gebhart/patrepeval huggingface dataset:
Subspecialization of Cxcr5+ T Cells (2001)

The T helper (Th) cell pool is composed of specialized cells with heterogeneous effector functions. Apart from Th1 and 2 cells, CXCR5+ T cells have been suggested to be another type of effector T cell specialized for B cell help. We show here that CXCR5+ T cells are heterogeneous, and we identify subsets of CXCR5+ CD4 T cells that differ in function and microenvironmental localization in secondary lymphoid tissues. CD57+CXCR5 T cells, hereafter termed germinal center Th (GC-Th) cells, are localized only in GCs, lack CCR7, and are highly responsive to the follicular chemokine B lymphocyte chemoattractant but not to the T cell zone EBI1-ligand chemokine. Importantly, GC-Th cells are much more efficient than CD57-CXCR5+ T cells or CXCR5- T cells in inducing antibody production from B cells. Consistent with their function, GC-Th cells produce elevated levels of interleukin 10 upon stimulation which, with other cytokines and costimulatory molecules, may help confer their B cell helper activity. Our results demonstrate that CXCR5+ T cells are functionally heterogeneous and that the GC-Th cells, a small subset of CXCR5+ T cells, are the key helpers for B cell differentiation and antibody production in lymphoid tissues.
Importance of Membrane- or Matrix-Associated Forms of M-CSF and RANKL/ODF in Osteoclastogenesis Supported by SaOS-4/3 Cells Expressing Recombinant PTH/PTHrP Receptors (2000)

SaOS-4/3, a subclone of the human osteosarcoma cell line SaOS-2, established by transfecting the human parathyroid hormone/parathyroid hormone-related protein (PTH/PTHrP) receptor complementary DNA (cDNA), supported osteoclast formation in response to PTH in coculture with mouse bone marrow cells. Osteoclast formation supported by SaOS-4/3 cells was completely inhibited by adding either osteoprotegerin (OPG) or antibodies against human macrophage colony-stimulating factor (M-CSF). Expression of messenger RNAs (mRNAs) for receptor activator of NF-kappaB ligand/osteoclast differentiation factor (RANKL/ODF) and both membrane-associated and secreted forms of M-CSF by SaOS-4/3 cells was up-regulated in response to PTH. SaOS-4/3 cells constitutively expressed OPG mRNA, expression of which was down-regulated by PTH. To elucidate the mechanism of PTH-induced osteoclastogenesis, SaOS-4/3 cells were spot-cultured for 2 h in the center of a culture well and then mouse bone marrow cells were uniformly plated over the well. When the spot coculture was treated for 6 days with both PTH and M-CSF, osteoclasts were induced exclusively inside the colony of SaOS-4/3 cells. Osteoclasts were formed both inside and outside the colony of SaOS-4/3 cells in coculture treated with a soluble form of RANKL/ODF (sRANKL/sODF) in the presence of M-CSF. When the spot coculture was treated with sRANKL/sODF, osteoclasts were formed only inside the colony of SaOS-4/3 cells. Adding M-CSF alone failed to support osteoclast formation in the spot coculture. PTH-induced osteoclast formation occurring inside the colony of SaOS-4/3 cells was not affected by the concentration of M-CSF in the culture medium. Mouse primary osteoblasts supported osteoclast formation in a similar fashion to SaOS-4/3 cells. These findings suggest that the up-regulation of RANKL/ODF expression is an essential step for PTH-induced osteoclastogenesis, and membrane- or matrix-associated forms of both M-CSF and RANKL/ ODF are essentially involved in osteoclast formation supported by osteoblasts/stromal cells.
Vascular endothelial growth factor pathway (2010)

Maitland, Michael L.; Lou, Xing Jian; Ramirez, Jacqueline; Desai, Apurva A.; Berlin, Dorit S.; McLeod, Howard L.; Weichselbaum, Ralph R.; Ratain, Mark J.; Altman, Russ B.; Klein, Teri E. Author Information
Dual‐frequency slotted triangular microstrip antenna with an inset microstrip‐line feed (2000)

