gebhart/patrepeval huggingface dataset:
Constitutive, long-term production of human interferons by hamster cells contalning multiple copies of a cloned interferon gene (1983)

Hybrid plasmids containing the mouse dihydrofolate reductase (dhfr) and a human interferon (either IFN-alpha 5 or IFN-gamma) coding sequence under the control of viral promoters were transfected into dhfr- Chinese hamster ovary (CHO) cells. dhfr+ colonies produced IFN at 10-1000 units X ml-1 X day-1. Clones selected in methotrexate had a 20-50-fold increase in the IFN-alpha 5 and dhfr DNA and mRNA content and secreted IFN at 20,000-100,000 units X ml-1 X day-1. SDS-polyacrylamide gel electrophoresis of partially purified 35S-HuIFN-gamma from CHO cells showed a multiple of labeled bands with a mobility corresponding to 22,400 to 23,400 daltons which was absent in the supernatants of non-transformed CHO cells. The higher apparent molecular weight of human IFN-gamma from CHO cells as compared to that of human IFN-gamma from E. coli (about 18,800) suggests that the former was glycosylated.
Distribution of kinetochore (centromere) antigen in mammalian cell nuclei. (1981)

Antigens associated with mammalian centromeres were localized at the high and electron microscopic levels using the peroxidase-labeled antibody method. The antibody used was of a type naturally occurring in the sera of patients with scleroderma. At the light microscopic level, it reacts specifically with the centromere regions of chromosomes in a variety of mammalian species and strains in discrete foci in interphase nuclei. We find that the number of foci approximates the number of chromosomes present in the various cell types. At the ultrastructural level, the antigenic foci are confirmed to lie in the kinetochore regions of each chromosome. In interphase nuclei, the antigenic foci were usually associated either with the inner surfaces of the nuclear envelope or with the nucleoli. These observations indicate that the centromere regions of the chromosomes in interphase are not randomly distributed within the nucleus but are usually fixed either to the inner surface of the nuclear envelope or to nucleoli.
Conformational Adaptation Drives Potent, Selective and Durable Inhibition of the Human Protein Methyltransferase DOT1L (2012)

DOT1L is the human protein methyltransferase responsible for catalyzing the methylation of histone H3 on lysine 79 (H3K79). The ectopic activity of DOT1L, associated with the chromosomal translocation that is a universal hallmark of MLL-rearranged leukemia, is a required driver of leukemogenesis in this malignancy. Here, we present studies on the structure-activity relationship of aminonucleoside-based DOT1L inhibitors. Within this series, we find that improvements in target enzyme affinity and selectivity are driven entirely by diminution of the dissociation rate constant for the enzyme-inhibitor complex, leading to long residence times for the binary complex. The biochemical K(i) and residence times measured for these inhibitors correlate well with their effects on intracellular H3K79 methylation and MLL-rearranged leukemic cell killing. Crystallographic studies reveal a conformational adaptation mechanism associated with high-affinity inhibitor binding and prolonged residence time; these studies also suggest that conformational adaptation likewise plays a critical role in natural ligand interactions with the enzyme, hence, facilitating enzyme turnover. These results provide critical insights into the role of conformational adaptation in the enzymatic mechanism of catalysis and in pharmacologic intervention for DOT1L and other members of this enzyme class.
A multi-method approach toward de novo glycan characterization: A Man-5 case study (2010)

