gebhart/patrepeval huggingface dataset:
Hybrid transactional memory (2006)

High performance parallel programs are currently difficult to write and debug. One major source of difficulty is protecting concurrent accesses to shared data with an appropriate synchronization mechanism. Locks are the most common mechanism but they have a number of disadvantages, including possibly unnecessary serialization, and possible deadlock. Transactional memory is an alternative mechanism that makes parallel programming easier. With transactional memory, a transaction provides atomic and serializable operations on an arbitrary set of memory locations. When a transaction commits, all operations within the transaction become visible to other threads. When it aborts, all operations in the transaction are rolled back.Transactional memory can be implemented in either hardware or software. A straightforward hardware approach can have high performance, but imposes strict limits on the amount of data updated in each transaction. A software approach removes these limits, but incurs high overhead. We propose a novel hybrid hardware-software transactional memory scheme that approaches the performance of a hardware scheme when resources are not exhausted and gracefully falls back to a software scheme otherwise.
Stability issues in OSPF routing (2001)

We study the stability of the OSPF protocol under steady state and perturbed conditions. We look at three indicators of stability, namely, (a) network convergence times, (b) routing load on processors, and (c) the number of route flaps. We study these statistics under three different scenarios: (a) on networks that deploy OSPF with TE extensions, (b) on networks that use subsecond HELLO timers, and (c) on networks that use alternative strategies for refreshing link-state information. Our results are based on a very detailed simulation of a real ISP network with 292 nodes and 765 links.
Overexpression of PD-L1 Significantly Associates with Tumor Aggressiveness and Postoperative Recurrence in Human Hepatocellular Carcinoma (2009)

Our data suggest for the first time that PD-L1 status may be a new predictor of recurrence for HCC patients and provide the rationale for developing a novel therapy of targeting the PD-L1/PD-1 pathway against this fatal malignancy.
Synthesis of a 2-Aminoimidazole Library for Antibiofilm Screening Utilizing the Sonogashira Reaction (2008)

The divergent synthesis of a 21-member library composed of 2-aminoimidazole compounds for evaluation as novel antibiofilm molecules is presented. The Sonogashira reaction was employed with three regioisomeric aryl iodides and 11 different alkynes to generate variously substituted diverse ring systems. Good to excellent yields (80-97%) for the reaction were obtained, and the products provide adequate handles for further manipulation into more advanced analogues.
Spectral Bounds for Sparse PCA: Exact and Greedy Algorithms (2005)

Sparse PCA seeks approximate sparse &amp;quot;eigenvectors&amp;quot; whose projections capture the maximal variance of data. As a cardinality-constrained and non-convex optimization problem, it is NP-hard and is encountered in a wide range of applied fields, from bio-informatics to finance. Recent progress has focused mainly on continuous approximation and convex relaxation of the hard cardinality constraint. In contrast, we consider an alternative discrete spectral formulation based on variational eigenvalue bounds and provide an effective greedy strategy as well as provably optimal solutions using branch-and-bound search. Moreover, the exact methodology used reveals a simple renormalization step that improves approximate solutions obtained by any continuous method. The resulting performance gain of discrete algorithms is demonstrated on real-world benchmark data and in extensive Monte Carlo evaluation trials.
Free-electron-laser-based biophysical and biomedical instrumentation (2003)

A survey of biophysical and biomedical applications of free-electron lasers (FELs) is presented. FELs are pulsed light sources, collectively operating from the microwave through the x-ray range. This accelerator-based technology spans gaps in wavelength, pulse structure, and optical power left by conventional sources. FELs are continuously tunable and can produce high-average and high-peak power. Collectively, FEL pulses range from quasicontinuous to subpicosecond, in some cases with complex superpulse structures. Any given FEL, however, has a more restricted set of operational parameters. FELs with high-peak and high-average power are enabling biophysical and biomedical investigations of infrared tissue ablation. A midinfrared FEL has been upgraded to meet the standards of a medical laser and is serving as a surgical tool in ophthalmology and human neurosurgery. The ultrashort pulses produced by infrared or ultraviolet FELs are useful for biophysical investigations, both one-color time-resolved spectroscopy and when coupled with other light sources, for two-color time-resolved spectroscopy. FELs are being used to drive soft ionization processes in mass spectrometry. Certain FELs have high repetition rates that are beneficial for some biophysical and biomedical applications, but confound research for other applications. Infrared FELs have been used as sources for inverse Compton scattering to produce a pulsed, tunable, monochromatic x-ray source for medical imaging and structural biology. FEL research and FEL applications research have allowed the specification of spin-off technologies. On the horizon is the next generation of FELs, which is aimed at producing ultrashort, tunable x rays by self-amplified spontaneous emission with potential applications in biology.
A Human Stem Cell Model of Early Alzheimer’s Disease Pathology in Down Syndrome (2012)

