gebhart/patrepeval huggingface dataset:
BASIC MORPHOGENETIC SYSTEM MODELING SHAPE CHANGES OF MIGRATING CELLS: HOW TO EXPLAIN FLUCTUATING LAMELLIPODIAL DYNAMICS (1995)

Migration of cells as leukocytes (white blood cells) or keratinocytes (outer epidermic cells) plays an important role in the response of (human) organisms to infections or injuries. When placed on two-dimensional substrata, these cells show extensive protrusions of so-called lamellipods, mostly around the whole cell periphery, inducing characteristic shape changes of the cell outline and subsequent translocation of the cell body. In order to explain the observed lamellipodial dynamics we investigate a "circular" model describing radial extension, L(t, x), of the cell periphery and density, a(t, x), of the underlying cortical polymer layer, consisting of actin and myosin filaments, as well as their contractile activity and their tangential transport velocity v(t, x). The resulting differential equations constitute a system of a non-local hyperbolic transport equation for a on the unit circle combined with a parabolic equation for L. Linear stability analysis as well as numerical simulations provide characteristic "morphogenetic behavior" of this model system, typically showing spatio-temporal patterns with one, two or more protrusions. One important feature of this morphogenetic system on the unit circle is the simple fact that stationary patterns might appear, but are stable only up to rotational shifts. This feature becomes effective, if we introduce stochastic perturbations of the PDE system, e.g. by adding a spatio-temporally correlated Gauss process to the rate term for actin assembly (thought to be induced by fluctuations of bound chemo-receptors which diffuse in the cell membrane). Then, depending on the choice of parameters, typical protrusion patterns transiently appear, or remain but are shifted circumferentially. Characteristic spatio-temporal auto-correlation results for these "model cells" can be compared to corresponding statistical results for "real cells".
Untersuchung der allergenen Prinzipien aus Kolophonium: Autoxidation, Synthese und Sensibilisierung (1992)

Investigation of the Allergenic Principles from Colophony: Autoxidation, Synthesis, and Sensitization The autoxidation of abietic acid ( 1a ), levopimaric acid ( 2a ), and dehydroabietic acid ( 3a ) was studied and the compounds 3a as well as (after esterification) 8b , 9b , 10b , 11b (from 1a ); 6b (from 2a ); and 4b , 5b (from 3a ) were isolated for the first time. Some derivatives ( 6a , 6b , 13b/14b , and 7b ) were semisynthezised. The isolated autoxidation products, the synthetic compounds and some polar fractions of natural colophony were tested for their sensitizing capacity. Compounds 4a, 10b, 16 , and 18 as well as the combined polar fraction A – D of colophony show enhanced sensitizing capacity. Methylation of the acids to the ester significantly reduces their activity.
Software platform virtualization in chemistry research and university teaching (2009)

Software virtualization in chemistry, mass spectrometry and cheminformatics is needed for software testing and development of software for different operating systems. In order to obtain maximum performance the virtualization software should be multi-core enabled and allow the use of multiprocessor configurations in the virtual machine environment. Server consolidation, by running multiple tasks and operating systems on a single physical machine, can lead to lower maintenance and hardware costs especially in small research labs. The use of virtual machines can prevent software virus infections and security breaches when used as a sandbox system for internet access and software testing. Complex software setups can be created with virtual machines and are easily deployed later to multiple computers for hands-on teaching classes. We discuss the popularity of bioinformatics compared to cheminformatics as well as the missing cheminformatics education at universities worldwide.
Endoplasmic Reticulum to Golgi Transport: Methods (2001)

Abstract Newly synthesized cargo proteins translocated into the endoplasmic reticulum (ER) are incorporated into small vesicular carriers that mediate transport to the Golgi, via pre‐Golgi intermediates along microtubule tracks. In vitro assays allow for the examination of factors that are required for and/or regulate the budding of vesicular carriers from the ER and the subsequent fusion of these vesicles with the Golgi.
The Effect of Potential and Temperature on Crevice Corrosion Incubation Time for Stainless Steels in Diluted Chloride Ion Environment (2009)

