gebhart/patrepeval huggingface dataset:
Adrenomedullin Induces Endothelium-Dependent Vasorelaxation via the Phosphatidylinositol 3-Kinase/Akt–Dependent Pathway in Rat Aorta (2001)

To study the mechanisms by which adrenomedullin (AM) induces endothelium-dependent vasorelaxation, we examined whether AM-induced endothelium-dependent vasodilation was mediated by the phosphatidylinositol 3-kinase (PI3K)/Akt-dependent pathway in rat aorta, because it was recently reported that PI3K/Akt was implicated in the activation of endothelial NO synthase. AM-induced vasorelaxation in thoracic aorta with intact endothelium was inhibited by pretreatment with PI3K inhibitors to the same level as that in endothelium-denuded aorta. AM elicited Akt phosphorylation in a time- and dose-dependent manner. AM-induced Akt phosphorylation was inhibited by pretreatment with a calmodulin-dependent protein kinase inhibitor as well as with PI3K inhibitors. When an adenovirus construct expressing a dominant-negative Akt mutant (Ad/dnAkt) was injected into abdominal aortas so that the mutant was expressed predominantly in the endothelium layer, AM-induced vasodilation was diminished to the same level as that in endothelium-denuded aortas. Finally, AM-induced cGMP production, which was used as an indicator for NO production, was suppressed by PI3K inhibition or by Ad/dnAkt infection into the endothelium. These results suggested that AM induced Akt activation in the endothelium via the Ca(2+)/calmodulin-dependent pathway and that this was implicated in the production of NO, which in turn induced endothelium-dependent vasodilation in rat aorta.
Single UM171 Expanded Cord Blood Transplant is Feasible, Safe, and Permits Transplantation of Better HLA Matched Cords with Very Low Transplant Related Mortality (2018)

Cord blood (CB) transplants are hampered by low cell dose and high transplant related mortality (TRM). UM171, a novel, potent agonist of hematopoietic stem cell (HSC) self-renewal could solve this hindrance, allowing for CB's lower risk of chronic GVHD and relapse to prevail. Hence, we initiated a trial to test the safety and efficacy of UM171 expanded CB (eCB). The procedure was designed to be be clinically viable. Patients (pts) received an ablative conditioning. On day(D)-7, CB was thawed and CD34+ selected. The CD34- lymphocyte containing fraction was cryopreserved and infused on D0. The CD34+ cells were placed in a closed culture system supplemented daily with UM171-containing media until D0, when cells were washed and infused. This culture system allowed for small culture volumes (median .6 liter), saving cost and labor. Between 6/16-8/17, 17 adults (median age 44 years) were transplanted. Net CD34 expansion was 36-fold. Median 1st day of 100 and 500 neutrophils were D+10 and D+19, respectively. Achieving 100 neutrophils was faster than expected and cell dose independent, suggesting that clinically meaningful expansion of an early repopulating myeloid progenitor is at saturation even with small CBs. In contrast, attaining 500 neutrophils was accelerated but dependent on infused CD34+ dose. Importantly, patients derived clinical benefit much earlier than engraftment of 500 neutrophils. For example, and when compared to our pts who received the same conditioning regimen with peripheral blood or marrow, eCB pts were free of fever much earlier (D+7 vs D+15 p < .001). Moreover, hospitalization was reduced by 11 days when compared to our non UM171 CB transplants. Furthermore, with a median follow up of 6 months (range 1-15), there has been no CMV disease, no PTLD, and only 1 grade 3-4 acute GVHD, 1 chronic GVHD (mild) and 1 TRM from alveolar hemorrhage. Full donor chimerism was achieved in all cell subsets. These results favorably compare to those of other expansion trials which utilize much larger (up to 20L) and longer (up to 21 days) cultures. Moreover, and in contrast to others, we have already initiated our dose reduction study with smaller, better HLA matched CBs, proven to reduce TRM. We offer 3 hypotheses as possible contributors for the favorable outcomes in our very high-risk patient group: i) 100 neutrophils, which are attained much earlier at D+10, provide significant defense against infection, ii) the graft contains a significant proportion of dendritic cell precursors (30-50%) which may activate Tregs and iii) because cell dose requirements are lower, 11/17 pts received a better HLA matched CB and 2 pts required a single CB instead of a double. In conclusion, this 1st trial positions UM171-expanded CB as a viable HSC source.
Hepatocyte Encapsulation for Enhanced Cellular Functions (2000)

