gebhart/patrepeval huggingface dataset:
Ibrutinib-Mediated Inhibition of cGVHD Pathogenic Pre-Germinal Center B-Cells and Follicular Helper Cells While Preserving Immune Memory and Th1 T-Cells (2018)

Background: Chronic graft-versus-host disease (cGVHD) is a life-threatening complication of allogeneic hematopoietic cell transplantation (allo-HCT). Recent studies point to the involvement of T and B cells in the pathogenesis of cGVHD. Ibrutinib is an irreversible inhibitor of Bruton's tyrosine kinase (BTK) and interleukin-2-inducible T-cell kinase (ITK). In a phase 1b/2 study, ibrutinib showed substantial clinical benefit in patients with cGVHD that had failed frontline therapy (Miklos et al. ASH 2016). Based on these data, ibrutinib is indicated by the US FDA for the treatment of adult patients with cGVHD after failure of ≥1 lines of systemic therapy. Methods: Blood samples from 42 patients with cGVHD that had failed frontline therapy were collected before and at multiple time-points after starting ibrutinib (420 mg daily). Correlative analyses included Nanostring gene expression profiling (GEP), Luminex- and ELISA-based plasma testing, CyTOF immunophenotyping, and ex-vivo T-cell stimulation assays. Results: In initial data from 8 patients using targeted Nanostring GEP, ibrutinib reduced inflammatory genes, including NFκB-1, and the chemokines, CXCL10, CCL7 and CCL3 by 2.6, 2.3, 25, and 1.8-fold over the first 3 months, respectively. Luminex plasma testing supported GEP results and unveiled several additional chemotactic, inflammatory, and fibrotic factors, which were down-modulated by ibrutinib, including CCL22, CXCL9, CXCL10, IL-8, sCD25, CCL4, and ST2. 42-parameter CyTOF single cell analysis showed a 10-fold reduction in absolute numbers of cGVHD-implicated pre-germinal center B-cells (CD19+, CD27+, CD38+, IgD+) and diminished Tfh, Th17, and total B cells by 2.6, 1.5, and 1.4-fold, respectively, over the first 90 days following ibrutinib. Relative numbers of CD4 and CD8 T-cells, class-switched B-cells, and CD14+ monocytes remained unchanged, and iNKT, Th1, and Treg cells increased incrementally by 1.8, 1.2, and 1.1-fold at day 90, respectively. Plasma IgG levels persisted while IgM significantly decreased corroborating an ibrutinib germinal center effect that did not deplete long-lived plasma cells. T cell reactivity against influenza increased and antibodies against EBV and tetanus remained unchanged. Single cell phosphorylation analysis showed that BTK and ITK signaling was attenuated following ibrutinib treatment in defined B and T cell subsets (Figure 1). PLCγ1/2 activation was simultaneously diminished in the pre-germinal center and plasmablast B-cell subsets. Conclusions: Ibrutinib selectively inhibits cGVHD pathogenic pre-germinal center B-cells and Tfh cells, while preserving immune memory and Th1 T-cells. These data support the clinical efficacy of ibrutinib in cGVHD and highlight ibrutinib's multifactorial mechanism of action in this disease.
An adaptive workflow coupled with Random Forest algorithm to identify intact N-glycopeptides detected from mass spectrometry (2014)

We implemented a supervised machine learning algorithm, Random Forest, in an automated workflow to identify N-glycopeptides using spectral features derived from ion trap-based LC-MS(2) data. The workflow streamlined high-confident N-glycopeptide spectral data and enabled adaptive model optimization with respect to different sampling strategies, training sample size and feature set. A critical evaluation of the features important for glycopeptide identification further facilitated effective feature selection for model improvement. Using split sample testing method from 577 high-confident N-glycopeptide spectral data, we demonstrated that an optimal true-positive rate, precision and false-positive rate of 73, 88 and 10%, respectively, can be attained for overall N-glycopeptide identification Availability and implementation: The workflow developed in this work and the application suite, Sweet-Heart, that the workflow supports for N-glycopeptide identification are available for download at http://sweet-heart.glycoproteomics.proteome.bc.sinica.edu.tw/.
Complement's participation in acquired immunity (2002)

