gebhart/patrepeval huggingface dataset:
Serum YKL-40, A New Prognostic Biomarker in Cancer Patients? (2006)

YKL-40, a member of the "mammalian chitinase-like proteins," is expressed and secreted by several types of solid tumors. The exact function of YKL-40 in cancer diseases is unknown and is an important objective of future studies. YKL-40 exhibits growth factor activity for cells involved in tissue remodeling processes. YKL-40 may have a role in cancer cell proliferation, survival, and invasiveness, in the inflammatory process around the tumor, angiogenesis, and remodeling of the extracellular matrix. YKL-40 is neither organ- nor tumor-specific. However, the present retrospective clinical studies of patients with eight different types of primary or advanced solid tumors suggest that serum concentration of YKL-40 may be a new biomarker in cancer patients used as a "prognosticator." Elevated serum YKL-40 is found in a subgroup of patients with different types of solid tumors, including several types of adenocarcinomas, small cell lung carcinoma, glioblastoma, and melanoma. The highest serum YKL-40 is detected in patients with advanced cancer and with the poorest prognosis. In many cases, serum YKL-40 provides independent information of survival. Serum YKL-40 cannot be used as a single screening test for cancer. The use of serum YKL-40 has not received Food and Drug Administration approval for use as a biomarker for cancer or any other disease. Large multicenter retrospective and prospective studies of patients with different types of cancer are required to determine: (a) if serum YKL-40 is a useful prognostic cancer biomarker, (b) if serum YKL-40 can be of value in monitoring patients with cancer in order to provide information about metastases before these are detected by routine methods, and (c) if serum YKL-40 can be useful for screening of cancer together with a panel of other cancer biomarkers and imaging techniques.
Cloning and sequencing of ATP sulfurylase from Penicillium chrysogenum. Identification of a likely allosteric domain. (1994)

Fungal (Penicillium chrysogenum) and yeast (Saccharomyces cerevisiae) ATP sulfurylases were shown to have very similar kinetic and chemical properties except that the fungal enzyme (a) contains a highly reactive Cys residue (SH-1) whose modification results in sigmoidal velocity curves (Renosto, F., Martin, R. L., and Segel, I. H. (1987) J. Biol. Chem. 262, 16279-16288) and (b) is allosterically inhibited by 3'-phosphoadenosine 5'-phosphosulfate (PAPS), while the yeast enzyme displays neither of these properties. The fungal enzyme subunit (64.3 kDa, 572 amino acids) is also larger than the yeast enzyme subunit (59.3 kDa, 521 amino acids). To correlate the unique allosteric properties of the fungal enzyme with specific structural features, we cloned and sequenced the ATP sulfurylase gene (aps) from P. chrysogenum. The yeast and fungal enzymes are homologous over the first 400 amino acids and contain two regions high in basic residues which are conserved in sulfurylases from Arabidopsis and the Riftia pachyptila (hydrothermal vent tube worm) chemolithotrophic symbiont. These regions may participate in forming the binding sites for MgATP2- and SO4(2-). The fungal enzyme has no sites for MgATP2- and SO4(2-). The fungal enzyme has no significant sequence homology to the yeast enzyme in the C-terminal 172 amino acids. This C-terminal region contains SH-1 (Cys-508) and has homology to MET14 (S. cerevisiae), CYSC (E. coli), and NODQ (Rhizobium meliloti), i.e. adenosine 5'-phosphosulfate (APS) kinase. The cumulative results suggest that (a) the allosteric PAPS binding site of P. chrysogenum ATP sulfurylase is located in the C-terminal domain of the protein and (b) that this domain may have evolved from APS kinase. In spite of the homology, this C-terminal region does not account for the APS kinase activity of P. chrysogenum. Fungal ATP sulfurylase has no significant homology to (or regulatory properties in common with) CYSD or CYSN, proteins reported to comprise E. coli ATP sulfurylase (Leyh, T., Vogt, T. F., and Suo, Y. (1992) J. Biol. Chem. 267, 10405-10410).
Age‐related decreases in NAD(P)H and glutathione cause redox declines before ATP loss during glutamate treatment of hippocampal neurons (2008)

