gebhart/patrepeval huggingface dataset:
Hyper-adhesion in desmosomes: its regulation in wound healing and possible relationship to cadherin crystal structure (2005)

The resistance of tissues to physical stress is dependent upon strong cell-cell adhesion in which desmosomes play a crucial role. We propose that desmosomes fulfil this function by adopting a more strongly adhesive state, hyper-adhesion, than other junctions. We show that the hyper-adhesive desmosomes in epidermis resist disruption by ethylene glycol bis(2-aminoethyl ether)-N,N,N'N'-tetraacetic acid (EGTA) and are thus independent of Ca2+. We propose that Ca2+ independence is the normal condition for tissue desmosomes. Ca2+ independence is associated with an organised arrangement of the intercellular adhesive material exemplified by a dense midline. When epidermis is wounded, desmosomes in the wound-edge epithelium lose hyper-adhesiveness and become Ca2+ dependent, i.e. readily dissociated by EGTA. Ca2+-dependent desmosomes lack a midline and show narrowing of the intercellular space. We suggest that this indicates a less-organised, weakly adhesive arrangement of the desmosomal cadherins, resembling classical cadherins in adherens junctions. Transition to Ca2+ dependence on wounding is accompanied by relocalisation of protein kinase C alpha to desmosomal plaques suggesting that an 'inside-out' transmembrane signal is responsible for changing desmosomal adhesiveness. We model hyper-adhesive desmosomes using the crystal packing observed for the ectodomain of C-cadherin and show how the regularity of this 3D array provides a possible explanation for Ca2+ independence.
The Embellum in Apluda mutica (2003)

Embellum of Apluda mutica was studied by light microscope. It was demonstrated that outer layer of 1-3 nucellar cells which enlarge in size and often protrude into the micropyle to form embellum at the functional megaspore stage. Both polygonum type and panicum type embryo sac have embellum. The length of embellum is about one to three times of its width in mature aposporous embryo sac, while its length is one to two times of its width in mature sexual embryo sac. The mature embellum cells in aposporous embryo sac were larger than that in sexual embryo sac. The larger embellum could be used as a secondary screening indicator for identifying aposporous embryo sac in Apluda mutica.
Dummy-atom modelling of stacked and helical nanostructures from solution scattering data (2018)

The availability of dummy-atom modelling programs to determine the shape of monodisperse globular particles from small-angle solution scattering data has led to outstanding scientific advances. However, there is no equivalent procedure that allows modelling of stacked, seemingly endless structures, such as helical systems. This work presents a bead-modelling algorithm that reconstructs the structural motif of helical and rod-like systems. The algorithm is based on a 'projection scheme': by exploiting the recurrent nature of stacked systems, such as helices, the full structure is reduced to a single building-block motif. This building block is fitted by allowing random dummy-atom movements without an underlying grid. The proposed method is verified using a variety of analytical models, and examples are presented of successful shape reconstruction from experimental data sets. To make the algorithm available to the scientific community, it is implemented in a graphical computer program that encourages user interaction during the fitting process and also includes an option for shape reconstruction of globular particles.
Isolation and Characterization of Circulating Type 1 Vaccine‐Derived Poliovirus from Sewage and Stream Waters in Hispaniola (2004)

Twenty-one cases of acute flaccid paralysis (AFP) were reported on the island of Hispaniola in 2000. Laboratory analysis confirmed the presence of circulating vaccine-derived poliovirus (cVDPV) type 1 in stool samples obtained from patients. As a complement to the active search for cases of AFP, environmental sampling was conducted during November and December 2000, to test for cVDPV in sewage, streams, canals, and public latrines. Fifty-five environmental samples were obtained and analyzed for the presence of polioviruses by use of cell culture followed by neutralization and reverse-transcription polymerase chain reaction. Of the 23 positive samples, 10 tested positive for poliovirus type 1, 7 tested positive for poliovirus type 2, 5 tested positive for poliovirus type 3, and 1 tested positive for both poliovirus type 2 and type 3. By sequence analysis of the complete viral capsid gene 1 (VP1), a 2.1%-3.7% genetic sequence difference between 7 type 1 strains and Sabin type 1 vaccine strain was found. Phylogenetic analysis showed that these viruses are highly related to cVDPV isolated from clinical cases and form distinct subclusters related to geographic region. Our findings demonstrate a useful role for environmental surveillance of neurovirulent polioviruses in the overall polio eradication program.
The Relevance of Drop Tester Accuracy (2007)