ステンレス鋼のすきま腐食発生時間tINCUにおよぼす電位と温度の影響を明らかにするために，試験直前に研磨したガラスすきま付き試験片を用いて460 ppm Cl－環境中298 K, 323 Kおよび353 Kの温度で定電位試験を実施した．その結果，いずれの温度においても，卑な電位で電解するほどtINCUは増大し，すきま腐食発生までに必要な電気量QINCUは同一温度であれば電位に対してほぼ一定値となるが，温度が高くなるとQINCUは小さくなる傾向を示した．これは，溶出した金属イオンの加水分解反応速度が温度の上昇にともなって増加しH＋濃度が高くなり，結果的に少ない金属イオン量で脱不動態化pHに達するたかまたは，不動態皮膜の化学的溶解速度が増加するためのどちらか一方または両方と考えられる．また，tINCUが電位依存性をもつ理由としては，すきま腐食発生に至るまでの平均的な金属の溶解電流密度iINCUが貴な電位ほど増大することに起因している．いずれのステンレス鋼とも，温度の上昇とともにtINCUおよびQINCUは低下するが，iINCUは逆に温度の上昇とともに増大した．これらのパラメータをArrheniusプロットし，各種ステンレス鋼のtINCU, iINCUおよびQINCUに関する見かけの活性化エネルギーを求め，すきま腐食発生過程の反応を推定した．
A novel SGCE gene mutation causing myoclonus dystonia in a family with an unusual phenotype (2011)

Abstract Background: Myoclonus dystonia is an autosomal dominant dystonia‐plus syndrome, characterized by symptom variability within families. Most often is the myoclonus the most debilitating symptom, and many patients report myoclonus reduction after alcohol intake. In several families, mutations in the SGCE gene have been identified. Method: We report of a three‐generation family with myoclonus dystonia displaying a varied phenotype and maternal imprinting. Additionally, this family displays some unusual clinical presentations including alcohol‐induced dystonia in an adult man, which will be discussed. Results: A novel mutation c.386T>C [p.I129T] was found within exon 3 of the SGCE gene in all three affected family members. In addition, two additional mutations [c.305G>A and IVS3+15G>A], judged to be polymorphisms in the SGCE gene, were found in two affected and one healthy family member. Conclusions: This report presents a novel mutation in the SGCE gene causing myoclonus dystonia and extends the phenotype of myoclonus dystonia to also include alcohol‐induced dystonia.
Expression of phaseolin cDNA genes in yeast under control of natural plant DNA sequences (1985)

We have constructed a strain of Saccharomyces cerevisiae that expresses two different members of the multigene family encoding phaseolin, the major seed storage glycoprotein from the French bean, Phaseolus vulgaris. Yeast vector plasmids have been engineered to include a Phaseolus DNA segment that contains the natural 5' and 3' plant genomic regulatory sequences flanking a cDNA copy of the protein-encoding region. Characterization of phaseolin transcripts isolated from transformed yeast cells revealed the presence of two classes of polyadenylylated RNA, approximately 1400 and 1800 bases, which initiate and terminate in plant DNA sequences. Protein extracts from transformants contain phaseolin-immunoreactive proteins similar in size to those isolated from plant tissue. These polypeptides are glycosylated in yeast and their molecular weights are consistent with the possibility that the phaseolin signal peptide has been cleaved to form the mature protein.
Abstract B257: Identification of new CYP26 inhibitors with efficacy in breast cancer xenograft models. (2013)