Age-related glutamate excitotoxicity depends in an unknown manner on active mitochondria, which are key determinants of the cellular redox potential. Compared with embryonic and middle-aged neurons, old-aged rat hippocampal neurons have a lower resting reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H) and a lower redox ratio (NAD(P)H/flavin adenine nucleotide). Glutamate treatment resulted in an initial increase in NAD(P)H concentrations in all ages, followed by a profound calcium-dependent, age-related decline in NAD(P)H concentration and redox ratio. With complex I of the electron transport chain inhibited by rotenone, treatment with glutamate or ionomycin only resulted in the increase in NAD(P)H fluorescence. High-performance liquid chromatography analysis of adenine nucleotides in brain extracts showed 50% less nicotinamide adenine dinucleotide (NADH) and almost twice as much oxidized nicotinamide adenine dinucleotide, demonstrating a more oxidized ratio in old than middle-aged brain. Resting glutathione content also declined with age and further decreased with glutamate treatment without accompanying changes in adenosine triphosphate levels. We conclude that age does not affect production of NADH by dehydrogenases but that old-aged neurons consume more NADH and glutathione, leading to a catastrophic decline in redox ratio.
Security considerations for workflow systems (2002)

Security services for workflow systems are becoming increasingly important for cross-domain interoperability in insecure environments. Workflow interfaces and system components involve the whole spectrum of security services including authentication, authorization, access control, data confidentiality and integrity, audit, non-repudiation, and administration. With the equipment of these services, workflow systems can be used in a broader range of enterprise applications. In this paper, we address many security issues in typical workflow systems and present a security model that utilizes the secure socket layer protocol and HTTPS tunneling mechanism. This model provides flexible security facilities that are suitable for application-to-application operations and data exchange over the Internet.
Hydrologic Factors in Wetland Water Treatment (2020)

A wide variety of wastewaters have been treated with wetland systems. Features of water movement in these systems distinguish them from conventional concrete-and-steel wastewater treatment facilities. The purpose of this chapter is to set forth current information on key hydrologic processes, and to examine implications on process performance. Hydrologicai complexity makes design and data interpretation difficult for wetland treatment systems. Attempts to set wetland operating depths may fail if vegetative resistance creates a significant slope to the wetland water sheet. Flow through a wetland system is augmented by precipitation and (negatively) evapotranspiration. Precipitation records are available for nearby sites, and the above outlines methods for estimating evapotranspiration. The chapter addresses what effect these gains or losses have on wetland hydrodynamics. A wetland system designed without regard for atmospheric augmentation may be under- or overdesigned, depending on degree of treatment and local climatic conditions in terms of water gains or losses.
Evaluation of&lt;tex&gt;$hboxSiO_2$&lt;/tex&gt;Antifuse in a 3D-OTP Memory (2004)

We have evaluated an antifuse technology used in a novel three-dimensional one-time-programmable (3D-OTP) nonvolatile solid-state memory. The 3D-OTP memory uses deposited polysilicon antifuse sandwiches to build its memory cells. The polysilicon based SiO/sub 2/ antifuse show different breakdown characteristics compared to conventional traditional gate oxides. Long-term storage tests show that this 3D-OTP solid-state memory not only can be a general purpose ROM, but also can be an ideal media for archiving.
Remote Ischemic Preconditioning of the Recipient Reduces Myocardial Ischemia-Reperfusion Injury of the Denervated Donor Heart via a Katp Channel-Dependent Mechanism (2005)

Remote ischemic preconditioning of the recipient, decreases ischemia-reperfusion injury in the brain dead donor heart following orthotopic heart transplantation via a Katp channel-dependent mechanism. This study suggests that a circulating effector persists after the rIPC stimulus is applied, and excludes an ongoing afferent neurogenic mechanism of cardioprotection.
Requirement for Phosphoinositide 3-Kinase p110δ Signaling in B Cell Antigen Receptor-Mediated Antigen Presentation (2007)

