gebhart/patrepeval huggingface dataset:
Step coverage comparison of Ti/TiN deposited by collimated and uncollimated physical vapor deposition techniques (1996)

The step coverage and grain structure of Ti/TiN films sputtered with and without a collimator in a contact/via hole structure were compared using transmission electron microscopy, microelectron diffraction, and Auger electron spectroscopy with field emission microanalysis capability on cross-section samples. The holes have widths ranging from 0.40 to 0.75 μm and aspect ratios from 2.3 to 1.4, respectively. It was found that collimated Ti/TiN films demonstrate reasonably uniform coverage along the sidewall and at the bottom of holes. Collimated Ti bottom coverage is sufficient to assure good contact resistance. In contrast, uncollimated Ti/TiN films demonstrate an overhang on the top sidewall of holes and show decreased coverage when approaching the bottom corner along the sidewall or along the bottom of holes. Film property differences at different regions of a hole using either collimated or uncollimated deposition techniques will also be discussed.
Identification of Mimotope Peptides Which Bind to the Mycotoxin Deoxynivalenol-Specific Monoclonal Antibody (1999)

Monoclonal antibody 6F5 (mAb 6F5), which recognizes the mycotoxin deoxynivalenol (DON) (vomitoxin), was used to select for peptides that mimic the mycotoxin by employing a library of filamentous phages that have random 7-mer peptides on their surfaces. Two phage clones selected from the random peptide phage-displayed library coded for the amino acid sequences SWGPFPF and SWGPLPF. These clones were designated DONPEP.2 and DONPEP.12, respectively. The results of a competitive enzyme-linked immunosorbent assay (ELISA) suggested that the two phage displayed peptides bound to mAb 6F5 specifically at the DON binding site. The amino acid sequence of DONPEP.2 plus a structurally flexible linker at the C terminus (SWGPFPFGGGSC) was synthesized and tested to determine its ability to bind to mAb 6F5. This synthetic peptide (designated peptide C430) and DON competed with each other for mAb 6F5 binding. When translationally fused with bacterial alkaline phosphatase, DONPEP.2 bound specifically to mAb 6F5, while the fusion protein retained alkaline phosphatase activity. The potential of using DONPEP.2 as an immunochemical reagent in a DON immunoassay was evaluated with a DON-spiked wheat extract. When peptide C430 was conjugated to bovine serum albumin, it elicited antibody specific to peptide C430 but not to DON in both mice and rabbits. In an in vitro translation system containing rabbit reticulocyte lysate, synthetic peptide C430 did not inhibit protein synthesis but did show antagonism toward DON-induced protein synthesis inhibition. These data suggest that the peptides selected in this study bind to mAb 6F5 and that peptide C430 binds to ribosomes at the same sites as DON.
Human capillary morphogenesis protein 2 functions as an anthrax toxin receptor (2003)

Bacillus anthracis secretes two bipartite toxins thought to be involved in anthrax pathogenesis and resulting death of the host. The current model for intoxication is that protective antigen (PA) toxin subunits bind a single group of cell-surface anthrax toxin receptors (ATRs), encoded by the tumor endothelial marker 8 (TEM8) gene. The ATR/TEM8-PA interaction is mediated by the receptor's extracellular domain related to von Willebrand factor type A or integrin inserted domains (VWA/I domains). A metal ion-dependent adhesion site (MIDAS) located within this domain of the ATR/TEM8 protein chelates a divalent cation critical for PA binding. In this report, we identify a second PA receptor encoded by capillary morphogenesis gene 2 (CMG2), which has 60% amino acid identity to ATR/TEM8 within the VWA/I domain, as well as a conserved MIDAS motif. A recombinant CMG2 protein bound PA and mediated toxin internalization when expressed on receptor-deficient cells. Binding between the CMG2 VWA/I domain and PA was shown to be direct and metal-dependent, although the cation specificity of this interaction is different than that observed with ATR/TEM8. Northern blot analysis revealed that CMG2 is widely expressed in human tissues, indicating that this receptor is likely to be relevant for disease pathogenesis. Finally, a soluble version of the CMG2 VWA/I domain inhibited intoxication of cells expressing endogenous toxin receptors when it was added to PA at a 3:1 ratio. These studies distinguish CMG2 as a second anthrax toxin receptor and identify a potent antitoxin that may prove useful for the treatment of anthrax.
Important Aspects of Well Control for Horizontal Drilling Including Deepwater Situations (1991)

