gebhart/patrepeval huggingface dataset:
Peripheral Vasoconstriction and Abnormal Parasympathetic Response to Sighs and Transient Hypoxia in Sickle Cell Disease (2011)

These data demonstrate significant disruption of autonomic nervous system balance, with marked parasympathetic withdrawal in response to transient hypoxia. They draw attention to an enhanced autonomic nervous system–mediated sigh–vasoconstrictor response in patients with sickle cell that could increase red cell retention in the microvasculature, promoting vasoocclusion.
Low power upconversion using MLCT sensitizers (2005)

Selective low energy excitation of the metal-to-ligand charge transfer (MLCT) transition in [Ru(dmb)(3)](2+)(dmb = 4,4'-dimethyl-2,2'-bipyridine) in the presence of anthracene or 9,10-diphenylanthracene yields easily visualized upconverted singlet fluorescence resulting from triplet-triplet annihilation at low excitation power.
Cognitive Neuroscience of Memory (1998)

The anatomical and neurophysiological bases of memory have been significantly advanced by integrative approaches bridging previously existing gaps between individual neuroscientific disciplines. The time- and content-based division of memory has been widely accepted: episodic and semantic memory, procedural memory and priming are frequently used terms. On the anatomical side, a division into forms of memory dependent on the limbic system (episodic and semantic information) and others (procedural memory and priming) being independent of these regions, has gained entrance into cognitive neuroscience as well. More disputed are ideas on the possible representation of stored information in the brain and on the existence of regions centrally implicated in its retrieval. Even more controversial are possible similarities between psychogenic and organic forms of amnesia. The present overview discusses these and related issues and points to some possibilities for integration. Last, but not least, this overview introduces the nine individual contributions making up this special issue on brain-memory interrelations.
Escherichia coli induces DNA damage in vivo and triggers genomic instability in mammalian cells (2010)

Escherichia coli is a normal inhabitant of the human gut. However, E. coli strains of phylogenetic group B2 harbor a genomic island called "pks" that codes for the production of a polyketide-peptide genotoxin, Colibactin. Here we report that in vivo infection with E. coli harboring the pks island, but not with a pks isogenic mutant, induced the formation of phosphorylated H2AX foci in mouse enterocytes. We show that a single, short exposure of cultured mammalian epithelial cells to live pks(+) E. coli at low infectious doses induced a transient DNA damage response followed by cell division with signs of incomplete DNA repair, leading to anaphase bridges and chromosome aberrations. Micronuclei, aneuploidy, ring chromosomes, and anaphase bridges persisted in dividing cells up to 21 d after infection, indicating occurrence of breakage-fusion-bridge cycles and chromosomal instability. Exposed cells exhibited a significant increase in gene mutation frequency and anchorage-independent colony formation, demonstrating the infection mutagenic and transforming potential. Therefore, colon colonization with these E. coli strains harboring the pks island could contribute to the development of sporadic colorectal cancer.
Nerve Growth Factor Signaling, Neuroprotection, and Neural Repair (2001)

Nerve growth factor (NGF) was discovered 50 years ago as a molecule that promoted the survival and differentiation of sensory and sympathetic neurons. Its roles in neural development have been characterized extensively, but recent findings point to an unexpected diversity of NGF actions and indicate that developmental effects are only one aspect of the biology of NGF. This article considers expanded roles for NGF that are associated with the dynamically regulated production of NGF and its receptors that begins in development, extends throughout adult life and aging, and involves a surprising variety of neurons, glia, and nonneural cells. Particular attention is given to a growing body of evidence that suggests that among other roles, endogenous NGF signaling subserves neuroprotective and repair functions. The analysis points to many interesting unanswered questions and to the potential for continuing research on NGF to substantially enhance our understanding of the mechanisms and treatment of neurological disorders.
Cloning and Sequencing of a Rhodothermus marinus Gene, bglA, Coding for a Thermostable β‐Glucanase and its Expression in Escherichia coli (1994)

