gebhart/patrepeval huggingface dataset:
Diagnostic value of cerebrospinal fluid anti–myelin basic protein in patients with multiple sclerosis (1986)

Prevalence and titer of total, free, and bound cerebrospinal fluid anti-myelin basic protein (MBP) antibodies as well as free/bound ratios were determined in four groups of patients with multiple sclerosis (MS) and three groups of controls. All patients with clinically active MS have elevated levels of total anti-MBP, which may be present in either free or bound form. Patients whose disease is in remission have undetectable anti-MBP levels, and some patients with clinically stable disease with residual disability may have detectable antibody titers. Chronically progressive MS is usually associated with high levels of antibody in the bound rather than the free form, resulting in a low or normal free/bound ratio. In contrast, MS exacerbations are characterized by relatively high levels of free anti-MBP in the cerebrospinal fluid, resulting in a high free/bound antibody ratio. Bound anti-MBP was also detected in elevated levels in 1 patient with subacute sclerosing panencephalitis and 2 of 8 patients with postinfectious encephalomyelitis. Although elevated levels of cerebrospinal fluid anti-MBP are not specific for MS, they are strongly associated with disease activity and may be involved in the pathogenesis of demyelination in patients with MS.
Protein Engineering Strategies for Selective Protein Purification (2005)

Abstract When producing and purifying recombinant proteins it is of importance to minimize the number of unit operations during the purification procedure. This is accomplished by increasing the selectivity in each step. Due to the high selectivity of affinity chromatography it has a widespread use in protein purification. However, most target proteins lack a suitable affinity ligand usable for capture on a solid matrix. A way to circumvent this obstacle is to genetically fuse the gene encoding the target protein with a gene encoding a purification tag. When the chimeric protein is expressed, the tag allows for specific capture of the fusion protein. In industrial‐scale production, extension of the target protein often is unwanted since it might interfere with the function of the target protein. Hence, a purification scheme developed for the native protein is desired. In this review, different fusion strategies used for protein purification are discussed. Also, the development of ligands for selective affinity purification of native target proteins is surveyed.
Hyaluronan&ndash;cisplatin conjugate nanoparticles embedded in Eudragit S100-coated pectin/alginate microbeads for colon drug delivery (2013)

Hyaluronan-cisplatin conjugate nanoparticles (HCNPs) were chosen as colon-targeting drug-delivery carriers due to the observation that a variety of malignant tumors overexpress hyaluronan receptors. HCNPs were prepared by mixing cisplatin with a hyaluronan solution, followed by dialysis to remove trace elements. The cells treated with HCNPs showed significantly lower viability than those treated with cisplatin alone. HCNPs were entrapped in Eudragit S100-coated pectinate/alginate microbeads (PAMs) by using an electrospray method and a polyelectrolyte multilayer-coating technique in aqueous solution. The release profile of HCNPs from Eudragit S100-coated HCNP-PAMs was pH-dependent. The percentage of 24-hour drug release was approximately 25.1% and 39.7% in pH 1.2 and pH 4.5 media, respectively. However, the percentage of drug released quickly rose to 75.6% at pH 7.4. Moreover, the result of an in vivo nephrotoxicity study demonstrated that Eudragit S100-coated HCNP-PAMs treatment could mitigate the nephrotoxicity that resulted from cisplatin. From these results, it can be concluded that Eudragit S100-coated HCNP-PAMs are promising carriers for colon-specific drug delivery.
Combined obeticholic acid and elafibranor treatment promotes additive liver histological improvements in a diet-induced ob/ob mouse model of biopsy-confirmed NASH (2019)

Obeticholic acid (OCA) and elafibranor (ELA) are selective and potent agonists for the farnesoid X receptor (FXR) and dual peroxisome proliferator-activated receptor α/δ (PPAR-α/δ), respectively. Both agents have demonstrated clinical efficacy in nonalcoholic steatohepatitis (NASH). The present study used OCA and ELA to compare the effects of mono- and combination therapies on metabolic and histological endpoints in Lep<sup>ob/ob</sup> mice with established diet-induced and biopsy-confirmed NASH (ob/ob-NASH). ob/ob-NASH mice were fed the AMLN diet high in trans-fat, fructose and cholesterol for 15 weeks, whereafter they received vehicle, OCA (30 mg/kg, PO, QD), ELA (3, 10 mg/kg, PO, QD), or combinations (OCA + ELA) for eight weeks. Within-subject comparisons were performed on histomorphometric changes, including fractional area of liver fat, galectin-3 and Col1a1. OCA and ELA monotherapies improved all quantitative histopathological parameters and OCA + ELA combinations exerted additive effects on metabolic and histological endpoints. In agreement with their different molecular mechanisms of action, OCA and ELA monotherapies elicited distinct hepatic gene expression profiles and their combination led to profound transcriptome changes associated with further improvements in lipid handling and insulin signaling, suppression of immune responses and reduced extracellular matrix formation. In conclusion, these findings provide preclinical proof-of-concept for combined FXR and PPAR-α/δ agonist-based therapies in NASH.
The Production and Directed Differentiation of Human Embryonic Stem Cells (2006)

