CD8(+) CTL line. ES-MS analysis was performed for peak 2B peptides from both types of cells. In the four consecutive fractions of peak 2B, at least 27 and 16 ion species of mass-to-charge (m/z) ratio between 760-1300 were detected in 1E4 and HER-2.J cells, respectively. The abundance of four 1E4 and six HER-2.J ions believed to be peptides in four consecutive HPLC fractions in this peak matched the CTL activity profile. Of these, two ions with actual m/z ratios 497.3-498.4 and 792.8-793.2, were found in the peak 2B from both types of cells. Since little is known about the tumor Ag recognized in human cancers, characterization of these ions may lead to identification of novel tumor Ag in breast and ovarian cancers. This may also be useful in developing quantitative approaches to the identification of tumor Ag and the determination of epitope density on tumor and normal cells. This may help characterize the relationship between tumor immunity and epitope tolerance in human epithelial cancers.
Decomposition and Reforming of Formic Acid on Supported Au Catalysts: Production of CO-Free H2 (2011)

The vapor-phase decomposition of formic acid was studied over Au supported on various materials, with the aim of producing CO-free H2. With regards to the decomposition and H2 formation, Au/SiO2 was found to be the most active catalyst. The reaction started at 373 K and was complete at 523 K. Depending on the nature of the supports, significant differences were experienced in the reaction pathways. On Au deposited on SiO2, CeO2, and carbon Norit, dehydrogenation predominated, whereas on Al2O3, ZSM-5, and TiO2-supported Au, dehydration of formic acid was favored. Pure CO-free H2 was obtained on Au/SiO2 and Au/CeO2 at and below 473 K. No changes in activity or selectivity were observed within ∼10 h. For most of the catalysts, the selectivity was improved by the addition of water to formic acid. In situ infrared spectroscopic studies revealed the formation of formate species even on Au/SiO2, located exclusively on Au particles. The decomposition of HCOOH over Au/SiO2 followed zero-order kinetics. The activation energy for the decomposition was 60.7 kJ mol–1, and that for H2 production was 58.5 kJ mol–1.
Na/K-ATPase Mimetic pNaKtide Peptide Inhibits the Growth of Human Cancer Cells (2011)

Cells contain a large pool of nonpumping Na/K-ATPase that participates in signal transduction. Here, we show that the expression of α1 Na/K-ATPase is significantly reduced in human prostate carcinoma as well as in several human cancer cell lines. This down-regulation impairs the ability of Na/K-ATPase to regulate Src-related signaling processes. A supplement of pNaKtide, a peptide derived from α1 Na/K-ATPase, reduces the activities of Src and Src effectors. Consequently, these treatments stimulate apoptosis and inhibit growth in cultures of human cancer cells. Moreover, administration of pNaKtide inhibits angiogenesis and growth of tumor xenograft. Thus, the new findings demonstrate the in vivo effectiveness of pNaKtide and suggest that the defect in Na/K-ATPase-mediated signal transduction may be targeted for developing new anticancer therapeutics.
Unusual lipid structures selectively reduce the toxicity of amphotericin B. (1988)

Ribbon-like structures result when amphotericin B interacts with lipid in an aqueous environment. At high ratios of amphotericin to lipid these structures, which are lipid-stabilized amphotericin aggregates, become prevalent resulting in a dramatic attenuation of amphotericin-mediated mammalian cell, but not fungal cell, toxicity. Studies utilizing freeze-etch electron microscopy, differential scanning calorimetry, 31P NMR, x-ray diffraction, and optical spectroscopy revealed that this toxicity attenuation is related to the macromolecular structure of the complexes in a definable fashion. It is likely that amphotericin in this specific form will have a much improved therapeutic utility.
Spatial Localizations of Mam22 and Mam12 in the Magnetosomes of Magnetospirillum magnetotacticum (2006)