A novel design of a slotted triangular microstrip antenna for dual-frequency operation is proposed and experimentally studied. By embedding an inverted V-shaped slot close to the vertex of a triangular microstrip patch, dual-frequency operation of the microstrip antenna can be achieved using an inset microstrip-line feed. The two operating frequencies have parallel polarization planes and broadside radiation characteristics. Also, the frequency ratio, in the range 1.37–1.59, of the two frequencies can be controlled by the length of the embedded slot. Details of the obtained dual-frequency performances are presented and discussed. © 2000 John Wiley & Sons, Inc. Microwave Opt Technol Lett 27: 318–320, 2000.
Amino Acid Racemization (1991)

In living tissue, all amino acids have L configuration, but after the death of an organism they undergo racemization which is a time-dependent process and therefore can be used for dating. The ratio of D to L amino acids found in a fossil is a measure of time elapsed since death. D/L ratios of protein hydrolysates can be determined by various enantioselective chromatographic techniques. Amino acid racemization is an inexpensive dating method and requires little material, e.g. 100 mg of mollusk shell, but the racemization rate depends on temperature, the type of material, and the biological species involved. A straightforward description of the kinetics is not possible. Absolute dating of a fossil is difficult or impossible but amino acid racemization is one more dating technique amongst many others. Suitable materials are mollusk shells, egg shells, foraminifera, and teeth.
Teaching with an intelligent electronic chalkboard (2004)

This paper presents E-Chalk, a software system which transforms a large touch sensitive screen into a smart teaching tool. The instructor writes on the screen using a special stylus and the software emulates a classical chalkboard. The lecturer can paste images to the board, can send queries to remote web services, can activate a computer algebra system, and can paste interactive Java Applets on the board. A copy of the lecture's audio, the board strokes (and an optional video) is stored on a server. The lecture is also transmitted live over the Internet and can be synchronized with teleconferencing systems for student feedback. The E-Chalk architecture is based on the metaphor of the classical chalkboard, enhanced by intelligent assistants running in the background. One assistant takes care of interpreting the handwritten input of the user. Another is a mathematical formula recognizer which processes handwritten queries for the algebraic server. A circuit simulator recognizes sketches of digital circuits and runs a simulation. An algorithm simulator accepts sketches of graphs as input and runs graph algorithms, animating them on the screen. Further assistants can be incorporated using the E-Chalk API. E-Chalk is being used in our electronic classroom containing a 6 meter long by 1.15 meter wide rear projection data wall.
CD79: A Review (2001)

CD79 is composed of CD79a and CD79b components expressed almost exclusively on B cells and B-cell neoplasms. CD79a and CD79b expression precedes immunoglobulin (Ig) heavy-chain gene rearrangement and CD20 expression during B-cell ontogeny and disappears later than CD20 in the late (plasma cell) stage of B-cell differentiation. Therefore, antibodies to CD79a and CD79b are useful in the differential diagnosis of B-cell neoplasms from T-cell neoplasms or myeloid neoplasms, or L and H lymphocyte predominance Hodgkin's lymphoma from classic Hodgkin's lymphoma. In addition, CD79a and CD79b antibodies are useful markers in the diagnosis of precursor B-acute lymphoblastic leukemia (pre-B-ALL) because many of these tumors are negative for other B-cell markers, such as CD20 and CD45RA. Furthermore, for B-cell neoplasms, wherein CD20 expression is aberrantly lost, such as in diffuse large B-cell lymphoma, or for B-cell neoplasms after CD20-antibody therapy, CD79a may be used as a first-line B-cell marker for the diagnosis. In this review, the authors discuss the molecular biology of CD79 and the frequency and usefulness of CD79 expression in these neoplasms.
Highly Efficient Mouse Genome Editing by CRISPR Ribonucleoprotein Electroporation of Zygotes (2016)

The CRISPR/Cas9 system has been employed to efficiently edit the genomes of diverse model organisms. CRISPR-mediated mouse genome editing is typically accomplished by microinjection of Cas9 DNA/RNA and single guide RNA (sgRNA) into zygotes to generate modified animals in one step. However, microinjection is a technically demanding, labor-intensive, and costly procedure with poor embryo viability. Here, we describe a simple and economic electroporation-based strategy to deliver Cas9/sgRNA ribonucleoproteins into mouse zygotes with 100% efficiency for in vivo genome editing. Our methodology, designated as CRISPR RNP Electroporation of Zygotes (CRISPR-EZ), enables highly efficient and high-throughput genome editing in vivo, with a significant improvement in embryo viability compared with microinjection. Using CRISPR-EZ, we generated a variety of editing schemes in mouse embryos, including indel (insertion/deletion) mutations, point mutations, large deletions, and small insertions. In a proof-of-principle experiment, we used CRISPR-EZ to target the tyrosinase (Tyr) gene, achieving 88% bi-allelic editing and 42% homology-directed repair-mediated precise sequence modification in live mice. Taken together, CRISPR-EZ is simple, economic, high throughput, and highly efficient with the potential to replace microinjection for in vivo genome editing in mice and possibly in other mammals.
Increasing update rates in the building walkthrough system with automatic model-space subdivision and potentially visible set calculations (1990)

