gebhart/patrepeval huggingface dataset:
The unfolded protein response (2006)

The endoplasmic reticulum (ER) is an intracellular organelle consisting of a membranous labyrinth network that extends throughout the cytoplasm of the cell and is contiguous with the nuclear envelope. In all eukaryotic cells, the ER is the site where folding and assembly occurs for proteins destined to the extracellular space, plasma membrane, and the exo/endocytic compartments. The ER is exquisitely sensitive to alterations in homeostasis, and provides stringent quality control systems to ensure that only correctly folded proteins transit to the Golgi and unfolded or misfolded proteins are retained and ultimately degraded. A number of biochemical and physiologic stimuli, such as perturbation in calcium homeostasis or redox status, elevated secretory protein synthesis, expression of misfolded proteins, sugar/glucose deprivation, altered glycosylation, and overloading of cholesterol can disrupt ER homeostasis, impose stress to the ER, and subsequently lead to accumulation of unfolded or misfolded proteins in the ER lumen. The ER has evolved highly specific signaling pathways called the unfolded protein response (UPR) to cope with the accumulation of unfolded or misfolded proteins. Recent discoveries of the mechanisms of ER stress signaling have led to major new insights into the diverse cellular and physiologic processes that are regulated by the UPR. This review summarizes the complex regulation of UPR signaling and its relevance to human physiology and disease.
Heparin-Coated Palmaz-Schatz Stents in Human Coronary Arteries (1996)

The implantation of stents coated with polyamine and end-point-attached heparin in stable patients with one significant de novo coronary lesion is well tolerated, is associated with no (sub)acute stent thrombosis, and results in a favorable event-free survival after 6 months.
Abstract 1022: Carfilzomib demonstrates broad antitumor activity in preclinical lung cancer models. (2013)

Abstract Carfilzomib (CFZ), is an irreversible inhibitor of the chymotrypsin-like activity of the proteasome that was recently FDA approved for treatment of refractory and relapsed multiple myeloma. Early Phase 1B studies of CFZ showed signs of clinical activity in a number of solid tumors, including non-small cell lung cancer (NSCLC) and small cell lung cancer (SCLC). We investigated the anti-tumor activity of CFZ monotherapy and in combination with cisplatin in NSCLC and SCLC cell lines and xenograft models. CFZ showed marked anti-proliferative activity in A549, H1993, H520, H460, H1299 NSCLC cell lines, with IC50 values after 96 hours of treatment ranging from 1.0 nM to 27 nM. CFZ + cisplatin resulted in antagonistic anti-proliferative activity in the NSCLC A549, H1993, and H520 cells, independent of sequence of drug administration. In vivo, CFZ monotherapy resulted in tumor growth inhibition in an A549 NSCLC murine xenograft model. In contrast, the SCLC cell lines SHP77 and H69 were more resistant to the anti-proliferative effects of CFZ, with IC50 values at 96 hours of 0.917 μM and &amp;gt;30 μM, respectively. In vitro, in the SHP-77 SCLC cell line CFZ + Cisplatin showed synergistic activity. In vivo, in a SHP-77 SCLC SCID murine xenograft model CFZ monotherapy resulted in an 8-day tumor growth delay to reach 1500 mm3. No additive or synergistic anti-tumor efficacy was observed for CFZ + cisplatin in this model. Western blot analysis from SHP-77 cell lines grown in vitro and treated with CFZ showed an increase in cleaved PARP and p53, supporting activation of apoptosis. We will report on inhibition of the chymotrypsin-like proteasome activity in CFZ-treated lung cancer cell lines. Together, these pre-clinical studies support further preclinical and clinical investigations of CFZ in NSCLC and SCLC, including novel CFZ + anti-cancer drug combinations. Citation Format: Amanda F. Baker, Barbara Sands, Lilliana Carbajal, Janet Anderl, Elena T. Chan, Christopher J. Kirk, Linda L. Garland. Carfilzomib demonstrates broad antitumor activity in preclinical lung cancer models. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 1022. doi:10.1158/1538-7445.AM2013-1022
AKR1C3 overexpression may serve as a promising biomarker for prostate cancer progression (2014)

