gebhart/patrepeval huggingface dataset:
InGaAsP-InP Semiconductor Microcavity Geometries for Annular Bragg Reflection, Optical Switching, and Sensing (2005)

One of the key mandates of modern optoelectronic research is the development of compact photonic integrated circuits, capable of performing many diverse functions for the generation, manipulation, and detection of light, all on a single chip. A key practical requirement for such circuits is the development of optical devices for the localization and processing of light within extremely small dimensions. In recent years, planar microring and microdisk resonators, in which light is confined by total internal reflection, have emerged as versatile photonic elements for filling this role. The high quality factors and long photon storage times associated with the whispering-gallery modes supported by these microcavities result in several technologically useful characteristics, including narrow-band filter response, and large resonant enhancement of the circulating electric field. These properties have been exploited in numerous passive and active device applications, including optical add/drop multiplexers, all-optical switches, and tunable lasers.

This thesis describes the study of several unique ring-based optical microcavity geometries based upon the indium gallium arsenide phosphide/indium phosphide alloy semiconductor material system, undertaken in an effort to explore new optoelectronic architectures for confining and manipulating light.

The first portion of this work involves the analysis and demonstration of a new microcavity geometry, in which cylindrical Bragg reflection is used for radial optical confinement, as an alternative to total internal reflection. In this class of structures, collectively known as annular Bragg resonators, light can be guided within a ring or pillar defect layer surrounded by cylindrical Bragg mirrors. Several microcavities based upon this configuration are designed and fabricated using a thin InGaAsP quantum well membrane. Using pulsed optical excitation, the characteristics of these structures as low threshold vertically emitting lasers is explored.

Second, a total internal reflection-based coupled waveguide-resonator geometry, having applications to low power optical switching and modulation, is analyzed. This geometry makes use of the hybrid integration of a Mach-Zehnder interferometer with a racetrack resonator. Switching takes place using the Mach-Zehnder to control the coupling parameters in the vicinity of the critical coupling condition. Characterization of the static and dynamic output response of a thermooptically actuated InGaAsP-InP hybrid switch device demonstrates good ON-OFF switching contrast, microsecond response time, and reduced switching power in comparison with a conventional Mach-Zehnder configuration.

Finally, this work concludes by examining both the annular Bragg resonator and hybrid switch geometries in application to chemical and biological sensing. Both microcavity devices are shown to possess unique characteristics making them ideal for sensitive monitoring of small changes in the refractive index of a chemical or biological analyte.
Simultaneous detection of the enzyme activities of GPx1 and GPx4 guide optimization of selenium in cell biological experiments (2020)

Selenium is a metalloid trace element essential for maintaining the optimal redox environment in cells and tissues. It is structurally incorporated into over 25 selenoproteins and enzymes. The glutathione peroxidase (GPx) family of enzymes has a critical role in human health because of its antioxidant function. The recommended daily allowance (RDA) for selenium intake in humans was established to maximize the activity of GPx in plasma. Suboptimal availability of selenium can limit the expression and activities of GPxs leading to a compromised redox environment. This can cause detrimental oxidative distress that could be prevented by increasing the availability of selenium. In cell culture studies, the medium is typically deficient in selenium; supplementation with selenium can increase selenoenzyme activities. However, the optimal level of supplementation in cell culture media has not been well characterized. We performed dose-response experiments for the activities of GPx1 and GPx4 vs. the level of selenium supplementation in cell culture medium. For this, we advanced an assay to determine the activities of both GPx1 and GPx4 efficiently in a single run. During the optimization process, we found that the observed activities of GPx1 and GPx4 depend greatly on the pH of the assay buffer; the observed activities increase with increasing pH, with pH 8 being optimal. Using the combination assay, we also found that the expression and activities for both GPx1 and GPx4 can be maximized in exponentially growing cells by supplementing cell culture media with ≈ 200 nM seleno-l-methionine, without concerns for toxicity. Optimizing the availability of selenium in cell culture to maximize the expression and activities GPx1 and GPx4 may allow for better translation of information from cell culture work to in vivo settings.
THE MENISCOFEMORAL LIGAMENTS ARE SECONDARY RESTRAINTS TO POSTERIOR DRAWER (2004)

