gebhart/patrepeval huggingface dataset:
Parallel genome-scale loss of function screens in 216 cancer cell lines for the identification of context-specific genetic dependencies (2014)

Using a genome-scale, lentivirally delivered shRNA library, we performed massively parallel pooled shRNA screens in 216 cancer cell lines to identify genes that are required for cell proliferation and/or viability. Cell line dependencies on 11,000 genes were interrogated by 5 shRNAs per gene. The proliferation effect of each shRNA in each cell line was assessed by transducing a population of 11M cells with one shRNA-virus per cell and determining the relative enrichment or depletion of each of the 54,000 shRNAs after 16 population doublings using Next Generation Sequencing. All the cell lines were screened using standardized conditions to best assess differential genetic dependencies across cell lines. When combined with genomic characterization of these cell lines, this dataset facilitates the linkage of genetic dependencies with specific cellular contexts (e.g., gene mutations or cell lineage). To enable such comparisons, we developed and provided a bioinformatics tool to identify linear and nonlinear correlations between these features.
Horse chestnut (Aesculus hippocastanum) pollen: a frequent cause of allergic sensitization in urban children (1992)

We investigated the incidence of allergic sensitization and the risk factors underlying sensitization in 214 urban children exposed to horse chestnut pollen. By means of the Phadezym RAST, we found IgE specific to horse chestnut pollen in 12.6% of the urban children, whereas it occurred in only 1.9% of control subjects recruited from a rural area. Reports of allergic symptoms in spring during the horse chestnut pollen load coincided with the presence of specific IgE in 5.1% of the urban group as against 1.4% of the recruited from the rural area. Environmental factors other than those related to urban living and higher horse chestnut pollen counts had no significant impact on allergic sensitization. Increased total IgE levels (greater than 100 kU/l), however, and the sensitization to pollen of other species significantly raised the odds for sensitization to chestnut pollen. They were highest in highly atopic children with sensitization to pollen, especially to that of plane trees (OR = 73.9). These results suggest the relevance of horse chestnut pollen because of the high allergic sensitization rate among urban children, and they should also be borne in mind when it comes to the planting of trees in urban areas.
pH‐insensitive glucose indicators (2008)

There is an urgent need for developing a biosensor that can real-time and noninvasively determine glucose concentration within living cells. In our previous study, we have engineered a glucose indicator protein (GIP) that can provide continuous glucose monitoring through a conformation change-induced Förster resonance-energy transfer measurement. Because of the pH-sensitivity of the fluorescent proteins used in the GIP construction, the GIP made from these fluorescent proteins is less tolerant to a pH change, especially to the acidic environment. It has been well documented that intracellular pH does not always remain the same, and it fluctuates in metabolism and other cellular activities and also differs between cellular compartments. To address these issues, we developed a GIP that can tolerate to pH change. This GIP was constructed by flanking a glucose binding protein with a cyan fluorescent protein and a pH-insensitive yellow fluorescent protein. Our experimental results indicated that the new GIP is more tolerant to pH change. The glucose response of this new GIP kept almost unchanged from pH 7.3 to 5.3, suggesting its capability of tolerating to acidic environment. This capability is desirable for intracellular glucose measurement.
ChemInform Abstract: Reaction on Water: A Greener Approach for the Thia Michael Addition on N‐Aryl Maleimides. (2011)

Abstract The Michael addition of thiols to N‐aryl maleimides (I) can be performed in water at ambient temperature.
Insulator-Superconductor Transition in 3D Granular Al-Ge Films (1997)

We report the results of high magnetic field study of granular 3D Al-Ge and demonstrate that intragranular superconductivity leads in truly insulating samples (with an exponentially diverging normal state resistivity), either to a global superconducting phase coherent state, or to a ``superconductor-insulator'' state with Cooper pairs totally localized within individual grains, depending on the strength of the intergranular Josephson coupling.
A comparison of methodologies for the non-invasive characterisation of commercial Li-ion cells (2019)

