gebhart/patrepeval huggingface dataset:
Microtiter Plate Assay for Assessment of Listeria monocytogenes Biofilm Formation (2002)

Listeria monocytogenes has the ability to form biofilms on food-processing surfaces, potentially leading to food product contamination. The objective of this research was to standardize a polyvinyl chloride (PVC) microtiter plate assay to compare the ability of L. monocytogenes strains to form biofilms. A total of 31 coded L. monocytogenes strains were grown in defined medium (modified Welshimer's broth) at 32 degrees C for 20 and 40 h in PVC microtiter plate wells. Biofilm formation was indirectly assessed by staining with 1% crystal violet and measuring crystal violet absorbance, using destaining solution. Cellular growth rates and final cell densities did not correlate with biofilm formation, indicating that differences in biofilm formation under the same environmental conditions were not due to growth rate differences. The mean biofilm production of lineage I strains was significantly greater than that observed for lineage II and lineage III strains. The results from the standardized microtiter plate biofilm assay were also compared to biofilm formation on PVC and stainless steel as assayed by quantitative epifluorescence microscopy. Results showed similar trends for the microscopic and microtiter plate assays, indicating that the PVC microtiter plate assay can be used as a rapid, simple method to screen for differences in biofilm production between strains or growth conditions prior to performing labor-intensive microscopic analyses.
Chemotactic activity of human recombinant granulocyte-macrophage colony-stimulating factor. (1987)

Recombinant human granulocyte-macrophage colony-stimulating factor (rhGM-CSF) seeded in the lower compartment of chemotaxis chambers induced migration of human peripheral blood monocytes and polymorphonuclear phagocytes. rhGM-CSF was active in inducing phagocyte migration at concentrations as low as 10 CML units/ml (corresponding to 0.002 microgram), and maximal activity was observed at 10(2)-10(4)/ml. Checkerboard analysis performed by seeding different concentrations of rhGM-CSF above and below the filter revealed that maximal induction of migration required a positive concentration gradient between the lower and upper compartment, and that rhGM-CSF elicited an actual chemotactic response in phagocytes. Human umbilical vein endothelial cells and blood large granular lymphocytes (LGL) responded poorly or not at all (endothelial cells) to rhGM-CSF under conditions in which appropriate reference chemoattractants were active. The chemotactic activity of rhGM-CSF may serve to recruit phagocytic cells from the blood compartment to amplify resistance against noxious agents.
Yellow fever virus envelope protein has two discrete type-specific neutralizing epitopes. (1997)

Two monoclonal antibody neutralization resistant (MAbR) variants of the yellow fever (YF) 17D-204 vaccine virus strain were selected using YF type-specific MAb B39. These B39R variants were compared with the variant virus selected by Lobigs et al. (Virology 161, 474-478, 1987) using a second YF-type specific MAb (2E10) which mapped to amino acid position 71/72 in the envelope (E) protein. Neutralization assays with a panel of MAbs suggested that these two YF-type-specific epitopes are located in two discrete regions of the folded E protein. Each of the B39R variants had a single nucleotide mutation which encoded an amino acid substitution at either position E-155 or E-158. Thus, YF type-specific epitopes map to both domain I (B39) and II (2E10) of the YF virus E protein. The B39 defined epitope represents the first flavivirus neutralizing epitope localized to this region of domain I of the E protein.
The Genomes of Bovine Papillomaviruses Types 3 and 4 are Colinear (1983)

The 7.2 kb genomic DNA of bovine papillomavirus type 3 (BPV-3) was molecularly cloned using its unique EcoRI site, and the 7.3 kb genome of BPV-4 was cloned using its single BamHI site. The viral genomes were compared by liquid hybridization, Southern blot hybridization and heteroduplex mapping. Low stringency hybridization conditions revealed that the genomes are colinear but the sequences are extensively mismatched. The relative alignment of the restriction endonuclease maps of the two viral genomes has been determined. It was found that the genomes as linearized for cloning are out of phase by 1.7 kb, so that the single EcoRI site of BPV-3 appears to coincide with the BPV-4 EcoRI site at 0.22 map units. It is concluded that the genomes of BPV-3 and BPV-4, both of which cause true epithelial warts, share the same physical organization but exhibit sequence divergence.
Transforming growth factor-?1 (1999)

