gebhart/patrepeval huggingface dataset:
Colon-specific antigen-p (CSAp). II: Further characterization in colorectal and pancreatic cancer (1982)

The physicochemical and immunological characteristics of colon-specific antigen-p (CSAp) in plasma and in colorectal and pancreatic tumors were investigated. CSAp in the plasma of a rectal cancer patient and in a colonic carcinoma xenografted in hamsters (GW-39 tumor) appeared to have similar chromatographic properties, being of a molecular size of 4 million or more. The activities of CSAp in both plasma and tumor were similarly destroyed by treatment with a thiol reagent. Finally, identical immunological reactions in radioimmunoassay and gel diffusion tests were obtained between the CSAp's in patient plasma and in GW-39 tumor tissue. Also CSAp in human pancreatic cancers xenografted in nude mice showed a precipitin line of complete identity with CSAp extracted from GW-39 human colonic carcinoma transplants. Thus, the CSAp's found in colorectal cancer patient plasma, in colonic carcinoma, and in pancreatic cancer tissues appear to be immunologically identical.
Development of vitellogenin measurement in the freshwater amphipod Gammarus fossarum: first step to propose a relevant biomarker for reproductive impact assessment of endocrine disruptors (2010)

Vitellogenin induction in aquatic male vertebrates has been used extensively as biomarker of exposure to endocrine disruptors exposure. Kidd and collaborator's works (2007) have recently shown that induction of this marker may caused long term population impact. Whereas this approach is well developed in vertebrates, few investigations were lead on aquatic invertebrates species although they represent about 95% of living species and play important roles in ecosystems. Moreover, because of evolutive distances in terms of molecular sequences and functional divergence between endocrine systems, invertebrates cannot be regarded as simple surrogates for vertebrates when considering biomarker responses related to toxic effect, and biomarkers or biomarkers-like should be re-confirmed and re-validated both for their molecular identification and for the interpretation in terms of biological function they could track. \nThis study was the first step for the development of endocrine disruptor biomarker in order to propose a tool for reproductive impact assessment in crustacean. For this, a analytical methodology using mass spectrometry has been proposed to detect and quantify vtg protein in this species. In female, the functionality of this protein has been checked by assessing the level of this protein during the vitellogenesis processes and after an exposure to methyl farnesoate. In the second step and to propose a methodology in males for biomonitoring studies, we investigated the impact of biotic (size, gametogenesis status) and abiotic (physico-chemical characteristics of water) factors to understand the natural variability of this marker. Effects of a suspected endocrine disruptor on the Vtg level in gammarid male and its impact on the spermatogenesis will be presented.
Classical Analysis of Degenerate Optomechanical Parametric Oscillators (2014)

Recent advances in the miniaturization of whispering gallery mode optical parametric oscillators have open the possibility of studying the interplay between parametric down-conversion and optomechanics, two of the most fundamental nonlinear optical processes. Even though a rigorous analysis of this scenario requires a fully quantum mechanical treatment where, e.g., the squeezing of the down-converted field or the cooling of the mechanical degree of freedom can be studied, having a clear idea of the classical properties of the system is useful or even necessary before starting such quantum mechanical analysis, and this is precisely what we offer in this work. We will restrict to the case of degenerate parametric down-conversion, obtaining then what we call a degenerate optomechanical parametric oscillator.
Roadmap and Challenges on the Next Generation of Thermal Interface Material for High Warpage Heterogonies Package (2022)

