gebhart/patrepeval huggingface dataset:
Biochip for K-ras Mutation Screening in Ovarian Cancer (2005)

Ovarian carcinoma is the fifth most common female cancer type and the most common cause of death from gynecologic malignancies in the Western world (1). The three members of the ras gene family, H- ras , K- ras , and N- ras , are among the most common oncogenes associated with human neoplasms (2). Mutations in the K- ras gene are frequently found in malignant neoplasms: 90% of adenocarcinomas of the pancreas; 50% of colon, 30% of lung, and 50% of thyroid tumors; and 30% of myeloid leukemia cases, respectively (3). K- ras -activating mutations occur in codons 12 and 13 and seldom in codon 61, and lead to constitutive activation of the protein by increasing GDP/GTP exchange or decreasing GTPase activity of the protein, thus leading to increased cell proliferation.

K- ras mutation frequencies seem to be highly related to tumor histology. In general, K- ras mutations occur more frequently in mucinous tumors, including borderline malignancies, than in nonmucinous tumors such as serous carcinomas (4)(5)(6)(7)(8). K- ras mutations are more common in borderline serous tumors than in serous carcinomas, suggesting distinct etiologies (5)(9)(10)(11).

A biochip application for detection of the 10 most common mutations of K- ras codons 12 and 13 (12) combines mutant-enriched amplification with a highly specific hybridization protocol. The chip appears suitable for the detection of K- ras mutations in human feces (12). An improved biochip platform, called GeneStiX (ViennaLab Labordiagnostika GmbH), is designed to meet the needs of molecular diagnostic applications. Up to 400 different DNA capture oligonucleotides can be immobilized on the tip of a special plastic stick contained in a cylindrical tube. This allows hybridization with low volumes in a closed system (tube) and the use of standard …
ChemInform Abstract: A NEW REAGENT FOR THE SELECTIVE, HIGH‐YIELD N‐DEALKYLATION OF TERTIARY AMINES: IMPROVED SYNTHESES OF NALTREXONE AND NALBUPHINE (1984)

Abstract Mit Hilfe von α‐Chlorethyloxy‐ carbonylchlorid (III) lassen sich tertiäre Amine wie (IV) über die Zwischenstufe der Carbamate (V) zu sekundären Aminen (VI) dealkylieren.
Synthesis and Antitumor Activity of Combretastatin Analogues (2011)

Plants, source of various bioactive compounds have played crucial role in development of several clinically useful anticancer agents’ viz., vincristin, vinblastin, camptothecin derivatives and taxol. Combretastatin, a potent anticancer molecule was first isolated from plant. In this continuation a series of combretastatin analogues has been synthesized on the basis of our butterfly model with two wings as aryl groups and connecting carbon chain as the body. In present study we have synthesized combretastatin analogues of different substitutions, showed potent anticancer activity against different cell lines in different fashion according to substitution. Compound 6 showed marked anticancer activity against colo-205 cell lines (colon cancer).
Targeting mediators of vascular injury in scleroderma (2002)

Increasing evidence suggests that the vasculopathy of scleroderma is mediated by a number of soluble factors and involves a complex interaction between endothelial cells, smooth muscle cells, extracellular matrix, intravascular coagulation factors, and circulating cells. Novel therapeutic approaches beyond vasodilator therapy are being developed by recognizing important molecular pathways involved in scleroderma vascular disease. The success of this strategy is most evident in pulmonary hypertension, an often fatal complication of scleroderma. In this article, the authors explore therapies for scleroderma that target endothelial cells, smooth muscle cells, reactive oxygen species, and circulating blood cells. The authors highlight clinical trials that have investigated the role of prostacyclin (and its analogues) and bosentan in managing scleroderma-related pulmonary hypertension. Finally, the authors look at the potential role of biomarkers as surrogate indicators of active vascular disease in scleroderma.
Nonlinear Shape Regression for Filtering Segmentation Results from Calcium Imaging (2018)

