gebhart/patrepeval huggingface dataset:
Glycan Dependence of Galectin-3 Self-Association Properties (2014)

Human Galectin-3 is found in the nucleus, the cytoplasm and at the cell surface. This lectin is constituted of two domains: an unfolded N-terminal domain and a C-terminal Carbohydrate Recognition Domain (CRD). There are still uncertainties about the relationship between the quaternary structure of Galectin-3 and its carbohydrate binding properties. Two types of self-association have been described for this lectin: a C-type self-association and a N-type self-association. Herein, we have analyzed Galectin-3 oligomerization by Dynamic Light Scattering using both the recombinant CRD and the full length lectin. Our results proved that LNnT induces N-type self-association of full length Galectin-3. Moreover, from Nuclear Magnetic Resonance (NMR) and Surface Plasmon Resonance experiments, we observed no significant specificity or affinity variations for carbohydrates related to the presence of the N-terminal domain of Galectin-3. NMR mapping clearly established that the N-terminal domain interacts with the CRD. We propose that LNnT induces a release of the N-terminal domain resulting in the glycan-dependent self-association of Galectin-3 through N-terminal domain interactions.
Uroscopy in the 21st century: high-field NMR spectroscopy (1997)

From the experiments described, it can be seen that there are different research approaches that can be taken and these are summarized in Table 1. Whereas much scientific research is principally hypothesis led, there remains, nevertheless, an important place for exploratory research. High resolution NMR can measure, directly and simultaneously, a wide range of endogenous metabolites in biological fluids and has the unique capability of providing structural information on the metabolites detected. It has proved to be a powerful research tool with which to study inherited metabolic diseases, renal disease, drug metabolism, and toxicity, and can be used to monitor the effects of drug therapy. For instance, by using a library of experimental toxins one can map the metabolic profile of site-specific nephron injury. With this approach in man one could eventually take an unknown disease such as Balkan nephropathy and predict the initial site of tubular injury, the mode of injury and therefore the kind of toxin capable of producing that injury. NMR spectroscopic techniques are still advancing rapidly, with ever increasing sensitivity and sophistication of NMR pulse sequences to enhance structural elucidation in complex mixtures. Given the advances in directly coupled HPLC-NMR and even HPLC-NMR-mass spectroscopy it is likely that these technologies in conjunction with pattern recognition will make major contribution to our understanding of renal processes and provide new diagnostic insights in the 21st century.
Improving security and performance for capability systems (2021)

This dissertation examines two major limitations of capability systems: an inability to support security policies that enforce confinement and a reputation for relatively poor performance when compared with non-capability systems. The dissertation examines why conventional capability systems cannot enforce confinement and proposes a new secure capability architecture, called SCAP, in which confinement can be enforced. SCAP is based on the earlier Cambridge Capability System, CAP. The dissertation shows how a non-discretionary security policy can be implemented on the new architecture, and how the new architecture can also be used to improve traceability of access and revocation of access. The dissertation also examines how capability systems are vulnerable to discretionary Trojan horse attacks and proposes a defence based on rules built into the command-language interpreter. System-wide garbage collection, commonly used in most capability systems, is examined in the light of the non-discretionary security policies and found to be fundamentally insecure. The dissertation proposes alternative approaches to storage management to provide at least some of the benefits of system-wide garbage collection, but without the accompanying security problems. Performance of capability systems is improved by two major techniques. First, the doctrine of programming generality is addressed as one major cause of poor performance. Protection domains should be allocated only for genuine security reasons, rather than at every subroutine boundary. Compilers can better enforce modularity and good programming style without adding the expense of security enforcement to every subroutine call. Second, the ideas of reduced instruction set computers (RISC) can be applied to capability systems to simplify the operations required. The dissertation identifies a minimum set of hardware functions needed to obtain good performance for a capability system. This set is much smaller than previous research had indicated necessary. A prototype implementation of some of the capability features is described. The prototype was implemented on a re-microprogrammed VAX-11/730 computer. The dissertation examines the performance and software compatibility implications of the new capability architecture, both in the context of conventional computers, such as the VAX, and in the context of RISC processors.
Impact of anthropogenic sources of pollution on the quality of the Dniester river in Ukraine (2022)