With the constant increases of power density in silicon year after year, there is a constant strive to provide better thermal management innovation to improve thermal design solutions for the high-power density. The Thermal Interface Material (TIM) is a first-order solution for thermal management of high-power density silicon. This TIM plays a crucial role in defining the solution, both thermally and mechanically. This study addresses the challenges of the next generation of thermal Interface material for high warpage heterogonies package. There is no question that Thermal Interface Materials (TIMs) materials have been helpful in coupling the IC packages thermally and mechanically to the thermal management solution and have addressed the issue of thermal contact optimally by displacing the air that is present between the irregular surfaces of the silicon and the heat spreader at the micro-level thereby decreasing the thermal contact resistance It also bridges the CTE (coefficient of thermal expansion) gap between two dissimilar materials. This work points out challenges that the TIM material has to overcome to maintain its thermal performance without degradation over time which depends on its intrinsic characteristics defined by the elongation, adhesion, thermal conductivity, and bond line thickness (BLT). As the power density and the sizes of the packages increase when these are surface mounted on the board, they exhibit warpage during its operation. The die side of the package can be warped by 10% to 30% in the operating range of 50°C to 100°C as compared to the warpage of standalone silicon die at 20°C, which was observed by analyzing a baseline FCBGA package using Digital Image Correlation (DIC) approach. This warpage also created the need for the higher BLT of the TIM to cover the entire die surface, and this will also induce high stresses and may also cause TIM delamination during the lifetime of the device. Hence there is a surface interaction between the die and the TIM that occurs due to the thermal and mechanical behavior of the package, which dictates the device lifetime and performance degradation. This study is given the roadmap of the first level of system-level interaction with the next generation of packages. Also, it reports the new finding on the impact of warpage and adhesion on the thermal interface resistance.
In-situ Lorentz Imaging of Room-Temperature Ferromagnetic Domains in Monolayer Vanadium-Doped WS2 (2022)

Journal Article In-situ Lorentz Imaging of Room-Temperature Ferromagnetic Domains in Monolayer Vanadium-Doped WS2 Get access Ariana Ray, Ariana Ray Cornell University, School of Applied and Engineering Physics, Ithaca, NY, USA Search for other works by this author on: Oxford Academic Google Scholar Mingzu Liu, Mingzu Liu Pennsylvania State University, Department of Physics, University Park, PA, USA Search for other works by this author on: Oxford Academic Google Scholar Boyang Zheng, Boyang Zheng Pennsylvania State University, Department of Physics, University Park, PA, USA Search for other works by this author on: Oxford Academic Google Scholar Da Zhou, Da Zhou Pennsylvania State University, Department of Physics, University Park, PA, USA Search for other works by this author on: Oxford Academic Google Scholar Vincent H Crespi, Vincent H Crespi Pennsylvania State University, Department of Physics, University Park, PA, USA Search for other works by this author on: Oxford Academic Google Scholar Mauricio Terrones, Mauricio Terrones Pennsylvania State University, Department of Physics, University Park, PA, USA Search for other works by this author on: Oxford Academic Google Scholar David A Muller David A Muller Cornell University, School of Applied and Engineering Physics, Ithaca, NY, USA Corresponding author: david.a.muller@cornell.edu Search for other works by this author on: Oxford Academic Google Scholar Microscopy and Microanalysis, Volume 28, Issue S1, 1 August 2022, Pages 1780–1782, https://doi.org/10.1017/S1431927622007048 Published: 01 August 2022
Development and Morphologic Aspects of the Cardiac Conduction System in Normal Hearts and Congenital Heart Defects (2021)

There is an inherent beauty to the cardiac conduction system. Its journey to creation is a remarkably complex process beginning in the second week of embryological development. By birth, there is a mature network of conduction tissue responsible for initiating and maintaining the cardiac heartbeat. Abnormalities in cardiogenesis, which result in congenital heart defects, produce various conduction system anomalies. Cardiologists, electrophysiologists, and surgeons must have an in-depth knowledge of the cardiac conduction system in normal and congenital hearts. In the following chapter, we provide insight into this complexity as we discuss the embryological origins and morphological aspects of the conduction system in both normal hearts and those with congenital heart defects.
Kilogram‐Scale Asymmetric Ruthenium‐Catalyzed Hydrogenation of a Tetrasubstituted Fluoroenamide (2011)

Abstract Ruthenium‐catalyzed asymmetric homogeneous hydrogenation (AHH) is used as the key step of a multi‐kilogram scale synthesis of an enantiomeric fluoropiperidine. The AHH of a tetrasubstituted β‐fluoroenamide is carried out under mild conditions using a Ru/Josiphos catalyst with high ee (98%).
RETRACTED: Cell–cell signaling in Xanthomonas campestris involves an HD-GYP domain protein that functions in cyclic di-GMP turnover (2006)

