gebhart/patrepeval huggingface dataset:
The effects of storage conditions on viability of Clostridium difficile vegetative cells and spores and toxin activity in human faeces (2003)

Storage temperature and multiple cycles of freezing (refrigeration)/thawing had minimal effects upon the viability of C difficile or its spores. Storage at 4 degrees C has no discernible effect on C difficile cytotoxin. However, storage at -20 degrees C has a detrimental effect upon C difficile cytotoxin, and multiple cycles of freezing and thawing may further adversely effect toxin titres.
Efficient runtime tracking of allocation sites in Java (2010)

Tracking the allocation site of every object at runtime is useful for reliable, optimized Java. To be used in production environments, the tracking must be accurate with minimal speed loss. Previous approaches suffer from performance degradation due to the additional field added to each object or track the allocation sites only probabilistically. We propose two novel approaches to track the allocation sites of every object in Java with only a 1.0% slow-down on average. Our first approach, the Allocation-Site-as-a-Hash-code (ASH) Tracker , encodes the allocation site ID of an object into the hash code field of its header by regarding the ID as part of the hash code. ASH Tracker avoids an excessive increase in hash code collisions by dynamically shrinking the bit-length of the ID as more and more objects are allocated at that site. For those Java VMs without the hash code field, our second approach, the Allocation-Site-via-a-Class-pointer (ASC) Tracker , makes the class pointer field in an object header refer to the allocation site structure of the object, which in turn points to the actual class structure. ASC Tracker mitigates the indirection overhead by constant-class-field duplication and allocation-site equality checks. While a previous approach of adding a 4-byte field caused up to 14.4% and an average 5% slowdown, both ASH and ASC Trackers incur at most a 2.0% and an average 1.0% loss. We demonstrate the usefulness of our low-overhead trackers by an allocation-site-aware memory leak detector and allocation-site-based pretenuring in generational GC. Our pretenuring achieved on average 1.8% and up to 11.8% speedups in SPECjvm2008.
Alloying and Dealloying Processes Involved in the Preparation of Metal Nanoshells through a Galvanic Replacement Reaction (2003)

The galvanic replacement reaction between Ag nanoparticles and an aqueous HAuCl4 solution has recently been demonstrated as a simple and convenient route to metal nanostructures with hollow interiors and highly crystalline walls (see, for example, Sun, Y.; Mayers, B. T.; Xia, Y. Nano Lett. 2002, 2, 481. Sun, Y.; Xia, Y. Science, 2002, 298, 2176). However, the details of morphological, compositional, structural, and spectral changes involved in the entire process of this template-engaged reaction is yet to be elucidated. The experimental results described in this letter indicate that the templating process proceeded through two distinctive steps: (i) formation of pinhole-free nanoshells with homogeneous, uniform walls of Au/Ag alloys via a combination of the replacement reaction and alloying; and (ii) formation of porous nanoshells (nanocages) through a dealloying process, in which Ag was selectively dissolved from the walls made of Au/Ag alloys. As alloying and dealloying proceeded, the surface plasmon resonance peaks of resultant metal nanostructures could be continuously tuned from ∼425 to ∼1030 nm.
Frames of reference and normal movement (1996)

Abstract Latash &amp; Anson propose that so-called abnormal movements may be stable and adaptive coordination and control solutions to task goals in action. Their interpretation of this established viewpoint is confused throughout in the persistent crossing of frames of reference, both in the description of movement and action and the proposed theory for motor control.
Two Independent Molecular Pathways for Recombinant Adeno-Associated Virus Genome Conversion Occur after UV-C and E4orf6 Augmentation of Transduction (1999)

