gebhart/patrepeval huggingface dataset:
Characteristic Structural Parameters for the γ‐Peptide 14‐Helix: Importance of Subunit Preorganization (2011)

Kristallographische Daten für einen Satz homologer Peptide, die aus Gabapentin und zwei bis sechs vororganisierten α-Aminosäureresten aufgebaut wurden (siehe Struktur des längsten Peptids), ermöglichen die Ableitung charakteristischer Parameter für die α-Peptid-14-Helix und liefern Richtlinien für die Charakterisierung einer 14-helicalen Faltung. Das Substitutionsmuster eines α-Rests dürfte starke Auswirkungen auf die Neigung zur 14-helicalen Faltung haben.
Enhanced composite adaptive IMC for boost pressure control of a turbocharged gasoline engine (2016)

Internal model control (IMC) offers an intuitive control structure and simple tuning philosophy, which makes it appealing to industrial applications. In our recent work [1], we proposed composite adaptive IMC (CAIMC) which simultaneously identified the model and the inverse in the IMC structure. It demonstrates good performance and auto-tuning capability in simulations and experiments. In this paper, an innovative approach is taken to express the IMC tracking error in terms of the modeling error and right-inverse modeling error, which analytically justifies the CAIMC design and its auto-tuning property. This new expression of the tracking error also suggests reformulation of the inverse model estimation problem, leading to enhanced CAIMC performance. The CAIMC from [1] and the enhanced CAIMC with the reformulated inverse are presented and compared, and applied to the boost-pressure control problem of a turbocharged gasoline engine. Results from simulations on a proprietary model and experiments on a vehicle with a turbocharged 2:0L engine are presented to demonstrate the advantages of the enhanced CAIMC.
High mTOR activity is a hallmark of reactive natural killer cells and amplifies early signaling through activating receptors (2017)

NK cell education is the process through which chronic engagement of inhibitory NK cell receptors by self MHC-I molecules preserves cellular responsiveness. The molecular mechanisms responsible for NK cell education remain unclear. Here, we show that mouse NK cell education is associated with a higher basal activity of the mTOR/Akt pathway, commensurate to the number of educating receptors. This higher activity was dependent on the SHP-1 phosphatase and essential for the improved responsiveness of reactive NK cells. Upon stimulation, the mTOR/Akt pathway amplified signaling through activating NK cell receptors by enhancing calcium flux and LFA-1 integrin activation. Pharmacological inhibition of mTOR resulted in a proportional decrease in NK cell reactivity. Reciprocally, acute cytokine stimulation restored reactivity of hyporesponsive NK cells through mTOR activation. These results demonstrate that mTOR acts as a molecular rheostat of NK cell reactivity controlled by educating receptors and uncover how cytokine stimulation overcomes NK cell education.
Modeling respiration from blood pressure waveform signals: an independent component approach (2003)

We describe a method for extracting the additive effect of respiration from arterial blood pressure and central venous pressure waveform signals. Our method estimates a finite impulse response (FIR) separating filter using an independent component approach, analogous to minimizing the coherence of the separated components. We compare the extracted respiration component with the impedance based respiration signal and with a respiration estimate extracted using an LMS-optimal bandpass filter of comparable order.
Planning with Submodular Objective Functions (2020)

We study planning with submodular objective functions, where instead of maximizing the cumulative reward, the goal is to maximize the objective value induced by a submodular function. Our framework subsumes standard planning and submodular maximization with cardinality constraints as special cases, and thus many practical applications can be naturally formulated within our framework. Based on the notion of multilinear extension, we propose a novel and theoretically principled algorithmic framework for planning with submodular objective functions, which recovers classical algorithms when applied to the two special cases mentioned above. Empirically, our approach significantly outperforms baseline algorithms on synthetic environments and navigation tasks.
Identification of a Sequence Element on the 3′ Side of AAUAAA Which Is Necessary for Simian Virus 40 Late mRNA 3′-End Processing (1985)