An efficient bioartificial liver-assisted device can sustain the lives of patients with acute liver failure. Among different configurations of the bioreactor design, hepatocyte encapsulation has important features that satisfy most requirements of the device. We have encapsulated rat hepatocytes in a two-layer polymeric membrane by complex coacervation using a simple setup and demonstrated enhanced cellular functions up to three times higher than those of the monolayer control. These microcapsules of the functioning hepatocytes have a 2- to 3-microm outer layer of synthetic polymer with 25% 2-hydroxyethyl methacrylate, 25% methacrylic acid, and 50% methyl methacrylate and an inner layer of positively charged modified collagen as a suitable substrate for the enhanced cellular functions. Permeable only to small molecules up to albumin, the microcapsules should allow unimpeded exchange of nutrients, oxygen, growth factors, and metabolites but prevent attack by immunoglobulins of the immune system, and no "skin effect" of the collagen has been observed. Mechanical properties of the microcapsules measured with a nano-indentation method suggest that the microcapsules should be suitable for use in a bioartificial liver-assisted device.
Supported copper catalysts for hydrogen transfer reactions involving allylic alcohols (2014)

International @ BIOVERT+TGE:MBE:CPI
Combination Therapies Including Cilofexor and Firsocostat for Bridging Fibrosis and Cirrhosis Attributable to NASH (2020)

In patients with bridging fibrosis and cirrhosis, 48 weeks of cilofexor/firsocostat was well tolerated, led to improvements in NASH activity, and may have an antifibrotic effect. This combination offers potential for fibrosis regression with longer-term therapy in patients with advanced fibrosis attributable to NASH.
Extending the Compatibility of the SP3 Paramagnetic Bead Processing Approach for Proteomics (2018)

The diversity in protein and peptide biochemistry necessitates robust protocols and reagents for efficiently handling and enriching these molecules prior to analysis with mass spectrometry (MS) or other techniques. Further exploration of the paramagnetic bead-based approach, single-pot solid-phase-enhanced sample preparation (SP3), is carried out toward updating and extending previously described conditions and experimental workflows. The SP3 approach was tested in a wide range of experimental scenarios, including (1) binding solvents (acetonitrile, ethanol, isopropanol, acetone), (2) binding pH (acidic vs neutral), (3) solvent/lysate ratios (50–200%, v/v), (4) mixing and rinsing conditions (on-rack vs off-rack rinsing), (5) Enrichment of nondenatured proteins, and (6) capture of individual proteins from noncomplex mixtures. These results highlight the robust handling of proteins in a broad set of scenarios while also enabling the development of a modified SP3 workflow that offers extended compatibility. The modified SP3 approach is used in quantitative in-depth proteome analyses to compare it with commercial paramagnetic bead-based HILIC methods (MagReSyn) and across multiple binding conditions (e.g., pH and solvent during binding). Together, these data reveal the extensive quantitative coverage of the proteome possible with SP3 independent of the binding approach utilized. The results further establish the utility of SP3 for the unbiased handling of peptides and proteins for proteomic applications.
S227 Messenger RNA SARS-CoV-2 Vaccines Affect the Gut Microbiome (2022)