Although transforming growth factor-β1 may prove to be an important new tumor marker in colorectal carcinoma, larger, prospective studies are needed to confirm this theory. See referenced original article on pages 554-61.
Combination Therapy with Anti–CTLA-4 and Anti–PD-1 Leads to Distinct Immunologic Changes In Vivo (2014)

Combination therapy concurrently targeting PD-1 and CTLA-4 immune checkpoints leads to remarkable antitumor effects. Although both PD-1 and CTLA-4 dampen the T cell activation, the in vivo effects of these drugs in humans remain to be clearly defined. To better understand biologic effects of therapy, we analyzed blood/tumor tissue from 45 patients undergoing single or combination immune checkpoint blockade. We show that blockade of CTLA-4, PD-1, or combination of the two leads to distinct genomic and functional signatures in vivo in purified human T cells and monocytes. Therapy-induced changes are more prominent in T cells than in monocytes and involve largely nonoverlapping changes in coding genes, including alternatively spliced transcripts and noncoding RNAs. Pathway analysis revealed that CTLA-4 blockade induces a proliferative signature predominantly in a subset of transitional memory T cells, whereas PD-1 blockade instead leads to changes in genes implicated in cytolysis and NK cell function. Combination blockade leads to nonoverlapping changes in gene expression, including proliferation-associated and chemokine genes. These therapies also have differential effects on plasma levels of CXCL10, soluble IL-2R, and IL-1α. Importantly, PD-1 receptor occupancy following anti-PD-1 therapy may be incomplete in the tumor T cells even in the setting of complete receptor occupancy in circulating T cells. These data demonstrate that, despite shared property of checkpoint blockade, Abs against PD-1, CTLA-4 alone, or in combination have distinct immunologic effects in vivo. Improved understanding of pharmacodynamic effects of these agents in patients will support rational development of immune-based combinations against cancer.
Annual Report to the Nation on the status of cancer, 1973–1999, featuring implications of age and aging on U.S. cancer burden (2002)

Despite the continuing decrease in cancer death rates and stabilization of cancer incidence rates, the overall growth and aging of the U.S. population can be expected to increase the burden of cancer in our nation.
Glycoprotein Synthesis: From Glycobiological Tools to Tailor-made Catalysts (1999)

The synthesis of pure, well-defined glycoproteins is essential to the study of the host of biological processes that they mediate. The use of a combined site-directed mutagenesis and chemical modification strategy allows the site-selective synthesis of homogenous glycoproteins, the determination of precise structureactivity relationships and the design of new synthetic catalysts. This general and powerful method is reviewed in the context of existing preparative techniques and the wide-ranging applications of glycoproteins are highlighted
Cell-mediated immunity to hepatitis B virus antigens in mice: correlation of in vivo and in vitro assays. (1986)

Cell mediated immunity (CMI) to hepatitis B viral antigens was studied in BALB/mice after immunization with purified hepatitis B surface antigen (HBsAg), or core antigen (HBcAg), with adjuvants. The two in vitro assays for cell-mediated immunity (CMI), utilizing lymph node cells, were release of interferon after exposure to antigen, and blast transformation of lymphocytes, and the in vivo assay was ear swelling at 24 h after local injection of antigen. Immunization with HBsAg or HBcAg with adjuvants induced antigen-specific cutaneous reactivity; if no adjuvants were given, immunization with HBcAg, but not HBsAg, induced cutaneous reactivity. CMI could be adoptively transferred by lymph node cells, but for only a limited period after immunization with HbsAg or HBcAg. The ability of lymph node cells from mice immunized with HBV antigens to transfer adoptively CMI correlated well with their production of interferon after challenge with antigen in vitro, but less well with blastogenesis after challenge with antigen in vitro, or with cutaneous reactivity to antigen in the donor mouse. Reliable antigen-specific lymphokine release assays, rather than blast transformation of lymphocytes or cutaneous reactivity after antigen challenge, are required to assess CMI to HBV antigens in the mouse and, by inference, in man.
The magnitude of the global problem of acute diarrhoeal disease: a review of active surveillance data. (1982)