HD-GYP is a protein domain of unknown biochemical function implicated in bacterial signaling and regulation. In the plant pathogen Xanthomonas campestris pv. campestris, the synthesis of virulence factors and dispersal of biofilms are positively controlled by a two-component signal transduction system comprising the HD-GYP domain regulatory protein RpfG and cognate sensor RpfC and by cell-cell signaling mediated by the diffusible signal molecule DSF (diffusible signal factor). The RpfG/RpfC two-component system has been implicated in DSF perception and signal transduction. Here we show that the role of RpfG is to degrade the unusual nucleotide cyclic di-GMP, an activity associated with the HD-GYP domain. Mutation of the conserved H and D residues of the isolated HD-GYP domain resulted in loss of both the enzymatic activity against cyclic di-GMP and the regulatory activity in virulence factor synthesis. Two other protein domains, GGDEF and EAL, are already implicated in the synthesis and degradation respectively of cyclic di-GMP. As with GGDEF and EAL domains, the HD-GYP domain is widely distributed in free-living bacteria and occurs in plant and animal pathogens, as well as beneficial symbionts and organisms associated with a range of environmental niches. Identification of the role of the HD-GYP domain thus increases our understanding of a signaling network whose importance to the lifestyle of diverse bacteria is now emerging.
Antenna terms and measurement techniques for active receiving arrays (2017)

The radio astronomical antenna engineering community has developed figures of merit and a measurement technique based on noise characterization for active array receivers. The figures of merit are included in the recent revision of IEEE Standard 145, and the measurement technique is proposed for inclusion as a test procedure in an upcoming update of Std. 149.
Towards an interdisciplinary methodology for service-oriented system engineering (2009)

Service concept is evolving as a broad idea recurrently discussed in recent years as it originates from many disciplines such as marketing, operations and computer science. Despite this interdisciplinary nature of service concept, existing methodologies for building service-oriented systems provide limited support to include a complete coverage of various engineering phases for a unified development and are therefore not directly applicable to service-oriented architectures. In particular, the design of coordination mechanisms between service providers and customers as well as the design of a common vocabulary in an inter-organizational setting is not adequately addressed. To face these shortcomings, in this position paper, we present an interdisciplinary approach integrating recently proposed methodologies into one coherent engineering methodology. The methodology aims to build a system that extends the basic find-bind-execute paradigm of Web services on an electronic market platform.
Targeted Sudan Black nanobubbles as photoacoustic contrast agents for breast cancer imaging (Conference Presentation) (2019)

Nanobubbles are a new class of ultrasound contrast agents. Unlike conventional microbubbles, their sub-micron (~200nm) diameter allows them to extravasate outside the vasculature and accumulate in the tumor interstitium. In this study, nanobubbles with shells loaded with Sudan Black (BNB) and DiD fluorescent dye were synthesized. These nanobubbles can be used to simultaneously enhance ultrasound and photoacoustic signals for in vivo breast tumor imaging. The nanobubbles consisted of lipid shells with a C3F8 gas core and were formed via self-assembly driven by mechanical agitation and size isolation via centrifugation. Herceptin antibody was conjugated to the BNB for targeting HER2-positive cells via standard EDC/NHS coupling chemistry. Human breast cancer cell lines (BT474 as HER2-positive and MDA-MB-231 as HER2-negative) were inoculated in the flanks of BALB/c-B17-Scid mice. Ultrasound and photoacoustic imaging (VevoLAZR, 21MHz, 720nm) were performed pre-injection and post-injection of the Herceptin conjugated BNB. The impact of Herceptin targeting was assessed by computing the PA frequency spectra and the non-linear contrast US images of the tumor regions. Photoacoustic images of the HER2-positive tumor showed an average of 6 dB increase in contrast signal 2 mins post-injection, while the HER2-negative MDA tumors showed a negligible change in image contrast, suggesting increased uptake of Herceptin labelled BNBs. The enhanced contrast is also confirmed by the non-linear contrast signals between positive and negative tumors. The photoacoustic technique can potentially be used to examine the kinetics of BNB extravasation. This work shows the potential of BNBs as multi-modal contrast agents capable of specialized tumor imaging in vivo.
The trend of disruption in the functional brain network topology of Alzheimer’s disease (2022)