The preliminary evidence for the involvement of complement in promoting primary humoral responses dates back over a quarter of a century. However, it is only in the course of the past decade or so that the detailed mechanisms underlying complement's influence have been characterized in depth. It is now clear that complement serves as a regulator of several B cell functions, including specific antibody production, antigen uptake, processing and presentation, and shaping of the B cell repertoire. Of key importance, in this respect, is the role played by the B cell-signaling triad consisting of the B cell receptor for antigen (BCR), a complex composed of the iC3b/C3d fragment-binding complement type 2 receptor (CR2, CD21) and its signaling element CD19 and the IgG-binding receptor FcgammaRIIb (CD32). The positive or negative outcome of signaling through this triad is determined by the context in which antigen is seen, be it alone or in association with natural or induced antibodies and/or C3-complement fragments. The aim of this review is to describe the present status of our understanding of complement's participation in acquired immunity and the regulation of autoimmune responses.
Transcribing Antarctic geological history (2018)

Thanks to the efforts of volunteer citizen scientist transcribers, Geoscience Australia's geological Antarctic field notebook collection is now available for all to access and enjoy.
In Search of Democracy: Reconciling Majority Rule, Minority Rights, and Group Rights in South Africa and the United States (1996)

We are born into certain groups, others we choose, and still others choose us.Life not subject to the call of groupness is as difficult for us to imagine as life not subject to the individuating
ChemInform Abstract: REACTIVE SILICA. XIII. ACTIVATION OF SILICA BY PYROLIZING CHEMISORBED TRICHLOROSILANE (1978)

Abstract Aktiviertes SiOQ ′ wird durch Chemisorption von HSiCl 3 und nachfolgendes Erhitzen auf 600°C dargestellt.
A Description and Evaluation of Various 3-D Models (1984)

Overcoming the limitations of polygonal techniques, parametric representations of curved lines and surfaces have evolved into powerful tools for today's computer graphics modeling applications.
Signal-to-noise ratio analysis of a digital polarimeter application to thermal imaging (1983)

A digital scanning polarimeter is described. It measures the local variations of the rotatory power of a thin liquid crystal target. This device is used for thermal imaging purposes. The incident scanning beam is split after traversing the target in two parts and then analyzed with two analyzers and detectors. Taking into account the photon noise, the existence of an optimal angle of the analyzer azimuth is shown. A numerical example is given.
Application of far-infrared spectroscopy to the structural identification of protein materials (2018)

Although far-infrared (IR) spectroscopy has been shown to be a powerful tool to determine peptide structure and to detect structural transitions in peptides, it has been overlooked in the characterization of proteins. Herein, we used far-IR spectroscopy to monitor the structure of four abundant non-bioactive proteins, namely, soybean protein isolate (SPI), pea protein isolate (PPI) and two types of silk fibroins (SFs), domestic Bombyx mori and wild Antheraea pernyi. The two globular proteins SPI and PPI result in broad and weak far-IR bands (between 50 and 700 cm-1), in agreement with those of some other bioactive globular proteins previously studied (lysozyme, myoglobin, hemoglobin, etc.) that generally only have random amino acid sequences. Interestingly, the two SFs, which are characterized by a structure composed of highly repetitive motifs, show several sharp far-IR characteristic absorption peaks. Moreover, some of these characteristic peaks (such as the peaks at 260 and 428 cm-1 in B. mori, and the peaks at 245 and 448 cm-1 in A. pernyi) are sensitive to conformational changes; hence, they can be directly used to monitor conformational transitions in SFs. Furthermore, since SF absorption bands clearly differ from those of globular proteins and different SFs even show distinct adsorption bands, far-IR spectroscopy can be applied to distinguish and determine the specific SF component within protein blends.
A Guided Tour of Selected Image Processing and Analysis Methods for Fluorescence and Electron Microscopy (2015)

