gebhart/patrepeval huggingface dataset:
TARP vaccination is associated with slowing in PSA velocity and decreasing tumor growth rates in patients with Stage D0 prostate cancer (2016)

T-cell receptor alternate reading frame protein (TARP) is a 58-residue protein over-expressed in prostate and breast cancer. We investigated TARP peptide vaccination's impact on the rise in PSA (expressed as Slope Log(PSA) or PSA Doubling Time (PSADT)), validated tumor growth measures, and tumor growth rate in men with Stage D0 prostate cancer. HLA-A*0201 positive men were randomized to receive epitope-enhanced (29-37-9V) and wild-type (27-35) TARP peptides administered as a Montanide/GM-CSF peptide emulsion or as an autologous peptide-pulsed dendritic cell vaccine every 3 weeks for a total of five vaccinations with an optional 6th dose of vaccine at 36 weeks based on immune response or PSADT criteria with a booster dose of vaccine for all patients at 48 and 96 weeks. 41 patients enrolled with median on-study duration of 75 weeks at the time of this analysis. Seventy-two percent of patients reaching 24 weeks and 74% reaching 48 weeks had a decreased Slope Log(PSA) compared to their pre-vaccination baseline (p = 0.0012 and p = 0.0004 for comparison of overall changes in Slope Log(PSA), respectively). TARP vaccination also resulted in a 50% decrease in median tumor growth rate (g): pre-vaccine g = 0.0042/day, post-vaccine g = 0.0021/day (p = 0.003). 80% of subjects exhibited new vaccine-induced TARP-specific IFNγ ELISPOT responses but they did not correlate with decreases in Slope Log(PSA). Thus, vaccination with TARP peptides resulted in significant slowing in PSA velocity and reduction in tumor growth rate in a majority of patients with PSA biochemical recurrence.
Geometry-Aware Network for Non-Rigid Shape Prediction from a Single View (2018)

We propose a method for predicting the 3D shape of a deformable surface from a single view. By contrast with previous approaches, we do not need a pre-registered template of the surface, and our method is robust to the lack of texture and partial occlusions. At the core of our approach is a {\it geometry-aware} deep architecture that tackles the problem as usually done in analytic solutions: first perform 2D detection of the mesh and then estimate a 3D shape that is geometrically consistent with the image. We train this architecture in an end-to-end manner using a large dataset of synthetic renderings of shapes under different levels of deformation, material properties, textures and lighting conditions. We evaluate our approach on a test split of this dataset and available real benchmarks, consistently improving state-of-the-art solutions with a significantly lower computational time.
Modulating molecular aggregation by facile heteroatom substitution of diketopyrrolopyrrole based small molecules for efficient organic solar cells (2015)

The correlation between molecular structures and aggregations provides insight for designing conjugated small molecules for solar cells.
High‐Optical‐Quality Blends of Anionic Polymethine Salts and Polycarbonate with Enhanced Third‐Order Non‐linearities for Silicon‐Organic Hybrid Devices (2012)

A series of anionic polymethine dyes with different aromatic counterions are prepared to improve their compatibility as guests in an amorphous polycarbonate host. When they are used as the cladding material for silicon hybrid slot waveguides, four-wave mixing wavelength conversion and two-photon absorption-based optical-power modulation are observed. Such guest-host materials may be attractive candidates for all-optical signal-processing applications.
Root Ideotype Influences Nitrogen Transport and Assimilation in Maize (2018)

