gebhart/patrepeval huggingface dataset:
Morphology of angiogenesis in human cancer: a conceptual overview, histoprognostic perspective and significance of neoangiogenesis (2005)

This paper reviews the histomorphological aspects of angiogenesis and neoangiogenesis, quantitative and qualitative, and their applications in prognostic evaluation of neoplastic diseases. The merits and weak points of intratumoral microvessel density (MVD), a widely regarded bona fide predictor of tumour growth, metastases and patient survival, are discussed. Total microvascular area (TVA) has been found useful in recent prognostic studies utilizing newer immunohistochemical vascular markers. Of particular significance is the fact that MVD and TVA are most predictive of patient outcome in those tumours that induce significant neoangiogenesis, namely carcinomas of breast and prostate, and haematological malignancies. In contrast, carcinomas of lung and urinary bladder do not show significant associations of MVD and TVA with poor prognosis, reflecting differences in angiogenic mechanisms. In gliomas, MVD appears to correlate with outcome in high‐grade, but not low‐grade tumours, and does not correlate with tumour cellularity in the infiltrating portions of the tumour, reflecting a paucity of neoangiogenesis and directional vascular growth. Recent studies have found CD105, Tie‐2/Tek and vascular endothelial growth factor receptors to be the best markers of neoangiogenesis. The vascular parameters so measured correlate better with overall and disease‐free survival in breast, colon and lung carcinoma than panendothelial markers such as CD31. A correlation of vascular patterns with prognosis has been established in ocular melanomas, glioblastomas and squamous carcinomas of head and neck region. Vascular networks with closed loops are closely associated with mortality due to metastases in uveal melanomas. Fewer bizarre glomeruloid vessels and prominent classical capillary pattern was an independent predictor of longer survival in glioblastoma. Therefore a judicious combination of quantitative and qualitative microscopic angiogenic parameters, with emphasis on neoangiogenesis and vascular patterns wherever applicable, should be an integral component of a more consistent tumour staging system for accurate prognostic evaluation of tumours, selection of optimal anti‐angiogenic therapy and pertinent research.
Searching in parallel for similar strings [biological sequences] (1994)

Distributed computation, probabilistic indexing and hashing techniques combine to create a novel approach to processing very large biological-sequence databases. Other data-intensive tasks could also benefit. Our indexing-based approach enables fast similarity searching through a large database of strings. Thanks to a redundant table-lookup scheme, recovering database items that match a test sequence requires minimal data access. We have implemented a uniprocessor version of this approach called Flash (Fast Lookup Algorithm for String Homology) as well as a distributed version, dFlash, using a cluster of seven non-dedicated workstations connected through a local area network. In this article, we present an approach for retrieving homologies in databases of proteins.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Measurement and Analysis of Engine Pressure Data (1975)

<div class="htmlview paragraph">This paper provides a user oriented description of techniques for the measurement and analysis of engine cylinder pressures. These techniques were developed for piezoelectric transducers and for digital systems of data acquisition and analysis. Test cell procedures are described for transducer preparation and calibration, and for association of each pressure with its appropriate crank angle. Techniques are also described for evaluating the accuracy of pressure data and for eliminating specific errors. Two examples of uses for pressure data are discussed: the calculation of heat release rate in conventional engines, and the computation of internal flows in divided chamber engines.</div>
Angiotensin II Controls Occludin Function and Is Required for Blood–Brain Barrier Maintenance: Relevance to Multiple Sclerosis (2007)