Microscopy imaging, including fluorescence micro scopy and electron microscopy, has taken a prominent role in life science research and medicine due to its ability to investigate the 3D interior of live cells and organisms. A long-term research in bio-imaging at the sub-cellular and cellular scales consists then in inferring the relationships between the dynamics of macromolecules and their functions. In this area, image processing and analysis methods are now essential to understand the dynamic organization of groups of interacting molecules inside molecular machineries and to address issues in fundamental biology driven by advances in molecular biology, optics and technology. In this paper, we present recent advances in fluorescence and electron microscopy and we focus on dedicated image processing and analysis methods required to quantify phenotypes for a limited number but typical studies in cell imaging.
Etiological Role of Estrogen Status in Renal Stone Formation (2002)

The lower risk of stone formation in women may be due to the lower urinary saturation of stone forming salts. Estrogen treatment may decrease the risk of stone recurrence in postmenopausal women by lowering urinary calcium and calcium oxalate saturation.
Evaluation of the Quality of Survey Data and its Visualization Using Dashboards (2020)

Surveys are a popular tool for decision-making support. However, the quality of survey results significantly affects the quality of decisions made on their basis. Firstly based on Shannon’s formula, we evaluated the average amount of information received from the group survey. Then we analyzed the information loss caused by omissions and duplication of answers to the questionnaire. Next on the modeled data, we showed the existence of a sufficient respondents’ number to reduce the effect of data distortion. Finally, we proposed to use various types of dashboards for visual assessing the appropriateness of data.
Pocket panorama: 3D GIS on a handheld device (2004)

Pocket Panorama, an original client-server application, provides mapping data and 3D terrain visualizations to a handheld pocket PC. The pocket PC acts as a client to a server PC, which contains all data and performs all display manipulations. The terrain visualization displayed on the client uses the GPS positions transmitted by the pocket PC. All exchanges use the HTTP protocol and remain independent of the network connection used. Within the United States, a networked pocket PC can automatically obtain high resolution maps or aerial photography around its position with a single click of the stylus from the Terraserver Web site.
All-angle negative refraction and evanescent wave amplification using one-dimensional metallodielectric photonic crystals (2006)

The authors numerically demonstrate all-angle negative refraction for propagating waves, as well as evanescent wave amplifications, using a one-dimensional photonic crystal consisting of metal-dielectric multilayers. Their structure has uniform surfaces parallel to the object plane and operates at the visible wavelength range. Using realistic material parameters including loss, they design a Ag–Si3N4 multilayer structure and verified its subwavelength resolution in the image formation process.
Macromedia Dreamweaver MX Unleashed (2002)

From the Publisher:
Macromedia Dreamweaver MX Unleashed is the first complete reference guide to cover Dreamweaver MX's new and powerful features that aid in server-side programming, as well as strategies for designing, managing and developing sophisticated Web sites.

A reference for advanced users on complex application development techniques, this book guides developers into the realm of dynamic sites enabling a richer experience for the end user.

Developers learn how to collect information from a user and personalize their Web experience and how to use Dreamweaver MX management tools that aren't thoroughly covered in other intermediate-level Dreamweaver books.
Design rules for interfacial thermal conductance: Building better bridges (2017)

We study the thermal conductance across solid-solid interfaces as the composition of an intermediate matching layer is varied. In the absence of phonon-phonon interactions, an added layer can make the interfacial conductance increase or decrease depending on the interplay between (1) an increase in phonon transmission due to better bridging between the contacts and (2) a decrease in the number of available conduction channels that must conserve their momenta transverse to the interface. When phonon-phonon interactions are included, the added layer is seen to aid conductance when the decrease in resistances at the contact-layer boundaries compensate for the additional layer resistance. For the particular systems explored in this work, the maximum conductance happens when the layer mass is close to the geometric mean of the contact masses. The surprising result, usually associated with coherent antireflection coatings, follows from a monotonic increase in the boundary resistance with the interface mass ratio. This geometric mean condition readily extends to a compositionally graded interfacial layer with an exponentially varying mass that generates the thermal equivalent of a broadband impedance matching network.
Tissue MicroArray Analyses of Pancreatic Duodenal Homeobox‐1 in Human Cancers (2005)