Magnetospirillum magnetotacticum possesses intracellular magnetite particles with a chain-like structure, termed magnetosomes. The bacterium expresses 22-kDa and 12-kDa magnetosome-associated proteins, termed Mam22 (MamA) and Mam12 (MamC), respectively. In this study, we investigated the structure of the purified magnetosomes with transmission electron microscopic techniques and found that the magnetosomes consisted of four compartments, i.e., magnetite crystal, magnetosomal membrane, interparticle connection, and magnetosomal matrix. Furthermore, we determined the precise localizations of Mam22 and Mam12 using immunogold staining of the purified magnetosomes and ultrathin sections of the bacterial cells. Interestingly, most Mam22 existed in the magnetosomal matrix, whereas Mam12 was strictly localized in the magnetosomal membrane. Moreover, the recombinant Mam22 was attached to the magnetosomal matrix of the Mam22-deficient magnetosomes prepared by alkaline treatment, such as 0.1 M Caps-NaOH buffer (pH 11.0). The spatial localization of the magnetosome-associated proteins in the magnetosomal chain provides useful information to elucidate the functional roles of these proteins.
Flexible Snooping: Adaptive Forwarding and Filtering of Snoops in Embedded-Ring Multiprocessors (2006)

A simple and low-cost approach to supporting snoopy cache coherence is to logically embed a unidirectional ring in the network of a multiprocessor, and use it to transfer snoop messages. Other messages can use any link in the network. While this scheme works for any network topology, a naive implementation may result in long response times or in many snoop messages and snoop operations. To address this problem, this paper proposes flexible snooping algorithms, a family of adaptive forwarding and filtering snooping algorithms. In these algorithms, a node receiving a snoop request may either forward it to another node and then perform the snoop, or snoop and then forward it, or simply forward it without snooping. The resulting design space offers trade-offs in number of snoop operations and messages, response time, and energy consumption. Our analysis using SPLASH-2, SPECjbb, and SPECweb workloads finds several snooping algorithms that are more cost-effective than current ones. Specifically, our choice for a high-performance snooping algorithm is faster than the currently fastest algorithm while consuming 9-17% less energy; our choice for an energy-efficient algorithm is only 3-6% slower than the previous one while consuming 36-42% less energy
You Only Look & Listen Once: Towards Fast and Accurate Visual Grounding (2019)

Visual Grounding (VG) aims to locate the most relevant region in an image, based on a flexible natural language query but not a pre-defined label, thus it can be a more useful technique than object detection in practice. Most state-of-the-art methods in VG operate in a two-stage manner, wherein the first stage an object detector is adopted to generate a set of object proposals from the input image and the second stage is simply formulated as a cross-modal matching problem that finds the best match between the language query and all region proposals. This is rather inefficient because there might be hundreds of proposals produced in the first stage that need to be compared in the second stage, not to mention this strategy performs inaccurately. In this paper, we propose an simple, intuitive and much more elegant one-stage detection based method that joints the region proposal and matching stage as a single detection network. The detection is conditioned on the input query with a stack of novel Relation-to-Attention modules that transform the image-to-query relationship to an relation map, which is used to predict the bounding box directly without proposing large numbers of useless region proposals. During the inference, our approach is about 20x ~ 30x faster than previous methods and, remarkably, it achieves 18% ~ 41% absolute performance improvement on top of the state-of-the-art results on several benchmark datasets. We release our code and all the pre-trained models at https://github.com/openblack/rvg.
Subcutaneous and visceral adipose tissue: structural and functional differences (2009)

Obesity is a heterogeneous disorder. Obese individuals vary in their body fat distribution, their metabolic profile and degree of associated cardiovascular and metabolic risk. Abdominal obesity carries greater risk of developing diabetes and future cardiovascular events than peripheral or gluteofemoral obesity. There are differences between adipose tissue present in subcutaneous areas (SCAT) and visceral adipose tissue (VAT) present in the abdominal cavity. These include anatomical, cellular, molecular, physiological, clinical and prognostic differences. Anatomically, VAT is present mainly in the mesentery and omentum, and drains directly through the portal circulaion to the liver. VAT compared with SCAT is more cellular, vascular, innervated and contains a larger number of inflammatory and immune cells, lesser preadipocyte differentiating capacity and a greater percentage of large adipocytes. There are more glucocorticoid and androgen receptors in VAT than in SCAT. VAT adipocytes are more metabolically active, more sensitive to lipolysis and more insulin-resistant than SCAT adipocytes. VAT has a greater capacity to generate free fatty acids and to uptake glucose than SCAT and is more sensitive to adrenergic stimulation, while SCAT is more avid in absorption of circulating free fatty acids and triglycerides. VAT carries a greater prediction of mortality than SCAT.
Synergistic design of DSP and power amplifiers for wireless communications (2001)