The virtual slide(s) for this article can be found here: http://www.diagnosticpathology.diagnomx.eu/vs/7748245591110149.
Expression of the gene cluster associated with the Escherichia coli pilus adhesin K99 (1995)

The biogenesis of the pilus adhesin K99 is dependent on the expression of eight contiguous genes, fanA to fanH. Transposon mutants were prepared by using TnlacZ and TnphoA, and selected transposon mutants were used to measure expression of each K99 gene. Expression of the K99 genes is likely controlled at the transcription level, since in general, there were no differences between the results obtained with the two transposons. fanC was the most highly expressed, and fanD was expressed at very low levels. The expression of TnlacZ fusions in fanA and fanB fusions was high. Deletion of fanA, fanB, and part of fanC abolished the expression of fanD but had no effect on the distal genes fanE to fanH. To locate the DNA regions required for expression of fanE to fanH, deletion mutations were prepared and the effects on expression of fanE to fanH were determined. The deletion of a segment between fanD and fanE abolished fanE and fanF expression but did not affect fanG and fanH. The deletion of a portion of fanF (approximately 1 kb proximal to fanG) abolished the expression of fanG and fanH. These results indicate the presence of regulatory elements proximal to fanE and to fanG. Putative promoters were identified in these regions by DNA homology and by primer extension. A stem-loop structure that may act as a transcriptional attenuator of fanF was also found at the beginning of fanF. These data confirm our previous model of K99 transcriptional organization.
Chiral discrimination by simple gas sensors (2002)

The discrimination of optical isomers (enantiomers) in the gas phase has been performed using thickness shear mode resonators (TSMRs). The selective coatings included both enantiomers ((S)- and (R)-receptor) of a Chirasil-Val(R)-derivative (stationary phase material in gas chromatography (GC)) with octyl-side chains. A successful discrimination of the enantiomers of different types of analytes (amino acids and lactates) was achieved. The results were in good agreement with GC-measurements. In addition different mixtures of the enantiomers of the respective analyte were investigated and the enantiomeric composition could be determined quantitatively with excellent reliability. Thus, the sensors allow an on-line-monitoring (not possible for GC) of enantiomeric purity.
Meta-Analysis: Glycosylated Hemoglobin and Cardiovascular Disease in Diabetes Mellitus (2004)

Pending confirmation from large, ongoing clinical trials, this analysis shows that observational studies are consistent with limited clinical trial data and suggests that chronic hyperglycemia is associated with an increased risk for cardiovascular disease in persons with diabetes.
Transporting Adult and Larval Gulf Menhaden and Techniques for Spawning in the Laboratory (1983)

Abstract Fifty-five adult gulf menhaden (Brevoortia patronus) were transported from Gulf Breeze, Florida, to Beaufort, North Carolina, in 30 h without mortality. The life-support features during transport included a 600-L cylindrical, unbaffled fish tank, a continuous-duty pump, a filter using crushed oyster shells and activated carbon, tris-buffered seawater, oxygen, and monitors for temperature, oxygen, and pH. Spawning, induced by temperature, photoperiod, and injections of human chorionic gonadotropin and carp pituitary, occurred following transport and occurred nine times from November 1982 through March 1982. Larvae from two spawns were transported to the Gulf of Mexico for shipboard feeding experiments.
Bexarotene and Erlotinib for Aerodigestive Tract Cancer (2005)

The recommended phase II doses are erlotinib 150 mg/d and bexarotene 400 mg/m2/d orally. These agents can be administered in combination at the recommended single-agent doses without added toxicity. Overall survival and clinical features of responding patients differ from prior reports of single-agent erlotinib treatment. These findings are encouraging and warrant further investigation of this regimen.
Synthesis and properties of N-acetimidoyl derivatives of glycine and sarcosine (1974)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and properties of N-acetimidoyl derivatives of glycine and sarcosineTaitzer WangCite this: J. Org. Chem. 1974, 39, 24, 3591–3594Publication Date (Print):November 1, 1974Publication History Published online1 May 2002Published inissue 1 November 1974https://pubs.acs.org/doi/10.1021/jo00938a031https://doi.org/10.1021/jo00938a031research-articleACS PublicationsRequest reuse permissionsArticle Views268Altmetric-Citations17LEARN 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
Harnessing Naturally Occurring Tumor Immunity: A Clinical Vaccine Trial in Prostate Cancer (2010)

