gebhart/patrepeval huggingface dataset:
Cell cycle control and cancer chemotherapy (1994)

As detailed information accumulates about how cell cycle events are regulated, we can expect new opportunities for application to cancer therapy. The altered expression of oncogenes and tumor suppressor genes that commonly occurs in human cancers may impair the ability of the cells to respond to metabolic perturbations of stress. Impaired cell cycle regulation would make cells vulnerable to pharmacologic intervention by drug regimens tailored to the defects existing in particular tumors. Recent findings that may become applicable to therapy are reviewed, and the possible form of new therapeutic stratagems is considered.
Projecting the transmission dynamics of SARS-CoV-2 through the post-pandemic period (2020)

Abstract There is an urgent need to project how transmission of the novel betacoronavirus SARS-CoV-2 will unfold in coming years. These dynamics will depend on seasonality, the duration of immunity, and the strength of cross-immunity to/from the other human coronaviruses. Using data from the United States, we measured how these factors affect transmission of human betacoronaviruses HCoV-OC43 and HCoV-HKU1. We then built a mathematical model to simulate transmission of SARS-CoV-2 through the year 2025. We project that recurrent wintertime outbreaks of SARS-CoV-2 will probably occur after an initial pandemic wave. We summarize the full range of plausible transmission scenarios and identify key data still needed to distinguish between them, most importantly longitudinal serological studies to determine the duration of immunity to SARS-CoV-2.
Starburst mid-flight: as the dust clears (database project) (1990)

The purpose of the Starburst project is to improve the design of relational database management systems and enhance their performance, while building an extensible system to better support nontraditional applications and to serve as a testbed for future improvements in database technology. The design and implementation of the Starburst system to date are considered. Some key design decisions and how they affect the goal of improved structure and performance are examined. How well the goal of extensibility has been met is examined: what aspects of the system are extensible, how extensions can be done, and how easy it is to add extensions. Some actual extensions to the system, including the experiences of the first real customizers, are discussed.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Channel architecture in maltoporin: dominance studies with lamB mutations influencing maltodextrin binding provide evidence for independent selectivity filters in each subunit (1989)

Maltoporin trimers constitute maltodextrin-selective channels in the outer membrane of Escherichia coli. To study the organization of the maltodextrin-binding site within trimers, dominance studies were undertaken with maltoporin variants of altered binding affinity. It has been established that amino acid substitutions at three dispersed regions of the maltoporin sequence (at residues 8, 82, and 360) resulted specifically in maltodextrin-binding defects and loss of maltodextrin channel selectivity; a substitution at residue 118 increased both binding affinity and maltodextrin transport. Strains heterodiploid for lamB were constructed in which these substitutions were encoded by chromosomal and plasmid-borne genes, and the relative level of maltoporin expression from these genes was estimated. Binding assays with bacteria forming maltoporin heterotrimers were performed in order to test for complementation between binding-negative alleles, negative dominance of negative over wild-type alleles, and possible dominance of negatives over the high-affinity allele. Double mutants with mutations affecting residues 8 and 118, 82 and 118, and 118 and 360 were constructed in vitro, and the dominance properties of the mutations in cis were also tested. There was no complementation between negatives and no negative dominance in heterotrimers. The high-affinity mutation was dominant over negatives in trans but not in cis. The affinity of binding sites in heterotrimer populations was characteristic of the high-affinity allele present and uninfluenced by the negative allele. These results are consistent with the presence of three discrete binding sites in a maltoporin trimer and suggest that the selectivity filter for maltodextrins is not at the interface between the three subunits.
Induction of antibodies to the Plasmodium falciparum merozoite surface protein-1 (MSP1) by cross-priming with heterologous MSP1s. (1994)

