gebhart/patrepeval huggingface dataset:
Genomic instability in human cancer: Molecular insights and opportunities for therapeutic attack and prevention through diet and nutrition (2015)

Genomic instability can initiate cancer, augment progression, and influence the overall prognosis of the affected patient. Genomic instability arises from many different pathways, such as telomere damage, centrosome amplification, epigenetic modifications, and DNA damage from endogenous and exogenous sources, and can be perpetuating, or limiting, through the induction of mutations or aneuploidy, both enabling and catastrophic. Many cancer treatments induce DNA damage to impair cell division on a global scale but it is accepted that personalized treatments, those that are tailored to the particular patient and type of cancer, must also be developed. In this review, we detail the mechanisms from which genomic instability arises and can lead to cancer, as well as treatments and measures that prevent genomic instability or take advantage of the cellular defects caused by genomic instability. In particular, we identify and discuss five priority targets against genomic instability: (1) prevention of DNA damage; (2) enhancement of DNA repair; (3) targeting deficient DNA repair; (4) impairing centrosome clustering; and, (5) inhibition of telomerase activity. Moreover, we highlight vitamin D and B, selenium, carotenoids, PARP inhibitors, resveratrol, and isothiocyanates as priority approaches against genomic instability. The prioritized target sites and approaches were cross validated to identify potential synergistic effects on a number of important areas of cancer biology.
Model Transient Networks from Strongly Hydrogen-Bonded Polymers (2009)

Random copolymers consisting of n-butyl acrylate backbones with quadruple hydrogen-bonding side chains based on 2-ureido-4[1H]-pyrimidinone (UPy) have been synthesized via controlled radical polymerization and postpolymerization functionalization. Through this synthetic strategy high UPy monomer content (15 mol %) can be reached while maintaining low polydispersity and excellent control over molecular weight, providing model reversible networks with well-defined molecular architecture. Despite low Tgs and a lack of entanglements or crystallinity, these materials behave as thermoplastic elastomers through the strong but reversible association of UPy groups. Bulk properties such as the plateau modulus, tensile modulus, and relaxation time scale are primarily determined by the average distance between UPy’s along the chain. Starting from a difunctional initiator, triblock copolymers can also be synthesized containing a homopolymer midblock and random copolymer end blocks, effectively concentrating the hydrogen-bonding groups near the chain ends. By controlling both the average composition and distribution of UPy’s along the polymer chain, macroscopic material properties such as stiffness and resistance to creep can be independently tuned.
Oxidation of alkoxyphenols. XXIX. Phototautomerism and dinierization of 4,6-Di-t-butyl-4a-hydroxy-8-methoxydibenzofuran-2(4aH)-one (1983)

In solution in non-polar solvents the title compound undergoes photochemical ring opening to its hydroxyphenylquinone tautomer. Oxidation of 3,3'-di-t-butyl-5,5'-dimethoxybiphenyl-2,2'-diol withvanadium oxytrifluoride in the presence of trifluoroacetic acid yields bisdibenzofurans. The crystal structures of 4,4',6,6'-tetra-t-butyl-2',8-dimethoxy-1,1'-bisdibenzofuran-2,8'-diol and of 4,6-di-t-butyl-4a-hydroxy-8-methoxydibenzofuran-2(4a H )-one have been determined.
A Mucin-Specific Protease Enables Molecular and Functional Analysis of Human Cancer-Associated Mucins (2018)

&lt;div&gt; &lt;div&gt; &lt;div&gt; &lt;p&gt;Mucins are a class of highly O-glycosylated proteins that are ubiquitously expressed on cellular surfaces and are important for human health, especially in the context of carcinomas. However, the molecular mechanisms by which aberrant mucin structures lead to tumor progression and immune evasion have been slow to come to light, in part because methods for selective mucin degradation are lacking. Here we employ high resolution mass spectrometry, polymer synthesis, and computational peptide docking to demonstrate that a bacterial protease, called StcE, cleaves mucin domains by recognizing a discrete peptide-, glycan-, and secondary structure- based motif. We exploited StcE’s unique properties to map glycosylation sites and structures of purified and recombinant human mucins by mass spectrometry. As well, we found that StcE will digest cancer-associated mucins from cultured cells and from ovarian cancer patient-derived ascites fluid. Finally, using StcE we discovered that Siglec-7, a glyco-immune checkpoint receptor, specifically binds sialomucins as biological ligands, whereas the related Siglec-9 receptor does not. Mucin-specific proteolysis, as exemplified by StcE, is therefore a powerful tool for the study of glycoprotein structure and function and for deorphanizing mucin-binding receptors. &lt;/p&gt; &lt;/div&gt; &lt;/div&gt; &lt;/div&gt;
Photoconductivity of 3,5-dinitrobenzoate of poly[1-phenyl-1-penten-3-yn-5-ol] (DN-PPPYO) blended with poly[4-(p-N,N-diphenylaminophenyl)-1-phenyl-1-buten-3-yne] (PPAPBEY) as a hole transporting polymer (1999)

