gebhart/patrepeval huggingface dataset:
Design of a slot array with perturbation walls for an alternating-phase fed single-layer waveguide array (2008)

This paper presents design of the slot array for grating lobe suppression. The slots arrayed at the center of the radiating waveguide are excited by the inductive wall, while the reflection from each slot is canceled out by the capacitive wall. Slot coupling and the condition of the reflection canceling are analyzed by using Ansoft HFSS. Then, the 16-slot array is designed at 25.33 GHz. Uniform aperture distribution and broadside radiation of the array is confirmed.
Inhibition of Antiapoptotic BCL-XL, BCL-2, and MCL-1 Proteins by Small Molecule Mimetics (2010)

Informatics and computational design methods were used to create new molecules that could potentially bind antiapoptotic proteins, thus promoting death of cancer cells. Apoptosis is a cellular process that leads to the death of damaged cells. Its malfunction can cause cancer and poor response to conventional chemotherapy. After being activated by cellular stress signals, proapoptotic proteins bind antiapoptotic proteins, thus allowing apoptosis to go forward. An excess of antiapoptotic proteins can prevent apoptosis. Designed molecules that mimic the roles of proapoptotic proteins can promote the death of cancer cells. The goal of our study was to create new putative mimetics that could simultaneously bind several antiapoptotic proteins. Five new small molecules were designed that formed stable complexes with BCL-2, BCL-XL, and MCL-1 antiapoptotic proteins. These results are novel because, to our knowledge, there are not many, if any, small molecules known to bind all three proteins. Drug-likeness studies performed on the designed molecules, as well as previous experimental and preclinical studies on similar agents, strongly suggest that the designed molecules may indeed be promising drug candidates. All five molecules showed "drug-like" properties and had overall drug-likeness scores between 81% and 96%. A single drug based on these mimetics should cost less and cause fewer side effects than a combination of drugs each aimed at a single protein. Computer-based molecular design promises to accelerate drug research by predicting potential effectiveness of designed molecules prior to laborious experiments and costly preclinical trials.
Molecular Sensors of Estrogen Receptor Conformations and Dynamics (2003)

The ligand-induced conformation of a nuclear receptor ligand-binding domain (LBD) is a principal factor leading to transcriptional activity and determining the pharmacological response. Using the estrogen receptor (ER) LBD-labeled site specifically with a fluorophore, we demonstrate that effects of ligand binding on the conformation and dynamics of this domain can be studied directly, in a quantitative and convenient fashion, by various fluorescence methods. Estrogen ligands of different pharmacological character-agonists, selective ER modulators (SERMs), and pure antagonists-each produce distinctive spectroscopic signatures, characteristic of the conformational or dynamic features of their ER-LBD complexes. We can directly follow the equilibrium of helix 12 positions through the degree of local fluorophore rotational freedom and receptor helicity near the C terminus of helix 11. We observe differences even between ligands within a specific pharmacological class, such as the SERMs raloxifene and trans-4-hydroxytamoxifen, highlighting the ability of these fluorescent receptor sensors to detect unique ER conformations induced even by closely related ligands, yet ones that produce distinctive biological activities in estrogen target cells. Fluorophore-labeled LBDs can serve as versatile molecular sensors predictive of ligand pharmacological character and should be broadly applicable to other members of the nuclear receptor superfamily.
<title>Self-aligned double and quadruple patterning layout principle</title> (2012)

Self-Aligned Double Patterning (SADP) has become one of the most promising processes for 20nm node technology and beyond. Despite its robustness against overlay, it is a challenging process for designers since predicting the wafer image instantly is almost impossible. Self-Aligned Quadruple Patterning (SAQP) is also critical technology for sub-10nm process but more complex than SADP, so it is too difficult to design a layout intuitively. Needless to say designing layout by applying N times sidewalls intuitively is impossible for almost everyone. In this paper, we clarify a new intuitive principle for SADP layout. The principle uses "Base patterns" painted in different two colors interchangeably. The proposed method enables us to design SADP layout simply by connecting and cutting fundamental pattern arbitrarily with a few restrictions. Another benefit is that either of two colors in the pattern can be used as mandrel. We can apply the principle to not only SAQP but also N times sidewall processes. Considering these advantages, layout formed by sidewall process becomes designer-friendly.
Effect of hypoosmotic stress on hybridoma cell growth and antibody production (1997)

