gebhart/patrepeval huggingface dataset:
Cellular differentiation is required for cAMP but not Ca(2+)-dependent Cl- secretion in colonic epithelial cells expressing high levels of cystic fibrosis transmembrane conductance regulator. (1992)

The gene responsible for cystic fibrosis (CF) has recently been cloned and sequenced. When transfected into CF epithelial cells, normal transcripts of this gene correct the underlying defect in CF, i.e. cAMP-dependent Cl- secretion is restored. Thus, the protein encoded by this gene, designated "cystic fibrosis transmembrane conductance regulator" (CFTR), somehow participates in the Cl- secretory response. In this paper we have correlated CFTR gene expression with cAMP and Ca(2+)-dependent Cl- secretion in unpolarized (parental) and polarized (Cl.19A) clones of the human colonic adenocarcinoma cell line HT-29. These cell lines were found to express equally high levels of CFTR mRNA at 4 days post-passage. In addition, protein expression (determined by immunoprecipitation) was also identical. The cAMP-generating agonist forskolin had little effect on 125I efflux from the unpolarized cells. In contrast, this agonist increased 125I efflux 3-fold in polarized cells. The lack of response in the unpolarized cells was not due to the inability of forskolin to raise cAMP levels. Neurotensin, a Ca(2+)-mobilizing agonist, stimulated 125I efflux from both cell lines. In the polarized cells, the magnitude of this response was attenuated at 8 days post-seeding. At this time, the undifferentiated line attained some cAMP responsiveness. This latter effect was paralleled by the appearance of monolayers within areas of the multicell layer. Cell-attached patch-clamp recording from apical membrane patches of polarized cells revealed the presence of a forskolin-stimulated 8-pS Cl- channel; no channel activity was observed in forskolin-stimulated unpolarized cells. Ca(2+)-activated Cl- channels were found in both cell lines. In agreement with the 125I efflux data, the single-channel activation response to [Ca2+]i was smaller in the polarized cell line. From these studies, we can conclude that CFTR expression, measured both at the mRNA and protein level, does not correlate with the colonocyte's ability to secrete chloride ions in response to a cAMP-generating agonist. Cyclic AMP-dependent Cl- secretion requires cellular polarization; specifically, the delineation of an apical membrane. Differences in the cellular location of CFTR during differentiation are likely to explain our results. In contrast, Ca(2+)-stimulated Cl- secretion occurred independently of cellular polarization but was reduced when the cells formed tight junctions.
Cytokinin Regulates the Activity of Reproductive Meristems, Flower Organ Size, Ovule Formation, and Thus Seed Yield in Arabidopsis thaliana (2011)

The size and activity of the shoot apical meristem is regulated by transcription factors and low molecular mass signals, including the plant hormone cytokinin. The cytokinin status of the meristem depends on different factors, including metabolic degradation of the hormone, which is catalyzed by cytokinin oxidase/dehydrogenase (CKX) enzymes. Here, we show that CKX3 and CKX5 regulate the activity of the reproductive meristems of Arabidopsis thaliana. CKX3 is expressed in the central WUSCHEL (WUS) domain, while CKX5 shows a broader meristematic expression. ckx3 ckx5 double mutants form larger inflorescence and floral meristems. An increased size of the WUS domain and enhanced primordia formation indicate a dual function for cytokinin in defining the stem cell niche and delaying cellular differentiation. Consistent with this, mutation of a negative regulator gene of cytokinin signaling, ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN 6, which is expressed at the meristem flanks, caused a further delay of differentiation. Terminal cellular differentiation was also retarded in ckx3 ckx5 flowers, which formed more cells and became larger, corroborating the role of cytokinin in regulating flower organ size. Furthermore, higher activity of the ckx3 ckx5 placenta tissue established supernumerary ovules leading to an increased seed set per silique. Together, the results underpin the important role of cytokinin in reproductive development. The increased cytokinin content caused an ~55% increase in seed yield, highlighting the relevance of sink strength as a yield factor.
Chromosome loss is the most frequent mechanism contributing to HLA haplotype loss in human tumors (1999)

