gebhart/patrepeval huggingface dataset:
A Guide to Fluorescent Protein FRET Pairs (2016)

Förster or fluorescence resonance energy transfer (FRET) technology and genetically encoded FRET biosensors provide a powerful tool for visualizing signaling molecules in live cells with high spatiotemporal resolution. Fluorescent proteins (FPs) are most commonly used as both donor and acceptor fluorophores in FRET biosensors, especially since FPs are genetically encodable and live-cell compatible. In this review, we will provide an overview of methods to measure FRET changes in biological contexts, discuss the palette of FP FRET pairs developed and their relative strengths and weaknesses, and note important factors to consider when using FPs for FRET studies.
Thermochemistry for the Dehydrogenation of Methyl-Substituted Ammonia Borane Compounds (2009)

Atomization energies at 0 K and heats of formation at 0 and 298 K are predicted for (CH3)H2N-BH3, (CH3)HN=BH2, (BH3)HN=CH2, (CH3)H2B-NH3, (CH3)HB=NH2, and (NH3)HB=CH2, as well as various molecules involved in the different bond-breaking processes, from coupled cluster theory (CCSD(T)) calculations. In order to achieve near-chemical accuracy (+/-1 kcal/mol), three corrections were added to the complete basis set binding energies based on frozen core CCSD(T) energies, corrections for core-valence, scalar relativistic, and first-order atomic spin-orbit effects. Scaled vibrational zero-point energies were computed with the MP2 method. The heats of formation were predicted for the respective dimethyl- and trimethyl-substituted ammonia boranes, their dehydrogenated derivatives, and the various molecules involved in the different bond breaking processes, based on isodesmic reaction schemes calculated at the G3(MP2) level. Thermodynamics for dehydrogenation pathways in the monomethyl-substituted molecules were predicted. Dehydrogenation across the B-N bond is more favorable as opposed to dehydrogenation across the B-C and N-C bonds. Methylation at N reduces the exothermocity of the dehydrogenation reaction and makes the reaction more thermoneutral, while methylation at B moves it away from thermoneutral. Various mixtures of CH3NH2BH3 and NH3BH3 were made, and their melting points were measured. The lowest melting mixture contained approximately 35% NH3BH3 by weight and melted at 35-37 degrees C.
Cytotoxic edema: mechanisms of pathological cell swelling (2007)

Cerebral edema is caused by a variety of pathological conditions that affect the brain. It is associated with two separate pathophysiological processes with distinct molecular and physiological antecedents: those related to cytotoxic (cellular) edema of neurons and astrocytes, and those related to transcapillary flux of Na+ and other ions, water, and serum macromolecules. In this review, the authors focus exclusively on the first of these two processes. Cytotoxic edema results from unchecked or uncompensated influx of cations, mainly Na+, through cation channels. The authors review the different cation channels that have been implicated in the formation of cytotoxic edema of astrocytes and neurons in different pathological states. A better understanding of these molecular mechanisms holds the promise of improved treatments of cerebral edema and of the secondary injury produced by this pathological process.
Transgenic overexpression of human IL-17E results in eosinophilia, B-lymphocyte hyperplasia, and altered antibody production (2002)

We have identified and cloned a novel human cytokine with homology to cytokines of the interleukin-17 (IL-17) family, which we have termed human IL-17E (hIL-17E). With the identification of several IL-17 family members, it is critical to understand the in vivo function of these molecules. We have generated transgenic mice overexpressing hIL-17E using an apolipoprotein E (ApoE) hepatic promoter. These mice displayed changes in the peripheral blood, particularly, a 3-fold increase in total leukocytes consisting of increases in eosinophils, lymphocytes, and neutrophils. Splenomegaly and lymphoadenopathy were predominant and included marked eosinophil infiltrates and lymphoid hyperplasia. CCR3(+) eosinophils increased in the blood and lymph nodes of the transgenic mice by 50- and 300-fold, respectively. Eosinophils also increased 8- to 18-fold in the bone marrow and spleen, respectively. In the bone marrow, most of the eosinophils had an immature appearance. CD19(+) B cells increased 2- to 5-fold in the peripheral blood, 2-fold in the spleen, and 10-fold in the lymph nodes of transgenic mice, whereas CD4(+) T lymphocytes increased 2-fold in both blood and spleen. High serum levels of the cytokines IL-2, IL-4, IL-5, granulocyte colony-stimulating factor, eotaxin, and interferon gamma were observed. Consistent with B-lymphocyte increases, serum immunoglobulin (Ig) M, IgG, and IgE were significantly elevated. Antigenic challenge of the transgenic mice with keyhole limpet hemocyanin (KLH) resulted in a decrease in anti-KLH IgG accompanied by increases of anti-KLH IgA and IgE. In situ hybridization of transgenic tissues revealed that IL-17Rh1 (IL-17BR/Evi27), a receptor that binds IL-17E, is up-regulated. Taken together, these data indicate that IL-17E regulates hematopoietic and immune functions, stimulating the development of eosinophils and B lymphocytes. The fact that hIL-17E overexpression results in high levels of circulating eosinophils, IL-4, IL-5, eotaxin, and IgE suggests that IL-17E may be a proinflammatory cytokine favoring Th2-type immune responses.
Binding and Functional Properties of Recombinant and Endogenous CXCR3 Chemokine Receptors (1998)