A gene library of the thermophilic eubacterium, Rhodothermus marinus, strain 21, was prepared in pUC18 and used to transform Escherichia coli. Of 5400 transformants, two produced halos on lichenan plates after Congo-red staining. Restriction mapping showed that the two clones shared an overlapping 1200-bp DNA fragment, which was used for DNA sequencing. Five potential methionine (Met) translational-initiation codons were identified. A putative signal peptide of 30 amino acids was identified with a hydrophobic core of nine hydrophobic amino acids. The molecular mass of the mature enzyme was estimated to be 29.7 kDa. A comparison of the primary protein sequence of beta-glucanase of Rhodothermus marinus with other glycosyl hydrolases showed 38.5% identity to the C-terminal part of the beta-1,3-glucanase of Bacillus circulans and limited identity to bacterial endo-beta-1,3-1,4-glucanases. The amino acid sequence showed high similarity to regions surrounding the catalytic Glu residue of bacterial beta-glucanases. A gene fragment of 889 bp containing the catalytic domain was overexpressed in E. coli using the pET23, T7-phage RNA polymerase system. The enzyme showed activity on lichenan, beta-glucan and laminarin but not on CMC cellulose or xylan. The expressed enzyme was purified by heat treatment of the host. The enzyme had a temperature and pH optima of 85 degrees C and pH 7.0, respectively, and was shown to retain full activity after incubation for 16 h at 80 degrees C and have a half life of 3 h at 85 degrees C.
Design and implementation of the blue gene/P snoop filter (2008)

As multi-core processors evolve, coherence traffic between cores is becoming problematic, both in terms of performance and power. The negative effects of coherence (snoop) traffic can be significantly mitigated through snoop filtering. Shielding each cache with a device that can squash snoop requests for addresses known not to be in cache improves performance significantly for caches that cannot perform normal load and snoop lookups simultaneously. In addition, reducing snoop lookups yields power savings. This paper describes the design of the Blue Gene/P snoop filters, and presents hardware measurements to demonstrate their effectiveness. The Blue Gene/P snoop filters combine stream registers and snoop caches to capture both the locality of snoop addresses and their streaming behavior. Simulations of SPLASH-2 benchmarks illustrate tradeoffs and strengths of these two techniques. Their combination is shown to be most effective, eliminating 94-99% of all snoop requests using very few stream registers and snoop cache lines. This translates into an average performance improvement of almost 20% for the NAS benchmarks running on an actual Blue Gene/P system.
microRNA-22 acts as a metastasis suppressor by targeting metadherin in gastric cancer (2014)

microRNA (miR)-22 has been reported to be downregulated in hepatocellular, lung, colorectal, ovarian and breast cancer, acting as a tumor suppressor. The present study investigated the potential effects of miR-22 on gastric cancer invasion and metastasis and the molecular mechanism. miR-22 expression was examined in tumor tissues of in 89 gastric cancer patients by in situ hybridization (ISH) analysis. Additionally, the association between miR-22 levels and clinicopathological parameters was analyzed. A luciferase assay was conducted for target identification. The ability of invasion and metastasis of gastric cancer cells in vitro and in vivo was evaluated by cell migration and invasion assays and in a xenograft model. The results showed that miR-22 was downregulated in the gastric cancer specimens and significantly correlated with the advanced clinical stage and lymph node metastasis. In addition, metadherin (MTDH) was shown to be a direct target of miR-22 and the expression of MTDH was inversely correlated with miR-22 expression in gastric cancer. Ectopic expression of miR-22 suppressed cell invasion and metastasis in vitro and in vivo. The present study suggested that miR-22 may be a valuable prognostic factor in gastric cancer. miR-22 inhibited gastric cancer cell invasion and metastasis by directly targeting MTDH. The novel miR-22/MTDH link confirmed in the present study provided a novel, potential therapeutic target for the treatment of gastric cancer.
A TMR Scheme for SEU Mitigation in Scan Flip-Flops (2007)

