gebhart/patrepeval huggingface dataset:
Benzoate Fermentation by the Anaerobic Bacterium Syntrophus aciditrophicus in the Absence of Hydrogen-Using Microorganisms (2001)

The anaerobic bacterium Syntrophus aciditrophicus metabolized benzoate in pure culture in the absence of hydrogen-utilizing partners or terminal electron acceptors. The pure culture of S. aciditrophicus produced approximately 0.5 mol of cyclohexane carboxylate and 1.5 mol of acetate per mol of benzoate, while a coculture of S. aciditrophicus with the hydrogen-using methanogen Methanospirillum hungatei produced 3 mol of acetate and 0.75 mol of methane per mol of benzoate. The growth yield of the S. aciditrophicus pure culture was 6.9 g (dry weight) per mol of benzoate metabolized, whereas the growth yield of the S. aciditrophicus-M. hungatei coculture was 11.8 g (dry weight) per mol of benzoate. Cyclohexane carboxylate was metabolized by S. aciditrophicus only in a coculture with a hydrogen user and was not metabolized by S. aciditrophicus pure cultures. Cyclohex-1-ene carboxylate was incompletely degraded by S. aciditrophicus pure cultures until a free energy change (DeltaG') of -9.2 kJ/mol was reached (-4.7 kJ/mol for the hydrogen-producing reaction). Cyclohex-1-ene carboxylate, pimelate, and glutarate transiently accumulated at micromolar levels during growth of an S. aciditrophicus pure culture with benzoate. High hydrogen (10.1 kPa) and acetate (60 mM) levels inhibited benzoate metabolism by S. aciditrophicus pure cultures. These results suggest that benzoate fermentation by S. aciditrophicus in the absence of hydrogen users proceeds via a dismutation reaction in which the reducing equivalents produced during oxidation of one benzoate molecule to acetate and carbon dioxide are used to reduce another benzoate molecule to cyclohexane carboxylate, which is not metabolized further. Benzoate fermentation to acetate, CO(2), and cyclohexane carboxylate is thermodynamically favorable and can proceed at free energy values more positive than -20 kJ/mol, the postulated minimum free energy value for substrate metabolism.
<title>Evolving neural network pattern classifiers</title> (1993)

This work investigates the application of evolutionary programming for automatically configuring neural network architectures for pattern classification tasks. The evolutionary programming search procedure implements a parallel nonlinear regression technique and represents a powerful method for evaluating a multitude of neural network model hypotheses. The evolutionary programming search is augmented with the Solis &amp; Wets random optimization method thereby maintaining the integrity of the stochastic search while taking into account empirical information about the response surface. A network architecture is proposed which is motivated by the structures generated in projection pursuit regression and the cascade-correlation learning architecture. Results are given for the 3-bit parity, normally distributed data, and the T-C classifier problems.
3′-End processing of pre-mRNA in eukaryotes (1999)

3'-Ends of almost all eukaryotic mRNAs are generated by endonucleolytic cleavage and addition of a poly(A) tail. In mammalian cells, the reaction depends on the sequence AAUAAA upstream of the cleavage site, a degenerate GU-rich sequence element downstream of the cleavage site and stimulatory sequences upstream of AAUAAA. Six factors have been identified that carry out the two reactions. With a single exception, they have been purified to homogeneity and cDNAs for 11 subunits have been cloned. Some of the cooperative RNA-protein and protein-protein interactions within the processing complex have been analyzed, but many details, including the identity of the endonuclease, remain unknown. Several examples of regulated polyadenylation are being analyzed at the molecular level. In the yeast Saccharomyces cerevisiae, sequences directing cleavage and polyadenylation are more degenerate than in metazoans, and a downstream element has not been identified. The list of processing factors may be complete now with approximately a dozen polypeptides, but their functions in the reaction are largely unknown. 3'-Processing is known to be coupled to transcription. This connection is thought to involve interactions of processing factors with the mRNA cap as well as with RNA polymerase II.
Boron neutron capture therapy: linkage of a boronated macromolecule to monoclonal antibodies directed against tumor-associated antigens (1989)