The 3,5-dinitrobenzoate of poly[1-phenyl-1-penten-3-yn-5-ol] (DN-PPPYO) blended with a charge transporting polymer, poly[4-(p-N,N-diphenylaminophenyl)-1-phenyl-1-buten-3-yne] (PPAPBEY), and polystyrene shows high photoconductivity due to the high concentration of the triphenylamine (TPA) moiety and the fully conjugated backbone as verified by xerographic measurements.
A systems biology study to tailored treatment in chronic heart failure (2017)

This thesis was part of the The BIOlogy STudy to TAilored Treatment in Chronic Heart Failure (BIOSTAT-CHF) project. BIOSTAT-CHF was a European, multicenter, multinational, prospective, observational study that was especially designed to find biological mechanisms involved with response to ESC guideline recommended pharmacological therapy. The aim and focus of this thesis was twofold. In the first part, we focused on individualized treatment of heart failure. We looked at what heart failure prediction models were published and which factors resulted in more accurate predictions. We tried to identify heart failure patients with low or high risk of mortality and/or heart failure related hospitalization. We also looked at which patients achieved recommended treatment doses for guideline recommended pharmacological therapy and which did not. In addition to this, we tried to estimate if a patient would benefit from receiving recommended treatment doses or not based on prediction models consisting solely on biomarkers. The second part, was of a more methodological nature. We looked at the consistency and robustness of different clustering methods, and we clustered patients based not on clinical, but pathophysiological parameters. We also developed two methods to analyze the enormous amounts of data collected in systems biology. The first method estimates possible existence of splice variants in gene expression data. The second method is a penalized canonical correlation analysis, which enables to analyze multiple high-dimensional datasets in such a way that a set of variables in one dataset correlates maximally with the sets of variables in all other datasets.
Response to Comment on “Analysis of the Cellular Mechanism of Antitumor Responses and Autoimmunity in Patients Treated with CTLA-4 Blockade” (2006)

In our article analyzing the cellular mechanisms of antitumor and autoimmune effects of CTLA-4 blockade ([1][1]), the cells that were tested were obtained ∼3 wk after the last dose of anti-CTLA-4 mAb. All patients had received many doses of anti-CTLA-4 Ab administered every 3 wk, and because the
Magnetic resonance imaging for the assessment of myocardial viability (2004)

The identification of myocardial viability in the setting of left ventricular (LV) dysfunction is crucial for the prediction of functional recovery following revascularization. Although echocardiography, positron emission tomography (PET), and nuclear imaging have validated roles, recent advances in cardiac magnetic resonance (CMR) technology and availability have led to increased experience in CMR for identification of myocardial viability. CMR has unique advantages in the ability of magnetic resonance spectroscopy (MRS) to measure subcellular components of myocardium, and in the image resolution of magnetic resonance proton imaging. As a result of excellent image resolution and advances in pulse sequences and coil technology, magnetic resonance imaging (MRI) can be used to identify the transmural extent of myocardial infarction (MI) in vivo for the first time. This review of the role of CMR in myocardial viability imaging describes the acute and chronic settings of ventricular dysfunction and concepts regarding the underlying pathophysiology. Recent advances in MRS and MRI are discussed, including the potential for dobutamine MRI to identify viable myocardium and a detailed review of the technique of delayed gadolinium (Gd) contrast hyperenhancement for visualization of viable and nonviable myocardium.
Notes and Comments: The Right to a Speedy Trial in Maryland (1976)

