gebhart/patrepeval huggingface dataset:
Transfer of Autoimmune Diabetes Mellitus with Splenocytes from Nonobese Diabetic (NOD) Mice (1986)

The nonobese diabetic (NOD) mouse, a model of human type I diabetes, develops insulitis beginning at 4-6 wk of age. By 30 wk of age, 72% of females and 39% of males develop spontaneous diabetes, apparently because of an overwhelming autoimmune response to the insulin-producing beta-cells within the islets. To identify the immune mechanism responsible for destruction of beta-cells in the NOD mouse, we developed an adoptive transfer protocol that induces diabetes in NOD mice at an age when spontaneous diabetes is rarely observed. Splenocytes from overtly diabetic NOD mice were unable to transfer diabetes to very young (less than or equal to 6 wk) irradiated NOD mice but effectively transferred diabetes to irradiated NOD mice greater than 6 wk of age. In such transfers, overt diabetes was induced within 12-22 days in greater than 95% (79/82) of the recipients. Thus, transfer of splenocytes to young mice induces them to become diabetic at a higher frequency and at a younger age than their untreated littermates. Equally successful transfers with as few as 5 X 10(6) spleen cells have been performed in male and female NOD mice, even though males display a lower spontaneous incidence of diabetes than females. Splenocytes obtained from diabetic mice maintained on insulin for up to 2 mo also transferred diabetes. Because NOD mice display increasing levels of insulitis with age, spleen cells obtained from nondiabetic NOD mice of different ages were tested for their ability to transfer diabetes.(ABSTRACT TRUNCATED AT 250 WORDS)
Rent3D: Floor-plan priors for monocular layout estimation (2015)

The goal of this paper is to enable a 3D “virtual-tour” of an apartment given a small set of monocular images of different rooms, as well as a 2D floor plan. We frame the problem as inference in a Markov Random Field which reasons about the layout of each room and its relative pose (3D rotation and translation) within the full apartment. This gives us accurate camera pose in the apartment for each image. What sets us apart from past work in layout estimation is the use of floor plans as a source of prior knowledge, as well as localization of each image within a bigger space (apartment). In particular, we exploit the floor plan to impose aspect ratio constraints across the layouts of different rooms, as well as to extract semantic information, e.g., the location of windows which are marked in floor plans. We show that this information can significantly help in resolving the challenging room-apartment alignment problem. We also derive an efficient exact inference algorithm which takes only a few ms per apartment. This is due to the fact that we exploit integral geometry as well as our new bounds on the aspect ratio of rooms which allow us to carve the space, significantly reducing the number of physically possible configurations. We demonstrate the effectiveness of our approach on a new dataset which contains over 200 apartments.
Using GOMS for user interface design and evaluation (1996)

Since the seminal book, The Psychology of Human-Computer Interaction , the GOMS model has been one of the few widely known theoretical concepts in human-computer interaction. This concept has spawned much research to verify and extend the original work and has been used in real-world design and evaluation situations. This article synthesizes the previous work on GOMS to provide an integrated view of GOMS models and how they can be used in design. We briefly describe the major variants of GOMS that have matured sufficiently to be used in actual design. We then provide guidance to practitioners about which GOMS variant to use for different design situations. Finally, we present examples of the application of GOMS to practical design problems and then summarize the lessons learned.
Nondeletional T-Cell Receptor Transgenic Mice: Model for the CD4+T-Cell Repertoire in Chronic Hepatitis B Virus Infection (2000)