Lithium-ion cells currently power almost all electronic devices and power tools; they are a key enabling technology for electric vehicles and are increasingly considered to be the technology of choice for grid storage. In line with this increased applicability, there is also an increase in the development of new commercial lithium-ion cell technologies that incorporate innovative functional components (electrode material compositions and electrolyte formulations) and designs, leading to a diverse range of performance characteristics. The uniqueness of each technology in-turn gives rise to unique evolutions of cell performance as the cell degrades because of usage. Non-destructively measuring and subsequently tracking the evolution of lithium-ion cell characteristics is valuable for both industrial engineers and academic researchers. To proceed in this regard, stakeholders have often devised their own procedures for characterising lithium-ion cells, typically without considering unification, comparability or compatibility. This makes the comparison of technologies complicated. This comprehensive review for the first time has analysed and discusses the various international standards and regulations for the characterisation and electrical testing of lithium-ion cells, specifically for high-power automotive and grid applications.
[Problems on the determination of intracellular free calcium concentration when measured by fura-2/AM in mast cells]. (1989)

When rat peritoneal mast cells which had been loaded with fluorescent Ca2+ indicator fura-2/AM were exposed to compound 48/80, fura-2 fluorescence was increased in the presence of 1mM extracellular Ca2+, but remained unchanged in the Ca2(+)-eliminated medium. Only in the presence of 1mM extracellular Ca2+, both fura-2 fluorescence and histamine release were increased in response to compound 48/80, depending on the concentration of the stimulant. Both of these responses were attenuated in the same degree by such release inhibitors as disodium cromoglycate and HSR-6071. Fluorescent microscopic observation of fura-2/AM-loaded mast cells revealed that fura-2 fluorescence was densely localized in the granules and the nucleus, but less in the cytoplasm. All these results strongly suggest that increase in the fura-2 fluorescence might not result from the increase in cytoplasmic free Ca2+ concentration, but from binding of fura-2, which had been released together with chemical mediators from granules following stimulation, to extracellular Ca2+. Therefore, it seems likely that the fura-2/AM loading method is inadequate to investigate whether or not the increase in cytoplasmic free Ca2+ concentration triggers release of chemical mediators from mast cells.
Neutrophil-Mediated Phagocytic Host Defense Defect in Myeloid Cftr-Inactivated Mice (2014)

Cystic fibrosis (CF) is a common and deadly inherited disease, caused by mutations in the CFTR gene that encodes a cAMP-activated chloride channel. One outstanding manifestation of the disease is the persistent bacterial infection and inflammation in the lung, which claims over 90% of CF mortality. It has been debated whether neutrophil-mediated phagocytic innate immunity has any intrinsic defect that contributes to the host lung defense failure. Here we compared phagosomal CFTR targeting, hypochlorous acid (HOCl) production, and microbial killing of the neutrophils from myeloid Cftr-inactivated (Myeloid-Cftr-/-) mice and the non-inactivated control (Cftrfl10) mice. We found that the mutant CFTR that lacked Exon-10 failed to target to the neutrophil phagosomes. This dysfunction resulted in impaired intraphagosomal HOCl production and neutrophil microbial killing. In vivo lung infection with a lethal dose of Pseudomonas aeruginosa caused significantly higher mortality in the myeloid CF mice than in the controls. The myeloid-Cftr-/- lungs were deficient in bacterial clearance, and had sustained neutrophilic inflammation and stalled transition from early to late immunity. These manifestations recapitulated the symptoms of human CF lungs. The data altogether suggest that myeloid CFTR expression is critical to normal host lung defense. CFTR dysfunction in neutrophils compromises the phagocytic innate immunity, which may predispose CF lungs to infection.
INDUCIBLE NITRIC OXIDE SYNTHASE mRNA EXPRESSION IN MURINE PERITONEAL MACROPHAGES, SPLENIC MACROPHAGES, and KUPFFER CELLS FOLLWING HEMORRHAGE (1995)