Radiation from outer space comprising of charged particles can affect transistors in integrated circuits resulting in a change in the state of transistors. This creates a temporary transient effect that corrupts logic within a circuit, and hence it is called a single event upset (SEU). The SEU if captured may lead to soft error. With the progress of microelectronic technology, the shrinkage of transistor sizes is enabling the integration of more transistors in a circuit, making them more vulnerable to soft errors. Any future attempt toward scaling will have to address the problems of circuit reliability which is affected by the increasing number of failures arising from soft errors. In this paper the authors present a novel register design which can detect and correct soft errors. The authors add a redundant latch to the existing structure of a flip-flop and functional data is simultaneously registered at multiple latches. The content of these multiple latches are fed to a majority voter, and if the content of any of these latches is corrupted by a soft error, it is filtered out through the majority voting circuit. This design provides tolerance over the entire vulnerability region of a flip-flop unlike other published solutions. This design can be operated as a simple scan flip-flop or scan hold flip-flop and thus is useful for system testability purposes. The detection and correction operation takes place concurrently, with 23% degradation in system performance
Renal Failure and Heatstroke (1995)

We report a fatal case of heatstroke in an obese boy who developed multi-organ failure. Six other cases of exertional heatstroke admitted to our hospital over the last 5 years were also reviewed. All of them showed some degree of renal impairment. The causes of renal failure are multifactorial, with rhabdomyolysis being the major mechanism. All cases except one responded to alkaline diuresis without the need for dialysis. Continuous venovenous hemofiltration appeared to be a good alternative in hemodynamically unstable patients. Renal function recovered completely after varying intervals in all surviving cases. Interestingly, rhabdomyolysis in our heatstroke patients was usually associated with hypokalemia or normokalemia instead of hyperkalemia. Mortality in our series was largely related to the long duration of hyperthermia and coma, the severity of disseminated intravascular coagulation, and the presence of cardiogenic shock and severe acidosis.
Towards trusted cloud computing (2009)

Cloud computing infrastructures enable companies to cut costs by outsourcing computations on-demand. How-ever, clients of cloud computing services currently have no means of verifying the confidentiality and integrity of their data and computation. To address this problem we propose the design of a trusted cloud computing platform (TCCP). TCCP en-ables Infrastructure as a Service (IaaS) providers such as Amazon EC2 to provide a closed box execution envi-ronment that guarantees confidential execution of guest virtual machines. Moreover, it allows users to attest to the IaaS provider and determine whether or not the ser-vice is secure before they launch their virtual machines. 1
Human macrophage response to UHMWPE, TiAlV, CoCr, and alumina particles: Analysis of multiple cytokines using protein arrays (2007)

Aseptic loosening of total joint replacements is believed to be initiated by a macrophage response to prosthetic wear debris. To better characterize the early response to clinically relevant wear debris, we challenged primary human macrophages from four donors with ultra high molecular weight polyethylene (UHMWPE), TiAlV, CoCr, and alumina particles. After a 24-h culture, protein arrays were used to quantify the secretion of 30 different cytokines and chemokines. Macrophages secreted detectable levels of nine mediators in culture: Interleukin-1alpha (IL-1alpha), tumor necrosis factor-alpha (TNF-alpha), IL-1beta, MCP-1, IL-8, IL-6, GM-CSF, IL-10, and IL-12p40. TiAlV particles were the most stimulatory, causing 5- to 900-fold higher cytokine expression compared with nonstimulated cells and uniquely eliciting high levels of IL-1alpha, IL-6, IL-10, and GM-CSF. CoCr and alumina were mildly stimulatory and typically elicited two- to fivefold greater levels than nonstimulated cells. Surprisingly, UHMWPE did not elicit a significant increase in cytokine release. Our data suggests that IL-1alpha, TNF-alpha, IL-1beta, and MCP-1 are the primary initiators of osteolysis and implicates metallic debris as an important trigger for their release.
ElephantTrap: A low cost device for identifying large flows (2007)

This paper describes the design of ElephantTrap, a device which aims to cache the largest flows (the "elephants") on a network link. ElephantTrap differs from previous work on identifying large flows in one crucial sense: it does not attempt to accurately estimate the size of the flows it is trapping. This leads to an extremely lightweight design and a surprisingly good performance. ElephantTrap can be employed in the line cards of switches and routers and be used for diagnostics, anomaly detection and traffic engineering.
Structure-based Incorporation of 6-Methyl-8-(2-deoxy-β-ribofuranosyl)isoxanthopteridine into the Human Telomeric Repeat DNA as a Probe for UP1 Binding and Destabilization of G-tetrad Structures (2003)