Two new protein-binding polyhedral boron derivatives, isocyanatoundecahydro-closo-dodecaborate(2-) (1) and isocyanato(trimethylamino)octahydro-closo-decaborate(1 -) (2), were synthesized. These anionic isocyanates have long hydrolysis half-lives at pH 7 and react readily with primary or secondary aliphatic amines resulting in spontaneous urea linkage. Utilizing 1, 1100 boron atoms (7.3% boron by weight) were incorporated per molecule of a polyclonal antibody directed against human thymocytes (anti-thymocyte globulin) without denaturation. However, immunoreactivity of the conjugates was lost. Reaction of 1 and 2 with polylysine yielded boronated macromolecules containing 21-28% boron by weight (up to 2000 boron atoms per molecule). Polylysine boronated with 2 was successfully linked to antibody molecules employing the heterobifunctional linking molecules N-succinimidyl 3-(2-pyridyldithio)propionate (SPDP) and m-maleimidobenzoyl sulfosuccinimide ester (sulfo-MBS). Separation of the conjugated antibody from the free boronated macromolecules and unconjugated antibody molecules has been achieved by gel filtration on a Sephacryl S-300 column. By linking boronated polylysine to antibodies, greater than 10(3) boron atoms were incorporated with the attachment of this species to one or more sites on the antibody molecule. The resulting immunoconjugates contained greater than 10(3) boron atoms per molecule, retained their immunoreactivity, and potentially might be useful for the selective delivery of large numbers of boron atoms to tumor cells.
Spleen Cells Transmit Osteopetrosis in Mice (1975)

Osteopetrosis was induced in lethally irradiated, normal mice of grey-lethal and microphthalmic stocks by cell infusions prepared from the spleens of osteopetrotic littermates. Failure of skeletal remodeling became evident within a few weeks after transplantation as calcified cartilage and bone accumulated excessively in the active metaphyses of the long bones. The massive lesions produced were extensively infiltrated with abnormal osteoclasts.
DU‐145 and PC‐3 human prostate cancer cell lines express androgen receptor: Implications for the androgen receptor functions and regulation (2006)

The majority of human prostate cancer cell lines, including the two "classical" cell lines DU-145 and PC-3, are reported to be androgen receptor (AR)-negative. However, other studies have provided evidence that the DU-145 and PC-3 cell lines express AR mRNA. These contradictory observations prompted us to investigate whether DU-145 and PC-3 cell lines express the androgen receptor. Using antipeptide antibodies directed against three distinct regions of the human AR protein and an improved method to detect AR protein in immunoblotting, we report that DU-145 and PC-3 cell lines express AR protein. We found that the relative levels of the AR mRNA and protein that were detected in DU-145 and PC-3 cell lines were lower than the LNCaP, an AR-positive cell line. Moreover, the antibody directed against the non-variant region (amino acids 299-315), but not the variant N- or C-terminal region (amino acids 1-20 and 900-919, respectively) of the human AR protein, detected the expression of AR in all prostate cancer cell lines. Notably, treatment of these cell lines with dihydrotestosterone (DHT) resulted in measurable increases in the AR protein levels and considerable nuclear accumulation. Although, treatment of DU-145 and PC-3 cells with DHT did not result in stimulation of the activity of an AR-responsive reporter, knockdown of AR expression in PC-3 cells resulted in decreases in p21(CIP1) protein levels, and a measurable decrease in the activity of the p21-luc-reporter. Our observations demonstrate the expression of AR protein in DU-145 and PC-3 prostate cancer cell lines.
Detection and subtyping of dengue 1–4 and yellow fever viruses by means of a multiplex RT‐nested‐PCR using degenerated primers (2006)

This test is able to detect and identify the four DENVs and YFV to a high level of sensitivity and specificity and can be used with clinical samples. This simple, reliable and easy-to-perform method able to detect and identify dengue 1-4 and YFV can be used in poor endemic countries.
Hydrophilic Polymers (1996)

