gebhart/patrepeval huggingface dataset:
Evaluation Of Myeloablative Therapy Followed By Autologous Stem Cell Transplantation In First Remission In Patients With Advanced Stage Follicular Lymphoma After Initial Immuno-Chemotherapy (R-CHOP) Or Chemotherapy Alone: Analysis Of 940 Patients Treated In Prospective Randomized Trials Of The German Low Grade Lymphoma Study Group (GLSG) (2013)

Abstract Background The anti-CD20 antibody rituximab has dramatically changed the treatment paradigms for advanced stage follicular lymphoma (FL) and has improved overall survival. The question whether myeloablative treatment followed by autologous stem cell transplantation (ASCT) in first remission may add further benefit in the era of initial rituximab-chemotherapy induction remains currently unsolved. Methods We report on the long-term outcome of 940 patients, randomized for treatment with ASCT versus IFN-alpha maintenance in first remission after initial therapy with MCP, CHOP or R-CHOP in two consecutive randomized trials for patients with advanced stage FL of the GLSG . Results A total of 472 patients, (38 with initial MCP therapy, 199 with initial CHOP therapy and 224 with initial R-CHOP therapy, 13 not documented), were randomized to receive ASCT. The remaining 468 patients were randomized for IFN-maintenance (39 with MCP, 201 with CHOP and 219 with R-CHOP, 7 not documented). The patient characteristics, the initial therapy and the quality of remission were well balanced between ASCT and IFN-maintenance. After a median follow up of 8.3 years 454 pts randomized for IFN-maintenance and 445 pts randomized for ASCT were evaluable for treatment failure. The estimated failure free survival at 10 years was 32% (95% CI 0.26-0.37) for IFN-alpha maintenance and 51% (95% CI 0.45-0.57) for ASCT. For patients assigned to CHOP or MCP (no rituximab during induction) the estimated failure free survival after 10 years was 18% for IFN-maintenance and 45% for ASCT (hazard ratio 0.49, 95% CI 0.39-0.61). Among the 423 evaluable patients assigned to R-CHOP the estimated failure free survival at 10 years was 53% for IFN-maintenance and 58% for ASCT (hazard ratio 0.77, 95% CI 0.56-1.07). Conclusions After a median follow up of more than 6 years in 423 patients assigned to R-CHOP, only a small improvement in time to treatment failure could be observed for ASCT compared to IFN-alpha maintenance. This is in strong contrast to patients treated with chemotherapy only (figure 1). The promising results for ASCT observed in the pre-rituximab era cannot be confirmed after initial immuno-chemotherapy. Since the use of ASCT is hampered by relevant toxic side effects, the actual data suggest that ASCT for patients with follicular lymphomas in first line therapy is of questionable benefit. Disclosures: Hiddemann: Roche: Honoraria, Membership on an entity’s Board of Directors or advisory committees, Research Funding. Dreyling:Roche: Honoraria, Research Funding. Hoster:Roche: Honoraria, Travel Support Other. Unterhalt:Roche: Travel Support Other.
Citrullinome of Porphyromonas gingivalis Outer Membrane Vesicles: Confident Identification of Citrullinated Peptides (2019)