To investigate the response of hybridoma cells to hypoosmotic stress, S3H5/gamma2bA2 and DB9G8 hybridomas were cultivated in the hypoosmolar medium [Dulbecco's modified Eagle's medium (DMEM) supplemented with 10% serum] resulting from sodium chloride subtraction. Both hybridomas showed similar responses to hypoosmotic stress in regard to cell growth and antibody production. The cell growth and antibody production at 276 mOsm/kg were comparable to those at 329 mOsm/kg (standard DMEM). Both cells grew well at 219 mOsm/kg, though their growth and antibody production were slightly decreased. When the osmolality was further decreased to 168 mOsm/kg, the cell growth did not occur. When subjected to hyperosmotic stress, both cells displayed significantly enhanced specific antibody productivity (q(Ab)). However, the cells subjected to hypoosmotic stress did not display enhanced q(Ab). Taken together, both hyperosmotic and hypoosmotic stresses depressed the growth of S3H5/gamma2bA2 and DB9G8 hybridomas. However, their response to hypoosmotic stress in regard to q(Ab) was different from that to hyperosmotic stress.
Co-effect of silk and amniotic membrane for tendon repair (2016)

The objective of the present study was to determine the feasibility and biocompatibility of a silk scaffold and a composite silk scaffold in terms of new tendon generation using a rabbit Achilles tendon model. The silk scaffold was constructed using a weaving machine, then soaked in a 1% collagen-hyaluronan (HA) solution and air-dried, whereas the composite silk scaffold was composed of a silk scaffold containing a lyophilized collagen-HA substrate. Tenocytes were cultured in vitro to compare cell populations in the two groups. The cellular densities on composite silk scaffolds were 40% higher on average than those on silk scaffolds in 30-day tenocyte cultures. The tendon scaffolds had implanted into Achilles tendon defects in 16 white New Zealand rabbits. Rabbits were randomly divided into the following three groups: group I, silk scaffold alone; group II, composite silk scaffold; and group III, composite silk scaffold wrapped by an amniotic membrane. Implants were harvested 2, 8, and 12 weeks post-implantation. Histological examinations were conducted using hematoxylin-eosin (H&E), Masson's trichrome, and by performing immunohistochemical staining for CD34. After 12 weeks, the three groups were distinguishable based on gross examination. The histological examination revealed more organized collagen fibrils in groups III, which showed a dense, parallel, linear organization of collagen bundles. CD34 staining revealed neoangiogenesis in groups III. The results of this research showed that collagen-HA substrates with amniotic membrane accelerate cellular migration and angiogenesis in neotendons.
The molecular defect of ferrochelatase in a patient with erythropoietic protoporphyria. (1992)

The molecular basis of an inherited defect of ferrochelatase in a patient with erythropoietic protoporphyria (EPP) was investigated. Ferrochelatase is the terminal enzyme in the heme biosynthetic pathway and catalyzes the insertion of ferrous iron into protoporphyrin IX to form heme. In Epstein-Barr virus-transformed lymphoblastoid cells from a proband with EPP, enzyme activity, an immunochemically quantifiable protein, and mRNA content of ferrochelatase were about one-half the normal level. In contrast, the rate of transcription of ferrochelatase mRNA in the proband's cells was normal, suggesting that decreased ferrochelatase mRNA is due to an unstable transcript. cDNA clones encoding ferrochelatase in the proband, isolated by amplification using the polymerase chain reaction, were found to be classified either into those encoding the normal protein or into those encoding an abnormal protein that lacked exon 2 of the ferrochelatase gene, indicating that the proband is heterozygous for the ferrochelatase defect. Genomic DNA analysis revealed that the abnormal allele had a point mutation, C----T, near the acceptor site of intron 1. This point mutation appears to be responsible for the post-transcriptional splicing abnormality resulting in an aberrant transcript of ferrochelatase in this patient.
Maximum entropy and conditional probability (1981)