Abstract : Pre-processing some building models can radically reduce the number of polygons processed during interactive building walkthroughs. New model-space subdivision and potentially visible set (PVS) calculation techniques, used in combination, reduce the number of polygons processed in a real building model by an average factor of 30, and a worst case factor of at least 3.25. A method of recursive model-space subdivision using binary space partitioning is presented. Heuristics are developed to guide the choice of splitting planes. The spatial subdivisions resulting from binary space partitioning are called cells. Cells correspond roughly to rooms. An observer placed in a cell may see features exterior to the cell through transparent portions of the cell boundary called portals. Computing the polygonal definitions of the portals is cast as a problem of computing a set difference operation on co-planar polygons. A plane-sweep algorithm to compute the set operations, union, intersection and difference, on co-planar sets of polygons is presented with an emphasis on handling real-world data. Two different approaches to computing the PVS for a cell are explored. The first uses point sampling and has the advantage that it is easy to trade time for results, but has the disadvantage of under-estimating the PVS. The second approach is to analytically compute a conservative over-estimation of the PVS using techniques similar to analytical shadow computation. An implementation of the Radiosity lighting model is described along with the issues involved in combining it with the algorithms described in this dissertation.
Mechanistic Analysis of the argE-Encoded N-Acetylornithine Deacetylase (2000)

The E. coli argE-encoded N-acetyl-L-ornithine deacetylase has been cloned, expressed, and purified in high yield. The substrate specificity of the enzyme is relatively broad, with a number of alpha-N-acyl-L-amino acids exhibiting activity, including both alpha-N-acetyl- and alpha-N-formylmethionine that exhibit higher activity than alpha-N-acetyl-L-ornithine. Sequence homolgy suggests that the enzyme is a member of the metal-dependent aminoacylase family, and the purified enzyme contains a single atom of zinc per monomer. The activity of this enzyme can be increased greater than 2-fold by the addition of zinc, or 8-fold by the addition of cobalt. This suggests that the enzyme can accommodate two metal ions at the active site. The pH dependence of the kinetic parameters has been determined and revealed the presence of two enzymic groups, one functioning as a general base and one functioning as a general acid. Solvent kinetic isotope effects on the hydrolysis of N-acetylornithine have been determined, and a linear proton inventory suggests that a single proton transfer occurs in a partially rate-limiting step. A chemical mechanism is proposed and compared with other mechanisms determined for other members of the aminoacylase family.
Elucidating the Detectivity Limits in Shortwave Infrared Organic Photodiodes (2018)

Abstract While only few organic photodiodes have photoresponse past 1 µm, novel shortwave infrared (SWIR) polymers are emerging, and a better understanding of the limiting factors in narrow bandgap devices is critically needed to predict and advance performance. Based on state‐of‐the‐art SWIR bulk heterojunction photodiodes, this work demonstrates a model that accounts for the increasing electric‐field dependence of photocurrent in narrow bandgap materials. This physical model offers an expedient method to pinpoint the origins of efficiency losses, by decoupling the exciton dissociation efficiency and charge collection efficiency in photocurrent–voltage measurements. These results from transient photoconductivity measurements indicate that the main loss is due to poor exciton dissociation, particularly significant in photodiodes with low‐energy charge‐transfer states. Direct measurements of the noise components are analyzed to caution against using assumptions that could lead to an overestimation of detectivity. The devices show a peak detectivity of 5 × 10 10 Jones with a spectral range up to 1.55 µm. The photodiodes are demonstrated to quantify the ethanol–water content in a mixture within 1% accuracy, conveying the potential of organics to enable economical, scalable detectors for SWIR spectroscopy.
Parenteral Plant Sterols and Intestinal Failure–associated Liver Disease in Neonates (2011)