Introduction: Messenger RNA vaccines for preventing SARS-CoV-2 infection are widely used yet their effect on the gut microbiome is not known. Low bifidobacteria levels have been linked with severe SARS-CoV-2 infection, inflammatory bowel disease, Clostridioides diffícile infection, obesity and aging. Preliminary case reports suggest fecal microbiota transplant could cure SARS-CoV-2 infection (1). A study by Bozkurt et al. showed that SARS-CoV-2 patients taking bifidiobacteria-containing probiotics had lower COVID-related hospitalization times (2). Methods: 34 subjects had stool collection prior to vaccination and one month post vaccination to evaluate the relative abundance of bifidobacteria in the gut. DNA was extracted, library was prepped, and enrichment and sequencing were done using metagenomic next generation sequencing. Results: Relative abundance of genus bifidobacteria significantly decreased to about half of original value after vaccination (P = 0.0065 via Wilcoxon signed rank test). Prior to vaccination, median (interquartile range) values of relative abundance for genus bifidobacteria were 1.13% (0.0016% to 2.52%) and after vaccination were 0.64% (0.0015% to 2.48%). Conclusion: Bifidobacteria, included in the $1 billion industry of probiotics, has been shown to be critical in inflammatory diseases, severe COVID-19, obesity, and the aging process. Our results, although preliminary suggest that SARS COV-2 mRNA vaccine decreases levels of bifidobacteria (P = 0.0065). Future studies will be needed to characterize the time course of this decrease in bifidobacteria abundance, its impact on human health, and whether or not similar findings are seen with other vaccines (Figure).Figure 1.: Bifidobacterium relative abundance decreases ( P = 0.0065) in subjects (n=34) after vaccination compared to before vaccination in the same subjects. Bars plot median; error bars plot interquartile range
Precision Irrigation/Fertilization in Orchards (2004)

The development of a spatially variable microsprinkler system was shown. The systemconsisted of individually addressable microsprinkler nodes and a drip line controller which issuedcommands to each node. A demonstration system was constructed and preliminary field tests wereconducted. Results show that individual microsprinkler control is possible and development willcontinue.
Cost-Effective Hyperparameter Optimization for Large Language Model Generation Inference (2023)

Large Language Models (LLMs) have sparked significant interest in their generative capabilities, leading to the development of various commercial applications. The high cost of using the models drives application builders to maximize the value of generation under a limited inference budget. This paper presents a study of optimizing inference hyperparameters such as the number of responses, temperature and max tokens, which significantly affects the utility/cost of text generation. We design a framework named EcoOptiGen which leverages economical hyperparameter optimization and cost-based pruning. Experiments with the GPT-3.5/GPT-4 models on a variety of tasks verify its effectiveness. EcoOptiGen is implemented in the `autogen' package of the FLAML library: \url{https://aka.ms/autogen}.
Supplementary Figure 4 from A Novel Epigenetic Signature for Early Diagnosis in Lung Cancer (2023)

&lt;p&gt;Epigenetic signature in lung cancer and non-tumoral paraffins classified based on histological subtypes.&lt;/p&gt;
Intraesophageal administration of GS-nitroxide (JP4-039) protects against ionizing irradiation-induced esophagitis. (2011)

intraesophageal GS-nitroxide radioprotection is mediated primarily through recovery of endogenous esophageal progenitor cells.
Learning to Perform Downlink Channel Estimation in Massive MIMO Systems (2021)

We study downlink (DL) channel estimation in a multi-cell Massive multiple-input multiple-output (MIMO) system operating in a time-division duplex. The users must know their effective channel gains to decode their received DL data signals. A common approach is to use the mean value as the estimate, motivated by channel hardening, but this is associated with a substantial performance loss in non-isotropic scattering environments. We propose two novel estimation methods. The first method is model-aided and utilizes asymptotic arguments to identify a connection between the effective channel gain and the average received power during a coherence block. The second one is a deep-learning-based approach that uses a neural network to identify a mapping between the available information and the effective channel gain. We compare the proposed methods against other benchmarks in terms of normalized mean-squared error and spectral efficiency (SE). The proposed methods provide substantial improvements, with the learning-based solution being the best of the considered estimators.
Supplementary Figure S7 from ERK Inhibitor LY3214996 Targets ERK Pathway–Driven Cancers: A Therapeutic Approach Toward Precision Medicine (2023)

&lt;p&gt;In vivo effect of treatment on body weight loss.&lt;/p&gt;
A linear array of processors with partially shared memory for parallel solution of PDE (1990)

We propose a multiprocessor architecture with partially shared memory blocks, which is, we think, best suited for the successive approximation of scientific computing problems, such as matrix operations, partial differential equations etc. The topology is a ring. But the system configuration is a subset of an orthogonal multiprocessor Scherson and Hwang have already proposed.We actually built an experimental system, on which we solved a heat conduction problem. The computing time is about 600 seconds in the case of 256x256 grid points.We conclude that the proposed system is a medium scale specific computer for simulations of physical systems, which is suitable for the coming era of personal and distributed computing.
A Floating Body Cell (FBC) fully Compatible with 90nm CMOS Technology Node for Embedded Applications (2006)

