gebhart/patrepeval huggingface dataset:
Droplet volume variability as a critical factor for accuracy of absolute quantification using droplet digital PCR (2017)

Accurate and precise nucleic-acid quantification is crucial for clinical and diagnostic decisions, as overestimation or underestimation can lead to misguided treatment of a disease or incorrect labelling of the products. Digital PCR is one of the best tools for absolute nucleic-acid copy-number determination. However, digital PCR needs to be well characterised in terms of accuracy and sources of uncertainty. With droplet digital PCR, discrepancies between the droplet volume assigned by the manufacturer and measured by independent laboratories have already been shown in previous studies. In the present study, we report on the results of an inter-laboratory comparison of different methods for droplet volume determination that is based on optical microscopy imaging and is traceable to the International System of Units. This comparison was conducted on the same DNA material, with the examination of the influence of parameters such as droplet generators, supermixes, operators, inter-cartridge and intra-cartridge variability, and droplet measuring protocol. The mean droplet volume was measured using a QX200™ AutoDG™ Droplet Digital™ PCR system and two QX100™ Droplet Digital™ PCR systems. The data show significant volume differences between these two systems, as well as significant differences in volume when different supermixes are used. We also show that both of these droplet generator systems produce droplets with significantly lower droplet volumes (13.1%, 15.9%, respectively) than stated by the manufacturer and previously measured by other laboratories. This indicates that to ensure precise quantification, the droplet volumes should be assessed for each system.
Ab Initio Evaluation of the Substitution Effect of the Hydrogen Bond Energy of the Watson−Crick Type Base Pair between 1-Methyluracil and Substituted 9-Methyladenine Derivatives (2001)

The substitution effect on hydrogen bond energy of the Watson−Crick type base pair between uracil and chemically modified adenine derivatives was evaluated by ab initio molecular orbital theory. Predicted hydrogen bond energies were compared with experimental binding constants in some cases, and the calculated hydrogen bond energies correlated well with the experimental binding constants. Thus, ab initio calculation is an effective method to estimate the stability of the base pair between chemically modified nucleic acid bases. In contrast to the substitution effect in uracil on hydrogen bond energy, no remarkable trend was observed in the relation between the substituent in adenine derivatives and the hydrogen bond energies. The adenine derivatives, which have a nitro group on the 8-position or an amino group on the 2-position, can form the most stable hydrogen bonds with uracil.
Bromodeoxyuridine Induces Senescence in Neural Stem and Progenitor Cells (2008)

Bromodeoxyuridine (BrdU) is a halogenated pyrimidine that incorporates into newly synthesized DNA during the S phase. BrdU is used ubiquitously in cell birthdating studies and as a means of measuring the proliferative index of various cell populations. In the absence of secondary stressors, BrdU is thought to incorporate relatively benignly into replicating DNA chains. However, we report here that a single, low-dose pulse of BrdU exerts a profound and sustained antiproliferative effect in cultured murine stem and progenitor cells. This is accompanied by altered terminal differentiation, cell morphology, and protein expression consistent with the induction of senescence. There is no evidence of a significant increase in spontaneous cell death; however, cells are rendered resistant to chemically induced apoptosis. Finally, we show that a brief in vivo BrdU regimen reduces the proliferative potential of subsequently isolated subependymal zone neurosphere-forming cells. We conclude, therefore, that BrdU treatment induces a senescence pathway that causes a progressive decline in the replication of rapidly dividing stem/progenitor cells, suggesting a novel and uncharacterized effect of BrdU. This finding is significant in that BrdU-incorporating neural stem/progenitor cells and their progeny should not be expected to behave normally with respect to proliferative potential and downstream functional parameters. This effect highlights the need for caution when results based on long-term BrdU tracking over multiple rounds of replication are interpreted. Conversely, the reliable induction of senescence in stem/progenitor cells in vitro and in vivo may yield a novel platform for molecular studies designed to address multiple aspects of aging and neurogenesis.
Phospholipases D1 and D2 Regulate Different Phases of Exocytosis in Mast Cells (2002)