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Infra-red microscopy of Cd(Zn)Te radiation detectors revealing their internal electric field structure under bias (1996)

This paper describes the use of the Pockels electro-optic effect to both visualise and measure the internal electric field present within CdZnTe detectors under normal bias conditions. Use was made of a silicon charge coupled device (CCD), as an image sensor, in conjunction with a 940 nm LED to illuminate a 3/spl times/3/spl times/5 mm detector crystal with polarised infra-red light. The experiment was arranged so that a /spl times/40 image of the crystal showing a contour plot of electric field intensity could be generated. Further, more precise E-field measurements, were obtained using a 1.2 /spl mu/m laser diode (LD) and a germanium photodiode detector. Together these experiments indicate substantially non-uniform electric fields within the detector crystals used.
A Central Role for the Armadillo Protein Plakoglobin in the Autoimmune Disease Pemphigus Vulgaris (2001)

In pemphigus vulgaris (PV), autoantibody binding to desmoglein (Dsg) 3 induces loss of intercellular adhesion in skin and mucous membranes. Two hypotheses are currently favored to explain the underlying molecular mechanisms: (a) disruption of adhesion through steric hindrance, and (b) interference of desmosomal cadherin-bound antibody with intracellular events, which we speculated to involve plakoglobin. To investigate the second hypothesis we established keratinocyte cultures from plakoglobin knockout (PG-/-) embryos and PG+/+ control mice. Although both cell types exhibited desmosomal cadherin-mediated adhesion during calcium-induced differentiation and bound PV immunoglobin (IgG) at their cell surface, only PG+/+ keratinocytes responded with keratin retraction and loss of adhesion. When full-length plakoglobin was reintroduced into PG-/- cells, responsiveness to PV IgG was restored. Moreover, in these cells like in PG+/+ keratinocytes, PV IgG binding severely affected the linear distribution of plakoglobin at the plasma membrane. Taken together, the establishment of an in vitro model using PG+/+ and PG-/- keratinocytes allowed us (a) to exclude the steric hindrance only hypothesis, and (b) to demonstrate for the first time that plakoglobin plays a central role in PV, a finding that will provide a novel direction for investigations of the molecular mechanisms leading to PV, and on the function of plakoglobin in differentiating keratinocytes.
Oxidative interactions between haemoglobin and membrane lipid. A liposome model (1984)

The relationship between haemoglobin and membrane oxidation was studied using liposomes containing haemoglobin (haemosomes) as a red cell model. Rapid oxidation occurred in haemosomes formed from purified haemoglobin and unsaturated lipid (egg phosphatidylcholines). After 3 h at 37 degrees C most of the haemoglobin was oxidized, predominantly to methaemoglobin with some haemichrome formation. The oxidation of haemoglobin was paralleled by membrane lipid peroxidation as measured by thiobarbituric acid reactivity. These changes were largely abolished by using freshly prepared haemolysate instead of purified haemoglobin, or when haemosomes were prepared with saturated phosphatidylcholines. In haemosomes consisting of fresh haemolysate and saturated phosphatidylcholine, the rate of haemoglobin oxidation at 37 degrees C corresponded to that of non-encapsulated haemolysate, and after 4 months storage at 4 degrees C 45% of oxyhaemoglobin was oxidized. In haemosomes prepared from purified haemoglobin and egg lecithin, alpha-tocopherol, catalase and ascorbate each protected against both haemoglobin oxidation and lipid peroxidation. Superoxide dismutase or reduced glutathione had no effect. In unsaturated-lipid haemosomes containing haemolysate, the rate of haemoglobin oxidation increased when catalase was inhibited or reduced glutathione was depleted, but after long term incubation only concurrent catalase-inhibition and glutathione depletion could increase thiobarbituric acid reactivity. These results demonstrate a close interdependence between haemoglobin oxidation and lipid peroxidation, and show that constituents of haemolysate strongly protect against both processes. H2O2 appears to be an important mediator, with its removal by either catalase or the glutathione/glutathione peroxidase system protecting against both oxidative changes.
Bright afterglow illuminator made of phosphorescent material and fluorescent fibers (2000)