Data from 24 published studies were anlayzed in order to estimate the annual morbidity and mortality from acute diarrheal diseases in the developing world. 22 of the studies involved frequent surveillance through home visits to families in communities; the other 2 were multicountry studies in which diarrhea mortality was calculated on the basis of death certificate information. Morbidity rates were found to be highest in the 6-11 month age group, while the mortality rates were greatest in infants under 1 year of age and children 1 year old. For children under 5 years of age, the median incidence of diarhhea was 2.2 episodes/child/year for all studies and 3.0 episodes/child/year for the studies that had the smallest populations and most frequent surveillance. Using 1980 population estimates, the estimated total yearly morbidity and mortality from diarrheal diseases for children under 5 years of age in Africa, Asia (excluding China), and Latin America were 744-1000 million episodes and 4.6 million deaths. (author's)
Removal of nonhydratable phospholipids from soybean oil (1971)

Abstract On the basis of the literature concerning the chemical and physicochemical properties of phosphatidic acid and phosphatidates, an experimental investigation of the conditions under which nonhydratable phospholipids (Mg/Ca‐phosphatidates) are removable from water degummed soybean oil was carried out. The experiments were carried out by mixing water‐degummed oil at different fixed pH values with buffer solutions with and without admixture of Ca ++ , Mg/Ca‐binding reagents and surfactants. The results indicate that the nonhydratable phospholipids can be removed in a chemically nonconverted state as a component of micelles or of mixed emulsifiers. Furthermore, the nonhydratable phospholipids are removable by conversion into dissociated form, i.e., by removal of Mg and Ca from the phosphatidates, which can be accomplished by acidulation or by treatment with Mg/Ca‐complexing or Mg/Ca‐precipitating reagents. Alkali‐refining experiments have shown that removal or chemical conversion of the nonhydratable phospholipids result in reduced emulsion formation and in improved separation of the deacidified oil from the emulsion layer and the soapstock.
CD11a-CD18 and CD102 interactions mediate human myeloma cell growth arrest induced by CD40 stimulation. (1996)

We have recently demonstrated that the CD40 molecule was expressed on both normal human plasma cells and most malignant plasma cells, i.e., myeloma cells. Thus, we have investigated its putative role in the proliferation of myeloma cells. We report that 7 of 15 myeloma cell lines were CD40+ but only one, XG2, presented a high level of CD40 expression. We show that the CD40 stimulation by anti-CD40 monoclonal antibodies (mAbs) of the interleukin 6-dependent myeloma cell line XG2 induced a total inhibition of its proliferation. This inhibition was also observed when cells were either cultured in the "CD40 system," where the anti-CD40 mAb has been immobilized on fibroblasts expressing Fc receptors or in the presence of a soluble chimeric CD40 ligand molecule. This inhibition of proliferation was neither accompanied by differentiation nor apoptosis. Triggering CD40 induced an homotypic aggregation of XG2 cells, and the inhibition of proliferation was totally prevented by a blocking anti-CD18 mAb. Although the CD11a-CD18 ligands, i.e., CD50, CD54, and CD102, were all expressed on XG2 cells, only a blocking anti-CD102 mAb inhibited the CD40-induced growth arrest. Our data demonstrate that CD40 triggering on XG2 cells induced a myeloma cell growth arrest mediated by lymphocyte function-associated antigen 1 and intercellular adhesion molecule 2 interactions.
KNAT1 and ERECTA Regulate Inflorescence Architecture in Arabidopsis (2002)

Plant architecture is dictated by morphogenetic factors that specify the number and symmetry of lateral organs as well as their positions relative to the primary axis. Mutants defective in the patterning of leaves and floral organs have provided new insights on the signaling pathways involved, but there is comparatively little information regarding aspects of the patterning of stems, which play a dominant role in architecture. To this end, we have characterized five alleles of the brevipedicellus mutant of Arabidopsis, which exhibits reduced internode and pedicel lengths, bends at nodes, and downward-oriented flowers and siliques. Bends in stems correlate with a loss of chlorenchyma tissue at the node adjacent to lateral organs and in the abaxial regions of pedicels. A stripe of achlorophyllous tissue extends basipetally from each node and is positioned over the vasculature that services the corresponding lateral organ. Map-based cloning and complementation studies revealed that a null mutation in the KNAT1 homeobox gene is responsible for these pleiotropic phenotypes. Our observation that wild-type Arabidopsis plants also downregulate chlorenchyma development adjacent to lateral organs leads us to propose that KNAT1 and ERECTA are required to restrict the action of an asymmetrically localized, vasculature-associated chlorenchyma repressor at the nodes. Our data indicate that it is feasible to alter the architecture of ornamental and crop plants by manipulating these genetically defined pathways.
Identification of Two Distinct Progenitor Populations in the Lateral Ganglionic Eminence: Implications for Striatal and Olfactory Bulb Neurogenesis (2003)

