gebhart/patrepeval huggingface dataset:
Identification of four novel T cell autoantigens and personal autoreactive profiles in multiple sclerosis (2022)

Multiple sclerosis (MS) is an inflammatory disease of the central nervous system (CNS), in which pathological T cells, likely autoimmune, play a key role. Despite its central importance, the autoantigen repertoire remains largely uncharacterized. Using a novel in vitro antigen delivery method combined with the Human Protein Atlas library, we screened for T cell autoreactivity against 63 CNS-expressed proteins. We identified four previously unreported autoantigens in MS: fatty acid-binding protein 7, prokineticin-2, reticulon-3, and synaptosomal-associated protein 91, which were verified to induce interferon-γ responses in MS in two cohorts. Autoreactive profiles were heterogeneous, and reactivity to several autoantigens was MS-selective. Autoreactive T cells were predominantly CD4<sup>+</sup> and human leukocyte antigen-DR restricted. Mouse immunization induced antigen-specific responses and CNS leukocyte infiltration. This represents one of the largest systematic efforts to date in the search for MS autoantigens, demonstrates the heterogeneity of autoreactive profiles, and highlights promising targets for future diagnostic tools and immunomodulatory therapies in MS.
Shared Table Access Pattern Analysis for Multi-Tenant Applications (2008)

With the rise of applications in the area of software as a service it becomes crucial to operate profitable even with small profit margins. The possibility of customers to switch between different hosted solutions makes the calculation of the total cost of ownership even more important. Not only the application design is an important factor in this calculation but as well the employed storage techniques used to create and maintain thousands of instances of the same application play one of the most important roles in this game. None of the well-known commercial of the shelf databases like MySQL, PostgreSQL, etc. provides an optimized solution for multi-tenancy problems. In this paper we analyze typical operations in the area of multi-tenant databases and show how they are wired together. Based on the analysis we propose an architecture for a multi-tenant storage engine capable to overcome the problems of typical relational databases in this area.
Abstract A10: Increased mesenchymal progenitor cells in RB1−/− bone (2009)

Abstract The retinoblastoma pathway is deregulated in 90% of human cancers owing to the mutation of one or more pathway members. Yet, the molecular pathogenesis of tumors with a loss of the retinoblastoma gene, RB1, (retinoblastoma and osteosarcoma) are poorly understood. To understand the role of pRb in tumor formation we have focused on a tissue in which malignancies commonly have RB1 deletions, bone. Human osteosarcoma cells, in general, exhibit no signs of terminal differentiation, and are defined by the ability to form bone. We hypothesize that osteosarcoma is caused by molecular/genetic disruptions of the osteogenic differentiation pathway. Homozygous null RB1 mice die during early embryonic day, E11.5-13.5, before any significant skeletal development or mineralization occurs. Therefore, we utilized the cre/lox system to create a bone targeted RB1 knockout animal. RB1−/− mice display defects in bone formation. Furthermore, isolation and characterization of primary calvarial cells (dorsal skull cells) from these animals show that pRb abates progression of pre-osteoblasts to mature osteoblasts. As osteoblasts are known progeny of primitive mesenchymal stem cells (MSC), we next asked if diminished differentiation resulted in an increase in MSCs. MSCs are pluripotent cells that can differentiate into a variety of cell types. I have shown in the absence of RB1, calvarial cells can differentiate into multiple lineages including bone and fat, where as cells fromWT littermates are restricted to the osteoblast lineage. Colony formation assays, a functional in vitro assay, suggest RB1−/− cells have increased progenitor cell number, and through sphere formation assays we have shown an increased self-renewal capacity. There is also a significantly larger population of Sca-1 (a stem cell marker) positive cells in RB1−/− cultures compared toWT littermates. In addition, utilization of microarray technology suggests a unique RB1 dependent gene expression pattern in osteogenesis. This is consistent with our previous work showing the necessity of the pRb/Runx2 (a master regulator in bone development) interaction to turn on osteocalcin transcription, a late marker in differentiation. We have begun to identify a possible mechanism for pRb regulation early in osteogenesis through the Hedgehog signaling pathway that explains the increased pluripotency of mesenchymal cells in the absence of RB1. Therefore, we have identified an increased number of bone progenitor cells that are pluripotent from RB1−/− mice, and a possible mechanism for pRb regulation early in osteogenesis and malignant tumor formation. Citation Information: Cancer Res 2009;69(23 Suppl):A10.
System Performance Modelling of Heterogeneous HW Platforms: An Automated Driving Case Study (2019)