The rat mast cell line RBL-2H3 contains both phospholipase D (PLD)1 and PLD2. Previous studies with this cell line indicated that expressed PLD1 and PLD2 are both strongly activated by stimulants of secretion. We now show by use of PLDs tagged with enhanced green fluorescent protein that PLD1, which is largely associated with secretory granules, redistributes to the plasma membrane in stimulated cells by processes reminiscent of exocytosis and fusion of granules with the plasma membrane. These processes and secretion of granules are suppressed by expression of a catalytically inactive mutant of PLD1 or by the presence of 50 mM 1-butanol but not tert-butanol, an indication that these events are dependent on the catalytic activity of PLD1. Of note, cholera toxin induces translocation of PLD1-labeled granules to the plasma membrane but not fusion of granules with plasma membrane or secretion. Subsequent stimulation of calcium influx with Ag or thapsigargin leads to rapid redistribution of PLD1 to the plasma membrane and accelerated secretion. Also of note, PLD1 is recycled from plasma membrane back to granules within 4 h of stimulation. PLD2, in contrast, is largely confined to the plasma membrane, but it too participates in the secretory process, because expression of catalytically inactive PLD2 also blocks secretion. These data indicate a two-step process: translocation of granules to the cell periphery, regulated by granule-associated PLD1, and a calcium-dependent fusion of granules with the plasma membrane, regulated by plasma membrane-associated PLD2 and possibly PLD1.
Rational low temperature synthesis and structural investigations of ultrathin bismuth nanosheets (2012)

A novel and convenient, template-free synthesis approach based on a low-temperature reduction route has been developed for the fabrication of high-yield ultrathin bismuth nanosheets for the first time by bottom-up self-assembly. Scanning electron microscopy and transmission electron microscopy observations of the product show uniform two-dimensional ultrathin nanosheets with high aspect ratios possessing lateral dimension up to several hundred nanometers. Results presented herein suggest a simple route for the large-scale production of ultrathin and flat Bi nanosheets, which may be beneficial to further electronics and as building blocks in catalysts, solar cells, batteries, electronic devices as well assisting as platforms for fundamental studies of physical/chemical properties in two-dimensional systems.
MULTIPLE INTRACRANIAL TUMORS (1939)

It has been recognized that some relationship exists between meningeal growths and those tumors which arise from the nerve sheaths or their components, but only recently has the nature of this association been given any considerable study. Most of the interest has evolved about that special form of generalized neurofibromatosis in which the central nervous system is predominantly affected. Mainly through the work of Harbitz, 1 Preiser and Davenport 2 and Schaltenbrand, 3 generalized von Recklinghausen's disease has been long recognized as a familial disorder. Only recently, however, has it been shown that central neurofibromatosis is also hereditary in that special form of the disease and may be transmitted as a dominant trait with little or none of the peripheral manifestations of the disorder. 4 A special variety of central neurofibromatosis, bilateral acoustic tumors, has been described by Gardner and Frazier 5 and Gardner 6 and also established on a
Control of photosynthetic membrane assembly in Rhodobacter sphaeroides mediated by puhA and flanking sequences (1989)

