gebhart/patrepeval huggingface dataset:
Modulation of cell spreading and cell-substrate adhesion dynamics by dystroglycan (2009)

Dystroglycan is a ubiquitously expressed cell adhesion protein. Its principal role has been determined as a component of the dystrophin-glycoprotein complex of muscle, where it constitutes a key component of the costameric cell adhesion system. To investigate more fundamental aspects of dystroglycan function in cell adhesion, we examined the role of dystroglycan in the dynamics and assembly of cellular adhesions in myoblasts. We show that beta-dystroglycan is recruited to adhesion structures and, based on staining for vinculin, that overexpression or depletion of dystroglycan affects both size and number of fibrillar adhesions. Knockdown of dystroglycan increases the size and number of adhesions, whereas overexpression decreases the number of adhesions. Dystroglycan knockdown or overexpression affects the ability of cells to adhere to different substrates, and has effects on cell migration that are consistent with effects on the formation of fibrillar adhesions. Using an SH3 domain proteomic screen, we identified vinexin as a binding partner for dystroglycan. Furthermore, we show that dystroglycan can interact indirectly with vinculin by binding to the vinculin-binding protein vinexin, and that this interaction has a role in dystroglycan-mediated cell adhesion and spreading. For the first time, we also demonstrate unequivocally that beta-dystroglycan is a resident of focal adhesions.
Spin Proximity Effect in Ultrathin Superconducting Be-Au Bilayers (2006)

We present a detailed study of the effects of interface spin-orbit coupling on the critical field behavior of ultrathin superconducting Be/Au bilayers. Parallel field measurements were made in bilayers with Be thicknesses in the range of d=2-30 nm and Au coverages of 0.5 nm. Though the Au had little effect on the superconducting gap, it produced profound changes in the spin states of the system. In particular, the parallel critical field exceeded the Clogston limit by an order of magnitude in the thinnest films studied. In addition, the parallel critical field unexpectedly scaled as [FORMULA: SEE TEXT], suggesting that the spin-orbit coupling energy was proportional to Delta0/d2. Tilted field measurements showed that, contrary to recent theory, the interface spin-orbit coupling induces a large in-plane superconducting susceptibility but only a very small transverse susceptibility.
10 Gbit/s penalty-free transmission over 48 km using 1.3-/spl mu/m wavelength electroabsorption modulated lasers (EML) for metro-loop transmission link (1996)

Summary form only given. Here we report the first penalty-free transmission results over 48 km of nondispersion-shifted fiber using a 1.3-/spl mu/m wavelength integrated electroabsorption modulated MQW laser (EML) device at a bit rate of 10 Gbit/s.
Reducing the complexity of virtual machine networking (2016)

Virtualization is an enabling technology that improves scalability, reliability, and flexibility. Virtualized networking is tackled by emulating or paravirtualizing network interface cards. This approach, however, leads to complexities (implementation and management) and has to conform to some limitations imposed by the Ethernet standard. RINA turns the current approach to virtualized networking on its head: instead of emulating networks to perform inter-process communication on a single processing system, it sees networking as an extension to local inter-process communication. In this article, we show how RINA can leverage a paravirtualization approach to achieve a more manageable solution for virtualized networking. We also present experimental results performed on IRATI, the reference open source implementation of RINA, which shows the potential performance that can be achieved by deploying our solution.
Benchmarking for Large-Scale Placement and Beyond (2004)

Over the last five years, the large scale integrated circuit placement community achieved great strides in the understanding of placement problems, developed new high-performance algorithms, and achieved impressive empirical results. These advances have been supported by a nontrivial benchmarking infrastructure, and future achievements are set to draw on benchmarking as well. In this paper, we review motivations for benchmarking, especially for commercial electronic design automation, analyze available benchmarks, and point out major pitfalls in benchmarking. Our empirical data offers perhaps the first comprehensive evaluation of several leading large-scale placers on multiple benchmark families. We outline major outstanding problems and discuss the future of placement benchmarking. Furthermore, we attempt to extrapolate our experience to circuit layout tasks beyond placement.
Engineering the acyltransferase substrate specificity of assembly line polyketide synthases (2013)

