gebhart/patrepeval huggingface dataset:
Binding at molecule/gold transport interfaces. I. Geometry and bonding (2003)

Density functional methods on cluster models are used to examine the nature of the geometry, bonding, and energetics involved in the formation of molecular thiol junctions at gold electrode interfaces. The two gold electrodes are modeled as four atom clusters, without geometric constraint. We observe that the geometry nearly always favors twofold coordination of the thiol to a nearly planar array of four gold atoms. There are four essential structural motifs, that seem to characterize these interactions for alkyne, alkane, xylyl, and benzene dithiols. Bonding interactions are relatively strong, and correspond to a polarized covalent interaction. Results are given for different charge and spin components on the molecular bridge.
Interlaced realtime channel-domain photoacoustic and ultrasound imaging (2011)

Photoacoustic imaging offers a new and complementary contrast mechanism to the traditional structural contrast of ultrasound. While the combination of these two modes has been demonstrated in the past with single-element transducers, array transducers offer clear advantages in both modes by eliminating mechanical scanning and allowing image formation from a single excitation. Given the abundance of commercially available ultrasound systems, it is desirable to use them as much as possible. However, these systems often only allow access to beamformed RF data. We discuss the applicability of ultrasound beamformers for photoacoustic imaging, and find that with only software-defined control over the speed of sound, walking aperture reconstruction is optimally performed using a speed correction factor of 1.414. When sector-scanning is used, a different strategy is required. We also demonstrate a new photoacoustic-ultrasound imaging system based on a Verasonics ultrasound array system. The system streams raw channel data to a 6-core PC at up to 1.4GB/s via PCI-Express, allowing interlaced ultrasound and photoacoustic data to be acquired and reconstructed at realtime rates. Using an L7-4 linear array transducer, we demonstrate the performance of this system and discuss potential applications. The system should provide new opportunities for clinical and pre-clinical imaging.
Mechanistic and Functional Shades of Mucins and Associated Glycans in Colon Cancer (2020)

Mucus serves as the chief protective barrier against pathogenic and mechanical insults in respiratory, gastrointestinal, and urogenital tracts. Altered mucin expression, the major component of mucus, in conjunction with differential glycosylation has been strongly associated with both benign and malignant pathologies of colon. Mucins and their associated glycans arbitrate their impact sterically as well as mechanically by altering molecular and microbial spectrum during pathogenesis. Mucin expression in normal and pathological conditions is regulated by nonspecific (dietary factors and gut microbiota) and specific (epigenetic and transcriptional) modulators. Further, recent studies highlight the impact of altering mucin glycome (cancer-associated carbohydrate antigens including Tn, Sialyl-Tn, Sialyl-Lew A, and Sialyl-Lewis X) on host immunomodulation, antitumor immunity, as well as gut microbiota. In light of emerging literature, the present review article digs into the impact of structural organization and of expressional and glycosylation alteration of mucin family members on benign and malignant pathologies of colorectal cancer.
[cDNA microarray technology as a laboratory examination method: a gene expression profiling test for analysis of drug resistance in tumor cells]. (2002)

cDNA microarray technology permits the simultaneous measurement of the expressions of thousands of genes. The technology is now an indispensable research tool in molecular biology, and the challenge is its development and usage as clinical diagnostic tools. cDNA microarray can be used to identify gene expression profiles in tumor cells which correlate strongly with the treatment responsiveness such as drug resistance and clinical outcome of the disease despite similar phenotypes. For the introduction of cDNA microarray into laboratory examination, many issues need to be resolved. Design of a diagnostic array must be developed with defined sequences based on interpretation of huge quantities of data from experimental arrays to predict treatment responsiveness. Assay quality must be improved in terms of detection sensitivity, reproducibility, and linear dynamic range for RNA quantitation. Generally available instruments, which are much less expensive and more practical, need to be developed. Along with the improvement of the assay as a laboratory examination method, cDNA microarray will facilitate the integration of diagnosis and therapeutics, and the introduction of individual medicines.
Using Eye-Tracking Technology to Capture Visual Attention during Interpretation of a Simulated Bedside Monitor (2015)