ABSTRACT The drilling of horizontal wells to improve oil and gas recovery and productivity has quickly become one of the most important and promising technology of the oil industry. This is reflected by the considerable number of technical papers published on this subject. Although these papers have been covered a great deal of aspects of horizontal drilling, one important subject remains almost unexplored: the well pressure control. The scope of this paper is to show important facets of the well control for horizontal wells, especially for deepwater ones, and to highlight some design and operational aspects to make the horizontal drilling safer. One important point analyzed in this paper was the pressure behavior inside a horizontal wellbore during a gas kick removal process. For this analysis, a numerical simulator of a gas kick based on the unsteady state flow of a two-phase mixture (gas and mud) has been developed and used to predict pressure at any point of the wellbore-choke line system. It has also been used to compute and to analyze the kick tolerance during the gas kick circulation process. Some other relevant points of the well control operation for horizontal wells that differ from those for vertical wells were also investigated.They include:swabbing effect when tripping out of the hole,shut-in pressures and pit gain,drillpipe pressure schedule during the kick removal process,and mud density design.
Bystander killing of breast cancer MCF‐7 cells by MDA‐MB‐231 cells exposed to 5‐fluorouracil is mediated via Fas (2007)

The major drawback with cancer therapy is the development of resistant cells within tumors due to their heterogeneous nature and due to inadequate drug delivery during chemotherapy. Therefore, the propagation of injury ("bystander effect" (BE)) from directly damaged cells to other cells may have great implications in cancer chemotherapy. The general advantage of the bystander cell killing phenomenon is the large therapeutic index that can be achieved. Experiments suggest that this phenomenon is detected in radiation therapy as well as in gene therapy in conjunction with chemotherapy. In the present study, we developed an original in vitro model dedicated to the exploration of bystander cytotoxicity induced during breast carcinoma chemotherapy. In brief, we investigated this perpetuation of injury on untreated bystander MCF-7 breast cancer cells which were coplated with 5-fluorouracil (5-FU)-treated MDA-MB-231 breast cancer cells. To achieve this goal, a specific in vitro coculture model which involved mixing of aggressive MDA-MB-231 breast cancer cells with enhanced green fluorescent protein (EGFP) expressing stable clone of non-metastatic MCF-7 breast cancer cells (MCF-EGFP), was used. A bystander killing effect was observed in MCF-EGFP cells cocultured with MDA-MB-231 cells pretreated with 5-FU. The striking decrease in MCF-EGFP cells, as detected by assaying for total GFP intensity, is mediated by activation of Fas/FasL system. The implication of Fas in MCF-EGFP cell death was confirmed by using antagonistic anti-FasL antibody that reverses bystander cell death by blocking FasL on MDA-MB-231 cells. In addition, inhibition of CD95/Fas receptor on the cell surface of MCF-EGFP cells by treatment with Pifithrin-alpha, a p53 specific transactivation inhibitor, partially abrogated the sensitivity of bystander MCF-EGFP cells. Our data, therefore, demonstrates that the Fas/FasL system could be considered as a new determinant for chemotherapy-induced bystander cell death in breast cancers.
Basal carcinoma of the breast revisited: an old entity with new interpretations (2008)