Polyketide natural products act as a broad range of therapeutics, including antibiotics, immunosuppressants and anti-cancer agents. This therapeutic diversity stems from the structural diversity of these small molecules, many of which are produced in an assembly line manner by modular polyketide synthases. The acyltransferase (AT) domains of these megasynthases are responsible for selection and incorporation of simple monomeric building blocks, and are thus responsible for a large amount of the resulting polyketide structural diversity. The substrate specificity of these domains is often targeted for engineering in the generation of novel, therapeutically active natural products. This review outlines recent developments that can be used in the successful engineering of these domains, including AT sequence and structural data, mechanistic insights and the production of a diverse pool of extender units. It also provides an overview of previous AT domain engineering attempts, and concludes with proposed engineering approaches that take advantage of current knowledge. These approaches may lead to successful production of biologically active 'unnatural' natural products.
IMMU-43. ZIKA VIRUS TO TREAT GLIOMA: TURNING COLD TUMORS HOT (2020)

Abstract GBM is a hallmark example of an immunotherapy-resistant tumor. Previously, we discovered that Zika virus (ZIKV) has a natural honing capacity to specifically kill GBM stem cells (GSCs). Using two syngeneic glioma models, GL261 and CT2A, we found that in vivo intratumoral ZIKV treatment reduces tumor size and extends median survival far beyond that expected for its anti-GSC effects; additionally, approximately 50% of mice were long-term survivors. We now report that ZIKV treatment is associated with an increase in tumor-specific CD8+ T cells and activated myeloid cells expressing MHC-II and NOS2. Treatment with CD8-depleting antibody abrogates the survival advantage conferred by ZIKV, demonstrating that CD8+ T cells are required for ZIKV efficacy. Remarkably, ZIKV treatment also confers protection against tumor re-challenge 1.5 years after the original treatment, and this too is dependent on CD8+ T cells. Lastly, in a bilateral tumor implantation model, intratumoral ZIKV treatment of one tumor increases overall survival, suggesting ZIKV is efficacious because it generates a global anti-tumor response. Building on the observation that ZIKV treatment increases CD8+ T cells in the tumor bed, we combined ZIKV with α-PD1 immunotherapy. We found survival was dramatically increased compared to either treatment alone. Finally, to improve safety of potential ZIKV treatment for patients, we generated an immune-sensitized virus. This strain remains efficacious as a single agent and in combination with immunotherapy in vivo. Overall, our results suggest ZIKV treatment addresses two key problems in our current treatment of GBM: it specifically targets highly resistant GSC and initiates a potent anti-tumor immune response against the remaining tumor. Our work reveals the mechanistic basis of ZIKV efficacy and demonstrates the potential for ZIKV as a therapy for GBM.
p53 mutations in the non-neoplastic mucosa of the human stomach showing intestinal metaplasia (1996)

In order to ascertain whether genetic alterations occur during the early stages of gastric carcinogenesis, abnormal accumulation of p53 protein and mutation of its gene in stomach tissue showing intestinal metaplasia were investigated using immunohistochemistry and polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) analysis. Immunohistochemistry detected 19 foci showing nuclear accumulation of p53 protein in non-neoplastic gastric mucosa in a total of 756 sections (477 of which contained intestinal metaplasia) from 16 resected stomachs containing gastric adenocarcinomas. Of these 19 p53-positive foci, 17 were diagnosed histologically as incomplete-type intestinal metaplasia and 2 as pseudopyloric glands in the regenerative mucosa. Furthermore, 14 such foci were detected in 6 patients with multiple gastric cancers. No correlation between high-iron diamine (HID)-positive sulfomucin production and p53-positive glands was observed. The DNAs were extracted selectively from these p53-positive metaplastic glands and examined for p53 mutations by PCR-SSCP analysis followed by direct sequencing. In only 10 lesions could exons; 5 to 8 be investigated completely, and of these, 4 were shown to possess p53 mutations, which were on exon 5 in 3 cases and on exon 7 in 1 case. These results indicate that irreversible genetic changes had already occurred in morphologically non-neoplastic gastric mucosa with intestinal metaplasia, and are consistent with the hypothesis that intestinal metaplasia, especially the incomplete type, may contain precursor lesions of gastric cancer.
Mapping surface plasmon propagation by collection-mode near-field microscopy (2011)

