gebhart/patrepeval huggingface dataset:
Iron intake, body iron stores and colorectal cancer risk in women: a nested case-control study (1999)

Accumulated evidence suggests that increased body iron stores may increase the risk of colorectal cancer, possibly via catalyzing oxidation reactions. We examined the relationship between iron status and colorectal cancer in a case-control study nested within the New York University Women's Health Study cohort. For 105 incident cases of colorectal cancer with an average follow-up of 4.7 years and 523 individually matched controls, baseline levels of serum iron, ferritin, total iron binding capacity (TIBC) and transferrin saturation were determined as indicators of body iron stores, and total iron intake was assessed based on their diet and supplement intake. Overall, there were no associations between the risk of colorectal cancer and any of these indices except for serum ferritin, which showed a significant inverse association. When analyzed by subsite, there was an increasing trend in risk of cancer of the proximal colon with increasing total iron intake (p-value for trend = 0.04). In addition, a significantly increased risk of colorectal cancer associated with higher total iron intake [odds ratio (OR) = 2.50; 95% confidence interval (CI): 1.06-5.87] was observed among subjects with higher intake of total fat. Our results do not support a role of increased body iron stores in the development of colorectal cancer, but suggest that luminal exposure to excessive iron may possibly increase the risk in combination with a high fat diet.
Inhibition of energy metabolism alters the processing of amyloid precursor protein and induces a potentially amyloidogenic derivative. (1994)

The cellular mechanisms which lead to the generation and pathological deposition of beta amyloid in Alzheimer's disease are unknown. In this report we describe the proteolytic processing of the amyloid precursor protein (APP) to an 11.5-kDa COOH-terminal derivative which contains the full-length beta amyloid sequence. This processing step normally occurs at low levels in parallel with APP maturation in the secretory pathway. Inhibition of oxidative energy metabolism by sodium azide or the mitochondrial uncoupler carbonyl cyanide m-chlorophenylhydrazone increased the proteolysis of APP to the 11.5-kDa derivative by about 80-fold with accumulation of this APP derivative in the Golgi complex. Agents which inhibit protein transport in the secretory pathway, including monensin and brefeldin A, also increased the production of the 11.5-kDa derivative. Inhibition of APP maturation demonstrated that the 11.5-kDa derivative could be produced by proteolysis of immature APP. These results demonstrate that APP processing to potentially amyloidogenic COOH-terminal derivatives occurs in either the endoplasmic reticulum or Golgi complex and can be modulated by the state of cellular energy metabolism. Deficits in oxidative energy metabolism have recently been found in the cerebral cortex of patients with Alzheimer's disease. These findings raise the possibility that energy-related metabolic stress may lead to altered metabolism of APP and contribute to amyloidosis in Alzheimer's disease.
ORK1, a potassium-selective leak channel with two pore domains cloned from Drosophila melanogaster by expression in Saccharomyces cerevisiae (1996)

A K+ channel gene has been cloned from Drosophila melanogaster by complementation in Saccharomyces cerevisiae cells defective for K+ uptake. Naturally expressed in the neuromuscular tissues of adult flies, this gene confers K+ transport capacity on yeast cells when heterologously expressed. In Xenopus laevis oocytes, expression yields an ungated K(+)-selective current whose attributes resemble the "leak" conductance thought to mediate the resting potential of vertebrate myelinated neurons but whose molecular nature has long remained elusive. The predicted protein has two pore (P) domains and four membrane-spanning helices and is a member of a newly recognized K+ channel family. Expression of the channel in flies and yeast cells makes feasible studies of structure and in vivo function using genetic approaches that are not possible in higher animals.
Optical waveguide switches in silicon based on Ge-indiffused waveguides (1994)

An optical waveguide switch based on single-moded Ge-indiffused waveguides with a lateral pin-diode structure for carrier injection has been realized. The switch is polarization independent and shows an on-off-ratio better than 16.5 dB at a wavelength of 1.3 μm. By time domain measurements the coexistence of the plasma dispersion and the thermo-optical effect is shown. Both effects are separated and quantified.
Structure of the hypothetical protein PF0899 fromPyrococcus furiosusat 1.85 Å resolution (2007)