In the wake of the Supreme Court's 1972 decision in Barker v. Wingo, Maryland appellate courts have enforced more rigorously the right of criminal defendants to a speedy trial. This article surveys the application and treatment of the Barker criteria by the Maryland courts in recent decisions.
First-principles calculations of band-edge electronic states of silicon quantum wires (1994)

Valence- and conduction-band-edge energies and effective masses of hydrogen-terminated silicon wires are calculated using a first-principles pseudopotential method, and the results are compared with effective-mass-theory (EMT) calculations. The first-principles result for the ordering of states at the valence-band maximum is different from the prediction of EMT. The magnitudes of the valence- and conduction-band effective masses for motion along the wire axis increase from their bulk values as the wire thickness decreases, but by much less than predicted by other calculations.
The volatile exudates from germinating pea seeds of different viability and vigor (1985)

Pea seeds var. Kriter were stored aseptically at 92% relative humidity and 30 °C. After 0, 4, 6, 8, or 10 weeks of storage, viability, vigor, and volatile exudates were determined on sublots of seeds. As storage time increased, vigor, as measured by dehydrogenase activity, growth of embryonic axes, and conductivity decreased. Later, viability also decreased. Imbibing and germinating pea seeds produced ethanol, acetaldehyde, and lesser amounts of methanol. No qualitative differences in volatile exudates were observed from germinating seeds regardless of age or storage condition. Nonaged seeds with highest vigor produced the smallest amounts of volatiles, but with increased aging the quantities of ethanol and acetaldehyde gradually increased. Dry seed produced small quantities of both volatiles. The amount of these compounds produced reached a maximum between 12 and 48 h of germination. Infestation of seed samples with Enterobacter cloacae or Trichoderma harzianum reduced the quantities of these compounds measured. These results indicate that determinations of acetaldehyde and ethanol in the space over germinating seeds by means of gas chromatography may be a useful seed vigor test.
Suppression of Prostate Cancer Nodal and Systemic Metastasis by Blockade of the Lymphangiogenic Axis (2008)

Lymph node involvement denotes a poor outcome for patients with prostate cancer. Our group, along with others, has shown that initial tumor cell dissemination to regional lymph nodes via lymphatics also promotes systemic metastasis in mouse models. The aim of this study was to investigate the efficacy of suppressive therapies targeting either the angiogenic or lymphangiogenic axis in inhibiting regional lymph node and systemic metastasis in subcutaneous and orthotopic prostate tumor xenografts. Both androgen-dependent and more aggressive androgen-independent prostate tumors were used in our investigations. Interestingly, we observed that the threshold for dissemination is lower in the vascular-rich prostatic microenvironment compared with subcutaneously grafted tumors. Both vascular endothelial growth factor-C (VEGF-C) ligand trap (sVEGFR-3) and antibody directed against VEGFR-3 (mF4-31C1) significantly reduced tumor lymphangiogenesis and metastasis to regional lymph nodes and distal vital organs without influencing tumor growth. Conversely, angiogenic blockade by short hairpin RNA against VEGF or anti-VEGFR-2 antibody (DC101) reduced tumor blood vessel density, significantly delayed tumor growth, and reduced systemic metastasis, although it was ineffective in reducing lymphangiogenesis or nodal metastasis. Collectively, these data clarify the utility of vascular therapeutics in prostate tumor growth and metastasis, particularly in the context of the prostate microenvironment. Our findings highlight the importance of lymphangiogenic therapies in the control of regional lymph node and systemic metastasis.
A Computational Study of Rhodium Pincer Complexes with Classical and Nonclassical Hydride Centres as Catalysts for the Hydroamination of Ethylene with Ammonia (2010)

The catalytic hydroamination of ethylene with ammonia was investigated by means of density functional theory (DFT) calculations. An initial computational screening of key reaction steps (C-N bond formation, N-H bond cleavage), which are assumed to be part of a catalytic cycle, was carried out for complexes with the [M(L)]-complex fragment (M=Rh, Ir; L=NCN, PCP; NCN=2,5-bis(dimethylaminomethyl)benzene, PCP=2,5-bis- (dimethylphosphanylmethyl)benzene). Based on the evaluation of activation barriers, this screening showed the rhodium compound with the NCN ligand to be the most promising catalyst system. A detailed investigation was carried out starting with the hypothetical catalyst precursor [Rh(NCN)(H)(2)(H(2))] (1). A variety of activation pathways to yield the catalytically active species [Rh(NCN)(H)(NH(2))] (5), as well as [Rh(NCN)(C(2)H(5))(NH(2))] (17), were identified. With 5 and 17 several closed catalytic cycles could be calculated. One of the calculated cycles is favoured kinetically and bond-forming events have activation barriers low enough to be put into practice. The calculations also show that for experimental realisation the synthesis of 1 is not necessary, as the synthesis of 17 would establish an active catalyst directly without the need for activation. Oligomerisation of ethylene would be possible in principle and would be expected as a competitive side reaction. Accordingly not only ethylamine would be observed in an experimental system, as amines with longer carbon chains also can be formed.
Praziquantel – 50 Years of Research (2023)