IP10 and MIG are two members of the CXC branch of the chemokine superfamily whose expression is dramatically up-regulated by interferon (IFN)-gamma. The proteins act largely on natural killer (NK)-cells and activated T-cells and have been implicated in mediating some of the effects of IFN-gamma and lipopolysaccharides (LPSs), as well as T-cell-dependent anti-tumor responses. Recently both chemokines have been shown to be functional agonists of the same G-protein-coupled receptor, CXCR3. We now report the pharmacological characterization of CXCR3 and find that, when heterologously expressed, CXCR3 binds IP10 and MIG with Ki values of 0.14 and 4.9 nM, respectively. The receptor has very modest affinity for SDF-1alpha and little or no affinity for other CXC-chemokines. The properties of the endogenous receptor expressed on activated T-cells are similar. Surprisingly, several CC-chemokines, particularly eotaxin and MCP-4, also compete with moderate affinity for the binding of IP10 to CXCR3. Eotaxin does not activate CXCR3 but, in CXCR3-transfected cells, can block IP10-mediated receptor activation. Eotaxin, therefore, may be a natural CXCR3 antagonist.
Some social implications of ubiquitous wireless networks (2000)

Wireless computer networks and the devices to communicate with them are about to become ubiquitous. A profusion of devices is likely to emerge quickly in specialized form factors, from handhelds to cheap, disposable sensors. Groups of people using these tools will gain new forms of social power, ways to organize and coordinate their interactions and exchanges just in time and just in place. Using these tools, people will be able to collectively construct a range of resources that were too difficult or expensive, or simply impossible to provide before. Simultaneously, these tools will gather a constellation of intimate data about each of us. Wireless devices will penetrate every nook and cranny of the social world, bringing the efficiency of information technology to the production of panoptic power. In the following, two sociological concepts, Power/Knowledge and social dilemmas, are used as a guide to the kinds of social institutions and relationships that are likely to emerge from the use of these tools.
Work-efficient nested data-parallelism (2002)

An apply-to-all construct is the key mechanism for expressing data-parallelism, but data-parallel programming languages like HPF and C* significantly restrict which operations can appear in the construct. Allowing arbitrary operations substantially simplifies the expression of irregular and nested data-parallel computations. The technique of flattening nested parallelism introduced by Blelloch, compiles data-parallel programs with unrestricted apply-to-all constructs into vector operations, and has achieved notable success, particularly with irregular data-parallel programs. However, these programs must be carefully constructed so that flattening them does not lead to suboptimal work complexity due to unnecessary replication in index operations. We present new flattening transformations that generate programs with correct work complexity. Because these transformations may introduce concurrent reads in parallel indexing, we developed a randomized indexing that reduces concurrent reads while maintaining work-efficiency. Experimental results show that the new rules and implementations significantly reduce memory usage and improve performance.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Identification of Anti-virulence Compounds That Disrupt Quorum-Sensing Regulated Acute and Persistent Pathogenicity (2014)