In previous studies, we demonstrated that rat insulin promoter (RIP)-driven gene therapy successfully targeted human pancreatic tumor PANC-1 cells and mouse insulinoma NIT-1 cells, which are both pancreatic duodenal homeobox-1 (PDX-1)-positive. The purpose of this study was to perform a human tissue array analysis to determine potential targets for RIP-driven gene therapy. A custom-designed tissue MicroArray analysis of various human cancer specimens was performed using a PDX-1 polyclonal antibody generated in our laboratory. The custom-designed Tissue MicroArray of human tumor specimens consists of human cancer specimens from different origins, such as the pancreas, breast, colon, prostate, kidney, liver, lung, and ovary. A panel of normal human specimens from 20 organs or tissues was used as a control. All tissues were fixed in formalin and embedded in paraffin. The immunohistochemistry studies of the cytoplasm and the nuclear expression levels were compared using the Loda method and blind reviews. Data are presented as the mean +/- SEM (p < 0.05 was considered significant by the unpaired student t-test). PDX-1 expression intensity was elevated in both benign and malignant tissues from the same patient with pancreas, breast, colon, prostate, and kidney cancers, whereas normal human tissues from control subjects without cancer did not express PDX-1. These results suggest that PDX-1 is an early marker for these cancers and could be potentially used as a diagnostic parameter and perhaps could be targeted by PDX-1-activated gene therapies, such as RIP-TK.
Use of Negative Dielectrophoresis for Selective Elution of Protein-Bound Particles (2011)

In this paper with the aid of negative dielectrophoresis force in conjunction with shear force and at an optimal sodium hydroxide concentration we demonstrated a switchlike functionality to elute specifically bound beads from the surface. At an optimal flow rate and sodium hydroxide concentration, negative dielectrophoresis turned on results in bead detachment, whereas when negative dielectrophoresis is off, the beads remain attached. This platform offers the potential for performing a bead-based multiplexed assay where in a single channel various regions are immobilized with a different antibody, each targeting a different antigen. To develop the proof of concept and to demonstrate the switchlike functionality in eluting specifically bound beads from the surface we looked at two different protein interactions. We chose interactions that were in the same order of magnitude in strength as typical antibody-antigen interactions. The first was protein G-IgG interaction, and the second was the interaction between anti-IgG and IgG.
Novel GLP-1 Fusion Chimera as Potent Long Acting GLP-1 Receptor Agonist (2010)

GLP-1 has a variety of anti-diabetic effects. However, native GLP-1 is not suitable for therapy of diabetes due to its short half-life (t1/2<2 min). To circumvent this, we developed a long-lasting GLP-1 receptor agonist by the fusion of GLP-1 with human IgG2 Fc (GLP-1/hIgG2). ELISA-based receptor binding assay demonstrated that GLP-1/hIgG2 had high binding affinity to the GLP-1R in INS-1 cells (Kd = 13.90±1.52 nM). Upon binding, GLP-1/hIgG2 was rapidly internalized by INS-1 cells in a dynamin-dependent manner. Insulin RIA showed that GLP-1/IgG2 dose-dependently stimulated insulin secretion from INS-1 cells. Pharmacokinetic studies in CD1 mice showed that with intraperitoneal injection (i.p.), the GLP-1/hIgG2 peaked at 30 minutes in circulation and maintained a plateau for >168 h. Intraperitoneal glucose tolerance test (IPGTT) in mice showed that GLP-1/hIgG2 significantly decreased glucose excursion. Furthermore, IPGTT performed on mice one week after a single drug-injection also displayed significantly reduced glucose excursion, indicating that GLP-1/hIgG2 fusion protein has long-lasting effects on the modulation of glucose homeostasis. GLP-1/hIgG2 was found to be effective in reducing the incidence of diabetes in multiple-low-dose streptozotocin-induced type 1 diabetes in mice. Together, the long-lasting bioactive GLP-1/hIgG2 retains native GLP-1 activities and thus may serve as a potent GLP-1 receptor agonist.
Mechanisms of Anterior Cruciate Ligament Injury in Basketball (2006)