Loss of heterozygosity (LOH) in the short arm of chromosome 6 (6p) was detected in samples obtained from colon (13.8%), larynx (17.6%) and melanoma (15.3%) tumors. The parallel study of HLA-antigen expression in tumor tissues using locus- and polymorphic-specific antibodies in combination with LOH microsatellite analysis on 6p allowed us to establish that LOH in chromosome 6 is a representative phenomenon in most tumor cells present in a given tumor tissue. In most cases, specific HLA alleles had been lost in a predominant population of tumor cells, indicating that LOH is a non-irrelevant mutation that probably confers a selective advantage for survival of the mutant cell. We also demonstrate that LOH frequently occurred through chromosome loss rather than somatic recombination. LOH at all loci studied on the p and q arms of chromosome 6 was observed in at least 56.2% (9/17) cases. This HLA-associated microsatellite analysis was a useful tool for classifying tumors as LOH-positive or -negative, and therefore to consider a patient as a potential non-responder or responder in a vaccination trial.
Activation of the Unfolded Protein Response in Infarcted Mouse Heart and Hypoxic Cultured Cardiac Myocytes (2006)

Endoplasmic reticulum (ER) stresses that reduce ER protein folding activate the unfolded protein response (UPR). One effector of the UPR is the transcription factor X-box binding protein-1 (XBP1), which is expressed on ER stress-mediated splicing of the XBP1 mRNA. XBP1 induces certain ER-targeted proteins, eg, glucose-regulated protein 78 (GRP78), that help resolve the ER stress and foster cell survival. In this study, we determined whether hypoxia can activate the UPR in the cardiac context. Neonatal rat ventricular myocyte cultures subjected to hypoxia (16 hours) exhibited increased XBP1 mRNA splicing, XBP1 protein expression, GRP78 promoter activation, and GRP78 protein levels; however, the levels of these UPR markers declined during reoxygenation, suggesting that the UPR is activated during hypoxia but not during reoxygenation. When cells were infected with a recombinant adenovirus (AdV) encoding dominant-negative XBP1 (AdV-XBP1dn), UPR markers were reduced; however, hypoxia/reoxygenation-induced apoptosis increased. Confocal immunocytofluorescence demonstrated that hypoxia induced GRP78 in neonatal rat and isolated adult mouse ventricular myocytes. Moreover, mouse hearts subjected to in vivo myocardial infarction exhibited increased GRP78 expression in cardiac myocytes near the infarct, but not in healthy cells distal to the infarct. These results indicate that hypoxia activates the UPR in cardiac myocytes and that XBP1-inducible proteins may contribute to protecting the myocardium during hypoxic stress.
Targeted Mutagenesis in Mammalian Cells Mediated by Intracellular Triple Helix Formation (1995)

As an alternative to standard gene transfer techniques for genetic manipulation, we have investigated the use of triple helix-forming oligonucleotides to target mutations to selected genes within mammalian cells. By treating monkey COS cells with oligonucleotides linked to psoralen, we have generated targeted mutations in a simian virus 40 (SV40) vector contained within the cells via intracellular triple helix formation. Oligonucleotide entry into the cells and sequence-specific triplex formation within the SV40 DNA deliver the psoralen to the targeted site. Photoactivation of the psoralen by long-wavelength UV light yields adducts and thereby mutations at that site. We engineered into the SV40 vector novel supF mutation reporter genes containing modified polypurine sites amenable to triplex formation. By comparing the abilities of a series of oligonucleotides to target these new sites, we show that targeted mutagenesis in vivo depends on the strength and specificity of the third-strand binding. Oligonucleotides with weak target site binding affinity or with only partial target site homology were ineffective at inducing mutations in the SV40 vectors within the COS cells. We also show that the targeted mutagenesis is dependent on the oligonucleotide concentration and is influenced by the timing of the oligonucleotide treatment and of the UV irradiation of the cells. Frequencies of intracellular targeted mutagenesis in the range of 1 to 2% were observed, depending upon the conditions of the experiment. DNA sequence analysis revealed that most of the mutations were T.A-to-A.T transversions precisely at the targeted psoralen intercalation site. Several deletions encompassing that site were also seen. The ability to target mutations to selected sites within mammalian cells by using modified triplex-forming oligonucleotides may provide a new research tool and may eventually lead to therapeutic applications.
Structure-activity relationship of antiestrogens. A study using triarylbutenone, benzofuran, and triarylfuran analogs as models for triarylethylenes and triarylpropenones (1989)