Regulatory agencies' expectations for biotherapeutic approval are becoming more stringent with regard to product characterization, where minor species as low as 0.1% of a given profile are typically identified. The mission of this manuscript is to demonstrate a multi-method approach toward de novo glycan characterization and quantitation, including minor species at or approaching the 0.1% benchmark. Recently, unexpected isomers of the Man(5)GlcNAc(2) (M(5)) were reported (Prien JM, Ashline DJ, Lapadula AJ, Zhang H, Reinhold VN. 2009. The high mannose glycans from bovine ribonuclease B isomer characterization by ion trap mass spectrometry (MS). J Am Soc Mass Spectrom. 20:539-556). In the current study, quantitative analysis of these isomers found in commercial M(5) standard demonstrated that they are in low abundance (<1% of the total) and therefore an exemplary "litmus test" for minor species characterization. A simple workflow devised around three core well-established analytical procedures: (1) fluorescence derivatization; (2) online rapid resolution reversed-phase separation coupled with negative-mode sequential mass spectrometry (RRRP-(-)-MS(n)); and (3) permethylation derivatization with nanospray sequential mass spectrometry (NSI-MS(n)) provides comprehensive glycan structural determination. All methods have limitations; however, a multi-method workflow is an at-line stopgap/solution which mitigates each method's individual shortcoming(s) providing greater opportunity for more comprehensive characterization. This manuscript is the first to demonstrate quantitative chromatographic separation of the M(5) isomers and the use of a commercially available stable isotope variant of 2-aminobenzoic acid to detect and chromatographically resolve multiple M(5) isomers in bovine ribonuclease B. With this multi-method approach, we have the capabilities to comprehensively characterize a biotherapeutic's glycan array in a de novo manner, including structural isomers at >/=0.1% of the total chromatographic peak area.
Chemistry and Biology of Galactofuranose‐Containing Polysaccharides (2009)

The thermodynamically less stable form of galactose-galactofuranose (Galf)-is essential for the viability of several pathogenic species of bacteria and protozoa but absent in this form in mammals, so the biochemical pathways by which Galf-containing glycans are assembled and catabolysed are attractive sites for drug action. This potential has led to increasing interest in the synthesis of molecules containing Galf residues, their subsequent use in studies directed towards understanding the enzymes that process these residues and the identification of potential inhibitors of these pathways. Major achievements of the past several years have included an in-depth understanding of the mechanism of UDP-galactopyranose mutase (UGM), the enzyme that produces UDP-Galf, which is the donor species for galactofuranosyltransferases. A number of methods for the synthesis of galactofuranosides have also been developed, and practitioners in the field now have many options for the initiation of a synthesis of glycoconjugates containing either alpha- or beta-Galf residues. UDP-Galf has also been prepared by a number of approaches, and it appears that a chemoenzymatic approach is currently the most viable method for producing multi-milligram amounts of this important intermediate. Recent advances both in the understanding of the mechanism of UGM and in the synthesis of galactofuranose and its derivatives are highlighted in this review.
Substituted isatoic anhydrides: selective inactivators of trypsin-like serine proteases (1986)

Derivatives of isatoic anhydride were prepared and tested as inhibitors of serine proteases. A number of isatoic anhydrides with positively charged substituents irreversibly inactivated several trypsin-like enzymes and preferentially inactivated trypsin over chymotrypsin. Further selectivity was obtained by introduction of an aromatic group on the N-1 position of isatoic anhydride. 7-(Aminomethyl)-1-benzylisatoic anhydride was prepared and was a selective inactivator of thrombin; thus it is possible to prepare derivatives of isatoic anhydride that are highly enzyme selective without attaching peptide recognition structures.
El conocimiento sobre los insectos que atacan el cafeto: una alternativa para la Educación Ambiental en la carrera de Agronomía. (2003)

Las acciones favorables al desarrollo de la Educacion Ambiental (E.A) se hanincrementado a escala internacional a partir de la Cumbre de la tierra, de maneraparticular en Cuba la Educacion Ambiental y todos los aspectos relacionados con elmedio ambiente se reflejan de forma sistematica con el Programa Nacional de medioambiente y desarrollo .
Interfacial Nucleic Acid Hybridization Studied by Random Primer 32P Labeling and Liquid-Phase Acoustic Network Analysis (1994)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInterfacial Nucleic Acid Hybridization Studied by Random Primer 32P Labeling and Liquid-Phase Acoustic Network AnalysisHongbo. Su, Krishna M. R. Kallury, Michael. Thompson, and Arthur. RoachCite this: Anal. Chem. 1994, 66, 6, 769–777Publication Date (Print):March 15, 1994Publication History Published online1 May 2002Published inissue 15 March 1994https://pubs.acs.org/doi/10.1021/ac00078a002https://doi.org/10.1021/ac00078a002research-articleACS PublicationsRequest reuse permissionsArticle Views176Altmetric-Citations91LEARN 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
Follicular large-cell lymphoma treated with intensive chemotherapy: an analysis of 89 cases included in the LNH87 trial and comparison with the outcome of diffuse large B-cell lymphoma. Groupe d'Etude des Lymphomes de l'Adulte. (1997)