Heterogeneous ribonucleoprotein A1 (hnRNP A1) is an abundant nuclear protein that participates in RNA processing, alternative splicing, and chromosome maintenance. hnRNP A1 can be proteolyzed to unwinding protein (UP1), a 22.1-kDa protein that retains a high affinity for purine-rich single-stranded nucleic acids, including the human telomeric repeat (hTR) d(TTAGGG)n. Using the structure of UP1 bound to hTR as a guide, we have incorporated the fluorescent guanine analog 6-MI at one of two positions within the DNA to facilitate binding studies. One is where 6-MI remains stacked with an adjacent purine, and another is where it becomes fully unstacked upon UP1 binding. The structures of both modified oligonucleotides complexed to UP1 were determined by x-ray crystallography to validate the efficacy of our design, and 6-MI has proven to be an excellent reporter molecule for single-stranded nucleic acid interactions in positions where there is a change in stacking environment upon complex formation. We have shown that UP1 affinity for d(TTAGGG)2 is approximately 5 nm at 100 mm NaCl, pH 6.0, and our binding studies with d(TTAGG(6-MI)TTAGGG) show that binding is only modestly sensitive to salt and pH. UP1 also has a potent G-tetrad destabilizing activity that reduces the Tm of the hTR sequence d(TAGGGT)4 from 67.0 degrees C to 36.1 degrees C at physiological conditions (150 mm KCl, pH 7.0). Consistent with the structures determined by x-ray crystallography, UP1 is able to bind the hTR sequence in solution as a dimer and supports a model for hnRNP A1 binding to nucleic acids in arrays that may make a contiguous set of anti-parallel single-stranded nucleic acid binding clefts. These data suggest that seemingly disparate roles for hnRNP A1 in alternative splice site selection, RNA processing, RNA transport, and chromosome maintenance reflect its ability to bind a purine-rich consensus sequence (nYAGGn) and destabilize potentially deleterious G-tetrad structures.
Protein identification from 2-DE gels by MALDI mass spectrometry (1997)

Two-dimensional electrophoresis (2-DE) allows the separation of proteins at the level of protein species, which are defined by their chemical structure. Each chemical modification leads to a new protein species. Prerequisites for investigations of protein species are reproducible sample preparation, large gels (20 × 30 cm and larger), high sensitive detection methods, automated evaluation of gels, and sensitive methods for identification of 2-DE-separated protein species. MALDI mass spectrometry with its sensitivity in the fmol range fits with the sensitivity of protein detection on 2-DE gels. Protein mass determination, peptide mass mapping, post-source decay sequencing, and ladder sequencing by MALDI-MS in combination with genome databases have the potential for complete structural investigation on the protein species level. The discrimination of 19 crystalline species of mouse eye lens and of 54 human heart heatshock protein 27 species shows the capacity of the combination of 2-DE with MALDI-MS. © 1997 John Wiley & Sons, Inc., Mass Spectrom Rev 16(3), 145–162, 1997
Evaluation of the microcirculation in hypertension and cardiovascular disease (2007)

The ability to investigate the microvascular structure and function is important in improving our understanding of pathophysiological processes in hypertension and related cardiovascular disease. A range of techniques are available or emerging for investigating different aspects of the microcirculation in animals and humans. Techniques such as experimental intravital microscopy and clinical intravital microscopy (e.g. orthogonal polarization spectral imaging) allow visualization at the level of single microvessels. Venous occlusion plethysmography can be used to measure blood flow in organs, and laser Doppler flowmetry to measure red cell flux in small areas of tissue. Positron emission tomography, myocardial contrast echocardiography, and magnetic resonance imaging provide three-dimensional imaging of local blood flow. The current and potential clinical usefulness of these different techniques is evaluated. The technical quality and availability for clinical use of some of the techniques should improve dramatically during the next few years. 'Molecular imaging'-the combination of these techniques with genetic, molecular, and computational approaches-offers great potential for use in research and in diagnosis and the monitoring of disease progression or the results of therapy. Closer attention to the microcirculation will ultimately improve the treatment and prevention of many of the most important forms of cardiovascular disease.
Albumin Suppresses Human Hepatocellular Carcinoma Proliferation and the Cell Cycle (2014)