Eye-Tracking technology is a tool for collecting data on a person’s visual attention and is suitable for psychological and physiological studies (e.g. reading and psychological response studies). The data captured can provide us a number of statistics regarding the participant’s interaction with stimuli. With selected areas of interest within visual stimuli provided to the participant, we can take numerous measurements (e.g. the time taken to first fixation, the total number of fixations, the total duration of all fixations etc.) The technology has already been used within healthcare-related research with positive outcomes in distinguishing patterns and metrics among different groups of users. Our hypothesis is that this data can be used to infer the competency of interpreters of clinical bedside monitors. A PhD study has been designed to capture the eye gaze and scan-path of nurses with mixed levels of expertise (nursing undergraduates to practicing nurses) whilst they interpret a simulated bedside monitor. During this recording, they will verbalise their interpretation and they will be given a score according to set criteria (validated by nursing experts at Ulster University). We expect this data when analysed will show quantitative differences that distinguish users as experts, competent and lacking competency. The captured data can be transformed into metrics for determining proficiency whilst reading and interpreting vital signs on a bedside monitor. These could be used within patient monitoring training as another form of assessment during a simulation.
BUCILLAMINE, A DIFFUSIBLE ANTIOXIDANT, PREVENTS ISCHEMIA/REPERFUSION INJURY IN AN EX-VIVO RAT LIVER MODEL. (2000)

Amersi, Farin F.1; Nelson, Sally K.2; Farmer, Douglas G.1; Kato, Hirohisa1; Melinek, Judy1; Zaky, Joseph1; Kupiec-Weglinski, Jerzy W.1; Horwitz, Lawrence D.3; Busuttil, Ronald W.1; Horwitz, Marcus A.4 Author Information
RANKL/RANK Pathway and Its Inhibitor RANK-Fc in Uterine Leiomyoma Growth (2018)

Treatment with the RANKL/RANK pathway inhibitor RANK-Fc significantly decreased human leiomyoma cell proliferation and tumor growth. This suggests that the RANKL/RANK pathway could serve as a potential target for the prevention and treatment of uterine leiomyoma.
Production Environment Laser Assisted Machining of Silicon Nitride (2010)

This chapter contains sections titled: Introduction Experimental Set Up & Testing Experimental Results and Discussion Conclusions Future Work Acknowledgements
Combined Structure Geometry and Anode Placement Effects on Cathodic Protection Effectiveness (2017)

Abstract An impressed current cathodic protection system was applied to an uncoated test sample. The test sample was chosen to represent an essential right angle feature of a common structure. Anode placement was quantitatively shown to affect the resulting surface polarization distribution. Two distinct types of local polarization depletion zones have been demonstrated. These regions of lesser polarization represent a locally insufficient amount of cathodic protection compared to criteria designated values. Conversely, for geometrically complex structures containing sharp features, the possibility of locally evolving hydrogen gas is also discussed.
Fast antenna-weights tracking algorithm of adaptive antenna array diversity receiver in W-CDMA reverse link (2002)

In wideband direct sequence code division multiple access (W-CDMA), employing an adaptive antenna array is a very promising technique to reduce severe multiple access interference (MAI) especially from high rate users. This paper proposes a fast and accurate two-step antenna-weight tracking algorithm incorporated in a pilot symbol-assisted coherent adaptive antenna array diversity (PSA-CAAAD) receiver and evaluates its performance both by computer simulations and laboratory experiments. In the proposed scheme, the receiver antenna weights are updated by using both an adaptive algorithm based on the minimum mean square error (MMSE) criterion and the signal-to-interference power ratio (SIR) measurements employing multiple sets of antenna weights (MSAW), in which other sets except for a master set of antenna weights are simply generated by a master set. Computer simulation results show that antenna weights of a four-antenna PSA-CAAAD receiver using the proposed beam-tracking algorithm tracks changes in the direction of arrival (DOA) of the desired user at up to 20 degrees per sec, which corresponds to 250 km/h at 200 m from a base station. We also confirm, based on experiments in a radio anechoic room, that the generated antenna weights can track the DOA changes of up to 12 degrees/sec.
Distance-Dependent Metal-Enhanced Intrinsic Fluorescence of Proteins Using Polyelectrolyte Layer-by-Layer Assembly and Aluminum Nanoparticles (2012)