Human embryonic stem cells (hESCs) are being rapidly produced from chromosomally euploid, aneuploid, and mutant human embryos that are available from in vitro fertilization clinics treating patients for infertility or preimplantation genetic diagnosis. These hESC lines are an important resource for functional genomics, drug screening, and, perhaps eventually, cell and gene therapy. The methods for deriving hESCs are well established and repeatable and are relatively successful with a ratio of 1:10 to 1:2 new hESC lines produced from 4- to 8-d-old morula and blastocysts and from isolated inner cell mass cell clusters of human blastocysts. The hESCs can be formed and maintained on human somatic cells in humanized serum-free culture conditions and for several passages in cell-free culture systems. The hESCs can be transfected with DNA constructs. Their gene expression profiles are being described and immunological characteristics determined. They may be grown indefinitely in vitro while maintaining their original karyotype and epigenetic status, but this needs to be confirmed from time to time in long-term cultures. hESCs spontaneously differentiate in the absence of the appropriate cell feeder layer, when overgrown in culture and when isolated from the ESC colony. All three major embryonic lineages are produced in differentiating flat attachment cultures and unattached embryoid bodies. Cell progenitors of interest can be identified by markers, expression of reporter genes, and characteristic morphology, and the cells thereafter enriched for progenitor types and further culture to more mature cell types. Directed differentiation systems are well developed for ectodermal pathways that result in neural and glial cells and the mesendodermal pathway for cardiac muscle cells and many other cell types including hematopoietic progenitors and endothelial cells. Directed differentiation into endoderm has been more difficult to achieve, perhaps because of the lack of markers of early progenitors in this lineage. There are reports of enriched cultures of keratinocytes, pigmented retinal epithelium, neural crest cells and motor neurons, hepatic progenitors, and cells that have some markers of gut tissue and pancreatic islet-like cells. The prospects for use of hESC derivatives in regenerative medicine are significant, and there is much optimism for their potential contributions to human regenerative medicine.
An investigation of the physiological roles and enzymatic properties of invertases in tobacco and hybrid poplar (2008)

Plant invertases (EC 3.2.1.26) represent a multi-gene family of β-fructofuranosidases that perform integral roles in several biochemical processes. The central importance of this family of enzymes to plant growth and development has made them a primary target of investigation in plant biology. Research has principally focused on sink-source interactions, and the potential to increase sink capacity in several economically important crop species, including potato and tomato. However, studies exploring the impacts of invertase mis-regulation on cellulose and lignin, the two most abundant biopolymers on earth, had not been conducted. Consequently, we investigated the effects of overexpressing yeast-derived invertases in tobacco and hybrid poplar. Transgenic tobacco expressing the yeast-derived invertases showed reduced height and interference in sink-source metabolism. In addition, some transgenic lines showed significant changes in cellulose and lignin content, providing evidence that sink capacity can be altered via the overexpression of this class of enzyme. In contrast, hybrid poplar expressing foreign invertase genes showed no visible phenotype, with only minor changes to the structural polymers cellulose and lignin, suggesting the mechanism of carbohydrate transport differs between tobacco and hybrid poplar. However, there was evidence for post-translational modification of the foreign invertases in hybrid poplar, which may also explain the difference in phenotypes observed. We suggest that the yeast-derived invertases may not be the most effective target to alter sink biopolymers, and that mis-regulating endogenous invertases may be a more suitable alternative. Consequently, we identified three cell-wall invertase genes in hybrid poplar and investigated their spatial and temporal expression profiles during the complete first year of growth. In addition, we heterologously expressed and characterized two hybrid poplar cell-wall invertase genes involved in vegetative growth. Collectively, the expression and functional characterization data suggest that one floral-specific and two vegetative cell-wall invertases exist in hybrid poplar. Of the two vegetative cell-wall invertases, one (PaxgINV1) appears to be involved in processes relating to dormancy, while the other (PaxgINV2) appears to be involved in phloem unloading and the seasonal reallocation of carbohydrate. We therefore hypothesize that PaxgINV2 may be a suitable target for future mis-regulation studies aimed at altering sink capacity.
Content-Based Representations of Audio Using Siamese Neural Networks (2018)