In a study of the structure-activity relationship (SAR) of antiestrogens use has been made of certain 1,2,3-triarylbutenones, of 2-arylbenzofurans carrying aryl or aroyl substituents at C3, and of 2,3,4-triarylfurans as conformationally constrained models for triarylethylene (TAE) and triarylpropenone (TAP) prototypes. The position-specific contributions of substituents to receptor affinity and to agonist-antagonist profiles were used as aids in characterizing the relative binding orientation of the prototypes. Although most compounds were found to be weak receptor ligands and poorly active in vivo, the following conclusions could be drawn about their SAR: (i) (Z)-TAPs and TAEs interact with the receptor in an analogous manner using the trans-stilbene core, with their agonist-antagonist profiles depending on the nature of other substructures. (ii) Incorporation into the benzofuran framework introduces a stereoelectronic constraint that compromises the normal binding interactions of TAE, as well as TAP, prototypes, resulting in their poor affinities and weak biological activities. (iii) (E)-TAPs can interact with the receptor through their S-cis conformation, but such a binding mode is unlikely to account for their behavior as antagonists.
Chronische Pudendale Neurostimulation zur Therapie der überaktiven Blase - eine Alternative zur sakralen Neuromodulation? (2005)

The BION-system and chronic pudendal nerve stimulation seem to be alternatives to sacral neuromodulation, however, patient selection is difficult as subchronic stimulation for a longer period of time is not possible so far.
A New Clone Sweeps Clean: the Enigmatic Emergence of Escherichia coli Sequence Type 131 (2014)

Escherichia coli sequence type 131 (ST131) is an extensively antimicrobial-resistant E. coli clonal group that has spread explosively throughout the world. Recent molecular epidemiologic and whole-genome phylogenetic studies have elucidated the fine clonal structure of ST131, which comprises multiple ST131 subclones with distinctive resistance profiles, including the (nested) H30, H30-R, and H30-Rx subclones. The most prevalent ST131 subclone, H30, arose from a single common fluoroquinolone (FQ)-susceptible ancestor containing allele 30 of fimH (type 1 fimbrial adhesin gene). An early H30 subclone member acquired FQ resistance and launched the rapid expansion of the resulting FQ-resistant subclone, H30-R. Subsequently, a member of H30-R acquired the CTX-M-15 extended-spectrum beta-lactamase and launched the rapid expansion of the CTX-M-15-containing subclone within H30-R, H30-Rx. Clonal expansion clearly is now the dominant mechanism for the rising prevalence of both FQ resistance and CTX-M-15 production in ST131 and in E. coli generally. Reasons for the successful dissemination and expansion of the key ST131 subclones remain undefined but may include increased transmissibility, greater ability to colonize and/or persist in the intestine or urinary tract, enhanced virulence, and more-extensive antimicrobial resistance compared to other E. coli. Here we discuss the epidemiology and molecular phylogeny of ST131 and its key subclones, possible mechanisms for their ecological success, implications of their widespread dissemination, and future research needs.
Fast hashing of variable-length text strings (1990)

Using only a few simple and commonplace instructions, this algorithm efficiently maps variable-length text strings small integers.
Porous polyurethanes synthesized within high internal phase emulsions (2009)