Etiological agents of acute, persistent, or relapsing clinical infections are often refractory to antibiotics due to multidrug resistance and/or antibiotic tolerance. Pseudomonas aeruginosa is an opportunistic Gram-negative bacterial pathogen that causes recalcitrant and severe acute chronic and persistent human infections. Here, we target the MvfR-regulated P. aeruginosa quorum sensing (QS) virulence pathway to isolate robust molecules that specifically inhibit infection without affecting bacterial growth or viability to mitigate selective resistance. Using a whole-cell high-throughput screen (HTS) and structure-activity relationship (SAR) analysis, we identify compounds that block the synthesis of both pro-persistence and pro-acute MvfR-dependent signaling molecules. These compounds, which share a benzamide-benzimidazole backbone and are unrelated to previous MvfR-regulon inhibitors, bind the global virulence QS transcriptional regulator, MvfR (PqsR); inhibit the MvfR regulon in multi-drug resistant isolates; are active against P. aeruginosa acute and persistent murine infections; and do not perturb bacterial growth. In addition, they are the first compounds identified to reduce the formation of antibiotic-tolerant persister cells. As such, these molecules provide for the development of next-generation clinical therapeutics to more effectively treat refractory and deleterious bacterial-human infections.
β-III Spectrin Is Critical for Development of Purkinje Cell Dendritic Tree and Spine Morphogenesis (2011)

Mutations in the gene encoding β-III spectrin give rise to spinocerebellar ataxia type 5, a neurodegenerative disease characterized by progressive thinning of the molecular layer, loss of Purkinje cells and increasing motor deficits. A mouse lacking full-length β-III spectrin (β-III⁻/⁻) displays a similar phenotype. In vitro and in vivo analyses of Purkinje cells lacking β-III spectrin, reveal a critical role for β-III spectrin in Purkinje cell morphological development. Disruption of the normally well ordered dendritic arborization occurs in Purkinje cells from β-III⁻/⁻ mice, specifically showing a loss of monoplanar organization, smaller average dendritic diameter and reduced densities of Purkinje cell spines and synapses. Early morphological defects appear to affect distribution of dendritic, but not axonal, proteins. This study confirms that thinning of the molecular layer associated with disease pathogenesis is a consequence of Purkinje cell dendritic degeneration, as Purkinje cells from 8-month-old β-III⁻/⁻ mice have drastically reduced dendritic volumes, surface areas and total dendritic lengths compared with 5- to 6-week-old β-III⁻/⁻ mice. These findings highlight a critical role of β-III spectrin in dendritic biology and are consistent with an early developmental defect in β-III⁻/⁻ mice, with abnormal Purkinje cell dendritic morphology potentially underlying disease pathogenesis.
Immunoadsorption patients with multiple sclerosis: an open‐label pilot study (2005)

Removal of immunoglobulins, including myelin-specific antibodies by immunoadsorption, seems to delay disease progression as defined by EDSS, MSFC and MRI, while the patients' quality of life did not deteriorate.
Enhancement of Jejunal Absorption of Heparinoid by Sodium Ethylenediaminetetraacetate in the Dog. (1962)

SummaryThe presence of NaEDTA in the lumen of isolated canine jejunal segments in situ produced significant enhancement of intestinal absorption of heparinoid as measured by the disappearance of heparinoid from the lumen. Increases in clotting time of recalcified citrated plasma accompanied the enhanced absorption and verified that the heparinoid had been absorbed without loss of anticoagulant activity.
Dermatofibroma is a clonal proliferative disease (2000)

Benign fibrous histiocytoma of the skin or dermatofibroma (DF) has been regarded as a fibrohistiocytic tumor. Whether DF is a neoplastic growth or a reactive process has not been settled. Since a neoplastic process is clonal in nature, clonal analysis of DF was conducted to see if DF is a clonal disease. Fresh specimens of 13 DFs and 2 hypertrophic scars obtained from female patients were studied. The adjacent nonlesional skin tissues served as controls. The clonal analysis was based on the methylation pattern of the polymorphic X-chromosome linked androgen-receptor gene (HUMARA). Eight DFs and 1 hypertrophic scar were heterozygous at the androgen receptor gene and could be analyzed. All 8 informative DFs showed a significant reduction in one of the allelic bands compared with the corresponding bands of the nonlesional tissue after Hha I digestion. Therefore, DF is a clonal proliferative disease. In contrast, 1 hypertrophic scar showed a polyclonal pattern of X-chromosome inactivation. We conclude that DF is a clonal disease favoring a neoplastic process.
Dose- and Schedule-Dependent Inhibition of the Mammalian Target of Rapamycin Pathway With Everolimus: A Phase I Tumor Pharmacodynamic Study in Patients With Advanced Solid Tumors (2008)

Everolimus achieved mTOR signaling inhibition at doses below the DLT. A dosage of 10 mg/d or 50 mg/wk is recommended for further development.
The Interactions between Fish Nodavirus and Fish Retrovirus during Co-infection (2004)