The hypothetical protein PF0899 is a 95-residue peptide from the hyperthermophilic archaeon Pyrococcus furiosus that represents a gene family with six members. P. furiosus ORF PF0899 has been cloned, expressed and crystallized and its structure has been determined by the Southeast Collaboratory for Structural Genomics (http://www.secsg.org). The structure was solved using the SCA2Structure pipeline from multiple data sets and has been refined to 1.85 A against the highest resolution data set collected (a presumed gold derivative), with a crystallographic R factor of 21.0% and R(free) of 24.0%. The refined structure shows some structural similarity to a wedge-shaped domain observed in the structure of the major capsid protein from bacteriophage HK97, suggesting that PF0899 may be a structural protein.
Modeling of the intrinsic retention characteristics of FLOTOX EEPROM cells under elevated temperature conditions (1995)

A model for the intrinsic retention characteristics of FLOTOX EEPROM cells is presented, which is based on the temperature dependence of the Fowler-Nordheim emission current. This model which has been successfully tested on single-poly-FLOTOX EEPROM cells, enables the device lifetime to be calculated for given memory operating conditions, instead of being extrapolated as is usually done. The sensitivity of the retention characteristics to several technological parameters is also investigated. It is expected that this intrinsic retention model (with minor modifications) will also be applicable to FLASH EEPROM cells.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
MazF-Mediated Cell Death in Escherichia coli : a Point of No Return (2004)

mazEF is a stress-induced toxin-antitoxin module, located on the chromosome of Escherichia coli, that we have previously described to be responsible for programmed cell death in E. coli. mazF specifies a stable toxin, and mazE specifies a labile antitoxin. Recently, it was reported that inhibition of translation and cell growth by ectopic overexpression of the toxin MazF can be reversed by the action of the antitoxin MazE ectopically overexpressed at a later time. Based on these results, it was suggested that rather than inducing cell death, mazF induces a state of reversible bacteriostasis (K. Pederson, S. K. Christensen, and K. Gerdes, Mol. Microbiol. 45:501-510, 2002). Using a similar ectopic overexpression system, we show here that overexpression of MazE could reverse MazF lethality only over a short window of time. The size of that window depended on the nature of the medium in which MazF was overexpressed. Thus, we found "a point of no return," which occurred sooner in minimal M9 medium than it did in the rich Luria-Bertani medium. We also describe a state in which the effect of MazF on translation could be separated from its effect on cell death: MazE overproduction could completely reverse the inhibitory effect of MazF on translation, while not affecting the bacteriocidic effect of MazF at all. Our results reported here support our view that the mazEF module mediates cell death and is part of a programmed cell death network.
Selectivity for maltose and maltodextrins of maltoporin, a pore‐forming protein of E. coli outer membrane (1987)

Homogenous maltoporin (lamB protein), an Escherichia coli outer membrane spanning protein, was incorporated in phospholipid planar bilayers. It generates aqueous channels distinct from those formed by the non-specific porin (OmpF) or by phosphoporin (phoE protein). The single conductance, 150 pS in 1 M NaCl, is much smaller than that of the porins. The channels, which are poorly selective for cations and voltage independent, are specifically inhibited by maltose and maltodextrins. This inhibition, observed in the absence of maltose binding protein, demonstrates that the selectivity of maltoporin for maltose and maltodextrins is an intrinsic property of the protein.
Immunocapture and Identification of Cell Membrane Protein Antigenic Targets of Serum Autoantibodies (2009)