Maize (<i>Zea mays</i>, L.) yield is strongly influenced by external nitrogen inputs and their availability in the soil solution. Overuse of nitrogen-fertilizers can have detrimental ecological consequences through increased nitrogen pollution of water and the release of the potent greenhouse gas, nitrous oxide. To improve yield and overall nitrogen use efficiency (NUE), a deeper understanding of nitrogen uptake and utilization is required. This study examines the performance of two contrasting maize inbred lines, B73 and F44. F44 was selected in Florida on predominantly sandy acidic soils subject to nitrate leaching while B73 was selected in Iowa on rich mollisol soils. Transcriptional, enzymatic and nitrogen transport analytical tools were used to identify differences in their N absorption and utilization capabilities. Our results show that B73 and F44 differ significantly in their genetic, enzymatic, and biochemical root nitrogen transport and assimilatory pathways. The phenotypes show a strong genetic relationship linked to nitrogen form, where B73 showed a greater capacity for ammonium transport and assimilation whereas F44 preferred nitrate. The contrasting phenotypes are typified by differences in root system architecture (RSA) developed in the presence of both nitrate and ammonium. F44 crown roots were longer, had a higher surface area and volume with a greater lateral root number and density than B73. In contrast, B73 roots (primary, seminal, and crown) were more abundant but lacked the defining features of the F44 crown roots. An F1 hybrid between B73 and F44 mirrored the B73 nitrogen specificity and root architecture phenotypes, indicating complete dominance of the B73 inbred. This study highlights the important link between RSA and nitrogen management and why both variables need to be tested together when defining NUE improvements in any selection program.
Kallikrein Gene Delivery Inhibits Vascular Smooth Muscle Cell Growth and Neointima Formation in the Rat Artery After Balloon Angioplasty (1999)

Tissue kallikrein cleaves kininogen substrate to produce vasoactive kinin peptides that have been implicated in the proliferation of vascular smooth muscle cells (VSMCs). To explore potential roles of the kallikrein-kinin system in vascular biology, we evaluated the effects of adenovirus-mediated human kallikrein gene delivery on the growth of primary cultured VSMCs and in balloon-injured rat artery in vivo. Kallikrein gene transfer into cultured rat VSMCs resulted in time-dependent secretion of recombinant human tissue kallikrein and inhibition of cell proliferation. Balloon angioplasty reduced endogenous rat tissue kallikrein mRNA and protein levels at the injured site. In rats that received adenovirus-mediated human kallikrein gene delivery, we observed a 39% reduction in intima/media ratio at the injured vessel after delivery compared with that of rats that received control virus (n=8, P<0.01). Icatibant, a specific bradykinin B(2) receptor antagonist, blocked the protective effect and reversed the intima/media ratio to that of the control rats (n=5, P<0.01). After gene delivery, human kallikrein mRNA was identified at the injured vessel and a 3-fold increase occurred in kininogenase activity. cAMP and cGMP levels in balloon-injured aorta increased significantly at 4, 7, and 14 days after kallikrein gene delivery, but icatibant abolished the increase. These results provide new insights into the role of the vascular kallikrein-kinin system and have significant implications for gene therapy to treat restenosis or atherosclerosis.
Exome Sequencing of Cell-Free DNA from Metastatic Cancer Patients Identifies Clinically Actionable Mutations Distinct from Primary Disease (2015)

The identification of the molecular drivers of cancer by sequencing is the backbone of precision medicine and the basis of personalized therapy; however, biopsies of primary tumors provide only a snapshot of the evolution of the disease and may miss potential therapeutic targets, especially in the metastatic setting. A liquid biopsy, in the form of cell-free DNA (cfDNA) sequencing, has the potential to capture the inter- and intra-tumoral heterogeneity present in metastatic disease, and, through serial blood draws, track the evolution of the tumor genome. In order to determine the clinical utility of cfDNA sequencing we performed whole-exome sequencing on cfDNA and tumor DNA from two patients with metastatic disease; only minor modifications to our sequencing and analysis pipelines were required for sequencing and mutation calling of cfDNA. The first patient had metastatic sarcoma and 47 of 48 mutations present in the primary tumor were also found in the cell-free DNA. The second patient had metastatic breast cancer and sequencing identified an ESR1 mutation in the cfDNA and metastatic site, but not in the primary tumor. This likely explains tumor progression on Anastrozole. Significant heterogeneity between the primary and metastatic tumors, with cfDNA reflecting the metastases, suggested separation from the primary lesion early in tumor evolution. This is best illustrated by an activating PIK3CA mutation (H1047R) which was clonal in the primary tumor, but completely absent from either the metastasis or cfDNA. Here we show that cfDNA sequencing supplies clinically actionable information with minimal risks compared to metastatic biopsies. This study demonstrates the utility of whole-exome sequencing of cell-free DNA from patients with metastatic disease. cfDNA sequencing identified an ESR1 mutation, potentially explaining a patient's resistance to aromatase inhibition, and gave insight into how metastatic lesions differ from the primary tumor.
The crystal and molecular structure of 8,2'-cycloadenosine trihydrate (1979)