Frequent occurrence of IFALD among neonates on PN displays an association to duration of PN and markedly increased serum PS, especially stigmasterol, in comparison to healthy neonates and children on PN. Striking accumulation of parenteral PS may contribute to IFALD among neonates.
Detection of Dekkera-Brettanomyces strains in sherry by a nested PCR method (1996)

Brettanomyces sp. and its ascosporogenous sexual state, Dekkera sp., have been well documented as spoilage microorganisms, usually associated with barrel-aged red wines. In this report, we describe the genetic characterization, on the basis of DNA content per cell, electrophoretic karyotyping, and mitochondrial DNA restriction patterns, of a Dekkera yeast strain isolated from sherries and of a number of other Brettanomyces and Dekkera strains. By using a genomic DNA fragment of the isolated Dekkera strain, we developed a two-step PCR method which directs the specific amplification of target DNA from this strain and from other Brettanomyces-Dekkera strains. The method efficiently amplified the target DNA from intact cells, obviating DNA isolation, and yielded a detection limit of fewer than 10 yeast cells in contaminated samples of sherry.
Pro‐apoptotic therapy with the oligonucleotide GenasenseTM (oblimersen sodium) targeting Bcl‐2 protein expression enhances the biological anti‐tumour activity of rituximab (2004)

New strategies have evolved in the treatment of patients with non-Hodgkin's lymphoma (NHL). Anti-sense oligonucleotides (ASO) and monoclonal antibody (mAb) therapy, though proven to be safe and effective, have not demonstrated to be curative when used as single agents. We tested an innovative combination strategy involving various mAbs and ASO against Bcl-2 (G3139) in aggressive preclinical models. G3139, under optimal transfection conditions, decreased the proliferation rate of lymphoma cells by 60-75% when compared with controls. In addition, apoptosis was demonstrated in Raji (25%) and DHL-4 cells (30%) treated with Genasense following downregulation of Bcl-2 protein. Downregulation of Bcl-2 by G3139 was associated with a higher degree of rituximab-associated, complement-mediated cytotoxicity and antibody dependent cellular cytotoxicity when compared with rituximab alone-treated controls. In vivo studies in severe combined immunodeficiency (SCID) mice clearly demonstrated synergistic activity between G3139 and rituximab. Treatment of lymphoma-bearing SCID mice with G3139 for two consecutive days prior to each rituximab dose resulted in better disease control and survival than treatment with either agent alone or controls. Our findings suggest that Bcl-2 downregulation by G3139, followed by the administration of rituximab is an efficient anti-tumour strategy associated with improved survival in lymphoma-bearing SCID mice.
The function of the SNP in the MMP1 and MMP3 promoter in susceptibility to endometriosis in China (2005)

Matrix metalloproteinases (MMPs) may contribute to the development of endometriosis. Genetic variations in several MMP promoters may influence the transcription and expression of MMPs. The purpose of the present study was to assess how gene polymorphisms in the MMP1 and MMP3 promoters affect the risk of development of endometriosis. We genotyped 100 women with endometriosis and 150 control subjects in North China. There was a significant difference in frequency of the MMP1 genotype between cases and controls (P=0.03). The 2G homozygote in endometriosis and controls was significantly different (P=0.02). The frequency of the 2G allele among affected women (79%) was significantly higher than among the healthy controls (66.9%; P=0.003). However, the overall genotype and allelotype distribution of the MMP3 single nucleotide polymorphism (SNP) in patients was not different from that of controls (P> or =0.05). MMP1 and MMP3 polymorphisms were in linkage disequilibrium in cases and controls (D'=0.47; P=0.00). The haplotype frequency distribution derived from these two polymorphisms was significantly different between cases and controls (P=0.00). The haplotype analysis suggested an implication of both MMP1 and MMP3 polymorphisms in the susceptibility to endometriosis. We conclude that the MMP1 promoter SNP and MMP 2G/6A haplotype may modify susceptibility to endometriosis, but that the MMP3 promoter SNP is unlikely to be associated with endometriosis in the population of North China.
Weighing nanoparticles in solution at the attogram scale (2014)