Alzheimer's disease (AD) is a progressive disorder associated with cognitive dysfunction that alters the brain's functional connectivity. Assessing these alterations has become a topic of increasing interest. However, a few studies have examined different stages of AD from a complex network perspective that cover different topological scales. This study used resting state fMRI data to analyze the trend of functional connectivity alterations from a cognitively normal (CN) state through early and late mild cognitive impairment (EMCI and LMCI) and to Alzheimer's disease. The analyses had been done at the local (hubs and activated links and areas), meso (clustering, assortativity, and rich-club), and global (small-world, small-worldness, and efficiency) topological scales. The results showed that the trends of changes in the topological architecture of the functional brain network were not entirely proportional to the AD progression. There were network characteristics that have changed non-linearly regarding the disease progression, especially at the earliest stage of the disease, i.e., EMCI. Further, it has been indicated that the diseased groups engaged somatomotor, frontoparietal, and default mode modules compared to the CN group. The diseased groups also shifted the functional network towards more random architecture. In the end, the methods introduced in this paper enable us to gain an extensive understanding of the pathological changes of the AD process.
Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations (2009)

The 82 base-pair deletion found in the rph-pyrE operon of many endpoints may function to relieve a pyrimidine biosynthesis defect present in MG1655. In contrast, a variety of regulators acquire mutations in the different endpoints, suggesting flexibility in overcoming regulatory challenges in the adaptation.
The XPRESS Challenge: Xray Projectomic Reconstruction -- Extracting Segmentation with Skeletons (2023)

The wiring and connectivity of neurons form a structural basis for the function of the nervous system. Advances in volume electron microscopy (EM) and image segmentation have enabled mapping of circuit diagrams (connectomics) within local regions of the mouse brain. However, applying volume EM over the whole brain is not currently feasible due to technological challenges. As a result, comprehensive maps of long-range connections between brain regions are lacking. Recently, we demonstrated that X-ray holographic nanotomography (XNH) can provide high-resolution images of brain tissue at a much larger scale than EM. In particular, XNH is wellsuited to resolve large, myelinated axon tracts (white matter) that make up the bulk of long-range connections (projections) and are critical for inter-region communication. Thus, XNH provides an imaging solution for brain-wide projectomics. However, because XNH data is typically collected at lower resolutions and larger fields-of-view than EM, accurate segmentation of XNH images remains an important challenge that we present here. In this task, we provide volumetric XNH images of cortical white matter axons from the mouse brain along with ground truth annotations for axon trajectories. Manual voxel-wise annotation of ground truth is a time-consuming bottleneck for training segmentation networks. On the other hand, skeleton-based ground truth is much faster to annotate, and sufficient to determine connectivity. Therefore, we encourage participants to develop methods to leverage skeleton-based training. To this end, we provide two types of ground-truth annotations: a small volume of voxel-wise annotations and a larger volume with skeleton-based annotations. Entries will be evaluated on how accurately the submitted segmentations agree with the ground-truth skeleton annotations.
Residual analysis of the water resonance signal in breast lesions imaged with high spectral and spatial resolution (HiSS) MRI: A pilot study (2014)

These promising AUC values suggest that analysis of the water-resonance in each HiSS image voxel using "residual analysis" could have high diagnostic utility and could be used to enhance current CADx methods and allow detection of breast cancer without the need to inject contrast agents.
Comparative study of dielectric spectroscopy measurements and anayses of oil and paper samples from a transformer undergoing repair (2005)

New methods, based on characterisation of dielectric response measurements, for assessing moisture content of pressboard and paper are gaining ground. However, there is a need for calibrating results with results from other techniques. This communication presents results from a study of a 19.5/6.8/6.8 kV - 40 MVA power transformer, which was opened on-site during maintenance work, thus allowing for collecting paper samples. Dielectric spectroscopy measurements were conducted before and after its opening. Results were compared with measurements on oil and paper samples. These showed that the moisture levels in the interior of the solid insulation were unchanged. Further, it was found that FDS measurements gave more accurate estimates of moisture levels than estimates based on oil analyses and equilibrium curves.
mce1 operon disruption is associated with changes in the lipid profile of M. tuberculosis (2006)