The merozoite surface protein-1 (MSP1) of Plasmodium falciparum possesses intervening conserved and nonconserved sequences. The relative importance of these sequences in providing T cell help for Ab production was investigated in a series of cross-priming studies using homologous and heterologous parasite MSP1 proteins. Cross-priming with heterologous MSP1s was as efficient as homologous immunizations in inducing anti-MSP1 Abs. Similar to homologous immunization, cross-priming with heterologous MSP1s induced primarily Abs to conserved epitopes. The specificities of the Abs were also similar for the two immunization regimens. Studies were also performed with use of the C-terminal p42 fragment of MSP1 expressed in baculovirus (BVp42). When BVp42 was used either as the priming Ag followed by boosting with homologous (or heterologous) MSP1 or as the booster Ag after priming with homologous (or heterologous) MSP1, much lower anti-BVp42 Ab titers were produced compared with priming/boosting with homologous or heterologous MSP1s or BVp42 alone. Thus, immunization with the complete parasite MSP1 induced a dominant, conserved Th epitope(s) specific for anti-p42 Ab production, and such determinant(s) was either located outside the p42 region or was not provided by the BVp42 because of possible differences in the processing of parasite MSP1 vs BVp42. Our data provided a strong rationale to identify and include conserved Th epitope(s) in MSP1 vaccines. Furthermore, a MSP1 vaccine on the basis of the C-terminal p42 fragment may benefit by the inclusion of additional Th epitopes to achieve effective boosting in the field.
Clinical applications of zolmitriptan (Zomig™, 311C90) (1997)

Zolmitriptan (Zomig, formerly 311C90) is a novel, oral antimigraine drug that is consistently effective and well tolerated in the acute treatment of migraine headache and its associated symptoms. The purpose of this article is to review data available from pharmacological and clinical trials with zolmitriptan and to summarize the clinically relevant features that distinguish this agent. We will review the attributes desirable in a migraine drug and use this as a template for assessing zolmitriptan. Zolmitriptan provides a new oral treatment option for physicians which should help improve patient outcomes.
The RNA recognition motif, a plastic RNA‐binding platform to regulate post‐transcriptional gene expression (2005)

The RNA recognition motif (RRM), also known as RNA-binding domain (RBD) or ribonucleoprotein domain (RNP) is one of the most abundant protein domains in eukaryotes. Based on the comparison of more than 40 structures including 15 complexes (RRM-RNA or RRM-protein), we reviewed the structure-function relationships of this domain. We identified and classified the different structural elements of the RRM that are important for binding a multitude of RNA sequences and proteins. Common structural aspects were extracted that allowed us to define a structural leitmotif of the RRM-nucleic acid interface with its variations. Outside of the two conserved RNP motifs that lie in the center of the RRM beta-sheet, the two external beta-strands, the loops, the C- and N-termini, or even a second RRM domain allow high RNA-binding affinity and specific recognition. Protein-RRM interactions that have been found in several structures reinforce the notion of an extreme structural versatility of this domain supporting the numerous biological functions of the RRM-containing proteins.
Immature rat ovaries become revascularized rapidly after autotransplantation and show a gonadotropin-dependent increase in angiogenic factor gene expression. (1994)

When the ovaries of 23-day-old juvenile rats are transplanted to an ectopic site, they recover within 1 week the ability to control gonadotropin secretion via steroid negative feedback. Vascular corrosion casting followed by scanning electron microscopy revealed that the transplanted ovary becomes profusely revascularized within 48 h after transplantation. Vascular ingrowth was accompanied by a 40- to 60-fold increase in expression of the genes encoding two angiogenic factors, vascular endothelial growth factor (VEGF) and transforming growth factor-beta 1 (TGF beta 1), as assessed by RNA blot hybridization of the corresponding mRNAs. Although TGF beta 3 mRNA levels also increased, no changes in the levels of mRNAs encoding other putative angiogenic factors, such as TGF alpha, basic fibroblast growth factor, and TGF beta 2, were observed. Hybridization histochemistry demonstrated that in intact ovaries, VEGF mRNA is mainly expressed in granulosa cells of the cumulus oophorus and thecal cells of large antral follicles. Transplantation is followed by an increase in mRNA abundance and a dramatic shift in cellular localization, so that the mRNA becomes predominantly expressed in cells of the outer ovarian cortex. In intact ovaries, low levels of TGF beta 1 mRNA were detected in thecal-interstitial cells; after transplantation, its expression also became more predominant in the ovarian outer cortex, but this change was not as marked as in the case of VEGF. Because ovarian autotransplantation is followed by a rapid increase in serum gonadotropin levels, experiments were conducted to determine the importance of this rise in the activation of VEGF and TGF beta 1 gene expression. After transplantation, some animals were treated with the LHRH antagonist Nal-Glu LHRH (50 micrograms/rat, once a day for 2 days) to prevent the posttransplantation rise in serum gonadotropins. Quantitation of VEGF and TGF beta 1 mRNA by RNase protection assay 48 h later showed that suppression of gonadotropin secretion diminished the increase in both VEGF and TGF beta 1 gene expression. Concomitant treatment with PMSG (8 IU/rat, single injection), which mainly bypasses the suppression of endogenous FSH levels, restored the TGF beta 1 mRNA response, but had no effect on VEGF mRNA. The results suggest that the increase in gonadotropin secretion following ovarian transplantation contributes to revascularization of the graft by up-regulating the gene expression of two major angiogenic factors.
Clodronate-liposome-mediated depletion of tumour-associated macrophages: a new and highly effective antiangiogenic therapy approach (2006)

