gebhart/patrepeval huggingface dataset:
Capabilities and Limitations of Plasma Polymerized Methylsilane (PPMS) All-Dry Lithography. (1998)

In this paper we report the results of a feasibility study of manufacturability of processes using plasma polymerized methylsilane (PPMS) as both a single-layer and a bilayer resist in both negative and positive tone development modes. PPMS has shown great promise as the basis for an all dry lithographic process. The photosensitive polymer is deposited in a low power plasma of methylsilane gas and is comprised of a Si-Si bonded network. PPMS undergoes efficient photo-oxidative crosslinking upon exposure to 248 or 193nm light in air to form an oxide-like material (PPMSO). We have identified several structural differences of films deposited at different temperatures and have correlated those differences to the air stability and the photosensitivity of PPMS films. We have also examined the effect of laser pulse power and repetition rate on the efficiency of exposure and conclude that the rate of oxygen diffusion into the film limits the effectiveness of high laser power for increasing the throughput of an exposure tool. We have concluded that positive tone PPMS processing is not practical because of the slow diffusion of oxygen through the film, required for effective photo-oxidation of PPMS to occur.
Ilizarov method of fixation for the management of pilon and distal tibial fractures in the compromised diabetic patient: A technique guide. (2014)

The purpose of this technique guide is to provide the foot and ankle surgeon with a comprehensive guide for reducing pilon and distal tibial fractures when dealing with the co-morbid patient and/or a soft tissue envelope that does not lend itself to ORIF. The senior author presents a relatively low complication rate (13% in the pilon group and 23% in the distal tibial group), with a low number of amputations (five out of 59 patients).
Hydrofluoric acid-treated tau PHF proteins display the same biochemical properties as normal tau. (1992)

Tau (tau) is a major constituent of paired helical filaments (PHF) found in Alzheimer's disease. The current study examines the possibility that the distinct properties of PHF-associated tau proteins (tau PHF) result from post-translational modifications of normal soluble tau (tau s). Following hydrofluoric acid (HF) treatment, tau PHF proteins are heat- and acid-stable, soluble in 2-(N-morpholino)ethanesulfonic acid buffers and display the same molecular weight, pI, and immunochemical properties as normal tau s. Alkaline phosphatase treatment of dissociated PHF results in similar, although less extensive, electrophoretic changes and a reduction in PHF-1 immunoreactivity. Therefore, phosphorylation of normal tau s appears to be responsible for the distinct properties of tau PHF. Although our results suggest that all of the normal tau isoforms are in PHF, the relative abundance of individual tau species differs in HF-treated PHF and tau s samples. Moreover, the loss of PHF following HF treatment suggests that post-translational modifications contribute to the structural stability of PHF.
Preparation and Characterization of a Polyelectrolyte Monolayer Covalently Attached to a Planar Solid Surface (1999)

A novel concept for the synthesis of molecularly thin polyelectrolyte layers covalently attached to planar solid surfaces is introduced. The polymer monolayers are generated directly at the surface by using self-assembled monolayers of an azo initiator and radical chain polymerization in situ. This "grafting from" approach yields surface-bound polymer molecules with a high molecular weight and with high graft densities of the attached chains ("brush"-like state). As an example for the preparation of a positively charged polyelectrolyte "brush" at first a monolayer of poly(4-vinylpyridine) (PVP) was generated at the surface, which was subsequently quarternized to yield a poly[4-vinyl-N-n-butylpyridinium] bromide (BuPVP) monolayer. The thickness of this resulting cationic monolayer can be controlled in a wide range, starting from 2 nm to more than 1000 nm in the solvent-free state.
Cross-Linked, Monodisperse, Micron-Sized Polystyrene Particles by Two-Stage Dispersion Polymerization (2005)

It is well-known that cross-linking agents such as divinylbenzene (DVB) interfere with the dispersion polymerization of styrene in ethanol, a reaction carried out in the presence of polymeric stabilizers such as poly(vinylpyrrolidone). Small amounts of DVB broaden the particle size distribution and lead to irregular particles, whereas modest amounts lead to coagulation. We report that many of these problems can be avoided if one delays the addition of the cross-linking agent until after the end of the nucleation stage of the reaction (e.g., at less than 5% monomer conversion). In this way one can obtain monodisperse polystyrene particles containing 1 wt % ethylene glycol dimethacrylate (EGDMA) as a cross-linker. A second set of problems arises if the cross-linking agent is consumed too early in the reaction, presumably because early network formation limits the swellability of the growing particles. These problems can be overcome by feeding DVB into the reaction over 12 h or by adding EGDMA in successive batches over 6 h. In this way, monodisperse particles with micrometer diameters, and a coefficient of variation of 2% or less, can be obtained containing up to 6 wt % cross-linker based on styrene.
The Electronic Influence of Ring Substituents and Ansa Bridges in Zirconocene Complexes as Probed by Infrared Spectroscopic, Electrochemical, and Computational Studies (2002)