Our previous studies of the 3'-end processing of simian virus 40 late mRNAs indicated the existence of an essential element (or elements) downstream of the AAUAAA signal. We report here the use of transient expression analysis to study a functional element which we located within the sequence AGGUUUUUU, beginning 59 nucleotides downstream of the recognized signal AAUAAA. Deletion of this element resulted in (i) at least a 75% drop in 3'-end processing at the normal site and (ii) appearance of readthrough transcripts with alternate 3' ends. Some flexibility in the downstream position of this element relative to the AAUAAA was noted by deletion analysis. Using computer sequence comparison, we located homologous regions within downstream sequences of other genes, suggesting a generalized sequence element. In addition, specific complementarity is noted between the downstream element and U4 RNA. The possibility that this complementarity could participate in 3'-end site selection is discussed.
Adaptive Immunotherapy with Autologous CD25-Depleted and CD3/CD28-Costimulated T-Cells Enhances Lymphocyte Recovery after Cyclophosphamide - Fludarabine Chemotherapy in Patients with Low-Grade Follicular Lymphoma. (2006)

Abstract BACKGROUND: Fludarabine-based chemotherapy combinations are highly effective in patients (pts) with low-grade follicular lymphoma (FL), but cause severe and long-lasting immunosuppression due to depletion of normal CD4+ T-cells. Aside from increasing the risk of serious infections, this toxicity may limit the ability of the immune system to eliminate minimal residual disease. Adoptive immunotherapy using autologous CD25-depleted, CD3/CD28-costimulated T-cells (ACTC) expanded ex vivo may enhance immune reconstitution and improve disease control. METHODS: We initiated a phase I study in pts with purine analog-naive relapsed/refractory FL (grades 1 and 2). After leukapheresis, pts receive 4 cycles of fludarabine (25 mg/m2) days 1–3 and cyclophosphamide (250 mg/m2) days 1–3. Four weeks after the last cycle, responding patients (CR/CRu, PR) receive escalating doses of ACTC prepared ex vivo from autologous T-cellss collected prior to chemotherapy and depleted of regulatory CD4+/CD25+ cells, then expanded and activated using anti-CD3 and anti-CD28. RESULTS: Eleven pts have been enrolled to date. Median age is 49 y (range: 33–64y). Median number of prior therapies is 2 (range: 1 – 3). Two pts were withdrawn from the study due to hematologic toxicity related to chemotherapy, one patient was withdrawn for progressive disease during chemotherapy, and one patient has not yet completed chemotherapy. Of the 7 pts completing chemotherapy and proceeding to T-cell infusion, 5 pts achieved a CR/CRu and 2 pts achieved a PR; 5 pts received 1 – 5 x 109 CD3+ cells and 2 patients received 5 – 10 x 109 CD3+ cells. There have been no adverse events related to T-cell infusions. Median follow-up after ACTC infusion is 19 mos (range: 3 – 26 mos). CD4+ counts increased in all patients by 1 month after T-cell infusion, with a median increase of 3.2 fold (range: 1.5 – 70, p= .028)(see figure). For patients at dose level 1, the median increase was 2.2 fold (n=4; range: 1.5 – 3.3); at dose level 2 it was 37 fold (n=2; range: 3.8 – 70). CD8+ counts also increased, with a median increase of 8.1 (range: 1.0 – 30, p= .046)(see figure). All 7 pts receiving ACTC were anergic to candida antigen by delayed type hypersensitivity (DTH) skin testing before chemotherapy. Four pts developed a positive DTH response to candida antigen 60 days after ACTC infusion. For patients receiving ACTC, median follow-up is 24 mos (range: 7 – 31 mos) with a median progression-free survival of 18 months which is significantly longer than the time to progression from last therapy (p= .024). CONCLUSIONS: ACTC infusion results in significant CD4+ and CD8+ numerical and functional lymphocyte recovery after cyclophosphamide-fludarabine chemotherapy in pts with low-grade FL. This compares very favorably to historical controls treated with fludarabine-based regimens. T-cell dose escalation is ongoing. Figure Figure
ChemInform Abstract: The Zeolate Ligand; Zeolite Encapsulated Semiconductor Nanomaterials (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
CytoMatrix for a reliable and simple characterization of lung cancer stem cells from malignant pleural effusions (2019)