Tumour-associated macrophages, TAMs, play a pivotal role in tumour growth and metastasis by promoting tumour angiogenesis. Treatment with clodronate encapsulated in liposomes (clodrolip) efficiently depleted these phagocytic cells in the murine F9 teratocarcinoma and human A673 rhabdomyosarcoma mouse tumour models resulting in significant inhibition of tumour growth ranging from 75 to >92%, depending on therapy and schedule. Tumour inhibition was accompanied by a drastic reduction in blood vessel density in the tumour tissue. Vascular endothelial growth factor (VEGF) is one of the major inducers of tumour angiogenesis and is also required for macrophage recruitment. The strongest effects were observed with the combination therapy of clodrolip and a VEGF-neutralising antibody, whereas free clodronate was not significantly active. Immunohistologic evaluation of the tumours showed significant depletion of F4/80+ and MOMA-1+ and a less pronounced depletion of CD11b+ TAMs. Blood vessel staining (CD31) and quantification of the vessels as well as TAMs and tumour-associated dendritic cells (TADCs) in the A673 model showed reduction rates of 85 to >94%, even 9 days after the end of therapy. In addition, CD11c+ TADCs, which have been shown to potentially differentiate into endothelial-like cells upon stimulation by tumour released growth and differentiation factors, were similarly reduced by clodrolip or antibody treatment. These results validate clodrolip therapy in combination with angiogenesis inhibitors as a promising novel strategy for an indirect cancer therapy aimed at the haematopoietic precursor cells that stimulate tumour growth and dissemination and as a tool to study the role of macrophages and dendritic cells in tumorigenesis.
Image coding using DCT of wavelet coefficients (2003)

A method to encode wavelet transformed (WT) images is described. WT decomposition of natural images preserves image structure within each subimage. Subsequent coding of this multiresolution representation can be achieved through techniques such as scalar/vector quantization (SQ/VQ). It is proposed that by transforming WT coefficients, a better result can be achieved in both compression ratio and output quality. Experimental results are presented to demonstrate the quality of the decoded images.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Template imprinting amphoteric polymer for the recognition of proteins (2004)

Abstract A selective recognizing of proteins with amphoteric polymer is essential for application in protein separations. An amphoteric polymer was synthesized by copolymerization of the two functional monomers with the crosslinker in the presence of the template proteins. After extraction of the template protein, the polymer was applied as chromatographic stationary phase, showing high resolution capacity. The molecular imprinting technique allows the formation of specific recognition sites in amphoteric polymers through the use of template protein. Protein is preferentially bound to a polymer made in the presence of the same protein. The recognition ability of an amphoteric polymer is attributed to imprinted cavities that complement proteins in shape and electrostatic interactions. © 2004 Wiley Periodicals, Inc. J Appl Polym Sci 95: 358–361, 2005
Bone Marrow Stem Cells Expressing Keratinocyte Growth Factor via an Inducible Lentivirus Protects against Bleomycin-Induced Pulmonary Fibrosis (2009)