Surface plasmon propagation along striped Gold structures has been investigated by collection-mode near-field microscopy, leading to map the field intensity at the structure surface and to assess the system behavior at the nanoscale.
THE PARTICLE FINITE ELEMENT METHOD — AN OVERVIEW (2004)

We present a general formulation for the analysis of fluid-structure interaction problems using the particle finite element method (PFEM). The key feature of the PFEM is the use of a Lagrangian description to model the motion of nodes (particles) in both the fluid and the structure domains. Nodes are thus viewed as particles which can freely move and even separate from the main analysis domain representing, for instance, the effect of water drops. A mesh connects the nodes defining the discretized domain where the governing equations, expressed in an integral form, are solved as in the standard FEM. The necessary stabilization for dealing with the incompressibility condition in the fluid is introduced via the finite calculus (FIC) method. A fractional step scheme for the transient coupled fluid-structure solution is described. Examples of application of the PFEM method to solve a number of fluid-structure interaction problems involving large motions of the free surface and splashing of waves are presented.
Analysis of standard and non-standard control modes for modular converters with synchronous modulation (2005)

The paper describes operation of cascaded (modular) converters with synchronous pulsewidth modulation (PWM), mainly for control regimes different from conventional volts/hertz control. Modular multilevel converter consists from three standard three-phase inverter modules along with an 0.33 p.u. output transformer. The proposed PWM method provides synchronisation of the voltage waveforms of each module and of the composed voltage at the output of the converter. The line-to-line output voltage of modular converter (with two, three or four levels in dependence of modulation index) has quarter-wave symmetry during the whole control range for both linear and non-linear control modes and regimes. Basic versions of continuous and discontinuous schemes of synchronous PWM, based on vector approach for determination of the pulse patterns, have been analysed and compared by simulations of the systems with low switching frequencies, which are used normally in high power systems
Self-starting additive pulse mode-locked erbium fibre ring laser (1992)

Nonlinear polarisation rotation has been used to additive pulse mode-lock (APM) a single loop erbium fibre ring laser. The system is fully self-starting without triggering and has been made to produce single pulses of 452 fs duration per round trip time.
Estradiol/progesterone-releasing vaginal rings for hormone replacement therapy in postmenopausal women (2003)

In order to investigate whether vaginal rings delivering estradiol and progesterone could prevent endometrial hyperplasia and relieve climacteric symptoms ,two variants of rings were used in 20 postmenopausal women with intact uteri for 4 months. One ring designated as PI-002 (n = 8) delivered in vitro estradiol 160 μg/day and progesterone 20 mg/day ,while the other (PI-003; n = 12) delivered the same dosage of estradiol but only half the progesterone (10 mg/day). Serum estrone ,estradiol and progesterone were measured at pretreatment ,weekly for 4 weeks ,and then monthly for 4 months. The incidence of hot flushes ,frequency of night sweats ,mood scores ,vaginal discharge and bleeding profiles were recorded. Endometrial thickness was monitored by ultrasonography. The mean estrone level was 50 pg/ml for 16 weeks. The mean serum estradiol level was 75 pg/ml for the first 4 weeks and gradually decreased to 50 pg/ml at 16 weeks. The mean progesterone level with the PI-002 ring was 5 ng/ml for the first 4 weeks and decreased to 3.5 ng/ml at 16 weeks. With the PI-003 ring ,the mean progesterone level was initially 3.5 ng/ml and then decreased to 2.5 ng/ml thereafter. Significant decreases in the incidence of hot flushes and night sweats as well as a striking improvement in mood scores were noted as early as 2 weeks after insertion. Three of the 20 women discontinued the treatment ,owing to ring expulsion. Increased vaginal discharge was observed with both rings in the first 6 weeks. Vaginal bleeding was more frequently apparent among users of the PI-002 ring ,although bleeding and spotting were confined to the first 6 weeks. Ultrasonographic monitoring of the endometrium constantly revealed a thickness of < 3 mm for both variants throughout use for 16 weeks. An estradiol/progesterone-releasing vaginal ring is a potential alternative to long-term hormone replacement therapy with minimum attention required. It provides effective protection against endometrial hyperplasia.
Pheromone Syntheses, LXXVIII. Synthesis of the Four Thermodynamically Stable Stereoisomers of 2,7‐Dimethyl‐1,6‐dioxaspiro[4.6]undecane, a Component of the Volatile Secretion from the Mandibular Glands of Andrena haemorrhoa F. (1985)