Phosphorescent oxides and fluorescent dyes were used together to create a fiber-type illuminator that glows in the dark without the need for electric power. Dye-doped polymer fibers, which were bundled at one end, were linearly arrayed in a polysiloxane resin that contained phosphorescent oxide particles. The phosphorescent resin continued to glow for a long time even after the excitation light was removed. Organic dyes in a polymer fiber were excited by the phosphorescence and emitted fluorescence toward the fiber end. Fluorescence from a number of dyes was combined in the long fiber, and, consequently a bright light beam emerged from the fiber end. Useful performance, i.e., high power density, narrow beam divergence, and long afterglow, is demonstrated by the prototype fiber illuminator.
Identification of a long non-coding RNA as a novel biomarker and potential therapeutic target for metastatic prostate cancer (2014)

Metastatic prostate cancer (PCa) is still an incurable disease. Long non-coding RNAs (lncRNAs) may be an overlooked source of cancer biomarkers and therapeutic targets. We therefore performed RNA sequencing on paired metastatic/non-metastatic PCa xenografts derived from clinical specimens. The most highly up-regulated transcript was LOC728606, a lncRNA now designated PCAT18. PCAT18 is specifically expressed in the prostate compared to 11 other normal tissues (p<0.05) and up-regulated in PCa compared to 15 other neoplasms (p<0.001). Cancer-specific up-regulation of PCAT18 was confirmed on an independent dataset of PCa and benign prostatic hyperplasia samples (p<0.001). PCAT18 was detectable in plasma samples and increased incrementally from healthy individuals to those with localized and metastatic PCa (p<0.01). We identified a PCAT18-associated expression signature (PES), which is highly PCa-specific and activated in metastatic vs. primary PCa samples (p<1E-4, odds ratio>2). The PES was significantly associated with androgen receptor (AR) signalling. Accordingly, AR activation dramatically up-regulated PCAT18 expression in vitro and in vivo. PCAT18 silencing significantly (p<0.001) inhibited PCa cell proliferation and triggered caspase 3/7 activation, with no effect on non-neoplastic cells. PCAT18 silencing also inhibited PCa cell migration (p<0.01) and invasion (p<0.01). These results position PCAT18 as a potential therapeutic target and biomarker for metastatic PCa.
Graph-Based Global Reasoning Networks (2018)

Globally modeling and reasoning over relations between regions can be beneficial for many computer vision tasks on both images and videos. Convolutional Neural Networks (CNNs) excel at modeling local relations by convolution operations, but they are typically inefficient at capturing global relations between distant regions and require stacking multiple convolution layers. In this work, we propose a new approach for reasoning globally in which a set of features are globally aggregated over the coordinate space and then projected to an interaction space where relational reasoning can be efficiently computed. After reasoning, relation-aware features are distributed back to the original coordinate space for down-stream tasks. We further present a highly efficient instantiation of the proposed approach and introduce the Global Reasoning unit (GloRe unit) that implements the coordinate-interaction space mapping by weighted global pooling and weighted broadcasting, and the relation reasoning via graph convolution on a small graph in interaction space. The proposed GloRe unit is lightweight, end-to-end trainable and can be easily plugged into existing CNNs for a wide range of tasks. Extensive experiments show our GloRe unit can consistently boost the performance of state-of-the-art backbone architectures, including ResNet, ResNeXt, SE-Net and DPN, for both 2D and 3D CNNs, on image classification, semantic segmentation and video action recognition task.
Analysis of Subpocket Selectivity and Identification of Potent Selective Inhibitors for Matriptase and Matriptase-2 (2014)