FLCL patients have a favorable response rate and survival when treated with intensive chemotherapy. Their outcome is similar to that of B-cell DLCL patients, and a long-term FFP is observed for a substantial number of patients. Some adverse prognostic factors (including those of the International Prognostic Index, bone marrow involvement, and beta-2 microglobulin) have been identified to define a subset of patients who require other therapeutic approach.
<title>Contamination removal from photomasks using a dry laser-assisted cleaning technology</title> (1996)

Photomask manufacturing for sub-0.5 micron ICs faces two principal challenges: efficient cleaning within cycle time requirements and minimization of water and chemical usage. A new technology using only deep ultraviolet photons and a flowing inert gas cleans state-of-the-art optical and x-ray photomasks. The technology uses no water or chemicals. Tools can handle single or multiple substrate sizes. There is no optical reflectivity change in the chrome. No damage is observed on chrome patterns from either backside or front side exposure whether the features are positioned horizontally or vertically. Our work to date indicates that this technology meets the cycle time requirements in the photomask manufacturing process.
Fast Regular Expression Matching Using FPGAs (2001)

This paper presents an efficient method for finding matches to a given regular expression in given text using FPGAs. To match a regular expression of length n, a serial machine requires 0(2^n) memory and takes 0(1) time per text character. The proposed approach reqiures only 0(n^2) space and still process a text character in 0(1) time (one clock cycle).The improvement is due to the Nondetermineistic Finite Automaton (NFA) used to perform the matching. As far as the authors are aware, this is the first prctical use of a nondeterministic state machine on programmable logic. Furthermore, the paper presents a simple, fast algorithm that quickly constructs the NFA for the given regular expression. Fast NFA construction is crucial because the NFA structure depends on the regular expression, which is known only at runtime. Implementations of the algorithm for conventional FPGAs and the self-reconfigurable Gate Array (SRGA) are described. To evaluate performance, the NFA logic was mapped onto the Virtex XCV100 FPGA and the SRGA. Also, the performance of GNU grep for matching regular expressions was evaluated on an 800 MHz Pentium III machine. The proposed approach was faster than best case grep performance in most cases. It was orders of magnitude faster than worst case grep performance. Logic for the largest NFA considered fit in less than a 1000 CLBs while DFA storage for grep in the worst case consumed a few hundred megabytes.
Dehydrooligopeptides. XI. Facile Syntheses of Various Kinds of Dehydrodi- and tripeptides, and Dehydroenkephalins Containing ΔTyr Residue by Using N-Carboxydehydrotyrosine Anhydride (1989)

Abstract Several kinds of N-free and protected N-carboxydehydrotyrosine anhydride (ΔTyr·NCA) derivatives, derived by both the cyclization of the corresponding N-benzyloxycarbonyldehydrotyrosine derivatives and the protection of the resulting ΔNCA, were employed for a one-pot dehydrooligopeptide (DHP) synthesis. As a result, various kinds of DHPs with a wide variety of combinations of sequences could be synthesized in fairly good yields. In addition, by utilizing the obtained information, two kinds of leucine-dehydroenkephalins containing a ΔTyr1 and both ΔTyr1 and ΔPhe4 residues were also synthesized.
Urinary Excretion Profiles of 11-Nor-9-Carboxy- 9-Tetrahydrocannabinol in Humans after Single Smoked Doses of Marijuana (1996)