The push towards automated and connected driving functionalities mandates the use of heterogeneous HW platforms in order to provide the required computational resources. For these platforms, the established methods for performance modelling in industry are no longer effective. In this paper, we propose an initial modelling concept for heterogeneous platforms which can then be fed into appropriate tools to derive effective performance predictions. The approach is demonstrated for a prototypical automated driving application on the Nvidia Tegra X2 platform.
Novel Petasis Boronic Acid Reactions with 1,3,5‐Tri‐oxygenated Benzenes. (2004)

Abstract For Abstract see ChemInform Abstract in Full Text.
Peripheral vision: Good for biological motion, bad for signal noise segregation? (2007)

Biological motion perception, having both evolutionary and social importance, is performed by the human visual system with a high degree of sensitivity. It is unclear whether peripheral vision has access to the specialized neural systems underlying biological motion perception; however, given the motion component, one would expect peripheral vision to be, if not specialized, at least highly accurate in perceiving biological motion. Here we show that the periphery can indeed perceive biological motion. However, the periphery suffers from an inability to detect biological motion signals when they are embedded in dynamic visual noise. We suggest that this peripheral deficit is not due to biological motion perception per se, but to signal/noise segregation.
Asymmetric Oxidation of a Dihydrothienopyrimidine (2017)

A robust catalytic asymmetric oxidation of prochiral sulfide 1 has been achieved by the use of a chiral titanium–hydrobenzoin complex. Reproducible reaction conditions were identified by screening reaction parameters and DOE optimization. The enantioselectivity was found to be mostly influenced by the amount of water and the time the catalyst was aged before addition of the sulfide.
An Efficient Analysis Technique For Dna Sequences Using Multiwindow Gabor Representations (2005)

Publication in the conference proceedings of EUSIPCO, Antalya, Turkey, 2005
1040. Towards Gene Correction Therapy for Wiskott-Aldrich Syndrome Using Designed Zinc Finger Endonucleases (2006)

Wiskott-Aldrich Syndrome (WAS) is a severe X-linked primary immunodeficiency resulting from mutations in a hematopoietic- specific and developmentally-regulated gene. WAS is a prime candidate for treatment by autologous hematopoietic stem cell (HSC) gene editing since this disorder is caused by a single gene defect and corrected cells should have a strong selective advantage in vivo, especially at the level of T lymphocyte precursors and perhaps even at the level of HSCs. Based on the efficient gene editing demonstrated by chimeric Zinc Finger Nucleases (ZFNs) at the IL2Rg locus (Urnov et al., 2005), ZFNs engineered to target exon 10 of the human WASP gene were similarly developed. These ZFNs were shown to efficiently bind and cleave the intended target sequences in vitro. In order to assess the efficiency of the WAS-ZFNs to bind their intended target site and mediate double strand DNA break formation in cells, we generated an integrated reporter system in HEK-293 cells. These cells contain a single integrated copy of a defective GFP reporter gene, disrupted by a portion of the WAS exon 10 sequence (GFP- WAS). We observed efficient repair ( 1%) of the GFP-WAS reporter by co-delivering the ZFN/donor constructs by lipofection. Examination of potential factors that influence the efficiency of gene correction revealed that delivery method and cell cycle status are key factors. Direct nuclear microinjection of the ZFNs/donor constructs into the GFP-WAS cells increased the repair rate by several fold (6%). We have subsequently delivered ZFNs/donors to normal human dermal fibroblasts (NHDFs) and primary hematopoietic CD34+ cells via microinjection. We are currently analyzing gene editing at the endogenous WAS locus in these cells. We have also developed an optimized reversible cell cycle synchronization procedure to allow for increased gene editing and improved cell expansion. Administration of either Vinblastine or Nocodazole (G2/M arrest agents) to the GFP-WAS cells significantly increased the gene correction efficiency (5-10 fold), but only Nocodazole treatment was fully reversible. We have also confirmed the reversible Nocodazole cell cycle synchronization in primary NHDFs. We now have available for these studies T (HTLV-I transformed) and B (EBV transformed) cell lines derived from a WAS patient. Experiments examining the efficiency of gene correction in these two patient lines are in progress. Authors B.R. Davis (Presenter), N.L. Prokopishyn, J. Rosenberg, M. DiCola, J. Brosius, R.M. Blaese, R.A. Metz have no financial affiliation with Sangamo BioSciences. Authors L. Zhang, J.C. Miller, K. Kim, F.D. Urnov, P.D. Gregory, M.C. Holmes are employees of Sangamo BioSciences, Inc.
Introduction to Microwave Measurements (2012)