The electronic influence of unbridged and ansa-bridged ring substituents on a zirconocene center has been studied by means of IR spectroscopic, electrochemical, and computational methods. With respect to IR spectroscopy, the average of the symmetric and asymmetric stretches (nu(CO(av))) of a large series of dicarbonyl complexes (Cp(R))(2)Zr(CO)(2) has been used as a probe of the electronic influence of a cyclopentadienyl ring substituent. For unbridged substituents (Me, Et, Pr(i), Bu(t), SiMe(3)), nu(CO(av)) on a per substituent basis correlates well with Hammett sigma(meta) parameters, thereby indicating that the influence of these substituents is via a simple inductive effect. In contrast, the reduction potentials (E degrees ) of the corresponding dichloride complexes (Cp(R))(2)ZrCl(2) do not correlate well with Hammett sigma(meta) parameters, thereby suggesting that factors other than the substituent inductive effect also influence E degrees. Ansa bridges with single-atom linkers, for example [Me(2)C] and [Me(2)Si], exert a net electron-withdrawing effect, but the effect is diminished upon increasing the length of the bridge. Indeed, with a linker comprising a three-carbon chain, the [CH(2)CH(2)CH(2)] ansa bridge becomes electron-donating. In contrast to the electron-withdrawing effect observed for a single [Me(2)Si] ansa bridge, a pair of vicinal [Me(2)Si] ansa bridges exerts an electron-donating effect relative to that from the single bridge. DFT calculations demonstrate that the electron-withdrawing effect of the [Me(2)C] and [Me(2)Si] ansa-bridges is due to stabilization of the cyclopentadienyl ligand acceptor orbital, which subsequently enhances back-donation from the metal. The calculations also indicate that the electron-donating effect of two vicinal [Me(2)Si] ansa bridges, relative to that of a single bridge, is a result of it enforcing a ligand conformation that reduces back-donation from the metal.
Enteral nutrients potentiate glucagon-like peptide-2 action and reduce dependence on parenteral nutrition in a rat model of human intestinal failure (2012)

Glucagon-like peptide-2 (GLP-2) is a nutrient-dependent, proglucagon-derived gut hormone that shows promise for the treatment of short bowel syndrome (SBS). Our objective was to investigate how combination GLP-2 + enteral nutrients (EN) affects intestinal adaption in a rat model that mimics severe human SBS and requires parenteral nutrition (PN). Male Sprague-Dawley rats were assigned to one of five groups and maintained with PN for 18 days: total parenteral nutrition (TPN) alone, TPN + GLP-2 (100 μg·kg(-1)·day(-1)), PN + EN + GLP-2(7 days), PN + EN + GLP-2(18 days), and a nonsurgical oral reference group. Animals underwent massive distal bowel resection followed by jejunocolic anastomosis and placement of jugular catheters. Starting on postoperative day 4, rats in the EN groups were allowed ad libitum access to EN. Groups provided PN + EN + GLP-2 had their rate of PN reduced by 0.25 ml/day starting on postoperative day 6. Groups provided PN + EN + GLP-2 demonstrated significantly greater body weight gain with similar energy intake and a safe 80% reduction in PN compared with TPN ± GLP-2. Groups provided PN + EN + GLP-2 for 7 or 18 days showed similar body weight gain, residual jejunal length, and digestive capacity. Groups provided PN + EN + GLP-2 showed increased jejunal GLP-2 receptor (GLP-2R), insulin-like growth factor-I (IGF-I), and IGF-binding protein-5 (IGFBP-5) expression. Treatment with TPN + GLP-2 demonstrated increased jejunal expression of epidermal growth factor. Cessation of GLP-2 after 7 days with continued EN sustained the majority of intestinal adaption and significantly increased expression of colonic proglucagon compared with PN + EN + GLP-2 for 18 days, and increased plasma GLP-2 concentrations compared with TPN alone. In summary, EN potentiate the intestinotrophic actions of GLP-2 by improving body weight gain allowing for a safe 80% reduction in PN with increased jejunal expression of GLP-2R, IGF-I, and IGFBP-5 following distal bowel resection in the rat.
Taxonomy of detection algorithms for hyperspectral imaging applications (2005)