Abstract Retinoids, such as the prototypical retinoid all trans retinoic acid (ATRA), have been used successfully in the treatment of acute promyelocytic leukemia (APL) patients. They have also been tested for efficacy in solid tumors, including breast cancer. Despite promising preclinical data, the clinical success of using ATRA for breast cancer patients has been limited so far. We hypothesize that this is largely due to three factors: (1) a lack of understanding of the patient population that is likely to respond to retinoid therapy, (2) a significant induction of retinoic acid metabolism with retinoid therapy, resulting in sub-optimal retinoid exposure in tumors and (3) the narrow therapeutic index of ATRA. Several recent studies indicate that breast cancer cells that express the Retinoic Acid Receptor Alpha (RARA) are more likely to respond to retinoic acid than cells without RARA expression. This provides a rationale for selection of patients that are likely to benefit from retinoid therapy in future clinical trials. The cytochrome P450 enzyme CYP26 is the key enzyme involved in ATRA metabolism. CYP26A1 expression is elevated in breast cancer tissue compared to normal tissue and CYP26A1 expression is negatively correlated with patient survival. Angion has identified orally bioavailable small molecule inhibitors of CYP26. Angion's lead inhibitor blocks retinoid metabolism in tumor cells and enhances serum and tumor retinoic acid levels. The compound shows robust single agent efficacy in several murine breast cancer xenograft models. By elevating endogenous serum and tumor retinoic acid levels in a physiological range, CYP26 inhibition therapy is likely to result in a better therapeutic index than systemic retinoid therapy. The identification of orally bioavailable, potent, and selective CYP26 inhibitors eliminates two major drawbacks of systemic retinoid therapy, and– in combination with new insights in selecting patients that are more likely to respond to retinoid therapy– may provide a new impetus for evaluation of retinoic acid signaling modulators as a treatment for breast cancer patients. Citation Information: Mol Cancer Ther 2013;12(11 Suppl):B257. Citation Format: Bert Oehlen, Gaifeng Ma, Siobhan McCormack, Dong Sung Lim, Jim Tarrant, Xiaokang Zhu, Bijoy Panicker, Itzhak D. Goldberg. Identification of new CYP26 inhibitors with efficacy in breast cancer xenograft models. [abstract]. In: Proceedings of the AACR-NCI-EORTC International Conference: Molecular Targets and Cancer Therapeutics; 2013 Oct 19-23; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2013;12(11 Suppl):Abstract nr B257.
A mechanistic kinetic model for the initiated anionic polymerization ofϵ‐caprolactam (1986)

Abstract The preparation of Nylon‐6 via the initiated anionic polymerization of EE‐caprolactam is characterized by rapid reaction rates displaying marked auto‐acceleration. A mechanistic approach has been taken to analyze the kinetics of this system and has resulted in the postulation that the auto‐acceleration is directly linked to a polymer chain degradation reaction. This reaction is significant even in the early stages of the polymerization and in many cases becomes the dominant mechanism for the production of reactive end groups, thereby controlling the overall reaction rate. A kinetic model is presented which is capable of differentiating between polymerizations carried out with different levels and ratios of catalyst and initiator, and contains but two rate constants—one for the propagation reaction and one for the degradation reaction. Predictions of the model are compared to experimental rate data derived from using both mono‐and difunctional initiators and close agreement is found.
Stereocontrolled Total Synthesis of (+)‐1‐Deoxynojirimycin (2009)

Abstract A highly efficient non‐chiral‐pool synthesis of (+)‐1‐deoxynojirimycin has been realized (24 % overall yield, 11 steps, complete stereocontrol). A novel one‐pot enol ether metathesis/hydroboration/oxidation sequence is used for the selective formation of the all‐ trans cyclic triol. (© Wiley‐VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009)
A Linear Time Active Learning Algorithm for Link Classification -- Full\n Version -- (2013)

We present very efficient active learning algorithms for link classification\nin signed networks. Our algorithms are motivated by a stochastic model in which\nedge labels are obtained through perturbations of a initial sign assignment\nconsistent with a two-clustering of the nodes. We provide a theoretical\nanalysis within this model, showing that we can achieve an optimal (to whithin\na constant factor) number of mistakes on any graph G = (V,E) such that |E| =\n\\Omega(|V|^{3/2}) by querying O(|V|^{3/2}) edge labels. More generally, we show\nan algorithm that achieves optimality to within a factor of O(k) by querying at\nmost order of |V| + (|V|/k)^{3/2} edge labels. The running time of this\nalgorithm is at most of order |E| + |V|\\log|V|.\n
Targeting amphiregulin (AREG) derived from senescent stromal cells diminishes cancer resistance and averts programmed cell death 1 ligand (PD‐L1)‐mediated immunosuppression (2019)