It is well-known that maximum entropy distributions, subject to appropriate moment constraints, arise in physics and mathematics. In an attempt to find a physical reason for the appearance of maximum entropy distributions, the following theorem is offered. The conditional distribution of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X_{l}</tex> given the empirical observation <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">(1/n)\sum^{n}_{i}=_{l}h(X_{i})=\alpha</tex> , where <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X_{1},X_{2}, \cdots</tex> are independent identically distributed random variables with common density <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</tex> converges to <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">f_{\lambda}(x)=e^{\lambda^{t}h(X)}g(x)</tex> (Suitably normalized), where <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\lambda</tex> is chosen to satisfy <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">\int f_{lambda}(x)h(x)dx= \alpha</tex> . Thus the conditional distribution of a given random variable <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">X</tex> is the (normalized) product of the maximum entropy distribution and the initial distribution. This distribution is the maximum entropy distribution when <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">g</tex> is uniform. The proof of this and related results relies heavily on the work of Zabell and Lanford.
Direct wafer temperature measurements for etch chamber diagnostics and process control (2003)

It is well known that wafer temperature has significant impact on plasma etching performance. Instability of (peak) wafer temperatures during process can be linked to such issues as post-metal etch residues, undercut or sloping sidewall profiles and inconsistent photoresist selectivity. Direct wafer temperature measurements can yield valuable diagnostic information. This information can be used to characterize the process as well as to improve process control. This paper presents two direct wafer measurement techniques which when used in combination can be powerful tools for chamber diagnostics, tool to tool matching, as well as process control in a production environment. Real time, in situ wafer temperature measurement using a thermal optical system is used to understand the effect of process parameters such as backside He cooling, RF power and gas flows on wafer temperature and temperature uniformity. This data is then correlated to measurements from a novel technique employing arrays of peak temperature indicators mounted on a single-use-instrumented wafer. The latter technique is ideal for quick chamber qualifications and day to day process control while the former can be used for more detailed chamber diagnostics and analysis of the thermal cycle during the etch process.
Design of “Smart” polymers that can direct intracellular drug delivery (2002)

Abstract One of the important characteristics of biological systems is their ability to change important properties in response to small environmental signals. The molecular mechanisms that biological molecules utilize to sense and respond provide interesting models for the development of “smart” polymeric biomaterials with biomimetic properties. An important example of this is the protein coat of viruses, which contains peptide units that facilitate the trafficking of the virus into the cell via endocytosis, followed by delivery of the genetic material out of the endosome into the cytoplasm, and from there into the nucleus. We have designed several new types of synthetic polymers to facilitate intracellular trafficking of drugs. One of these has been designed to mimic the specific peptides on viral coats that facilitate endosomal escape. Another has been designed to contain pH‐degradable bonds, facilitating endosomal escape of the drug only after the bonds are degraded at the acidic pHs of the endosomes. Both types of polymer are responsive to the lowered pH within endosomes, leading to disruption of the endosomal membrane and release of important biomolecular drugs such as DNA, RNA, peptides and proteins to the cytoplasm before they are trafficked to lysosomes and degraded by lysosomal enzymes. In this article, we review our work on the design, synthesis and action of such smart, pH‐sensitive polymers. Copyright © 2003 John Wiley & Sons, Ltd.
CEA-specificity of CEA-reactive monoclonal antibodies. Immunochemical and immunocytochemical studies. (1986)