Previously reported studies indicate that aluminum nanostructured substrates can potentially find widespread use in metal-enhanced fluorescence (MEF) applications particularly in the UV or near-UV spectral region toward label-free detection of biomolecules. MEF largely depends on several factors, such as chemical nature, size, shape of the nanostructure and its distance from the fluorophore. A detailed understanding of the MEF and its distance-dependence are important for its potential application in biomedical sensing. Our goal is to utilize intrinsic protein fluorescence for label-free binding assays. This is made possible by the use of metallic nanostructures which provide localized excitation and enhanced fluorescence of UV fluorophores and will also provide a way to separate the surface-bound proteins from the bulk samples. We evaluated varied probe distances from plasmonic nanostructures by the well-established layer-by-layer (LbL) technique. The investigated proteins were adsorbed on different numbers of alternate layers of poly(styrene sulfonate) (PSS) and poly(allylamine hydrochloride) (PAH). Bovine serum albumin (BSA) was electrostatically attached to the positively charged PAH layer, and goat and rabbit IgG were attached to negatively charged PSS layer. We obtained a maximum of a ~ 9 fold increase in fluorescence intensity from BSA at a distance of ~9 nm from the Al nanostructured surface. Approximately 6- and 7- fold increases were observed from goat and rabbit IgG at a distance of ~8 nm, respectively. The minimum lifetimes were about 3-fold shorter than those on bare control quartz slides for all three proteins. The time-resolved intensity decays were analyzed with a lifetime distribution model to understand the distance effect on the metal-fluorophore interaction in detail. The present study indicates the distance dependence nature of metal-enhanced intrinsic fluorescence of proteins and potential of LbL assembly to control the metal-to-fluorophore distance in the UV wavelength region.
Self-Supervised Contrastive Learning with Adversarial Perturbations for Robust Pretrained Language Models (2021)

This paper improves the robustness of the pretrained language model BERT against word substitution-based adversarial attacks by leveraging self-supervised contrastive learning with adversarial perturbations. One advantage of our method compared to previous works is that it is capable of improving model robustness without using any labels. Additionally, we also create an adversarial attack for word-level adversarial training on BERT. The attack is efficient, allowing adversarial training for BERT on adversarial examples generated on the fly during training. Experimental results on four datasets show that our method improves the robustness of BERT against four different word substitution-based adversarial attacks. Furthermore, to understand why our method can improve the model robustness against adversarial attacks, we study vector representations of clean examples and their corresponding adversarial examples before and after applying our method. As our method improves model robustness with unlabeled raw data, it opens up the possibility of using large text datasets to train robust language models.
RNA Silencing of Mycotoxin Production in <i>Aspergillus</i> and <i>Fusarium</i> Species (2005)

Mycotoxins are natural fungal products that are defined by their harmful effects on humans and animals. Aflatoxin contamination of maize by Aspergillus species and trichothecene contamination of small grains by Fusarium species are two of the most severe mycotoxin problems in the United States. We are investigating RNA silencing in an effort to identify novel ways to control mycotoxin contamination of crops. Transformation of two Aspergilli (A. flavus and A. parasiticus) and a Fusarium (F. graminearum) with inverted repeat transgenes (IRT) containing sequences of mycotoxin-specific regulatory genes suppressed mycotoxin production in all three plant-pathogenic fungi. This atoxigenic phenotype was stable during infection on corn and wheat, and importantly, F. graminearum IRT strains were less virulent on wheat than were wild type. The IRT did not alter physiological characteristics of the fungi, such as spore production and growth rate on solid media. These results indicate that RNA silencing exists in Aspergillus and Fusarium plant pathogens and suggest that RNA silencing technology may be a useful tool for eliminating mycotoxin contamination of agricultural products.
Chain contribution to the Seebeck coefficient in<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">YBa</mml:mi></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">Cu</mml:mi></mml:mrow><mml:mrow><mml:mn>3</mml:mn></mml:mrow></mml:msub></mml:mrow></mml:math><mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML" display="inline"><mml:mrow><mml:msub><mml:mrow><mml:mi mathvariant="normal">O</mml:mi></mml:mrow><mml:mrow><mml:mn>7</mml:mn><mml:mi mathvariant="normal">−</mml:mi><mml:mi mathvariant="normal">δ</mml:mi></mml:mrow></mml:msub></mml:mrow></mml:math> (1995)