<i>Porphyromonas gingivalis</i> is a key pathogen in chronic periodontitis and has recently been mechanistically linked to the development of rheumatoid arthritis via the activity of peptidyl arginine deiminase generating citrullinated epitopes in the periodontium. In this project the outer membrane vesicles (OMV) from <i>P. gingivalis</i> W83 wild-type (WT), a W83 knock-out mutant of peptidyl arginine deiminase (ΔPPAD), and a mutant strain expressing PPAD with the active site cysteine mutated to alanine (C351A), have been analyzed using a two-dimensional HFBA-based separation system combined with LC-MS. For optimal and positive identification and validation of citrullinated peptides and proteins, high resolution mass spectrometers and strict MS search criteria were utilized. This may have compromised the total number of identified citrullinations but increased the confidence of the validation. A new two-dimensional separation system proved to increase the strength of validation, and along with the use of an in-house build program, <i>Citrullia,</i> we establish a fast and easy semi-automatic (manual) validation of citrullinated peptides. For the WT OMV we identified 78 citrullinated proteins having a total of 161 citrullination sites. Notably, in keeping with the mechanism of OMV formation, the majority (51 out of 78) of citrullinated proteins were predicted to be exported via the inner membrane and to reside in the periplasm or being translocated to the bacterial surface. Citrullinated surface proteins may contribute to the pathogenesis of rheumatoid arthritis. For the C351A-OMV a single citrullination site was found and no citrullinations were identified for the ΔPPAD-OMV, thus validating the unbiased character of our method of citrullinated peptide identification.
CoIL: Coordinate-Based Internal Learning for Tomographic Imaging (2021)

We propose Coordinate-based Internal Learning (CoIL) as a new deep-learning (DL) methodology for continuous representation of measurements. Unlike traditional DL methods that learn a mapping from the measurements to the desired image, CoIL trains a multilayer perceptron (MLP) to encode the complete measurement field by mapping the coordinates of the measurements to their responses. CoIL is a self-supervised method that requires no training examples besides the measurements of the test object itself. Once the MLP is trained, CoIL generates new measurements that can be used within most image reconstruction methods. We validate CoIL on sparse-view computed tomography using several widely-used reconstruction methods, including purely model-based methods and those based on DL. Our results demonstrate the ability of CoIL to consistently improve the performance of all the considered methods by providing high-fidelity measurement fields.
Identification and in silico analysis of the origin recognition complex in the human fungal pathogen Candida albicans (2018)

Abstract DNA replication in eukaryotes is initiated by the orchestrated assembly and association of initiator proteins (heterohexameric Origin Recognition Complex, ORC) on the replication origins. These functionally conserved proteins play significant roles in diverse cellular processes besides their central role in ignition of DNA replication at origins. While Candida albicans , a major human fungal pathogen, is an ascomycetous, asexual, diploid budding yeast but it is significantly diverged from a much better studied model organism Saccharomyces cerevisiae . The components of the DNA replication machinery in C. albicans remain largely uncharacterized. Identification of factors required for DNA replication is essential for understanding the evolution of the DNA replication machinery. We identified the putative ORC homologs in C. albicans and determined their relatedness with those of other eukaryotes including several yeast species. Our extensive in silico studies demonstrate that the domain architecture of CaORC proteins share similarities with the ORC proteins of S. cerevisiae . We dissect the domain organization of ORC (trans-acting factors) proteins that seem to associate with DNA replication origins in C. albicans . We present a model of the 3D structure of CaORC4 to gain further insights of this protein’s function.
Microwave spectra of noble gas-pyridine dimers: argon-pyridine and krypton-pyridine (1989)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTMicrowave spectra of noble gas-pyridine dimers: argon-pyridine and krypton-pyridineT. D. Klots, T. Emilsson, R. S. Ruoff, and H. S. GutowskyCite this: J. Phys. Chem. 1989, 93, 4, 1255–1261Publication Date (Print):February 1, 1989Publication History Published online1 May 2002Published inissue 1 February 1989https://pubs.acs.org/doi/10.1021/j100341a017https://doi.org/10.1021/j100341a017research-articleACS PublicationsRequest reuse permissionsArticle Views221Altmetric-Citations89LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access options Get e-Alerts
Infrared Conformational Study of Poly(ethylene glycol)-Bound Homooligoglycines in the Solid State and in Solution (1980)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTInfrared Conformational Study of Poly(ethylene glycol)-Bound Homooligoglycines in the Solid State and in SolutionClaudio Toniolo, Gian M. Bonora, V. N. Rajasekharan Pillai, and Manfred MutterCite this: Macromolecules 1980, 13, 3, 772–774Publication Date (Print):May 1, 1980Publication History Published online1 May 2002Published inissue 1 May 1980https://pubs.acs.org/doi/10.1021/ma60075a051https://doi.org/10.1021/ma60075a051research-articleACS PublicationsRequest reuse permissionsArticle Views54Altmetric-Citations6LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Jigs and Lures: Associating Web Queries with Strongly-Typed Entities (2011)