Human cellular models of Alzheimer's disease (AD) pathogenesis would enable the investigation of candidate pathogenic mechanisms in AD and the testing and developing of new therapeutic strategies. We report the development of AD pathologies in cortical neurons generated from human induced pluripotent stem (iPS) cells derived from patients with Down syndrome. Adults with Down syndrome (caused by trisomy of chromosome 21) develop early-onset AD, probably due to increased expression of a gene on chromosome 21 that encodes the amyloid precursor protein (APP). We found that cortical neurons generated from iPS cells and embryonic stem cells from Down syndrome patients developed AD pathologies over months in culture, rather than years in vivo. These cortical neurons processed the transmembrane APP protein, resulting in secretion of the pathogenic peptide fragment amyloid-β42 (Aβ42), which formed insoluble intracellular and extracellular amyloid aggregates. Production of Aβ peptides was blocked by a γ-secretase inhibitor. Finally, hyperphosphorylated tau protein, a pathological hallmark of AD, was found to be localized to cell bodies and dendrites in iPS cell-derived cortical neurons from Down syndrome patients, recapitulating later stages of the AD pathogenic process.
Monoclonal antibodies to human intermediate filament proteins. II. Distribution of filament proteins in normal human tissues. (1984)

Monoclonal antibodies generated against different human intermediate filament (IF) proteins were assayed on fixed, embedded tissue by the biotin-avidin-immunoperoxidase method for evaluation of the tissue specificity of these antibodies. An antibody (43 beta E8) made to fibroblast IF protein stains mesenchymal tissue such as endothelium, histiocytes, stromal fibroblasts, and Schwann cells but does not stain epithelium, skeletal muscle, lymphocytes, or neurons. Three different anti-cytokeratin antibodies decorate epithelium in three unique patterns. One (35 beta H11) stains all nonsquamous epithelium but fails to recognize squamous epithelium. Antibody 34 beta E12 stains the full thickness of squamous epithelium and ductular epithelium but does not react with hepatocytes, pancreatic acinar cells, proximal renal tubules, or endometrial glands. Antibody 34 beta B4 stains only the suprabasal portion of squamous epithelium. None of these three anti-cytokeratin antibodies reacts with nerve or mesenchymal tissue. Two anti-neurofilament antibodies recognize only neurons, failing to react with epithelial or mesenchymal tissue. We conclude that these anti-intermediate filament antibodies can be used as tissue-specific markers. Neoplasms retain the same intermediate filament patterns as the normal parental tissue; therefore, these antibodies can be used as diagnostic aids in surgical pathology.
Wandering in dementia sufferers (1991)

Abstract Ninety‐two patients with dementia were thoroughly assessed by domiciliary interview and a period of day hospital attendance which included the completion of Camdex and Camcog schedules. Domiciliary visit letters described getting lost outside the home as a problem in 20.6% of patients, and inside the home in 3.3% of patients. The corresponding figures obtained from interviews were 36.9% and 28.3%. According to interview data, patients with senile dementia of Alzheimer's type were more likely to get lost outside the home than those with vascular dementia and there was no correlation between the severity of cognitive impairment and the prevalence of getting lost outside the home.
Variation of Stoichiometric Ratios and Their Correlation for Monitoring and Control of Animal Cell Cultures (1998)