A shape filter is presented to repair segmentation results obtained in calcium imaging of neurons in vivo. This post-segmentation algorithm can automatically smooth the shapes obtained from a preliminary segmentation, while precluding the cases where two neurons are counted as one combined component. The shape filter is realized using a square-root velocity to project the shapes on a shape manifold in which distances between shapes are based on elastic changes. Two data-driven weighting methods are proposed to achieve a trade-off between shape smoothness and consistency with the data. Intuitive comparisons of proposed methods via projection onto Cartesian maps demonstrate the smoothing ability of the shape filter. Quantitative measures also prove the superiority of our methods over models that do not employ any weighting criterion.
The phase composition and workability of electrodeposited Fe-Zn alloy. (1983)

Electrodeposited Fe-Zn alloy was studied with respect to the phase composition and workability.(1) The phase composition was investigated in the range of 10-30% Fe. The η phase was a main phase up to 13% Fe and extended further to 20% Fe. The δ1 phase appeared from 10% Fe and became a main phase in the range of 13-20% Fe. The δ1 phase was present up to 28% Fe. The Γ phase appeared from 10% Fe, but remained to a small extent up to 15% Fe. The Γ phase became a main phase in the range over 21% Fe and the sole one observed in the range over 28% Fe.(2) Depending on the bath used, different phase compositions which contain the same Fe in ehe deposit were found.(3) The phase composition determined workability of the deposit, which was evaluated in terms of draw bead test. The η phase exhibited good workability. In contrast, the δ1+Γ phases lowered the workability of the deposit. Since the presence of the η phase improves workability, it is desirable that the deposit contains the η phase to some extent from the viewpoint of workability.
Effects of tobacco glycoprotein (TGP) on the immune system. I. TGP is a T-independent B cell mitogen for murine lymphoid cells. (1985)

It has been shown that tobacco glycoprotein (TGP), a polyphenol-rich glycoprotein antigen purified from cured tobacco leaves, is mitogenic for lymphoid cells in the spleen, peripheral blood, and bone marrow, but not for thymus cells. The proliferative response is not reduced by treatment of spleen cells or peripheral blood lymphocytes with anti-Thy-1.2 and complement, and spleen cells from the congenitally athymic (nu/nu) CD-1 proliferate as vigorously in response to TGP as do spleen cells from their heterozygous nu/+ littermates. In addition, TGP induces differentiation of mouse spleen cells into antibody-secreting cells, the majority of which secrete IgM, and the remainder mainly IgG and a few IgA. The differentiation into antibody-secreting cells induced by TGP occurs with spleen cells from nu/nu mice. It is concluded that TGP is a T-independent B cell mitogen for mouse lymphoid cells. On the basis of the ability of spleen cells from the LPS-nonresponder C3H/HEJ mice to respond to TGP with proliferation and differentiation into antibody-secreting cells, it is concluded that the effects of TGP are distinct from those of LPS and cannot be due to contamination of the TGP preparation with LPS.
ChemInform Abstract: KATHODISCHE SPALTUNG VON KOHLENSTOFF‐SAUERSTOFF‐BINDUNGEN 3. MITT. REDUKTION VON PINAKOLEN AN DER QUECKSILBERELEKTRODE, EINE MOEGLICHKEIT ZUR ELEKTROCHEMISCHEN SPALTUNG VON KOHLENSTOFF‐KOHLENSTOFF‐BINDUNGEN (1975)

Abstract Bei der elektrochemischen Reduktion von Pinakolen oder α‐Glykolen [z.B. 1,2‐Dimethyl‐1,2‐bis(biphenylyl)‐glykol, 9,9′‐Dihydroxy‐9 ,9 ′‐bifluoren] in protischen Lösungsmitteln werden sowohl die C‐O‐Bindungen als auch die zentrale C‐C‐Bindung gespalten, wobei sich die Reduktionsstufen nicht voneinander trennen lassen.
Chelating Tendencies of Aminomethylenephosphonic-N,N-diacetic Acid (1958)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTChelating Tendencies of Aminomethylenephosphonic-N,N-diacetic AcidN. Ockerbloom and A. E. MartellCite this: J. Am. Chem. Soc. 1958, 80, 10, 2351–2354Publication Date (Print):May 1, 1958Publication History Published online1 May 2002Published inissue 1 May 1958https://pubs.acs.org/doi/10.1021/ja01543a002https://doi.org/10.1021/ja01543a002research-articleACS PublicationsRequest reuse permissionsArticle Views74Altmetric-Citations8LEARN 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
Ethanol increases histone H3‐K4 methylation and decreases histone H3‐K9 acetylation in conjunction with increased p16 gene expression in the normal colonic epithelial cells (2009)