The lateral ganglionic eminence (LGE) is known to give rise to striatal projection neurons as well as interneurons, which migrate in the rostral migratory stream (RMS) to populate the granule cell and glomerular layers of the olfactory bulb. Because all of these neuronal subtypes express Distalless-related (DLX) homeobox proteins during their differentiation, we set out to further characterize progenitors in the Dlx-positive domain of the LGE. Previous studies have shown that the LIM homeobox protein Islet1 (ISL1) marks the LGE subventricular zone (SVZ) and differentiating striatal projection neurons. However, ISL1 is not expressed in neurons of the developing olfactory bulb or the RMS. We show here that the dorsal-most portion of the Dlx-expressing region of the LGE SVZ lacks ISL1 cells. This dorsal domain, however, contains cells that express the ETS transcription factor Er81, which is also expressed in granule and periglomerular cells of the developing and adult olfactory bulb. Moreover, the adult SVZ and RMS contain numerous Er81-positive cells. Fate-mapping studies using Dlx5/6-cre transgenic mice demonstrate that Er81-positive cells in the granule cell and glomerular layers of the olfactory bulb derive from the Dlx-expressing SVZ region. These findings suggest that the LGE SVZ contains two distinct progenitor populations: a DLX(+);ISL1(+) population representing striatal progenitors and a DLX(+);Er81(+) population comprising olfactory bulb interneuron progenitors. In support of this, mice mutant for the homeobox genes Gsh2 and Gsh1/2, which show olfactory bulb defects, exhibit dramatically reduced numbers of Er81-positive cells in the LGE SVZ as well as in the olfactory bulb mantle.
Breast cancer stem cells: tools and models to rely on (2009)

There is increasing evidence for the "cancer stem cell (CSC) hypothesis", which holds that cancers are driven by a cellular component that has stem cell properties, including self-renewal, tumorigenicity and multi-lineage differentiation capacity. Researchers and oncologists see in this model an explanation as to why cancer may be so difficult to cure, as well as a promising ground for novel therapeutic strategies. Given the specific stem cell features of self-renewal and differentiation, which drive tumorigenesis and contribute to cellular heterogeneity, each marker and assay designed to isolate and characterize CSCs has to be functionally validated. In this review, we survey tools and markers available or promising to identify breast CSCs. We review the main models used to study breast CSCs and how they challenge the CSC hypothesis.
Zur Anpassung des KSE-Vertrages an neue Sicherheitsstrukturen in Europa. (II): Die Folgen des zukünftigen KSE-Vertrages: Zugewinn an konventioneller Stabilität für ganz Europa (1997)

Die neuen Kernelemente des zukünftigen KSE-Vertragssystems, d.h. nationale und territoriale Obergrenzen, spezielle stabilisierende Maßnahmen und mehr Effizienz bei wechselseitiger militärischer Information und Verifikation (siehe im einzelnen Teil I), werden zusammenwirkend in ganz Europa einen Zugewinn an konventioneller Stabilität eröffnen. Es ist zu erwarten, daß das neue KSE-Vertragssystem erhebliche Anreize für eine Absenkung nationaler Obergrenzen schaffen wird. (BIOst-Dok)
Total synthesis of long DNA sequences: Synthesis of a contiguous 32-kb polyketide synthase gene cluster (2004)

To exploit the huge potential of whole-genome sequence information, the ability to efficiently synthesize long, accurate DNA sequences is becoming increasingly important. An approach proposed toward this end involves the synthesis of approximately 5-kb segments of DNA, followed by their assembly into longer sequences by conventional cloning methods [Smith, H. O., Hutchinson, C. A., III, Pfannkoch, C. & Venter, J. C. (2003) Proc. Natl. Acad. Sci. USA 100, 15440-15445]. The major current impediment to the success of this tactic is the difficulty of building the approximately 5-kb components accurately, efficiently, and rapidly from short synthetic oligonucleotide building blocks. We have developed and implemented a strategy for the high-throughput synthesis of long, accurate DNA sequences. Unpurified 40-base synthetic oligonucleotides are built into 500- to 800-bp "synthons" with low error frequency by automated PCR-based gene synthesis. By parallel processing, these synthons are efficiently joined into multisynthon approximately 5-kb segments by using only three endonucleases and "ligation by selection." These large segments can be subsequently assembled into very long sequences by conventional cloning. We validated the approach by building a synthetic 31,656-bp polyketide synthase gene cluster whose functionality was demonstrated by its ability to produce the megaenzyme and its polyketide product in Escherichia coli.
Hive - a petabyte scale data warehouse using Hadoop (2010)

