gebhart/patrepeval huggingface dataset:
Human Papillomavirus 16 E6-specific CD45RA+ CCR7+ High Avidity CD8+ T Cells Fail to Control Tumor Growth Despite Interferon-γ Production in Patients With Cervical Cancer (2007)

We defined the nature of the cellular immune response in 5 women with human papillomavirus (HPV) 16+cervical carcinoma at a single time point when surgery was performed for treatment. To monitor the differences in T-cell recognition, 2 approaches of tetramer-guided technology were employed: (i) the in situ localization of major histocompatibility complex class I peptide complexes in the tumor lesions and (ii) the ex vivo sorting of HLA-A*0201-restricted and HPV16 E6-reactive T cells. CD8 T cells from the periphery (peripheral blood lymphocytes), the tumor (tumor-infiltrating lymphocytes), and T cells harvested from draining lymph nodes (T-LN) were analyzed. HPV16 E6 tetramer-sorted lymphocytes from the different anatomic sites recognized an HLA-A*0201-restricted E6 peptide irrespective of the type of antigen-presenting cells used for stimulation as determined by interferon-gamma production: autologous tumor cells, HLA-A*0201 surrogate antigen-presenting cells pulsed with the nominal peptide, and an HLA-A*0201-matched human dendritic cell line transgenic for HPV16 E6. Further analysis showed that the HPV16 E6-reactive CD8 T cells were of high avidity defined by blocking with an anti-CD8-alpha specific monoclonal antibody. We found that HPV16 E6-reactive T cells reside preferentially within the CD45RA+ CCR7+ T-cell subpopulation of tumor-infiltrating lymphocyte, peripheral blood lymphocyte, and T-LN in cervical cancer patients, suggesting that successful immune surveillance of HPV16+ tumor cells in cervical cancer patients is impaired. The CD45RA+/CCR7+ phenotype of HPV antigen-reactive T cells may serve as an indicator of dysfunctional T cells, despite effective interferon-gamma production in response to HPV antigens.
Osprey: Worldwide Sentinel Species for Assessing and Monitoring Environmental Contamination in Rivers, Lakes, Reservoirs, and Estuaries (2009)

Abstract In the United States, many fish and wildlife species have been used nationwide to monitor environmental contaminant exposure and effects, including carcasses of the bald eagle (Haliaeetus leucocephalus), the only top avian predator regularly used in the past. Unfortunately, bald eagles are sensitive to investigator intrusion at the nest. Thus, the osprey (Pandion haliaetus) is evaluated as a potential sentinel species for aquatic ecosystems. Several characteristics support the choice of the osprey as a sentinel species, including: (1) fish-eating diet atop the aquatic food web, (2) long-lived with strong nest fidelity, (3) adapts to human landscapes (potentially the most contaminated), (4) tolerates short-term nest disturbance, (5) nests spatially distributed at regular intervals, (6) highly visible nests easily located for study, (7) ability to accumulate most, if not all, lipophilic contaminants, (8) known sensitivity to many contaminants, and (9) nearly a worldwide distribution. These osprey traits have been instrumental in successfully using the species to understand population distribution, abundance, and changes over time; the effects of various contaminants on reproductive success; how contaminants in prey (fish on biomass basis) contribute to egg concentrations (i.e., biomagnification factors); and spatial residue patterns. Data summarized include nesting population surveys, detailed nesting studies, and chemical analyses of osprey egg, organ, blood, and feather samples for contaminants that bioaccumulate and/or biomagnify in aquatic food webs; and biochemical evaluations of blood and various organs. Studies in the United States, Canada, Mexico, Europe, and elsewhere have shown the osprey to be a useful sentinel species for monitoring selected environmental contaminants, including some emerging contaminants in lakes, reservoirs, rivers, and estuaries. Notes Henny, C. J., Kaiser, J. L., and Grove, R. A. 2008b. PCDDs, PCDFs, PCBs, OC insecticides and mercury in fish and osprey eggs from Willamette River, Oregon (1993, 2001 and 2006) with calculated biomagnification factors. Ecotoxicology.
Simple equivalent circuit for the nonlinear surface-wave convolver (1972)