The objective of this study was to determine whether disturbances in one‐carbon metabolism could modify p16 gene expression through histone modifications. NCM460, human colonic epithelial cells, were incubated in media 1) deficient in folate, methionine and choline, 2) with 100μM Adox (adenosine‐2', 3′‐dialdehyde, an S‐adenosylhomocysteine hydrolase inhibitor), and 3) with 100mM ethanol, which inhibits methionine synthesis and reduces methyl group availability. Histone methylation at histone H3 lysine 4 (H3‐K4) and acetylation at lysine 9 (H3‐K9), both known to be increased in active genes, were measured by Western blotting and p16 gene expression by RT‐PCR. Ethanol increased H3‐K4 trimethylation (p=0.005) and decreased H3‐K9 acetylation (p<0.0001) in a time‐dependent fashion. These changes in histone modifications were paralleled with increased p16 expression (p=0.003). Adox decreased H3‐K9 acetylation time‐dependently (p=0.004) without any change in p16 expression. Folate/methionine/choline deficiency didn't produce any changes in this in vitro culture model. This study demonstrates that in this normal colonic cell line, ethanol, which inhibits one‐carbon metabolism, alters H3‐K4 trimethylation and H3‐K9 acetylation in conjunction with an increase in p16 expression. Grant Funding Source NIH R21 AA016681
Gunn effect oscillator modules using microstrip circuits (1968)

Microwave oscillator modules for operation at X and S-band have been designed which use Gunn devices as the rf power source. More than 10 mW CW at X-band and 20 watts pulsed at S-band has been obtained. The microstrip circuit, together with the necessary filters and blocking capacitor, is produced on an alumina substrate in a single operation using photolithographic techniques. Electronic tuning is achieved by the incorporation of a series mounted varactor diode. Microstrip circulators have been developed for use in both TR and injection locking applications. The design of the circuit elements and their combination to achieve the optimum output power and tuning range is discussed. The injection locking characteristic and the variation of frequency and output power with temperature are described.
“Hybrid DAC” Approach to Increasing Dynamic Range and Signal to Noise in IRSP Systems (2019)

We propose and show preliminary test results on a system to improve dynamic range and signal to noise ratio (SNR) in an infrared (IR) light-emitting diode (LED) display system by splitting the digital-to-analog conversion between the close-support electronics (CSE) and the read-in integrated-circuit (RIIC).
Pharmacodynamic and clinical activity of RGX-104, a first-in-class immunotherapy targeting the liver-X nuclear hormone receptor (LXR), in patients with refractory malignancies. (2018)