Abstract The title compounds (2 R ,5 S ,7 R )‐ 1 , (2 S ,5 S ,7 R )‐ 1 , (2 R ,5 R ,7 S )‐ 1 , and (2 S ,5 R ,7 S )‐ 1 were synthesized from ethyl ( S )‐lactate ( 3 ) and the ( R )‐ or ( S )‐enantiomers of ethyl 3‐hydroxybutanoate ( 4a ). The formation of the spiro acetal 1 from 2b proceeds stereoselectively. Various spiro acetals with axial S ‐chirality at the spiro center were shown to be dextrorotatory at 589 nm.
A now Schendyloid chilopod from California (1946)

(Uploaded by Plazi from the Biodiversity Heritage Library) No abstract provided.
Biological treatment of industrial wastes in a photobioreactor (2006)

An algal-bacterial consortium was tested for the treatment from a coke factory. A Chlorella vulgaris strain and a phenol-degrading Alcaligenes sp. were first isolated from the wastewater treatment plant to serve as inocula in the subsequent biodegradation tests. Batch tests were then conducted with samples from the real wastewater or using a synthetic wastewater containing 325 mg phenol/l and 500 mg NH4+/l as target pollutants. Direct biological treatment of the real wastewater was not possible due to the toxicity of organic compounds. Activated carbon adsorption and UV(A-B)-irradiation were efficient in detoxifying the effluent for subsequent biological treatment as inoculation of pretreated samples with the algal-bacterial consortium was followed by complete phenol removal and NH4+ removal of 45%. Complete phenol removal and 33% NH4+ removal were achieved during the fed-batch treatment of artificial wastewater at 6 d hydraulic retention time (HRT). Under continuous feeding at 3.6 d HRT, phenol and NH4+ removal dropped to 58 and 18%, respectively. However, complete phenol removal and 29% NH4+ removal were achieved when 8 g NaHCO3/l was added to the artificial wastewater to enhance algal growth. This study confirms the potential of solar-based industrial wastewater treatment based on solar-based UV pretreatment followed by algal-bacterial biodegradation.
KNOWS: Cognitive Radio Networks Over White Spaces (2007)

FCC has proposed to allow unlicensed operations in the TV broadcast bands. This portion of the spectrum has several desirable properties for more robust data communication as compared to the ISM bands. However, there are a number of challenges in efficiently using the TV bands. For example, the available spectrum is fragmented, and its availability may vary over time. In this paper, we present a cognitive radio system, called KNOWS, to address these challenges. We present the design of our prototype, which includes a new hardware platform and a spectrum-aware Medium Access Control (MAC) protocol. We have implemented the MAC protocol in QualNet, and our results show that in most scenarios KNOWS increases the throughput by more than 200% when compared to an IEEE 802.11 based system.
Can Mathematics and Computational Modeling Help Treat Deep Tissue Injuries? (2019)

<b>Objective:</b> Improving the treatment of deep tissue injuries, such as burns, by the use of computational modeling, instead of by animal experiments. <b>Approach:</b> Development of mathematical relations between various parameters and processes. Furthermore, solving the resulting problems through the use of numerical methods, such as finite-element methods. <b>Results:</b> Using our framework, we are able to simulate wound contraction in two dimensions, in which the wound area is followed over time. Our studies indicate that the degree of contraction can be reduced if the appearance of myofibroblasts is inhibited and if their apoptosis is enhanced. Furthermore, after skin grafting, splinting procedures are to be continued as long as TG-beta like growth factor levels are significant. <b>Innovation:</b> A morphoelasticity-based and computational-probabilistic framework for studying the evolution of burn injuries. <b>Conclusion:</b> The current framework is able to reproduce the time evolution of the wound area as observed in clinical results for skin grafts.
Mechanism of L-leucyl-L-leucine methyl ester-mediated killing of cytotoxic lymphocytes: dependence on a lysosomal thiol protease, dipeptidyl peptidase I, that is enriched in these cells. (1990)

