gebhart/patrepeval huggingface dataset:
VIBRATIONAL SPECTRA OF RESONANCE STABILIZED ANIONS. $(C_{n}O_{n})^{-2}$ (1962)

Raman and infrared spectra are reported for resonance stabilized anions, $(C_{n}O_{n})^{-2} (n = 4, 5$ and 6). All the spectra are very simple, indicating high symmetry. For $(C_{4}O_{4})^{-2}$ and $(C_{5}O_{5})^{-2}$, the data fit very well with symmetrical planar models having $D_{\\rm 4b}$ and $D_{\\rm 5b}$ symmetry. However, the $D_{\\rm 6b}$ structure seems to be unlikely for $(C_{6}O_{6})^{-2}$. Tentative assignments are given for the main vibrational frequencies of $(C_{4}O_{4})^{-2}$ and $(C_{5}O_{5})^{-2}$. On the basis of this assignment, a normal coordinate treatment was carried out using a Urey-Badley force field. Agreements between observed and calculated frequencies are fairly good. The force constants obtained in this calculation show that the C---C and C---O bond characters are intermediate between pure single and pure double bonds, indicating that conjugation is complete over the anions. Furthermore, it was found the C---C double bond character increases and C---O double bond character decreases as the ring size becomes smaller. This is an accordance with results obtained from M. O. calculation. The repulsion force constant for non-bonded C atoms increases rapidly going from $(C_{5}O_{5})^{-2}$ to $(C_{4}O_{4})^{-2}$ as expected. Some abnormal values are obtained for bending force constants. However, these are improved in some degree by a modification of the simple Urey-Bradley force field in which flexibility of the C---C bond is taken into consideration.
A Framework for Ubiquitous Content Sharing (2009)

Examining three content-sharing scenarios reveals requirements for a generic content-sharing framework. The SharedLife framework helps combine different content types and balance user control versus effort when sharing information.
80 fs pulses from a stretched-pulse Yb 3+ :silica fibre laser (1996)

We report the first demonstration of ultrashort pulse generation in a Ytterbium:silica fibre laser. The self-starting, stretched-pulse laser system produces 100 pJ, transform-limited, 80 fs pulses and represents a key step in the development of an all-solid-state, Yb3+-based, high power amplified system.
Identification and characterization of a new gene family induced during macrophage activation (1991)

In this report, we describe the primary structure and regulation of two novel IFN-gamma-inducible genes expressed during the process of macrophage activation. We used the RAW 264.7 cell line to prepare a cDNA library, from which inducible genes were selected by differential hybridization. Two cDNA clones, mag-1 and mag-2 (for macrophage-activation gene-1 and -2), were induced by IFN-gamma treatment in both RAW 264.7 cells and thioglycolate-elicited peritoneal macrophages, but not in the noncytolytic cell line, WEHI-3. A comparison of the nucleotide and deduced amino acid sequences of clones mag-1 and mag-2 with sequences in available data bases revealed no homologs. However, comparison of mag-1 and mag-2 sequences with each other revealed that these genes are homologous, with conserved residues concentrated at the amino terminus. Kinetic analyses revealed similar temporal patterns of induction of mRNA expression for these genes after IFN-gamma treatment. In addition, the genes showed distinct response patterns to the macrophage-activating stimuli IFN-gamma and LPS used either alone or in combination. Analysis of a panel of cell types of various lineages demonstrated that expression of these genes was associated with cellular activation in multiple cell types. As a result of the sequence similarities between these genes, we propose that they define a new family of IFN-gamma-regulated genes in macrophages.
Effect of nifedipine on changes in fibrinogen and von Willebrand factor in haemodialysis patients treated with recombinant human erythropoietin (1995)