A unified, simplified, and concise overview of spectral target detection algorithms for hyperspectral imaging applications is presented. We focus on detection algorithms derived using established statistical techniques and whose performance is predictable under reasonable assumptions about hyperspectral imaging data. The emphasis on a signal processing perspective enables us to better understand the strengths and limitations of each algorithm, avoid unrealistic performance expectations, and apply an algorithm properly and sensibly.
Formation of brome mosaic virus RNA-dependent RNA polymerase in yeast requires coexpression of viral proteins and viral RNA. (1995)

In this report we show that yeast expressing brome mosaic virus (BMV) replication proteins 1a and 2a and replicating a BMV RNA3 derivative can be extracted to yield a template-dependent BMV RNA-dependent RNA polymerase (RdRp) able to synthesize (-)-strand RNA from BMV (+)-strand RNA templates added in vitro. This virus-specific yeast-derived RdRp mirrored the template selectivity and other characteristics of RdRp from BMV-infected plants. Equivalent extracts from yeast expressing 1a and 2a but lacking RNA3 contained normal amounts of 1a and 2a but had no RdRp activity on BMV RNAs added in vitro. To determine which RNA3 sequences were required in vivo to yield RdRp activity, we tested deletions throughout RNA3, including the 5',3', and intercistronic noncoding regions, which contain the cis-acting elements required for RNA3 replication in vivo. RdRp activity was obtained only from cells expressing 1a, 2a, and RNA3 derivatives retaining both 3' and intercistronic noncoding sequences. Strong correlation between extracted RdRp activity and BMV (-)-strand RNA accumulation in vivo was found for all RNA3 derivatives tested. Thus, extractable in vitro RdRp activity paralleled formation of a complex capable of viral RNA synthesis in vivo. The results suggest that assembly of active RdRp requires not only viral proteins but also viral RNA, either to directly contribute some nontemplate function or to recruit essential host factors into the RdRp complex and that sequences at both the 3'-terminal initiation site and distant internal sites of RNA3 templates may participate in RdRp assembly and initiation of (-)-strand synthesis.
Massive Apoptosis of Thymocytes in T-Cell-Deficient Id1 Transgenic Mice (1999)

Id1 is an inhibitor of a group of basic helix-loop-helix transcription factors, collectively called E proteins, which includes E12, E47, E2-2, and HEB. We have generated transgenic mice in which Id1 is specifically expressed in T cells. The total number of thymocytes in these mice is less than 4% of that in wild-type mice. The majority of the transgenic thymocytes are CD4 and CD8 double negative and bear the cell surface markers of multipotent progenitor cells. A small number of thymocytes, however, differentiate into CD4 or CD8 single-positive T cells, which also display different characteristics from their wild-type counterparts. More importantly, apoptotic cells constitute about 50% of the total thymocytes. These apoptotic thymocytes have rearranged their T-cell receptor genes, suggesting that they are differentiating T cells. This finding has raised the possibility that the T-cell deficiency in Id1 transgenic mice is the result of a massive apoptosis of differentiating T cells triggered by Id1 expression as opposed to a developmental block at the earliest progenitor stage. The progenitor cells accumulated in the transgenic mice might have survived because they are not susceptible to the apoptotic signals. Despite the massive cell death of the thymocytes at young ages, Id1 transgenic mice frequently develop T-cell lymphoma later in their life span, and lymphomagenesis appears to occur at different stages of T-cell development. Taken together, our data suggest that E proteins, being the targets of Id1, are essential regulators for normal T-cell differentiation and tumor suppression.
Expression of membrane-type matrix metalloproteinases 4, 5, and 6 in mouse corneas infected with P. aeruginosa. (2001)