Interpretation of marijuana-positive urine tests requires an understanding of the excretion pattern of marijuana metabolites in humans. However, limited urinary excretion data from controlled clinical studies of marijuana use are available. In this study, six subjects smoked a single marijuana cigarette (placebo, 1.75% delta 9-tetrahydrocannabinol [THC], or 3.55% THC) each week while residing on the clinical ward of the Addiction Research Center. Individual urine specimens were collected for 7 days after drug administration and analyzed for 11-nor-9-carboxy-delta 9-tetrahydrocannabinol (THCCOOH) by gas chromatography-mass spectrometry (GC-MS) with a limit of detection of 0.5 ng/mL. Substantial intersubject variability in patterns of THCCOOH excretion was noted between subjects and between doses. Mean THCCOOH concentrations in the first urine collections were 47 +/- 22.3 ng/mL and 75.3 +/- 48.9 ng/mL after the 1.75 and 3.55% THC cigarettes, respectively. Mean peak urine THCCOOH concentrations averaged 89.8 +/- 31.9 ng/mL and 153.4 +/- 49.2 ng/mL after smoking of approximately 15.8 mg and 33.8 mg THC, respectively. The mean times of peak urine concentration were 7.7 +/- 0.8 h after the 1.75% THC and 13.9 +/- 3.5 h after the 3.55% THC dose. Mean GC-MS THCCOOH detection times for the last positive urine sample after the smoking of a single 1.75 or 3.55% THC cigarette were 33.7 +/- 9.2 h and 88.6 +/- 9.5 h, respectively, when a 15-ng/mL cutoff concentration was used. An average of 93.9 +/- 24.5 micrograms THCCOOH (range, 34.6-171.6 micrograms) was excreted by each subject during the 7-day period after smoking of a single 1.75% THC cigarette. The average amount of THCCOOH excreted in the same time period after the high dose was 197.4 +/- 33.6 micrograms (range, 107.5-305.0 micrograms). This represented an average of only 0.54 +/- 0.14% and 0.53 +/- 0.09% of the original amount of THC in the low-and high-dose cigarettes, respectively. These data provide a detailed complication of THCCOOH concentrations in urine after administration of marijuana that may aid in the interpretation of urine cannabinoid results.
Metastatic Pancreatic Cancer: American Society of Clinical Oncology Clinical Practice Guideline (2016)

A multiphase computed tomography scan of the chest, abdomen, and pelvis should be performed. Baseline performance status and comorbidity profile should be evaluated. Goals of care, patient preferences, treatment response, psychological status, support systems, and symptom burden should guide decisions for treatments. A palliative care referral should occur at first visit. FOLFIRINOX (leucovorin, fluorouracil, irinotecan, and oxaliplatin; favorable comorbidity profile) or gemcitabine plus nanoparticle albumin-bound (NAB) -paclitaxel (adequate comorbidity profile) should be offered to patients with Eastern Cooperative Oncology Group performance status (ECOG PS) 0 to 1 based on patient preference and support system available. Gemcitabine alone is recommended for patients with ECOG PS 2 or with a comorbidity profile that precludes other regimens; the addition of capecitabine or erlotinib may be offered. Patients with an ECOG PS ≥ 3 and poorly controlled comorbid conditions should be offered cancer-directed therapy only on a case-by-case basis; supportive care should be emphasized. For second-line therapy, gemcitabine plus NAB-paclitaxel should be offered to patients with first-line treatment with FOLFIRINOX, an ECOG PS 0 to 1, and a favorable comorbidity profile; fluorouracil plus oxaliplatin, irinotecan, or nanoliposomal irinotecan should be offered to patients with first-line treatment with gemcitabine plus NAB-paclitaxel, ECOG PS 0 to 1, and favorable comorbidity profile, and gemcitabine or fluorouracil should be offered to patients with either an ECOG PS 2 or a comorbidity profile that precludes other regimens. Additional information is available at www.asco.org/guidelines/MetPC and www.asco.org/guidelineswiki.
Identification by Affinity Chromatography of Boar Sperm Membrane-Associated Proteins Bound to Immobilized Porcine Zona Pellucida. Mapping of the Phosphorylethanolamine-Binding Region of Spermadhesin AWN (1995)