A simple equivalent circuit for the centre-plate nonlinear acoustic-surface-wave convolver has been derived. This model has been tested experimentally and used to separate the magnitude of the nonlinear electromechanical coupling constant for the circuit response of the device.
Non-Metathesis Ruthenium-Catalyzed C−C Bond Formation (2001)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNon-Metathesis Ruthenium-Catalyzed C−C Bond FormationBarry M. Trost, F. Dean Toste, and Anthony B. PinkertonView Author Information Department of Chemistry, Stanford University, Stanford, California 94305 Cite this: Chem. Rev. 2001, 101, 7, 2067–2096Publication Date (Web):June 19, 2001Publication History Received29 December 2000Published online19 June 2001Published inissue 1 July 2001https://pubs.acs.org/doi/10.1021/cr000666bhttps://doi.org/10.1021/cr000666bresearch-articleACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views10929Altmetric-Citations736LEARN 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 SUBJECTS:Anions,Catalysts,Hydrocarbons,Inorganic carbon compounds,Ruthenium Get e-Alerts
Increasing atmospheric CO2 reduces metabolic and physiological differences between isoprene‐ and non‐isoprene‐emitting poplars (2013)

Isoprene, a volatile organic compound produced by some plant species, enhances abiotic stress tolerance under current atmospheric CO2 concentrations, but its biosynthesis is negatively correlated with CO2 concentrations. We hypothesized that losing the capacity to produce isoprene would require stronger up-regulation of other stress tolerance mechanisms at low CO2 than at higher CO2 concentrations. We compared metabolite profiles and physiological performance in poplars (Populus × canescens) with either wild-type or RNAi-suppressed isoprene emission capacity grown at pre-industrial low, current atmospheric, and future high CO2 concentrations (190, 390 and 590 ppm CO2 , respectively). Suppression of isoprene biosynthesis led to significant rearrangement of the leaf metabolome, increasing stress tolerance responses such as xanthophyll cycle pigment de-epoxidation and antioxidant levels, as well as altering lipid, carbon and nitrogen metabolism. Metabolic and physiological differences between isoprene-emitting and suppressed lines diminished as growth CO2 concentrations rose. The CO2 dependence of our results indicates that the effects of isoprene biosynthesis are strongest at pre-industrial CO2 concentrations. Rising CO2 may reduce the beneficial effects of biogenic isoprene emission, with implications for species competition. This has potential consequences for future climate warming, as isoprene emitted from vegetation has strong effects on global atmospheric chemistry.
Performance evaluation of the PennPET explorer with expanded axial coverage (2023)

<i>Objective.</i>This work evaluated the updated PennPET Explorer total-body (TB) PET scanner, which was extended to 6 rings with updated readout firmware to achieve a 142 cm axial field of view (AFOV) without 7.6 cm inter-ring axial gaps.<i>Approach.</i>National Electrical Manufacturers Association (NEMA) NU 2-2018 measurements were performed with modifications including longer phantoms for sensitivity and count-rate measurements and additional positions for spatial resolution and image quality. A long uniform phantom and the clinical trials network (CTN) phantom were also used.<i>Main results.</i>The total sensitivity increased to 140 kcps MBq<sup>-1</sup>for a 70 cm line, a gain of 1.8x compared to the same system with axial gaps; an additional 47% increase in total counts was observed with a 142 cm line at the same activity per cm. The noise equivalent count rate (NECR) increased by 1.8x without axial gaps. The peak NECR is 1550 kcps at 25 kBq cc<sup>-1</sup>for a 140 cm phantom; due to increased randoms, the NECR is lower than with a 70 cm phantom, for which NECR is 2156 kcps cc<sup>-1</sup>at 25 kBq cc<sup>-1</sup>and continues increasing. The time-of-flight resolution is 250 ps, increasing by <10 ps at the highest activity. The axial spatial resolution degrades by 0.6 mm near the center of the AFOV, compared to 4 mm resolution near the end. The NEMA image quality phantom showed consistent contrast recovery throughout the AFOV. A long uniform phantom demonstrated axial uniformity of uptake and noise, and the CTN phantom demonstrated quantitative accuracy for both<sup>18</sup>F and<sup>89</sup>Zr.<i>Significance</i>. The performance evaluation of the updated PennPET Explorer demonstrates significant gains compared to conventional scanners and shows where the current NEMA standard needs to be updated for TB-PET systems. The comparisons of systems with and without inter-ring gaps demonstrate the performance trade-offs of a more cost-effective TB-PET system with incomplete detector coverage.
A Case Study on the Usage of the Value Blueprint for Ecosystem Design (2015)