There is increasing interest in the role of antibodies targeting specific membrane proteins in neurological and other diseases. The target(s) of these pathogenic antibodies is known in a few diseases, usually when candidate cell surface proteins have been tested. Approaches for identifying new antigens have mainly resulted in the identification of antibodies to intracellular proteins, which are often very useful as diagnostic markers for disease but unlikely to be directly involved in disease pathogenesis because they are not accessible to circulating antibodies. To identify cell surface antigens, we developed a "conformational membrane antigen isolation and identification" strategy. First, a cell line is identified that reacts with patient sera but not with control sera. Second, intact cells are exposed to sera to allow the binding of presumptive autoantibodies to their cell surface targets. After washing off non-bound serum components, the cells are lysed, and immune complexes are precipitated. Third, the bound surface antigen is identified by mass spectrometry. As a model system we used a muscle cell line, TE671, that endogenously expresses muscle-specific tyrosine receptor kinase (MuSK) and sera or plasmas from patients with a subtype of the autoimmune disease myasthenia gravis in which patients have autoantibodies against MuSK. MuSK was robustly detected as the only membrane protein in immunoprecipitates from all three patient samples tested and not from the three MuSK antibody-negative control samples processed in parallel. Of note, however, there were many intracellular proteins found in the immunoprecipitates from both patients and controls, suggesting that these were nonspecifically immunoprecipitated from cell extracts. The conformational membrane antigen isolation and identification technique should be of value for the detection of highly relevant antigenic targets in the growing number of suspected antibody-mediated autoimmune disorders. The approach would also be very suitable for the analysis of human or experimental antitumor responses.
Enhancement of metastatic ability by ectopic expression of ST6GalNAcI on a gastric cancer cell line in a mouse model (2012)

ST6GalNAcI is a sialyltransferase responsible for the synthesis of sialyl Tn (sTn) antigen which is expressed in a variety of adenocarcinomas including gastric cancer especially in advanced cases, but the roles of ST6GalNAcI and sTn in cancer progression are largely unknown. We generated sTn-expressing human gastric cancer cells by ectopic expression of ST6GalNAcI to evaluate metastatic ability of these cells and prognostic effect of ST6GalNAcI and sTn in a mouse model, and identified sTn carrier proteins to gain insight into the function of ST6GalNAcI and sTn in gastric cancer progression. A green fluorescent protein-tagged human gastric cancer cell line was transfected with ST6GalNAcI to produce sTn-expressing cells, which were transplanted into nude mice. STn-positive gastric cancer cells showed higher intraperitoneal metastatic ability in comparison with sTn-negative control, resulting in shortened survival time of the mice, which was mitigated by anti-sTn antibody administration. Then, sTn-carrying proteins were immunoprecipitated from culture supernatants and lysates of these cells, and identified MUC1 and CD44 as major sTn carriers. It was confirmed that MUC1 carries sTn also in human advanced gastric cancer tissues. Identification of sTn carrier proteins will help understand mechanisms of metastatic phenotype acquisition of gastric cancer cells by ST6GalNAcI and sTn.
Integrated Droplet Analysis System with Electrospray Ionization-Mass Spectrometry Using a Hydrophilic Tongue-Based Droplet Extraction Interface (2010)

This paper describes a simple, robust, and integrated microchip-based system for droplet analysis with electrospray ionization-mass spectrometry (ESI-MS) detection. The microchip integrated multiple modules including a droplet generator, a droplet extraction interface, and a monolithic ESI emitter. The novel droplet extraction interface based on hydrophilic tongue structure was developed. The interface could transfer droplets from segmented phase to aqueous phase with high reliability and high controllability by coupling with a back pressure regulator. The flow injection mode was adopted to introduce the transferred droplets to the ESI emitter for minimizing the cross-contamination between droplets and achieving droplet matrix modification. The system performance was evaluated using angiotensin as a model sample, and high sensitivity (<1 μM) and a good reproducibility of 5.2% RSD (n = 7) were obtained. The present device was further applied in the online monitoring of droplet-based microreaction for alkylation of peptide.
Crystallization and initial X-ray analysis of xylose isomerase from Thermotoga neapolitana (1997)

Crystals of xylose isomerase from the hyperthermophile Thermotoga neapolitana have been grown using the microbatch method under oil from solutions containing Jeffamine ED 4000 as precipitant. The space group of the crystals is C222(1) with cell dimensions a = 161.8, b = 121.9, c = 98.9 A and they contain two monomers in the asymmetric unit. The crystals diffract beyond 2.7 A.
Statistical techniques for diagnosing CIN using fluorescence spectroscopy: SVD and CART (1995)