Floating body cell (FBC) is a one-transistor memory cell on SOI substrate, which aims high density embedded memory on SOC. In order to verify this memory cell technology, a 128Mb SOI DRAM with FBC has been designed and successfully developed. The memory cell design and the experimental results, such as the signal and the retention characteristics, are reviewed. The results of the fabricated SOI DRAM and the prospect as embedded memory are also discussed
Energy Principles and Finite Element Methods for Pure Traction Linear Elasticity (2011)

Abstract A conforming finite element discretization of the pure traction elasticity boundary value problem results in a singular linear system of equations. The singularity of the linear system is removed through various approaches. In this report, we consider an alternative approach in which discrete finite element formulations are derived directly from the principle of minimum potential energy. This point of view turns out to be particularly well suited to handle the rigid body modes, which are the source of the singularity in the finite element linear system. Our approach allows us to formulate a regularized potential energy principle and show that the associated weak problem is coercive in H1(Ω). This guarantees nonsingular problems, enables simplified solution algorithms and leads to more efficient and robust preconditioners for the iterative solution linear equations.
BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions (2010)

BiGG addresses a need in the systems biology community to have access to high quality curated metabolic models and reconstructions. It is freely available for academic use at http://bigg.ucsd.edu.
Extraction, purification and characterization of an arabinogalactan from frost (riverbank) grape (Vitis riparia Michx.) stems (2023)

This study investigated the extraction and properties of an arabinogalactan polysaccharide from frost grape (FGP) as a potential alternative to gum arabic (GA). Collection date, solvent:feed ratio (S:F), chip size, C-18 filtration, ultrafiltration, freeze drying versus spray drying, methanol pre-extraction, and water absorption were examined. Sugar composition, elemental analysis, dietary fiber content, emulsification activity index (EAI), emulsification stability index (ESI), and viscosity were used to evaluate the extracts. Exudates collected in March from live stems were viscous with high percentage solids and FGP, while May collections were watery with low percentage solids and FGP. Frost grape stems were collected, chipped, and classified by size. The extraction system utilized pressure or vacuum to increase contact between the chips and extraction water. A S:F ratio of ca. 24% gave an excellent yield of FGP. Chips between 1.8 and 3.8 mm gave the highest mass yields. Pre-extracting the chips with methanol and C-18 filtration of the water extract both yielded a lighter product. The EAI for the FGP was higher than that for GA; however, its ESI was lower. Ultrafiltration of the crude extract separated glucose, fructose, and sucrose from the FGP. FGP with glucose, fructose, and sucrose adsorbed water and became darker.
Session details: Industrial research on evaluation and modeling of computer systems (2010)

No abstract available.
Global Call for Free Academic Movement for International Dialogue (2012)

The recent meeting of the International Diabetes Federation (IDF), the World Diabetes Congress 2011, took place in Dubai in December 2011. The fact that Dubai was chosen as the venue for this international congress became controversial because it was perceived by some prospective attendees that it might limit participation based on nationality or religion as a result of strict entry laws and/or fear for the security of some participants.

On the other hand, the choice by the IDF was a logical one because of the fact that the Emirates and other countries in the Gulf region have an unusually high frequency of diabetes. In this region, diabetes is epidemic, with approximately 25% of the adult population affected. As a result, the physicians and Ministries of Health had a great need and strong desire to promote prevention and treatment of diabetes and its associated disorders in this region.

The IDF widely publicized that the meeting was open to anyone who wanted to attend and that all would receive permits to enter the country and have their security assured. However, as the date of the meeting approached, it turned out that some Israeli passport holders, not applying via the IDF, were not able to acquire visas to enter Dubai. In addition, there were some technical difficulties on the website which made it difficult to register via the IDF Internet site. It also appears that the Israel Diabetes Association, whose members were most …
Human activities control the source of eroded organic carbon in lake sediments over the last 100 years: Evidence from stable isotope fingerprinting (2023)