The stoichiometry of animal cell cultures is examined with respect to its variation and suitability for process monitoring and control. In addition to the two often used stoichiometric ratios, i.e., lactate yield from glucose (Lac/Glc) and ammonium yield from glutamine (NH4+/Gln), five other less well characterzied ones, i.e., ammonium yield from the total consumption of amino acids (NH4+/TAA), consumption of total amino acids to glutamine (TAA/Gln), essential amino acids to glutamine (EAA/Gln), glutamine to glucose (Gln/Glc), and oxygen to glucose (OUR/Glc), are also considered. A comparison of a number of cell lines including hybridoma, BHK, and CHO cells under a wide range of experimental conditions revealed that all the cell lines have similar patterns of variation of stoichiometry. In steady states of continuous culture, Lac/Glc and Gln/Glc are primarily determined by the residual glucose concentration while TAA/Gln and EAA/Gln correlate well with the residual glutamine concentration. Ammonium formation not only is a function of glutamine concentration but also is affected by the consumption of other amino acids, particularly at low residual glutamine concentrations. NH4+/TAA turned out to be a more suitable parameter to describe the ammonium formation. Large variations of all these stoichiometric ratios are found under conditions of relatively low residual concentrations of glucose and glutamine (both ca. < 0.2-0.5 mM). Above these concentrations the stoichiometric ratios are relatively constant and are independent of the cell lines. Thus, the correlations for these stoichiometric ratios may be directly used to control the nutrient concentration at low levels which are otherwise on-line difficult to determine. A stoichiometric equation is also derived for oxygen consumption. It is found that the metabolism of amino acids can significantly contribute to the consumption of oxygen. A correlation is obtained for OUR/Glc which may be used for the monitoring and control of mammalian cell cultures.
Polymorphisms of the Tumor Suppressor GeneLSAMPare Associated with Left Main Coronary Artery Disease (2008)

Previous association mapping on chromosome 3q13-21 detected evidence for association at the limbic system-associated membrane protein (LSAMP) gene in individuals with late-onset coronary artery disease (CAD). LSAMP has never been implicated in the pathogenesis of CAD. We sought to thoroughly characterize the association and the gene. Non-redundant single nucleotide polymorphisms (SNPs) across the gene were examined in an initial dataset (168 cases with late-onset CAD, 149 controls). Stratification analysis on left main CAD (N = 102) revealed stronger association, which was further validated in a validation dataset (141 cases with left main CAD, 215 controls), a third control dataset (N = 255), and a family-based dataset (N = 2954). A haplotype residing in a novel alternative transcript of the LSAMP gene was significant in all independent case-control datasets (p = 0.0001 to 0.0205) and highly significant in the joint analysis (p = 0.00004). Lower expression of the novel alternative transcript was associated with the risk haplotype (p = 0.0002) and atherosclerosis burden in human aortas (p = 0.0001). Furthermore, silencing LSAMP expression in human aortic smooth muscle cells (SMCs) substantially augmented SMC proliferation (p<0.01). Therefore, the risk conferred by the LSAMP haplotype appears to be mediated by LSAMP down-regulation, which may promote SMC proliferation in the arterial wall and progression of atherosclerosis.
Low-Dose Ionizing Radiation Decreases the Frequency of Neoplastic Transformation to a Level below the Spontaneous Rate in C3H 10T1/2 Cells (1996)

We have previously shown that chronic exposure of plateau-phase C3H 10 T1/2 cells to (60)Co gamma radiation at doses as low as 10 cGy protected the cells against neoplastic transformation by a subsequent large acute radiation exposure. We have also shown that this induced resistance to neoplastic transformation correlated with an increased ability to repair radiation-induced chromosome breaks. We now show that a single exposure of quiescent cells to doses as low as 0.1 cGy also reduces the risk of neoplastic transformation, from the spontaneous level to a rate three- to fourfold below that level. Higher doses, up to 10 cGy at the same dose rate (0.24 cGy/min), did not reduce the neoplastic transformation frequency further. This protective effect was seen only in irradiated cells that were allowed to incubate at 37 degrees C before release from contact inhibition. Cells released into low-density subcultures immediately after irradiation had unchanged neoplastic transformation frequencies. These results demonstrate that low or chronic exposure to radiation can induce processes which protect the cell against naturally occurring as well as radiation-induced alterations that lead to cell transformation. If similar processes are induced in human cells, the results also suggest that a single low dose, at background or occupational exposure levels, may in some circumstances reduce rather than increase cancer risk, a conclusion inconsistent with the linear no-threshold model of cancer risk from radiation.
Phylogeny of mRNA capping enzymes (1997)