A quantitative measure of intraepithelial neoplasia which can be made in vivo without tissue removal would be clinically significant in chemoprevention studies. Our group is working to develop such a technique based on fluorescence spectroscopy. Using empirically based algorithms, we have demonstrated that fluorescence is discriminating normal cervix from low- and high-grade cervical dysplasias with similar performance to colposcopy in expert hands. These measurements can be made in vivo, in near real time, and results can be obtained without biopsy. This paper describes a new method using automated analysis of fluorescence emission spectra to classify cervical tissue into multiple diagnostic categories. First, data is reduced using the singular value decomposition (SVD), yielding a set of orthogonal basis vectors. Each patient's emission spectrum is then fit by linear least squares regression to the basis vectors, producing a set of coefficients for each patient. Based on these coefficient values, the classification and regression tree (CART) method predicts the patient's classification. These results suggest that laser-induced fluorescence can be used to automatically recognize and differentially diagnose cervical intraepithelial neoplasia (CIN) at colposcopy. This method of analysis is general in nature, and can analyze fluorescence spectra of suspected intraepithelial neoplasms from other organ sites. As a more complete understanding of the biochemical and morphologic basis of tissue spectroscopy is developed, it may also be possible to use fluorescence spectroscopy of the cervix as a surrogate endpoint biomarker in Phase I and II chemoprevention trials.
Visual function after monocular implantation of apodized diffractive multifocal or single-piece monofocal intraocular lens (2010)

The multifocal IOL provided better near visual acuity and more spectacle independence than the monofocal IOL.
Antiviral and antimetabolic activities of neplanocins (1985)

Of a series of carbocyclic analogs of adenosine, in which the ribose moiety was replaced by a cyclopentenyl ring, neplanocin A, or (-)-9-[trans-2, trans-3-dihydroxy-4-(hydroxymethyl)cyclopent-4-enyl]adenine proved particularly effective in inhibiting the multiplication of DNA viruses (i.e., vaccinia), (-)RNA viruses (i.e., parainfluenza, measles, and vesicular stomatitis), and double-stranded RNA viruses (i.e., reo) in vitro in cell culture. Depending on the cells used, the MIC of neplanocin A for these viruses ranged from 0.01 to 4 micrograms/ml, and depending on the parameter used to assess toxicity for the host cell, the specificity index of neplanocin A ranged from 50 to 4,000. As postulated before for other adenosine analogs, neplanocin A may owe its antiviral action to inhibition of S-adenosylhomocysteine hydrolase, hence perturbation of transmethylation reactions. In vivo, neplanocin A afforded only marginal protection against a lethal infection of mice with vesicular stomatitis virus.
Coding and decoding: Seismic data modeling, acquisition and processing (2007)

We present a method for coding and decoding seismic data acquired, based on the concept of multishooting. In this concept, waves generated simultaneously from several locations at the surface of the earth, near the sea surface, at the sea floor, or inside a borehole propagate in the subsurface before being recorded at sensor locations as mixtures of various signals. The coding and decoding method for seismic data described here works with both instantaneous mixtures and convolutive mixtures. Furthermore, the mixtures can be undedetemined [i.e., the number of mixtures (K) is smaller than the number of seismic sources (I) associated with a multi‐shot] or determined [i.e., the number of mixtures is equal to or greater than the number of sources). When mixtures are determined, we can reorganize our seismic data as zero‐mean random variables and use the independent component analysis (ICA) or, alternatively, the principal component analysis (PCA) to decode. We can also alternatively take advantage of the sparsity of seismic data in our decoding process. When mixtures are underdetermined and the number of mixtures is at least two, we utilize higher‐order statistics to overcome the underdeterminacy. Alternatively, we can use the constraint that seismic data are sparse to overcome the underdeterminacy. When mixtures are underdetermined and limited to single mixtures, we use a priori knowledge about seismic acquisition to computationally generate additional mixtures from the actual recorded mixtures. Then we organize our data as zero‐mean random variables and use ICA or PCA to decode the data. The a priori knowledge includes source encoding, seismic acquisition geometries, and reference data collected for the purpose of aiding the decoding processing. The coding and decoding processes described can be used to acquire and process real seismic data in the field or in laboratories, and to model and process synthetic data.
A single amino acid substitution in transmembrane helix VI results in overexpression of the human GnRH receptor (1998)