The BCR serves to both signal cellular activation and enhance uptake and presentation of Ags by B cells; however, the intracellular signaling mechanisms linking the BCR to Ag presentation functions have been controversial. PI3Ks are critical signaling enzymes controlling many cellular processes, with the p110delta isoform playing a critical role in BCR signaling. In this study, we used pharmacological and genetic approaches to evaluate the role of p110delta signaling in Ag presentation by primary B lymphocytes. It was found that activation of allogeneic T cells is significantly reduced when B cells are pretreated with global PI3K inhibitors, but was intact when p110delta signaling was specifically inactivated. In contrast, inactivation of p110delta significantly impaired the ability of B cells to activate T cells in a BCR-mediated Ag uptake and presentation model. Prestimulation of p110delta-inactivated B cells with anti-CD40 or LPS could not rescue their BCR-mediated Ag presentation ability to normal levels. p110delta signaling was required for efficient presentation of either anti-Ig or protein Ag via a lysozyme-specific BCR. p110delta-inactivated B cells were able to internalize Ag normally, and no defects in association of Ag with lysosome-associated membrane protein 1(+) late endosomes were observed; however, these cells were less effective in forming polarized conjugates with Ag-specific T cells. Our data demonstrate a role for p110delta signaling in B cell Ag presentation function, implicating 3-phosphoinositides and their targets in the latter stages of this process.
Strain compensated InGaAs-GaAsP-InGaP laser (1996)

The performance characteristics of InGaAs-GaAsP-InGaP strain compensated laser emitting near 1 μm are reported. The ridge waveguide lasers have room temperature threshold current of 18 mA and differential quantum efficiency of 0.45 W/A/facet. The linewidth enhancement factor is smaller and gain coefficient is larger for these strain compensated lasers compared to that for conventional strained layer laser. This may be due to higher effective compressive strain in the light emitting layer of these devices which reduces the effective mass. The observed larger gain coefficient is consistent with the measured larger relaxation oscillation frequency of these lasers compared to that for a conventional strained layer laser.
Notalgia paresthetica: the unreachable itch (2013)

The published cases and studies suggest symptoms of NP are due to a cutaneous sensory neuropathy. Treatments addressing the condition as such are more successful than traditional itch therapies. In many cases, a simple explanation for the persistent pruritus is satisfactory for patients. For very distressing cases, therapy should address the condition as a benign sensory neuropathy. Further studies are needed to evaluate which treatments have the greatest potential for providing symptom relief.
A Superior Method for the Reduction of Secondary Phosphine Oxides (2005)

[reaction: see text] Diisobutylaluminum hydride (DIBAL-H) and triisobutylaluminum have been found to be outstanding reductants for secondary phosphine oxides (SPOs). All classes of SPOs can be readily reduced, including diaryl, arylalkyl, and dialkyl members. Many SPOs can now be reduced at cryogenic temperatures, and conditions for preservation of reducible functional groups have been found. Even the most electron-rich and sterically hindered phosphine oxides can be reduced in a few hours at 50-70 degrees C. This new reduction has distinct advantages over existing technologies.
Membrane covered electrically isolated through-wafer via holes (2001)

An electrically isolated through-wafer via hole, covered by a membrane, has been realized by standard integrated circuits processes together with deep silicon etching. The deep silicon etching was performed by the Bosch silicon etch process in a Plasma-Therm etch system. The via structures were made in double-sided polished 300 µm thick silicon wafers and had widths down to 20 µm, which correspond to an aspect ratio of 15. The fact that the via structures are electrically isolated makes them a suitable start-point to realize interconnections through a wafer. Furthermore, the application field of the via structure is broadened by the flexibility in the design of the structure, which makes it possible to apply an almost arbitrary membrane material onto the via structure at the end of the process.
Cell and molecular neurobiology of presenilins: A role for the endoplasmic reticulum in the pathogenesis of Alzheimer's disease? (1997)

Mutations in genes encoding presenilin-1 (PS-1) and presenilin-2 (PS-2) cause many cases of autosomal dominant inherited forms of early-onset Alzheimer's disease (AD). PSs are expressed in neurons throughout the nervous system, with differences in abundance among cell populations. PS-1 and PS-2 each have six to eight transmembrane domains and are localized mainly in the endoplasmic reticulum (ER). PSs may interact with cytoskeletal proteins and beta-amyloid precursor protein (APP) in ways consistent with roles in membrane trafficking and APP processing. Expression of mutant PSs in cultured cells and transgenic mice results in increased production of an amyloidogenic-cytotoxic form of amyloid beta-peptide (Abeta). Neural cells expressing mutant PSs exhibit increased sensitivity to apoptosis induced by trophic factor withdrawal and Abeta. The proapoptotic action of mutant PSs involves perturbed calcium release from ER stores and increased levels of oxidative stress. PS mutations may also suppress neurotransmitter synthesis in cholinergic neurons, suggesting a role in regulation of neuronal phenotype. Homology of PSs with the C. elegans gene sel-12 and phenotypic similarities of PS-1 and Notch knockout mice suggest a developmental role for PSs in somitogenesis. Collectively, the emerging data suggest intriguing roles of PSs in neuronal plasticity and cell death and highlight the importance of the ER as a regulatory site involved in the pathogenesis of neuronal degeneration in AD.
HIV-1 Directly Kills CD4+ T Cells by a Fas-independent Mechanism (1998)