Abstract ASTM D 5276-98 “Standard Test Method for Drop Test of Loaded Containers by Free Fall,” [1] was written as the general test specification for permitting free-fall drop tests for packaged products. One of the fundamental characteristics for drop testers used to perform ASTM D 5276 is that they must produce a flat drop with tolerance limit set at ±2 deg. For drops other than flat drops, such as edges and corners, tolerance limits of ±5 deg have been specified. Although most drop testers are calibrated during manufacturing, they are often not checked for accuracy at their lab locations. This is primarily due to the lack of a calibration standard. This paper investigates the importance of drop test accuracy and reports observations, measurements, and documentation of changes in acceleration and velocity change measured on a test specimen as it is subjected to drops with increasing deviation from the desired impact orientation. A statistical analysis of accelerations as impact orientations deviated is provided and statistical trends in the data as impact angles change are reported. The results suggested that the existing tolerances for performing drops within ±2 deg as recommended by ASTM D 5276 are acceptable for flat drops and the tolerances for performing edge and corner drops within ±5 deg are not acceptable as they can result in larger deviations as the offset is increased beyond ±2 deg.
Detection and Quantification of GPCR mRNA: An Assessment and Implications of Data from High-Content Methods (2019)

G protein-coupled receptors (GPCRs) are the largest family of membrane receptors and targets for approved drugs. The analysis of GPCR expression is, thus, important for drug discovery and typically involves messenger RNA (mRNA)-based methods. We compared transcriptomic complementary DNA (cDNA) (Affymetrix) microarrays, RNA sequencing (RNA-seq), and quantitative polymerase chain reaction (qPCR)-based TaqMan arrays for their ability to detect and quantify expression of endoGPCRs (nonchemosensory GPCRs with endogenous agonists). In human pancreatic cancer-associated fibroblasts, RNA-seq and TaqMan arrays yielded closely correlated values for GPCR number (∼100) and expression levels, as validated by independent qPCR. By contrast, the microarrays failed to identify ∼30 such GPCRs and generated data poorly correlated with results from those methods. RNA-seq and TaqMan arrays also yielded comparable results for GPCRs in human cardiac fibroblasts, pancreatic stellate cells, cancer cell lines, and pulmonary arterial smooth muscle cells. The magnitude of mRNA expression for several Gq/11-coupled GPCRs predicted cytosolic calcium increase and cell migration by cognate agonists. RNA-seq also revealed splice variants for endoGPCRs. Thus, RNA-seq and qPCR-based arrays are much better suited than transcriptomic cDNA microarrays for assessing GPCR expression and can yield results predictive of functional responses, findings that have implications for GPCR biology and drug discovery.
CD73-Generated Extracellular Adenosine Creates Microenvironmental Conditions Favoring Growth and Survival of Chronic Lymphocytic Leukemia Cells (2011)

Abstract Abstract 621 CD39 (ecto-nucleoside-triphosphate-diphosphohydrolase-1) and CD73 (5'-nucleotidase) are surface enzymes with extracellular catalytic sites. CD39 hydrolyses ATP/ADP to AMP, which is then converted to adenosine (ADO) by CD73. Once ADO is released in the extracellular milieu, it may re-enter the cell or engage different types of purinergic receptors, eliciting potent autocrine and paracrine cytoprotective, anti-inflammatory and immunosuppressive effects. Several lines of evidence suggest that the tumor microenvironment is marked by increased turnover of extracellular nucleotides and nucleosides, as well as by upregulation of ecto-enzymes that dismantle them. These alterations are believed to contribute to increasing local concentrations of ADO, creating local conditions that favor tumor expansion. We have investigated expression of CD39/CD73 by chronic lymphocytic leukemia (CLL) cells and evaluated the functional significance of the autocrine ADO production in supporting the survival of the leukemic cells and their expansion. Immunohistochemical analyses of lymph node biopsies indicated that CD39 was widely expressed by neoplastic cells, as well as by surrounding non-neoplastic stroma. On the contrary, CD73 was largely restricted to CLL proliferation centers and to cells with a prolymphocyte / para-immunoblast morphology, suggesting that ADO generation is confined to specific tissue niches and to specific cell subpopulations. The highest intensity of expression was scored by Ki-67+ CLL cells, in close association with T lymphocytes and localized to perivascular areas, where recirculation to and from lymphoid organs occurs. When analyzed in the peripheral blood, CD39 was constantly expressed, while CD73 was present in approximately 30% of cases and associated with markers of aggressive disease. CD39+/CD73+ CLL cells could selectively produce ADO from ADP, in a time- and concentration-dependent way. RT-PCR data indicated that CLL express high levels of A2A ADO receptor, further elevated in proliferating leukemic cells. Ligation of the A2A receptor by extracellular ADO or by the selective agonist CGS21680 increased cytoplasmic cAMP levels. The functional consequence was the inhibition of CXCL12-mediated chemotaxis, suggesting that the adenosinergic axis contributes to keeping CLL cells in a growth-favorable environment where they were attracted by CXCL12. Furthermore, activation of the axis conferred significant protection from spontaneous and/or fludarabine-induced apoptosis. The contribution of CD73 in regulating ADO production was confirmed by using a selective enzyme inhibitor. These results are consistent with the existence of an adenosinergic loop, active in selected CLL patients, creating conditions in the lymph node microenvironment that favor the development, maintenance and progression of the leukemia. Disclosures: No relevant conflicts of interest to declare.
Inhibition of TNFR1 signaling by P60 PLAD protein ameliorates skin lesions in lupus MRL/lpr mice (50.24) (2009)