3095 Background: RGX-104 is a small-molecule LXR agonist that modulates innate immunity via transcriptional activation of the ApoE gene. RGX-104 depletes myeloid derived suppressor cells (MDSCs) and stimulates dendritic cells (DCs), activating cytotoxic lymphocytes (CTLs) with anti-tumor activity as monotherapy and in combination with checkpoint blockade in murine models. Methods: We are conducting a Phase 1 dose escalation and expansion study of RGX-104 in patients with refractory solid tumors. Safety, PK, PD, and efficacy are being assessed. Results: RGX-104 was dosed orally in 23 patients with a broad array of tumors on 5 cohorts at doses ranging from 120 mg QD for 3 of 4 weeks to 200 mg BID continuously. Following single dosing, PK analysis demonstrated high inter-patient variability with t1/2 from 6 – 8 hr. ApoE gene expression measured in whole blood leukocytes correlated with RGX-104 dose and exposure, demonstrating robust LXR target engagement. Peripheral immune-cell monitoring revealed substantial MDSC depletion (CD33+CD15+HLA-DR-/low; median 78% decrease), DC stimulation (HLA-DR+Lin-; median 34% increase in PD-L1) and CTL activation (median 257% increase in PD-1+GITR+ CD8+ T-cells) in 10/12 evaluable patients. Peak PD effects began ~2 weeks after RGX-104 initiation. Three patients experienced grade 3-4 neutropenia and 1 patient had grade 3 elevated cholesterol, reversible with a statin, likely on-target adverse events. A patient with a platinum-refractory, high-grade neuroendocrine carcinoma with small cell features had a 53% reduction in index hepatic metastases--a partial response pending confirmation, and 5 patients had stable disease at 8 weeks. Conclusions: Proof of principle has been demonstrated for immunologic and anti-tumor activity of the first-in-class LXR-agonist RGX-104 in advanced cancer patients. RGX-104 was well tolerated at doses up to 160mg BID and demonstrated robust PD effects on ApoE expression and relevant immune cell populations. Dose escalation with a PD-1 inhibitor has begun with plans to study RGX-104 both as monotherapy and in combination with a PD-1 inhibitor in select malignancies. Clinical trial information: NCT02922764.
A High Relaxivity Magnetic Resonance Imaging Contrast Agent Targeted to Serum Albumin (2008)

EP-647 is a serum albumin-targeted magnetic resonance imaging contrast agent comprising a GdDTPA (DTPA, diethylenetriaminepentaacetate) chelate for magnetic resonance signal generation linked via a phosphodiester to a substituted biphenyl for albumin targeting. Albumin binding and relaxivity are higher than the benchmark magnetic resonance angiographic agent MS-325. EP-647 binds primarily to a unique site on serum albumin that is different from the MS-325 site and the binding sites of other drugs.
Symbolic transformations of heart rate variability preserve information about cardiac autonomic control (2015)

Traditional measures of heart rate variability (HRV) in the time or frequency domain (e.g. standard deviation of normal-to-normal intervals, SDNN, or the high frequency component of spectral analysis, HF) may be used to track vagal and sympathetic modulation directed to the sinus node. In this study, we assess the ability of symbolic analysis to monitor cardiac autonomic regulation during two autonomic challenges (phenylephrine and nitroprusside; low and high dose of atropine). To assess the effect of the coarse graining procedure, symbolic series obtained from four different transformations over the original series and the series of successive differences of the original values. The analysis focused on patterns of length 3 and exploited a redundancy reduction strategy to group patterns into a small number of families. It turns out that each symbolic series created by the four transformations still contained sufficient dynamical features to quantify differences of cardiovascular changes during the pharmacological challenges. The symbolic series created by transformations of the beat-to-beat interview, i.e RR interval series, showed that patterns without variations (0V) appear more often during a high dose of atropine compared to rest or to a low dose of atropine. Furthermore, patterns with two unlike variations (2UV) appear more often during a low dose of atropine and less often during a high dose of atropine. Differences of nitroprusside and phenylephrine could also be assessed by patterns with these variations. In conclusion, the changes of cardiovascular regulation during pharmacological challenges can be assessed by the analysis of symbolic dynamics derived from the RR interval series independently of the specific symbolic transformation.
Assessing the construct validity of five nutrient profiling systems using diet modeling with linear programming (2013)

Nutrient profiling classifies individual food products according to their nutrient content. According to the WHO (World Health Organization), validation is a key step in the development of a nutrient profiling system. The aim was to assess the construct validity of five European nutrient profiling systems (Choices, Keyhole, (AFSSA), European Commission (EC) system and FoodProfiler). Construct validity was assessed for each of the five-selected nutrient profiling systems by testing whether healthy foods (that is, identified as eligible by the system) make healthy diets, and unhealthy foods (that is, non-eligible) make unhealthy diets, using diet modeling. The AFSSA, EC and FoodProfiler systems were identified as valid, but differences in their levels of permissiveness suggested some misclassified food products. The two other systems failed the construct validity assessment. Among these three systems, the EC system is the less demanding in terms of nutritional information, it would, therefore, be the easiest to implement for regulating nutrition and health claims in Europe.
Formation of Nanowires by Self-Assembly on Highly Oriented Pyrolytic Graphite (HOPG) (2004)