The mechanism by which HIV-1 induces CD4(+) T cell death is not known. A fundamental issue is whether HIV-1 primarily induces direct killing of infected cells or indirectly causes death of uninfected bystander cells. This question was studied using a reporter virus system in which infected cells are marked with the cell surface protein placental alkaline phosphatase (PLAP). Infection by HIV-PLAP of peripheral blood mononuclear cells (PBMCs) and T cell lines leads to rapid depletion of CD4(+) T cells and induction of apoptosis. The great majority of HIV-induced T cell death in vitro involves direct loss of infected cells rather than indirect effects on uninfected bystander cells. Because of its proposed role in HIV-induced cell death, we also examined the Fas (CD95/Apo1) pathway in killing of T cells by HIV-1. Infected PBMCs or CEM cells display no increase in surface Fas relative to uninfected cells. In addition, HIV-1 kills CEM and Jurkat T cells in the presence of a caspase inhibitor that completely blocks Fas-mediated apoptosis. HIV-1 also depletes CD4+ T cells in PBMCs from patients who have a genetically defective Fas pathway. These results suggest that HIV-1 induces direct apoptosis of infected cells and kills T cells by a Fas-independent mechanism.
Isolation and characterization of cell clones producing various amounts of bovine leukosis virus. (1985)

Several single-cell clones were isolated from lamb kidney cell line (FLK) persistently infected with bovine leukosis virus (BLV). The clones differed in the amount of produced virus, some clones were highly virus productive, others produced less virus. The restriction analysis of cell DNA from clones revealed the existence of several numbers of integrated BLV-DNA proviruses in various cell clones. In some cell clones the unintegrated proviral DNA was observed. The proviral BLV sequences were found to be integrated in reiterated DNA in some cell clones. There was no apparent relationship between the number of integrated BLV proviruses and the extent of virus production. The origin of the different numbers of integrated BLV proviruses in various cell clones is discussed.
Leukotrienes (1987)

There is evidence that phospholipid-derived mediators play important roles in inflammation. The generation and action of lipoxygenase products (leukotrienes and lipoxins) together with the interactions of the leukotrienes with other inflammatory mediators are discussed in this chapter, with particular reference to inflammation of the airways, heart and blood vessels. Since the detection of lipoxygenase products in vivo has proved more difficult than in various perfused preparations in vitro, the responses of these mediators in vitro is mainly described in an attempt to explain their mechanism of action.
Visible to infrared plasmonic absorption from silver nanostructures enabled by microreactor-assisted solution deposition (2016)

The ability to control the morphology of silver films is critical since optical properties of silver films largely depend on their morphology. Due to their ability to precisely tailor the growth mechanism, vacuum-based processes have been widely used to control the morphology of silver films. In this study, we report the use of a continuous flow microreactor deposition process for the formation of silver films. Colloidal silver nanocrystals along with smaller reactive silver species are generated in the microreactor. These in situ silver reactants were delivered directly onto the glass substrate to form silver nanostructures at room temperature. The morphology of the silver nanostructure is transitioned from isolated irregular silver nanocrystals to a continuous silver nanocrystalline film as the deposition period increases. The UV-vis-NIR spectra of the resulting silver nanostructures vary correspondingly with their morphology. In particular, a broadband absorption from visible to near infrared is shown for the spectrum of the silver nanostructure close to the percolation threshold. Highly conductive silver films are also obtained as surface coverage was far beyond the percolation threshold. The utility of silver nanostructures with different morphologies is also demonstrated via surface enhanced Raman scattering (SERS) of Rhodamine B. This study demonstrates the capability of the continuous flow microreactor-assisted solution deposition process to fabricate silver nanostructures that can be useful in various applications.
Filter synthesis for periodically coupled microring resonators (2000)