Numerous environmental influences have been demonstrated to enhance recombinant adeno-associated virus (rAAV) transduction. Such findings are the foundation of developing new and innovative strategies to improve the efficiency of rAAV as a gene therapy vector. Several of these environmental factors included genotoxic stresses such as UV and y irradiation as well as certain adenoviral gene products such as E4orf6. The mechanisms by which these environmental stimuli increase rAAV transduction are only partially understood but have been suggested to involve both endocytosis and uptake of virus to the nucleus, as well as conversion of single-stranded DNA viral genomes to double-stranded expressible forms. Two molecular intermediates of rAAV genomes, which have been demonstrated to correlate with transgene expression and/or the persistence of rAAV, include both replication form (Rf) monomers and dimers as well as circular intermediates. In the present study, we demonstrate that augmentation of rAAV transduction by UV irradiation and the adenoviral protein E4orf6 correlates with distinct increases in either circular or replication form intermediates, respectively. UV irradiation of primary fibroblasts at 15 J/m2 resulted in a 15-fold induction of head-to-tail circular intermediates, with minimal induction of replication form rAAV genomes. In contrast, E4orf6-augmented rAAV transduction was correlated with the formation of replication form intermediates, with no alteration in the abundance of circular intermediates. These findings demonstrate that rAAV transduction can occur through two independent molecular pathways that convert single-stranded AAV genomes to expressible forms of DNA.
Frequently increased epidermal growth factor receptor (EGFR) copy numbers and decreased BRCA1 mRNA expression in Japanese triple-negative breast cancers (2008)

TNBCs have an aggressive clinical course, and EGFR and BRCA1 might be candidate therapeutic targets in this disease.
Effects of Concentration, Crystal Structure, Magnetism, and Electronic Structure Method on First-Principles Oxygen Vacancy Formation Energy Trends in Perovskites (2014)

Systematic prediction of the redox reaction energetics of large sets of 3d transition metal oxides is imperative to the selection of oxygen carrier candidates in applications ranging from chemical looping to solid oxide fuel cell (SOFC) cathode design. In particular, the energetic study of oxygen vacancy formation in unmixed perovskites with La, alkali, and alkaline A-site metal cations—as well as 3d transition metal B-site cations—is a crucial first step in understanding the energetic tunability afforded by cation doping in ABO3 materials. An assessment of the relative oxygen vacancy formation energetics of LaBO3, SrBO3, and similar materials that serve as a guideline for predicting energetics in related systems is completed below using density functional theory (DFT). This assessment illustrates which simplifications can be made in the prediction of energetics trends without affecting trend order. The independent consideration of oxygen vacancy concentration, crystal structure, and antiferromagnetic (AFM) magnetism revealed that these factors in DFT calculations had no effect on trend order. However, the ferromagnetic (FM) SrBO3 trend order was affected between SrMnO3 and SrFeO3 as a function of defect concentration. Moreover, energetic trends were also formed by adding constant, incremental values of the Hubbard U parameter contributing to the 3d orbitals of perovskite B-sites. Calculation of U parameters was done by linear response theory or by a literature review of previous research.
[A simple and rapid modified--new method for SNP typing by fragment length discrepant allele specific PCR]. (2005)

FLDAS-PCR is a simple, rapid and efficient new method for SNP typing. During FLDAS-PCR, specific primers with a mismatch at the third or fourth 3'-terminal base have more power to identify two alleles.
Nucleotide sequence of the rat low density lipoprotein receptor cDNA (1989)

Journal Article Nucleotide sequence of the rat low density lipoprotein receptor cDNA Get access L.Y. Lee, L.Y. Lee Search for other works by this author on: Oxford Academic PubMed Google Scholar W.A. Mohler, W.A. Mohler Search for other works by this author on: Oxford Academic PubMed Google Scholar B.L. Schafer, B.L. Schafer Search for other works by this author on: Oxford Academic PubMed Google Scholar J.S. Freudenberger, J.S. Freudenberger Search for other works by this author on: Oxford Academic PubMed Google Scholar N. Byrne-Connolly, N. Byrne-Connolly Search for other works by this author on: Oxford Academic PubMed Google Scholar K.B. Eager, K.B. Eager Search for other works by this author on: Oxford Academic PubMed Google Scholar S.T. Mosley, S.T. Mosley Search for other works by this author on: Oxford Academic PubMed Google Scholar J.K. Leighton, J.K. Leighton 1Hepatobiliary Research Center, University of Colorado Health Science CenterDenver, CO 80262, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar R.N. Thrift, R.N. Thrift 1Hepatobiliary Research Center, University of Colorado Health Science CenterDenver, CO 80262, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar R.A. Davis, R.A. Davis 1Hepatobiliary Research Center, University of Colorado Health Science CenterDenver, CO 80262, USA Search for other works by this author on: Oxford Academic PubMed Google Scholar ... Show more R.D. Tanaka R.D. Tanaka To whom correspondence should be addressed Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 17, Issue 3, 11 February 1989, Pages 1259–1260, https://doi.org/10.1093/nar/17.3.1259 Published: 11 February 1989 Article history Received: 12 December 1988 Published: 11 February 1989
Natriuretic Peptides Suppress Vascular Endothelial Cell Growth Factor Signaling to Angiogenesis* (2001)