Chronicity after infection with the hepatitis B virus (HBV) can occur for a variety of reasons. However, once established, chronicity may be maintained by high levels of viral proteins circulating in the serum. To examine the characteristics of T cells capable of coexisting with the secreted hepatitis B e antigen (HBeAg), T-cell receptor (TCR) transgenic (Tg) mice were produced. To ensure that HBeAg-specific T cells would not be deleted in the presence of serum HBeAg, the TCR alpha- and beta-chain genes used to produce the TCR-Tg mice were derived from T-cell hybridomas produced from immunizing HBeAg-Tg mice. A TCR-Tg lineage (11/4-12) was produced that possessed a high frequency ( approximately 67%) of CD4(+) T cells that expressed a Tg TCR specific for the HBeAg. As predicted, when 11/4-12 TCR-Tg mice were bred with HBeAg-Tg mice no deletion of the HBeAg-specific CD4(+) T cells occurred in the thymus or the spleen. Functional analysis of the TCR-Tg T cells revealed that the HBeAg-specific CD4(+) T cells escaped deletion in the thymus and periphery by virtue of low avidity. Regardless of their low avidity, HBeAg-specific TCR-Tg T cells could be activated by exogenous HBeAg, as measured by cytokine production in vitro and T-helper-cell function for anti-HBe antibody production in vitro and in vivo. Furthermore, activated TCR-Tg HBeAg-specific T cells polarized to the Th1 subset were able to elicit liver injury when transferred into HBeAg or HBcAg-Tg recipients. Therefore, HBeAg-specific CD4(+) T cells that can survive deletion or anergy in the presence of circulating HBeAg nonetheless are capable of being activated and of mediating liver injury in vivo. The 11/4-12 TCR-Tg lineage may serve as a monoclonal model for the HBe/HBcAg-specific CD4(+) T-cell repertoire present in chronically infected HBV patients.
Cell Type-Specific and Site Directed N-Glycosylation Pattern of FcγRIIIa (2011)

Human leukocyte receptor IIIa (hFcγRIIIa) plays a prominent role in the elimination of tumor cells by antibody-based cancer therapies. In previous studies, a major impact of the presence of carbohydrates at Asn-162 on the binding between the receptor and the Fc part of wild type fucosylated or glycoengineered nonfucosylated antibodies has been shown. In this study, we performed a site directed carbohydrate analysis at hFcγRIIIa derived from human embryonic kidney (HEK) and Chinese hamster ovary (CHO) cells, respectively. Using mass spectrometry (MS) and a multienzyme protein digest, we analyzed the proteolysis-generated glycopeptides in detail. We could show that hFcγRIIIa expressed by HEK cells was mostly bearing multifucosylated biantennary Asn162-glycans with a major fraction terminating with GalNAc residues replacing the more common Gal. We could demonstrate that the glycan antennae with terminal GalNAc could be sialylated as indicated by a novel reporter ion HexNAcHexNAcNeuAc(+) (m/z 698.28) using a source induced dissociation (SID) scan in the MS cycle. In contrast to the hFcγRIIIa Asn-162 glycosylation pattern from HEK cells, the CHO cells derived receptor contains bi- and triantennary galactosylated and highly sialylated carbohydrates. Our data suggest that the type of expression host system was a dominating factor for formation of distinct glycopatterns of hFcγRIIIa, while the protein sequence and the site of glycosylation remained unchanged for both types of cells. Using surface plasmon resonance (SPR) interaction analysis, we show that the cell type and site specific glycosylation pattern of hFcγRIIIa influences its binding behavior to immunoglobulin molecules.
Calorimetric Measurement of the Energy Difference Between Two Solid Surface Phases (1995)

A recently designed single-crystal surface calorimeter has been deployed to measure the energy difference between two solid surface structures. The clean Pt{100} surface is reconstructed to a stable phase in which the surface layer of platinum atoms has a quasi-hexagonal structure. By comparison of the heats of adsorption of CO and of C(2)H(4) on this stable Pt{100}-hex phase with those on a metastable Pt{100}-(1x1) surface, the energy difference between the two clean phases was measured as 20 +/- 3 and 25 +/- 3 kilojoules per mole of surface platinum atoms.
Web services for digital rights management and copyright protection in digital media (2008)

The paper focuses on the implementation of an advanced digital rights management (DRM) system which supported by web services offers copyright protection and management of digital media. The main components of the DRM system are a digital image library, which offers specialized services for storing and searching and a copyright protection and digital rights management subsystem for the digitized media based on innovative watermarking and web technologies.
Migration of neutrophils across endothelial monolayers is stimulated by treatment of the monolayers with interleukin-1 or tumor necrosis factor- alpha . (1989)