The introduction of global gene expression analysis in breast cancer research has focused attention onto a repeatedly described subgroup of invasive breast cancer, the basal-like carcinomas. This subgroup is characterised by the expression of high-molecular weight cytokeratins 5, 14 and 17; using immunohistochemical diagnosis, it represents approximately 7-20% of invasive breast cancers. Some of these tumours fulfil the criteria of grade 3 invasive ductal carcinoma, the so-called triple negative carcinomas. However, other rare subgroups of metaplastic, medullary and myoepithelial carcinomas also belong to this entity. Even though the initial clinical prognostic relevance of basal-like breast cancers may have been overestimated, its distinctive biology generates many questions regarding the pathogenesis, chemosensitivity and optimal clinical management of this subgroup. Physiological progenitor cells within the normal female breast share essential immunohistochemical features with basal-like breast cancers. Although the exact relationship between subgroups of normal breast cells and their respective malignant counterparts is still under investigation, the major hallmarks of physiological progenitor cells are either maintained or reactivated by distinct genetic changes in basal breast cancer cells. This review will discuss the impact of these findings on our global understanding of breast cancer pathogenesis, especially from the perspective of its potential histogenesis. Clinical consequences and potential future research directions driven by the definition of basal breast cancers will also be discussed.
Absence of particle and fiber release from commercial transfusion blood microfilters. (1978)

The past years have triggered considerable scientific efforts towards the predictive analysis of the reliability of solder connections in micro-electronics. Undoubtedly, the replacement of the classical Sn-Pb solder alloy by a lead-free alternative constitutes the main motivation for this. This paper concentrates on the theoretical, computational and experimental multi-scale analysis of the microstructure evolution and degradation of the conventional solder material Sn-Pb and its most promising lead-free alternative, a Sn-Ag-Cu (SAC) alloy. Special attention is given to the thermal anisotropy of bulk SAC and the interfacial fatigue failure of SAC interconnects.
The Montgomery inverse and its applications (1995)

The Montgomery inverse of b module a is b/sup -1/2/sup n/ mod a, where n is the number of bits in a. The right-shifting binary algorithm for modular inversion is shown naturally to compute the new inverse in fewer operations than the ordinary modular inverse. The new inverse facilitates recent work by Koc on modular exponentiation and has other applications in cryptography.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Pneumatic Flap Performance for a 2D Circulation Control Airfoil, Steady and Pulsed (2005)

Circulation Control technologies have been around for 65 years, and have been successfully demonstrated in laboratories and flight vehicles alike, yet there are few production aircraft flying today that implement these advances. Circulation Control techniques may have been overlooked due to perceived unfavorable trade offs of mass flow, pitching moment, cruise drag, noise, etc. Improvements in certain aspects of Circulation Control technology are the focus of this paper. This report will describe airfoil and blown high lift concepts that also address cruise drag reduction and reductions in mass flow through the use of pulsed pneumatic blowing on a Coanda surface. Pulsed concepts demonstrate significant reductions in mass flow requirements cor Circulation Control, as well as cruise drag concepts that equal or exceed conventional airfoil systems.
DNS Security (DNSSEC) NextSECure (NSEC) RDATA Format (2004)

This document redefines the wire format of the Type Bit Map field in
the DNS NextSECure (NSEC) resource record RDATA format to cover the
full resource record (RR) type space. [STANDARDS-TRACK]
The Thyroid Hormone Receptor- -Selective Agonist GC-1 Differentially Affects Plasma Lipids and Cardiac Activity (2000)

Thyroid hormones influence the function of many organs and mediate their diverse actions through two types of thyroid hormone receptors, TRα and TRβ. Little is known about effects of ligands that preferentially interact with the two different TR subtypes. In the current study the comparison of the effects of the novel synthetic TRβ-selective compound GC-1 with T3 at equimolar doses in hypothyroid mice revealed that GC-1 had better triglyceride-lowering and similar cholesterol-lowering effects than T3. T3, but not GC-1, increased heart rate and elevated messenger RNA levels coding for the If channel (HCN2), a cardiac pacemaker that was decreased in hypothyroid mice. T3 had a larger positive inotropic effect than GC-1. T3, but not GC-1, normalized heart and body weights and messenger RNAs of myosin heavy chain α and β and the sarcoplasmic reticulum adenosine triphosphatase (Serca2). Additional dose-response studies in hypercholesteremic rats confirmed the preferential effect of GC-1 on TRβ-mediated parameters by showing a much higher potency to influence cholesterol and TSH than heart rate. The preferred accumulation of GC-1 in the liver vs. the heart probably also contributes to its marked lipid-lowering effect vs. the absent effect on heart rate. These data indicate that GC-1 could represent a prototype for new drugs for the treatment of high lipid levels or obesity.
Alternative splicing in the fragile X gene FMR1 (1993)