Expression of MT4-, MT5-, and MT6-MMP was induced in corneas infected with P. aeruginosa. Immunohistochemistry showed predominant immunoreactivity of MT4- and MT5-MMP in the substantia propria. Previous histologic studies have revealed different patterns of inflammatory cell infiltration with an increased number of polymorphonuclear neutrophils (PMNs) during the early stage of inflammation and increased macrophages during the late stage. These results indicate a good correlation between the overexpression of the MT-MMPs in the infected corneas and the inflammatory response-that is, leukocyte infiltration-indicating that inflammatory cells such as macrophages and PMNs may play a role in the upregulation of MT-MMPs during corneal infection, which in turn can cause the destruction of corneal tissue.
A SIMPLE METHOD OF ESTIMATING FIFTY PER CENT ENDPOINTS12 (1938)

Journal Article A SIMPLE METHOD OF ESTIMATING FIFTY PER CENT ENDPOINTS Get access L.J. REED, L.J. REED Search for other works by this author on: Oxford Academic PubMed Google Scholar H. MUENCH H. MUENCH Search for other works by this author on: Oxford Academic PubMed Google Scholar American Journal of Epidemiology, Volume 27, Issue 3, May 1938, Pages 493–497, https://doi.org/10.1093/oxfordjournals.aje.a118408 Published: 01 May 1938 Article history Received: 26 October 1937 Published: 01 May 1938
The seroepidemiology of genogroup 1 and genogroup 2 Norwalk-like viruses in Italy (1999)

Southampton virus (SV) and Lordsdale viruses (LV) are small round structured viruses characterised recently and belong to two separate genogroups. The capsid genes of these viruses were expressed in insect cells using recombinant baculoviruses. Both SV (genogroup 1) and LV (genogroup 2) capsid proteins self-assembled to form virus-like particles (VLPs). The VLPs were used in a standard enzyme-linked immunosorbent assay (ELISA) to screen for antibodies to SV and LV in 1,729 age-stratified human sera collected in Verona, Italy between January and November 1996. SV VLPs were labile compared with LV VLPs. There was a large difference in the prevalence of SV (28.7%) compared with LV (91.2%). However, presentation of SV VLPs using chicken egg yolk antibody-coated wells (IgY capture ELISA) with a subset of serum samples from patients (0-19 years) increased the number of positive sera significantly (50.5%), indicating that SV antigen integrity is an important factor in the assay. Recent reverse transcription-polymerase chain reaction (RT-PCR) studies have shown that LV is circulating currently and analysis of IgY capture ELISA data showed greater reactivity for LV than SV, reflecting a genuinely lower rate of recent infection by this genogroup 1 virus.
MAX Inactivation in Small Cell Lung Cancer Disrupts MYC–SWI/SNF Programs and Is Synthetic Lethal with BRG1 (2013)

Our knowledge of small cell lung cancer (SCLC) genetics is still very limited, amplification of L-MYC, N-MYC, and C-MYC being some of the well-established gene alterations. Here, we report our discovery of tumor-specific inactivation of the MYC-associated factor X gene, MAX, in SCLC. MAX inactivation is mutually exclusive with alterations of MYC and BRG1, the latter coding for an ATPase of the switch/sucrose nonfermentable (SWI/SNF) complex. We demonstrate that BRG1 regulates the expression of MAX through direct recruitment to the MAX promoter, and that depletion of BRG1 strongly hinders cell growth, specifically in MAX-deficient cells, heralding a synthetic lethal interaction. Furthermore, MAX requires BRG1 to activate neuroendocrine transcriptional programs and to upregulate MYC targets, such as glycolysis-related genes. Finally, inactivation of the MAX dimerization protein, MGA, was also observed in both non-small cell lung cancer and SCLC. Our results provide evidence that an aberrant SWI/SNF-MYC network is essential for lung cancer development.
A rapid and effective procedure for screening protease mutants (1996)

We describe a simple and effective procedure to screen for active proteases among a large number of mutants. First, the mutants are genetically tested by the protease activity produced in the periplasm of transformed bacteria which supplies the cells with a nitrogen source by hydrolyzing a protein applied to plates. Then a less sensitive activity staining and an X-ray film digestion assay are used to verify and estimate the activity of the mutants that proved to be positive in the first step. Depending essentially on the level of periplasmic protease activity, the method can detect both the activity and the stability of the expressed enzymes. We calibrated the method with transformants that produce wild-type trypsin, chymotrypsin and trypsin mutants of known activity. Using this method we found two active revertants of the inactive Asn102 trypsin mutant, by screening approximately 4.4 x 10(4) random mutants that were generated by the polymerase chain reaction on a cDNA fragment. This procedure should be useful in searching for proteases of novel specificity and/or reaction chemistry engineered by random mutagenesis, and also for in vitro evolution studies.
Molecular cloning of cDNA for the carcinoma-associated antigen GA733-2. (1990)