To study the effects of the cytokines IL-1 and TNF-alpha on the transendothelial migration of neutrophils, human umbilical vein endothelial cells (HUVEC) were grown to confluence on connective tissue prepared from human amniotic membrane. Pretreatment of HUVEC-amnion cultures with rIL-1 beta (7.5 ng/ml) or rTNF-alpha (5 ng/ml) for 4 h resulted in rapid migration of from 20 to 50% of subsequently added neutrophils across the endothelial monolayer. In contrast, only 3 +/- 3% of added neutrophils penetrated the HUVEC monolayer in the absence of any stimulus. The number of neutrophils that migrated across cytokine-treated HUVEC was similar to the number that traversed untreated monolayers in response to gradients of FMLP; in addition, it was only 35% less than the number of neutrophils that migrated in response to leukotriene B4. No consistent additive effect was seen when migration was induced by both cytokine pretreatment of the HUVEC and a chemotactic gradient. The number of neutrophils that migrated across IL-1-treated cultures was proportional to the number added over the range of 2.5 x 10(5) to 4 x 10(6) neutrophils. When used at optimal concentrations, IL-1 and TNF-alpha were equally effective in stimulating neutrophil migration; no additive effect was seen when HUVEC were pretreated with optimal doses of both cytokines together. Direct addition of IL-1 or TNF-alpha to a 1-h migration assay had no effect on neutrophil adhesion to or migration across HUVEC, either in the presence or absence of a chemotactic gradient. Stimulation of neutrophil transendothelial migration in this system did not appear to be caused by adsorption of cytokine by the amniotic tissue, nor was it due to contamination of the cytokine preparations by LPS. These results suggest that IL-1 and TNF-alpha, generated at sites of inflammation, may act upon the endothelium to promote emigration of neutrophils from the vasculature.
Comparative enzymology of 11β-hydroxysteroid dehydrogenase type 1 from six species (2005)

11beta-Hydroxysteroid dehydrogenase type 1 (11beta-HSD1), catalyzing the intracellular activation of cortisone to cortisol, is currently considered a promising target to treat patients with metabolic syndrome; hence, there is considerable interest in the development of selective inhibitors. For preclinical tests of such inhibitors, the characteristics of 11beta-HSD1 from the commonly used species have to be known. Therefore, we determined differences in substrate affinity and inhibitor effects for 11beta-HSD1 from six species. The differences in catalytic activities with cortisone and 11-dehydrocorticosterone were rather modest. Human, hamster and guinea-pig 11beta-HSD1 displayed the highest catalytic efficiency in the oxoreduction of cortisone, while mouse and rat showed intermediate and dog the lowest activity. Murine 11beta-HSD1 most efficiently reduced 11-dehydrocorticosterone, while the enzyme from dog showed lower activity than those from the other species. 7-ketocholesterol (7KC) was stereospecifically converted to 7beta-hydroxycholesterol by recombinant 11beta-HSD1 from all species analyzed except hamster, which showed a slight preference for the formation of 7alpha-hydroxycholesterol. Importantly, guinea-pig and canine 11beta-HSD1 displayed very low 7-oxoreductase activities. Furthermore, we demonstrate significant species-specific variability in the potency of various 11beta-HSD1 inhibitors, including endogenous compounds, natural chemicals and pharmaceutical compounds. The results suggest significant differences in the three-dimensional organization of the hydrophobic substrate-binding pocket of 11beta-HSD1, and they emphasize that species-specific variability must be considered in the interpretation of results obtained from different animal experiments. The assessment of such differences, by cell-based test systems, may help to choose the appropriate animal for safety and efficacy studies of novel potential drug candidates.
Virtual memory mapped network interface for the SHRIMP multicomputer (1994)

The network interfaces of existing multicomputers require a significant amount of software overhead to provide protection and to implement message passing protocols. This paper describes the design of a low-latency, high-bandwidth, virtual memory-mapped network interface for the SHRIMP multicomputer project at Princeton University. Without sacrificing protection, the network interface achieves low latency by using virtual memory mapping and write-latency hiding techniques, and obtains high bandwidth by providing a user-level block data transfer mechanism. We have implemented several message passing primitives in an experimental environment, demonstrating that our approach can reduce the message passing overhead to a few user-level instructions.
A Regulatory Role for TRAF1 in Antigen-induced Apoptosis of  T Cells (1997)