The m7GpppN cap structure of eukaryotic mRNA is formed cotranscriptionally by the sequential action of three enzymes: RNA triphosphatase, RNA guanylyltransferase, and RNA (guanine-7)-methyltransferase. A multifunctional polypeptide containing all three active sites is encoded by vaccinia virus. In contrast, fungi and Chlorella virus encode monofunctional guanylyltransferase polypeptides that lack triphosphatase and methyltransferase activities. Transguanylylation is a two-stage reaction involving a covalent enzyme-GMP intermediate. The active site is composed of six protein motifs that are conserved in order and spacing among yeast and DNA virus capping enzymes. We performed a structure-function analysis of the six motifs by targeted mutagenesis of Ceg1, the Saccharomyces cerevisiae guanylyltransferase. Essential acidic, basic, and aromatic functional groups were identified. The structural basis for covalent catalysis was illuminated by comparing the mutational results with the crystal structure of the Chlorella virus capping enzyme. The results also allowed us to identify the capping enzyme of Caenorhabditis elegans. The 573-amino acid nematode protein consists of a C-terminal guanylyltransferase domain, which is homologous to Ceg1 and is strictly conserved with respect to all 16 amino acids that are essential for Ceg1 function, and an N-terminal phosphatase domain that bears no resemblance to the vaccinia triphosphatase domain but, instead, has strong similarity to the superfamily of protein phosphatases that act via a covalent phosphocysteine intermediate.
Combining Novel Biomolecules and Stimuli‐Sensitive Biomaterials into New Recognition‐Response Biomaterial Systems (1988)

An important present and emerging trend in biomaterials development is the synthesis of polymers which combine capabilities of biologic recognition ("biomimetic") with sensitivity to small environmental changes ("stimuli-responsive"). This short article highlights some of the many opportunities and challenges in this exciting area.
[Differentially expressed genes in prostate cancer and benign prostatic hyperplasia]. (2004)

The study of the differentially expressed genes in PCa and BPH should help to understand the molecular mechanism of PCa and identify the markers for diagnostic and therapeutic use.
CC-1065 (NSC 298223), a most potent antitumor agent: kinetics of inhibition of growth, DNA synthesis, and cell survival. (1982)

CC-1065 (NSC 298223) is the most cytotoxic agent tested against cells in culture in our laboratory. The 50% lethal doses for exponentially growing B16 melanoma and Chinese hamster ovary cells were 0.44 and 0.14 ng/ml, respectively, as compared to 35 and 500 ng/ml for Adriamycin. In the human tumor-cloning assay, 1-hr exposure to CC-1065 (0.1 ng/ml) caused greater than or equal to 50% lethality in a broad spectrum of tumors. The dose-survival curves for B16 and Chinese hamster ovary cells were characterized by an initial shoulder followed by an exponential decline with increasing dose. CC-1065 was more lethal to exponentially growing B16 cells (50% lethal dose = 0.44 ng/ml) than to plateau-phase cells (50% lethal dose = 1.2 ng/ml). CC-1065 inhibited DNA synthesis much more than did RNA or protein synthesis. After a 2-hr incubation with drug, inhibition of DNA synthesis was low immediately (0 hr) after drug exposure and reached maximum inhibition about 20 hr later. The doses for 50% inhibition of growth (0.18 ng/ml), survival (0.44 ng/ml), and DNA synthesis (0.15 ng/ml) were in the same range, whereas RNA synthesis was inhibited 50% at a much higher dose (5 ng/ml).
New Immunosuppressive Drugs: Mechanistic Insights and Potential Therapeutic Advances (1993)

Together with CsA, the new macrolide immunosuppressants FK506 and rapamycin have proved to be valuable tools in providing new information about key molecular events that underlie lymphocyte activation and degranulation. Studies of their mechanisms of action have pinpointed the phosphatase calcineurin and protein kinases as important signaling mediators in T-cell activation. Other new immunosuppressive drugs, including leflunomide, mycophenolate mofetil, brequinar sodium and deoxyspergualin exhibit diverse inhibitory effects on cells of the immune system and offer considerable promise as adjunctive therapeutic immunosuppressants. FK506 appears to be both a valuable therapeutic alternative to liver or kidney retransplantation and an alternative primary immunosuppressant to CsA in hepatic (especially) and renal transplantation. There is now good evidence that immunosuppressive drugs, both old and new, permit the establishment of donor-derived, multi-lineage cell chimerism following organ transplantation.
Using Compuserve (1994)