Six different classes of water-soluble polyphosphazenes have been synthesized and characterized. Several of the new polymers have been cross-linked to yield materials that absorb water to form hydrogels. This chapter examines the underlying concepts used in this work and describes the use of this chemistry to prepare new materials with controlled surface structures and with special properties such as lower critical solution temperatures, bioerodibility, or biocompatibility. The incorporation of these polymers into membranes or microencapsules is also described.
Lipoxins: novel series of biologically active compounds formed from arachidonic acid in human leukocytes. (1984)

Trihydroxytetraenes, a novel series of oxygenated derivatives formed from arachidonic acid in human leukocytes, were recently isolated [Serhan, C. N., Hamberg, M. & Samuelsson, B. (1984) Biochem. Biophys. Res. Commun. 118, 943-949]. The structure of the major compound was established--i.e., 5,6,15L-trihydroxy-7,9,11,13-icosatetraenoic acid. The present study reports the structure of a second member of the trihydroxytetraene series of compounds--i.e., 5D,14,15L-trihydroxy-6,8,10,12-icosatetraenoic acid. When added to human neutrophils, 5,6,15L-trihydroxy-7,9,11,13-icosatetraenoic acid stimulated superoxide anion generation and degranulation at submicromolar concentrations without provoking a substantial aggregation response. With respect to superoxide anion generation, 5,6,15L-trihydroxy-7,9,11,13-icosatetraenoic acid proved to be as potent as leukotriene B4. In contrast, the compound was approximately 2 orders of magnitude less potent than either leukotriene B4 or fMet-Leu-Phe at provoking degranulation. The results indicate that interaction(s) between the 5- and 15-lipoxygenase pathways of human leukocytes leads to formation of a new series of oxygenated derivatives of arachidonic acid that may be involved in regulating specific cellular responses. The trivial names lipoxin A (5,6,15L-trihydroxy-7,9,11,13-icosatetraenoic acid) and lipoxin B (5D,14,15L-trihydroxy-6,8,10,12-icosatetraenoic acid) are proposed for the new compounds.
Expression of cyr61, a growth factor-inducible immediate-early gene. (1990)

A set of immediate-early genes that are rapidly activated by serum or purified platelet-derived growth factor in mouse 3T3 fibroblasts has been previously identified. Among these genes, several are related to known or putative transcription factors and growth factors, supporting the notion that some of these genes encode regulatory molecules important to cell growth. We show here that a member of this set of genes, cyr61 (originally identified by its cDNA 3CH61), encodes a 379-amino-acid polypeptide rich in cysteine residues. cyr61 can be induced through protein kinase C-dependent and -independent pathways. Unlike many immediate-early genes that are transiently expressed, the cyr61 mRNA is accumulated from the G0/G1 transition through mid-G1. This expression pattern is due to persistent transcription, while the mRNA is rapidly turned over during the G0/G1 transition and in mid-G1 at the same rate. In logarithmically growing cells, the cyr61 mRNA level is constant throughout the cell cycle. Cyr61 contains an N-terminal secretory signal sequence; however, it is not detected in the culture medium by immunoprecipitation. Cyr61 is synthesized maximally at 1 to 2 h after serum stimulation and has a short half-life within the cell.
The Role of Hsp70 in Cancer: A Study of the Hsp70 / Akt Relationship (2012)