Abstract PolyHIPE are highly porous, emulsion‐templated polymers typically synthesized via free‐radical polymerization within a water‐in‐oil (W/O) high internal phase emulsion (HIPE) whose dispersed, aqueous phase occupies more than 74% of the volume. The synthesis of a polyHIPE containing biodegradable polymers is not straightforward because the presence of both an organic phase and an aqueous phase within the HIPE limits the type of polymerization reactions that can be used. This article describes the synthesis of polyHIPE containing biodegradable poly(ε‐caprolactone) (PCL) groups through the step‐growth reaction of a diisocyanate with a flexible PCL triol to form a crosslinked polyurethane. The reaction of the diisocyanate with the water in the HIPE produced urea groups and large bubbles from the generation of CO 2 . The polymer walls between these bubbles consisted of a porous, emulsion‐templated structure. Polymerization with an excess of diisocyanate produced a significant enhancement in the amounts of urea and CO 2 . The reduction in the flexible PCL content and the enhancement in the rigid urea content produced an increase in wall modulus that was over 20‐fold. The ability to synthesize polyHIPE through such step‐growth reactions is an important advance in the adaptation of polyHIPE for such applications as tissue engineering. © 2009 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 47: 5806–5814, 2009
Antigen contacts by Ni-reactive TCR: typical αβ chain cooperation versus α chain-dominated specificity (2000)

VB17(+) TCR dominate in Ni-driven T cell cultures from highly Ni-sensitized patients. Using transfection of TCR from three CD4(+), VB17(+), Ni-specific human T cell clones, we studied their Ni-MHC contacts by site-directed TCR mutation and combination of alpha and ss chains between different TCR. All three TCR exhibited N-nucleotide-determined Arg-Asp motifs in their CDR3-ss sequences. Two of them were specifically restricted to HLA-DR13, while the third one accepted a variety of HLA-DR alleles. The highly similar alpha or ss chains of the DR13-restricted TCR were interchangable without loss of specificity, but alpha or ss chains of other TCR were not tolerated. Mutations of their Arg-Asp motif revealed loss of reactivity upon exchanging Asp for Glu or Ala and of Arg for Ala but not of Arg for Lys or the Ni binding His. Reactivity was also destroyed by mutation of alpha chain position 51, proposed as a general contact site for MHC. Hence, in these two TCR the Arg-Asp motif is clearly involved in contacting Ni-MHC complexes, and close cooperation between alpha and ss chain is required. In contrast, the third TCR retained Ni reactivity upon mutation of alpha chain position 51 or of its ss chain Arg-Asp motif, which rather affected the pattern of DR cross-restriction. Moreover, its alpha chain paired with various ss chains from other, even mouse TCR, irrespective of their specificity, retaining Ni reactivity as well as promiscuous HLA-DR restriction. This preponderance of an alpha chain in defining specificity indicates fundamental differences in Ni interactions of individual TCR and implies that ss chain similarities may not necessarily result from antigen selection.
Impedance matrix localization produces a sparse moment method matrix (1990)

Basis and testing functions for moment-method calculations that make the resulting matrix sparse are discussed. Recent numerical results have verified theoretical predictions that a moment-method matrix with N/sup 2/ elements can be replaced by one with 100N nonzero elements. This technique is unlike some other techniques (e.g. k-space, differential equation, etc.) in that this is done without increasing N from its usual moment-method value. This technique also differs from many of these techniques (e.g. k-space. Rokhlin's factorization, etc.) because the resulting matrix is truly sparse, permitting solutions using efficient preconditioners for iterative techniques and possibly sparse direct techniques. For large moment-method problems (N>10000), the resulting savings in memory and execution time are both greater than a factor of 100. This impedance matrix localization technique applies to any moment-method formulation. >
Granulocytes and cultured human fibroblasts express common acute lymphoblastic leukemia-associated antigens (1983)

We have investigated the expression of the common acute lymphoblastic leukemia antigen (cALLA) by nonlymphoid cells, using a new murine monoclonal antibody (designated 24.1), specific for cALLA. This antibody completely blocks the binding of monoclonal anti-cALLA antibody J-5. Furthermore, antibody 24.1 binds to cALLA with greater affinity and induces a greater degree of antigenic modulation than antibody J-5. With antibody 24.1, we have demonstrated that normal cultured marrow and skin fibroblasts and mature granulocytes express cALLA. By immune precipitation and polyacrylamide gel electrophoresis, cALLA from fibroblasts has a slightly lower molecular weight and cALLA from granulocytes a slightly higher molecular weight than cALLA from cultured human leukemic cell lines. Quantitative studies indicate, however, that cALLA expression is approximately 3-fold and 20-fold lower, respectively, on normal granulocytes and skin fibroblasts than on NALM-6 cells. cALLA may be expressed by cells with widespread distribution in multiple organ systems. These findings emphasize that differentiation markers that appear to be tumor or tissue specific may be found on cells of diverse origin.
Molecular analysis of the aroA gene of Pasteurella multocida and vaccine potential of a constructed aroA mutant (1992)