The size of data sets being collected and analyzed in the industry for business intelligence is growing rapidly, making traditional warehousing solutions prohibitively expensive. Hadoop is a popular open-source map-reduce implementation which is being used in companies like Yahoo, Facebook etc. to store and process extremely large data sets on commodity hardware. However, the map-reduce programming model is very low level and requires developers to write custom programs which are hard to maintain and reuse. In this paper, we present Hive, an open-source data warehousing solution built on top of Hadoop. Hive supports queries expressed in a SQL-like declarative language - HiveQL, which are compiled into map-reduce jobs that are executed using Hadoop. In addition, HiveQL enables users to plug in custom map-reduce scripts into queries. The language includes a type system with support for tables containing primitive types, collections like arrays and maps, and nested compositions of the same. The underlying IO libraries can be extended to query data in custom formats. Hive also includes a system catalog - Metastore - that contains schemas and statistics, which are useful in data exploration, query optimization and query compilation. In Facebook, the Hive warehouse contains tens of thousands of tables and stores over 700TB of data and is being used extensively for both reporting and ad-hoc analyses by more than 200 users per month.
Effects of a metabotropic glutamate agonist, trans-ACPD, on cortical epileptiform activity (1992)

The effect of the metabotropic glutamate receptor agonist trans-1-amino-1,3,cyclopentanedicarboxylic acid (trans-ACPD) on epileptiform activity induced in rat neocortical slices by exposure to Mg(2+)-free medium was examined. Trans-ACPD dose dependently (10-200 microM) decreased the frequency of spontaneous epileptiform events whilst increasing both the duration of afterpotentials and the number of afterbursts associated with single events. This effect on afterpotentials and afterbursting was particularly pronounced in 14-17 day-old rats and was blocked by the sigma ligand ditolyguanidine (DTG) 10 microM. The putative metabotropic glutamate receptor antagonist L-AP3 did not antagonise the actions of trans-ACPD. The results suggest a role for metabotropic glutamate receptors in epilepsy, possibly in the transition from interictal to ictal activity.
Calculation of Minimal Detectable Activity for Scintillation Detection Systems (1987)

This paper analyzes the statistical approach to the determinoJion of minimum detectable radioactivity for nuclear medicine counting data. Based upon measurements of the background level and de­ tector counting efficiency this method allows calculation of the counting time necessary to detect a specified minimum amount of radioactivity. This method is important both in the application of bioassay measurements of radimion workers for measuring thyroid burden and in the measurement of radioactive wipe test samples.
Generation of Novel Rat and Human Pluripotent Stem Cells by Reprogramming and Chemical Approaches (2010)

Although embryonic stem cells (ESCs) have been established from mice since 1981, attempts to derive its counterparts from various other mammals, including rats, have not succeeded. Recently, induced pluripotent stem cells (iPSCs) have been generated from both mouse and human somatic cells by genetic transduction. We had successfully established novel rat iPSCs (riPSCs), which can be homogenously maintained by LIF and a cocktail of ALK5 inhibitor, GSK3 inhibitor and MEK inhibitor. riPSCs share conventional mouse ESC characteristics and most importantly can contribute extensively to chimeras. We also generated novel human iPSCs (hiPSCs) with "mouse ESC-like" characteristics, which can be surprisingly maintained in culture in the presence of MEK inhibitor and ALK5 inhibitor.
Nonlinear pulse shaping and causality (1993)

A nonlinear phase shift is applied to a spectrum of an ultrafast input signal after dispersing it in space. It is shown that when the input is a pulse pair, the output contains new pulses, which are formed both in front of and behind the original pair. We show the analogy between this experiment and photon echoes and discuss the causal properties of this system.
Synthesis of Functionalised Phenylalanines Using Rhodium Catalysis in Water (2003)

Abstract The efficient synthesis of substituted phenylalanine‐type amino acids using a rhodium‐catalysed, conjugate addition of arylboronic acids is described. The reactions are run in water and use a low loading (0.5 mol %) of rhodium catalyst.