The goal of this chapter is to provide the latest, state-of-the-art methods and techniques for acquiring the optimum measurements of the myriad of microwave components. It focuses on the practical microwave engineer facing modern, practical problems. Throughout the discussion of measurements a six-step procedure will be followed that applies to most measurement problems. When approaching a measurement these steps are: pretest, optimize, calibrate, measure, analyze and save data. The idealized analysis of many components is described in the chapter, but the descriptions are extended to some of the real-world detriments that cause these components' behavior to vary from the expected analytical response. Many of the relevant parameters used in microwave components are derived from the fundamental measurements of voltage and current on the ports. Power parameters, noise figure and noise parameters and distortion parameters are described have been under the assumption that the device under test (DUT) is linear. Controlled Vocabulary Terms distortion; microwave circuits; signal to noise ratio
CD uniformity improvement by active scanner corrections (2002)

As resolution shrinks, also the demands for litho CD Uniformity are becoming tighter. In replicating the mask pattern into photoresist, a sequence of modules within the patterning cluster (coat, expose, develop, etch) is responsible for CD non-uniformity. So far, the strategy has been to make the contribution of each of these modules as small as possible. The CD Uniformity can be improved in a more efficient way by compensating the various error sources with adapted dose profiles on the scanner. An inventory is made of the requirements for this compensation mechanism. In more detail a description is given how the scanner can apply these dose corrections. With experiments, the feasibility of the concept is proven. Improvements in CD Uniformity over 5nm are demonstrated, both on test structures as well as on real device layers.
SoSharP: Recommending Sharing Policies in Multiuser Privacy Scenarios (2017)

Users often share information about others; sometimes this inadvertently violates others' privacy. Thus, here the authors propose SoSharP, an agent-based approach to help users maintain their own and others' privacy by guiding a selection of sharing policies in multiuser scenarios. SoSharP learns incrementally and asks for users' input only when required, reducing users' effort.
Cover Feature: Reactions of a Polyhalide Ionic Liquid with Copper, Silver, and Gold (ChemistryOpen 1/2019) (2018)

The Cover Feature shows how coinage metals such as gold, silver, and copper are rapidly dissolved under mild and safe conditions by the ionic liquid 1-hexyl-3-methylimidiazolim dibromoiodide ([C6C1Im][Br2I]), forming metal(I)–dibromo anionic complexes together with molecular iodine, as proven by X-ray photoelectron spectroscopy, etching experiments, and gas-phase analysis. Trihalide ionic liquids are shown to be promising candidates for precious-metal etching and leaching media, and may also open new possibilities for Au(I) catalysis. More information can be found in the Full Paper by F. Maier and co-workers on page 15 in Issue 1, 2019 (DOI: 10.1002/open.201800149).
Clinical usefulness of transarterial chemoembolization response prior to liver transplantation as predictor of optimal timing for living donor liver transplantation (2018)

In selected patients who showed good response to pre-LT TACE, a shorter time interval between TACE and LDLT may be associated with higher recurrence free survival, cancer specific survival, and overall survival.
Isolation and Characterization of cDNA Clones Encoding Class I Chitinase in Suspension Cultures of Rice Cell (1994)

We have cloned and determined the nucleotide sequences of full-length cDNA clones for chitinase, CH6 and CH16, whose sizes were about 1.1 kb with signal peptides, from rice cell suspension cultures. Northern blot analysis with CH16 as a probe showed that the chitinase transcript reached maximum at 8 h after elicitor-treatment and their sizes were about 1.1 kb, demonstrating that these clones were induced by elicitor.
Retinoblastoma protein activation of interleukin 8 expression inhibits tumor cell survival in nude mice. (2000)