Ecosystems are an important aspect of today’s software business. Different companies aim to create an ecosystem around their products so that they can benefit from this. Unfortunately, creating such ecosystems is not an easy task. One of the few tools that can be used to facilitate this process is Adner’s Value Blueprint. This tool allows a company to identify the different types of risks that it faces during the establishment of an ecosystem. Adner presents several examples of blueprints he has built and provides some guidelines to create new ones. Given the potential of the approach in addressing some of the issues faced by ecosystem designers, we decided to assess the usage of the Value Blueprint through a case study using data from the Apple Watch ecosystem. We report our results from the Apple ecosystem, and more importantly, our evaluation of the value blueprint tool. We conclude by providing recommendations for practitioners interested in establishing their own ecosystems and researchers interested in the design of ecosystems.
Estradiol acts via the estrogen receptor in the sexual differentiation of the rat brain, but what does this complex do? (1993)

Journal Article Estradiol acts via the estrogen receptor in the sexual differentiation of the rat brain, but what does this complex do? Get access R A Gorski R A Gorski Search for other works by this author on: Oxford Academic Google Scholar Endocrinology, Volume 133, Issue 2, 1 August 1993, Pages 431–432, https://doi.org/10.1210/endo.133.2.8344187 Published: 01 August 1993
Meta-analysis of 16S rRNA Microbial Data Identified Distinctive and Predictive Microbiota Dysbiosis in Colorectal Carcinoma Adjacent Tissue (2020)

As research focusing on the colorectal cancer fecal microbiome using shotgun sequencing continues, increasing evidence has supported correlations between colorectal carcinomas (CRCs) and fecal microbiome dysbiosis. However, large-scale on-site and off-site (surrounding adjacent) tissue microbiome characterization of CRC was underrepresented. Here, considering each taxon as a feature, we demonstrate a machine learning-based method to investigate tissue microbial differences among CRC, colorectal adenoma (CRA), and healthy control groups using 16S rRNA data sets retrieved from 15 studies. A total of 2,099 samples were included and analyzed in case-control comparisons. Multiple methods, including differential abundance analysis, random forest classification, cooccurrence network analysis, and Dirichlet multinomial mixture analysis, were conducted to investigate the microbial signatures. We showed that the dysbiosis of the off-site tissue of colonic cancer was distinctive and predictive. The AUCs (areas under the curve) were 80.7%, 96.0%, and 95.8% for CRC versus healthy control random forest models using stool, tissue, and adjacent tissue samples and 69.9%, 91.5%, and 89.5% for the corresponding CRA models, respectively. We also found that the microbiota ecologies of the surrounding adjacent tissues of CRC and CRA were similar to their on-site counterparts according to network analysis. Furthermore, based on the enterotyping of tissue samples, the cohort-specific microbial signature might be the crux in addressing classification generalization problems. Despite cohort heterogeneity, the dysbiosis of lesion-adjacent tissues might provide us with further perspectives in demonstrating the role of the microbiota in colorectal cancer tumorigenesis.<b>IMPORTANCE</b> Turbulent fecal and tissue microbiome dysbiosis of colorectal carcinoma and adenoma has been identified, and some taxa have been proven to be carcinogenic. However, the microbiomes of surrounding adjacent tissues of colonic cancerous tissues were seldom investigated uniformly on a large scale. Here, we characterize the microbiome signatures and dysbiosis of various colonic cancer sample groups. We found a high correlation between colorectal carcinoma adjacent tissue microbiomes and their on-site counterparts. We also discovered that the microbiome dysbiosis in adjacent tissues could discriminate colorectal carcinomas from healthy controls effectively. These results extend our knowledge on the microbial profile of colorectal cancer tissues and highlight microbiota dysbiosis in the surrounding tissues. They also suggest that microbial feature variations of cancerous lesion-adjacent tissues might help to reveal the microbial etiology of colonic cancer and could ultimately be applied for diagnostic and screening purposes.
Non-contact Vital Signs Monitoring through Visible Light Sensing (2018)