Exposure of murine or human lymphocytes to L-leucyl-L-leucine methyl ester (Leu-Leu-OMe) results in selective killing of cytotoxic lymphocytes, whereas helper T cells and B cells remain functionally intact. Cytolytic lymphocytes incubated in the presence of toxic concentrations of Leu-Leu-OMe were found to contain membranolytic metabolites of the structure (Leu-Leu)n-OMe, where n greater than or equal to 3. The sensitivity of cytotoxic lymphocytes to Leu-Leu-OMe was found to be dependent upon production of these metabolites by a lysosomal thiol protease, dipeptidyl peptidase I, which is present at far higher levels in cytotoxic lymphocytes than in cells without cytolytic potential or not of bone marrow origin. Thus, this granule enzyme is required for the unique effects of Leu-Leu-OMe and may provide a target for the development of other immunotherapeutic agents designed to delete cytotoxic lymphocyte responses.
Grangeat-type helical half-scan computerized tomography algorithm for reconstruction of a short object (2003)

Currently, cone-beam computerized tomography (CT) and micro-CT scanners are under rapid development for major biomedical applications. Half-scan cone-beam image reconstruction algorithms assume only part of a scanning turn, and are advantageous in terms of temporal resolution and image artifacts. While the existing half-scan cone-beam algorithms are in the Feldkamp framework, we have published a half-scan algorithm in the Grangeat framework for a circular trajectory [Med. Phys. 30, 689-700 (2003)]. In this paper, we extend our previous work to a helical case without data truncation. We modify the Grangeat's formula for utilization and estimation of Radon data. Specifically, we categorize each characteristic point in the Radon space into singly, doubly, triply sampled, and shadow regions, respectively. A smooth weighting strategy is designed to compensate for data redundancy and inconsistency. In the helical half-scan case, the concepts of projected trajectories and transition points on meridian planes are introduced to guide the design of weighting functions. Then, the shadow region is recovered via linear interpolation after smooth weighting. The Shepp-Logan phantom is used to verify the correctness of the formulation, and demonstrate the merits of the Grangeat-type half-scan algorithm. Our Grangeat-type helical half-scan algorithm is not only valuable for quantitative and/or dynamic biomedical applications of CT and micro-CT, but also serves as an intermediate step towards solving the long object problem.
Imaging Wet Individual Single Walled Carbon Nanotube at Atomic Level (2008)

Wet individual Single walled carbon nanotube was observed at an atomic level with high resolution. This observation was achieved in a liquid cell containing water using a modified non-contact mode atomic force microscopy (NC-AFM) which, we believed, becomes the powerful tool for imaging nano-material in atomic scale. Consequently, the topography image showed many hexagons network of carbon atoms forming the outer surface of SWCNT. The analysis of the scanned SWCNT, by NC-AFM probe, revealed the presence of two sites of an armchair and zigzag structures.
Improving allergy alerting in a computerized physician order entry system. (2000)

Computerized physician order entry has been shown to reduce the frequency of serious medication errors. Decision support tools such as alerting functions for patient medication allergy are a key part of these applications. However, optimal performance requires iterative refinement. As systems become increasingly complex, mechanisms to monitor their performance become increasingly critical. We analyzed trend data obtained over a five-year period that showed decreasing compliance to allergy alert functions within computerized order entry. Many medication-allergy pairs were being consistently overridden. Renewal policies affecting reordering narcotics also contributed heavily to this trend. Each factor revealed a system-wide trend that could result in suggestions for policy or software change. Monitoring trends such as these is very important to maintain software correctness and ensure user trust in alerting systems, so users remain responsive to computerized alerts.