Aging is characterized by a progressive loss of physiological integrity, while cancer represents one of the primary pathological factors that severely threaten human lifespan and healthspan. In clinical oncology, drug resistance limits the efficacy of most anticancer treatments, and identification of major mechanisms remains a key to solve this challenging issue. Here, we highlight the multifaceted senescence-associated secretory phenotype (SASP), which comprises numerous soluble factors including amphiregulin (AREG). Production of AREG is triggered by DNA damage to stromal cells, which passively enter senescence in the tumor microenvironment (TME), a process that remarkably enhances cancer malignancy including acquired resistance mediated by EGFR. Furthermore, paracrine AREG induces programmed cell death 1 ligand (PD-L1) expression in recipient cancer cells and creates an immunosuppressive TME via immune checkpoint activation against cytotoxic lymphocytes. Targeting AREG not only minimized chemoresistance of cancer cells, but also restored immunocompetency when combined with classical chemotherapy in humanized animals. Our study underscores the potential of in vivo SASP in driving the TME-mediated drug resistance and shaping an immunosuppressive niche, and provides the proof of principle of targeting major SASP factors to improve therapeutic outcome in cancer medicine, the success of which can substantially reduce aging-related morbidity and mortality.
Electro-Thermal Modelling of High Power Light Emitting Diodes Based on Experimental Device Characterisation (2008)

This paper presents a 3D finite element model for the electro-thermal analysis of high power light emitting diodes (LEDs). The proposed model and implementation approach require basic electrical and optical parameters that may be experimentally derived with the aid of advanced post-processing techniques. Extensive experimental validation reveals the capability of the model to accurately simulate self-heating, current crowding, forward voltage and other relevant performance indicators.
Langmuir Studies of the Sublimation of Strontium Fluoride and Barium Fluoride Single Crystals (1965)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTLangmuir Studies of the Sublimation of Strontium Fluoride and Barium Fluoride Single CrystalsRenato G. Bautista and John L. MargraveCite this: J. Phys. Chem. 1965, 69, 5, 1770–1771Publication Date (Print):May 1, 1965Publication History Published online1 May 2002Published inissue 1 May 1965https://pubs.acs.org/doi/10.1021/j100889a518https://doi.org/10.1021/j100889a518research-articleACS PublicationsRequest reuse permissionsArticle Views59Altmetric-Citations4LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Chemosensitivity and DNA repair in BRCA1 deficient murine mammary epithelial cells (2005)

Proc Amer Assoc Cancer Res, Volume 46, 2005

4390 

Breast cancer is the second leading cause of cancer death among US women. Inherited mutations in the BRCA1 tumor suppressor gene result in a 50-85% lifetime risk for developing breast cancer and an increased risk for ovarian and prostate cancer. While these germline mutation carriers account for 5% of breast cancer cases, emerging evidence suggests that up to 30% of sporadic breast cancers exhibit epigenetic silencing of BRCA1 by promoter hypermethylation and other mechanisms. These BRCA1 associated tumors are frequently estrogen receptor (ER) negative and often carry mutations of the p53 tumor suppressor protein. The lack of ER renders BRCA1 deficient cancers ineffective targets of hormonal manipulations, therefore making chemotherapy the only treatment option available to patients with metastatic disease. The BRCA1 protein has been implicated in many cellular processes, yet its specific mechanism of tumor suppression remains unclear. BRCA1 plays a role in several DNA repair pathways including nucleotide excision repair (NER). We have demonstrated, by an MTT chemosensitivity assay, that Brca1 deficient murine mammary epithelial cells (MMECs) are 3-fold more sensitive to ultraviolet-C (UV-C) radiation, 10-fold more sensitive to cisplatin, and 25-fold more sensitive to gemcitabine chemotherapy than the isogenic, Brca1 positive parental cell line. In addition, Brca1 deficient cells demonstrate decreased repair of UV-C induced cyclobutane pyrimidine dimers in genomic DNA. Loss of Brca1 expression leads to blunted UV-C induced expression of the damaged-DNA binding proteins xeroderma pigmentosum complementation group C (XPC), but not DDB2, which is mutated in xeroderma pigmentosum complementation group E (XPE). These results confirm our earlier findings that Brca1 is involved in global genomic NER, and affects this process through regulation of DNA damage recognition protein gene expression. In addition, the altered chemosensitivity observed in BRCA1 deficient cells raises the possibility that individuals with BRCA1 deficient cancers may benefit from treatment with agents not traditionally used to treat breast cancer.
Quantification of Human Herpesvirus 6 in Immunocompetent Persons and Post-mortem Tissues from AIDS Patients by PCR (1996)