This paper presents a non-contact vital signs (respiration and heartbeat) monitoring system that utilizes visible light sensing (VLS) technology. We have for the first time demonstrated the ability to wirelessly (non-contact) sense vital signs using only reflected incoherent light signals from a human subject. The VLS-based system is implemented by using simple visible light source, photodetector and data acquisition/processing unit, and is used with the developed signal processing algorithms to turn slight variations in reflected light power into accurate measurements of respiration and heart rate. To assess the accuracy of our method, the results were compared with reliable measurements using a contact-based monitoring device (ground truth). More than 94% of accuracy was observed in test results including both breathing and heartbeat rates in different scenarios as compared to the state-of-the-art baseline methods such as contact-based vitals monitoring devices. These competitive results have demonstrated that VLS-based vitals monitoring innovation is indeed a viable, powerful, attractive, low-cost and safe method. This study represents a substantive departure from the traditional ways of doing non-contact vitals monitoring methods (e.g., radio-frequency-based radars and imaging-based cameras) and is poised to make big contributions to this area. Since vital signs monitoring is a ubiquitous element of medicine, this work would also impact the entire health care community, from patients in their homes, to doctor's offices, to large medical institutions and industries. This technology has potential to address numerous conditions and situations in which vital signs are critical indicators such as sleep apnea and human-computer-interaction applications.
Competing interactions in dispersions of superparamagnetic nanoparticles (2001)

We study the magnetic properties of dispersions of uniformly sized, chemically synthesized cobalt nanoparticles (NP's), observing a crossover from a blocked state to a superparamagnetic one with increasing temperature. By analyzing magnetization data, we determine the distributions of NP volumes and anisotropies, and establish that variations in the shapes of the magnetic cores of the NP's generate the anisotropy governing the crossover. We characterize the frustrated low-temperature state produced by the competition between dipolar interactions and anisotropy at sufficiently high NP density through remanent magnetization measurements, and explain the results through analysis of a simple model.
The role of sub-peatland critical zone structure on the hydrology of northern peatlands (2023)

The hydrology of northern peatlands is increasingly recognized to be influenced by groundwater flow between peat and underlying mineral sediments. These hydrologic fluxes have been measured in peatlands of central and northern Maine where peatlands formed in depressions within the complex landscape left after the last glacial ice retreat. Although most of these peatlands formed on top of a low permeability confining glaciomarine clay, surface digital elevation maps and subsurface geophysical datasets (ground penetrating radar, electromagnetic and resistivity imaging) indicate that, in places, they are often in hydrogeological contact with eskers (glacial outwash deposits) and possibly even directly in contact with bedrock. Hydrogeological datasets, including direct hydraulic head observations and indirect observations of seepage fluxes, support the case that these points of hydrogeological contact exert a profound influence on the surface hydrology, including pool formation, and ecology of these peatland systems. The unique properties of peat, including the formation of pipe structures, result in highly focused discharges of mineralized water as evidenced from temperature sensing and aqueous geochemistry data (specific conductance, dissolved iron, dissolved manganese). These pipe networks may exert a control on carbon cycling in peatlands via the delivery of nutrients, or possibly by serving as conduits for the release of free phase gas stored in the deep peat. Preliminary observations using gas traps lend support to this hypothesis.
Bioenergetic Impairment in Congenital Muscular Dystrophy Type 1A and Leigh Syndrome Muscle Cells (2017)