A reaction center H- strain (RCH-) of Rhodobacter sphaeroides, PUHA1, was made by in vitro deletion of an XhoI restriction endonuclease fragment from the puhA gene coupled with insertion of a kanamycin resistance gene cartridge. The resulting construct was delivered to R. sphaeroides wild-type 2.4.1, with the defective puhA gene replacing the wild-type copy by recombination, followed by selection for kanamycin resistance. When grown under conditions known to induce intracytoplasmic membrane development, PUHA1 synthesized a pigmented intracytoplasmic membrane. Spectral analysis of this membrane showed that it was deficient in B875 spectral complexes as well as functional reaction centers and that the level of B800-850 spectral complexes was greater than in the wild type. The RCH- strain was photosythetically incompetent, but photosynthetic growth was restored by complementation with a 1.45-kilobase (kb) BamHI restriction endonuclease fragment containing the puhA gene carried in trans on plasmid pRK404. B875 spectral complexes were not restored by complementation with the 1.45-kb BamHI restriction endonuclease fragment containing the puhA gene but were restored along with photosynthetic competence by complementation with DNA from a cosmid carrying the puhA gene, as well as a flanking DNA sequence. Interestingly, B875 spectral complexes, but not photosynthetic competence, were restored to PUHA1 by introduction in trans of a 13-kb BamHI restriction endonuclease fragment carrying genes encoding the puf operon region of the DNA. The effect of the puhA deletion was further investigated by an examination of the levels of specific mRNA species derived from the puf and puc operons, as well as by determinations of the relative abundances of polypeptides associated with various spectral complexes by immunological methods. The roles of puhA and other genetic components in photosynthetic gene expression and membrane assembly are discussed.
β‐Cell replacement as a treatment for type 1 diabetes: an overview of possible cell sources and current axes of research (2016)

To efficiently treat type 1 diabetes, exogenous insulin injections currently represent the main approach to counter chronic hyperglycaemia. Unfortunately, such a therapeutic approach does not allow for perfectly maintained glucose homeostasis and, in time, cardiovascular complications may arise. Therefore, seeking alternative/improved treatments has become a major health concern as an increasing proportion of type 2 diabetes patients also require insulin supplementation. Towards this goal, numerous laboratories have focused their research on β-cell replacement therapies. Herein, we will review the current state of this research area and describe the cell sources that could potentially be used to replenish the depleted β-cell mass in diabetic patients.
Heat Shock–Induced Protection of Renal Proximal Tubular Epithelial Cells from Cold Storage and Rewarming Injury (2006)

Cold storage and reperfusion injury to transplanted kidneys contributes to increased incidence of delayed graft function and may have a negative impact on graft survival. This study examined the mechanisms by which previous heat shock protects against cell death in an in vitro model of kidney storage. Cold storage is mimicked by incubating human renal proximal tubular epithelial (HK-2) cells in University of Wisconsin solution at 4 degrees C with and without subsequent rewarming. Heat shock was induced by incubation of cells at 42 degrees C for 1 h. Altered protein expression was measured by Western blot, and cell viability and apoptosis were measured by propidium iodide DNA staining using flow cytometry. The specific role of heat-shock protein 70 (HSP-70) was determined both by siRNA knockdown and by stable overexpression approaches. Cold storage and rewarming-induced cell death was associated with decreased expression of HSP-70, HSP-90, HSP-27, and Bcl-2. Previous heat shock significantly reduced HK-2 cell death after cold storage and rewarming and was associated with the maintenance of HSP-70, HSP-27, and Bcl-2 protein levels. Blocking heat stress-induced HSP-70 with siRNA did not significantly block the protective effect of heat stress against cold storage and rewarming cell death; however, overexpression of HSP-70 protected HK-2 cells from this stress. It is concluded that previous heat shock protects HK-2 cells from cold storage and rewarming injury. siRNA inhibition of HSP-70 induction did not block the protective effect of heat shock, indicating that HSP-70 is not essential to the heat stress-induced protective effect reported in this study.
Characterization of the collagen in the hexagonal lattice of Descemet's membrane: its relation to type VIII collagen. (1990)

To investigate the nature of the hexagonal lattice structure in Descemet's membrane, monoclonal antibodies were raised against a homogenate of bovine Descemet's membranes. They were screened by immunofluorescence microscopy to obtain antibodies that label Descement's membrane. Some monoclonal antibodies labeled both Descemet's membrane and fine filaments within the stroma. In electron microscopy, with immunogold labeling on a critical point dried specimen, the antibodies labeled the hexagonal lattices and long-spacing structures produced by the bovine corneal endothelial cells in culture; 6A2 antibodies labeled the nodes of the lattice and 9H3 antibodies labeled the sides of the lattice. These antibodies also labeled the hexagonal lattice of Descemet's membrane in situ in ultrathin frozen sectioning. In immunofluorescence, these antibodies stained the sclera, choroid, and optic nerve sheath and its septum. They also labeled the dura mater of the spinal cord, and the perichondrium of the tracheal cartilage. In immunoblotting, the antibodies recognized 64-kD collagenous peptides both in tissue culture and in Descemet's membrane in vivo. They also recognized 50-kD pepsin-resistant fragments from Descemet's membranes that are related to type VIII collagen. However, they did not react either in immunoblotting or in immunoprecipitation with medium of subconfluent cultures from which type VIII collagen had been obtained. The results are discussed with reference to the nature of type VIII collagen, which is currently under dispute. This lattice collagen may be a member of a novel class of long-spacing fibrils.
Electrochemical planarization of interconnect metallization (2005)