The aim of this work was to evaluate the capability of lactoferrin- and antitransferrin-modified long circulating liposomes to deliver the hydrophilic peptide senktide, a selective NK3 receptor agonist unable to cross the blood brain barrier, to central nervous system by using an indirect method based on in vivo microdialysis studies to estimate the responsiveness of nucleus accumbens shell dopamine to senktide. To this purpose, senktide was encapsulated in different targeted and not-targeted stealth liposomes prepared using film hydration method. Formulations were characterized in terms of morphology, size distribution, zeta potential, encapsulation efficiency, and antibody presence on the liposome surface. In vivo microdialysis studies were performed injecting intravenously the senktide-loaded liposomes and comparing obtained dopamine levels with those found with the free senktide given intracerebroventricularly. Results showed that all vesicles were spherical, small in size (around 120 nm), homogeneously dispersed, and slightly negatively charged. TEM analysis, using an anti IgG secondary antibody with 10nm gold nanoparticles at its distal end, demonstrated the successful linkage of the antibody on the liposomal surface. Intravenously administered in rats, senktide-loaded targeted stealth liposomes elicited a significant increase of dialysate dopamine in the nucleus accumbens shell, which was comparable to that of the free senktide given intracerebroventricularly when antitransferrin-targeted liposomes were tested. On the contrary, control stealth liposomes did not affect dopamine levels. Senktide brain levels were higher using the antitransferrin-targeted liposomes in comparison with the lactoferrin ones, while the opposite was obtained in the liver tissue where the highest senktide accumulation was always found.
Improved Lower Bounds for Coded Caching (2017)

Caching is often used in content delivery networks as a mechanism for reducing network traffic. Recently, the technique of coded caching was introduced whereby coding in the caches and coded transmission signals from the central server were considered. Prior results in this area demonstrate that carefully designing the placement of content in the caches and designing appropriate coded delivery signals from the server allow for a system where the delivery rates can be significantly smaller than conventional schemes. However, matching upper and lower bounds on the transmission rate have not yet been obtained. In this paper, we derive tighter lower bounds on the coded caching rate than were known previously. We demonstrate that this problem can equivalently be posed as a combinatorial problem of optimally labeling the leaves of a directed tree. Our proposed labeling algorithm allows for significantly improved lower bounds on the coded caching rate. Furthermore, we study certain structural properties of our algorithm that allow us to analytically quantify improvements on the rate lower bound for general values of the problem parameters. This allows us to obtain a multiplicative gap of at most four between the achievable rate and our lower bound.
New, Halogen-Free Ionic Liquids — Synthesis, Properties and Applications (2002)

Typical ionic liquids consist of halogen containing anions such as [AlCl4]−, [PF6]−, [BF4]−, [CF3SO3]− or [(CF3SO2)2N]−. However for many technical applications the presence of halogen atoms in the ionic liquid's anion may cause serious concerns if the hydrolysis stability of the anion is poor (e. g. for chloroaluminate and hexafluorophosphate systems) or if a thermal treatment of the spent ionic liquid is desired. In both cases additional effort is needed to avoid the liberation of toxic and highly corrosive HF or HCl into the environment. In our contribution, we present synthesis, properties and application of several new alkylsulfate and arylsulfonate ionic liquids. The described systems are characterized by their easy synthesis from technically available raw materials. Some candidates combine low melting points with high hydrolysis stability and acceptable viscosity.
Chip Level Adaptive Equalization for Satellite High Speed Downlink Packet Access (S-HSDPA) (2007)