Vascular endothelial cell growth factor (VEGF) is essential for angiogenesis. Atrial natriuretic peptide (ANP) inhibits the production of VEGF, but whether this important vascular peptide also inter- rupts VEGF signaling to angiogenesis is unknown. In cultured bovine aortic endothelial cells, VEGF significantly stimulated extracellular signal-regulated protein kinase activity and phosphorylation, which was inhibited 60% by coincubation with ANP or a natriuretic peptide clearance receptor specific ligand (NPRC), C-type NAP-(4-23) [C-ANP-(4-23)]. VEGF also stimulated c-Jun N-terminal kinase (JNK) and p38 activities/phosphorylation that were prevented by the two natriuretic peptides (NP). A specific NP guanylate cyclase (GC) receptor antagonist, HS-142-1, blocked the actions of ANP [but not those of C-ANP-(4-23)], supporting the involvement of both GC and NPRC receptors. VEGF and expression of constituitively active JNK each stimulated the synthesis of cyclin D1 and increased the activity of the cyclin-dependent kinase-4, which was inhibited 55% by ANP. VEGF induced endothelial cell proliferation and migration, which was significantly blocked by NP or by expressing a dominant negative JNK-1. VEGF stimulated human microvascular endothelial cells to form capillary tubes, which was significantly inhibited by expressing dominant negative JNK-1 and by NP. Therefore, VEGF induction of critical steps in angiogenesis is enhanced through JNK activation. The actions are significantly prevented by NP, which act through both the NPRC and GC receptors to block growth factor signaling. Thus, NP are candidate antiangiogenesis factors that inhibit both the synthesis and function of VEGF.
Molecular Interactions, T‐Cell Subsets and a Role of the CD4/CD8:p56lck Complex in Human T‐Cell Activation (1989)

Several T-cell structures are capable of generating intracellular signals linked to T-cell proliferation. Crosslinking of CD2, CD4 and CD45 with Ti/CD3 to several of these antigens can augment the minimal signal induced by antigen binding to the Ti/CD3 complex. Importantly, some of these regulatory structures (CD4, CD8 and CD45) are also expressed on subsets of T cells with distinct activation requirements and functional programs (helper, suppressor, suppressor-inducer and cytotoxic function). The CD4+ CD45RA+ (2H4+) subset responds well to self-Ia, poorly to soluble antigen and possesses suppressor-inducer function. A reciprocal subset CD4+ CD45RA- (4B4+) is preferentially activated by soluble recall antigens and possesses helper function. Each of these subsets can be distinguished by virtue of the differential expression of CD45 antigens. Importantly, the anti-2H4 antibody which reacts with a specific region near the N-terminus of two CD45 isoforms can effectively block its function. Crosslinking of CD4 with the Ti/CD3 complex preferentially activated the CD4+ CD45+ RA- subset, while soluble antibodies to CD2 preferentially affected the CD45 CD45RA+ subset. Thus, CD3 and CD4 more effectively synergize in the activation process on the CD4+ CD45RA- subset, a result consistent with the ability of this subpopulation to respond to recall antigens. The regulatory role of the CD4, CD8 and CD45 antigens may be mediated by an interactive network of protein-tyrosine phosphorylation and dephosphorylation. We have shown the CD4 and CD8 antigens to be associated with the T cell-specific protein-tyrosine kinase (p56lck). p56lck is a member of a family of protein-tyrosine kinases with an established ability to activate and transform mammalian cells. The CD4/CD8:p56lck complex is catalytically active as shown by its ability to phosphorylate various members of the Ti/CD3 complex. By contrast, the CD45 antigens possess protein-tyrosine phosphatase activity within their intracellular domains and are postulated to function by virtue of a regulatory interaction with CD4/CD8:p56lck and its potential substrates. Thus, the differences in the response of the CD4+ CD45RA+/- subsets to various stimuli and the expansion of T-cell subsets with distinct immunoregulatory programs may be governed by a pathway of tyrosine-mediated events.
Cleavage of p15 protein in vitro by human immunodeficiency virus type 1 protease is RNA dependent (1994)