SHOCK®: Injury, Inflammation, and Sepsis: Laboratory and Clinical Approaches includes studies of novel therapeutic approaches, such as immunomodulation, gene therapy, nutrition, and others. The mission of the Journal is to foster and promote multidisciplinary studies, both experimental and clinical in nature, that critically examine the etiology, mechanisms and novel therapeutics of shock-related pathophysiological conditions. Its purpose is to excel as a vehicle for timely publication in the areas of basic and clinical studies of shock, trauma, sepsis, inflammation, ischemia, and related pathobiological states, with particular emphasis on the biologic mechanisms that determine the response to such injury. Making such information available will ultimately facilitate improved care of the traumatized or septic individual. SHOCK® is also privileged to have fourteen distinguished Associate Editors, as well as a diverse group of editorial board members from various parts of the world, who enjoy the respect and admiration of their colleagues in their areas of investigation. The Official Journal of the Shock Society, the European Shock Society, the Indonesian Shock Society, the International Federation of Shock Societies, and the Official and International Journal of the Japan Shock Society
Improved Random-Binning Exponent for Distributed Hypothesis Testing (2023)

Consider the problem of distributed binary hypothesis testing with two terminals, where the decision is made at one of them (the "receiver"). We study the exponent of the error probability of the second type. Previously, an achievable exponent was derived by Shimokawa, Han, and Amari using a "quantization and binning" scheme. We propose a simple modification on the receiver's decision rule in this scheme to attain a better exponent.
Application of solid‐phase extraction coupled to an NMR flow‐probe in the analysis of HPLC fractions (2001)

Abstract The design and use of a system consisting of a disposable solid‐phase extraction cartridge coupled to an NMR flow‐probe (SPE–NMR) is demonstrated. Fractions obtained from high‐performance liquid chromatography of an extract of Habanero pepper ( Capsicum chinense ) were analysed. The fractions were loaded on SPE cartridges and the compounds were eluted with deuterated methanol directly into the NMR flow‐probe. Good‐quality NMR spectra were acquired and the structure of the compounds could be determined. The main advantages with SPE–NMR are the simple handling of small amounts of samples, the removal of polar additives and solvents from the preceding separation step allowing optimal conditions for both the chromatography and the NMR spectroscopy and the possibility of automating the procedure. Hence the method can facilitate the structural characterization of small amounts of natural products in complex mixtures. Copyright © 2001 John Wiley &amp; Sons, Ltd.
PDGFRalpha is an oncofetal target in human hepatocellular cancer (2007)

Hepatocellular cancer (HCC) is a disease of poor prognosis. Owing to the similarities between the processes of development and carcinogenesis, we utilized early developing livers to recognize differentially expressed genes and analyzed their expression in HCC. Livers from various mouse embryos (E11-E18) were utilized for gene and protein analysis. Patient HCC tissues (n=22), normal adjacent preneoplastic tissue and normal livers were examined for PDGFRα by Western and Real-Time PCR. The upstream effectors such as PDGF-A and PDGF-C were also examined. Finally, therapeutic effect of anti-PDGFRα antibody (MAb3G3; ImClone) was investigated on human hepatoma cells. A significantly higher expression of PDGFRα is observed during early liver development (p<0.001). 14/22 (>60%) of HCC samples showed a 1.5–7-fold increase in total PDGFRα levels as compared to controls (p<0.01). 17/21 additional samples revealed cytoplasmic PDGFRα and activated-PDGFRα (Tyr754) staining in tumors only. PDGFRα gene expression was increased in 3, PDGF-AA in 3 and PDGF-CC in 4 patients with elevated PDGFRα protein. Hep3B and HepG2 cells, which showed elevated and activated PDGFRα, when treated with MAb3G3, showed significant decrease in cell proliferation and survival (p<0.01). Thus around 70% of HCC patients had elevated PDGFRα levels in the tumor core, due to diverse mechanisms and its inhibition, might have therapeutic consequences in HCC.
Opportunities and challenges for Minnesota sewn product manufacturers (2017)