In this paper, we focus on the problem of content-based retrieval for audio, which aims to retrieve all semantically similar audio recordings for a given audio clip query. This problem is similar to the problem of query by example of audio, which aims to retrieve media samples from a database, which are similar to the user-provided example. We propose a novel approach which encodes the audio into a vector representation using Siamese Neural Networks. The goal is to obtain an encoding similar for files belonging to the same audio class, thus allowing retrieval of semantically similar audio. Using simple similarity measures such as those based on simple euclidean distance and cosine similarity we show that these representations can be very effectively used for retrieving recordings similar in audio content.
The 2007 National Asthma Education and Prevention Program Asthma Guidelines: Accelerating Their Implementation and Facilitating Their Impact on Children With Asthma (2009)

Nearly 2 decades have elapsed since the National Center for Health Statistics raised concerns regarding the trends in increasing asthma prevalence. Additional research highlighted the large racial disparities and geographic variations in asthma morbidity and mortality rates. Although there was little national consensus on the care of children with asthma at the time, there were improvements in the understanding of the mechanisms and treatment of asthma. It was in this context that the National Heart, Lung, and Blood Institute launched the National Asthma Education and Prevention Program, which convened its first panel of experts to create the national consensus clinical practice guidelines on the treatment of asthma. More than 15 years have passed since the publication of those first guidelines and, in August 2007, the National Heart, Lung, and Blood Institute released its newest updates, which are the product of the National Asthma Education and Prevention Program third expert panel. The release of the updated guidelines serves as an occasion to examine important issues regarding the dissemination and clinical implementation of National Asthma Education and Prevention Program guidelines. The goals of this report are to examine the adoption of earlier versions of the National Asthma Education and Prevention Program guidelines and to suggest opportunities for rapid adoption of the newly released guidelines.
Gaussian split Ewald: A fast Ewald mesh method for molecular simulation (2005)

Gaussian split Ewald (GSE) is a versatile Ewald mesh method that is fast and accurate when used with both real-space and k-space Poisson solvers. While real-space methods are known to be asymptotically superior to k-space methods in terms of both computational cost and parallelization efficiency, k-space methods such as smooth particle-mesh Ewald (SPME) have thus far remained dominant because they have been more efficient than existing real-space methods for simulations of typical systems in the size range of current practical interest. Real-space GSE, however, is approximately a factor of 2 faster than previously described real-space Ewald methods for the level of force accuracy typically required in biomolecular simulations, and is competitive with leading k-space methods even for systems of moderate size. Alternatively, GSE may be combined with a k-space Poisson solver, providing a conveniently tunable k-space method that performs comparably to SPME. The GSE method follows naturally from a uniform framework that we introduce to concisely describe the differences between existing Ewald mesh methods.
Quantitative and in vivo activity of adenoviral-producing cells made by cotransduction of a replication-defective adenovirus and a replication-enabling plasmid. (1997)

Achieving limited recombinant viral replication may provide a means of amplifying viral-mediated gene transfer in vivo. We have previously shown that cotransduction of an E1-defective adenovirus with a plasmid containing the deleted E1 functions into prostate carcinoma cells resulted in E1-defective virus production by those cells. The studies described here have extended these findings to more firmly establish the capacity of the trans complementation approach to achieve amplification of recombinant viral transgene expression. The recombinant virus used for all the studies was AdCMV-luc which contained a luciferase expression cassette; the replication-enabling plasmid, pE1, encoded the E1 functions deleted from AdCMV-luc. Quantitative in vitro studies with the HeLa cell line showed that for each plaque forming unit of AdCMV-luc originally exposed to the cells, 0.54 x 10(3) new replication-defective viruses were detected in supernatants and lysates over the following 4 days. Multiple cell lines were shown to support new virus production following cotransduction of AdCMV-luc and pE1. Small numbers of replication-competent viruses were detected in the lysates and supernatants from the cotransduced cells such that for every 10(5) replication-defective viruses approximately two replication-competent viruses were produced. Tumor nodules produced by engrafting a mixture of AdCMV-luc/pE1-cotransduced HeLa cells with uninfected HeLa cells yielded much higher levels of luciferase expression than control tumors containing mixtures of cells infected with AdCMV-luc alone. In total, these results demonstrate new virus production by cells receiving a replication-defective adenovirus and a replication-enabling plasmid are capable of amplifying recombinant viral transgene expression in vivo.
Gate-all-around silicon nanowire 25-stage CMOS ring oscillators with diameter down to 3 nm (2010)

We demonstrate the world's first top-down CMOS ring oscillators (ROs) fabricated with gate-all-around (GAA) silicon nanowire (NW) FETs having diameters as small as 3 nm. NW capacitance shows size dependence in good agreement with that of a cylindrical capacitor. AC characterization shows enhanced self-heating below 5 nm.
Generation of monoclonal antibodies to a human natural killer clone. Characterization of two natural killer-associated antigens, NKH1A and NKH2, expressed on subsets of large granular lymphocytes. (1985)