Disrupting the mce1 operon in M. tuberculosis causes a hypervirulent phenotype and a reduced ability to stimulate Th1 type immunity in mice, suggesting that the mce1 operon is associated with persistence of the bacterium. Upon investigation of lipid extracts from wild-type (wt), mutant, and complemented strains (comp), it was observed that lipids were present on the cell surface of the mutant that were not observed in the wt or comp strains (Figure 1). The accumulating lipids were characterized as the free mycolic acids by high performance mass spectrometry. The genes encoded in mce1, include one fatty acid CoA ligase, three predicted integral membrane proteins, as well as 9 proteins likely to be associated with the cytoplasmic membrane. Six proteins within the operon have homology to the MKL family of ABC transporters. Current investigations are aimed at determining if a defect in lipid transport is causing the accumulation of the lipids on the cell surface. Further investigations are underway to determine the role of the free mycolic acids during infection. MDL and JAL thank the NIH (GM47356) for funding. SC and LWR thank Ellison Medical Foundation (Senior Global ID award) for funding Total lipid extracts from M.tuberculosis: Wild-type, k/o and complemented strains. All spectra are scaled to the peak denoted with a ‘*’.
A generalized transducing thiophage (TPC-1) of a facultative sulfur chemolithotrophic bacterium,Bosea thiooxidansCT5, of Î±-Proteobacteria, isolated from Indian soil (2003)

We have isolated and characterized a double-stranded DNA bacteriophage (TPC-1) of Bosea thiooxidans, a facultative sulfur chemolithotrophic bacterium. The name 'thiophage' is introduced for phage(s) infecting sulfur chemolithotrophic bacteria. Electron micrographs showed the phage particle with an icosahedral head and a very short wedge-like tail. TPC-1 is classified as the C1 morphotype of the Podoviridae family. Restriction map and terminal ends detection by end fill labeling of the TPC-1 genomic DNA showed that the genome is linear with 5' protruding cohesive termini. Contour length mapping of the DNA genome also revealed it to be a linear fragment with size ( approximately 44 kb) corresponding with the size estimated from restriction fragment analyses and proved the non-redundant nature of the linear genome topology. In colorless sulfur chemolithotrophic microorganisms, TPC-1 is the first report of a generalized transducing thiophage.
Supplementary Tables 1-2 from <i>TMPRSS2-ERG</i> Gene Fusion Is Not Associated with Outcome in Patients Treated by Prostatectomy (2023)

Supplementary Tables 1-2 from &lt;i&gt;TMPRSS2-ERG&lt;/i&gt; Gene Fusion Is Not Associated with Outcome in Patients Treated by Prostatectomy
Rapamycin generates anti-apoptotic human Th1/Tc1 cells via autophagy for induction of xenogeneic GVHD (2010)

Murine T cells exposed to rapamycin maintain flexibility towards Th1/Tc1 differentiation, thereby indicating that rapamycin promotion of regulatory T cells (Tregs) is conditional. The degree to which rapamycin might inhibit human Th1/Tc1 differentiation has not been evaluated. In the presence of rapamycin, T cell costimulation and polarization with IL-12 or IFN-α permitted human CD4+ and CD8+ T cell differentiation towards a Th1/Tc1 phenotype; activation of STAT1 and STAT4 pathways essential for Th1/Tc1 polarity was preserved during mTOR blockade but instead abrogated by PI3 kinase inhibition. Such rapamycin-resistant human Th1/Tc1 cells: (1) were generated through autophagy (increased LC3BII expression; phenotype reversion by autophagy inhibition via 3-MA or siRNA for Beclin1); (2) expressed anti-apoptotic bcl-2 family members (reduced Bax, Bak; increased phospho-Bad); (3) maintained mitochondrial membrane potentials; and (4) displayed reduced apoptosis. In vivo, type I polarized and rapamycin-resistant human T cells caused increased xenogeneic graft-versus-host disease (x-GVHD). Murine recipients of rapamycin-resistant human Th1/Tc1 cells had: (1) persistent T cell engraftment; (2) increased T cell cytokine and cytolytic effector function; and (3) T cell infiltration of skin, gut, and liver. Rapamycin therefore does not impair human T cell capacity for type I differentiation. Rather, rapamycin yields an anti-apoptotic Th1/Tc1 effector phenotype by promoting autophagy.