gebhart/patrepeval huggingface dataset:
Comparisons of Aluminum and Silica Elution from Various Glass Vials (2015)

To understand the risk of particle formation in glass vials, we investigated the correlation between vial surface condition and alminum (Al) or silicon (Si) elution using various suppliers' vials with or without surface treatment. The elution of Si, which can also be an indicator of Al elution, consists of two phases; the first phase is influenced by roughness of the glass surface at the time of filling, and the second phase is dependent on the fundamental elution rate from the glass tube. When vials were filled with citrate buffer at pH 7, vials with varied surface conditions showed the most obvious differences in Al and Si elution. Sulfur-treated vials showed slightly lower Al and Si elution than the non-treated vials. It is considered that this effect of the sulfur treatment on elution is due to the surface being smoothed during heat treatment after the washing process. Different from the sulfur treatment, silicon dioxide (SiO2)-coated vials hardly showed any Al elution as long as the surface was fully coated with the SiO2 layer. It was found that the protective effect of the SiO2 layer against Al elution is more effective in a vial filled with a solution having a lower pH, due to the lower Si dissolving rate occurring at a lower pH. As shown above, pre-measuring the Si and Al present in a citrate buffer at pH 7 placed within a glass container can be a useful tool for selecting the appropriate container for liquid drugs.
Efficient Bacterial Expression of Bovine and Porcine Growth Hormones (1983)

cDNAs prepared using poly(A)mRNA from pituitaries and containing the coding sequences for bovine and porcine growth hormones (bGH and pGH) were cloned in bacteria. The primary structures of the peptide hormones derived from the nucleotide sequences of the respective cDNAs show approximately 90% homology. The cloned cDNAs were modified using synthetic DNA to construct expression vectors for efficient bacterial production of the mature animal growth hormones.
Inverse correlation of the up‐regulation of FZD10 expression and the activation of β‐catenin in synchronous colorectal tumors (2009)

We investigated the immunohistochemical expression patterns of Frizzled homolog 10 (FZD10), a cell-surface receptor for molecules in the Wnt pathway, in tissue samples derived from 104 patients with colorectal cancers (CRCs). There was no immunoreactivity for FZD10 in normal colonic mucosa, and only tumor cells in polyps and CRC tissues showed spotted immunostaining patterns in apical sides of the cytoplasm. In metastatic liver lesions, tumor cells showed cytoplasmic immunostaining similar to primary lesions, whereas normal liver parenchyma showed almost no immunostaining. Frequencies of FZD10-immunopositive cells in tumor tissues were significantly higher in CRCs than those in polyps (3.3 +/- 10.3% vs 20.5 +/- 31.7%, P = 0.0016), and almost equivalent with those in metastatic liver lesions (33.2 +/- 39.7% vs 26.4 +/- 33.4%, P = 0.133). Analyses of paired samples (polyps and CRCs, or CRCs and metastatic liver lesions from the same patient) suggested that a subset of CRCs possessed intrinsic genetic mechanisms causing the evolution of FZD10-positive clones during tumor progression, making FZD10 a promising candidate for molecular imaging and a target for therapy. To our surprise, cancer cells immunopositive for FZD10 showed significantly less nuclear accumulation of beta-catenin, compared to FZD10-immunonegative cancer cells, and there was a strong inverse correlation between nuclear immunostaining scores for beta-catenin expression and expression patterns of FZD10 (P = 0.0002), suggesting that FZD10 has a distinct role from other FZDs in canonical Wnt signal transduction.
CLOCK-Pro: an effective improvement of the CLOCK replacement (2005)