Investigations on praziquantel (PZQ) started fifty years ago by a cooperation between Bayer AG and Merck KGaA. Until today PZQ is the drug of choice for schistosomiasis in human medicine and used in many combinations with antinematode drugs in veterinary medicine. The Sm.TRPM<sub>PZQ</sub> , a Ca<sup>2+</sup> -permeable transient receptor potential (TRP) channel, has been discovered as primary target of PZQ during the last decade. Furthermore, there is a short overview of routes of large-scale synthesis of racemic and pure (R)-PZQ. Until now racemic PZQ is used in veterinary and human medicine. In 2012 the Pediatric Praziquantel Consortium started PZQ chemistry and process development of pure (R)-PZQ for human application. It is hoped that (R)-PZQ will become available for pediatric use soon. The knowledge of the binding pocket of PZQ in Sm.TRPM<sub>PZQ</sub> allows to design synthesis of PZQ-derivatives of the next generation for a target-site directed screening. A similar screening should also be started for Fasciola hepatica TRPM<sub>PZQ</sub> .
Antibody-Dependent Cellular Cytotoxicity against Primary HIV-Infected CD4+T Cells Is Directly Associated with the Magnitude of Surface IgG Binding (2012)

Antibody (Ab)-dependent cellular cytotoxicity (ADCC) is thought to potentially play a role in vaccine-induced protection from HIV-1. The characteristics of such antibodies remain incompletely understood. Furthermore, correlates between ADCC and HIV-1 immune status are not clearly defined. We screened the sera of 20 HIV-1-positive (HIV-1(+)) patients for ADCC. Normal human peripheral blood mononuclear cells were used to derive HIV-infected CD4(+) T cell targets and autologous, freshly isolated, natural killer (NK) cells in a novel assay that measures granzyme B (GrB) and HIV-1-infected CD4(+) T cell elimination (ICE) by flow cytometry. We observed that complex sera mediated greater levels of ADCC than anti-HIV-1 envelope glycoprotein (Env)-specific monoclonal antibodies and serum-mediated ADCC correlated with the amount of IgG and IgG1 bound to HIV-1-infected CD4(+) T cells. No correlation between ADCC and viral load, CD4(+) T cell count, or neutralization of HIV-1(SF162) or other primary viral isolates was detected. Sera pooled from clade B HIV-1(+) individuals exhibited breadth in killing targets infected with HIV-1 from clades A/E, B, and C. Taken together, these data suggest that the total amount of IgG bound to an HIV-1-infected cell is an important determinant of ADCC and that polyvalent antigen-specific Abs are required for a robust ADCC response. In addition, Abs elicited by a vaccine formulated with immunogens from a single clade may generate a protective ADCC response in vivo against a variety of HIV-1 species. Increased understanding of the parameters that dictate ADCC against HIV-1-infected cells will inform efforts to stimulate ADCC activity and improve its potency in vaccinees.
Genome mining in myxobacteria and actinobacteria : studies of natural products and their biosynthetic pathways (2020)