Studies of the electropolishing of copper are reviewed. Recent work intended to demonstrate the electrochemical planarization of the overburden in electroplated copper interconnect metallization is emphasized. Furthermore, two common reaction mechanisms invoked to explain the mass-transfer limitation required to achieve electropolishing are outlined and discussed within the context of anodic leveling, which has been more recently called electrochemical planarization. Finally, scaling arguments are used to demonstrate practical considerations for tool development and to speculate about uncertainties in anodic leveling theories.
Leptin Induces the Hepatic High Density Lipoprotein Receptor Scavenger Receptor B Type I (SR-BI) but Not Cholesterol 7α-Hydroxylase (Cyp7a1) in Leptin-deficient (ob/ob) Mice (2003)

Cholesterol elimination from the body involves reverse cholesterol transport from peripheral tissues in which the elimination of high density lipoprotein (HDL) and low density lipoprotein (LDL) cholesterol by the liver and subsequent biliary excretion as free cholesterol and bile acids are important. In situations of peripheral fat and cholesterol accumulation, such as obesity, these pathways may be overloaded, contributing to increased cholesterol deposition. Leptin has an important role in obesity, suppressing food intake and increasing energy expenditure. This hormone, which is absent in genetically obese ob/ob mice, is also thought to be involved in the coordination of lipid excretion pathways, although available data are somewhat inconsistent. We therefore studied the expression of the hepatic HDL receptor, scavenger receptor class B type I (SR-BI), and the LDL receptor as well as the rate-limiting enzyme in bile acid synthesis, cholesterol 7alpha-hydroxylase (Cyp7a1), in leptin-deficient ob/ob mice and their wild-type controls. In ob/ob mice, protein levels of both LDL receptor and SR-BI were reduced, whereas LDL receptor mRNA levels were increased and those of SR-BI were reduced, regardless of challenge with a 2% cholesterol diet. In ob/ob mice, the enzymatic activity and mRNA for Cyp7a1 were reduced, and the increase in response to dietary cholesterol was blunted. Upon short-term (2 days) treatment with leptin, a dose-dependent increase was seen in the SR-BI protein and mRNA, whereas the Cyp7a1 protein and mRNA were reduced. Our findings indicate that leptin is an important regulator of hepatic SR-BI expression and, thus, HDL cholesterol levels, whereas it does not stimulate Cyp7a1 and bile acid synthesis.
VEGF-A/VEGFR-2 Signaling Leading to cAMP Response Element-Binding Protein Phosphorylation Is a Shared Pathway Underlying the Protective Effect of Preconditioning on Neurons and Endothelial Cells (2009)