Purpose This study aims to explore domestic sewn product manufacturing in Minnesota. There is a renewed interest from consumers in products Made in America, thus some manufactures are taking advantage of the opportunities to produce locally. Design/methodology/approach Fourteen companies from across the state that ranged in size and product type were interviewed about the motivations, opportunities and challenges they experience with domestic manufacturing. A content analysis was conducted on the qualitative data. Findings The themes of personal values and economics emerged under motivations; the local economy, control and uniqueness were revealed as opportunities; and challenges included the themes of manufacturing resources and costs. Originality/value This group of Minnesota manufacturers holds strong values that drive them to balance the opportunities and challenges of domestic manufacturing. There is no evidence to determine if sustainability is a concern or a motivating factor.
Novel Carboxylated Pyrrole- and Carbazole-Based Monomers. Synthesis and Electro-Oxidation Features (2006)

Carboxylated pyrrole (Pyr, a index)- and carbazole (Cbz, b index)-containing monomers 6-7a/b and 9a/b have been readily synthesized from the monobenzyl ester of L-glutamic acid and triamine 2 using Clauson-Kaas and amide coupling reactions. In contrast to Pyr-containing compounds 6-7a, and 9a, the three Cbz-containing monomers 6-7b, and 9b have been found electroactive and were successfully electropolymerized on a Pt electrode resulting in the deposition of corresponding insoluble electroconducting polyCOOH polyCbz-films poly(6-7b) and poly(9b).
Wearable Biomedical Systems: Research to Reality (2007)

The field of wearable biomedical systems (WBS) has of late been generating a lot of interest in the research and business communities since its early beginnings in the mid-nineties. However, the technology is yet to enter the marketplace and realize its original goal of enhancing the quality of life for individuals through enhanced real-time biomedical monitoring. In this paper, we propose a framework for analyzing the transition of WBS from research to reality. We begin with a look at the evolution of the field and describe the key components of a WBS. We then analyze the key issues encompassing the technical, medical, economic, public policy and business facets from the viewpoints of various stakeholders in the continuum. We conclude with a plan of action for transitioning WBS from "research to reality."
Evolution of intraperitoneal hydrostatic pressure following peritoneal catheter implantation. (1993)

Intraperitoneal hydrostatic pressure (IPP) was measured in 10 patients for 15 days (until day 15) following peritoneal catheter implantation. Tenckhoff catheters were surgically implanted using a transrectal approach. The patients began peritoneal dialysis (PD) immediately, initially with small intraperitoneal fluid volumes (500 mL), gradually increasing to reach 2000 mL by day 7. In one patient PD was delayed until day 7 because of an initial leakage of dialysate. Inspiratory and expiratory IPP were measured daily, with the zero point fixed at the midaxillary line with the patient in the supine position. Despite the small intraperitoneal fluid volumes used initially (500 mL), IPP was much higher in the first 3 days following implantation than in the next 12 days (17 +/- 3 cm of water vs 11 +/- 1 cm of water). IPP remained high until day 3, then gradually decreased in a linear fashion until day 12, despite the increased intraperitoneal volumes used, and then remained constant. In conclusion, IPP was found to be significantly higher for 3 days following intraperitoneal catheter implantation, whichever intraperitoneal volume was used. This may be due to tense abdominal muscles from pain caused by the surgery or because of reduced intraperitoneal compliance at the beginning of PD.
A global initiative to improve the care of underserved people with spinal disorders deserves support (2018)

was convened by World Spine Care (WSC), a charity, founded by Joan and Scott Haldeman in 2008. With the support of an international team of dedicated like-minded clinicians and researchers, WSC has established spine care programs in four underserved communities in low-and middle-income countries. Over 50 volunteers have donated their time and expertise from 6 weeks to 1 year providing care and establishing public education programs for people who have minimal or no access to spine care. The mission of WSC is "to improve lives in underserved communities through sustainable, integrated, evidence-based, spine care".
Integral Equations and Other Field Representations (2012)