8,2'-Cycloadenosine, C IoHi~NsO4.3H20, is a modified
arabinosyladenosine nucleoside which has been cyclized
at the C(8) and 0(2') atoms. THe trihydrate
crystallizes in the orthorhombic space group P2~2~2~,
with a = 8.680 (2), b = 5.991 (2), c = 27.203 (4) A, Z
= 4. The structure was refined to R = 0.0672 for 1411
unique reflections, photographically recorded. The
arabinofuranose ring has a flattened C(4')-endo-C(3')-
exo pucker. The conformation about C(4')-C(5') is
gauche-gauche, and that about the sugar-base bond is
high anti. The crystal structure involves extensive
base-base hydrogen bonding, N(1), N(6) and N(7) all
being participants.
Transgenic expression of the dicotyledonous pattern recognition receptor EFR in rice leads to ligand-dependent activation of defense responses (2014)

Plant plasma membrane localized pattern recognition receptors (PRRs) detect extracellular pathogen-associated molecules. PRRs such as Arabidopsis EFR and rice XA21 are taxonomically restricted and are absent from most plant genomes. Here we show that rice plants expressing EFR or the chimeric receptor EFR::XA21, containing the EFR ectodomain and the XA21 intracellular domain, sense both Escherichia coli- and Xanthomonas oryzae pv. oryzae (Xoo)-derived elf18 peptides at sub-nanomolar concentrations. Treatment of EFR and EFR::XA21 rice leaf tissue with elf18 leads to MAP kinase activation, reactive oxygen production and defense gene expression. Although expression of EFR does not lead to robust enhanced resistance to fully virulent Xoo isolates, it does lead to quantitatively enhanced resistance to weakly virulent Xoo isolates. EFR interacts with OsSERK2 and the XA21 binding protein 24 (XB24), two key components of the rice XA21-mediated immune response. Rice-EFR plants silenced for OsSERK2, or overexpressing rice XB24 are compromised in elf18-induced reactive oxygen production and defense gene expression indicating that these proteins are also important for EFR-mediated signaling in transgenic rice. Taken together, our results demonstrate the potential feasibility of enhancing disease resistance in rice and possibly other monocotyledonous crop species by expression of dicotyledonous PRRs. Our results also suggest that Arabidopsis EFR utilizes at least a subset of the known endogenous rice XA21 signaling components.
Towards Virtualization of Software-Defined Networks: A Journey in Three Acts (2019)

Today's networks lack the support to satisfy the highly diverse and fast changing demands of emerging applications and services. The paradigms Network Virtualization (NV) and Software-Defined Networking (SDN) can potentially overcome this impasse. The virtualization of software-defined networks is expected to bring dynamic resource sharing with guaranteed performance through NV and programmability through SDN; for the first time, tenants can program their requested network resources according to their service demands in a timely manner. However, the virtualization of SDN-based networks introduces new challenges for operators, e.g., a virtualization layer that provides low and guaranteed control plane latencies for tenants. Moreover, tenants' expectations range from a fast, nearly-instantaneous provisioning of virtual networks to predictable operations of virtual networks. With this paper, we give a comprehensive overview of the thesis, which can be split into three parts - a journey in three acts. The thesis first presents a measurement procedure and a flexible virtualization layer design for the virtualization of software-defined networks. Focusing on the control plane, it introduces mathematical models for analyzing four virtualization layer architectures. Third, for a fast and efficient virtual network provisioning on the data plane, the thesis proposes optimization systems using Machine Learning and Neural Computation.
Measurement of the transverse momentum distribution of Drell–Yan lepton pairs in proton–proton collisions at $$\sqrt{s}=13\,$$TeV with the ATLAS detector (2020)