The human immunodeficiency virus (HIV) gag polyprotein is processed by the viral protease to yield the structural proteins of the virus. One of these structural proteins, p15, and its protease cleavage products, p7 and p6, are believed to be responsible for the viral RNA binding which is prerequisite for assembly of infectious virions. To better understand potential interactions between viral RNA, p15, and the HIV protease, we have synthesized p15 in an in vitro system and studied its processing by the viral protease. Using this system, we demonstrate that p15 synthesized in vitro is properly cleaved by the HIV protease in an RNA-dependent reaction. Mutation of cysteine residues in either zinc-binding domain of the p7 portion of p15 does not alter the RNA-dependent cleavage, but mutation of three basic residues located between the zinc-binding domains blocks HIV protease susceptibility. The results support a previously unrecognized role for the interaction of RNA and nucleocapsid-containing gag precursors that may have important consequences for virus assembly.
Cardiomyocyte remodelling during myocardial hibernation and atrial fibrillation: prelude to apoptosis (1999)

Cardiomyocyte dedifferentiation, but not extensive degeneration through apoptosis, can be observed in chronic hibernating myocardium and chronic fibrillating atrium. Dedifferentiation may be the best way to survive prolonged exposure to the unfavourable conditions imposed by increased wall stress, a relative lowered oxygen environment, or both.
Single 19F Probe for Simultaneous Detection of Multiple Metal Ions Using miCEST MRI (2014)

The local presence and concentration of metal ions in biological systems has been extensively studied ex vivo using fluorescent dyes. However, the detection of multiple metal ions in vivo remains a major challenge. We present a magnetic resonance imaging (MRI)-based method for noninvasive detection of specific ions that may be coexisting, using the tetrafluorinated derivative of the BAPTA (TF-BAPTA) chelate as a (19)F chelate analogue of existing optical dyes. Taking advantage of the difference in the ion-specific (19)F nuclear magnetic resonance (NMR) chemical shift offset (Δω) values between the ion-bound and free TF-BAPTA, we exploited the dynamic exchange between ion-bound and free TF-BAPTA to obtain MRI contrast with multi-ion chemical exchange saturation transfer (miCEST). We demonstrate that TF-BAPTA as a prototype single (19)F probe can be used to separately visualize mixed Zn(2+) and Fe(2+) ions in a specific and simultaneous fashion, without interference from potential competitive ions.
Alzheimer's Disease: Insolubility of Partially Purified Paired Helical Filaments in Sodium Dodecyl Sulfate and Urea (1982)

A method is described for the partial purification of the paired helical filaments that accumulate progressively in human neurons in Alzheimer's disease (senile dementia). Paired helical filaments have unusual solubility characteristics, including insolubility in sodium dodecyl sulfate, urea, reducing agent, and guanidine, which prevent analysis of their molecular composition by gel electrophoresis. The paired helical filaments appear to contain covalent bonds other than disulfide, which cross-link individual filaments into a rigid intracellular polymer. Thus, paired helical filaments appear to represent an example in neurons of an insoluble cross-linked protein. Covalently cross-linked protein polymers occur in lens senile cataracts and in terminally differentiated skin keratinocytes, suggesting that there may be a common mechanism for remodeling some structural proteins during cell aging.
Combination Treatment with Intralesional Cidofovir and Viral-DNA Vaccination Cures Large Cottontail Rabbit Papillomavirus-Induced Papillomas and Reduces Recurrences (2001)

We used the cottontail rabbit papillomavirus (CRPV) New Zealand White rabbit model to test a combination treatment of large established papillomas with intralesional cidofovir and DNA vaccination to cure sites and reduce recurrences. Intralesional 1% (wt/vol) (0.036 M) cidofovir treatment of rabbit papillomas led to elimination, or "cure," of the papillomas over a 6- to 8-week treatment period (N. D. Christenson, M. D. Pickel, L. R. Budgeon, and J. W. Kreider, Antivir. Res. 48:131-142, 2000). However, recurrences at periods from 1 to 8 weeks after treatment cessation were observed at approximately 50% of cured sites. DNA vaccinations with CRPV E1, E2, E6, and E7 were initiated either after or at the time of intralesional treatments, and the recurrence rates were observed. When DNA vaccinations were started after intralesional cures, recurrence rates were similar to those of vector-vaccinated rabbits. A small proportion of recurrent sites subsequently regressed (4 out of 10, or 40%) in the vaccinated group versus no regression of recurrences in the vector-immunized group (0 out of 19, or 0%), indicating partial effectiveness. In contrast, when DNA vaccinations were conducted during intralesional treatments, a significant reduction of recurrences (from 10 out of 19, or 53%, of sites in vector-immunized rabbits to 3 out of 20, or 15%, of sites in viral-DNA-immunized rabbits) was observed. DNA vaccination without intralesional treatments had a minimal effect on preexisting papillomas. These data indicated that treatment with a combination of antiviral compounds and specific immune stimulation may lead to long-term cures of lesions without the ensuing problem of papilloma recurrence.
The Efficient and Enantiospecific Total Synthesis of Cyclopenta[b]phenanthrenes Structurally‐Related to Neurosteroids (2010)