The Hsp70 family of molecular chaperones is essential for\nprotein folding, re-folding misfolded client proteins, clearance\nof aberrant client proteins, and can also inhibit programmed\ncell death. There are two major cytosolic members of this\nfamily: the constitutive Hsc70, and the inducible Hsp72. Under\nstress conditions the Hsp70 family protects the cell from\nprotein related damage by the induction of Hsp72. Hsc70 and\nHsp72 are highly homologous with minor differences in\nsubstrate binding. In cancers, Hsp72 is commonly induced and\nthis induction is thought to aid in cancer cell survival. In these\nstudies we demonstrate the differential regulation of the prosurvival\nkinase Akt by Hsc70 and Hsp72. We demonstrate that\nof the two cytosolic forms, Hsp72 is the primary Akt regulator.\nUsing a phenothiazine class inhibitor of Hsp70-family activity,\nmethylene blue, we demonstrate dose dependent decreases in\nthe levels of Akt; produced breast cancer specific cell death.\nThis cell death could be rescued by the use of an Hsp70 family ATPase stimulating compound, SW02. We also demonstrate a\nsimilar phenotype with a rhodacyanine class Hsp70 family\ninhibitor, YM-1, also capable of reducing Akt and causing\ncancer specific cytotoxicity. The resulting Akt decreases were\nsufficient to block a tamoxifen-resistance pathway, allowing\npreviously resistant cells to regain sensitivity to tamoxifen.\nThese results demonstrate the capabilities of Hsp70 family\ninhibitors as potent compounds for the treatment of breast\ncancer.
In vivo investigation of the transcription, processing, endonucleolytic activity, and functional relevance of the spatial distribution of a plant miRNA (2004)

We show, with miR171, that plant miRNA genes are modular independent transcription units in which the fold-back pre-miRNA is sufficient for miRNA processing, and that the upstream region contains highly specific promoter elements. Processing depends on flanking sequences within the miRNA stem-loop precursor rather than the miRNA sequence itself, and mutations affecting target pairing at the center and 5' but not 3' region of the miRNA compromise its function in vivo. Inactivation of the SDE1 RNA-dependent-RNA-polymerase was mandatory for accurate representation of miRNA activity by sensor constructs in Arabidopsis. Work in sde1 background revealed a near-perfect spatial overlap between the patterns of miR171 transcription and activity, supporting the idea that plant miRNAs enable cell differentiation.
Representing shape with spatial pyramid kernel (2007)

The objective of this paper is classifying images by the object categories they contain, for example motorbikes or dolphins. There are three areas of novelty. First, we introduce a descriptor that represents local image shape and its spatial layout, together with a spatial pyramid kernel. These are designed so that the shape correspondence between two images can be measured by the distance between their descriptors using the kernel. Second, we generalize the spatial pyramid kernel, and learn its level weighting parameters (on a validation set). This significantly improves classification performance. Third, we show that shape and appearance kernels may be combined (again by learning parameters on a validation set). <br> Results are reported for classification on Caltech-101 and retrieval on the TRECVID 2006 data sets. For Caltech-101 it is shown that the class specific optimization that we introduce exceeds the state of the art performance by more than 10%.
Laser writing of copper lines from metalorganic films (1987)

Direct writing of high-purity copper lines has been achieved by photothermal decomposition of copper formate films under ambient conditions using a focused argon ion laser (514 nm) beam on a scanning quartz or silicon substrate. The fast decomposition kinetics of the precursor allows use of writing speeds as high as 1 cm/s for deposition of micron-thick copper films. There is negligible oxidation of the copper after decomposition in the presence of air due to the rapid heating and cooling of the deposit during laser writing.
The photochemical synthesis of a tricyclo[2.2.0.02,5]hexane (1976)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTThe photochemical synthesis of a tricyclo[2.2.0.02,5]hexaneEdward C. Alexander and Joseph UlianaCite this: J. Am. Chem. Soc. 1976, 98, 14, 4324–4325Publication Date (Print):July 1, 1976Publication History Published online1 May 2002Published inissue 1 July 1976https://pubs.acs.org/doi/10.1021/ja00430a059https://doi.org/10.1021/ja00430a059research-articleACS PublicationsRequest reuse permissionsArticle Views216Altmetric-Citations10LEARN 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
Neural deficits contribute to respiratory insufficiency in Pompe disease (2009)