We studied the factors affecting the selectivity of peptidomimetic inhibitors of the highly homologous proteases matriptase and matriptase-2 across subpockets using docking simulations. We observed that the farther away a subpocket is located from the catalytic site, the more pronounced its role in selectivity. As a result of our exhaustive virtual screening, we biochemically validated novel potent and selective inhibitors of both enzymes.
"Missed pill" conception: fact or fiction? (1985)

A study of 19 healthy nulliparous women 20-30 years who were using the low dose combined oral contraceptive (OC) demonstrated ovarian folliculogenesis during the 7-day withdrawal in 28 day cycles. This makes the genuine occurrence of conceptions seem less mythical. All of the women had normal menstrual histories before OC use. They had been on treatment for at least 3 months and had regular monthly withdrawal bleeds. Ultrasonographic examination of the ovaries was performed on the last day of 1 pack (day 21) on the last pill day (day 28) and on the 7th day of the next pack (day 7). An Elscint Dynex sector scanner with a 3.5 MHz probe was used which is capable of measuring down to 1.5 mm. All subjects showed some ovarian follicular activity by the last day of the pill-free phase and half developed multiple follicles with a dominant follicular diameter of 7 mm or greater the diameter seen on day 7 of the normal cycle. Continuation of the gonadotrophin stimulation of these dominant follicles would have led to ovulation. By the 7th day of the new pack the follicular appearance had returned to the dormant condition shown by the 1st scan in all but 1 subject and she showed reduction in follicular diameter. No pills were missed by any subject during the study cycles. In 2 subjects small cysts were detected at the 1st scan and at the 2nd and 3rd examinations unaffected by the development and regression of the other follicles. 1 subject inadvertently missed a on day 5 of a cycle after completing the study. She was examined 24 hours later and a 10 mm follicle was seen. She was unable to attend for further examination. With the current 21 day pack it is strongly recommended that alternative contraception be used when a is missed during the first 7 days of a pack even if the woman has been using OC for some time. This is most likely not necessary when a is missed later in the course. Women using OCs should also be warned of the danger of delaying restarting treatment after the 7 free days.
Sensemaking in Organizations (1996)

The Nature of Sensemaking Seven Properties of Sensemaking Sensemaking in Organizations Occasions for Sensemaking The Substance of Sensemaking Belief-Driven Processes of Sensemaking Action-Driven Processes of Sensemaking The Future of Sensemaking
The Design Of Fiber Optic Sensors For Measuring Hydrodynamic Parameters (2002)

We present an approximate analytic model that has been developed for examining hydrodynamic flow near the surface of a fiber optic sensor. An analysis of the conservation of momentum, the continuity equation and the Navier-Stokes equation for compressible flow was used to develop expressions for the velocity and the density as a function of the distance along the flow and above a two dimensional flat surface. When examining the flow near the surface, these expressions can be used to estimate the sensitivity required to perform direct optical measurements and to parameterize the shear force for indirect optical measurements. The use of these results allows for direct modeling of sensors using the optical properties of the flow field. Future work includes analyzing the optical parametric design of fiber optic sensors, modeling sensors to utilize those parameters for optimal measurements involving different mixtures of fluid flow.
Preparation and Properties of Octenyl Succinic Anhydride Modified Early <b><i>Indica</i></b> Rice Starch (2006)

Abstract Octenyl succinic anhydride (OSA) modified early indica rice starch was prepared in aqueous slurry systems and the major factors affecting the esterification were investigated systematically. The physicochemical properties of the products were determined by means of Fourier transform infrared (FT‐IR) spectroscopy, scanning electron microscopy (SEM), X‐ray diffraction and Rapid Visco Analyser (RVA). The results indicated that the suitable parameters for the preparation of OSA starch from early indica rice starch in aqueous slurry systems were as follows: concentration of starch slurry 35% (in proportion to water, w/w), reaction period 4 h, pH of reaction system 8.5, reaction temperature 35°C, amount of OSA 3% (in proportion to starch, w/w). The degree of substitution (DS) was 0 018 and the reaction efficiency (RE) was 78%. FT‐IR spectroscopy showed characteristic absorption of the ester carbonyl groups in the OSA starch at 1724 cm ‐1 . SEM and X‐ray diffraction revealed that OSA groups acted by first attacking the surface and some pores formed, but OSA modification caused no change in the crystalline pattern of rice starch up to DS 0.046. RVA results indicated that the starch derivatives gelatinized at shorter time to achieve higher viscosities with increased OSA modification.
Environmental vulnerability and resilience: Social differentiation in short‐ and long‐term flood impacts (2020)