Abstract Skin disease is the second most common manifestation in patients with systemic lupus erythematosus (SLE). The etiology of skin injury remains unclear. There is urgent need to understand better the pathogenesis of skin lesions and to develop effective, non-toxic therapy for cutaneous lupus erythematosus. MRL/lpr mice develop pathology similar to human SLE including skin lesions. To understand whether tumor necrosis factor (TNF) contributes to the pathogenesis of cutaneous lupus erythematosus, we treated lupus MRL/lpr mice with TNF receptor (R) defined PLAD protein. P60 PLAD inhibits the function of TNFR1, whereas P80 PLAD inhibits the function of TNFR2. We found that P60 PLAD protein significantly inhibited skin injury but P80 PLAD failed to do so in MRL/lpr mice. Both PLAD proteins promoted the development of proteinuria. Immunohistochemistry studies of skin lesions demonstrated that TNFR1 but not TNFR2 in expressed in the skin lesion of MRL/lpr mice. P60 PLAD significantly inhibited NF-kB, MCP-1 and iNOS expression by skin keratinocytes. Our results indicate that TNFR1 contributes to the development of skin lesions in lupus-prone mice suggest that it can be targeted successfully to treat cutaneous SLE.
Atom interferometry using wavepackets with constant spatial separations (2006)

We demonstrate a standing wave light pulse sequence that places atoms into a superposition of displaced wavepackets with precisely controlled displacements that remain constant for times as long as 1 s. The separated wavepackets are subsequently recombined resulting in atom interference patterns that probe energy differences of approximately 10^-34 J, and can provide acceleration measurements that are insensitive to platform vibrations.
Plenoptic Imaging and Vision using Angle Sensitive Pixels (2017)

Computational cameras with sensor hardware co-designed with computer vision and graphics algorithms are an exciting recent trend in visual computing. In particular, most of these new cameras capture the plenoptic function of light, a multidimensional function of radiance for light rays in a scene. Such plenoptic information can be used for a variety of tasks including depth estimation, novel view synthesis, and inferring physical properties of a scene that the light interacts with. In this thesis, we present multimodal plenoptic imaging, the simultaenous capture of multiple plenoptic dimensions, using Angle Sensitive Pixels (ASP), custom CMOS image sensors with embedded per-pixel diffraction gratings. We extend ASP models for plenoptic image capture, and showcase several computer vision and computational imaging applications. First, we show how high resolution 4D light fields can be recovered from ASP images, using both a dictionary-based machine learning method as well as deep learning. We then extend ASP imaging to include the effects of polarization, and use this new information to image stress-induced birefringence and remove specular highlights from light field depth mapping. We explore the potential for ASPs performing time-of-flight imaging, and introduce the depth field, a combined representation of time-of-flight depth with plenoptic spatio-angular coordinates, which is used for applications in robust depth estimation. Finally, we leverage ASP optical edge filtering to be a low power front end for an embedded deep learning imaging system. We also present two technical appendices: a study of using deep learning with energy-efficient binary gradient cameras, and a design flow to enable agile hardware design for computational image sensors in the future.
576 NL-201, a de novo IL-2 and IL-15 agonist, demonstrates enhanced in vivo antitumor activity in combination with multiple cancer immunotherapies (2020)