SSN-1 cell line was used for many research of NNV, but it was SnRV-persistently infected. Lee et al. (2002) infected GF-1, which could also be infected by NNV, with the supernatant of SSN-1, and then got a SnRV-persistently infected cell line called SGF-1. Next, SGF-1 was used to investigate the interactions of the viral co-infection. The goal of this research was to study the interactions between NNV and SnRV during co-infection. The experiment revealed that the RT of SnRV reverse transcripted both positive singlestrand RNAs of NNV to high identified cDNA, but there was no primer binding site for SnRV RT recognizing in the RNA of NNV. To observe the daily change of co-infection, I found that the cDNA of NNV could be detected from the 3rd day, and the RNA of SnRV could not be detected after the 4th day. In addition, the titers of NNV in the supernatant during the 3rd to 5th day were much different between detected with GF-1 and SGF-1. Therefore, I supposed that the third day after NNV infecting was the important point of the change. The details of discussions were in the article.
Cathepsin B-Labile Dipeptide Linkers for Lysosomal Release of Doxorubicin from Internalizing Immunoconjugates:  Model Studies of Enzymatic Drug Release and Antigen-Specific In Vitro Anticancer Activity (2002)

The anticancer drug doxorubicin (DOX) has been linked to chimeric BR96, an internalizing monoclonal antibody that binds to a Lewis(y)-related, tumor-associated antigen, through two lysosomally cleavable dipeptides, Phe-Lys and Val-Cit, giving immunoconjugates 72 and 73. A self-immolative p-aminobenzyloxycarbonyl (PABC) spacer between the dipeptides and the DOX was required for rapid and quantitative generation of free drug. DOX release from model substrate Z-Phe-Lys-PABC-DOX 49 was 30-fold faster than from Z-Val-Cit-PABC-DOX 42 with the cysteine protease cathepsin B alone, but rates were identical in a rat liver lysosomal preparation suggesting the participation of more than one enzyme. Conjugates 72 and 73 showed rapid and near quantitative drug release with cathepsin B and in a lysosomal preparation, while demonstrating excellent stability in human plasma. Against tumor cell lines with varying levels of BR96 expression, both conjugates showed potent, antigen-specific cytotoxic activity, suggesting that they will be effective in delivering DOX selectively to antigen-expressing carcinomas.
Sur le changement macrolinguistique survenu entre 1300 et 1900 dans le domaine d'oïl. Une étude diachronique d'inspiration dialectométrique1 (2008)

With the supply of 4 figures and 24 closely interpreted dialectometrical maps, this paper analyses the
linguistic change of the geolinguistic deep structures in Northern France (Domaine d’Oil) between 1300 and
1900. As a matter of fact, the result will show – with some well explainable exceptions – the great stability of
these deep structures.
The two empirical bases are, on the one hand, the scripta-atlas of the Amsterdam Romanist Anthonij Dees
of Northern France (published in 1980) and the “Atlas linguistique de la France” (ALF) of Jules Gillieron and
Edmond Edmont (1902-1910). Whereas the Dees-atlas is based on the philological exploitation of 3300
medieval non literary documents (charters) and therefore refers to written materials, the ALF contains oral
materials which have been collected by field work and standardized interviews with competent dialect speakers.
For to comparison of the two empirical levels (scripturality and orality) we use well experienced methods
of the “Salzburg School of Dialectometry” like similarity maps, parameter maps, interpoint maps, correlation
maps and trees.
How to fast-track your meaningful use effort. (2011)

While there is no shortcut to meaningful use, getting the fundamentals right is essential to smoothing the way to qualifying for incentives.
Nucleotide sequence of the nfo gene of Escherichia coli K-12 (1988)

The nfo gene of Escherichia coli K-12 which encodes endonuclease IV has been sequenced. The predicted gene product has a molecular weight of 31,562, in good agreement with the size of the gene product estimated by maxicell analysis. The nfo promoter was mapped by primer extension of in vivo transcripts. Inspection of the nucleotide sequence revealed no regions of potential secondary structure corresponding to a transcriptional terminator downstream from the structural gene; however, there was a potential open reading frame immediately downstream from the nfo structural gene.
Limiting Legislative Terms (1992)

This DOI is not currently attached to any metadata records. DOIs can’t actually ever be deleted (they’re persistent), but sometimes our members create DOIs in error. We do have a process to approximate deletion which we follow only in rare cases where the DOI has been genuinely created in error, and most crucially, if the DOI has never been published anywhere online or in print and never otherwise distributed to or communicated with anyone (authors, readers, reviewers, etc.
In vivo imaging flow cytometer (2007)