Many investigations have revealed that a low recurrence rate of hepatocellular carcinoma (HCC) is associated with high serum albumin levels in patients; therefore, high levels of serum albumin are a major indicator of a favorable prognosis. However, the mechanism inhibiting the proliferation of HCC has not yet been elucidated, so we investigated the effect of serum albumin on HCC cell proliferation. Hep3B was cultured in MEM with no serum or containing 5 g/dL human albumin. As control samples, Prionex was added to generate the same osmotic pressure as albumin. After 24-h incubation, the expressions of α-fetoprotein (AFP), p53, p21, and p57 were evaluated with real-time PCR using total RNA extracted from the liver. Protein expressions and the phosphorylation of Rb (retinoblastoma) were determined by Western blot analysis using total protein extracted from the liver. For flow cytometric analysis of the cell cycle, FACS analysis was performed. The percentages of cell cycle distribution were evaluated by PI staining, and all samples were analyzed employing FACScalibur (BD) with appropriate software (ModFit LT; BD). The cell proliferation assay was performed by counting cells with using a Scepter handy automated cell counter (Millipore). The mRNA levels of AFP relative to Alb(-): Alb(-), Alb(+), and Prionex, were 1, 0.7 ± 0.2 (p < 0.001 for Alb(-)), and 1 ± 0.3, respectively. The mRNA levels of p21 were 1, 1.58 ± 0.4 (p = 0.007 for Alb(-) and p = 0.004 for Prionex), and 0.8 ± 0.2, respectively. The mRNA levels of p57 were 1, 4.4 ± 1.4 (p = 0.002 for Alb(-) and Prionex), and 1.0 ± 0.1, respectively. The protein expression levels of Rb were similar in all culture media. The phosphorylation of P807/811 and P780 of Rb protein was reduced in Alb(+). More cells in the G0/G1 phase and fewer cells in S and G2/M phases were obtained in Alb(+) than in Alb(-) (G0/G1: 60.9%, 67.7%, 61.5%; G2/M: 16.5%, 13.1%, 15.6%; S: 22.6%, 19.2%, 23.0%, Alb(-), Alb(+), Prionex, respectively). The same results were obtained in HepG2. Cell proliferation was inhibited in 5 g/dL albumin medium in both HepG2 cells and Hep3B cells in 24 h culture by counting cell numbers. The presence of albumin in serum reduces the phosphorylation of Rb proteins and enhances the expression of p21 and p57, following an increase in the G0/G1 cell population, and suppresses cell proliferation. These results suggest that albumin itself suppresses the proliferation of hepatocellular carcinoma.
Novel Oncolytic Agent GLV-1h68 Is Effective Against Malignant Pleural Mesothelioma (2008)

Malignant pleural mesothelioma (MPM) is a fatal disease with a median survival of less than 14 months. For the first time, a genetically engineered vaccinia virus is shown to produce efficient infection, replication, and oncolytic effect against MPM. GLV-1h68 is a replication-competent engineered vaccinia virus carrying transgenes encoding Renilla luciferase, green fluorescent protein (both inserted at the F14.5L locus), beta-galactosidase (inserted at the J2R locus, which encodes thymidine kinase), and beta-glucuronidase (at the A56R locus, which encodes hemagglutinin). This virus was tested in six human MPM cell lines (MSTO-211H, VAMT, JMN, H-2373, H-2452, and H-2052). GLV-1h68 successfully infected all cell lines. For the most sensitive line, MSTO-211H, expression of green fluorescent protein (GFP) started within 4 hr with increasing intensity over time until nearly 100% of cells expressed GFP at 24 hr. All cell lines were sensitive to killing by GLV-1h68, with the degree of sensitivity predictable by infectivity assay. Even the most resistant cell line exhibited 44 +/- 3.8% cell survival by day 7 when infected at a multiplicity of infection of 1.0. Viral proliferation assays demonstrated 2-to 4-fold logarithmic replication of GLV-1h68 in the cell lines tested. In an orthotopic model, GLV-1h68 effectively prevented development of cachexia and tumor-related morbidity, reduced tumor burden, and cured MPM in both early and late treatment groups. GLV-1h68 was successfully used to treat MPM in vitro and in an orthotopic model (in vivo). These promising results warrant clinical investigation of GLV-1h68 as a novel agent in the treatment of MPM.