Loss of retinoblastoma protein (Rb) has been implicated in the formation of a variety of human malignancies. Restoration of Rb expression in the cell lines representing these tumors eliminates or significantly reduces tumorigenicity in nude mice, but the mechanism for this Rb effect is unknown. Results from this study indicated that Rb expression reduced tumor cell survival in nude mice by dramatically enhancing interleukin 8 (IL-8) secretion. IL-8 secreted by the Rb-transformed cells attracted neutrophils in vitro and tumor-infiltrating neutrophils in vivo, which is consistent with the Rb-mediated tumor regression being dependent on IL-8. The apparent, contradictory roles of IL-8 as a protumorigenic and antitumorigenic cytokine are discussed.
Boosting Self-Supervised Embeddings for Speech Enhancement (2022)

Self-supervised learning (SSL) representation for speech has achieved state-of-the-art (SOTA) performance on several downstream tasks. However, there remains room for improvement in speech enhancement (SE) tasks. In this study, we used a cross-domain feature to solve the problem that SSL embeddings may lack fine-grained information to regenerate speech signals. By integrating the SSL representation and spectrogram, the result can be significantly boosted. We further study the relationship between the noise robustness of SSL representation via clean-noisy distance (CN distance) and the layer importance for SE. Consequently, we found that SSL representations with lower noise robustness are more important. Furthermore, our experiments on the VCTK-DEMAND dataset demonstrated that fine-tuning an SSL representation with an SE model can outperform the SOTA SSL-based SE methods in PESQ, CSIG and COVL without invoking complicated network architectures. In later experiments, the CN distance in SSL embeddings was observed to increase after fine-tuning. These results verify our expectations and may help design SE-related SSL training in the future.
Immunization against Foot-and-Mouth Disease with Synthetic Peptides Representing the C-terminal Region of VP1 (1988)

Foot-and-mouth disease virus challenge experiments in guinea-pigs and immunoassays with a range of peptides equivalent to either or both of the sequences 141 to 158 and 200 to 213 of VP1 showed the most effective structure, in terms of protection, to be one in which both 'sites' were present with a minimum of additional amino acids. An 80 residue peptide comprising amino acids 134 to 213 was considerably less effective than 40 or 45 residue peptides. The major site for the induction of protection was deduced to be in the region 141 to 158. Thus, protection with the 40 or 45 residue peptide did not appear to be due to the presence of antibody directed solely to the 200 to 213 sequence. Finally, induction of antibody to the latter site appeared to be dependent on both the size of the peptide and the disposition of 'sites' within it.
Verschiedene nachhaltige Kohlenstoffnanopunkte für die freie radikalische Photopolymerisation, die Photo‐ATRP und die Photo‐CuACC Chemie (2021)

Abstract Kohlenstoffnanopunkte ( CD s), die aus unterschiedlicher Biomasse stammen, besitzen unterschiedliche Reaktivitäten hinsichtlich der Sensibilisierung der Photo‐ATRP‐ und der Photo‐CuAAC‐Reaktion bei Verwendung von sichtbarem Licht. Die radikalische Polymerisation von Tri(propylenglykol)diacrylat zeigte auch eine gute Effizienz bei Verwendung von CD s in Kombination mit einem Iodoniumsalz unter Einsatz von LEDs, die entweder bei 405 nm, 525 nm oder 660 nm emittieren. Photo‐ATRP‐Experimente bestätigten die kontrollierten Polymerisationsbedingungen unter Verwendung von Cu II im ppm‐Maßstab, was zu Dispersitäten zwischen 1.06 und 1.10 führte. Die selektive Reaktion der Kettenenden wurde erfolgreich durch Kettenverlängerung und Blockcopolymerisation nachgewiesen, wobei der lebende Charakter der Polymerisation unter Verwendung eines CD s bestätigt wurde, der aus Färberlack (“lac dye”) synthetisiert wurde und olefinische Einheiten in der ursprünglichen Biomasse enthielt. Eine Globalanalyse der zeitaufgelösten Fluoreszenzmessungen zeigte das Auftreten mehrerer emittierender Spezies, die zur Reaktivität der angeregten Zustände beitrugen. Unterschiedliche zytotoxische Antworten wurden von MCF‐10A‐Zellen in einem Durchflusszytometrie‐Assay nachgewiesen (400 μg mL −1 ). Somit war die Lebensfähigkeit der Zellen im Fall von CD‐2 – CD‐5 höher als 80 %, während die von CD‐1 bei etwa 70 % lag.
Synthesis and anticancer activities of 4-oxobenzopyrano[2,3-d]pyrimidines (1999)