The FMR1 gene, associated with fragile X syndrome, has recently been cloned and the sequence of partial cDNA clones is known. We have determined additional cDNA sequences both at the 5' and 3' end. We have characterized the expressed gene by means of RT-PCR in various tissues and have found that alternative splicing takes place in the FMR1 gene, which does not seem to be tissue specific. When the different alternative splicing events are combined, 12 distinct mRNA products could result from FMR1 expression in each tested tissue. In all these transcripts the open reading frame is maintained until the same stop codon. At the 3' end alternative use of polyadenylation signals is found. The alternative splicing allows functional diversity of the FMR-1 gene. Whether all the possible proteins will be synthesized and whether they will be functionally active has to be determined.
Efficient foreign gene expression in Chlamydomonas reinhardtii mediated by an endogenous intron (1998)

Summary Heterologous genes introduced into the nuclear genome of Chlamydomonas reinhardtii are often poorly expressed. To understand the molecular mechanisms underlying this effect, we examined the influence of various factors on the expression of a chimeric transgene that confers resistance to zeomycin. This marker comprises the bacterial ble gene flanked by 5′ and 3′ sequences from the Chlamydomonas RBCS2 gene. We found that the frequency with which transformants are recovered is significantly increased when ble is fused to shorter versions of the RBCS2 promoter and when Chlamydomonas introns are introduced into the coding region of ble. The latter effect is particularly evident in the case of the first intron of RBCS2 , which dramatically stimulates the transformation frequency and the level of ble expression. We found that this improvement is mediated in part by an enhancer element within the intron sequence, and that this element acts in an orientation‐independent manner and is effective when placed either upstream or downstream of the promoter. Our results demonstrate that stable high‐level expression of a foreign gene in Chlamydomonas is possible, and highlight a potential role of introns as modulators of gene expression in this alga.
American Joint Committee on Cancer prognostic factors consensus conference (2000)

The TNM categories and stage groupings for colorectal carcinoma published in the current AJCC manual have clinical and academic value. However, a few categories require subdivision to provide increasing discrimination for individual patients. The serum marker CEA should be added to the staging system, whereas multiple other factors should be recorded as part of good clinical practice. Although many molecular and oncogenic markers show promise to supplement or modify the current staging systems eventually, to the authors' knowledge none have yet been evaluated sufficiently to recommend their inclusion in the TNM system.
A geometric method for calibration of the image center (2011)

A geometric approach is proposed to calibrate the image center (also called principle point) of a camera, which is independent of other intrinsic parameters such as the focal length, distortion coefficients, and so on. The basic idea arises from intuitive experience that when the camera moves backward, the path of a static feature point will evolute as a straight line toward the principle point in the image space. The presented method does not require a precise calibration block, and it is insensitive to radical distortion and the variation of focal length. Both linear and nonlinear least square methods are exploited to obtain stable and accurate calibration results. Experiments are conducted to validate the proposed technique.
Preclinical Studies of Lymphocyte Gene Therapy for Mild Hunter Syndrome (Mucopolysaccharidosis Type II) (1996)