Defined by monoclonal antibody GA733, the GA733-2 antigen is a cell surface 40-kDa glycoprotein associated with human carcinomas of various origins. Molecular clones for the GA733-2 antigen were isolated from a colorectal carcinoma cell line cDNA library using the high-efficiency COS cell expression system. A 1.4-kilobase cDNA species was enriched by immunoselection with monoclonal antibody. The authenticity of individual clones was established by immunologic and sequence criteria. At the amino acid sequence level, GA733-2 was found to be greater than 99% identical to the previously described KSA antigen defined by monoclonal antibody KS1/4. The amino acid sequence derived from the previously described GA733-related gene, GA733-1, was found to be 49% identical to GA733-2. The positions of 12 cysteine residues in the extracellular domains of the two GA733 antigens are conserved, as is the overall distribution of hydrophobic and hydrophilic residues. A 1.45-kilobase transcript of the GA733-2/KSA gene was found to be expressed in cell lines derived from colorectal and pancreatic carcinoma.
Energy Deregulation: Licensing Tumors to Grow (2006)

Taking their cue from a controversial, 80-year-old theory of cancer, scientists are reexamining how tumors fuel their own growth and finding new ways to cut off their energy supply. (Read more.)
Passive Immunization Against Cachectin/Tumor Necrosis Factor Protects Mice from Lethal Effect of Endotoxin (1985)

A highly specific polyclonal rabbit antiserum directed against murine cachectin/tumor necrosis factor (TNF) was prepared. When BALB/c mice were passively immunized with the antiserum or with purified immune globulin, they were protected against the lethal effect of the endotoxin lipopolysaccharide produced by Escherichia coli. The prophylactic effect was dose-dependent and was most effective when the antiserum was administered prior to the injection of the endotoxin. Antiserum to cachectin/TNF did not mitigate the febrile response of endotoxin-treated animals, and very high doses of endotoxin could overcome the protective effect. The median lethal dose of endotoxin in mice pretreated with 50 microliters of the specific antiserum was approximately 2.5 times greater the median lethal dose for controls given nonimmune serum. The data suggest that cachectin/TNF is one of the principal mediators of the lethal effect of endotoxin.
Proteome analysis of cerebrospinal fluid proteins in Alzheimer patients (2002)

By comparing the CSF proteome between Alzheimer disease (AD) patients and controls it may be possible to identify proteins that play a role in the disease process and thus to study the pathogenesis of AD. We used mini-gel technology in a two-dimensional electrophoresis procedure, sensitive SYPRO Ruby staining and mass spectrometry for clinical screening of disease-influenced CSF proteins in 15 AD patients and 12 controls. The levels of six proteins and their isoforms, including proapolipoprotein, apolipoprotein E, beta-2 microglobulin, retinol-binding protein, transthyretin, and ubiquitin, were significantly altered in CSF of AD patients. The most prominently altered proteins were the apolipoproteins, especially proapolipoprotein.
B Cell Maturation Antigen, the Receptor for a Proliferation-Inducing Ligand and B Cell-Activating Factor of the TNF Family, Induces Antigen Presentation in B Cells (2005)

B cell maturation Ag (BCMA), a member of the TNFR superfamily expressed on B cells, binds to a proliferation-inducing ligand (APRIL) and B cell-activating factor of the TNF family (BAFF) but the specific B cell responses regulated by BCMA remain unclear. This study demonstrates that ligation of A20 B cells transfected with BCMA induces the expression of CD40, CD80/B7-1, CD86/B7-2, MHC class II, and CD54/ICAM-1, which subsequently enhances the presentation of OVA peptide Ag to DO11.10 T cells. BCMA expression in murine splenic B cells can be induced with IL-4 and IL-6, allowing subsequent treatment with APRIL or agonist anti-BCMA to similarly induce Ag presentation. A comparative analysis of hybrid receptors of TNFR2 fused to the cytoplasmic domains of APRIL/BAFF receptors found that only BCMA, but not transmembrane activator and calcium-modulator and cyclophilin ligand interactor or BAFF-R, is capable of activating Ag presentation. Although all three receptors can trigger NF-kappaB signaling, only BCMA activates the JNK pathway conferring on BCMA the specific ability to activate this Ag presentation response.