We have identified boar sperm membrane components recovered by affinity chromatography on a porcine zona pellucida affinity column. The major zona pellucida-bound proteins were spermadhesins AWN and AQN-3, the heparin-binding protein pAIF, and a homolog of the mouse milk fat globule membrane protein. All these proteins are phospholipid-binding proteins peripherally associated with the plasma membrane. Our data suggest that coating proteins tightly bound to the external lipid bilayer may act as major zona pellucida-binding molecules. Using a synthetic peptide approach we show that the regions of spermadhesin AWN comprising residues 6-12 and 104-108 possess affinity for phosphorylethanolamine. These two amino acid sequences are in close proximity in the predicted structural model for AWN, and in opposite location to its carbohydrate-recognition domain. Taken together, our data provide further evidence for the possible involvement of members of the porcine spermadhesin protein family in gamete interaction and suggest a model for the ultrastructural disposition of functional domains of spermadhesin AWN bound to the sperm surface.
Embryonic origin of the adult hematopoietic system: advances and questions (2011)

Definitive hematopoietic stem cells (HSCs) lie at the foundation of the adult hematopoietic system and provide an organism throughout its life with all blood cell types. Several tissues demonstrate hematopoietic activity at early stages of embryonic development, but which tissue is the primary source of these important cells and what are the early embryonic ancestors of definitive HSCs? Here, we review recent advances in the field of HSC research that have shed light on such questions, while setting them into a historical context, and discuss key issues currently circulating in this field.
Midkine inhibits apoptosis via extracellular signal regulated kinase (ERK) activation in PC12 cells. (1999)

Midkine (MK) is a new member of the family of heparin-binding neurotrophic factors. MK has several important biological effects and plays an important role in the development and survival of neurons. The mechanism by which MK exerts its neurotrophic actions, however has not been sufficiently clarified. To understand the intracellular pathway activated by MK, we established an apoptosis-induction system with the neuronal cell line PC12 and studied the involvement of the mitogen-activated protein kinase (MAPK) cascade in neuroprotective actions of MK. We demonstrate here that MK rescued PC12 cells from apoptosis induced by serum deprivation in a dose-dependent manner. MK also activated extracellular signal-regulated kinases 1 and 2 (ERK1 and ERK2), which are well known as signal transducer acting downstream several receptors. PD98059, an inhibitor of MAPK kinase (MAPKK), inhibited ERK activation and also prevented the trophic effect of MK. These results indicate that MK exerts its neuroprotective actions mainly via ERK activation.
Gastrointestinal luminal polyamines: cellular accumulation and enterohepatic circulation (1990)

The concentration of polyamines contained in the lumen of the gut was quantified. The duodenum and jejunum of the rat contained 2-3 mM putrescine and 1-2 mM cadaverine, whereas in the ileum and colon the concentration of these polyamines was significantly less. In addition, the concentrations of spermine and spermidine in the intestinal lumen were low to undetectable. Putrescine in the lumen of the gut was over 90% free with only 10% or less bound to protein. The activity of the enzymes responsible for the synthesis of polyamines was also measured. In contrast to concentration, enzyme activity was found to be high in the ileum, cecum, and colon and nonexistent in the duodenal and jejunal lumen. This suggested the potential for enterohepatic circulation of polyamines that were synthesized by the colonic microflora and transported to the proximal gut via the portal circulation and biliary tree. Indeed, when [14C]putrescine was instilled into the lumen of the gut, it was secreted in pancreaticobiliary secretions. Upper and lower jejunum and colon all supported enterohepatic circulation of polyamines, whereas it was absent in the ileum. Polyamine accumulation in IEC-6 cells grown under in vitro conditions was also measured. Putrescine was transported under time- and temperature-dependent but sodium-independent conditions. The transporter displayed little selectivity for the various polyamines and compounds with related structures but did not recognize amino acids. The Michaelis constant for putrescine accumulation was 1.26 x 10(-6) M with a maximal velocity of the enzyme reaction of 5,184 pmol putrescine.mg protein-1.h-1.(ABSTRACT TRUNCATED AT 250 WORDS)