<b>Purpose:</b> An <i>in vivo</i> flow cytometer was developed recently, providing quantification of fluorescently labeled cells in live animals without extracting blood samples. This non-invasive procedure allows continuously tracking a cell population of interest over long periods of time to examine its dynamic changes in the circulation. However, it has not been shown that counting signals arise from individual cells. Furthermore, cell morphology and cell-cell interaction in the blood stream (e.g. aggregation) are not visualized. Here we describe an imaging <i>in vivo</i> flow cytometer. <b>Material and Methods:</b> Fluorescence images are obtained simultaneously with quantitative information on a DiD-labeled cell population. As fluorescent cells pass through the slit of light focused across a blood vessel, the excited fluorescence is detected confocally. This cell counting signal triggers a strobe beam and an intensified CCD camera to capture a snapshot image of the cell as it moves down-stream from the slit. <b>Results:</b> Nearly all peaks counted as circulating T-cells originate from individual cells, while cell aggregates were rarely observed (<2%). Counting signal amplitude variation is attributed to uneven dye-loading among cells. We identify non-T-cells by their abnormal shape and size. Cell velocity was measured by determining the traveled distance from the slit within the delay of the strobe pulse or by applying multiple strobe pulses during the integration time of the CCD camera. <b>Conclusions:</b> An improved <i>in vivo</i> imaging flow cytometer can be a useful tool for studying cell populations in circulation.
Polyamine Transport as a Target for Treatment ofPneumocystisPneumonia (2009)

Polyamine levels are greatly increased in alveolar macrophages (AMs) during Pneumocystis pneumonia (PCP), leading to increased production of H(2)O(2), which causes AMs to undergo apoptosis. One of the mechanisms by which polyamine levels in AMs are elevated is enhanced uptake of exogenous polyamines. In this study, the possibility of targeting polyamine uptake as a treatment for PCP was examined. Four anthracene- and one benzene-polyamine conjugates that are potential polyamine transport inhibitors, including N1-anthracen-9-ylmethyl-butane-1,4-diamine; N-(4-aminobutyl)-N-anthracen-9-ylmethylbutane-1,4-diamine; N-[4-(4-aminobutylamino)butyl]-N-anthracen-9-ylmethylbutane-1,4-diamine; N-(4-amino-butyl)-N'-(10-[[4-(4-amino-butylamino)butylamino]-methyl]anthracen-9-ylmethyl)butane-1,4-diamine (44-Ant-44); and benzene-polyamine conjugate N-(4-amino-butyl)-N'-(4-[[4-(4-amino-butylamino)butylamino]-methyl]benzyl)butane-1,4-diamine (44-Bn-44), were tested. Compounds 44-Ant-44 and 44-Bn-44 were found to have a very low toxicity to AMs in vitro and were evaluated for their therapeutic effect on PCP in vivo. Sprague-Dawley rats infected with P. carinii for 28 days were intranasally instilled with 50 microl of a 1 mM solution of 44-Bn-44 or 44-Ant-44 every 2 days. Twenty-one days after initiation of the treatment, three to five rats from each group were sacrificed and examined for lung pathology, organism burden, and apoptosis of AMs. Both 44-Bn-44 and 44-Ant-44 reduced organism burdens; however, only 44-Ant-44 decreased the severity of the infection with reduced lung inflammation, increased clearance of exudates, increased air space, and decreased apoptosis of AMs. 44-Ant-44 also significantly prolonged the survival of treated animals. These results suggest that polyamine uptake is a potential target for treatment of PCP.
Acyl Dipeptides as Reversible Caspase Inhibitors. Part 2. Further Optimization. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.
Scalability Bugs (2017)

We highlight the problem of scalability bugs, a new class of bugs that appear in "cloud-scale" distributed systems. Scalability bugs are latent bugs that are cluster-scale dependent, whose symptoms typically surface in large-scale deployments, but not in small or medium-scale deployments. The standard practice to test large distributed systems is to deploy them on a large number of machines ("real-scale testing"), which is difficult and expensive. New methods are needed to reduce developers' burdens in finding, reproducing, and debugging scalability bugs. We propose "scale check," an approach that helps developers find and replay scalability bugs at real scales, but do so only on one machine and still achieve a high accuracy (i.e., similar observed behaviors as if the nodes are deployed in real-scale testing).