With the ever-growing performance gap between memory systems and disks, and rapidly improving CPU performance, virtual memory (VM) management becomes increasingly important for overall system performance. However, one of its critical components, the page replacement policy, is still dominated by CLOCK, a replacement policy developed almost 40 years ago. While pure LRU has an unaffordable cost in VM, CLOCK simulates the LRU replacement algorithm with a low cost acceptable in VM management. Over the last three decades, the inability of LRU as well as CLOCK to handle weak locality accesses has become increasingly serious, and an effective fix becomes increasingly desirable. Inspired by our I/O buffer cache replacement algorithm, LIRS [13], we propose an improved CLOCK replacement policy, called CLOCK-Pro. By additionally keeping track of a limited number of replaced pages, CLOCK-Pro works in a similar fashion as CLOCK with a VM-affordable cost. Furthermore, it brings all the much-needed performance advantages from LIRS into CLOCK. Measurements from an implementation of CLOCK-Pro in Linux Kernel 2.4.21 show that the execution times of some commonly used programs can be reduced by up to 47%.
Gene Transfer Method for Transient Gene Expression, Stable Transformation, and Cotransformation of Suspension Cell Cultures (1985)

A new method was developed to study transient gene expression, stable transformation, and cotransformation in suspension cells, such as mouse myeloma and erythroleukemia cells. This method involves attachment of cells to a concanavalin A-coated tissue culture dish, treatment of cells with DEAE-dextran to adsorb plasmid DNA to the attached cells, and finally treatment with a 40% solution of polyethylene glycol to facilitate the uptake of DNA by the cells. Plasmids pSV2cat and pSV2neo were used as markers to optimize the conditions for transient gene expression and stable transformation, respectively, of mouse myeloma and erythroleukemia cells. This method was successfully used to obtain cotransformants of mouse myeloma cells.
A survey of CORDIC algorithms for FPGA based computers (1998)

The current trend back toward hardware intensive signal processing has uncovered a relative lack of understanding of hardware signal processing architectures. Many hardware efficient algorithms exist, but these are generally not well known due to the dominance of software systems over the past quarter century. Among these algorithms is a set of shift-add algorithms collectively known as CORDIC for computing a wide range of functions including certain trigonometric, hyperbolic, linear and logarithmic functions. While there are numerous articles covering various aspects of CORDIC algorithms, very few survey more than one or two, and even fewer concentrate on implementation in FPGAs. This paper attempts to survey commonly used functions that may be accomplished using a CORDIC architecture, explain how the algorithms work, and explore implementation specific to FPGAs.
Fabrication of multiply-stacked structures of Si quantum-dots embedded in SiO/sub 2/ by combination of low-pressure CVD and remote plasma treatments (2004)

Silicon nanocrystals embedded in Si02 network have attracted a great deal of interest as quantum dots with discrete charged states and their application to the floating gate of MOS memories [l]. For the multivalued capability of the Si dots floating gate MOS devices, the growth control of Si quantum dots (Si-QDs) with an areal density as high as - 10l2 cmm2 on an ultrathin Si02 layer is a crucial factor. In our previous work, we demonstrated the self-assembling formation of Si-QDs on ultrathin SO2 layers by controlling the early stages of low-pressure chemical vapor deposition (LPCVD) using a SiH4 gas [2].
A Randomized, Double-blind, Placebo-controlled Trial of Augmentation With an Extended Release Formulation of Methylphenidate in Outpatients With Treatment-Resistant Depression (2006)

We examined the efficacy and tolerability of augmentation with an extended release formulation of methylphenidate (OROS MPH, Concerta) in patients with major depression who were nonresponders or partial responders to antidepressants. Sixty subjects with treatment-resistant depression (TRD) participated in a 4-week, randomized, double-blind, placebo-controlled study of augmentation with methylphenidate (18-54 mg/d). The preexisting antidepressant dose was unchanged. The primary efficacy measure was change in the 21-item Hamilton Depression Rating Scale from randomization to end of treatment. Data were analyzed with intent-to-treat with last observation carried forward approach. There were no statistically significant differences between the methylphenidate (n = 30) and placebo (n = 30) groups in reduction in 21-item Hamilton Depression Rating Scale scores (drug, -6.9; placebo, -4.7) from baseline to end of treatment (F1,47 = 1.24, P = 0.22), although responders were numerically higher in the extended-release methylphenidate group (40.0%) than in the placebo group (23.3%). On the secondary efficacy measures of changes in Clinical Global Impression-Improvement and Severity scores and Beck Depression Inventory-Second Edition, the drug failed to separate from placebo, although the proportion of responders in the drug group were numerically higher than placebo. There were no significant differences in weight, heart rate, and blood pressure changes between the 2 groups. The common adverse events were loss of appetite, nausea, headache, and anxiety. The mean dose of drug was 34.2 mg/d. The study did not demonstrate a statistically significant benefit for augmentation with methylphenidate in TRD. Combination of methylphenidate with antidepressants was well tolerated. Adequately powered, randomized, controlled trials are necessary to fully evaluate the efficacy of extended-release methylphenidate in TRD.
Accelerated immunopathological response of mice infected with Mycobacterium tuberculosis disrupted in the mce1 operon negative transcriptional regulator (2007)