Electrodeposition on Highly Oriented Pyrolytic Graphite (HOPG) steps has been proven to be an easy method for the preparation of metal (Pd, Cu, Ag etc) and metal oxide or sulfide (MoO2, MnO2, MoS2) nanowires in recent years. These wires can be transferred on to other insulating substrates like polymers (eg, PDMS) and epoxy or cyano acrylate glues, to be used as sensors, for example palladium for the detection of hydrogen. The main problem during their conductivity measurements is to make macroscopic contacts to these wires. Normally, silver paints are used to form contact between transferred wires, which however provides only poor control of size and reproducibility. In order to improve this, we attempt to connect the wires, by evaporating micro pads of 200-300 nm thick film of Al and 200- 400 nm thick Au through a nano stencil. The stencil used in these experiments is made of a 200 nm SiN membrane with apertures ranging from 250 nm to hundreds of micrometers. We studied several implementations of the micro-nano fabrication techniques such as follows: The structures were deposited on bare HOPG surface (before nanowire formation), HOPG surface after nano wire formation, and on glass wafer spin coated with PDMS. We also evaporated metal contacts over nanowires, which were transferred from HOPG to PDMS coated glass. Wires used in these experiments have average diameters of 50-60 nm. The distance between the sample and stencil plays a key role in the sharpness of the structures formed by shadow evaporation. The current limitation during the deposition of micro pads through stencil is the spreading of metal at the sides of the structures. This was most pronounced on graphite surface after nanowire formation and on PDMS surface with wires. This may be because after deposition of wires, the surface becomes rougher and is no more flat as bare HOPG or spin coated PDMS, so that this prevents close enough contact between substrate and stencil. The distance between sample and the stencil is kept as small as possible- in the micrometer range- to avoid spreading of the deposited structures. When stencil evaporation of 200 nm thick Au was done over wires transferred to PDMS, cracks in the gold film were observed on the polymer. This could be a result of the expansion and further contraction of PDMS during thermal evaporation and/or mechanical manipulation. In the presentation, we will show details of microelectrode formation on HOPG using the nanostencil and nanowire formation by electrochemical method.
A Short Course on Virology / Vectorology / Gene Therapy (2003)

For people starting off in the field of gene therapy, the encountered terminology is often quite confusing. Moreover, the background on basic virology may be modest. The following introduction provides a head start to any novice willing to gain more in-depth knowledge on the subject. The development of gene therapy is also addressed from a historical perspective.
Photoacoustic waves at reflecting interfaces (2003)

The properties of photoacoustic waves generated outside acoustically reflecting boundaries can be found using Green’s function solutions to the wave equation for pressure. Here, Green’s functions are used to calculate the time profiles of photoacoustic waves generated in the fluid surrounding an incompressible sphere with a vanishing thermal expansivity. The Green’s function method is also applied to determination of the properties of the photoacoustic wave generated in the atmosphere of a planet caused by rotation of the planet in the radiation emitted by the sun.
Solvent effects on the nitrogen and β-hydrogen hyperfine splitting constants of aminoxyl radicals obtained in spin trapping experiments (1982)

The nitrogen and β-hydrogen hyperfine splitting constants (hfsc) for phenyl, 4-nitrophenyl, 4-pyridyl, benzoyl, and trichloromethyl spin adducts of α-phenyl tert-butyl nitrone (PBN) as well as for the tert-butoxyl adduct of 5,5-dimethylpyrroline-N-oxide (DMPO) have been obtained as a function of solvent (30 solvents). A useful linear relationship between the β-H hfsc and the N-hfsc of each aminoxyl is found except for the benzoyl adduct of PBN. Some speculations regarding the structural significance of these correlations is presented.