Aim: To test the hypothesis that the meniscofemoral ligaments (MFLs) make a significant contribution to resisting anteroposterior and rotatory laxity of the posterior cruciate ligament (PCL) deficient knee. Methods: The anterior and posterior MFLs of eight cadaveric knees were identified using previously described dissection techniques [1], which were shown not to affect overall knee stability in control studies. These specimens were tested for anteroposterior and rotatory laxity in a materials testing machine. The posterior cruciate ligament was then divided, followed by division of the MFLs. Laxity results were obtained for intact, PCL-deficient and PCL/MFL-deficient knees. Results were analysed using repeated measures analysis of variance and paired t tests. Results: Division of the MFLs in the PCL-deficient knee significantly increased posterior laxity between 15o and 90o of flexion (p 0.2). Discussion: Previous studies have demonstrated a high prevalence of the MFLs in knees1 and that these ligaments have a strength similar to the posterior fibre bundle of the PCL [2]. The current in vitro study suggests that they contribute to overall resistance to posterior drawer, especially in the PCL-deficient knee. If this is confirmed in vivo, patients with PCL injuries may have a reduced posterior drawer sign if their MFLs are intact, and this may result in a more stable knee. Thus the MFLs should be accurately identified and assessed during MRI scanning and arthroscopy [3]. Conclusion: This is the first study demonstrating a function for the MFLs as secondary restraints to posterior drawer in the PCL-deficient knee. The integrity of these structures should be assessed during both MRI scanning and arthroscopy of PCL-injured patients, as this may affect the diagnosis and management of such injuries.
Recent Advances of Pullulan and/or Dextran-Based Materials for Bone Tissue Engineering Strategies in Preclinical Studies: A Systematic Review (2022)

Bone tissue engineering (BTE) strategies are increasingly investigated to overcome the limitations of currently used bone substitutes and to improve the bone regeneration process. Among the natural polymers used for tissue engineering, dextran and pullulan appear as natural hydrophilic polysaccharides that became promising biomaterials for BTE. This systematic review aimed to present the different published applications of pullulan and dextran-based biomaterials for BTE. An electronic search in Pubmed, Scopus, and Web of Science databases was conducted. Selection of articles was performed following PRISMA guidelines. This systematic review led to the inclusion of 28 articles on the use of pullulan and/or dextran-based biomaterials to promote bone regeneration in preclinical models. Sixteen studies focused on dextran-based materials for bone regeneration, six on pullulan substitutes and six on the combination of pullulan and dextran. Several strategies have been developed to provide bone regeneration capacity, mainly through their fabrication processes (functionalization methods, cross-linking process), or the addition of bioactive elements. We have summarized here the strategies employed to use the polysaccharide scaffolds (fabrication process, composition, application usages, route of administration), and we highlighted their relevance and limitations for BTE applications.
On optimizing subspaces for face recognition (2009)

We propose a subspace learning algorithm for face recognition by directly optimizing recognition performance scores. Our approach is motivated by the following observations: 1) Different face recognition tasks (i.e., face identification and verification) have different performance metrics, which implies that there exist distinguished subspaces that optimize these scores, respectively. Most prior work focused on optimizing various discriminative or locality criteria and neglect such distinctions. 2) As the gallery (target) and the probe (query) data are collected in different settings in many real-world applications, there could exist consistent appearance incoherences between the gallery and the probe data for the same subject. Knowledge regarding these incoherences could be used to guide the algorithm design, resulting in performance gain. Prior efforts have not focused on these facts. In this paper, we rigorously formulate performance scores for both the face identification and the face verification tasks, provide a theoretical analysis on how the optimal subspaces for the two tasks are related, and derive gradient descent algorithms for optimizing these subspaces. Our extensive experiments on a number of public databases and a real-world face database demonstrate that our algorithm can improve the performance of given subspace based face recognition algorithms targeted at a specific face recognition task.
Introducing sub-wavelength pixel THz camera for the understanding of close pixel-to-wavelength imaging challenges (2012)

