gebhart/patrepeval huggingface dataset:
Biodegradable Bioadherent Microcapsules for Orally Administered Sustained Release Vaccines (1997)

This research focuses on the development of an orally administered microencapsulated vaccine against botulinum neurotoxin type A using the non-toxic C-fragment of the neurotoxin (Bot-Ac). The research focuses on the production through recombinant techniques and the incorporation of a known bioadhesive, vitelline protein B (vpb), into the microsphere preparations to enhance uptake of the microspheres by the M cells located in the Peyer's patches. The results demonstrate that vpB can be produced at 170-350 mg/L in a Pichia pastoris expression system. iso, microspheres that contain 10% vpB generate a higher serum IgG level than microspheres that do not contain - B when administered either orally or subcutaneously. Whether vpB is acting as a true bioadhesive is still under study through the use of Peyer's patch uptake experiments. For comparison it was also determined that when 2.0 g of 10 mm microspheres containing 89.9% BSA /10.0% vpB /0.1% Bot-Ac were administered subcutaneously, detectable serum IgG level was generated at 17 weeks post-immunization.
Activation of the Platelet-Derived Growth Factor-Receptor Enhances Survival of Murine Bone Endothelial Cells (2004)

The activation of the microvascular endothelial cell platelet-derived growth factor (PDGF) receptor (PDGF-R) by PDGF has been implicated in neoplastic angiogenesis. Here, we established cultures of murine bone microvascular endothelial cells and examined their response to stimulation with PDGF BB ligand and to blockade of PDGF-R signaling with the tyrosine kinase inhibitor STI571 (Gleevec). The addition of STI571 to cultures of bone endothelial cells blocked PDGF BB-induced phosphorylation in a dose-dependent manner and completely abrogated the activation of downstream targets Akt and ERK1/2. Coadministration of STI571 and Taxol also induced the activation of procaspase-3 and significant apoptosis. These data suggest that phosphorylation of PDGF-R stimulates survival pathways in bone endothelial cells and that by selectively inhibiting PDGF-R signaling with STI571, the cells are rendered sensitive to Taxol treatment. The therapeutic combination of STI571 and Taxol may be a powerful tool for targeting tumor-associated endothelial cells in the skeletal compartment.
Biomechanical evaluation of predictive parameters of progression in adolescent isthmic spondylolisthesis: a computer modeling and simulation study (2012)

Progression of the slippage is mostly affected by a movement and an increase of stresses at the lumbosacral junction in accordance with spino-pelvic parameters. The statistical results provide evidence that pelvic incidence is a predictive parameter to determine progression in isthmic spondylolisthesis.
Oncogenic HER2 fusions in gastric cancer (2015)

Our results provide the molecular basis of a novel resistance mechanism to trastuzumab-based anti-HER2 therapy, supporting additional molecule stratification within HER2-positive GC patients for more effective therapy options.
Prevention of Photoresist Pattern Collapse by Using Liquid Carbon Dioxide (2001)

Photoresist polymers with high aspect ratios are presently cleaned with aqueous solutions. For high aspect ratios, the pattern collapses during the drying step. The origin of resist pattern collapse is the surface tension of the rinse liquid. Following a theoretical model, we present the results of a preliminary analysis on using environmentally benign liquid carbon dioxide (CO2) as a cleaning solvent. To avoid the likelihood of pattern collapse, the relative size of the actual pattern spacing (S) should be larger than the minimum allowable pattern spacing (d), which can be calculated based on the properties of the rinse liquid and the mechanical properties of the resist material. The use of CO2 as a rinse liquid should help prevent the resist pattern collapse problem.
Synthesis of triazole-linked morpholino oligonucleotides via Cu<sup>I</sup> catalysed cycloaddition (2016)

Triazole-linked morpholino ((TL)MO) oligonucleic acids were synthesised using the Cu(I) catalysed (3 + 2) azide-alkyne cycloaddition (CuAAC) reaction. The modified DNA analogues were incorporated into 13-mer sequences via solid phase synthesis. UV melting experiments showed that the (TL)MO modification gives higher Tm values than the corresponding (TL)DNA modification.
Operation-based merging (1992)

Existing approaches for merging the results of parallel development activities are limited. These approaches can be characterised as state-based: only the initial and final states are considered. This paper introduces operation-based merging, which uses the operations that were performed during development. In many cases operation-based merging has advantages over state-based merging, because it automatically respects the data-type invariants of the objects, is extensible for arbitrary object types, provides better conflict detection and allows for better support for solving these conflicts. Several algorithms for conflict detection are described and compared.
Adaptive Circuit Approaches to Low-Power Multi-Level/Cell FeFET Memory (2020)