Mycobacterium tuberculosis causes a variety of clinical outcomes determined by host as well as bacterial factors. M. tuberculosis disrupted in the mce1 operon causes increased mortality in immunocompetent mice. This operon is negatively regulated by mce1R (Rv0165c). We studied the role of mce1R in infection outcome in mice. At 5 x 10(4) tail vein infectious dose, the median survival time (MST) of mice infected with the mce1R mutant M. tuberculosis H37Rv was 293 days, while mice infected with the wild-type H37Rv survived more than 350 days (P < 0.0001). At a higher dose (5 x 10(6)), the MST of mutant-infected mice was 32 days, compared with 127 days for wild type-infected mice (P < 0.0001). With either tail vein or aerosol infection, mutant-infected mice developed larger granulomatous lesions in their lungs than mice infected with the wild type. Mutant-infected mice were unable to control the bacterial burden in the first 4 weeks of infection, but even after achieving control later, these mice succumbed to granulomatous pneumonia. These observations suggest that the early deregulated expression of the mce1 operon products determines later granulomatous tissue response. mce1 operon may homeostatically regulate the cell wall architecture in vivo that elicits a steady-state granuloma tissue response permitting M. tuberculosis to establish a long-term infection.
CD43 potentiates CD3‐induced proliferation of murine intestinal intraepithelial lymphocytes (2001)

The involvement of CD43 in cell proliferation of murine intestinal intraepithelial lymphocytes (IEL) has been studied in in vitro CD3-stimulated cell cultures. In the presence of either IL-2 or IL-15, CD3 stimulation of IEL resulted in low levels of proliferation as measured by thymidine incorporation, whereas no proliferation occurred upon CD3 stimulation in the absence of cytokines. The combination of both cytokines to IEL cultures synergistically enhanced CD3-induced proliferation by approximately threefold that of cultures supplemented with either cytokine alone. Most importantly, however, proliferation of IEL was significantly greater when CD3 stimulation occurred in conjunction with CD43 triggering, indicating that CD43 functions as a coactivational signal for murine IEL. These findings indicate that a spectrum of potential proliferative responses exist among murine IEL depending on the types and combinations of signals received, and that because under normal conditions murine IEL are largely devoid of CD28 expression, a classical T-cell coactivational molecule, the capacity for high-level IEL proliferation may reside with CD43.
Synthesis and properties of ENA® oligonucleotides targeted to human telomerase RNA subunit (2005)

Oligonucleotides uniformly modified with 2'-O,4'-C-ethylene-bridged nucleic acid (ENA) units were synthesized using the phosphoramidite method on a hundred-milligram scale for the evaluation of thermodynamic and chemical properties. The properties of these ENA oligonucleotides with the sequences targeted to human telomerase RNA subunit (hTR) were compared with those of GRN163, which is an oligonucleotide modified with N3'-P5' thiophosphoramidates. The melting temperatures of the duplexes of ENA oligonucleotides with complementary RNA were higher than that of the duplex of GRN163. Moreover, ENA oligonucleotide ENA-13 was more highly stable than GRN163 under acidic conditions (pH 5.0). ENA-13, which contained contiguous guanine sequences, could not form a G-quadruplex, which formation is not feasible for binding to hTR as an antisense molecule. The above findings suggest that ENA oligonucleotides may be useful for antisense therapeutic applications.
Encapsulation of Small Polar Guests in Molecular Apple Peels (2007)