ClinicalTrials.gov NCT00289341.
Curcumin Prevents Dopaminergic Neuronal Death Through Inhibition of the c-Jun N-Terminal Kinase Pathway (2010)

Recent studies have shown that the c-Jun N-terminal kinase (JNK) signaling pathway is involved in dopaminergic neuronal degeneration, and direct blockade of JNK by specific inhibitors may prevent or effectively slow the progression of Parkinson disease (PD). Previous studies have revealed that the natural phenolic compound curcumin can reduce inflammation and oxidation, which makes it a potential therapeutic agent for neurodegenerative diseases. In this study, we investigated whether curcumin protects against 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine- (MPTP) or 1-methyl-4-phenylpyridnium ion- (MPP(+)) induced dopaminergic neurotoxicity in C57BL/6N mice or SH-SY5Y cells by inhibiting JNK pathways both in vivo and in vitro. Curcumin treatment significantly improved behavioral deficits, and enhanced the survival of tyrosine hydroxylase-positive neurons in the substantia nigra (SN) in the MPTP-induced PD model mice. Most importantly, curcumin treatment significantly inhibited MPTP/MPP(+)-induced phosphorylation of JNK1/2 and c-Jun, and cleaved caspase-3. Our study suggests that the neuroprotective effect of curcumin is not related simply to its antiinflammatory and antioxidant properties, but involves other mechanisms, particularly by targeting the JNK pathways.
Enzyme plus light therapy to repair DNA damage in ultraviolet-B-irradiated human skin (2000)

Ultraviolet-B (UVB) (290-320 nm) radiation-induced cyclobutane pyrimidine dimers within the DNA of epidermal cells are detrimental to human health by causing mutations and immunosuppressive effects that presumably contribute to photocarcinogenesis. Conventional photoprotection by sunscreens is exclusively prophylactic in nature and of no value once DNA damage has occurred. In this paper, we have therefore assessed whether it is possible to repair UVB radiation-induced DNA damage through topical application of the DNA-repair enzyme photolyase, derived from Anacystis nidulans, that specifically converts cyclobutane dimers into their original DNA structure after exposure to photoreactivating light. When a dose of UVB radiation sufficient to induce erythema was administered to the skin of healthy subjects, significant numbers of dimers were formed within epidermal cells. Topical application of photolyase-containing liposomes to UVB-irradiated skin and subsequent exposure to photoreactivating light decreased the number of UVB radiation-induced dimers by 40-45%. No reduction was observed if the liposomes were not filled with photolyase or if photoreactivating exposure preceded the application of filled liposomes. The UVB dose administered resulted in suppression of intercellular adhesion molecule-1 (ICAM-1), a molecule required for immunity and inflammatory events in the epidermis. In addition, in subjects hypersensitive to nickel sulfate, elicitation of the hypersensitivity reaction in irradiated skin areas was prevented. Photolyase-induced dimer repair completely prevented these UVB radiation-induced immunosuppressive effects as well as erythema and sunburn-cell formation. These studies demonstrate that topical application of photolyase is effective in dimer reversal and thereby leads to immunoprotection.
Blocking the hedgehog pathway inhibits hepatoblastoma growth # (2008)

This study demonstrates, for the first time, the frequent occurrence of GLI1 and PTCH1 overexpression and HHIP promoter methylation in early childhood HB, thus indicating a key role for Hh signaling activation in the malignant transformation of embryonal liver cells.
Precipitation hardening in a cast Mg-rare earth alloy (1992)