A quantitative competitive PCR assay for human herpesvirus 6 (HHV-6) was developed. Firstly, viral burden was determined in the blood of 25 healthy persons. Using 1 microgram of DNA, the prevalence of HHV-6 was 36% (9/25). Eight persons had viral loads of < or = 32 HHV-6 genomes/microgram DNA. The viral burden in the ninth individual was 1.2 x 10(6) HHV-6 genome copies/microgram DNA, which remained constant over a period of 10 months. This demonstrates the persistence of a high HHV-6 load in the absence of apparent disease. Secondly, HHV-6 burden was determined in 100 post-mortem tissues from seven AIDS patients and three controls. For all tissues combined, there was a statistically significant higher median viral load in AIDS patients (56 copies/microgram DNA, range 0-43321) compared to controls (10 copies/microgram DNA, range 0-423) (P = 0.04). The precision and reproducibility of this assay will allow hypotheses concerning the pathogenic potential of HHV-6 to be tested quantitatively.
Formation of Bile Acids from Cholesterol in the Rabbit: Bile Acids and Steroids 29 (1955)

Summary. The conversion of cholesterol into desoxycholic and cholic acids in a rabbit has been demonstrated. These acids are excreted in the bile mainly as conjugates with glycine. Fractionation of the labeled material excreted in the farces after the administration of labeled cholesterol has shown that no glycocholicorglyco‐desoxycholic acid was present. Several unidentified compounds have been formed, presumably by the action of intestinal microorganisms.
Elastohydrodynamic Line-Contact of Compressible Shear Thinning Fluids With Consideration of the Surface Roughness (2010)

Applications involving highly loaded elastohydrodynamic lubrication (EHL), particularly when the lubricant experiences shear thinning, operating with small film thicknesses may necessitate consideration of surface asperities. A modified Reynolds equation with provision for surface roughness and shear thinning is treated to predict the pressure and surface asperity effect in an EHL line-contact. The unknown in the Reynolds equation is the hydrodynamic pressure instead of the total pressure to ensure that the pressure boundary condition at the outlet is properly posed. The Carreau viscosity model is used for characterizing the shear thinning behavior, Patir and Cheng flow factors for taking into the influence of roughness on the lubricating film, and Greenwood–Trip for determination of pressure at the asperity level. The modified Reynolds equation is solved for the hydrodynamic pressure instead of the total pressure with appropriately defined boundary conditions.
Exciton interaction in the photosystem I reaction center from spinach chloroplasts. Absorption and circular dichroism difference spectra (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTExciton interaction in the photosystem I reaction center from spinach chloroplasts. Absorption and circular dichroism difference spectraKenneth D. Philipson, Vicki L. Sato, and Kenneth SauerCite this: Biochemistry 1972, 11, 24, 4591–4595Publication Date (Print):November 1, 1972Publication History Published online1 May 2002Published inissue 1 November 1972https://pubs.acs.org/doi/10.1021/bi00774a027https://doi.org/10.1021/bi00774a027research-articleACS PublicationsRequest reuse permissionsArticle Views168Altmetric-Citations67LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Hierarchy of spin and valley symmetry breaking in quantum Hall single-layer graphene (2010)

Several microscopic mechanisms for breaking the fourfold degeneracy of the central Landau level in a single-layer graphene is examined. We consider valley-scattering random potential, Zeeman interaction, and electron-phonon coupling as potential candidates to break the SU(4) symmetry of the Coulomb exchange interaction. A phase diagram is worked out, giving either the ``spin-first'' or ``valley-first'' splitting of the central Landau levels depending on the relative strengths of the electron-phonon coupling and the Zeeman interaction. Existence of a midgap band at the domain wall separating Landau levels of opposite valley polarity is demonstrated.