S-HSDPA is a concept that modifies terrestrial HSDPA in order to increase the throughput for S-UMTS and SDMB systems. In this paper, we consider S-HSDPA transmitted signals from GEO satellites via the IMR channel to the UE. The IMR channel is a highly dispersive multipath fading channel, and for this reason, the orthogonality between spreading signatures is lost, resulting in a reduction of average achievable throughput. In order to improve the performance, we investigate the performance of a linear chip level equalizer introduced at the receiver side. The results presented here highlight the advantage of the low complexity CPICH NLMS equalizer in comparison to a conventional RAKE receiver. The CPICH NLMS equalizer successfully increases the throughput of the SHSDPA by retaining the signal orthogonality with a relatively small increase in computational complexity.
Two-surface plasticity Model and Its Application to Spring-back Simulation of Automotive Advanced High Strength Steel Sheets (2011)

A two‐surface isotropic‐kinematic hardening law was developed based on a two‐surface plasticity model previously proposed by Lee et al., (2007, Int. J. Plast. 23, 1189–1212). In order to properly represent the Bauschinger and transient behaviors as well as permanent softening during reverse loading with various pre‐strains, both the inner yield surface and the outer bounding surface expand (isotropic hardening) and translate (kinematic hardening) in this two‐surface model. As for the permanent softening, both the isotropic hardening and the kinematic hardening evolution of the outer bounding surface were modified by introducing softening parameters. The numerical formulation was also developed based on the incremental plasticity theory and the developed constitutive law was implemented into the commercial finite element program, ABAQUS/Explicit and ABAQUS/Standard using the user‐defined material subroutines. In this work, a dual phase (DP) steel was considered as an advanced high strength steel sheet and uni‐axial tension tests and uni‐axial tension‐compression‐tension tests were performed for the characterization of the material property. For a validation purpose, the developed two‐surface plasticity model was applied to the 2‐D draw bending test proposed as a benchmark problem of the NUMISHEET 2011 conference and successfully validated with experiments.
Factors Affecting the Longevity and Strength in an In Vitro Model of the Bone–Ligament Interface (2010)

The interfaces between musculoskeletal tissues with contrasting moduli are morphologically and biochemically adapted to allow the transmission of force with minimal injury. Current methods of tissue engineering ligaments and tendons do not include the interface and this may limit the future clinical success of engineered musculoskeletal tissues. This study aimed to use solid brushite cement anchors to engineer intact ligaments from bone-to-bone, creating a functional musculoskeletal interface in vitro. We show here that modifying anchor shape and cement composition can alter both the longevity and the strength of an in vitro model of the bone-ligament interface: with values reaching 23 days and 21.6 kPa, respectively. These results validate the use of brushite bone cement to engineer the bone-ligament interface in vitro and raise the potential for future use in ligament replacement surgery.
Genomic analyses for age at menarche identify 389 independent signals and indicate BMI-independent effects of puberty timing on cancer susceptibility (2016)

Abstract The timing of puberty is a highly polygenic childhood trait that is epidemiologically associated with various adult diseases. Here, we analyse 1000-Genome reference panel imputed genotype data on up to ~370,000 women and identify 389 independent signals (all P&lt;5×10 −8 ) for age at menarche, a notable milestone in female pubertal development. In Icelandic data from deCODE, these signals explain ~7.4% of the population variance in age at menarche, corresponding to one quarter of the estimated heritability. We implicate over 250 genes via coding variation or associated gene expression, and demonstrate enrichment across genes active in neural tissues. We identify multiple rare variants near the imprinted genes MKRN3 and DLK1 that exhibit large effects on menarche only when paternally inherited. Disproportionate effects of variants on early or late puberty timing are observed: single variant and heritability estimates are larger for early than late puberty timing in females. The opposite pattern is seen in males, with larger estimates for late than early puberty timing. Mendelian randomization analyses indicate causal inverse associations, independent of BMI, between puberty timing and risks for breast and endometrial cancers in women, and prostate cancer in men. In aggregate, our findings reveal new complexity in the genetic regulation of puberty timing and support new causal links with adult cancer risks.
Optimal Sensor Placement for Source Localization: A Unified ADMM Approach (2022)