Measurements of the Seebeck coefficient \ensuremath{\alpha}(T) and the resistivity R(T) of polycrystalline ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{7\mathrm{\ensuremath{-}}\mathrm{\ensuremath{\delta}}}$ quenched from different temperatures ${\mathit{T}}_{\mathit{q}}$ and of polycrystalline (${\mathrm{Y}}_{1\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{Ca}}_{\mathit{x}}$)(${\mathrm{Ba}}_{2\mathrm{\ensuremath{-}}\mathit{x}}$${\mathrm{La}}_{\mathit{x}}$)${\mathrm{Cu}}_{3}$${\mathrm{O}}_{6.96\ifmmode\pm\else\textpm\fi{}0.01}$ were made to distinguish the contributions to \ensuremath{\alpha}(T) from the Cu(1)O chains and the ${\mathrm{CuO}}_{2}$ sheets. The ${\mathrm{CuO}}_{2}$ sheets give a positive contribution to \ensuremath{\alpha}(T) that is composed of a weakly temperature-dependent part ${\mathrm{\ensuremath{\alpha}}}_{0}$ that decreases sensitively with increasing oxidation and an enhancement part \ensuremath{\delta}\ensuremath{\alpha} that gives a broad maximum to \ensuremath{\alpha}(T) at a ${\mathit{T}}_{\mathrm{max}}$\ensuremath{\approxeq}140 \ifmmode^\circ\else\textdegree\fi{}C. These two features together have been shown to distinguish the superconductive compositions from the parent and overdoped compositions in other copper-oxide supeconductors. In fully oxidized ${\mathrm{YBa}}_{2}$${\mathrm{Cu}}_{3}$${\mathrm{O}}_{6.96}$, the contribution to \ensuremath{\alpha}(T) from the ${\mathrm{CuO}}_{2}$ sheets is obscured by a dominant, competitive negative contribution to \ensuremath{\alpha}(T) from the chains that has a similar, but negative, \ensuremath{\delta}\ensuremath{\alpha} enhancement.
On Burnett coefficients in periodic media (2006)

The aim of this work is to demonstrate a curious property of general periodic structures. It is well known that the corresponding homogenized matrix is positive definite. We calculate here the next order Burnett coefficients associated with such structures. We prove that these coefficients form a tensor which is negative semidefinite. We also provide some examples showing degeneracy in multidimension.
Low-power design of sequential circuits using a quasi-synchronous derived clock (2002)

This paper presents a novel circuit design technique to reduce the power dissipation in sequential circuits by generating a quasi-synchronous derived clock from the master clock and using it to isolate the flip flops in the circuit from the unwanted triggering action of the master clock. An example design of a decimal counter demonstrates the large power saving and improved performance of the resulting circuit.
Green Building and Sustainable Infrastructure: Sustainability Education for Civil Engineers (2010)

This paper discusses a framework for incorporating sustainable design/thinking as a new civil engineering course and experiences from the pilot offering. Important areas are outlined to aid all engineers in understanding sustainability in context with traditional engineering principles. Green-building rating systems were used to introduce the concepts of sustainability in buildings and infrastructure, highlighted by presentations from green-building professionals. By providing a better understanding of sustainability through education, civil engineers can provide proactive solutions to a growing global infrastructure.
STRUCTURE OF CHONDROCYTE UNDER TENSILE STRAIN (2006)