Cancer stem cells (CSCs) are a subpopulation with the properties of extensive self-renewal, capability to generate differentiated cancer cells and resistance to therapies. We have previously shown that malignant pleural effusions (MPEs) from patients with non-small-cell lung cancer (NSCLC) represent a valuable source of cancer cells that can be grown as three-dimensional (3D) spheroids enriched for stem-like features, which depend on the activation of the Yes-associated protein-transcriptional coactivator with PDZ-binding motif (YAP-TAZ)/Wnt-βcatenin/stearoyl-CoA desaturase 1 (SCD1) axis. Here, we describe a novel support, called CytoMatrix, for the characterization of limited amounts of cancer cells isolated from MPEs of patients with NSCLC. Our results show that this synthetic matrix allows an easy and fast characterization of several epithelial cellular markers. The use of CytoMatrix to study CSCs subpopulation confirms that SCD1 protein expression is enhanced in 3D spheroids when compared with 2D adherent cell cultures. YAP/TAZ nuclear-cytoplasmic distribution analysed by CytoMatrix in 3D spheroids is highly heterogeneous and faithfully reproduces what is observed in tumour biopsies. Our results confirm and extend the robustness of our workflow for the isolation and phenotypic characterization of primary cancer cells derived from the lung MPEs and underscore the role of SCD1.
ChemInform Abstract: Synthesis of N‐Allylhydroxamic Acids via (3,3)‐Sigmatropic Rearrangement (1994)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
HSP90 facilitates oncogenic alterations of metabolism in B-cell lymphomas (2020)

ABSTRACT HSP90 is critical for maintenance of the cellular proteostasis. In cancer cells, HSP90 also becomes a nucleating site for the stabilization of multiprotein complexes including signaling pathways and transcription complexes. Here, we described a novel role of HSP90 in the cytosolic compartmentalization of metabolic pathways in proliferating cancer cells. We found that HSP90 assists in the organization of metabolic enzymes into non-membrane-bound functional compartments termed metabosomes. Under experimental conditions that conserved the cellular proteostasis, we demonstrated that the compartmentalizing activity of HSP90 is critical to sustain the coordinated synthesis of multiple metabolites required for energy production, maintenance of the cellular biomass and secretion of immunometabolites. Conversely, inhibition of the nucleating capacity of HSP90 modified the topology of cytosolic metabosomes before protein degradation was apparent decreasing the efficiency of MYC-driven metabolic pathways. Inhibition of HSP90 decreases cancer metabolism in B-cell lymphoma cells and patients providing a novel mechanism of activity for this class of drugs.
371 How Do Case Type, Length of Stay, and Comorbidities Affect Medicare Diagnosis-Related Group Reimbursement for Minimally Invasive Surgery for Deformity? (2016)

INTRODUCTION: We investigated Medicare diagnosis-related group (DRG)-based reimbursement for minimally invasive surgery (MIS) deformity procedures in our study group hospitals based on length of stay and presence of comorbid conditions (CC). METHODS: DRG-based reimbursement was obtained for MIS anterior, posterior, and circumferential 1-level and multilevel fusion for listhesis and deformity cases with and without CC from 12 institutions throughout the United States. The 3 most common MIS procedures were analyzed to compare reimbursement based on DRG coding: (1) fusion via anterior or posterior only; (2) fusion anterior with fixation posterior percutaneous (no dorsal fusion); and (3) fusion combined anterior and posterior. RESULTS: The number of levels fused does not affect the reimbursement for all cases. Cases 1 and 2 without CC, 3-day stay reimbursed $41 404 vs 8-day reimbursed $42 808. Cases 1 and 2 with CCs, 3-day stay reimbursed $54 476 vs 8-day stay reimbursed $55 881. Case 3 without CC, 3-day stay reimbursed $47 992 vs 8-day stay reimbursed $49 397. Case 3 with CC, 3-day reimbursed $61 806 vs 8-day reimbursed $63 212. The increased payment for an 8-day stay was $1405 or $281 per day. If a deformity case 1 or 2 is coded incorrectly as a degenerative case the decrease in payment was $9769 lower (−24%) with no CC and $22 841 lower (−42%) with CC. CONCLUSION: Regardless the direct costs, Medicare DRG-based reimbursement was the same for single and multilevel MIS deformity cases. The use of posterior percutaneous fixation without dorsal fusion resulted in a 13% to 16% lower reimbursement compared with the addition of a posterior arthrodesis. Coding a deformity case as degenerative by the hospital resulted in 24% to 42% lower DRG-based reimbursement. In today's challenging environment it is important that physicians and hospitals better understand procedure and coding issues in order to be able to continue to offer complex spinal surgeries cost-effectively to our patients.
Distinct Effects of Ligand-Induced PDGFRα and PDGFRβ Signaling in the Human Rhabdomyosarcoma Tumor Cell and Stroma Cell Compartments (2013)