Source localization plays a key role in many applications including radar, wireless and underwater communications. Among various localization methods, the most popular ones are Time-Of-Arrival (TOA), Time-Difference-Of-Arrival (TDOA), Angle-Of-Arrival (AOA) and Received Signal Strength (RSS) based. Since the Cram&#x00E9;r-Rao lower bounds (CRLB) of these methods depend on the sensor geometry explicitly, sensor placement becomes a crucial issue in source localization applications. In this paper, we consider finding the optimal sensor placements for the TOA, TDOA, AOA and RSS based localization scenarios. We first unify the three localization models by a generalized problem formulation based on the CRLB-related metric. Then a <i>u</i>nified op<i>t</i>imization fra<i>m</i>ework for <i>o</i>ptimal <i>s</i>ensor placemen<i>t</i> (UTMOST) is developed through the combination of the alternating direction method of multipliers (ADMM) and majorization-minimization (MM) techniques. Unlike the majority of the state-of-the-art works, the proposed UTMOST neither approximates the design criterion nor considers only uncorrelated noise in the measurements. It can readily adapt to to different design criteria (i.e. A, D and E-optimality) with slight modifications within the framework and yield the optimal sensor placements correspondingly. Extensive numerical experiments are performed to exhibit the efficacy and flexibility of the proposed framework.
Direct Characterization of Enzyme–Substrate Complexes by Using Electrosonic Spray Ionization Mass Spectrometry (2004)

Der bessere Weg: Die Elektroschall-Spray-Ionisierung ist bei der Desolvatisierung effizienter als die Elektrospray-Ionisierung und liefert bei der Ionisierung nichtkovalenter Komplexe großer Biomoleküle normalerweise einfach geladene Ionen. Die binären und ternären Komplexe von Imidazol-3-glycerinphosphat-Synthase (IGPS) mit ihren Inhibitoren scheinen die native Lösungskonformation beim Übergang in die Gasphase beizubehalten (siehe Bild).
Common genetic variation at the IL1RL1 locus regulates IL-33/ST2 signaling (2013)

The suppression of tumorigenicity 2/IL-33 (ST2/IL-33) pathway has been implicated in several immune and inflammatory diseases. ST2 is produced as 2 isoforms. The membrane-bound isoform (ST2L) induces an immune response when bound to its ligand, IL-33. The other isoform is a soluble protein (sST2) that is thought to be a decoy receptor for IL-33 signaling. Elevated sST2 levels in serum are associated with an increased risk for cardiovascular disease. We investigated the determinants of sST2 plasma concentrations in 2,991 Framingham Offspring Cohort participants. While clinical and environmental factors explained some variation in sST2 levels, much of the variation in sST2 production was driven by genetic factors. In a genome-wide association study (GWAS), multiple SNPs within IL1RL1 (the gene encoding ST2) demonstrated associations with sST2 concentrations. Five missense variants of IL1RL1 correlated with higher sST2 levels in the GWAS and mapped to the intracellular domain of ST2, which is absent in sST2. In a cell culture model, IL1RL1 missense variants increased sST2 expression by inducing IL-33 expression and enhancing IL-33 responsiveness (via ST2L). Our data suggest that genetic variation in IL1RL1 can result in increased levels of sST2 and alter immune and inflammatory signaling through the ST2/IL-33 pathway.
Exposure of the Gestating Mother to Sympathetic Stress Modifies the Cardiovascular Function of the Progeny in Male Rats (2023)

These data suggest permanent changes to the heart's adrenergic response after rat progeny were stressed in the uterus.