Understanding the redistribution of soil organic carbon (OC) driven by erosion contributes to the global carbon budget and watershed management. Quantifying the sources of eroded OC in sediments provides new insights to addressing this issue. However, limited quantitative information on the factors influencing OC sources has constrained the behavior of regulating the OC exported from the watershed. Here, we explored the sources of OC in lake sediments over the last 100 years and quantified the effects of climate change and human activities on OC sources. Results from the stable isotope fingerprinting and MixSIAR model indicated that phragmites (30.34%) and croplands (21.48%) were consistently the main OC sources. Therefore, efforts should be concentrated on controlling soil erosion from cropland and managing the endogenous environment. In addition, the partial least squares pathways (PLS-PM) and random forests revealed that human activities (Path coefficients (r<sub>∂</sub>): 0.45 to 0.61) have controlled the OC sources over the last hundred years. Agricultural activities, urbanization, and land use change altered the quality of OC sources by affecting the vegetation productivity in source areas. The quantity of OC sources was also influenced by underlying surface and surface connectivity changes. The effects of climate change (temperature (r<sub>∂</sub>): -0.41 to 0.1; precipitation (r<sub>∂</sub>): 0.1 to 0.29) on OC sources have not been significant, but their long-term effects cannot be ignored. These findings provide a better insight into the origin and behavior of OC in lake sediments under global change, which is crucial for basin management and lake governance.
A Fluorescent Ligand-Binding Alternative Using Tag-lite® Technology (2010)

G-protein-coupled receptors (GPCRs) are crucial cell surface receptors that transmit signals from a wide range of extracellular ligands. Indeed, 40% to 50% of all marketed drugs are thought to modulate GPCR activity, making them the major class of targets in the drug discovery process. Binding assays are widely used to identify high-affinity, selective, and potent GPCR drugs. In this field, the use of radiolabeled ligands has remained so far the gold-standard method. Here the authors report a less hazardous alternative for high-throughput screening (HTS) applications by the setup of a nonradioactive fluorescence-based technology named Tag-lite(®). Selective binding of various fluorescent ligands, either peptidic or not, covering a large panel of GPCRs from different classes is illustrated, particularly for chemokine (CXCR4), opioid (δ, µ, and κ), and cholecystokinin (CCK1 and CCK2) receptors. Affinity constants of well-known pharmacological agents of numerous GPCRs are in line with values published in the literature. The authors clearly demonstrate that the Tag-lite binding assay format can be successfully and reproducibly applied by using different cellular materials such as transient or stable recombinant cells lines expressing SNAP-tagged GPCR. Such fluorescent-based binding assays can be performed with adherent cells or cells in suspension, in 96- or 384-well plates. Altogether, this new technology offers great advantages in terms of flexibility, rapidity, and user-friendliness; allows easy miniaturization; and makes it completely suitable for HTS applications.
Coupled-Cavity Laser System for Active Tracking of a Remote Target (2003)

We demonstrated that an optimal LADAR scheme requires a wavefront phase conjugate mirror (PCM) for efficient operation. Such a system can be built by using PC four-wave mixing (FWM) in a coupled-cavity laser scheme (CCLS). This provides a solution to the problem of maintaining mutual coherence between the pump and signal beams at arbitrary lengths of the partial cavities, as well as oscillation initiation in the entire system. The proposed CCLS can be used for tracking a remote target.
Hop functions downstream of Nkx2.1 and GATA6 to mediate HDAC-dependent negative regulation of pulmonary gene expression (2006)

Hop is an unusual homeodomain protein that was first identified in the developing heart where it functions downstream of Nkx2.5 to modulate cardiac gene expression. Hop functions through interactions with histone deacetylase (HDAC) 2 to mediate repression of cardiac-specific genes, and recent studies show that HDAC activity and HDAC2 expression are decreased in people with chronic obstructive pulmonary disease. Here, we show that Hop is expressed in airway epithelium coincident with HDAC2, and expression is induced by the combination of dexamethasone and cAMP in parallel with induction of surfactant protein gene expression. Hop functions in the developing pulmonary airway, acting downstream of Nkx2.1 and GATA6, to negatively regulate surfactant protein expression. Loss of Hop expression in vivo results in defective type 2 pneumocyte development with increased surfactant production and disrupted alveolar formation. Thus Hop represents a novel regulator of pulmonary maturation that is induced by glucocorticoids to mediate functionally important HDAC-dependent negative feedback regulation.