The blood-brain barrier (BBB) restricts molecular and cellular trafficking between the blood and the CNS. Although astrocytes are known to control BBB permeability, the molecular determinants of this effect remain unknown. We show that angiotensinogen (AGT) produced and secreted by astrocytes is cleaved into angiotensin II (AngII) and acts on type 1 angiotensin receptors (AT1) expressed by BBB endothelial cells (ECs). Activation of AT1 restricts the passage of molecular tracers across human BBB-derived ECs through threonine-phosphorylation of the tight junction protein occludin and its mobilization to lipid raft membrane microdomains. We also show that AGT knock-out animals have disorganized occludin strands at the level of the BBB and a diffuse accumulation of the endogenous serum protein plasminogen in the CNS, compared with wild-type animals. Finally, we demonstrate a reduction in the number of AGT-immunopositive perivascular astrocytes in multiple sclerosis (MS) lesions, which correlates with a reduced expression of occludin similarly seen in the CNS of AGT knock-out animals. Such a reduction in astrocyte-expressed AGT and AngII is dependent, in vitro, on the proinflammatory cytokines tumor necrosis factor-alpha and interferon-gamma. Our study defines a novel physiological role for AngII in the CNS and suggests that inflammation-induced downregulation of AngII production by astrocytes is involved in BBB dysfunction in MS lesions.
Orthodontic retention patterns in the United Kingdom (2009)

Vacuum retainers are popular in NHS, hospital and private practice. Bonded retainers are more commonly used in private practice than in other settings.
Formation Mechanism of Freestanding CH<sub>3</sub>NH<sub>3</sub>PbI<sub>3</sub> Functional Crystals: In Situ Transformation vs Dissolution–Crystallization (2014)

To date, the formation mechanism of organolead halide CH3NH3PbI3 perovskites based on the efficient sequential reaction route has remained virtually unexplored. Such a synthetic method usually yields high-performance solar cells with an efficiency over 15%, and the identification of the crystal growth mechanism is crucial for understanding the chemical reaction process and further improving the light converting efficiency. Herein, we develop a versatile and facile approach based on sequential reaction to produce freestanding CH3NH3PbI3 crystals as a model for crystal growth mechanism studies. It was found that the in situ transformation and dissolutioncrystallization mechanisms play competing roles in determining the characteristics of products that are largely depend on the chemical reaction kinetics. Such a method can also be readily used for synthesis of freestanding CH3NH3PbI3 crystals with controllable morphological characteristics, such as cuboids, rods, wires, and plates. The synthetic strategy as well as the crystal growth mechanisms exemplified here can also serve in the design and development of more sophisticated organolead halide perovskites as well as further optimization across a range of possible domains of applications.
Risk Estimation for Healthy Women from Breast Cancer Families (2004)

Risk estimation in breast cancer families is often estimated by use of the Claus tables. We analyzed the family histories of 196 counselees; compared the Claus tables with the Claus, the BRCA1/2, the BRCA1/2/ models; and performed linear regression analysis to extend the Claus tables with characteristics of hereditary breast cancer. Finally, we compared the Claus extended method with the Claus, the BRCA1/2, and the BRCA1/2/u models. We found 47% agreement for Claus table versus Claus model; 39% agreement for Claus table versus BRCA1/2 model; 48% agreement for Claus table versus BRCA1/2/u model; 37% agreement for Claus extended method versus Claus model; 44% agreement for Claus extended model versus BRCA1/2 model; and 66% agreement for Claus extended method versus BRCA1/2/u model. The regression formula (Claus extended method) for the lifetime risk for breast cancer was 0.08 + 0.40 (*) Claus Table + 0.07 (*) ovarian cancer + 0.08 (*) bilateral breast cancer + 0.07 (*) multiple cases. This new method for risk estimation, which is an extension of the Claus tables, incorporates information on the presence of ovarian cancer, bilateral breast cancer, and whether there are more than two affected relatives with breast cancer. This extension might offer a good alternative for breast cancer risk estimation in clinical practice.
Adsorption of PRG4 on commercially available contact lenses (2013)