Conventional guidelines and approximations useful in macro-scale system design can become invalidated when applied to the smaller scales. An illustration of this is when camera pixel size becomes smaller than the diffraction-limited resolution of the incident light. It is sometimes believed that there is no benefit in having a pixel width smaller than the resolving limit defined by the Raleigh criterion, 1.22 &lambda; F/#. Though this rarely occurs in today's imaging technology, terahertz (THz) imaging is one emerging area where the pixel dimensions can be made smaller than the imaging wavelength. With terahertz camera technology, we are able to achieve sub-wavelength pixel sampling pitch, and therefore capable of directly measuring if there are image quality benefits to be derived from sub-wavelength sampling. Interest in terahertz imaging is high due to potential uses in security applications because of the greater penetration depth of terahertz radiation compared to the infrared and the visible. This paper discusses the modification by INO of its infrared MEMS microbolometer detector technology toward a THz imaging platform yielding a sub-wavelength pixel THz camera. Images obtained with this camera are reviewed in this paper. Measurements were also obtained using microscanning to increase sampling resolution. Parameters such as imaging resolution and sampling are addressed. A comparison is also made with results obtained with an 8-12 &#956;m band camera having a pixel pitch close to the diffractionlimit.
Phylogenetic landscape of Monkeypox Virus (MPV) during the early outbreak in New York City, 2022 (2023)

Monkeypox (MPOX) is a zoonotic disease endemic to regions of Central/Western Africa. The geographic endemicity of MPV has expanded, broadening the human-monkeypox virus interface and its potential for spillover. Since May 2022, a large multi-country MPV outbreak with no proven links to endemic countries has originated in Europe and has rapidly expanded around the globe, setting off genomic surveillance efforts. Here, we conducted a genomic analysis of 23 MPV-infected patients from New York City during the early outbreak, assessing the phylogenetic relationship of these strains against publicly available MPV genomes. Additionally, we compared the genomic sequences of clinical isolates versus culture-passaged samples from a subset of samples. Phylogenetic analysis revealed that MPV genomes included in this study cluster within the B.1 lineage (Clade IIb), with some of the samples displaying further differentiation into five different sub-lineages of B.1. Mutational analysis revealed 55 non-synonymous polymorphisms throughout the genome, with some of these mutations located in critical regions required for viral multiplication, structural and assembly functions, as well as the target region for antiviral treatment. In addition, we identified a large majority of polymorphisms associated with GA > AA and TC > TT nucleotide replacements, suggesting the action of human APOBEC3 enzyme. A comparison between clinical isolates and cell culture-passaged samples failed to reveal any difference. Our results provide a first glance at the mutational landscape of early MPV-2022 (B.1) circulating strains in NYC.
The Dependence of Multijunction Solar Cell Performance on the Number of Quantum Dot Layers (2014)

The performance improvements of adding InAs quantum dots (QDs) in the middle subcell of a lattice matched triple-junction InGaP/InGaAs/Ge photovoltaic device are studied using the simulated external quantum efficiency, photocurrent, open circuit voltage, fill factor, and efficiency under standard testing conditions. The QDs and wetting layer are modeled using an effective medium consisting of trap states for the former and low confinement potentials for the latter. Although the efficiency stabilizes for more than 100 layers of QDs for the structure studied, the efficiency achieves an absolute efficiency of 31.1% under one sun illumination for 140 layers of QDs. This corresponds to a relative increase of 1.3% compared with a control structure with no QD layers. The performance of the device depends intricately on the magnitude of the confinement potentials representing the wetting layer.
Combined effect of mechanical stressors and channel orientation on mobility in FDSOI n and p MOSFETs (2012)