Physical characterization of nanoparticles is required for a wide range of applications. Nanomechanical resonators can quantify the mass of individual particles with detection limits down to a single atom in vacuum. However, applications are limited because performance is severely degraded in solution. Suspended micro- and nanochannel resonators have opened up the possibility of achieving vacuum-level precision for samples in the aqueous environment and a noise equivalent mass resolution of 27 attograms in 1-kHz bandwidth was previously achieved by Lee et al. [(2010) Nano Lett 10(7):2537-2542]. Here, we report on a series of advancements that have improved the resolution by more than 30-fold, to 0.85 attograms in the same bandwidth, approaching the thermomechanical noise limit and enabling precise quantification of particles down to 10 nm with a throughput of more than 18,000 particles per hour. We demonstrate the potential of this capability by comparing the mass distributions of exosomes produced by different cell types and by characterizing the yield of self-assembled DNA nanoparticle structures.
Thermal modeling, heat mitigation, and radiative cooling for double-clad fiber amplifiers (2018)

We report a detailed formalism aimed at the thermal modeling and heat mitigation in high-power double-clad fiber amplifiers. Closed form analytical formulas are developed that take into account the spatial profile of the amplified signal and pump in the double-clad geometry, the presence of the amplified spontaneous emission, and the possibility of radiative cooling due to anti-Stokes fluorescence emission. The formalism is applied to a high-power Yb-doped silica fiber amplifier. The contributions to the heat-load from the pump-signal quantum defect, as well as the pump and signal parasitic absorptions are compared to the radiative cooling. It is shown that for realistic cases, the local heat generation in kiloWatt-class fiber amplifiers is either dominated by the quantum defect or the parasitic absorption depending on the pump wavelength. In conventional designs, radiative cooling can be substantial only in properly designed amplifiers, when the pump power is tens of watts or lower, unless the parasitic absorption is reduced compared to the commonly reported values in the literature. We also explore the impact of the non-ideal quantum efficiency of the gain material. The developed formalism can be used to design fiber amplifiers and lasers for optimal heat mitigation, especially due to radiative cooling.
Proton energy optimization and reduction for intensity-modulated proton therapy (2014)

Intensity-modulated proton therapy (IMPT) is commonly delivered via the spot-scanning technique. To 'scan' the target volume, the proton beam is controlled by varying its energy to penetrate the patient's body at different depths. Although scanning the proton beamlets or spots with the same energy can be as fast as 10-20 m s(-1), changing from one proton energy to another requires approximately two additional seconds. The total IMPT delivery time thus depends mainly on the number of proton energies used in a treatment. Current treatment planning systems typically use all proton energies that are required for the proton beam to penetrate in a range from the distal edge to the proximal edge of the target. The optimal selection of proton energies has not been well studied. In this study, we sought to determine the feasibility of optimizing and reducing the number of proton energies in IMPT planning. We proposed an iterative mixed-integer programming optimization method to select a subset of all available proton energies while satisfying dosimetric criteria. We applied our proposed method to six patient datasets: four cases of prostate cancer, one case of lung cancer, and one case of mesothelioma. The numbers of energies were reduced by 14.3%-18.9% for the prostate cancer cases, 11.0% for the lung cancer cases and 26.5% for the mesothelioma case. The results indicate that the number of proton energies used in conventionally designed IMPT plans can be reduced without degrading dosimetric performance. The IMPT delivery efficiency could be improved by energy layer optimization leading to increased throughput for a busy proton center in which a delivery system with slow energy switch is employed.
The Antibacterial Lectin RegIIIγ Promotes the Spatial Segregation of Microbiota and Host in the Intestine (2011)

The mammalian intestine is home to ~100 trillion bacteria that perform important metabolic functions for their hosts. The proximity of vast numbers of bacteria to host intestinal tissues raises the question of how symbiotic host-bacterial relationships are maintained without eliciting potentially harmful immune responses. Here, we show that RegIIIγ, a secreted antibacterial lectin, is essential for maintaining a ~50-micrometer zone that physically separates the microbiota from the small intestinal epithelial surface. Loss of host-bacterial segregation in RegIIIγ(-/-) mice was coupled to increased bacterial colonization of the intestinal epithelial surface and enhanced activation of intestinal adaptive immune responses by the microbiota. Together, our findings reveal that RegIIIγ is a fundamental immune mechanism that promotes host-bacterial mutualism by regulating the spatial relationships between microbiota and host.