<h3>Background</h3> NL-201 is a de novo IL-2 and IL-15 receptor agonist designed with enhanced affinity for IL-2Rβγ and no binding interface for IL-2Rα (CD25). Previously, we reported that NL-201 stimulates selective proliferation of CD8+ effector T cells and NK cells, leading to increased CD8:Treg and NK:Treg ratios in the tumor microenvironment. As a result, NL-201 treatment led to robust single-agent antitumor activity in syngeneic murine tumor models at well-tolerated doses. <h3>Methods</h3> Here, we evaluated the antitumor activity of NL-201 in combination with established and exploratory cancer immunotherapies, including tumor-targeting monoclonal antibodies and immune checkpoint inhibitors (CPIs). Specifically, we evaluated NL-201 in combination with an anti-gp75 antibody (TA99) in a murine melanoma model, or anti-PD-1 and anti-PD-L1 antibodies in a CPI-resistant murine colon cancer model. <h3>Results</h3> NL-201 synergizes with TA99, anti-PD-1, and anti-PD-L1 to inhibit tumor growth more effectively than either agent alone. The synergy of NL-201 with TA99 may result from enhanced NK-mediated antibody-dependent cellular cytotoxicity (ADCC), while the synergy with CPIs may result from CD8+ T cell stimulation, which can turn ‘cold’ tumor microenvironments ‘hot’. <h3>Conclusions</h3> The broad activity of NL-201 across diverse tumor models and its potential to be combined with a variety of established and exploratory cancer immunotherapies to achieve synergistic antitumor activity highlights the opportunity for NL-201 to become a critical component of future immunotherapy regimens.
Superoxide release and cellular gluthatione peroxidase activity in leukocytes from children with persistent asthma (2004)

Asthma is an inflammatory condition characterized by the involvement of several mediators, including reactive oxygen species. The aim of the present study was to investigate the superoxide release and cellular glutathione peroxidase (cGPx) activity in peripheral blood granulocytes and monocytes from children and adolescents with atopic asthma. Forty-four patients were selected and classified as having intermittent or persistent asthma (mild, moderate or severe). The spontaneous or phorbol myristate acetate (PMA, 30 nM)-induced superoxide release by granulocytes and monocytes was determined at 0, 5, 15, and 25 min. cGPx activity was assayed spectrophotometrically. The spontaneous superoxide release by granulocytes from patients with mild (N = 15), moderate (N = 12) or severe (N = 6) asthma was higher at 25 min compared to healthy individuals (N = 28, P < 0.05, Duncan test). The PMA-induced superoxide release by granulocytes from patients with moderate (N = 12) or severe (N = 6) asthma was higher at 15 and 25 min compared to healthy individuals (N = 28, P < 0.05 in both times of incubation, Duncan test). The spontaneous or PMA-induced superoxide release by monocytes from asthmatic patients was similar to healthy individuals (P > 0.05 in all times of incubation, Duncan test). cGPx activity of granulocytes and monocytes from patients with persistent asthma (N = 20) was also similar to healthy individuals (N = 10, P > 0.05, Kruskal-Wallis test). We conclude that, under specific circumstances, granulocytes from children with persistent asthma present a higher respiratory burst activity compared to healthy individuals. These findings indicate a risk of oxidative stress, phagocyte auto-oxidation, and the subsequent release of intracellular toxic oxidants and enzymes, leading to additional inflammation and lung damage in asthmatic children.
Growth and multiplication of white skeletal muscle fibres in carp larvae in relation to somatic growth rate (1997)