The age hardening and precipitation behaviour of a cast Mg--1.3 rare earth alloy has been investigated. Ageing of solution treated and quenched specimens for 3 h at elevated temperatures resulted i ...
Three-dimensional optical bit-memory recording and reading with a photorefractive crystal: analysis and experiment (1996)

We analyze the three-dimensional refractive-index distribution that is induced locally when a laser beam is focused onto a very small region in a photorefractive crystal. The formation of the index distribution is deduced from the temporal behavior of the electron density distribution in the crystal under non-steady-state conditions. The density distribution is computed by the use of a set of the recurrence relations that was derived from Kukhtarev’s equations, which describe the transport of electrons in time. In particular, we calculated the index distribution formed in Fe-doped LiNbO3 crystals. To verify the validity of our analysis, we read, by using a phase-contrast microscope, refractive-index dots that were recorded in Fe-doped LiNbO3 crystals. Agood agreement was obtained between experimental results and the calculated phase-contrast images when the characteristics of the imaging system are taken into account. We also found that the induced index change is largest when the c axis of the LiNbO3 crystal is oriented parallel to the polarization direction of the reading beam. Under this optimal condition, we succeeded in recording up to 10 layers of readable data in a LiNbO3 crystal.
Current regulatory (draft) guidance on chiral medicinal products: Canada, EEC, Japan, United States (1994)

The rapid development of stereospecific analytical, synthetic, and preparative methods has profoundly changed the prospects for development and application of chiral medicinal products. This has induced regulatory agencies, e.g., in Canada, the EEC, Japan, and the United States, to prepare guidance on this subject. The present draft documents are discussed, with emphasis on the two most important cases: (1) New racemates: How many extra requirements are justified? (2) Development of a single enantiomer from an approved racemate: how few are acceptable? At the moment the opportunities for early harmonisation are favourable and the formulation of one international guidance document seems feasible.
Percutaneous aortic valve replacement: will we get there? (2001)

Percutaneous implantation of a biological valve in the pulmonary position has recently enlarged the field of interventional cardiovascular catheterisation.1 Aortic valve disease is much more frequent than pulmonary valve disease and therefore a non-surgical approach for aortic valve replacement would be attractive. The percutaneous approach is obviously difficult because of the proximity of the aortic valve to the coronary orifices. We set out to develop a stent for valve implantation which avoids obstructing the coronary orifices. We describe here our initial experience using the new device for percutaneous valve replacement of the aortic valve in an animal study.

A newly designed stent with a deployment strategy in two steps was developed. The first step assures the orientation of the stent in the aortic orifice. The second acts as a support for the implantable valve. A naturally valved bovine jugular vein segment was mounted as previously described inside this stent (Numed, Osypka).2The venous wall was then reduced along the commissures in order to remove the wall in front of the coronary orifices (fig 1).



Figure 1 
Left: venous …
Split-EGFP Screens for the Detection and Localisation of Protein–Protein Interactions in Living Yeast Cells (2010)

Proteomics aims to identify and classify the proteins present in a particular cell or tissue. However, we know that proteins rarely function alone and knowledge of which proteins interact with which other proteins is vital if we wish to understand how cells work. The budding yeast, Saccharomyces cerevisiae, is a well-established model for studying protein-protein interactions, and a number of methods have been developed to do this. A method for the in vivo detection and localisation of interacting pairs of proteins in living yeast cells is presented. The method relies on the ability of fragments of enhanced green fluorescent protein (EGFP) to reassemble if brought into close proximity. The reassembled EGFP regains the ability to fluoresce, and this fluorescence can be detected providing evidence of interaction and information about its location. S. cerevisiae is an ideal organism to apply this method to due to the relative ease with which its genome can be manipulated. The method described enables the modification of S. cerevisiae genes at the 3'-end with DNA encoding fragments of EGFP. Consequently, the expression levels of the proteins are unlikely to be affected and thus the method is unlikely to result in false positives. In addition to the protocol for labelling and detection of interacting pairs of yeast proteins, methods for simple tests for the effects of the labelling on the organism's function are presented.
Expression of c-kit receptor in human cholangiocarcinoma and in vivo treatment with imatinib mesilate in chimeric mice (2006)

c-kit expression is detectable at a moderate to low protein level in biliary tract cancer. Imatinib mesilate exerts marked effects on tumor growth in vitro and in vitro dependent on the level of c-kit expression.
Tumor-Selective Gene Expression in a Hepatic Metastasis Model after Locoregional Delivery of a Replication-Competent Retrovirus Vector (2006)