This paper finds that social differentiation in flood impacts is relatively small soon after a flood, with some surprising results such as professionals and homeowners badly affected in the short‐term – but widens over time, with socially disadvantaged groups displaying less recovery. The paper concludes that vulnerability and resilience to flooding are sensitive to financial resources, institutional support (chiefly from a landlord), and capacity to deal with disruption (chiefly time availability, which is low among professionals and high among retired people). An implication of these findings is that existing indices of flood vulnerability that use multiple measures of social deprivation should be used with caution, as not all conventional aspects of social deprivation are necessarily associated with greater vulnerability to flood impacts.
XLP: A Cross-Layer Protocol for Efficient Communication in Wireless Sensor Networks (2010)

Severe energy constraints of battery-powered sensor nodes necessitate energy-efficient communication in Wireless Sensor Networks (WSNs). However, the vast majority of the existing solutions are based on the classical layered protocol approach, which leads to significant overhead. It is much more efficient to have a unified scheme, which blends common protocol layer functionalities into a cross-layer module. In this paper, a cross-layer protocol (XLP) is introduced, which achieves congestion control, routing, and medium access control in a cross-layer fashion. The design principle of XLP is based on the cross-layer concept of initiative determination, which enables receiver-based contention, initiative-based forwarding, local congestion control, and distributed duty cycle operation to realize efficient and reliable communication in WSNs. The initiative determination requires simple comparisons against thresholds, and thus, is very simple to implement, even on computationally constrained devices. To the best of our knowledge, XLP is the first protocol that integrates functionalities of all layers from PHY to transport into a cross-layer protocol. A cross-layer analytical framework is developed to investigate the performance of the XLP. Moreover, in a cross-layer simulation platform, the state-of-the-art layered and cross-layer protocols have been implemented along with XLP for performance evaluations. XLP significantly improves the communication performance and outperforms the traditional layered protocol architectures in terms of both network performance and implementation complexity.
Improving the Maintenance Planning of Heavy Trucks using Constraint Programming (2013)

Maintenance planning of heavy trucks at Scania is presently done using static cyclic plans where each maintenance occasion contains a xed set of components. Using vehicle operational data gained fr ...
Decomposition Methods for Differential Equations: Theory and Applications (2009)

Exploring iterative operator-splitting methods, this work describes the analysis of numerical methods for evolution equations based on temporal and spatial decomposition methods. It generalizes the numerical analysis with respect to the consistency and stability to nonlinear, stiff, and spatial decomposed splitting problems.
A Novel Architecture to Build Ideal-linearity Neuromorphic Synapses on a Pure Logic FinFET Platform Featuring 2.5ns PGM-time and 10<sup>12</sup> Endurance (2019)

In this work, we will explore pure logic FinFET devices to realize the functionality of linear weight tuning capability as electric synapses. The unit cell of this new FinFET synapse is composed of two identical FinFETs in series; one serves as control and the other one as storage. This new FinFET synapse exhibits ideal linearity with nearly infinity training cycles (>10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">12</sup> ), much lower programming voltage, 0.85V, and faster speed, 2.5ns. It can also analogically increase or decrease the transistor's V <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">th</sub> to vary the drain conductance. As far as the analog performance is concerned, it performs excellent linearity and a wide tuning-window (20×) of weight-tuning capability. 1kb synaptic array has also been designed. The spice-simulated results have shown that new FinFET synaptic array can expand the array-size to 64×64, exhibiting 300× of SNR, w.r.t. that of RRAM array. Finally, the training of the neural network based on the proposed FinFET synapse can achieve 97.43% accuracy as high as the GPU one does.