We report an efficient synthesis of cyclopenta[b]phenanthrenes functionalized at C-3 and C-8 from an optically pure Hajos-Parrish ketone. The key step is a neutral alumina catalyzed Michael addition of a Hajos-Parrish ketone derivative (4) to 1,7-octadien-3-one (2) in 98% yield. This Michael addition product went through Krapcho decarbomethoxylation, aldol condensation, lithium liquid ammonia reduction, Wacker oxidation and acid catalyzed cyclization to form cyclopenta[b]phenanthrene (1a) in 37% overall yield for the 7 steps.
Molecular Genetics of Neurodegenerative Dementias (2016)

Neurodegenerative dementias are clinically heterogeneous, progressive diseases with frequently overlapping symptoms, such as cognitive impairments and behavior and movement deficits. Although a majority of cases appear to be sporadic, there is a large genetic component that has yet to be fully explained. Here, we review the recent genetic and genomic findings pertaining to Alzheimer's disease, frontotemporal dementia, Lewy body dementia, and prion dementia. In this review, we describe causal and susceptibility genes identified for these dementias and discuss recent research pertaining to the molecular function of these genes. Of particular interest, there is a large overlap in clinical phenotypes, genes, and/or aggregating protein products involved in these diseases, as well as frequent comorbid presentation, indicating that these dementias may represent a continuum of syndromes rather than individual diseases.
Early Neuromuscular Blockade in the Acute Respiratory Distress Syndrome (2019)

Among patients with moderate-to-severe ARDS who were treated with a strategy involving a high PEEP, there was no significant difference in mortality at 90 days between patients who received an early and continuous cisatracurium infusion and those who were treated with a usual-care approach with lighter sedation targets. (Funded by the National Heart, Lung, and Blood Institute; ROSE ClinicalTrials.gov number, NCT02509078.).
Towards an Area-Efficient Implementation of a High ILP EDGE Soft Processor (2018)

In-order scalar RISC architectures have been the dominant paradigm in FPGA soft processor design for twenty years. Prior out-of-order superscalar implementations have not exhibited competitive area or absolute performance. This paper describes a new way to build fast and area-efficient out-of-order superscalar soft processors by utilizing an Explicit Data Graph Execution (EDGE) instruction set architecture. By carefully mapping the EDGE microarchitecture, and in particular, its dataflow instruction scheduler, we demonstrate the feasibility of an out-of-order FPGA architecture. Two scheduler design alternatives are compared.
Retrovirus-mediated transduction of adult hepatocytes. (1988)

Retrovirus-mediated gene transfer was used to develop a method for introducing genes into primary cultures of adult rat hepatocytes. Subconfluent monolayers of hepatocytes, cultured in hormonally defined media on different matrix substrata, were infected with helper-free stocks of a replication-defective retrovirus that constitutively expresses high levels of beta-galactosidase. Retrovirus-mediated transduction was measured by two methods: (i) an in situ cytochemical stain that specifically detects the expression of viral expressed beta-galactosidase, and (ii) Southern blot analysis, which measures the relative copy number of integrated provirus. Maximal transduction efficiency of approximately equal to 25% was achieved when the cells were infected after 3 days in culture; matrix had little effect on transduction efficiency. Enzyme cytochemical (catalase and glucose 6-phosphatase) and peroxidase immunocytochemical (asialoglycoprotein and UDP-glucuronosyltransferase) analyses of the cultures indicated that greater than 95% of cells were hepatocytes. The demonstration of hepatocyte-specific organelles in cells expressing the viral-directed beta-galactosidase provided unambiguous evidence for the transduction of hepatocytes. These methods should be useful in the development of liver-directed somatic gene therapy and in the study of liver-specific gene regulation.