The aroA gene from Pasteurella multocida was cloned by complementation of the Escherichia coli aroA mutant AB2829 with a DNA library constructed in pUC18. The nucleotide sequence of the P. multocida aroA gene indicated an open reading frame encoding a protein of 441 amino acids, which showed a high degree of homology with the amino acid sequences of various other bacterial AroA proteins. The cloned P. multocida aroA gene was inactivated by insertion of a kanamycin-resistance gene and reintroduced by allelic exchange into the chromosome of P. multocida using the suicide vector pJM703.1. The P. multocida aroA mutant was highly attenuated in a mouse model. Mice immunized intraperitoneally with two doses of live P. multocida aroA mutant were completely protected against a lethal parental strain challenge.
A Concise Method for the Preparation of Peptide and Arginine-Rich Peptide-Conjugated Antisense Oligonucleotide (2003)

Peptide-oligonucleotide conjugates were synthesized using two strategies: a mimetic signal peptide-conjugated oligonucleotide was assembled stepwise on CPG by using 2,2-dimethyl-3-hydroxypropionic acid as a linker. To solve the precipitation problem in the coupling reaction caused by the electrostatic interaction of arginine-rich peptides and oligonucleotide, oligonucleotides were absorbed on an anion-exchange resin, and then the on-resin fragment was applied for the conjugation with arginine-rich peptide. The peptide-antisense oligonucleotides showed permeability to the cell membrane of HepG-2 cells.
Multiplication and Movement ofXylella fastidiosaWithin Grapevine and Four Other Plants (1995)

Xylella fastidiosa, a xylem-limited bacterium that causes Pierce's disease of grapevine and other plant diseases, has numerous symptomless hosts. The multiplication and spread of X. fastidiosa within grapevine (Vitis vinifera) and four other reported plant hosts that were preferred plants for insect vectors (Himalayan blackberry, Rubus discolor ; California mugwort, Artemisia douglasiana ; watergrass, Echinochloa crusgalli; and Bermuda grass, Cynodon dactylon) were assessed after vector inoculation. The bacterium was detected by culture and enzyme-linked immunosorbent assay. The incubation times required before first detection in grape, blackberry, mugwort, and watergrass were 4, 32, 30, and 18 days, respectively. The maximum bacterial concentration (CFU per gram) and percentage of infection in these species were >10 8 (100%), 1 x 10 7 (58%), 2 x 10 6 (20%), and 4 x 10 5 (31%), respectively. Systemic movement of X. fastidiosa distal to the inoculation site was detected only in grapevine and blackberry. The bacterium was never detected in inoculated Bermuda grass. The wide range in the capacities of these hosts to support the bacterium's multiplication and spread suggests that the epidemiological importance of plant host species for the spread of Pierce's disease varies greatly.
Chemical constituents ofCentella asiatica (2007)

Studies on the chemical constituents of the aerial part of Centella asiatica have led to the isolation of three new compounds, named centellin (1), asiaticin (2), and centellicin (3). Their structures have been elucidated through spectral studies including 2D NMR experiments (HMQC, HMBC, (1)H-(1)H COSY, NOESY and J resolved).
Checking the correctness of memories (2002)

The notion of program checking is extended to include programs that alter their environment, in particular, programs that store and retrieve data from memory. The model considered allows the checker a small amount of reliable memory. The checker is presented with a sequence of requests (online) to a data structure which must reside in a large but unreliable memory. The data structure is viewed as being controlled by an adversary. The checker is to perform each operation in the input sequence using its reliable memory and the unreliable data structure so that any error in the operation of the structure will be detected by the checker with high probability. Checkers for various data structures are presented. Lower bounds of log n on the amount of reliable memory needed by these checkers, where n is the size of the structure, are proved.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>