Abstract This paper describes precision measurements of the transverse momentum $$p_\mathrm {T}^{\ell \ell }$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>p</mml:mi><mml:mrow><mml:mi>T</mml:mi></mml:mrow><mml:mrow><mml:mi>ℓ</mml:mi><mml:mi>ℓ</mml:mi></mml:mrow></mml:msubsup></mml:math> ( $$\ell =e,\mu $$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mi>ℓ</mml:mi><mml:mo>=</mml:mo><mml:mi>e</mml:mi><mml:mo>,</mml:mo><mml:mi>μ</mml:mi></mml:mrow></mml:math> ) and of the angular variable $$\phi ^{*}_{\eta }$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>ϕ</mml:mi><mml:mi>η</mml:mi><mml:mrow><mml:mrow/><mml:mo>∗</mml:mo></mml:mrow></mml:msubsup></mml:math> distributions of Drell–Yan lepton pairs in a mass range of 66–116 GeV. The analysis uses data from 36.1 fb $$^{-1}$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msup><mml:mrow/><mml:mrow><mml:mo>-</mml:mo><mml:mn>1</mml:mn></mml:mrow></mml:msup></mml:math> of proton–proton collisions at a centre-of-mass energy of $$\sqrt{s}=13\,$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msqrt><mml:mi>s</mml:mi></mml:msqrt><mml:mo>=</mml:mo><mml:mn>13</mml:mn><mml:mspace/></mml:mrow></mml:math> TeV collected by the ATLAS experiment at the LHC in 2015 and 2016. Measurements in electron-pair and muon-pair final states are performed in the same fiducial volumes, corrected for detector effects, and combined. Compared to previous measurements in proton–proton collisions at $$\sqrt{s}=7$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:msqrt><mml:mi>s</mml:mi></mml:msqrt><mml:mo>=</mml:mo><mml:mn>7</mml:mn></mml:mrow></mml:math> and $$8\,$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mrow><mml:mn>8</mml:mn><mml:mspace/></mml:mrow></mml:math> TeV, these new measurements probe perturbative QCD at a higher centre-of-mass energy with a different composition of initial states. They reach a precision of 0.2 $$\%$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>%</mml:mo></mml:math> for the normalized spectra at low values of $$p_\mathrm {T}^{\ell \ell }$$ <mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:msubsup><mml:mi>p</mml:mi><mml:mrow><mml:mi>T</mml:mi></mml:mrow><mml:mrow><mml:mi>ℓ</mml:mi><mml:mi>ℓ</mml:mi></mml:mrow></mml:msubsup></mml:math> . The data are compared with different QCD predictions, where it is found that predictions based on resummation approaches can describe the full spectrum within uncertainties.
A 200μW Eddy Current Displacement Sensor with 6.7nmRMS Resolution (2020)

This paper describes a low-power eddy current displacement sensor intended for safety-critical touch applications. A sensing inductor is incorporated into a digital PLL to efficiently digitize the displacement of a flexible metal foil. At a stand-off distance of 500μm, the sensor achieves 6.7nm resolution in a 3kHz bandwidth over a 43μm range. It consumes 200μW from a 1.8V supply, which represents a 35× improvement on the state of the art.
TGF-β and basement membrane matrigel stimulate the chondrogenic phenotype in osteoblastic cells derived from fetal rat calvaria (1996)