Tumor necrosis factor receptor (TNFR)-associated factor 2 (TRAF2) and TRAF1 were found as components of the TNFR2 signaling complex, which exerts multiple biological effects on cells such as cell proliferation, cytokine production, and cell death. In the TNFR2-mediated signaling pathways, TRAF2 works as a mediator for activation signals such as NF-kappaB, but the role of TRAF1 has not been previously determined. Here we show in transgenic mice that TRAF1 overexpression inhibits antigen-induced apoptosis of CD8(+) T lymphocytes. Our results demonstrate a biological role for TRAF1 as a regulator of apoptotic signals and also support the hypothesis that the combination of TRAF proteins in a given cell type determines distinct biological effects triggered by members of the TNF receptor superfamily.
Convenient assay for interferons (1981)

A convenient assay for interferons based on reduction of cytopathic effect was developed. The number of manipulations and the lengths of the various incubation steps were reduced to a minimum. The assay is simple to perform and can be completed within 16 h. Moreover, it can be used with various types of cells and a variety of viruses.
Inhibition of hsc70-catalysed clathrin uncoating by HSJ1 proteins (1996)

The uncoating of clathrin-coated vesicles can be mediated in vitro by the 'uncoating ATPase' that has been identified as the constitutive 70 kDa heat shock protein (hsp70), hsc70. It is now established that the activity of hsp70 proteins can be regulated by another family of molecular chaperones, the DnaJ family. In this study, we have investigated the effects of DnaJ-like proteins (the human neuron-specific proteins HSJ1a and HSJ1b) on clathrin uncoating. In order to measure the kinetics of clathrin release from coated vesicles, we have developed a quantitative, two-site ELISA for clathrin triskelions and demonstrated that stoichiometric amounts of HSJ1 proteins inhibit the initial burst of hsc70-mediated clathrin uncoating by over 40%. This inhibition is not a consequence of ADP binding by hsc70 or the aggregation of hsc70, but correlates with an increase in the hsc70 associated with the coated vesicle fraction, suggesting that the inhibition is a consequence of a non-productive stabilization of hsc70 with a component of the coated vesicle fraction. These results strongly suggest that HSJ1 proteins interfere with an endogenous DnaJ-like protein that is involved in uncoating. Recent evidence suggests that the brain-specific vesicle-associated protein auxilin could play such a role. Although we find no evidence for auxilin in our coated vesicle preparation, our results predict that an auxilin-like protein will be a general factor in clathrin uncoating.
Baker's Yeast as a Reagent in Organic Synthesis (1990)

This review examines the use of baker's yeast as a reagent in organic synthesis, with an emphasis on the developments of the last 15 years. The transformations of various classes of compounds are examined, for example, reduction or formation of double bonds, acyloin condensation. The equivalent microbial transformations are compared in relevant cases. 1. Introduction 2. Reduction of β-Keto Esters 3. Reduction of other Keto Acid Derivatives 4. Reduction of α-Hydroxy Aldehydes and Ketones to Vicinal Diols 5. Reduction of Ketones with a Sulfur Containing Functional Group on the α-Carbon 6. Reduction of β-Diketones 7. Reduction of Carbon-Carbon Double Bonds 7.1. Preparation of Bifunctional Chiral Synthetic Building Blocks 7.2. Reduction of Trisubstituted Double Bonds of Larger Synthetic Intermediates 7.3. Reduction of other Trisubstituted Double Bonds 8. Formation of Carbon-Carbon Bonds 8.1. Acyloin Condensation 8.2. Enzymatic Cyclization of Squalenoids 8.3. Carbon-Carbon Bond Formation through Michael-Type Addition 9. Reduction of Carbonyl Groups for the Preparation of Optically Active Fluorinated Compounds 10. Reduction of Heterocyclic Ketones 11. Reduction of Aromatic and Unsaturated Ketones 12. Kinetic Resolution of Cyclic Racemic Ketones 13. Reduction of Nitro Containing Compounds 14. Ester Hydrolysis 15. Water Addition Across the Double Bond of α,β-Unsaturated Aldehydes 16. Dehydrogenation of Unnatural Fatty Acids
Corner-field induced drain leakage in thin oxide MOSFETs (1987)