Aim: The aim of this study is to visualize the structural changes of both the matrix collagen meshwork and the chondrocyte cytoskeleton of articular cartilage when it is subjected to tensile strain. Materials and Methods: Dumbbell-shape specimens were harvested from the articular surface of the femur. Specimens were placed with the articular surface uppermost each in individual mini tension device and subjected to a graded series of tensile strains, whilst being observed with phase contrast light microscopy. Thereafter each specimen was fixed in its particular position of strain, and stained with fluorochrome conjugated primary antibodies specific for actin and vimentin and with DAPI for nuclear staining for observation by confocal laser scanning microscopy (CLSM). Results: Phase contrast microscopy visualized the reorganization of the matrix which became aligned parallel to the direction of strain, resulting in the deformation of the chondrocyte and their nuclei into an elliptical shape. CLSM demonstrated the reorganization of the matrix and chondrocyte cytoskeleton; at no strain, the vimentin meshwork spanned the cytoplasm from plasma membrane to nuclear membrane. At 20% strain, the vimentin meshwork became aligned parallel to the direction of strain and the nucleus was deformed into elliptical shape. Discussions: There are two possibilities to explain the structural changes in the chondrocyte under tensile strain. 1.The collagen meshwork becomes aligned parallel to the direction of tensile strain, squeezing the chondrocyte into the observed elliptical shape subsequently with the cytoskeleton reorganizing in response to it. 2.The collagen meshwork transfers the tensile strain through the plasma membrane to the vimentin meshwork which reorganizes and subsequently results in the changes in chondrocyte morphology. Further explanation is required to test the above two hypotheses.
The microbial biofilm composition on peripherally inserted central catheters: A comparison of polyurethane and hydrophobic catheters collected from paediatric patients (2020)

More diverse pathogens were present on the colonised peripherally inserted central catheter collected from the patient with central line-associated bloodstream infection. Microbial biofilm composition did not appear to be affected by the design of peripherally inserted central catheter biomaterials or antibiotic therapy. However, the diversity of the microbial communities appeared to decrease with dwell time.
PPAR-<i>γ</i>Impairment Alters Peroxisome Functionality in Primary Astrocyte Cell Cultures (2014)

Peroxisomes provide glial cells with protective functions against the harmful effects of H2O2 on neurons and peroxisome impairment results in nervous lesions. Agonists of the γ -subtype of the Peroxisome-Proliferator-Activated-Receptors (PPAR) have been proposed as neuroprotective agents in neurodegenerative disorders. Nevertheless, the role of PPAR- γ alterations in pathophysiological mechanisms and the relevance of peroxisome functions in the PPAR- γ effects are not yet clear. In a primary cell culture of rat astrocytes, the irreversible PPAR- γ antagonist GW9662 concentration-dependently decreased the activity of catalase, the most important antioxidant defense enzyme in peroxisomes. Catalase functionality recovered in a few days and the PPAR- γ agonist rosiglitazone promoted reversal of enzymatic damage. The reversible antagonist G3335 reduced both the activity and expression of catalase in a rosiglitazone-prevented manner. G3335 reduced also the glutathione reductase expression, indicating that enzyme involved in glutathione regeneration was compromised. Neither the PPAR- α target gene Acyl-Coenzyme-A-oxidase-1 nor the mitochondrial detoxifying enzyme NADH:ubiquinone-oxidoreductase (NDFUS3) was altered by PPAR- γ inhibition. In conclusion, PPAR- γ inhibition induced impairment of catalase in astrocytes. A general decrease of the antioxidant defenses of the cell suggests that a PPAR- γ hypofunction could participate in neurodegenerative mechanisms through peroxisomal damage. This series of experiments could be a useful model for studying compounds able to restore peroxisome functionality.
A novel cell selection scheme using positioning information for heterogeneous wireless system (2014)

Heterogeneous wireless systems such as a combination of mobile broadband wireless access (MBWA) and wireless local area network (WLAN) are candidates to attain the large capacity in the next generation mobile communication systems. For capacity expansion, small cells of multiple wireless network are deployed densely in these systems. Because a number of the cells overlap, users must discover lots of cells at once for cell selection. As a result, radio resources are much used for cell selection and cell selection errors occur in dense small cell environment. In this paper, we propose the cell selection scheme for data traffic optimization in such an environment. The proposed scheme uses positioning information and the average of signal strength for cell selection. Using positioning information, users can select the cell which has a better channel quality fast and easily. It is considered that the proposed scheme is useful to optimize data traffic offloading in the heterogeneous wireless network. We study the 50 % user throughput and the system throughput of the proposed scheme by comparing with the conventional scheme which uses measured instantaneous signal strength. The simulation results show that the proposed scheme can improve the 50 % user throughput by 68% in comparison with the conventional scheme. Also, the system throughput is enhanced by 10 % compared with the conventional scheme. These performances can be achieved by feasible positioning accuracy.