Many common diseases of the gas exchange surface of the lung have no specific treatment but cause serious morbidity and mortality. Idiopathic Pulmonary Fibrosis (IPF) is characterized by alveolar epithelial cell injury, interstitial inflammation, fibroblast proliferation and collagen accumulation within the lung parenchyma. Keratinocyte Growth Factor (KGF, also known as FGF-7) is a critical mediator of pulmonary epithelial repair through stimulation of epithelial cell proliferation. During repair, the lung not only uses resident cells after injury but also recruits circulating bone marrow-derived cells (BMDC). Several groups have used Mesenchymal Stromal Cells (MSCs) as therapeutic vectors, but little is known about the potential of Hematopoietic Stem cells (HSCs). Using an inducible lentiviral vector (Tet-On) expressing KGF, we were able to efficiently transduce both MSCs and HSCs, and demonstrated that KGF expression is induced in a regulated manner both in vitro and in vivo. We used the in vivo bleomycin-induced lung fibrosis model to assess the potential therapeutic effect of MSCs and HSCs. While both populations reduced the collagen accumulation associated with bleomycin-induced lung fibrosis, only transplantation of transduced HSCs greatly attenuated the histological damage. Using double immunohistochemistry, we show that the reduced lung damage likely occurs through endogenous type II pneumocyte proliferation induced by KGF. Taken together, our data indicates that bone marrow transplantation of lentivirus-transduced HSCs can attenuate lung damage, and shows for the first time the potential of using an inducible Tet-On system for cell based gene therapy in the lung.
Mapping of Heavy Chain Genes for Mouse Immunoglobulins M and D (1980)

A single DNA fragment containing both mu and delta immunoglobulin heavy chain genes has been cloned from normal BALB/c mouse liver DNA with a new lambda phage vector Charon 28. The physical distance between the membrane terminal exon of mu and the first domain of delta is 2466 base pairs, with delta on the 3' side of mu. A single transcript could contain a variable region and both mu and delta constant regions. The dual expression of immunoglobulins M and D on spleen B cells may be due to alternate splicing of this transcript.
Comparison of flurpiridaz F 18 PET injection and Tc-99m labeled SPECT myocardial perfusion imaging for identifying severity and extent of stress induced myocardial ischemia in phase 2 clinical trials (2011)

444 Objectives Flurpiridaz F 18 is a novel PET myocardial perfusion imaging (MPI) tracer. In this multi-center Phase 2 study, rest-stress flurpiridaz F 18 PET and SPECT MPI were compared for evaluation of stress induced myocardial perfusion abnormalities in patients (Pts) with coronary artery disease (CAD). Methods 84 Pts from 21 centers, underwent coronary angiography and rest-stress flurpiridaz F 18 PET (PET) and SPECT MPI. Tc-99m labeled tracer was used for all stress and 81% of rest SPECT. The mean age of Pts was 64.5 years (range: 36-85) and 68 were males. In each Pt, 17 myocardial segments were visually scored on rest and stress images by 3 independent, blinded readers. For each Pt, summed difference scores (SDS) were determined from segmental scores. Percent narrowing in each coronary artery was quantitatively and blindly determined and ≥50% luminal diameter narrowing was considered significant. Of the 84 Pts, 52 had CAD and 32 had insignificant CAD or normal coronary arteries. Results There were 105 diseased coronary arteries in 52 patients; 40 left anterior descending, 30 left circumflex and 35 right coronary arteries. In patients with at least one diseased artery, the mean±SD PET SDS score ranged among the three readers from 6.8±5.75 to 9.4±7.51 and the SPECT SDS score ranged from 4.1±4.75 to 5.7±6.51. The differences in SDS scores between PET and SPECT were statistically significant in all readers (p Conclusions These data suggest that as compared to Tc-99m SPECT, flurpiridaz F 18 PET MPI demonstrates more severe and extensive stress induced perfusion abnormalities in myocardial regions that are supplied by diseased coronary arteries and in patients with multivessel CAD. Research Support Lantheus Medical Imagin
Neutrophil Apoptosis: Selective Regulation by Different Ligands of Integrin αMβ2 (2008)