We have calculated the combined effect of biaxial and uniaxial strain in FDSOI MOSFETs for different channel orientations using a comprehensive Monte Carlo simulator. Our results confirm that tensile uniaxial strain improves the electron mobility of sSOI channels, with low impact of channel orientation, or silicon thickness, i.e., biaxial and uniaxial strains have cumulative effects. In the case of holes, the effect of compressive uniaxial strain strongly depends on the channel orientation and on the Ge mole fraction of the sSOI channel: for low x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ge</sub> , compressive uniaxial strain enhances the hole mobility (cumulative effects); for high x <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Ge</sub> , compressive uniaxial strain cancels the mobility enhancement achieved by the biaxial strain.
Trafficking of prion proteins through a caveolae-mediated endosomal pathway (2003)

To understand the posttranslational conversion of the cellular prion protein (PrPC) to its pathologic conformation, it is important to define the intracellular trafficking pathway of PrPC within the endomembrane system. We studied the localization and internalization of PrPC in CHO cells using cryoimmunogold electron microscopy. At steady state, PrPC was enriched in caveolae both at the TGN and plasma membrane and in interconnecting chains of endocytic caveolae. Protein A-gold particles bound specifically to PrPC on live cells. These complexes were delivered via caveolae to the pericentriolar region and via nonclassical, caveolae-containing early endocytic structures to late endosomes/lysosomes, thereby bypassing the internalization pathway mediated by clathrin-coated vesicles. Endocytosed PrPC-containing caveolae were not directed to the ER and Golgi complex. Uptake of caveolae and degradation of PrPC was slow and sensitive to filipin. This caveolae-dependent endocytic pathway was not observed for several other glycosylphosphatidyl inositol (GPI)-anchored proteins. We propose that this nonclassical endocytic pathway is likely to determine the subcellular location of PrPC conversion.
A Stochastic Algorithm for Self-Organization of Autonomous Swarms (2006)

In earlier work of the authors simulation results indicated the possibility of achieving self-organization of autonomous vehicles through Gibbs sampler-based simulated annealing. However, the dynamic graph structure associated with the network evolution presents challenges in convergence analysis. In this paper a novel algorithm is presented and shown to yield desired global configurations with primarily local interactions. Its convergence speed is provided in terms of the Gibbs potential function. The analytical results are further verified through simulation.
Pyruvate Dehydrogenase Kinase as a Potential Therapeutic Target for Malignant Gliomas (2013)

Metabolic aberrations in the form of altered flux through key metabolic pathways are the major hallmarks of several life-threatening malignancies including malignant gliomas. These adaptations play an important role in the enhancement of the survival and proliferation of gliomas at the expense of the surrounding normal/healthy tissues. Recent studies in the field of neurooncology have directly targeted the altered metabolic pathways of malignant tumor cells for the development of anti-cancer drugs. Aerobic glycolysis due to elevated production of lactate from pyruvate regardless of oxygen availability is a common metabolic alteration in most malignancies. Aerobic glycolysis offers survival advantages in addition to generating substrates such as fatty acids, amino acids and nucleotides required for the rapid proliferation of cells. This review outlines the role of pyruvate dehydrogenase kinase (PDK) in gliomas as an inhibitor of pyruvate dehydrogenase that catalyzes the oxidative decarboxylation of pyruvate. An in-depth investigation on the key metabolic enzyme PDK may provide a novel therapeutic approach for the treatment of malignant gliomas.
Production of conjugated linoleic acid by Propionibacterium freudenreichii ssp. shermanii (2002)