The initial characterization of two monoclonal antibodies directed at antigens selectively expressed on large granular lymphocytes (LGL) is reported in the present paper. These two reagents, anti-natural killer (NK) H1A and anti-NKH2, were obtained following immunization of mouse spleen cells with a cloned human NK cell line termed JT3. In fresh human peripheral blood, both anti-NKH1A and anti-NKH2 selectively reacted with cells that appeared morphologically as large granular lymphocytes. However, complement lysis studies and two color fluorescence analysis demonstrated that some LGL express both antigens and other cells express only NKH1A or NKH2. Functional analysis of these subsets indicated that the population of NKH1A+ cells contains the entire pool of NK active lymphocytes, whereas expression of NKH2 antigen appeared to delineate a unique subpopulation of LGL which, in a resting state, display a low degree of spontaneous cytotoxicity. Expression of NKH1A and NKH2 was also investigated using a series of nine well characterized human NK clones. All NK clones were found to be NKH1A+ and four out of nine also expressed NKH2. These results strongly supported the view that NKH1A is a "pan-NK" associated antigen, and indicated that at least a fraction of cloned NKH2 + LGL are strongly cytotoxic. Anti-NKH1A was shown to have the same specificity as the previously described N901 antibody and was found here to precipitate a 200,000-220,000-mol wt molecule in SDS-polyacrylamide gel electrophoresis (PAGE) analysis. Anti-NKH2 was specific for a structure that migrates at 60,000 mol wt in SDS-PAGE analysis under reducing conditions. Two color immunofluorescence analysis of NKH1A, NKH2, and other NK-associated antigens (Leu7 and B73.1) demonstrated variable degrees of coexpression of these antigens, which confirmed that NKH1A and NKH2 define distinct cell surface structures. Anti-NKH1A and anti-NKH2 appear to be useful reagents for characterizing LGL present in human peripheral blood and for identifying functionally relevant subsets within this heterogeneous population of cytotoxic lymphocytes.
Increasing the instruction fetch rate via multiple branch prediction and a branch address cache (2014)

research-article Share on Increasing the instruction fetch rate via multiple branch prediction and a branch address cache Authors: Tse-Yu Yeh Univ. of Michigan, Ann Arbor Univ. of Michigan, Ann ArborView Profile , Deborah T. Marr Univ. of Michigan, Ann Arbor Univ. of Michigan, Ann ArborView Profile , Yale N. Patt Univ. of Michigan, Ann Arbor Univ. of Michigan, Ann ArborView Profile Authors Info & Claims ACM International Conference on Supercomputing 25th Anniversary VolumeJune 2014 Pages 183–192https://doi.org/10.1145/2591635.2667167Online:01 August 1993Publication History 1citation357DownloadsMetricsTotal Citations1Total Downloads357Last 12 Months9Last 6 weeks1 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteGet Access
Rapid Quantification of Adult and Developing Mouse Spatial Vision Using a Virtual Optomotor System (2004)

The virtual optomotor system provides a simple and precise method for rapidly quantifying mouse vision. Behavioral measures of vision in mice are essential for interpreting the results of experiments designed to reveal the cellular and molecular mechanisms of vision and visual development and for evaluating potential treatments for visual diseases.
Performance assessment of photon migration instruments: the MEDPHOT protocol (2005)

We propose a comprehensive protocol for the performance assessment of photon migration instruments. The protocol has been developed within the European Thematic Network MEDPHOT (optical methods for medical diagnosis and monitoring of diseases) and is based on five criteria: accuracy, linearity, noise, stability, and reproducibility. This protocol was applied to a total of 8 instruments with a set of 32 phantoms, covering a wide range of optical properties.
NGAL Controls the Metastatic Potential of Anaplastic Thyroid Carcinoma Cells (2012)

Our results indicate NGAL as a novel target of nuclear factor-κB prometastatic activity in thyroid cancer through enhancement of MMP-9 enzymatic activity.
Repeated Administration of Synthetic Oligodeoxynucleotides Expressing CpG Motifs Provides Long-Term Protection against Bacterial Infection (1999)

Synthetic oligodeoxynucleotides (ODN) expressing unmethylated CpG motifs stimulate an innate immune response characterized by the production of polyreactive immunoglobulin M antibodies and immunomodulatory cytokines. This immune response has been shown to protect mice from challenge by Listeria monocytogenes and Francisella tularensis for up to 2 weeks. By repeatedly administering CpG ODN two to four times/month, we found that this protection could be maintained indefinitely. Protection was associated with a significant increase in the number of spleen cells that could be triggered by subsequent pathogen exposure to secrete gamma interferon and interleukin-6 in vivo (P < 0.01). ODN-treated animals remained healthy and developed neither macroscopic nor microscopic evidence of tissue damage or inflammation. Thus, repeated administration of CpG ODN may provide a safe means of conferring long-term protection against infectious pathogens.