Four carcinoembryonic antigen (CEA) reactive monoclonal antibodies Parlam 1, 4, 5 and 6 were studied in respect to reactivity with CEA and its cross-reacting antigens (NCA-1, NCA-2, BGP). In immunochemical studies (ELISA and SDS-PAGE followed by immunoblotting) Parlam 4 did not react with these crossreacting antigens, whereas Parlam 1, 5, and 6 demonstrated variable reactivity with these antigens. As expected, by immunocytochemistry Parlam 1, 5, and 6 stained bile canaliculi in the liver (due to crossreactivity with BGP), pneumocytes and splenic tissue (NCA-1) to an extent comparable with the results in biochemical tests. In contrast with the immunochemical observations, however, Parlam 4 showed slight but distinct reactivity with splenic granulocytes (NCA-1) and hepatic bile canaliculi (BGP). Relative epitope specificity of the monoclonal antibodies was tested in blocking experiments. These showed that Parlam 1 and 5 detect the same epitope on CEA as they block each others binding completely. In other combinations monoclonal antibodies block each others binding only partially, indicating that they detect different or partially overlapping epitopes. These results suggest that CEA specific epitopes may partly overlap with epitopes on crossreacting antigens. In this context, we propose that on crossreacting antigens epitopes exist that are structurally similar to epitopes on CEA or that some epitopes on CEA may consist of a spatial configuration which involves CEA specific as well as non-CEA specific structures. The antibody will show the highest affinity towards CEA, as this molecule contains the uniquely matching or complete epitope and lower affinity towards the crossreacting antigen with an imperfectly matching or only partially available epitope.
Use of basiliximab as a cyclosporin-sparing agent in palmoplantar pustular psoriasis with myalgia as an adverse effect (2002)

British Journal of DermatologyVolume 147, Issue 3 p. 606-607 Use of basiliximab as a cyclosporin-sparing agent in palmoplantar pustular psoriasis with myalgia as an adverse effect H.K. Bell, H.K. Bell Department of Dermatology, Link 10 C, Royal Liverpool University Hospital, Prescot Street, Liverpool L7 8XP, U.K.Search for more papers by this authorR.A.G. Parslew, R.A.G. Parslew Department of Dermatology, Link 10 C, Royal Liverpool University Hospital, Prescot Street, Liverpool L7 8XP, U.K.Search for more papers by this author H.K. Bell, H.K. Bell Department of Dermatology, Link 10 C, Royal Liverpool University Hospital, Prescot Street, Liverpool L7 8XP, U.K.Search for more papers by this authorR.A.G. Parslew, R.A.G. Parslew Department of Dermatology, Link 10 C, Royal Liverpool University Hospital, Prescot Street, Liverpool L7 8XP, U.K.Search for more papers by this author First published: 04 October 2002 https://doi.org/10.1046/j.1365-2133.2002.48452.xCitations: 12 Correspondence: Dr Hazel Bell. E-mail: fam.shaw@virgin.net Read the full textAboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume147, Issue3September 2002Pages 606-607 RelatedInformation
Variability and Prognostic Values of Virologic and CD4 Cell Measures in Human Immunodeficiency Virus Type 1‐Infected Patients with 200–500 CD4 Cells/mm<sup>3</sup>(ACTG 175) (1998)

Virologic measurements are increasingly used to evaluate prognosis and treatment responses in human immunodeficiency virus (HIV) type 1 infection. Markers of HIV-1 replication, including infectious HIV-1 titer from peripheral blood mononuclear cells, serum HIV-1 p24 antigen, plasma HIV-1 RNA, CD4 cell numbers, and viral syncytium-inducing (SI) phenotype, were determined in 391 virology substudy participants in AIDS Clinical Trials Group study 175. The subjects had 200-500 CD4 cells/mm3. All markers of viral replication significantly correlated with one another and were inversely related to CD4 cell number. Disease progression to an AIDS-defining event or death or loss of >50% of CD4 cells was associated with infectious HIV-1 titer (P < .001), HIV-1 RNA (P < .001), and HIV-1 p24 antigen (P = .007). In multivariate proportional hazards models, p24 antigen was never significant when HIV-1 RNA level was included. In a model containing infectious HIV-1 titer (P = .038), HIV-1 RNA (P < .001), SI phenotype (P < .001), and CD4 cell number (P = .18), only the virologic parameters remained significantly associated with progression.
IscR‐dependent gene expression links iron‐sulphur cluster assembly to the control of O <sub>2</sub> ‐regulated genes in <i>Escherichia coli</i> (2006)