Abstract Skeletal muscle has high energy requirement and alterations in metabolism are associated with pathological conditions causing muscle wasting and impaired regeneration. Congenital muscular dystrophy type 1A (MDC1A) is a severe muscle disorder caused by mutations in the LAMA2 gene. Leigh syndrome (LS) is a neurometabolic disease caused by mutations in genes related to mitochondrial function. Skeletal muscle is severely affected in both diseases and a common feature is muscle weakness that leads to hypotonia and respiratory problems. Here, we have investigated the bioenergetic profile in myogenic cells from MDC1A and LS patients. We found dysregulated expression of genes related to energy production, apoptosis and proteasome in myoblasts and myotubes. Moreover, impaired mitochondrial function and a compensatory upregulation of glycolysis were observed when monitored in real-time. Also, alterations in cell cycle populations in myoblasts and enhanced caspase-3 activity in myotubes were observed. Thus, we have for the first time demonstrated an impairment of the bioenergetic status in human MDC1A and LS muscle cells, which could contribute to cell cycle disturbance and increased apoptosis. Our findings suggest that skeletal muscle metabolism might be a promising pharmacological target in order to improve muscle function, energy efficiency and tissue maintenance of MDC1A and LS patients.
Microarray Platform for Profiling Enzyme Activities in Complex Proteomes [J. Am. Chem. Soc. 2004, 126, 15640−15641]. (2005)

ADVERTISEMENT RETURN TO ISSUEPREVAddition/CorrectionNEXTORIGINAL ARTICLEThis notice is a correctionMicroarray Platform for Profiling Enzyme Activities in Complex Proteomes [J. Am. Chem. Soc. 2004, 126, 15640−15641].Stephan A. Sieber, Tony S. Mondala, Steven R. Head, and Benjamin F. CravattCite this: J. Am. Chem. Soc. 2005, 127, 11, 4114Publication Date (Web):February 26, 2005Publication History Published online26 February 2005Published inissue 1 March 2005https://pubs.acs.org/doi/10.1021/ja0506915https://doi.org/10.1021/ja0506915correctionACS PublicationsCopyright © 2005 American Chemical Society. This publication is available under these Terms of Use. Request reuse permissions This publication is free to access through this site. Learn MoreArticle Views388Altmetric-Citations1LEARN 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 PDF (16 KB) Get e-Alertsclose Get e-Alerts
Positive Emotions Preferentially Engage an Auditory–Motor “Mirror” System (2006)

Social interaction relies on the ability to react to communication signals. Although cortical sensory-motor "mirror" networks are thought to play a key role in visual aspects of primate communication, evidence for a similar generic role for auditory-motor interaction in primate nonverbal communication is lacking. We demonstrate that a network of human premotor cortical regions activated during facial movement is also involved in auditory processing of affective nonverbal vocalizations. Within this auditory-motor mirror network, distinct functional subsystems respond preferentially to emotional valence and arousal properties of heard vocalizations. Positive emotional valence enhanced activation in a left posterior inferior frontal region involved in representation of prototypic actions, whereas increasing arousal enhanced activation in presupplementary motor area cortex involved in higher-order motor control. Our findings demonstrate that listening to nonverbal vocalizations can automatically engage preparation of responsive orofacial gestures, an effect that is greatest for positive-valence and high-arousal emotions. The automatic engagement of responsive orofacial gestures by emotional vocalizations suggests that auditory-motor interactions provide a fundamental mechanism for mirroring the emotional states of others during primate social behavior. Motor facilitation by positive vocal emotions suggests a basic neural mechanism for establishing cohesive bonds within primate social groups.