The field integral representations given in the previous chapter, although of sufficient generality, are often inconvenient and possibly inefficient for specific applications. Also, their integrands are highly singular, requiring special treatment when the observation point is in the source region. This difficulty cannot be eliminated, but any reduction in the integrand&apos;s singularity is desirable for achieving higher accuracies in numerical computations involving such integrals. Obviously, a variety of field representations, integral equations, and formal solutions could be derived, many of which can be applicable only to a specific situation. This chapter will consider some alternative field representations to construct integral equations that are among the most frequently used. First, we shall develop three-dimensional representations. Many of the two-dimensional representations can then be reduced from the three-dimensional ones. However, for scattering applications a larger variety of two-dimensional representations is available primarily because the topic has been extensively studied.
Differences in the redistribution of concanavalin A and wheat germ agglutinin binding sites on mouse neuroblastoma cells (1979)

Concanavalin A (Con A), wheat germ agglutinin (WGA), and Ricinus communis agglutinin (RCA) bound with either 125I, fluorescent dyes, or fluorescent polymeric microspheres were used to quantitate and visualize the distribution of lectin binding sites on mouse neuroblastoma cells. As viewed by fluorescent light and scanning electron microscopy, over 10(7) binding sites for Con A, WGA, and RCA appeared to be distributed randomly over the surface of differentiated and undifferentiated cells. An energy-dependent redistribution of labeled sites into a central spot occurred when the cells were labeled with a saturating dose of fluorescent lectin and maintained at 37 degrees C for 60 min. Reversible labeling using appropriate saccharide inhibitors indicated that the labeled sites had undergone endocytosis by the cell. A difference in the mode of redistribution of WGA or RCA and Con A binding sites was observed in double labeling experiments. When less than 10% of the WGA or RCA lectin binding sites were labeled, only these labeled sites appeared to be removed from the cell surface. In contrast, when less than 10% of the Con A sites were labeled, both labeled and unlabeled Con A binding sites were removed from the cell surface. Cytochalasin B uncoupled the coordinate redistribution of labeled and unlabeled Con A sites, suggesting the involvement of microfilaments. Finally, double labeling experiments employing fluorescein-tagged Con A and rhodamine-tagged WGA indicate that most Con A and WGA binding sites reside on different membrane components and redistribute independenty of each other.
Trust-to-Trust Design of a New Internet (2017)

The internet's original design, guided by the end-to-end design principle, pushed all application-specific logic and complexity to the edges of the network and kept the core of the network focused on the simple task of delivering data. The original end-to-end principle, however, did not explicitly account for trust and security. There are several central points of trust and failure on the traditional internet. These include root servers for the Domain Name System (DNS) and public-key infrastructure like Certificate Authorities (CAs) that publish security certificates. Further, the success of cloud hosted services in the last decade means that most user data is stored on remote servers and end-users need to trust these remote servers for correct execution of their applications. In this thesis, we present a new internet architecture that explicitly follows the trust-to-trust design principle, i.e., end-users don't need to trust the core of the network for anything, and end-users can use applications and services in a fully decentralized way. We make the observation that cryptocurrency blockchains, like Bitcoin, can be used to bootstrap trust for new nodes joining a network. We identify the various limitations, like high latency and limited bandwidth, of contemporary blockchains and discuss how our architecture can scale by moving most operations outside of the blockchain layer. We detail our experience of running a large production system on top of a cryptocurrency blockchain and how that experience guided our design. We present the implementation of a new decentralized internet, called Blockstack, that takes the trust-to-trust architecture from a theoretical concept to a production system. Deploying new systems by modifying production blockchains is hard because it requires coordination and agreement from several parties. We introduce virtualchains, a virtual blockchain constructed by processing data from underlying blockchains, to enable the seamless introduction of new functionality on top of blockchains without requiring any consensus-breaking changes. Blockstack is already powering several fully decentralized applications, like OpenBazaar; it's released as open-source software and, to date, more than 70,000 domains have been registered on it.
ChemInform Abstract: REACTION OF DIMETHYLSILYLENE WITH ALLYLIC METHYL SULFIDES (1981)

Abstract Das durch Photolyse von Dodekamethylcyclohexasilan erzeugte Dimethylsilylen reagiert mit dem Allylmethylsulfid (I) regiospezifisch zu dem Produkt (II).
ChemInform Abstract: Regioselective Fluorination of CB11H‐12, CB9H‐10, and B10H‐102 (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.