A morphometric analysis of white axial muscle of common carp Cyprinus carpio was undertaken in order to quantify increase in fibre size, fibre nuclei and fibre number in relation to somatic growth rate during early life. In fast‐growing carp larvae fed zooplankton, length and height of fibres from the central part of dorsolateral muscle increased at the same rate (0.75) relative to the total length of the larvae during the first 2 weeks of feeding. During this period, the number of nuclei per fibre increased threefold while the number of nuclei per unit fibre surface remained constant. In fast‐growing larvae fed a formulated diet, the total cross‐sectional area of one epaxial quadrant of white muscle and the total area of white fibres increased at almost the same rate (3.15; 3.23) relative to larval total length during the first 28 days of exogenous feeding. The total number of white fibres increased faster (2.07) relative to the total length of larvae than the mean area of white fibres (1.16). Hyperplasia accounted for 64% of muscle growth in these larvae. The proportion of fibres with a width &lt; 10 μm decreased from 72% at first feeding to 14% 28 days later, while the proportion of fibres with a width &gt;20 μm which was 0% at first feeding increased up to 34% in the same time. The recruitment of new white fibres seemed to be almost the same in the whole muscle quadrant at first feeding and 18 or 28 days later but, 8 days after first feeding, a transient significant recruitment of new fibres was shown at the apex of the myotome. Comparisons between fast‐ and slow‐growing groups of larvae showed that for a given larval total length: (1) the mean width of central white fibres was higher and the proportion of central fibres with a width &lt;10 μm was lower in slow‐growing larvae than in fast‐growing ones; (2) the total number of white fibres was lower for a higher total cross‐sectional area of white muscle in slow‐growing larvae than in fast‐growing ones. These results suggest that, in Cyprinus carpio larvae, slow‐growing conditions are related to a decreased contribution of hyperplasia to muscle growth.
Isobaric Analog Resonances in theZn68(p, n)Ga68Reaction from 4 to 5 MeV (1970)

Two pairs of isobaric analog resonances near 4.1- and 4.9-MeV proton bombarding energy, respectively, have been studied in the $^{68}\mathrm{Zn}(p, n)^{68}\mathrm{Ga}$ reaction. Differential cross sections were measured at 2.5, 30, and 130\ifmmode^\circ\else\textdegree\fi{} for neutrons which leave $^{68}\mathrm{Ga}$ in the ground state and 180-keV first excited state in the bombarding energy region from 4.00 to 4.15 MeV. Analog resonances at 4.075 and 4.098 MeV were analyzed according to the Robson theory. Eleven levels in $^{68}\mathrm{Ga}$ up to an excitation energy of 1.088 MeV were identified in time-of-flight spectra. Hauser-Feshbach analyses were done on the angular distributions of neutrons leaving $^{68}\mathrm{Ga}$ in 4 and 6 residual nucleus states at 4.400 and 4.512 MeV, respectively, an energy region where no analog resonances appear. Excitation functions for seven neutron groups were measured at 100\ifmmode^\circ\else\textdegree\fi{} in the bombarding energy region 4.7 to 5.0 MeV, where two analog resonances, at 4.87 and 4.92 MeV, were seen. An analysis according to the theory of Robson was performed on these resonances in order to obtain spins, parities, and resonance parameters.
Efficient Authenticated Encryption for Hybrid Hard Drives Based on GCM (2008)

Hybrid hard drives (HHD) are coming up with potential high viability in mobile computing. It's quite necessary to put forward an efficient secure scheme for hybrid hard drives. NAND Flash of HHD is made full use as a container and a buffer for metadata. We propose an efficient combined scheme based on Galois/Counter Mode (GCM) to protect hard disk data by authenticated encryption, and build a secure architecture for HHD. Our results show that we not only protect the disk data by authenticated encryption, but also gain high performance. According to the simulation results, for the best of our methods, the performance overhead is less than 18%, which is efficient and acceptable practically.
Distribution and movement of trichloroethylene in ground water in the Tucson area, Arizona (1987)

In 1981, investigations of ground-water quality around Tucson International Airport revealed a number of wells that pumped water contaminated by trichloroethylene.
Delay minimization through joint routing and resource allocation in cognitive radio-based mesh networks (2012)

We consider wireless mesh networks in which the nodes are utilizing cognitive radios and try to opportunistically gain access to spectrum resources. In such networks, the timely delivery of the traffic is a challenging task due to the licensed (primary) users' activities and their traffic characteristics. To overcome this challenge we propose an algorithm that minimizes the end-to-end delay through joint routing and spectrum resources allocation. The network is analyzed from a queueing theory perspective to capture the effects of dynamic spectrum availability on mesh network's traffic. The joint routing and resource allocation problem is formulated as a non-linear integer programming problem, for which we propose a decentralized solution based on the Lagrangian dual problem. Results demonstrate the performance of our proposed algorithm, as well as the efficiency of the decentralized implementation.