Three aromatic oligoamides have been prepared that have alternating 1,6-diaminopyridine and 1,6-pyridinedicarboxylic acid units at the center of the sequence and two 8-amino-2-quinolinecarboxylic acid units at each extremity. The three oligomers differ in the number--3, 5, or 7-of pyridine units in the sequence. They were designed to adopt helically folded conformations in solution and in the solid state. The sequence of monomers was chosen so that the diameter of the helix is larger in the center than at each extremity, and hence they resemble helically wrapped apple peels. According to modeling studies, the pyridine units were expected to define a polar hollow within the helix that is large enough to accommodate small polar guests, whereas the quinoline units at each end of the oligomeric sequences were expected to completely cap the hollow and transform the helix cavities into a closed shell that may act as a capsule. Crystallographic studies demonstrate that the oligomers do fold into helices that define a cavity isolated from the surrounding medium in the solid state. Depending on the number of pyridine rings, one or two water molecules are bound within the capsules. The crystal structure of a capsule fragment shows that MeOH can also be hosted by the largest oligomer. Solution NMR studies confirm that binding of water also occurs in solution with the same stoichiometry as observed in the solid state. The capsules have distinct signals depending on whether they are empty, half-full, or full, and these species are in slow exchange on the NMR timescale at low temperature. Indeed, the binding and release of water molecules requires a significant conformational distortion of the helix that slows down these processes. The addition of small polar molecules such as methanol, hydrazine, hydrogen peroxide, or formic acid to the largest capsule leads to the observation of new sets of NMR signals of the capsules that were assigned to complexes with these guests. However, water appears to be the preferred guest.
Rapid Charge Transport in Dye‐Sensitized Solar Cells Made from Vertically Aligned Single‐Crystal Rutile TiO2 Nanowires (2012)

A rapid solvothermal approach was used to synthesize aligned 1D single-crystal rutile TiO(2) nanowire (NW) arrays on transparent conducting substrates as electrodes for dye-sensitized solar cells. The NW arrays showed a more than 200 times faster charge transport and a factor four lower defect state density than conventional rutile nanoparticle films.
Predominant T-helper 1 cytokine profile of hepatitis B virus nucleocapsid-specific T cells in acute self-limited hepatitis B (1997)

The cytokine pattern secreted by T cells on viral antigen recognition is believed to exert a profound influence on both the type of disease caused by the infecting agent and the final outcome of the viral infection. To characterize the cytokine pattern associated with spontaneous resolution of acute hepatitis B, we analyzed interferon gamma (IFN-gamma), interleukin (IL)-4, and IL-5 production by a wide series of hepatitis B virus (HBV) nucleocapsid-specific T-cell lines (34 lines) and T-cell clones (71 clones) derived from the peripheral blood of 13 patients during the acute or recovery phase of hepatitis B (2 and 7 of them were studied only in the recovery or the acute phase, respectively, and 4 during both). Most T-cell lines (67%) and clones (77%) isolated during the acute phase of infection expressed a T-helper (Th) 1 cytokine profile dominated by the production of IFN-gamma. A larger proportion (74%) of T-cell lines produced several years after resolution of hepatitis was able to secrete not only IFN-gamma, but also IL-4 and IL-5 (Th0-like cells). Results indicate that the antigen-specific fraction of peripheral blood T cells in acute self-limited hepatitis B selectively secrete Th1-type eytokines, suggesting that Th1-mediated effects may contribute not only to liver cell injury, but probably also to recovery from disease and successful control of infection.
Interstitial Fluid and Lymph Formation and Transport: Physiological Regulation and Roles in Inflammation and Cancer (2012)