Co-design of digital signal-processing (DSP) algorithms and power-amplifier characteristics can lead to improved efficiency and linearity through a variety of strategies including: predistortion, DSP control over bias conditions, particularly the power supply voltage, and DSP generation of digital input signals for switching amplifiers. This paper discusses several amplifier architectures that exemplify these approaches, including: bias-controlled amplifiers, linear amplification with nonlinear component amplifiers, and class-S amplifiers. We envision for the future a generation of "smart power amplifiers," in which DSP optimization of amplifier parameters is carried out for changing environments.
Cutting Edge: Roles of Toll-Like Receptor 4 and IL-23 in IL-17 Expression in Response to Klebsiella pneumoniae Infection (2003)

Local production of IL-17 is a significant factor in effective host defense against Gram-negative bacteria. However, the proximal events mediating IL-17 elaboration by T cells remain unclear. In this study, we show in vivo that intact Toll-like receptor 4 signaling in the lung is required for induction of both the p19 transcript of IL-23 and IL-17 protein elaboration in response to Klebsiella pneumoniae. Although IL-17 is widely considered a CD4(+) T cell product, we also demonstrate significant in vitro IL-17 production by CD8(+) T cells after culture in medium from dendritic cells exposed to these bacteria. The dominant portion of this IL-17-inducing activity for both CD4(+) and CD8(+) T cells is IL-23. These data demonstrate the critical signaling pathway for IL-17 induction in the host response to Gram-negative pulmonary infection and suggest a direct role for IL-23 in CD8(+) T cell IL-17 production.
What do we mean by validating a prognostic model? (2000)

Prognostic models are used in medicine for investigating patient outcome in relation to patient and disease characteristics. Such models do not always work well in practice, so it is widely recommended that they need to be validated. The idea of validating a prognostic model is generally taken to mean establishing that it works satisfactorily for patients other than those from whose data it was derived. In this paper we examine what is meant by validation and review why it is necessary. We consider how to validate a model and suggest that it is desirable to consider two rather different aspects - statistical and clinical validity - and examine some general approaches to validation. We illustrate the issues using several case studies.
Transcriptional and Functional Profiling of Human Embryonic Stem Cell-Derived Cardiomyocytes (2008)

Human embryonic stem cells (hESCs) can serve as a potentially limitless source of cells that may enable regeneration of diseased tissue and organs. Here we investigate the use of human embryonic stem cell-derived cardiomyocytes (hESC-CMs) in promoting recovery from cardiac ischemia reperfusion injury in a mouse model. Using microarrays, we have described the hESC-CM transcriptome within the spectrum of changes that occur between undifferentiated hESCs and fetal heart cells. The hESC-CMs expressed cardiomyocyte genes at levels similar to those found in 20-week fetal heart cells, making this population a good source of potential replacement cells in vivo. Echocardiographic studies showed significant improvement in heart function by 8 weeks after transplantation. Finally, we demonstrate long-term engraftment of hESC-CMs by using molecular imaging to track cellular localization, survival, and proliferation in vivo. Taken together, global gene expression profiling of hESC differentiation enables a systems-based analysis of the biological processes, networks, and genes that drive hESC fate decisions, and studies such as this will serve as the foundation for future clinical applications of stem cell therapies.
Characterization and optimization of acoustic filter performance by experimental design methodology (2005)

Acoustic cell filters operate at high separation efficiencies with minimal fouling and have provided a practical alternative for up to 200 L/d perfusion cultures. However, the operation of cell retention systems depends on several settings that should be adjusted depending on the cell concentration and perfusion rate. The impact of operating variables on the separation efficiency performance of a 10-L acoustic separator was characterized using a factorial design of experiments. For the recirculation mode of separator operation, bioreactor cell concentration, perfusion rate, power input, stop time and recirculation ratio were studied using a fractional factorial 2(5-1) design, augmented with axial and center point runs. One complete replicate of the experiment was carried out, consisting of 32 more runs, at 8 runs per day. Separation efficiency was the primary response and it was fitted by a second-order model using restricted maximum likelihood estimation. By backward elimination, the model equation for both experiments was reduced to 14 significant terms. The response surface model for the separation efficiency was tested using additional independent data to check the accuracy of its predictions, to explore robust operation ranges and to optimize separator performance. A recirculation ratio of 1.5 and a stop time of 2 s improved the separator performance over a wide range of separator operation. At power input of 5 W the broad range of robust high SE performance (95% or higher) was raised to over 8 L/d. The reproducible model testing results over a total period of 3 months illustrate both the stable separator performance and the applicability of the model developed to long-term perfusion cultures.
Two single-base-pair substitutions causing desensitization to tryptophan feedback inhibition of anthranilate synthase and enhanced expression of tryptophan genes of Brevibacterium lactofermentum (1987)