Platelet-derived growth factor receptors (PDGFR) α and β have been suggested as potential targets for treatment of rhabdomyosarcoma, the most common soft tissue sarcoma in children. This study identifies biologic activities linked to PDGF signaling in rhabdomyosarcoma models and human sample collections. Analysis of gene expression profiles of 101 primary human rhabdomyosarcomas revealed elevated PDGF-C and -D expression in all subtypes, with PDGF-D as the solely overexpressed PDGFRβ ligand. By immunohistochemistry, PDGF-CC, PDGF-DD, and PDGFRα were found in tumor cells, whereas PDGFRβ was primarily detected in vascular stroma. These results are concordant with the biologic processes and pathways identified by data mining. While PDGF-CC/PDGFRα signaling associated with genes involved in the reactivation of developmental programs, PDGF-DD/PDGFRβ signaling related to wound healing and leukocyte differentiation. Clinicopathologic correlations further identified associations between PDGFRβ in vascular stroma and the alveolar subtype and with presence of metastases. Functional validation of our findings was carried out in molecularly distinct model systems, where therapeutic targeting reduced tumor burden in a PDGFR-dependent manner with effects on cell proliferation, vessel density, and macrophage infiltration. The PDGFR-selective inhibitor CP-673,451 regulated cell proliferation through mechanisms involving reduced phosphorylation of GSK-3α and GSK-3β. Additional tissue culture studies showed a PDGFR-dependent regulation of rhabdosphere formation/cancer cell stemness, differentiation, senescence, and apoptosis. In summary, the study shows a clinically relevant distinction in PDGF signaling in human rhabdomyosarcoma and also suggests continued exploration of the influence of stromal PDGFRs on sarcoma progression.
MMSE-Based Throughput Control Algorithm for Generalized PF Scheduling (2012)

In this paper, we propose a minimum mean square error (MMSE)-based throughput control algorithm for generalized proportional fair (PF) scheduling. The algorithm determines mobile users' scheduling parameters so that the mean square error between expected throughputs and demanded throughputs is minimized. To do this, we simplify a function that predicts users' throughput, formulate a quadratically constrained quadratic problem, and find scheduling parameters that satisfy the first order necessary conditions of the problem.
Fully printed silicon field effect transistors (2009)

This letter demonstrates the use of a traditional screen printing approach for the fabrication of silicon field effect transistors. Using purely additive patterning technologies at room temperature conditions, with no additional postprocessing steps, transistors have been produced on paper substrates that have performance characteristics comparable to amorphous silicon thin film transistors. Insulated gate field effect transistors employing n type silicon in the semiconductor layer operate in accumulation mode with effective carrier mobilities in the range 0.3 to 0.7 cm2 (V s)−1.
Role of Gas6 receptors in platelet signaling during thrombus stabilization and implications for antithrombotic therapy (2005)