A new type of leakage current between drain and substrate (n-well) in thin oxide (120A-285A) n- and p-channel MOSFET's fabricated with standard CMOS n-well process is investigated. Experimental results indicate that the origin of this leakage is due to band-to-band tunneling occurring at the deep-depleted drain junction corner. It is shown that the tunneling <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">I-V</tex> behavior can be adequately described by the analytical expression of <tex xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">J = B_{1}E_{si} \exp (-B_{2}/E_{si})</tex> . The critical drain voltage corresponding to the onset of tunneling is empirically found to be 1.3 V higher in p-channel than in n-channel. Device structures with graded junctions, such as double-diffused and LDD, are also studied and demonstrated to be effective in suppressing this leakage current.
Heart Failure and Midrange Ejection Fraction (2016)

Patients with HF with midrange LVEF demonstrate a distinct clinical profile from HFpEF and HFrEF patients, with objective measures of functional capacity similar to HFpEF. Within the midrange LVEF HF population, recovered systolic function is a marker of more favorable prognosis.
Compatibility of the selective area growth of GaN nanowires on AlN-buffered Si substrates with the operation of light emitting diodes (2015)

AlN layers with thicknesses between 2 and 14 nm were grown on Si(111) substrates by molecular beam epitaxy. The effect of the AlN layer thickness on the morphology and nucleation time of spontaneously formed GaN nanowires (NWs) was investigated by scanning electron microscopy and line-of-sight quadrupole mass spectrometry, respectively. We observed that the alignment of the NWs grown on these layers improves with increasing layer thickness while their nucleation time decreases. Our results show that 4 nm is the smallest thickness of the AlN layer that allows the growth of well-aligned NWs with short nucleation time. Such an AlN buffer layer was successfully employed, together with a patterned SiOx mask, for the selective-area growth (SAG) of vertical GaN NWs. In addition, we fabricated light-emitting diodes (LEDs) from NW ensembles that were grown by means of self-organization phenomena on bare and on AlN-buffered Si substrates. A careful characterization of the optoelectronic properties of the two devices showed that the performance of NW-LEDs on bare and AlN-buffered Si is similar. Electrical conduction across the AlN buffer is facilitated by a high number of grain boundaries that were revealed by transmission electron microscopy. These results demonstrate that grainy AlN buffer layers on Si are compatible both with the SAG of GaN NWs and LED operation. Therefore, this study is a first step towards the fabrication of LEDs on Si substrates based on homogeneous NW ensembles.
Differences between stereo and motion behaviour on synthetic and real-world stereo sequences (2008)

Performance evaluation of stereo or motion analysis techniques is commonly done either on synthetic data where the ground truth can be calculated from ray-tracing principals, or on engineered data where ground truth is easy to estimate. Furthermore, these scenes are usually only shown in a very short sequence of images. This paper shows why synthetic scenes may not be the only testing criteria by giving evidence of conflicting results of disparity and optical flow estimation for real-world and synthetic testing. The data dealt with in this paper are images taken from a moving vehicle. Each real-world sequence contains 250 image pairs or more. Synthetic driver assistance scenes (with ground truth) are 100 or more image pairs. Particular emphasis is paid to the estimation and evaluation of scene flow on the synthetic stereo sequences. All image data used in this paper is made publicly available at http: //www.mi.auckland.ac.nz/EISATS.
Characterization of chromatin accessibility with a transposome hypersensitive sites sequencing (THS-seq) assay (2016)

Chromatin accessibility captures in vivo protein-chromosome binding status, and is considered an informative proxy for protein-DNA interactions. DNase I and Tn5 transposase assays require thousands to millions of fresh cells for comprehensive chromatin mapping. Applying Tn5 tagmentation to hundreds of cells results in sparse chromatin maps. We present a transposome hypersensitive sites sequencing assay for highly sensitive characterization of chromatin accessibility. Linear amplification of accessible DNA ends with in vitro transcription, coupled with an engineered Tn5 super-mutant, demonstrates improved sensitivity on limited input materials, and accessibility of small regions near distal enhancers, compared with ATAC-seq.