Our results thus show that locoregional infusion of RCR vectors can be used to deliver therapeutic genes selectively to tumor cells in the liver while sparing normal hepatocytes and without dissemination to extrahepatic normal tissues.
Correlated Equilibrium as an Expression of Bayesian Rationality (1987)

Correlated equilibrium is formulated in a manner that does away with the dichotomy usually perceived between the "Bayesian" and the "game-theoretic" view of the world.From the Bayesian viewpoint, probabilities should be assignable to everything, including the prospect of a player choosing a certain strategy in a certain game.The so-called "game-theoretic" viewpoint holds that probabilities can only be assigned to events not governed by rational decision makers; for the latter, one must substitute an equilibrium (or other game-theoretic) notion.The current formulation synthesizes the two viewpoints: Correlated equilibrium is viewed as the result of Bayesian rationality; the equilibrium condition appears as a simple maximization of utility on the part of each player, given his information.A feature of this approach is that it does not require explicit randomization on the part of the players.Each player always chooses a definite pure strategy, with no attempt to randomize; the probabilistic nature of the strategies reflects the uncertainty of other players about his choice.Examples are given.
Excision of hypoxanthine from DNA containing dIMP residues by the Escherichia coli, yeast, rat, and human alkylpurine DNA glycosylases. (1994)

The deamination of adenine residues in DNA generates hypoxanthine, which is mutagenic since it gives rise to an A.T to G.C transition. Hypoxanthine is removed by hypoxanthine DNA glycosylase activity present in Escherichia coli and mammalian cells. Using polydeoxyribonucleotides or double-stranded synthetic oligonucleotides that contain dIMP residues, we show that this activity in E. coli is associated with the 3-methyladenine DNA glycosylase II coded for by the alkA gene. This conclusion is based on the following facts: (i) the two enzymatic activities have the same chromatographic behavior on various supports and they have the same molecular weight, (ii) both are induced during the adaptive response, (iii) a multicopy plasmid bearing the alkA gene overproduces both activities, (iv) homogeneous preparation of AlkA has both enzymatic activities, (v) the E. coli alkA- mutant does not show any detectable hypoxanthine DNA glycosylase activity. Under the same experimental conditions, but using different substrates, the same amount of AlkA protein liberates 1 pmol of 3-methyladenine from alkylated DNA and 1.2 fmol of hypoxanthine from dIMP-containing DNA. The Km for the latter substrate is 420 x 10(-9) M as compared to 5 x 10(-9) M for alkylated DNA. Hypoxanthine is released as a free base during the reaction. Duplex oligodeoxynucleotides containing hypoxanthine positioned opposite T, G, C, and A were cleaved efficiently. ANPG protein, APDG protein, and MAG protein--the 3-methyladenine DNA glycosylases of human, rat, and yeast origin, respectively--were also able to release hypoxanthine from various DNA substrates containing dIMP residues. The mammalian enzyme is by far the most efficient hypoxanthine DNA glycosylase of all the enzymes tested.
One-step shaping of NiTi biomaterial by selective laser melting (2007)

NiTi alloy has excellent biocompatibility. This paper presents a novel technology of direct shaping of this promising biomaterial with selective laser melting (SLM). The frequently encountered defects of the SLM metal alloy parts such as non-fully melting, thermal deformation and balling were analyzed theoretically and experimentally, and the microstructure of the parts was analyzed on microscope. The results show that an appropriate selection of laser mode and scanning strategy assures a satisfying quality of the final parts; they also reveal that the SLM technology can be expected as a potential technology to directly manufacture the artificial implant of NiTi alloys.