Pompe disease is a severe form of muscular dystrophy due to glycogen accumulation in all tissues, especially striated muscle. Disease severity is directly related to the deficiency of acid alpha-glucosidase (GAA), which degrades glycogen in the lysosome. Respiratory dysfunction is a hallmark of the disease, muscle weakness has been viewed as the underlying cause, and the possibility of an associated neural contribution has not been evaluated previously. Therefore, we examined behavioral and neurophysiological aspects of breathing in 2 animal models of Pompe disease--the Gaa(-/-) mouse and a transgenic line (MTP) expressing GAA only in skeletal muscle, as well as a detailed analysis of the CNS in a Pompe disease patient. Glycogen content was elevated in the Gaa(-/-) mouse cervical spinal cord. Retrograde labeling of phrenic motoneurons showed significantly greater soma size in Gaa(-/-) mice vs. isogenic controls, and glycogen was observed in Gaa(-/-) phrenic motoneurons. Ventilation, assessed via plethysmography, was attenuated during quiet breathing and hypercapnic challenge in Gaa(-/-) mice (6 to >21 months of age) vs. controls. We confirmed that MTP mice had normal diaphragmatic contractile properties; however, MTP mice had ventilation similar to the Gaa(-/-) mice during quiet breathing. Neurophysiological recordings indicated that efferent phrenic nerve inspiratory burst amplitudes were substantially lower in Gaa(-/-) and MTP mice vs. controls. In human samples, we demonstrated similar pathology in the cervical spinal cord and greater accumulation of glycogen in spinal cord compared with brain. We conclude that neural output to the diaphragm is deficient in Gaa(-/-) mice, and therapies targeting muscle alone may be ineffective in Pompe disease.
The lateral ganglionic eminence is the origin of cells committed to striatal phenotypes: neural transplantation and developmental evidence (1994)

In order to determine whether the lateral ganglionic eminence (LGE) of the fetal telencephalon is the primary source of striatal precursors in striatal transplants and tissue cultures, cells derived exclusively from the LGE of fetal rat brains were transplanted into the quinolinic-acid-lesioned striatum of adult rats. After 2-3 months they produced grafts that were almost entirely AChE-positive as well as DARPP-32-, TH-, and calbindin-immunoreactive. The grafts were integrated into the host striatum so that host corticofugal fiber tracts interdigitated with graft tissues similar to the way they penetrate the gray matter of the normal striatum. Fast Blue dye injected into the ipsilateral globus pallidus of LGE grafted produced retrogradely labeled neurons within the grafts, but Fluorogold dye injected into the ipsilateral substantia nigra did not. In a separate experiment using DARPP-32-immunohistochemstry as a striatal marker, fetal (E16) and neonatal (P2) rat brains showed DARPP-32 immunoreactivity in the LGE but not in the adjacent medial ganglionic eminence (MGE). In summary, both fetal LGE cells and LGE grafts express specific striatal markers, and LGE grafts integrate into the host striatum and innervate the major striatal efferent target within the host brain. These data suggest that the LGE is the origin of cells committed to striatal phenotypes in the developing brain.
Reducing the Migration Times of Multiple VMs on WANs Using a Feedback Controller (2013)

Virtual machine (VM) migration is affected by network latency and throughput, which are highly fluctuating and unpredictable in wide-area networks (WANs). Hence, it is difficult to statically minimize the time required to transfer a large number of VMs across WAN. The goal of this work is to migrate as many VMs as possible during a given period of time and it is motivated by disaster recovery scenarios. One approach is to migrate a large number of VMs in parallel, but this leads to long migration times of each individual VM. Long migration times are problematic in catastrophic circumstances where resources are limited and can fail within a short period of time. Thus, it is important to shorten both the total time required to migrate multiple VMs and the migration time of individual VMs. Due to network performance fluctuations, the optimal number of parallel migrations changes over time. This work proposes a feedback-based controller that adapts to the number of parallel VM migrations in response to changes in a WAN. The controller implements an algorithm inspired by the TCP congestion avoidance algorithm in order to regulate the number of VMs in transit depending on the network conditions. Experiments using a prototype controller confirm that it is possible to control the migration of a set of VMs shortening both the total and individual migration times. The experiments show that the controller shortens the individual migration time by up to 5.7 fold compared to that of the static VM migrations where the number of parallel migrations does not change until all migrations are completed. The contributions of this work are 1) introducing migration strategies for multiple VMs on WANs and 2) proposing a hypervisor-independent controller that adapts to network bandwidth fluctuations in disaster scenarios.