IscR is an iron-sulphur (Fe-S) cluster-containing transcription factor that represses transcription of the operon containing its own gene and the iscSUA-hscBA-fdx genes, whose products are involved in Fe-S cluster biogenesis. In this study, global transcriptional profiling of Escherichia coli IscR(+) and IscR(-) strains grown under aerobic and anaerobic conditions indicated that 40 genes in 20 predicted operons were regulated by IscR. DNase I footprinting and/or in vitro transcription reactions identified seven new promoters under direct IscR control. Among these were genes encoding known or proposed functions in Fe-S cluster biogenesis (sufABCDSE, yadR and yhgI) and Fe-S cluster-containing anaerobic respiratory enzymes (hyaABCDEF, hybOABCDEFG and napFDAGHBC). The finding that IscR repressed expression of the hyaA, hybO and napF promoters specifically under aerobic growth conditions suggests a new mechanism to explain their upregulation under anaerobic growth conditions. Phylogenetic footprinting of the DNase I protected regions of seven promoters implies that there are at least two different classes of IscR binding sites conserved among many bacteria. The findings presented here indicate a more general role of IscR in the regulation of Fe-S cluster biogenesis and that IscR contributes to the O(2) regulation of several promoters controlling the expression of anaerobic Fe-S proteins.
Content of <b><i>trans,trans</i></b>‐2,4‐decadienal in deep‐fried and pan‐fried potatoes (2006)

Abstract Trans , trans ‐2,4‐decadienal is a by‐product of frying oil that is also transferred to fried food. This aldehyde has been found and quantified both in frying oils and fumes generated during frying. Furthermore, it has been reported that 2,4‐decadienal has cytotoxic and genotoxic effects and promotes LDL oxidation. In the present work trans , trans ‐2,4‐decadienal was detected directly in fried potatoes (french‐fries). Moreover, the influence of frying conditions (deep‐frying, pan‐frying), the oil type (olive oil, sunflower oil, cottonseed oil, palm oil and a vegetable shortening) and the degree of thermal deterioration (eight successive frying sessions without replenishment) on the production of 2,4‐decadienal in oil and potatoes was studied. The isolation of the aldehyde was performed by methanol extraction, while the identification and quantification was performed by RP‐HPLC. The quantity of trans , trans ‐2,4‐decadienal produced during successive pan‐frying demonstrated a peak at the third and fourth frying session. The highest concentration of trans , trans ‐2,4‐decadienal was detected in potatoes fried in sunflower oil, and the lowest in olive oil. The quantity of trans , trans ‐2,4‐decadienal in fried potatoes decreased during successive deep‐frying at the seventh frying session or remained stable, except for cottonseed oil. The quantity of trans , trans ‐2,4‐decadienal in fried potatoes was considered to be dependent on the oil used, on the frying process and, to a lesser extent, on the oil deterioration. In all cases tested, the highest concentration of trans , trans ‐2,4‐decadienal was detected during deep‐frying. The unsaturation degree of the frying oil was considered to promote the formation of trans , trans ‐2,4‐decadienal. Considering the quantity of 2,4‐decadienal found in french‐fries and in the respective frying medium, direct quantification of 2,4‐decadienal is required in order to make an estimation of intake from french‐fries.
Detection of and compensation for shadows in colored urban aerial images (2004)

A new method for shadow detection in colored urban aerial images is proposed. First, a new imaging model of shadows is presented, which indicates that hue values of shadowed image areas are larger than those of these areas non-shadowed. Based on this model, a thresholding technique is employed to detect shadowed areas. After detection, the Retinex technique is applied to shadowed and non-shadowed areas individually to compensate for shadows. Experiment results show the effectiveness of the proposed method.
In situ identification of allospecific B cells using pentamers (2008)

To the editor:

We recently published a report in Blood documenting that, in allosensitized murine recipients, preformed antibody is the initial barrier to bone marrow engraftment.[1][1] We now demonstrate a novel method to detect alloantibody secreting cells in situ in our allosensitization model