Erythropoietin (EPO) therapy in haemodialysis patients may be associated with the development of hypertension and vascular access thrombosis. Raised levels of fibrinogen and von Willebrand factor have been implicated in the pathophysiology of thrombosis under these circumstances. The effect of nifedipine, used to treat EPO therapy-related hypertension, on levels of fibrinogen and von Willebrand factor antigen (vWf) was studied in a group of 21 EPO-treated haemodialysis patients. Significant increments in both fibrinogen and vWf following EPO therapy were observed in the 13 patients who did not receive nifedipine (fibrinogen (median range), pre-EPO: 3.73 (2.41-6.38) mg/ml, post-EPO: 4.59 (3.03-8.80) mg/ml, P < 0.05; vWf pre-EPO: 183 (118-374)% normal, post-EPO: 253 (124-392)% normal, P < 0.01). Similar changes were not seen in the eight nifedipine-treated patients (fibrinogen, pre-EPO: 3.35 (2.58-6.32) mg/ml, post-EPO: 3.36 (2.69-7.20) mg/ml, P = NS; vWf, pre-EPO: 176 (104-298)% normal, post-EPO: 175 (82-371)% normal, P = NS). These effects were independent of blood pressure control. The use of nifedipine to treat EPO therapy-related hypertension may therefore potentially help to reduce the risk of vascular access thrombosis.
Nur77, a member of the steroid receptor superfamily, antagonizes negative feedback of ACTH synthesis and secretion by glucocorticoid in pituitary corticotrope cells (1998)

Nur77 is a member of the steroid receptor superfamily and is known to be expressed in animals under stress. We studied the role of nur77 in the regulation of the hypothalamic-pituitary-adrenal (HPA) axis during the stress response using a murine pituitary corticotrope cell line, AtT-20. Corticotropin-releasing hormone (CRH), a stress mediator in the HPA axis, induced the expression of nur77 transiently in AtT-20 cells. Gel shift assay showed that nur77 bound to negative glucocorticoid responsive element (nGRE) in the promoter of the human proopiomelanocortin (POMC) gene and the formation of the nur77-nGRE complex increased after treatment of the cells with CRH. Negative GRE is known to be necessary for the negative regulation by glucocorticoid of the POMC gene expression. In stable transformants of AtT-20 cells expressing a human homolog of nur77, NAK-1, at a high level, glucocorticoid-mediated inhibition of both POMC mRNA induction and ACTH secretion was significantly lower than that in the NAK-1-non-expressing cells (P < 0.001). These results strongly suggest that nur77 antagonizes the negative feedback effect of glucocorticoid on the synthesis and secretion of ACTH in pituitary corticotropes. This suggests that nur77 plays an important role in the pituitary gland in the biological adaptation to overcome stress.
A Quantitative Assessment of Osteoinductivity of Human Demineralized Bone Matrix (1997)

Demineralized bone matrix (DBM) is widely used in the repair of pathologies associated with skeletal defects and periodontal diseases. The present study was directed at establishing in vivo and in vitro models for a quantitative assessment of the osteoinductivity of DBM before clinical use. Athymic mice were used in an in vivo assay to overcome the species limitations (for human DBM) found in xenogeneic animal models. Calcium contents of explants, as an indicator of new bone formation, were assayed and expressed as a change in the weight percent calcium in the explant as compared to the weight percent of calcium in the implanted material. A total of 82 mice (2 implants per mouse) were used in this study. Significant amounts of new bone were induced in this animal model in response to implantation of DBM. Muscular implantation was found to be more osteoinductive (increases of 10.0 +/- 0.4 calcium weight percent of explant) than subcutaneous implantation (increases of 1.62 +/- 0.27 calcium weight percent of explant) and new bone formation in muscular implantation sites of athymic mice mimics endochondral bone formation. Between weeks 1 to 4, the weight of explanted materials did not significantly differ from the weight of the implanted material; however, by week 5 the explant weight began to increase. Calcium deposition over the 5 weeks of implantation increased in a nearly linear fashion. Consequently week 4 was chosen as the optimum time for explantation in the in vivo assay in that sufficient calcium levels had been achieved without a significant increase in explant dry weight. Aliquots of 10, 20, 30, and 40 mg per implantation site were used in dose response studies in the in vivo bioassay. Dose response curves with DBM exhibited maximal activity at the 20 mg DBM implant dose in the in vivo bioassay. An in vitro bioassay was also developed where human periosteal (HPO) cells were chosen because osteoprogenitor cells found in bone repair typically come from periosteal tissue. Alkaline phosphatase (ALP) activity in confluent cell cultures of HPO cells exposed to DBM, as an indicator of osteoblast induction, reached its highest level on day 5 of DBM treatment. Aliquots of 2, 5, 10, 20, 30, and 40 mg DBM per flask were chosen in dose response studies using the in vitro bioassay. These dose response studies with DBM revealed that quantities approximating 5 to 10 mg DBM in the in vitro model provided for maximal levels of ALP in cell extracts. A linear correlation (R2 = 0.7397) was demonstrated between the in vivo calcium remineralization assay and the in vitro ALP assay of osteoinductivity of DBM, suggesting that the in vitro assay can be used to quantitatively assess the osteoinductive potential of DBM where production and distribution of clinically usable DBM dictates rapid analysis.
Molecular Cloning and Genomic Analysis of Mouse GalNAc 2,6-Sialyltransferase (ST6GalNAc I) (2000)