INTRODUCTION Contact lens wear can cause corneal damage, which destabilizes the tear film that protects the ocular surface and may lead to Dry Eye Syndrome [1]. Contact lens-induced Dry Eye Syndrome causes significant discomfort and affects the quality of life of millions worldwide [2,3]. A possible cause of this discomfort is increased friction between ocular tissues [4]. Proteoglycan 4 (PRG4) is a mucin-like glycoprotein that was originally found in synovial fluid, but has also recently been discovered on the eye. It was shown to function as an effective boundary lubricant for the ocular surfaces [4], specifically between the cornea and eyelid or a contact lens [5]. However, these initial studies were not performed in the presence of tear film proteins, which can accumulate on contact lenses with wear causing discomfort [6]. The objectives of this project were to determine if PRG4 adheres to commercially available contact lenses, and to clarify whether PRG4 is able to maintain its boundary-lubricating ability at a cornea-contact lens biointerface in the presence of tear film proteins. METHODS A western blot was performed to measure adhesion of PRG4 on contact lenses. Samples were prepared by soaking commercial contact lenses Air Optix Aqua (AO), Acuvue Oasys (OAS), Acuvue 2 (Av2) in native bovine PRG4 overnight. The lenses were then rinsed three times in saline to remove excess PRG4, and then heated to 70°C to release PRG4 adhered to the lenses. These samples were loaded onto a gel and immunostained to test for presence of PRG4. The lubricity of commercially available contact lenses OAS and Acuvue TruEye (TE) was analyzed using a custom cornea-contact lens friction test. Lenses were soaked in an artificial tear solution (ATS) or ATS doped with PRG4 (ATS+PRG4), sent from collaborators at the University of Waterloo, to challenge the lenses to a proteinaceous condition. Friction tests measure axial load and torque to calculation friction coefficients for these lubrication conditions. RESULTS Figure 1. Image of a western blot membrane showing PRG4 adhesion of OAS, AO, and Av2 soaked in native PRG4. Western blots showed strong PRG4 adhesion (denoted by the density of the PRG4 bands) on silicone hydrogel contact lenses (OAS and AO), and little adhesion on a conventional hydrogel lens (Av2). AO clearly held onto PRG4 the best (Figure 1). Kinetic friction coefficients were not significantly different for the ATS and ATS+PRG4 conditions. Values of were higher for TE than OAS (0.35±0.18 TE; 0.28±0.14 OAS mean±SEM). DISCUSSION AND CONCLUSIONS PRG4 is known to have difficulty sticking to hydrophilic surfaces, such as Av2 conventional hydrogel lenses. Adding silicone to a lens makes it more hydrophobic, allowing PRG4 to better adhere to it [6]. PRG4 had no apparent effect in ATS, possibly due to PRG4 getting bound up in the hydrophobic lipids in ATS before adhering to the lens. Future experiments may examine soaking a contact lens in PRG4 first, before testing in ATS to prevent this, or testing a used contact lens.
Beam deflecting optical switch using volumetric thermal gratings (1984)

Volumetric thermal gratings were created in liquid and gaseous media and were used to efficiently deflect laser beams. In gaseous media, a low-input energy requirement and high switching efficiency make this type of switch a good candidate for a practical device. The switch is scalable to large apertures and has low insertion loss.
Synthesis of nucleic-acid base containing norbornene derivatives as monomers for ring-opening-metathesis–polymerization (2001)

A series of norbornene derivatives containing nucleic-acid bases (thymine, adenine, cytosine, guanine, or uracil) have been prepared as monomers for ring-opening-metathesis–polymerization (ROMP). Many of the initially prepared monomers had poor solubility but this could be overcome by appropriate choice of a linker between the norbornene and base units. Some of the monomers were successfully polymerised to give homopolymers derived from nucleic-acid bases.
Differences in Metabolite-Detecting, Adrenergic, and Immune Gene Expression After Moderate Exercise in Patients With Chronic Fatigue Syndrome, Patients With Multiple Sclerosis, and Healthy Controls (2011)

Postexercise mRNA increases in metabolite-detecting receptors were unique to patients with CFS, whereas both patients with MS and patients with CFS showed abnormal increases in adrenergic receptors. Among patients with MS, greater fatigue was correlated with blunted immune marker expression.
Full waveform inversion and the truncated Newton method: quantitative imaging of complex subsurface structures (2014)