Several 2-aryl-4-oxoxbenzopyrano[2,3-d]pyrimidines have previously been shown to exhibit in vivo antitumor activity in mice with P388 lymphocytic leukemia. In the present study, a series of novel substituted benzopyrano[2,3-d]pyrimidines have been prepared and tested for cytotoxic activity against a panel of cancer cell lines including the P388 lymphocytic leukemia cell line. The unsubstituted parent compound, some methoxylated derivatives and a cyclohexyl derivative all exhibited potent cytotoxic activity (IC50 values 0.3-0.64 microM). A number of derivatives, including the unsubstituted parent pyrimidine, were shown to cause a significant perturbation in cell cycle kinetics with an observed 2- to 3-fold increase in cells in the G2/M phase of the cell cycle. Furthermore, a polymethoxylated derivative, 2-(3,4,5-trimethoxyphenyl)-9-methoxy-4-oxo-2,3-dihydrobenzopyrano[ 2,3-d]pyrimidine 13, was shown to be selectively active against a number of human ovarian cell lines.
Neonatal hyperbilirubinemia and the role of unbound bilirubin (2021)

Total serum bilirubin is inadequate to optimize care of the term and preterm infant with hyperbilirubinemia. A rapid, accurate, and more effective indicator of bilirubin neurotoxicity is needed to manage jaundiced infants and for the universal screening of newborn infants. Future measurements of free bilirubin unattached to albumin will improve the management of neonatal hyperbilirubinemia.
Quasi-deterministic millimeter-wave channel models in MiWEBA (2016)

This article introduces a quasi-deterministic channel model and a link level-focused channel model, developed with a focus on millimeter-wave outdoor access channels. Channel measurements in an open square scenario at 60 GHz are introduced as a basis for the development of the model and its parameterization. The modeling approaches are explained, and their specific area of application is investigated.
Quantitative Evaluation for Computational Cost of CG-FMM on Typical Wiregrid Models (2010)

The conjugate gradient-fast multipole method (CG-FMM) is one of the powerful methods for analysis of large-scale electromagnetic problems. It is also known that CPU time and computer memory can be reduced by CG-FMM but such computational cost of CG-FMM depends on shape and electrical properties of an analysis model. In this paper, relation between the number of multipoles and number of segments in each group is derived from dimension of segment arrangement in four typical wiregrid models. Based on the relation and numerical results for these typical models, the CPU time per iteration and computer memory are quantitatively discussed. In addition, the number of iteration steps, which is related to condition number of impedance matrix and analysis model, is also considered from a physical point of view.
System identification of closed-loop cardiovascular control: effects of posture and autonomic blockade (1997)

We applied system identification to the analysis of fluctuations in heart rate (HR), arterial blood pressure (ABP), and instantaneous lung volume (ILV) to characterize quantitatively the physiological mechanisms responsible for the couplings between these variables. We characterized two autonomically mediated coupling mechanisms [the heart rate baroreflex (HR baroreflex) and respiratory sinus arrhythmia (ILV-HR)] and two mechanically mediated coupling mechanisms [the blood pressure wavelet generated with each cardiac contraction (circulatory mechanics) and the direct mechanical effects of respiration on blood pressure (ILV-->ABP)]. We evaluated the method in humans studied in the supine and standing postures under control conditions and under conditions of beta-sympathetic and parasympathetic pharmacological blockades. Combined beta-sympathetic and parasympathetic blockade abolished the autonomically mediated couplings while preserving the mechanically mediated coupling. Selective autonomic blockade and postural changes also altered the couplings in a manner consistent with known physiological mechanisms. System identification is an "inverse-modeling" technique that provides a means for creating a closed-loop model of cardiovascular regulation for an individual subject without altering the underlying physiological control mechanisms.