cDNA clones encoding mouse GalNAc alpha2,6-sialyltransferase (ST6GalNAc I) were isolated from a mouse submaxillary gland cDNA library. The deduced amino acid sequence of cDNA clones is 526 amino acids in length and has highly conserved motifs among sialyl transferases, sialyl motifs L, S, and VS. The expressed recombinant enzyme exhibited similar substrate specificity to chicken ST6GalNAc I. The mouse ST6GalNAc I gene was expressed in submaxillary gland, mammary gland, colon, and spleen. The mouse ST6GalNAc I gene was also cloned from a mouse genomic library, which was divided into 9 exons spanning over 8 kilobases of genomic DNA. The genomic structure of the mouse ST6GalNAc I gene was similar to that of the mouse ST6GalNAc II gene. Unlike the ST6GalNAc II gene, however, which has a housekeeping gene-like promoter with GC-rich sequences, the ST6GalNAc I gene has two promoters and they do not contain GC-rich sequences but contain putative binding sites for tumor-associated transcription factors such as c-Myb, c-Myc/Max, and c-Ets. Analysis of the 5'-RACE PCR products suggested that the mouse ST6GalNAc I gene expression is regulated by these two promoters in tissue-specific manners.
Fat reduction to prevent prostate cancer: waiting for more evidence? (2001)

Complementary medicine has become an important area of interest for patients and researchers around the world. The utilization of some of these therapies by many individuals makes it imperative to understand whether they have any role in treatment of cancer or other diseases. Some of such therapies may play a role in the prevention of prostate cancer. Clinical trials are addressing this issue, and whether these products could also improve prognosis of prostate cancer. That dietary fat reduction may help to prevent prostate cancer is supported by numerous case-control studies reported over the past several decades, but recent prospective studies suggest that the impact of fat reduction in this regard may not be great. Clinicians should be careful not to suggest such a benefit until more research provides a better picture of the situation. Breast cancer is probably the best example of why more research into dietary changes for reduction in cancer risk is needed. Once believed to play a significant role, recent prospective studies suggest that dietary fat reduction may have little effect on breast cancer prevention, although some interesting insights have been gained with regard to the method of meat preparation and the influence of genetics. Fat reduction, together with soy products or other plant estrogen foods, may have a symbiotic relationship. Numerous healthy lifestyle changes incorporated and practiced at one time (healthy diet, attainment and maintenance of normal weight, soy consumption, among others) may hold some promise in the area of cancer prevention. In the meantime any healthy lifestyle or dietary change should be encouraged, because it may reduce the risk of cardiovascular disease, which is still the number one cause of mortality. It is also an important cause of morbidity and mortality in cancer patients. Regardless, complementary medicine should probably be discussed with any patient who is initiating or undergoing conventional treatment, because of the cardiovascular benefits and overall potential impact on all-cause mortality. Whether such therapies impact on prostate carcinoma remains to be determined through additional prospective investigations.
Structural Organization of the Gene Encoding the Neuroendocrine Chaperone 7B2 (1996)

The neuroendocrine-specific polypeptide 7B2 is a constituent of the regulated secretary pathway. Recently, 7B2 was found to function as a molecular chaperone for prohormone convertase PC2. This report describes the genomic organization of the 7B2 gene which consists of six exons. Exon I corresponds to the 5'-untranslated mRNA region, while exons 2 and 3 encode the signal peptide and the amino-terminal half of the 7B2 protein that is distantly related to a subclass of molecular chaperones. The carboxy-terminal half of 7B2, responsible for its inhibitory action on PC2, is encoded by exons 4-6. Primer-extension analysis showed that the human 7B2 gene is transcribed from multiple transcription-initiation sites. The human 7B2 gene promoter contains a cAMP-responsive element, an AP-1 site, and several Pit-1/GHF-1-binding domains and heat-shock-element-like sequences but no obvious TATA or CAAT boxes. Of further interest is the finding of two DNA elements which are common to the promoter regions of the 7B2 gene and other genes selectively expressed in neuroendocrine tissues.
Giardiasis in mice: studies on the characteristics of chronic infection in C3h/He mice. (1981)