Neutrophils undergo spontaneous apoptosis, but their survival can be extended during inflammatory responses. alpha(M)beta(2) is reported either to delay or accelerate neutrophil apoptosis, but the mechanisms by which this integrin can support such diametrically opposed responses are poorly understood. The abilities of closely related alpha(M)beta(2) ligands, plasminogen and angiostatin, derived from plasminogen, as well as fibrinogen and its two derivative alpha(M)beta(2) recognition peptides, P1 and P2-C, differed markedly in their effects on neutrophil apoptosis. Plasminogen, fibrinogen, and P2-C suppressed apoptosis via activation of Akt and ERK1/2 kinases, while angiostatin and P1 failed to activate these prosurvival pathways and did not prevent neutrophil apoptosis. Using cells transfected with alpha(M)beta(2) or its individual alpha(M) or beta(2) subunits, and purified receptors and its constituent chains, we show that engagement of both subunits with prosurvival ligands is essential for induction of the prosurvival response. Hence, engagement of a single integrin by closely related ligands can induce distinct signaling pathways, which can elicit distinct cellular responses.
Ion activities and potassium uptake mechanisms of glial cells in guinea‐pig olfactory cortex slices. (1987)

1. Double-barrelled ion-sensitive micro-electrodes were used to measure changes in the intracellular activities of K+, Na+ and Cl- (aiK, aiNa, aiCl) in glial cells of slices from guinea-pig olfactory cortex during repetitive stimulation of the lateral olfactory tract. 2. Base-line levels of aiK, aiNa and aiCl were about 66, 25 and 6 mM, respectively, for cells with resting potentials higher than -80 mV. During stimulation, intraglial aiK and aiCl increased, whereas aiNa decreased. Within about 2 min after stimulation the ion activities returned to their base-line levels. 3. The Cl- equilibrium potential was found to be close to the membrane potential (Em). There was also a strong correlation between changes of Em and aiCl. These observations indicate a high Cl- conductance of the glial cell membrane. 4. In the presence of Ba2+, the usual depolarizing response of the glial cells to a rise of the extracellular K+ activity (aeK) reversed into a membrane hyperpolarization. Furthermore, Ba2+ strongly reduced the stimulus-related rise of intraglial aiK. An additional application of ouabain blocked both the membrane hyperpolarization as well as the remaining rise of aiK. 5. In conclusion, our data show that glial cells in guinea-pig olfactory cortex slices possess at least two mechanisms of K+ accumulation. One mechanism is sensitive to the K+ channel blocker Ba2+ and might be a passive KCl influx. The other appears to be the electrogenic Na+/K+ pump, which can be activated by excess extracellular K+.
Normalized shape and location of perturbed craniofacial structures in the Xenopus tadpole reveal an innate ability to achieve correct morphology (2012)

Our data suggest a model in which craniofacial structures use a measuring mechanism to assess and adjust their location relative to other local organs. Understanding the correction mechanisms at work in this system could lead to the better understanding of the adaptive decision-making capabilities of living tissues and suggest new approaches to correct birth defects in humans.
Direct labeling of RNA with multiple biotins allows sensitive expression profiling of acute leukemia class predictor genes (2004)

Direct labeling of RNA is an expedient method for labeling large quantities (e.g. micrograms) of target RNA for microarray analysis. We have developed an efficient labeling system that uses T4 RNA ligase to attach a 3'-biotinylated donor molecule to target RNA. Microarray analyses indicate that directly labeled RNA is uniformly labeled, has higher signal intensity than comparable labeling methods and achieves high transcript detection sensitivity. The labeled donor molecule we have developed allows the attachment of multiple biotins, which increases target signal intensity up to 30%. We have used this direct-labeling method to detect previously discovered class predictor genes for two types of cancer: acute myeloid leukemia (AML) and acute lymphoblastic leukemia (ALL). In order to test the sensitivity of direct RNA labeling, we analyzed the AML and ALL expression profiles for predictor genes that were previously found to show elevated expression in the disease state. Direct labeling of AML poly(A) RNA detects 90% of the class predictor genes that are detected by the IVT-based target amplification method used to discover the genes. These results indicate that the detection sensitivity, simplicity (single tube reaction) and speed (2 h) of this direct labeling protocol may be ideal for diagnostic applications that do not require target amplification.