ABSTRACT Full waveform inversion is a powerful tool for quantitative seismic imaging from wide‐azimuth seismic data. The method is based on the minimization of the misfit between observed and simulated data. This amounts to the solution of a large‐scale nonlinear minimization problem. The inverse Hessian operator plays a crucial role in this reconstruction process. Accounting accurately for the effect of this operator within the minimization scheme should correct for illumination deficits, restore the amplitude of the subsurface parameters, and help to remove artefacts generated by energetic multiple reflections. Conventional minimization methods (nonlinear conjugate gradient, quasi‐Newton methods) only roughly approximate the effect of this operator. In this study, we are interested in the truncated Newton minimization method. These methods are based on the computation of the model update through a matrix‐free conjugate gradient solution of the Newton linear system. We present a feasible implementation of this method for the full waveform inversion problem, based on a second‐order adjoint state formulation for the computation of Hessian‐vector products. We compare this method with conventional methods within the context of 2D acoustic frequency full waveform inversion for the reconstruction of P‐wave velocity models. Two test cases are investigated. The first is the synthetic BP 2004 model, representative of the Gulf of Mexico geology with high velocity contrasts associated with the presence of salt structures. The second is a 2D real data‐set from the Valhall oil field in North sea. Although, from a computational cost point of view, the truncated Newton method appears to be more expensive than conventional optimization algorithms, the results emphasize its increased robustness. A better reconstruction of the P‐wave velocity model is provided when energetic multiple reflections make it difficult to interpret the seismic data. A better trade‐off between regularization and resolution is obtained when noise contamination of the data requires one to regularize the solution of the inverse problem.
Multiscale Vessel Tracking (2004)

A method is presented that uses a vectorial multiscale feature image for wave front propagation between two or more user defined points to retrieve the central axis of tubular objects in digital images. Its implicit scale selection mechanism makes the method more robust to overlap and to the presence of adjacent structures than conventional techniques that propagate a wave front over a scalar image representing the maximum of a range of filters. The method is shown to retain its potential to cope with severe stenoses or imaging artifacts and objects with varying widths in simulated and actual two-dimensional angiographic images.
Exploring the interactome of EF-hand proteins (2010)

EF-hand proteins are central in many cellular processes being the main group of Ca2+-sensing and buffering proteins in the cell. In the work presented in this thesis we study ligand interactions of three EF-hand proteins; calmodulin, calbindin D28k and secretagogin. We have developed a screening method using proteins arrays and validation of targets with surface plasmon resonance. With have applied this method to the two proteins calmodulin and secretagogin. In a study of calmodulin interacting proteins we find 72 novel human calmodulin targets and determine the strength of their interaction with calmodulin. The relevance of the interactions is confirmed for four of the novel targets with co-immunoperciptations using cultured brain cells. For four of proteins we also determine the calmodulin binding sites. One of the calmodulin binding proteins found in the screen is the protein STIM1 which is essential for sensing and refilling the ER calcium stores. We show that the C-terminal of this protein binds to calmodulin and hypothesize that this process could be important in the termination of the refilling process. Using the same screening method in a study of secretagogin interacting proteins we identify nine novel target proteins and also show the interaction of three of them in brain tissue with GST-pull downs. The fact that six of the novel targets are proteins which are important in vesicle handling processes corroborates the theory that secretagogin is involved in secretion. We also study the protein calbindin D28k and show that the protein can bind three Zn2+-ions. The binding is associated with a small conformational change and we show that histidine 80 is involved in the coordination of one of the ions. We make the hypothesis that the biological role of the Zn2+-binding is to buffer the ions to protect the cell from high concentrations which can trigger apoptosis.
Hydrogen Production in <i>Chlamydomonas</i>: Photosystem II-Dependent and -Independent Pathways Differ in Their Requirement for Starch Metabolism  (2009)