When C3H/He mice are dosed orally with fecal cysts or trophozoites of the intestinal parasite, Giardia muris, they become chronically infected, whereas BALB/c (or DBA/2) mice rapidly eliminate their infection. The ability to eliminate a primary infection or resist a challenge infection was not related to levels of serum IgA antibody directed against a crude extract of trophozoites. The possibility that the development of host-protective immunity may either be delayed or absent in C3H/He mice was investigated by 2 types of experiment: 1) BALB/c and C3H/He mice were drug-cured at various times after a primary infection and assessed for their ability to resist reinfection, and 2) the ability of infected female mice to protect their suckling young was assessed. Under these experimental conditions, no significant difference in the kinetics of development of resistance to a challenge infection was noted. Thus, mice of both strains were capable of resisting a challenge infection after drug-cured and infected mothers were able to protect their suckling young from a challenge infection. Drug-cured long-term infected mice were resistant to a challenge of either cysts or trophozoites obtained from either 1-wk infected nude mice or long-term infected C2H/He mice. Thus, it is unlikely that the explanation for chronic infection oif C3H/He mice is that variants or a modified population of G. muris trophozoites arise to which C3H/He mice have a defective response. The possibility that G. muris is able to suppress host-protective responses in chronically-infected C3H/He mice but not in BALB/c mice is discussed.
Reversible stability switching of a hairpin DNA via a photo-responsive linker unit (2009)

We have designed and synthesized a novel photo-responsive linker unit, 4,4'-bis(hydroxymethyl)-azobenzene, which was introduced to the loop oligonucleotide in a DNA hairpin and was able to reversibly control the stability of the whole hairpin structure via UV or visible light irradiation.
Nectin-3, a New Member of Immunoglobulin-like Cell Adhesion Molecules That Shows Homophilic and Heterophilic Cell-Cell Adhesion Activities (2000)

We have isolated a novel cell-cell adhesion system localized at cadherin-based adherens junctions (AJs). This system consists of at least nectin, a Ca(2+)-independent immunoglobulin-like adhesion molecule, and afadin, an actin filament-binding protein, that connects nectin to the actin cytoskeleton. Nectin constitutes a family consisting of two members, nectin-1 and -2. We have isolated here a third member of the nectin family and named it nectin-3. Nectin-3 has three splicing variants, nectin-3alpha (biggest), -3beta (middle), and -3gamma (smallest). Like nectin-1 and -2, nectin-3alpha consists of three extracellular immunoglobulin-like domains, a transmembrane segment, and a cytoplasmic region with the C-terminal consensus motif for binding to the PDZ domain. Nectin-3alpha formed a cis-homo-dimer and showed Ca(2+)-independent trans-homo-interaction to cause homophilic cell-cell adhesion. Nectin-3alpha furthermore showed trans-hetero-interaction with nectin-1 or -2 but did not form a cis-hetero-dimer with nectin-1 or -2. Nectin-1 did not show trans-hetero-interaction with nectin-2. The affinity of trans-hetero-interaction of nectin-3alpha with nectin-1 or -2 was higher than that of trans-homo-interaction of nectin-1, -2, or -3alpha. Nectin-2 and -3 were ubiquitously expressed, whereas nectin-1 was abundantly expressed in brain. Nectin-3alpha was colocalized with nectin-2 at cadherin-based AJs and interacted with afadin. These results indicate that the nectin family consists of at least three members, nectin-1, -2, and -3, all of which show homophilic and heterophilic cell-cell adhesion activities and are localized at cadherin-based AJs.
Water intoxication and hyponatremic encephalopathy from the use of an oxytocin nasal spray. A case report. (1985)

Many nursing women returning to a full-time job and desiring to continue to breast feed are using oxytocin nasal sprays to facilitate breast emptying during the work day. Very few complications have been reported from its use, and the preparation has been assumed to be innocuous. However, we encountered a nursing mother whose life appears to have been jeopardized by the excessive and unmonitored application of such a spray. The patient was hospitalized for a viral illness and given a large quantity of intravenous fluid. In association with excessive self-administration of an oxytocin nasal spray, she developed severe water intoxication, with hyponatremic encephalopathy and convulsions. During the same hospitalization the patient subsequently developed a Guillain-Barré type of peripheral polyneuritis. The syndrome of inappropriate secretion of antidiuretic hormone has been reported to accompany the neurologic manifestations of the Guillain-Barré syndrome and may have been the cause of the convulsions. However, the temporal associations in this case strongly favor the unmonitored use of the oxytocin nasal spray as etiologic.
Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival (2014)