Mechanisms regulating thrombus stabilization remain largely unknown. Here, we report that loss of any 1 of the Gas6 receptors (Gas6-Rs), i.e., Tyro3, Axl, or Mer, or delivery of a soluble extracellular domain of Axl that traps Gas6 protects mice against life-threatening thrombosis. Loss of a Gas6-R does not prevent initial platelet aggregation but impairs subsequent stabilization of platelet aggregates, at least in part by reducing “outside-in” signaling and platelet granule secretion. Gas6, through its receptors, activates PI3K and Akt and stimulates tyrosine phosphorylation of the β(3) integrin, thereby amplifying outside-in signaling via α(IIb)β(3). Blocking the Gas6-R–α(IIb)β(3) integrin cross-talk might be a novel approach to the reduction of thrombosis.
Additions and Corrections - Cofacial Assembly of Partially Oxidized Metallomacrocycles as an Approach to Controlling Lattice Architecture in Low-Dimensional Molecular Solids. Synthesis and Properties of Cofacially Joined Silicon and Germanium Hemiporphyrazine Polymers (1985)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAdditions and Corrections - Cofacial Assembly of Partially Oxidized Metallomacrocycles as an Approach to Controlling Lattice Architecture in Low-Dimensional Molecular Solids. Synthesis and Properties of Cofacially Joined Silicon and Germanium Hemiporphyrazine PolymersCarl Dirk and Tobin MarksCite this: Inorg. Chem. 1985, 24, 18, 2870Publication Date (Print):August 1, 1985Publication History Published online22 September 2003Published inissue 1 August 1985https://pubs.acs.org/doi/10.1021/ic00212a600https://doi.org/10.1021/ic00212a600research-articleACS PublicationsRequest reuse permissionsArticle Views20Altmetric-Citations-LEARN 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
Effect of pulse parameters on visual nervous system (2001)

In a visual prosthesis, the visual nervous system of blind people are stimulated electrically in order to reconstruct their sense of sight. However electrical power supply to an internal device is limited. Therefore, it is very important to study efficient electrical stimulation. In our study, various pulse types were applied to the lateral geniculate nucleus (LGN) to record the neural responses from the visual cortex (V1) of cats. Experimental results revealed that the inversion of polarity of electric current pulse was effective in electrical stimulation to the LGN.
Active Immunoprophylaxis and Vaccine Augmentations Mediated by a Novel Plasmid DNA Formulation (2019)

Plasmid DNA (pDNA) gene delivery is a highly versatile technology that has the potential to address a multitude of unmet medical needs. Advances in pDNA delivery to host tissue with the employment of in vivo electroporation (EP) have led to significantly enhanced gene expression and the recent demonstration of clinical efficacy with the platform. Building upon this platform, this study reports that enzyme-mediated modification of the muscle tissue extracellular matrix structure at the site of pDNA delivery operates in a synergistic manner with EP to enhance both local and systemic gene expression further. Specifically, administration of chondroitinase ABC (Cho ABC) to the site of intramuscular delivery of pDNA led to transient disruption of chondroitin sulfate scaffolding barrier, permitting enhanced gene distribution and expression across the tissue. The employment of Cho ABC in combination with CELLECTRA<sup>®</sup> intramuscular EP resulted in increased gene expression by 5.5-fold in mice and 17.98-fold in rabbits. The study demonstrates how this protocol can be universally applied to an active prophylaxis platform to increase the in vivo production of functional immunoglobulin G, and to DNA vaccine protocols to permit drug dose sparing. The data indicate the Cho ABC formulation to be of significant value upon combination with EP to drive enhanced gene expression levels in pDNA delivery protocols.
Mesoscale convective systems as a source of electromagnetic signals registered by ground-based system and DEMETER (Detection of Electro-Magnetic Emissions Transmitted from Earthquake Regions) satellite (2021)

Abstract. Mesoscale convective systems (MCSs) are especially visible in the summertime when there is an advection of warm maritime air from the west. Advection of air masses is enriched by water vapour, the source of which can be found over the Mediterranean Sea. In propitious atmospheric conditions, and thus significant convection, atmospheric instability or strong vertical thermal gradient leads to the development of strong thunderstorm systems. In this paper, we discuss one case of MCSs, which generated a significant amount of +CG (cloud-to-ground), −CG and intracloud (IC) discharges. We have focused on the ELF (extremely low frequency; &lt; 1 kHz) electromagnetic field measurements, since they allow us to compute the charge moments of atmospheric discharges. Identification of the MCSs is a complex process, due to many variables which have to be taken into account. For our research, we took into consideration a few tools, such as cloud reflectivity, atmospheric soundings and data provided by PERUN (Polish system of the discharge localisation system), which operates in a very high frequency (VHF) range (113.5–114.5 MHz). Combining the above-described measurement systems and tools, we identified a MCS which occurred in Poland on 23 July 2009. Furthermore, it fulfilled our requirements since the thunderstorm crossed the path of the DEMETER (Detection of Electro-Magnetic Emissions Transmitted from Earthquake Regions) overpass.