To explore the feasibility of ex vivo lymphocyte gene therapy for mild Hunter syndrome (mucopolysaccharidosis type II), we evaluated retrovirus-mediated gene transfer of the iduronate-2-sulfatase (IDS) coding sequence into peripheral blood lymphocytes from enzyme-deficient individuals (PBLMPS). Moloney murine leukemia virus-derived retroviral vectors were constructed by inserting the IDS cDNA under transcriptional regulation of the long terminal repeat (LTR) (in vector L2SN) or the cytomegalovirus (CMV) early promoter (vector LNC2). High-titer virus-producer cells were generated using amphotropic PA317 packaging cells. After 3 days of in vitro stimulation of T lymphocytes with anti-CD3 antibody and interleukin-2 (IL-2), PBLMPS were transduced once on each of the next 3 days. Seven to 21 days later, cultured PBLMPS were evaluated for gene transfer and IDS specific activity. Heterogeneous populations of L2SN-transduced PBLMPS had high levels of IDS enzyme activity (456 U/mg per hr +/- SD 292) despite a gene transfer efficiency of 5% or less. Owing to overexpression of IDS in that percentage of PBLMPS successfully transduced, IDS activity was increased above the deficiency found in patients with Hunter syndrome (< 20 U/mg per hr) to a level comparable with that of normal individuals (mean activity of uncultured normal leukocytes 807 U/mg per hr; SD 252). Reduced 35SO4-glucosaminoglycan (GAG) accumulation was observed in PBLMPS that had been transduced with L2SN, or when PBLMPS were grown in medium that had been "conditioned" by growth of L2SN-transduced cells. This latter result indicated that metabolic cross-correction occurred by means of intercellular enzyme transfer. These studies of retrovirus-mediated expression and metabolic correction, finding near-normal levels of IDS in cultured PBLMPS and metabolic correction, demonstrate the potential for treatment of mild, nonneuropathic Hunter syndrome by means of ex vivo lymphocyte gene therapy.
The inducible expression of dominant-negative epidermal growth factor receptor-CD533 results in radiosensitization of human mammary carcinoma cells. (1999)

Ionizing radiation activates the epidermal growth factor receptor (EGFR) and downstream signaling involving the cytoprotective mitogen-activated protein kinase (MAPK) pathway. In our effort to investigate the role of EGFR in cellular responses to radiation, we generated mammary carcinoma cell clones, MCF-TR5-EGFR-CD533 and MDA-TR15-EGFR-CD533, that inducibly express EGFR-CD533, a truncated EGFR mutant lacking mitogenic and transformation activity. EGFR-CD533 expression inhibits radiation- and EGF-induced EGFR autophosphorylation and MAPK activation and, therefore, functions as a dominant-negative mutant without blocking the expression of EGFR or erbB-2, another member of the erbB receptor Tyr kinase family. Expression of EGFR-CD533 only minimally inhibited cell growth and did not alter radiosensitivity to single radiation exposures. However, repeated 2 Gy radiation exposures of cells, under conditions of EGFR-CD533 expression, essentially abolished their ability for subsequent cell growth. These results identify the inhibition of EGFR function through genetic manipulation as a potential therapeutic maneuver. The concept of such an intervention would be the radiosensitization of cells by counteracting a radiation-induced cytoprotective proliferation response.
Structural Selection in G‐Quartet‐Based Hydrogels and Controlled Release of Bioactive Molecules (2007)

A guanosine-5'-hydrazide can entrap biologically interesting molecules such as acyclovir, vitamin C, and vancomycin into its hydrogel network. Controlled release of these molecules was monitored by 1H NMR spectroscopy. The hydrazide may potentially form mixed G-G quartets with analogous compounds containing a guanine group. 1H NMR spectroscopy was used to study the inclusion of various guanine derivatives into the hydrogel. The structural selectivity was found to depend strongly on both the shape and the charge of the additive and may arise from the strong cohesion of the supramolecular architecture of the gel and the resulting resistance to perturbation by foreign bodies. Hydrogels thus offer a promising medium for highly selective, controlled release of bioactive substances.
In vitro systems for inducers of cartilage and bone development. (1990)

Murine condylar cartilages of perinatal mice were cultured in the form of organ or tissue cultures on top of collagen sponges in medium containing 10% fetal calf serum. Cultures were treated with increasing concentrations of recombinant human growth hormone, recombinant IGF-I, insulin, TGF beta-1, FGF and recombinant fragments of human parathyroid hormone. All the above agents [except for the fragments rPTH (28-48) and (53-84)] were found to be mitogenic as they accelerated the proliferative activity of the condylar stem cells. IGF-I and insulin also stimulated the synthesis of cartilage proteoglycans. Growth hormone also supported de novo osteogenesis in vitro.