Somatic missense mutations can initiate tumorogenesis and, conversely, anti-tumor cytotoxic T cell (CTL) responses. Tumor genome analysis has revealed extreme heterogeneity among tumor missense mutation profiles, but their relevance to tumor immunology and patient outcomes has awaited comprehensive evaluation. Here, for 515 patients from six tumor sites, we used RNA-seq data from The Cancer Genome Atlas to identify mutations that are predicted to be immunogenic in that they yielded mutational epitopes presented by the MHC proteins encoded by each patient's autologous HLA-A alleles. Mutational epitopes were associated with increased patient survival. Moreover, the corresponding tumors had higher CTL content, inferred from CD8A gene expression, and elevated expression of the CTL exhaustion markers PDCD1 and CTLA4. Mutational epitopes were very scarce in tumors without evidence of CTL infiltration. These findings suggest that the abundance of predicted immunogenic mutations may be useful for identifying patients likely to benefit from checkpoint blockade and related immunotherapies.
Sound Classification in Hearing Aids Inspired by Auditory Scene Analysis (2005)

A sound classification system for the automatic recognition of the acoustic environment in a hearing aid is discussed. The system distinguishes the four sound classes "clean speech," "speech in noise," "noise," and "music." A number of features that are inspired by auditory scene analysis are extracted from the sound signal. These features describe amplitude modulations, spectral profile, harmonicity, amplitude onsets, and rhythm. They are evaluated together with different pattern classifiers. Simple classifiers, such as rule-based and minimum-distance classifiers, are compared with more complex approaches, such as Bayes classifier, neural network, and hidden Markov model. Sounds from a large database are employed for both training and testing of the system. The achieved recognition rates are very high except for the class "speech in noise." Problems arise in the classification of compressed pop music, strongly reverberated speech, and tonal or fluctuating noises.
Transcription and translation : a Practical Approach (1984)

Introduction Expression of exogenous DNA in mammalian cells Expression of exogenous DNA in xenopus oocytes Transcription of eukaryotic genes in whole-cell extract Transcription of RNA in isolated nuclei Transcription of chromatin In vivo gene expression systems in prokaryotes Coupled transcription-translation in prokaryotic cell-free systems Purification of eukaryotic messenger RNA Translation of prokaryotic messenger RNA in cell-free extracts Translation of eukaryotic messenger RNA in xenopus oocytes Appendices Index
Capillary Isoelectric Focusing-Mass Spectrometry Method for the Separation and Online Characterization of Intact Monoclonal Antibody Charge Variants (2017)

We report a new online capillary isoelectric focusing-mass spectrometry (CIEF-MS) method for monoclonal antibody (mAb) charge variant analysis using an electrokinetically pumped sheath-flow nanospray ion source and a time-of-flight MS with pressure-assisted chemical mobilization. To develop a successful, reliable CIEF-MS method for mAb, we have selected and optimized many critical, interrelating reagents and parameters that include (1) MS-friendly anolyte and catholyte; (2) a glycerol enhanced sample mixture that reduced non-CIEF electrophoretic mobility and band broadening; (3) ampholyte selected for balancing resolution and MS sensitivity; (4) sheath liquid composition optimized for efficient focusing, mobilization, and electrospray ionization; (5) judiciously selected CIEF running parameters including injection amount, field strength, and applied pressure. The fundamental premise of CIEF was well maintained as verified by the linear correlation (R<sup>2</sup> = 0.99) between pI values and migration time using a mixture of pI markers. In addition, the charge variant profiles of trastuzumab, bevacizumab, infliximab, and cetuximab, obtained using this CIEF-MS method, were corroborated by imaged CIEF-UV (iCIEF-UV) analyses. The relative standard deviations (RSD) of absolute migration time of pI markers were all less than 5% (n = 4). Triplicate analyses of bevacizumab showed RSD less than 1% for relative migration time to an internal standard and RSD of 7% for absolute MS peak area. Moreover, the antibody charge variants were characterized using the online intact MS data. To the best of our knowledge, this is the first time that direct online MS detection and characterization were achieved for mAb charge variants resolved by CIEF as indicated by a well-established linear pH gradient and correlated CIEF-UV charge variant profiles.