Although none of the mutant receptors exhibited constitutive activity, mutation of Phe-2 72 in transmembrane helix VI to Leu increased cell surface receptor numbers, with unchanged affinities for radiolabeled agonist, superagonist and antagonist peptides compared with wild type receptor. The cell surface receptor stability and rate of internalization were similar for wild type and F272L GnRH receptors. Thus a single amino acid mutation in transmembrane helix VI causes an increase in cell surface receptor numbers, which appears to result from an increased rate of receptor protein translation, processing or insertion into membranes.
Differences in membrane pore formation by peptaibols (2003)

The efficiencies of membrane pore formation by 14 naturally occurring peptaibols and two structurally modified ampullosporins were compared using an artificial bilayer membrane model. Major differences were found in the dependence on peptide sequences and the constituting amino acids. Alamethicin F-30, chrysospermins C/D, paracelsin and texenomycin A displayed higher activity by several orders of magnitude in comparison with smaller peptaibols containing < 17 amino acids such as ampullosporins, trichofumins. bergofungins and cephaibols. Biological activities such as the induction of pigment formation by the fungus Phoma destructiva and long acting hypothermia and depression of locomotor activity in mice were correlated with moderate membrane permeabilization. No or weak membrane activities corresponded with biological inactivity. Highly membrane-active structures such as alamethicin F-30, chrysospermin C, texenomycin A and paracelsin A displayed antibiotic effects against the fungus and toxicity in mice.
Highly specific inhibition of IGF-I-stimulated differentiation by an antisense oligodeoxyribonucleotide to myogenin mRNA. No effects on other actions of IGF-T. (1990)

Myogenin is a member of the recently discovered family of muscle determination genes that have been shown to induce myogenic differentiation in nonmuscle cells and to be closely correlated with terminal differentiation in myoblasts. An antisense oligodeoxyribonucleotide complementary to the first five codons of myogenin blocks the stimulation of terminal myogenic differentiation by insulin-like growth factor I (IGF-I). This effect exhibits a high degree of specificity on two levels; exchanging the positions as few as 2 of the 15 bases in the oligomer abolishes its activity, and none of the other processes stimulated by IGF-I in L6A1 myoblasts are affected by the presence of the oligomer. These processes include cell proliferation as well as incorporation of leucine, uridine, and thymidine into macromolecules. The specificity, ease, and convenience of this approach indicates its potential applicability to studies on actions of other putative controlling genes in other systems.
Perspective Article: Tissue repair, contraction, and the myofibroblast (2005)

After the first description of the myofibroblast in granulation tissue of an open wound by means of electron microscopy, as an intermediate cell between the fibroblast and the smooth muscle cell, the myofibroblast has been identified both in normal tissues, particularly in locations where there is a necessity of mechanical force development, and in pathological tissues, in relation with hypertrophic scarring, fibromatoses and fibrocontractive diseases as well as in the stroma reaction to epithelial tumors. It is now accepted that fibroblast/myofibroblast transition begins with the appearance of the protomyofibroblast, whose stress fibers contain only beta- and gamma-cytoplasmic actins and evolves, but not necessarily always, into the appearance of the differentiated myofibroblast, the most common variant of this cell, with stress fibers containing alpha-smooth muscle actin. Myofibroblast differentiation is a complex process, regulated by at least a cytokine (the transforming growth factor-beta1), an extracellular matrix component (the ED-A splice variant of cellular fibronectin), as well as the presence of mechanical tension. The myofibroblast is a key cell for the connective tissue remodeling that takes place during wound healing and fibrosis development. On this basis, the myofibroblast may represent a new important target for improving the evolution of such diseases as hypertrophic scars, and liver, kidney or pulmonary fibrosis.