Primary cultures of fetal rat calvarial cells contain a spectrum of osteogenic phenotypes including undifferentiated mesenchymal cells, osteoprogenitor cells, and osteoblasts. We recently demonstrated that rat calvarial osteoblast-like cells grown on basement membrane undergo profound morphological changes resembling a canalicular network in bone. In the present study, we examined the effect of reconstituted basement membrane Matrigel on chondroblastic versus osteoblastic differentiation of different cell subpopulations obtained by five consecutive enzymatic digestions of rat calvarial cell populations. We found that the appearance of canalicular cell processes decreased with the later digests. When cells from the fourth and fifth digest were grown on top of Matrigel for 7 days, the majority of the cell aggregates displayed chondrocytic characteristics but none of the cells became hypertrophic. When individual chondroblastic cell aggregates were subsequently transferred from Matrigel to plastic, they started expressing types I and X collagens, alkaline phosphatase, and osteocalcin. Within the next 7 days (days 8-14 of the experiment), the majority of cells increased in size, and at day 17 on plastic (day 24 of the experiment) mineralized bone nodules formed. The chondroblastic differentiation of calvarial cells grown on Matrigel could be inhibited by a specific transforming growth factor-beta 1 (TGF-beta 1) but not by a TGF-beta 2 antibody. Addition of recombinant TGF-beta 1 to similar cultures promoted the appearance of chondroblastic cell aggregates. The cartilage phenotype could not, on the contrary, be promoted by growing the cells on other extracellular matrices such as a collagen I gel. We suggest that TGF-beta 1 in concert with the basement membrane extracellular matrix induces chondroblastic differentiation of rat calvarial osteoprogenitor cells.
Synthesis and characterization of a homoleptic actinide alkyl. The heptamethylthorate(IV) ion: a complex with seven metal-carbon .sigma. bonds (1984)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthesis and characterization of a homoleptic actinide alkyl. The heptamethylthorate(IV) ion: a complex with seven metal-carbon .sigma. bondsHarald Lauke, Paul J. Swepston, and Tobin J. MarksCite this: J. Am. Chem. Soc. 1984, 106, 22, 6841–6843Publication Date (Print):October 1, 1984Publication History Published online1 May 2002Published inissue 1 October 1984https://pubs.acs.org/doi/10.1021/ja00334a062https://doi.org/10.1021/ja00334a062research-articleACS PublicationsRequest reuse permissionsArticle Views180Altmetric-Citations39LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information Get e-Alerts
Natural killer T cell immunotherapy combined with IL-15-expressing oncolytic virotherapy and PD-1 blockade mediates pancreatic tumor regression (2022)

TThese results demonstrate that NKT cell immunotherapy combined with oncolytic VSV-IL-15 virotherapy and PD-1 blockade enhances tumor control and presents a promising treatment strategy for targeting pancreatic cancer.
Physical and Chemical Characterization and Immunologic Properties ofSalmonella entericaSerovar Typhi Capsular Polysaccharide-Diphtheria Toxoid Conjugates (2009)

Typhoid fever remains a serious public health problem in developing countries, especially among young children. Recent studies showed more than 50% of typhoid cases are in children under 5 years old. Licensed vaccines, such as Salmonella enterica serovar Typhi capsular Vi, did not confer protection against typhoid fever for this age group. Vi conjugate, prepared by binding Vi to Pseudomonas aeruginosa recombinant exoprotein A (rEPA), induces protective levels of antibody at as young as 2 years old. Because of the lack of regulatory precedent for rEPA in licensing vaccines, we employed diphtheria toxoid (DT) as the carrier protein to accommodate accessibility in developing countries. Five lots of Vi-DT conjugates were prepared using adipic acid dihydrazide (ADH) as the linker. All 5 lots showed consistency in their physical and chemical characteristics and final yields. These Vi-DT conjugates elicited levels of IgG anti-Vi in young mice significantly higher than those in mice injected with Vi alone and induced a booster response upon reinjection. This booster effect was absent if the Vi replaced one of the two conjugate injections. Vi-DT was stable under repeated freeze-thaw (20 cycles). We plan to perform clinical evaluation of the safety and immunogenicity of Vi-DT when added to the infant combination vaccines.
K3 - A First Look at The New Direct Electron Detection Camera from Gatan Company (2018)

Much of the success of modern cryo-Electron microscopy is the result of advances in electron detector, specifically the advent of direct electron detectors Of particular utility has been the Gatan K2 camera that was the first camera to provide single electron detection at practical dose rates, resulting in dramatic improvements in DQE and reduction in noise. The K2 also introduced the concept of superresolution where the electrons can be registered to sub-pixel resolution. Despite the very high internal readout rate of the K2 camera (400 frames/sec), electron coincidence loss reduces DQE at doses above 3-5 e-/pixel/second, requiring prolonged exposures The high frame rate does not only increase the DQE, but also allows to correct for beam-induced sample motion by making an alignment of the individual frames before averaging [3],