The interstitium describes the fluid, proteins, solutes, and the extracellular matrix (ECM) that comprise the cellular microenvironment in tissues. Its alterations are fundamental to changes in cell function in inflammation, pathogenesis, and cancer. Interstitial fluid (IF) is created by transcapillary filtration and cleared by lymphatic vessels. Herein we discuss the biophysical, biomechanical, and functional implications of IF in normal and pathological tissue states from both fluid balance and cell function perspectives. We also discuss analysis methods to access IF, which enables quantification of the cellular microenvironment; such methods have demonstrated, for example, that there can be dramatic gradients from tissue to plasma during inflammation and that tumor IF is hypoxic and acidic compared with subcutaneous IF and plasma. Accumulated recent data show that IF and its convection through the interstitium and delivery to the lymph nodes have many and diverse biological effects, including in ECM reorganization, cell migration, and capillary morphogenesis as well as in immunity and peripheral tolerance. This review integrates the biophysical, biomechanical, and biological aspects of interstitial and lymph fluid and its transport in tissue physiology, pathophysiology, and immune regulation.
DNA Tile Based Self‐Assembly: Building Complex Nanoarchitectures (2006)

DNA tile based self-assembly provides an attractive route to create nanoarchitectures of programmable patterns. It also offers excellent scaffolds for directed self-assembly of nanometer-scale materials, ranging from nanoparticles to proteins, with potential applications in constructing nanoelectronic/nanophotonic devices and protein/ligand nanoarrays. This Review first summarizes the currently available DNA tile toolboxes and further emphasizes recent developments toward self-assembling DNA nanostructures with increasing complexity. Exciting progress using DNA tiles for directed self-assembly of other nanometer scale components is also discussed.
Bandgap and transport properties of Si/sub 1-x/Ge/sub x/ by analysis of nearly ideal Si/Si/sub 1-x/Ge/sub x//Si heterojunction bipolar transistors (1989)

Si/Si/sub 1-x/Ge/sub x//Si N-p-N heterojunction bipolar transistors (HBTs) produced by a chemical vapor deposition technique, limited-reaction processing, were analyzed using electrical measurements to determine properties of strained Si/sub 1-x/Ge/sub x/. The band discontinuities between Si and strained Si/sub 1-x/Ge/sub x/ were found by measuring the collector and base currents as a function of temperature. The electron diffusion coefficient in p-type Si/sub 1-x/Ge/sub x/ was extracted by measuring the change in collector current with Si/sub 1-x/Ge/sub x/ base width. The electron diffusion coefficient perpendicular to the heterointerface in the strained Si/sub 1-x/Ge/sub x/ layers studied here is smaller than that in Si doped to the same level. The reverse leakage currents at the base-emitter junction of the HBTs are smaller than the leakage at the collector-base junction, but in Si control transistors the situation is reversed. The high leakage currents at the collector-base junction in the HBTs are believed to result from the preferred accumulation of misfit dislocations at the strained interface closest to the substrate.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Comparison of Western blot (immunoblot) and glycoprotein G-specific immunodot enzyme assay for detecting antibodies to herpes simplex virus types 1 and 2 in human sera (1988)

Sera from patients with culture-proven genital herpes infections were tested for herpes simplex virus type 1 (HSV-1)- and HSV-2-specific antibodies by both a Western blot (immunoblot) technique (WBA) and immunodot enzyme assays (IEAs) specific for HSV-1 or HSV-2 glycoprotein G (gG). Of 137 serum samples tested, none was mistyped by either WBA or IEA. Both tests were most sensitive with sera obtained at least 21 days after onset of primary HSV-2 infections or sera drawn during recurrent HSV-2 genital episodes: 75 of 76 (99%) such serum samples were positive for HSV-2 antibody by WBA and 73 of 76 (96%) were positive by IEA. Of sera drawn earlier than 21 days from onset of primary genital HSV-2, antibodies to HSV-2 were detected in 25% by WBA and 8% by IEA. In patients with culture-proven primary genital HSV-1 infection, WBA detected antibodies to HSV-1 proteins in 16 of 17 (94%) serum samples drawn at least 21 days after onset of primary genital HSV-1 infection, compared with 9 of 17 (53%) serum samples tested for gG-1 by IEA. Both WBA and IEA are accurate and sensitive tests for HSV-2 antibody in patients convalescing from a first episode or having symptomatic or asymptomatic recurrent genital herpes. WBA was more sensitive than IEA in detecting seroconversion following primary HSV-1 genital herpes, although both assays may miss persons undergoing early seroconversion to HSV-2.