A 5-fluorotryptophan-resistant mutant, termed 1041, was isolated from Brevibacterium lactofermentum AJ12036. The anthranilate synthase of 1041 was insensitive to feedback inhibition by tryptophan, and the specific activities of the anthranilate synthase and anthranilate phosphoribosyltransferase of 1041 were 29- and 23-fold higher than those in parental strain AJ12036, respectively. A single-base change (adenine to cytosine) that resulted in a Ser-to-Arg substitution was found in the trpE structural gene of 1041. This substitution was identified as the cause of the desensitization to feedback inhibition by tryptophan of anthranilate synthase in 1041. Another substitution (guanine to adenine) was found at a position in which a mutation would destabilize the rho-independent terminator structure within the putative attenuator. The enhanced synthesis of tryptophan enzymes in 1041 could be caused by this substitution in the attenuator.
Assessment of the Tissue Distribution of Transplanted Human Endothelial Progenitor Cells by Radioactive Labeling (2003)

Although only a small proportion of radiolabeled EPCs are detected in nonischemic myocardium, myocardial infarction increases homing of transplanted EPCs in vivo profoundly. Radiolabeling might eventually provide an useful tool for monitoring the fate of transplanted progenitor cells and for clinical cell therapy.
Decrease of Intrathyroidal CD161+V.ALPHA.24+V.BETA.11+ NKT Cells in Graves' disease (2008)

To clarify changes in the intrathyroidal natural killer T (NKT) cell subset, which prevents autoimmunity in patients with Graves' disease (GD), we examined intrathyroidal and peripheral lymphocytes in 11 patients with GD and peripheral lymphocytes in nine healthy volunteers using three-color flow cytometry. The proportion of CD161 (+) T cell receptor Valpha24 (+) Vbeta11 (+) cells, which represent the NKT cell subset, was lower in the thyroid of patients with GD than in the peripheral blood of the same patients and in the peripheral blood of healthy subjects. These results indicate that the proportion of intrathyroidal NKT cells is decreased in patients with GD and that this decrease may contribute to incomplete regulation of autoreactive T cells in GD.
USING GRAPHICAL MODELS AND GENOMIC EXPRESSION DATA TO STATISTICALLY VALIDATE MODELS OF GENETIC REGULATORY NETWORKS (2000)

We propose a model-driven approach for analyzing genomic expression data that permits genetic regulatory networks to be represented in a biologically interpretable computational form. Our models permit latent variables capturing unobserved factors, describe arbitrarily complex (more than pair-wise) relationships at varying levels of refinement, and can be scored rigorously against observational data. The models that we use are based on Bayesian networks and their extensions. As a demonstration of this approach, we utilize 52 genomes worth of Affymetrix GeneChip expression data to correctly differentiate between alternative hypotheses of the galactose regulatory network in S. cerevisiae. When we extend the graph semantics to permit annotated edges, we are able to score models describing relationships at a finer degree of specification.
The convalescent sera option for containing COVID-19 (2020)

As of early 2020, humanity is confronting a pandemic in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). SARS-CoV-2 causes coronavirus disease, abbreviated as COVID-19. At the time of this writing, SARS-CoV-2 is spreading in multiple countries, threatening a pandemic that will affect billions of people. This virus appears to be a new human pathogen. Currently there are no vaccines, monoclonal antibodies (mAbs), or drugs available for SARS-CoV-2, although many are in rapid development and some may be available in a short time. This Viewpoint argues that human convalescent serum is an option for prevention and treatment of COVID-19 disease that could be rapidly available when there are sufficient numbers of people who have recovered and can donate immunoglobulin-containing serum.
Early Detection and Biomarkers in Pancreatic Cancer (2007)

Major advances in cancer control will be greatly aided by early detection for diagnosing and treating cancer in its preinvasive state before metastasis. Unfortunately, for pancreatic ductal adenocarcinoma (PDAC), which is the fourth leading cause of cancer-related death in the United States, effective early detection and screening are currently not available and tumors are typically diagnosed at a late stage, frequently after metastasis. Partly because of low sensitivity/specificity, existing biomarkers such as CA19-9 are not adequate as early detection markers of pancreatic cancer. Thus, a great need exists for new biomarkers for pancreatic cancer. This article focuses on recent developments in the identification of new serum protein biomarkers that are useful in the early detection of PDAC.