Under sulfur deprivation conditions, the green alga Chlamydomonas reinhardtii produces hydrogen in the light in a sustainable manner thanks to the contribution of two pathways, direct and indirect. In the direct pathway, photosystem II (PSII) supplies electrons to hydrogenase through the photosynthetic electron transport chain, while in the indirect pathway, hydrogen is produced in the absence of PSII through a photosystem I-dependent process. Starch metabolism has been proposed to contribute to both pathways by feeding respiration and maintaining anoxia during the direct pathway and by supplying reductants to the plastoquinone pool during the indirect pathway. At variance with this scheme, we report that a mutant lacking starch (defective for sta6) produces similar hydrogen amounts as the parental strain in conditions of sulfur deprivation. However, when PSII is inhibited by 3-(3,4-dichlorophenyl)-1,1-dimethylurea, conditions where hydrogen is produced by the indirect pathway, hydrogen production is strongly reduced in the starch-deficient mutant. We conclude that starch breakdown contributes to the indirect pathway by feeding electrons to the plastoquinone pool but is dispensable for operation of the direct pathway that prevails in the absence of DCMU. While hydrogenase induction was strongly impaired in the starch-deficient mutant under dark anaerobic conditions, wild-type-like induction was observed in the light. Because this light-driven hydrogenase induction is DCMU insensitive and strongly inhibited by carbonyl cyanide-p-trifluoromethoxyphenylhydrazone or 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone, we conclude that this process is regulated by the proton gradient generated by cyclic electron flow around PSI.
Evaluation of Nickel/Palladium-Finished ICs With Lead-Free Solder Alloys (2001)

A nickel/palladium (Ni/Pd) lead finish for integrated circuits (IC) was introduced in 1989. In 1998, solderability test results were published on Ni/Pd-finished components using a Sn/Ag/Cu/Sb lead-free (Pb-free) solder paste and printed wiring board (PWB) pads coated with organic solderability preservative (OSP). Since then, a number of other Pb-free solder alloys have been introduced. This evaluation shows soldering and reliability performance of Ni/Pd-finished components with the leading Pb-free solder alloys now being considered by the electronics industry. The ICs tested were 20-pin small-outline integrated circuit (SOIC) and 56-pin shrink small-outline package (SSOP) gull-wing leaded devices finished with four-layer Ni/Pd. The solder alloys were Sn/Pb/Ag (control), Sn/Ag/Cu, Sn/Bi, Sn/Ag/Cu/Sb, Sn/Zn/Bi, and Sn/Zn. The land pads on the test PWB were coated with an OSP. Using Pb-free Ni/Pd-finished components, a Pb-free solder alloy, and an OSP coating, a Pb-free assembly was achieved and evaluated. Additionally, Ni/Pd/Au-finished IC leads were soldered using the Sn/Ag/Cu paste. Evaluations of each alloy included visual appearance, lead pull before and after
Bi-directional wireless power transfer technology for wireless sensor/power networks (2013)

This study approaches a new proposal for “the wireless power networks (WPNs)”. Injecting the wireless ad-hoc networks with newly bi-directional power transfer has the advantage of stabilizing networks operation when a power source happens to broke down. This research putting network at forefront, proves that make a fundamental demonstration for bi-directional wireless power transfer (BD-WPT) system using an electric resonant coupler to an experimental level of WPNs. There is also the fact that, a space modeling deliberates an equivalent circuit of the coupler. WPNs are thought to make a large contribution to stable operation, and consequently making save wireless sensor networks.
RNA replicons derived from poliovirus are directly oncolytic for human tumor cells of diverse origins. (2001)

The failure and/or toxicity of conventional therapies for many types of human cancers underscore the need for development of safe and effective alternative treatments. Toward this goal, we describe the direct oncolytic activity of RNA-based vectors derived from poliovirus, termed replicons, which are genetically incapable of producing infectious virus. These replicons are cytopathic in vitro for human tumor cells originating from brain, breast, lung, ovary, and skin (melanoma). The cytopathic effects in a malignant glioma cell line were associated with nuclear DNA condensation, indicative of cells undergoing apoptosis. Injection of replicons into established xenograft flank tumors in scid mice resulted in oncolytic activity and extended survival. Inoculation of replicons into established intracranial xenograft tumors in scid mice resulted in tumor infection within 8 h and extended survival. Histological analysis revealed that replicons had infected tumor cells at the site of inoculation and, most importantly, diffused to infect tumor cells that had metastasized from the initial site of implantation. The wide spectrum of cytopathic activity for human tumors combined with effective distribution after in vivo inoculation establishes the therapeutic potential of poliovirus replicons for a variety of cancers.