Preconditioning protects endothelial cells as well as neurons from ischemic injury. In 7-d-old rat pups, ligating the carotid artery 1 h before hypoxia damaged the ipsilateral cerebral hemisphere; in contrast, ligating the artery 24 h before hypoxia provided complete neuroprotection. The protective effect of the 24 h artery ligation preconditioning model requires the activation of cAMP response element-binding protein (CREB). We tested the hypothesis that vascular endothelial growth factor (VEGF)-A/VEGF receptor-2 (VEGFR-2) signaling that leads to CREB activation is the shared pathway underlying the protective effect of preconditioning in neurons and endothelial cells. VEGF-A, VEGFR-1, or VEGFR-2 was inhibited by antisense oligodeoxynucleotides (ODNs) in vivo and by a VEGF-A neutralizing antibody or VEGFR-2 inhibitor in vitro. CREB phosphorylation (pCREB) and VEGF-A and VEGFR-2 expression were increased and colocalized in vascular endothelial cells and neurons in the ipsilateral cerebral cortex 24 h after ligation. The antisense ODN blockades of VEGF-A and VEGFR-2 decreased pCREB and reduced the protection of 24 h ligation preconditioning. Furthermore, oxygen-glucose deprivation (OGD) preconditioning upregulated VEGF-A, VEGFR-2, and pCREB levels and protected immortalized H19-7 neuronal cells and b.End3 vascular endothelial cells against 24 h OGD cell death. Blocking VEGF-A or VEGFR-2 reduced CREB activation and the effects of OGD preconditioning in neuronal cells and endothelial cells. Transfecting a serine-133 phosphorylation mutant CREB also inhibited the protective effect of OGD preconditioning. We conclude that VEGF-A/VEGFR-2 signaling leading to CREB phosphorylation is the shared pathway underlying the preconditioning-induced protective effect in neurons and vascular endothelial cells in the developing brain.
A convenient synthesis of cis-Mo(CO)4L2 derivatives (L = Group 5a ligand) and a qualitative study of their thermal reactivity toward ligand dissociation (1978)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTA convenient synthesis of cis-Mo(CO)4L2 derivatives (L = Group 5a ligand) and a qualitative study of their thermal reactivity toward ligand dissociationDonald J. Darensbourg and Robin L. KumpCite this: Inorg. Chem. 1978, 17, 9, 2680–2682Publication Date (Print):September 1, 1978Publication History Published online1 May 2002Published inissue 1 September 1978https://pubs.acs.org/doi/10.1021/ic50187a062https://doi.org/10.1021/ic50187a062research-articleACS PublicationsRequest reuse permissionsArticle Views9827Altmetric-Citations230LEARN 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
Intrinsic Decomposition of Image Sequences from Local Temporal Variations (2015)

We present a method for intrinsic image decomposition, which aims to decompose images into reflectance and shading layers. Our input is a sequence of images with varying illumination acquired by a static camera, e.g. an indoor scene with a moving light source or an outdoor timelapse. We leverage the local color variations observed over time to infer constraints on the reflectance and solve the ill-posed image decomposition problem. In particular, we derive an adaptive local energy from the observations of each local neighborhood over time, and integrate distant pairwise constraints to enforce coherent decomposition across all surfaces with consistent shading changes. Our method is solely based on multiple observations of a Lambertian scene under varying illumination and does not require user interaction, scene geometry, or an explicit lighting model. We compare our results with several intrinsic decomposition methods on a number of synthetic and captured datasets.
Strategies to improve the response rate of thermosensitive PNIPAAm hydrogels (2008)

Poly(N-isopropylacrylamide) (PNIPAAm) hydrogel is one of the most extensively studied thermosensitive hydrogels, it displays a lower critical solution temperature (LCST) at around 33 °C in aqueous solution and undergoes an abrupt thermoreversible change in volume as the external temperature cycles around this critical temperature. The fast response rate of hydrogels is critically important in some applications, such as artificial organs, actuators, and on–off switches. In this article, we review different strategies, including physical and chemical strategies, for improving the response kinetics of PNIPAAm-based hydrogels. Based on the numerous strategies, the factors that are essential to achieve the fast response rate are identified.
Thermal tunability of monolithic polymer microcavities (2008)

We demonstrate the thermal tunability of the emission of polymer embedded in microcavities. The large thermo-optic coefficients of a conjugated polymer is combined with the possibility to tailor the emission properties by means of cavities acting as optical filters. Both the transmission and the photoluminescence spectra of the polymer in cavities can be finely tuned with slopes up to about −0.2nm∕°C. Such an effect could be exploited to realize thermally tunable organic light-emitting devices for optical communication or sensing applications.