The theory of filter synthesis using periodically coupled microring resonators is developed as a means to overcome the fabrication sensitivities inherent in conventional higher-order filters, while still achieving desirable spectral characteristics. Each resonator in the array can compensate for deficiencies in any of the others. These filters exhibit a boxlike shape and very high extinction ratios.
Comparison of the mechanical characteristics of polymerized caprolactam and monofilament nylon loops constructed in parallel strands or as braided ropes versus cranial cruciate ligaments of cattle (2013)

The 3-stranded cords of 450-lb test monofilament nylon fishing line most closely approximated the strength of the CCL. Marked increases in elongation occur when large-sized materials are constructed in braided configurations, and this elongation would likely not provide stability in CCL-deficient stifle joints. Additional studies are needed to determine whether any of these materials are suitable CCL replacements in cattle.
Orthogonal complex filter banks and wavelets: some properties and design (1999)

Previous wavelet research has primarily focused on real-valued wavelet bases. However, complex wavelet bases offer a number of potential advantageous properties. For example, it has been suggested that the complex Daubechies wavelet can be made symmetric. However, these papers always imply that if the complex basis has a symmetry property, then it must exhibit linear phase as well. In this paper, we prove that a linear-phase complex orthogonal wavelet does not exist. We study the implications of symmetry and linear phase for both complex and real-valued orthogonal wavelet bases. As a byproduct, we propose a method to obtain a complex orthogonal wavelet basis having the symmetry property and approximately linear phase. The numerical analysis of the phase response of various complex and real Daubechies wavelets is given. Both real and complex-symmetric orthogonal wavelet can only have symmetric amplitude spectra. It is often desired to have asymmetric amplitude spectra for processing general complex signals. Therefore, we propose a method to design general complex orthogonal perfect reconstruct filter banks (PRFBs) by a parameterization scheme. Design examples are given. It is shown that the amplitude spectra of the general complex conjugate quadrature filters (CQFs) can be asymmetric with respect the zero frequency. This method can be used to choose optimal complex orthogonal wavelet basis for processing complex signals such as in radar and sonar.
Studies on pyrophosphates. Part III. A new method for the synthesis of nucleotide coenzymes by means of di-n-butylphosphiothioyl bromide. (1976)

Di-n-butylphosphinoyl bromide reacts with nucleotides to afford the corresponding nucleoside phosphoric di-n-butylphosphinothioic anhydrides in almost quantitative yields. These mixed anhydrides are stable even in the presence of water, but in the presence of silver salts they react readily with phosphoric acid, pyrophosphoric acid, or nucleotides to give the corresponding nucleoside di- and tri-phosphates, or nucleotide coenzymes in high yields, respectively. In the absence of the phosphates, the mixed anhydrides react with silver nitrate to form the corresponding nucleoside 3′,5′-cyclic phosphates in high yields.
High Frequency of PIK3R1 and PIK3R2 Mutations in Endometrial Cancer Elucidates a Novel Mechanism for Regulation of PTEN Protein Stability (2011)

We demonstrate that phosphatidylinositol 3-kinase (PI3K) pathway aberrations occur in >80% of endometrioid endometrial cancers, with coordinate mutations of multiple PI3K pathway members being more common than predicted by chance. PIK3R1 (p85α) mutations occur at a higher rate in endometrial cancer than in any other tumor lineage, and PIK3R2 (p85β), not previously demonstrated to be a cancer gene, is also frequently mutated. The dominant activation event in the PI3K pathway appears to be PTEN protein loss. However, in tumors with retained PTEN protein, PI3K pathway mutations phenocopy PTEN loss, resulting in pathway activation. KRAS mutations are common in endometrioid tumors activating independent events from PI3K pathway aberrations. Multiple PIK3R1 and PIK3R2 mutations demonstrate gain of function, including disruption of a novel mechanism of pathway regulation wherein p85α dimers bind and stabilize PTEN. Taken together, the PI3K pathway represents a critical driver of endometrial cancer pathogenesis and a novel therapeutic target.