The kinetics of linoleic acid isomerization to conjugated linoleic acid (CLA) by Propionibacterium freudenreichii ssp. shermanii JS was studied in pH-controlled batch and fedbatch fermentations. In batch fermentations supplemented with 600-2 000 g . mL -1 linoleic acid, the rate of CLA formation was highest during the exponential phase of growth. By the end of the batch fermentations, high amounts of CLA corresponding to 80-87% conversion were accumulated with initial linoleic acid concentrations up to 2 000 g . mL -1 . In fed-batch fermentations, where 600 g . mL -1 linoleic acid was added into the culture after exponential growth, a rapid but short conversion period occurred. Thus, both actively growing and non-growing cultures were able to effectively form CLA. However, the production rates per cell were significantly higher in growing cultures. This isomerization reaction could be a detoxification system for linoleic acid in the propionibacterium strain studied. conjugated linoleic acid / linoleic acid isomerization / Propionibacterium freudenreichii ssp. shermanii Rsum -Production d'acide linolique conjugu par Propionibacterium freudenreichii ssp. shermanii. La cintique d'isomrisation de l'acide linolique en acide linolique conjugu (ALC) par Propionibacterium freudenreichii ssp. shermanii JS a t tudie au cours de fermentations batch et batch aliment, pH contrl. En fermentations batch supplmentes avec 600-2 000 g . mL -1 d'acide linolique, le taux de formation d'ALC tait plus lev au cours de la phase exponentielle de croissance. la fin des fermentations batch, des quantits leves d'ALC correspondant une conversion de 80-87 % taient accumules, avec des concentrations initiales d'acide linolique allant jusqu' 2 000 g . mL -1 . En fermentations batch aliment, o 600 g . mL -1 d'acide linolique taient ajouts dans la culture aprs la phase exponentielle de croissance, une priode de croissance 91
Guest Editors' Introduction: Special Section on Learning Deep Architectures (2013)

There has been a resurgence of research in the design of deep architecture models and learning algorithms, i.e., methods that rely on the extraction of a multilayer representation of the data. Often referred to as deep learning, this topic of research has been building on and contributing to many different research topics, such as neural networks, graphical models, feature learning, unsupervised learning, optimization, pattern recognition, and signal processing. Deep learning is also motivated and inspired by neuroscience and has had a tremendous impact on various applications such as computer vision, speech recognition, and natural language processing. The clearly multidisciplinary nature of deep learning led to a call for papers for a special issue dedicated to learning deep architectures.
Combinatorial approach in the design of multifunctional polymeric nano-delivery systems for cancer therapy (2014)

There have been significant advances in our understanding of cancer as a disease at the molecular level. Combined with improved diagnostic systems, the concept of personalized medicine was introduced where therapy for every patient can be customized according to their disease profile. The nanotechnology approach for formulation design and the advent of drug delivery systems for small molecules and biologics has contributed to the development of personalized medicine. Despite the progress, effective management and treatment of cancer remains a clinical challenge. The majority of drug delivery vectors that have undergone clinical trials have been discontinued prematurely because of poor therapeutic outcomes, off-target effects and non-specific toxicity due to the components of the formulation itself. Therefore, there is an urgent unmet requirement for a systematic approach to design drug delivery vectors that not only deliver the cargo to the desired site of action, but are also highly biocompatible and non-toxic. The past decade has seen the evolution of a combinatorial approach to drug delivery, a concept that has been classically successful in drug discovery research. In the present review, we summarize the wet-lab and in silico strategies to designing libraries of biocompatible delivery materials using combinatorial chemistry and support this strategy with pre-clinical success stories in cancer therapy.
Infections in Kidney Transplant Recipients (2016)

Kidney transplant is the most common type of organ transplantation worldwide. In preparation for transplantation, appropriate infectious disease testing of the donor and recipient is required. In the posttransplant period, infections within the first 1 month generally include urinary tract infection, pneumonia, and wound infections. There is increasing prevalence of multidrug-resistant bacterial infections after kidney transplantation. Syndromes of specific interest in kidney transplant recipients include asymptomatic bacteriuria, recurrent UTI, and candiduria. Kidney transplant recipients are predisposed to several opportunistic viral infections including cytomegalovirus, BK virus, adenovirus, and parvovirus. There are also increasing number of HIV-positive recipients undergoing kidney transplant and there needs to be special attention to drug interactions in this population. Finally, infection prevention for kidney transplant recipients includes chemoprophylaxis and vaccinations.
ChemInform Abstract: Hydrochlorination of Acetylene Catalyzed by Gold (2012)

Abstract Review: 63 refs.