From the Publisher:
This thorough tour of CompuServe focuses on the business user-the one who needs specific information but has little time and money to spend looking for it. This book gives up-to-date coverage of the wealth of resources available on CompuServe, which now has over 1.4 million subscribers.
Loaded with tips and advice to maximize the user's time online
Covers interface software such as CompuServe Information Manager for Windows and OzCis
The only CompuServe book aimed at the business or technical user
Hematopoiesis-restricted minor histocompatibility antigens HA-1- or HA-2-specific T cells can induce complete remissions of relapsed leukemia (2003)

Donor lymphocyte infusion (DLI) into patients with a relapse of their leukemia or multiple myeloma after allogeneic stem cell transplantation (alloSCT) has been shown to be a successful treatment approach. The hematopoiesis-restricted minor histocompatibility antigens (mHAgs) HA-1 or HA-2 expressed on malignant cells of the recipient may serve as target antigens for alloreactive donor T cells. Recently we treated three mHAg HA-1- and/or HA-2-positive patients with a relapse of their disease after alloSCT with DLI from their mHAg HA-1- and/or HA-2-negative donors. Using HLA-A2HA-1 and HA-2 peptide tetrameric complexes we showed the emergence of HA-1- and HA-2-specific CD8(+) T cells in the blood of the recipients 5-7 weeks after DLI. The appearance of these tetramer-positive cells was followed immediately by a complete remission of the disease and restoration of 100% donor chimerism in each of the patients. Furthermore, cloned tetramer-positive T cells isolated during the clinical response specifically recognized HA-1 and HA-2 expressing malignant progenitor cells of the recipient and inhibited the growth of leukemic precursor cells in vitro. Thus, HA-1- and HA-2-specific cytotoxic T lymphocytes emerging in the blood of patients after DLI demonstrate graft-versus-leukemia or myeloma reactivity resulting in a durable remission. This finding implies that in vitro generated HA-1- and HA-2-specific cytotoxic T lymphocytes could be used as adoptive immunotherapy to treat hematological malignancies relapsing after alloSCT.
Polymeric nano- and microparticle technologies for oral gene delivery (2007)

Gene therapy refers to local or systemic administration of a nucleic acid construct that can prevent, treat and even cure diseases by changing the expression of genes that are responsible for the pathological condition. Oral gene therapy has significant promise for treatment of local diseases such as inflammatory bowel disease and for systemic absorption of the expressed protein therapeutics. In addition, efficient oral delivery of DNA vaccines can have significant impact in disease prevention. The use of polymeric gene delivery vectors promises the translation of this experimental medical concept into clinical reality. This review addresses the challenges and opportunities in the development of polymer-based nano- and microparticle technologies for oral gene therapy. Specifically, the discussion is focused on different synthetic and natural polymers used for formulating nano- and microparticle technologies and the use of these delivery systems for oral DNA administration for therapeutic and vaccination purposes.
Rescue of Recombinant Marburg Virus from cDNA Is Dependent on Nucleocapsid Protein VP30 (2005)

Here we report recovery of infectious Marburg virus (MARV) from a full-length cDNA clone. Compared to the wild-type virus, recombinant MARV showed no difference in terms of morphology of virus particles, intracellular distribution in infected cells, and growth kinetics. The nucleocapsid protein VP30 of MARV and Ebola virus (EBOV) contains a Zn-binding motif which is important for the function of VP30 as a transcriptional activator in EBOV, whereas its role for MARV is unclear. It has been reported previously that MARV VP30 is able to support transcription in an EBOV-specific minigenome system. When the Zn-binding motif was destroyed, MARV VP30 was shown to be inactive in the EBOV system. While it was not possible to rescue recombinant MARV when the VP30 plasmid was omitted from transfection, MARV VP30 with a destroyed Zn-binding motif and EBOV VP30 were able to mediate virus recovery. In contrast, rescue of recombinant EBOV was not supported by EBOV VP30 containing a mutated Zn-binding domain.