Preventive programs to enhance knee control should focus on avoiding valgus motion and include distractions resembling those seen in match situations.
The effect of conditioning temperature and exogenous xylanase addition on the viscosity of wheat-based diets and the performance of broiler chickens (2005)

1. A total of 1920 Ross broiler chicks were used in a 6 treatment by 8 replicate growth study to investigate the effect of conditioning temperature and exogenous xylanase addition on diet characteristics and bird performance. 2. Increasing conditioning temperature from 80 to 90 degrees C increased the viscosity of the diets by approximately 6 mPa.s and reduced body weight gain of the broiler chickens by 7%. 3. Furthermore, there was a significant interaction between temperature and the addition of exogenous xylanase, with a proportionately greater positive response to added xylanase in the diets that were pelleted at higher temperatures. 4. Addition of exogenous xylanase also increased the proportion of soluble arabinoxylan in the feed and reduced dietary viscosity, which is likely to be related to the degree of polymerisation of the soluble carbohydrate. 5. These results suggest that conditioning temperature should be considered as a factor when attempting to predict the response of broilers to added xylanase, especially when high-viscosity or 'low-quality' wheat is being used. 6. It can be concluded that pelleting wheat-based diets above 80 degrees C can compromise bird performance and that, if higher temperatures are to be employed, the use of exogenous xylanase is critical to maintain productivity.
Mechanisms underlying the therapeutic effect of fractional laser on photoaging (2014)

Fractional laser has been widely accepted as a treatment modality for a variety of skin conditions including photoaging,acne scars and pigmentary diseases.Based on the theory of local photothermolysis,fractional laser creates multiple microthermal zones (MTZs) surrounded by normal skin,followed by fast migration,proliferation and epithelialization of keratinocytes,which allows the timely wound healing with minimal downtime.This article presents an overview of recent advances in the treatment of skin photoaging with fractional laser,with an emphasis on histological changes and molecular mechanisms underlying fractional resurfacing.

Key words: 
Light;  Cell aging;  Fractional laser;  Treatment outcome
Management of penetrating juxtahepatic inferior vena cava injuries under total vascular occlusion. (1997)

Total vascular occlusion with selective use of aortic cross-clamping yielded 70 percent survival in an injury that historically has been associated with survival of 20 percent or less. Minimization of visceral ischemia is accomplished by occluding the aorta only after complete isolation of the inferior vena cava.
Empathy Institutionalized: Sociocultural Dialogue as a Strategic Peacebuilding Initiative (2017)

A common adage used in psychological exploration tells us that “If you want to know the end, look at the beginning.” While typically employed to emphasize the importance of upbringing and environment on personal outcomes, this phrase can be equally applicable in examining the ways in which society has developed over time to produce our polarized sociopolitical culture of today. This work explores from an integrative psychosocial perspective the potential that exists in working to define a new “end” by shaping a new “beginning,” through going directly to the institutions that comprise our own beginnings— schools. Through a combined research lens of peace studies and developmental psychology, this presentation will examine in detail the capacities of sociocultural dialogue as a strategic peacebuilding initiative, specifically in the context of institutionalized education. Through initiating relevant, age-appropriate conversational opportunities for our youngest minds to encounter and understand difference, this method would thus essentially strive to serve as an embedded, ongoing strategic peacebuilding initiative that assumes a preventative rather than reactionary approach to conflicts in perspective. In using an interdisciplinary approach to both inform frameworks and measure outcomes of implementing developmentally appropriate sociocultural dialogues in early educational settings, we gain a heightened understanding of the ways in which these types of dialogues can contribute to increased levels of empathy—ultimately working, from the beginning, to pre-emptively instill qualities capable of bridging the divides which we have clearly seen to emerge in the end.