Bacterial resistance to antibiotics drives the need for incessant research efforts to discover substitutes for ineffective antibiotics. Soil-dwelling Myxobacteria and Actinobacteria provide many biologically active natural products that can be developed into new treatment options. In postgenomic era, the natural product discovery is often based on the genome mining approach combined with genetic engineering used also in this work. This thesis presents two novel natural products, myxopentacin and myxoglucamide, produced by Cystobacterineae sp. MCy9003, a representative of a novel myxobacterial genus. The nonribosomal peptide myxopentacin features rare cispentacin and pseudoarginine moieties, incorporated by a unique assembly mechanism. The glycolipopeptide myxoglucamide contains an unusual vinyl moiety and its biosynthesis involves multiple biochemical transfomations. In addition, this thesis describes the identification of the biosynthetic gene cluster in Streptomyces hagronensis, responsible for the production of the known antibiotic globomycin, a signal peptidase II inhibitor. Furthermore, the genome of the antibiotic fidaxomicin producer Actinoplanes deccanensis was genetically engineered to acquire desired shunt products for further semi-synthesis. Finally, the biosynthetic pathway of the atypical tetracycline chelocardin, regarding cyclization and C6- methylation, was characterized via gene knockout and site-directed mutagenesis in Amycolatopsis sulphurea.
Control of Cell Behavior by Aligned Micro/Nanofibrous Biomaterial Scaffolds Fabricated by Spinneret‐Based Tunable Engineered Parameters (STEP) Technique (2008)

STEP by STEP: A method for depositing customized single and multilayer biomaterial scaffolds (see image) using point-to-point and continuous techniques is described. Proliferation and migration of mouse C2C12 progenitor cells occurs along the fiber axis on single-layered scaffolds and on double-layered orthogonal scaffolds spreading along the two layers, and right-angle transitions can be seen.
Epoxidation of Alkenes Catalyzed by Iron(III) Schiff Base Chelates. A Monooxygenase Model (1989)

Abstract Iron(III) Schiff base chelates [Fe2(PA2ppd)2Cl4]Cl2 (1), [Fe2(PA2mpd)2Cl4]Cl2 (2), and [Fe(PA2opd)Cl2]Cl (3), were synthesized, where (PA2ppd), (PA2mpd), and (PA2opd) are the Schiff bases derived from 2-pyridinecarbaldehyde (PA), and p-phenylenediamine (ppd), m-phenylenediamine (mpd), and o-phenylenediamine (opd) respectively. The complexes 1, 2, and 3 catalyzed the epoxidation of alkenes with iodosylbenzene as an oxidant providing a chemical model for cytochrome P-450. The binuclear complexes (1, 2) were superior to the mononuclear complex (3) as the catalyst for epoxidation of norbornene. Addition of pyridine bases increased the rates, and yields of epoxidation.
Update of >300W high power LPP-EUV source challenge for semiconductor HVM (2020)

Gigaphoton develops CO2-Sn-LPP EUV light source which is the most promising solution as the 13.5nm high power light source for HVM EUVL. Unique and original technologies including; combination of pulsed CO2 laser and Sn droplets, dual wavelength laser pulses for shooting and debris mitigation by magnetic field have been applied. We have developed first practical source for HVM; “GL200E” 1) in 2014. Then it is demonstrated which high average power CO2 laser more than 20kW at output power in cooperation with Mitsubishi Electric2). Pilot#1 is up running and it demonstrates HVM capability; EUV power recorded at 111W on average (117W in burst stabilized, 95% duty) with 5% conversion efficiency for 22 hour operation in October 20163). Availability is achievable at 89% (2 weeks average), also superior magnetic mitigation has demonstrated promising mirror degradation rate (= 0.5%/Gp) at 100W or higher power operation with dummy mirror test. We have demonstrated &gt;300W operation data (short-term) and actual collector mirror reflectivity degradation rate is less than 0.15%/Gp by using real collector mirror around 125W (at I/F clean) in burst power &gt; 10 Billion pulses operation4). Also we will update latest challenges for &gt;250W average long-term operation with collector mirror at the conference. REFERENCE 1) Hakaru Mizoguchi, et. al.: “Sub-hundred Watt operation demonstration of HVM LPP-EUV source”, Proc. SPIE 9048, (2014) 2) Yoichi Tanino et.al.:” A Driver CO2 Laser Using Transverse-flow CO2 Laser Amplifiers”, EUV Symposium 2013, ( Oct.6-10.2013, Toyama) 3) Hakaru Mizoguchi, et al: ” High Power HVM LPP-EUV Source with Long Collector Mirror Lifetime”, EUVL Workshop 2017, (Berkley, 12-15, June, 2017) 4) Hakaru Mizoguchi et al.:” Challenge of &gt;300W high power LPP-EUV source with long collector mirror lifetime for semiconductor HVM”, Proc. SPIE 11323, Extreme Ultraviolet (EUV) Lithography XI (2019) [11323-28]