Ferroelectric FETs (FeFETs) have emerged as a promising multi-level/cell (MLC) nonvolatile memory (NVM) candidate for low-power applications. This originates from the advantages of both efficient memory access and intrinsic device-level in-memory computing flexibilities. However, there still exist challenges for FeFET MLC NVM: (i) high power consumption in read operations due to high-gain requirement for sense amplifiers during sensing, and (ii) high latency and energy consumption in write operations with conventional recursive program-and-verify. Targeting at lower power, less latency, and higher density, this work investigates and optimizes the read and write approaches to MLC FeFET NVM design: (i) Adaptive FeFET memory State Mapping (ASM) between the FeFET drain-source current and the digital states to increase the sensing margin; (ii) Adaptive FeFET Gate Biasing (AGB) read methods that adopt the optimized FeFET gate voltage to boost the sensible dynamic range and to store more levels of states per cell; (iii) Adaptive Prediction-based Direct (APD) write methods that minimize the program-andverify activities. Evaluations show significant latency and energy improvement. Furthermore, the number of sensible levels of states per cell is also increased with an enhanced dynamic sensing range and an enhanced sensing margin.
Heavy-Oil Production Enhancement by Encouraging Sand Production (2000)

Abstract Dramatic increases in oil production rates have been achieved in many Canadian heavy oil reservoirs. These reservoirs are 30% porosity unconsolidated sandstones with oil ranging from 500 to 12,000 cP viscosity. Furthermore, many of these reservoirs have proven to be almost impossible to exploit economically with horizontal wells or with thermal processes. After reviewing the mechanics of CHOP (Cold Heavy Oil Production), the production history of the Luseland Field in Saskatchewan is reviewed. This is almost a unique case history because conventional production, horizontal wells, and CHOP have all been attempted in a small geographic area. Encouraging sanding resulted in over a four-fold increase in oil production rate and a total extraction ratio now just in excess of 11% overall. An aggressive CHOP program implemented after many years of conventional production and after a six-well horizontal production program achieved this increase. Conventional production was marginally economic, but the horizontal wells were failures. Several other case histories are summarized to demonstrate that CHOP wells in these reservoirs are usually just as productive as much more costly horizontal wells. We believe that CHOP technology is a far better option than thermal stimulation or horizontal wells in many cases where the reservoir state and rock properties are suitable.
The nature and functional significance of dentin extracellular matrix proteins (1995)

Odontoblasts are responsible for formation of predentin, which is transformed to dentin when apatite crystals are formed and the fibrillar matrix becomes mineralized. Odontoblasts are specialized cells that synthesize and secrete a unique set of non-collagenous proteins (NCPs), as well as the collagenous matrix largely comprised of type I collagen. The NCPs consist of dentin specific and mineralized tissue specific proteins, as well as other proteins that are found in a variety of tissues. Three dentin specific proteins have been recognized to date: dentin phosphoprotein (DPP), also called phosphophoryn, AG1 (dentin matrix protein 1, Dmp1) and dentin sialoprotein (DSP). DPP appears to be made by odontoblasts and appears at the mineralization front within a short time. It may be secreted via odontoblastic processes. DPP binds to collagen and potentially initiates formation of apatite crystals. A second DPP function appears to be to bind to the 100 face of growing apatite crystals and to inhibit or slow their growth; thus, DPP may play a dual role by initiating mineralization and then affecting the crystal growth and perhaps the habit of the crystals. Although no function has been ascribed to AG1 or DSP, they should prove to be important markers for the odontoblast phenotype. A recent unique finding is that two separate genes appear to code for more than one DSP mRNA; other transcripts may result from differential splicing. Examples of mineralized tissue specific proteins expressed by osteoblasts as well as odontoblasts are bone sialoprotein (BSP) and osteocalcin. Some NCPs expressed by osteoblasts, odontoblasts and several other tissues include osteopontin (OPN) and the chondroitin sulfate containing proteoglycans, decorin and biglycan. We propose that characterization of odontoblasts in tissues and cultures should rely upon utilization of sets of markers for the above NCPs and their mRNAs. Similar approaches are commonly used in investigations on osteoblasts. Finally, dentin (like bone) contains other molecules such as growth factors, and serum derived proteins, found within the matrix; no functional significance has yet been placed upon this finding. Future experiments should focus upon the elucidation of the three dimensional structures of the collagenous fibrillar network and of the NCPs to determine the relationships to mineralization. The role played by odontoblasts in controlling extracellular events, such as by selective secretory routes, will require careful exploration.
Evidence for a phylogenetic connection between Coccidioides immitis and Uncinocarpus reesii (Onygenaceae) (1994)

Coccidioides immitis is an anomaly amongst the human systemic fungal pathogens. Its unique parasitic cycle has contributed to confusion over its taxonomy. Early investigators mistakenly suggested that the pathogen is a protist, while others agreed it to be a fungus but placed it in four different divisions of the Eumycota. The taxonomy of C. immitis is still unresolved. Ultrastructural examinations of its parasitic and saprobic phases have revealed features that are diagnostic of the ascomycetous fungi. Moreover, striking similarities between the kind of asexual reproduction (i.e. arthroconidium formation) of this pathogen and certain anamorphic and teleomorphic members of the genus Malbranchea have suggested a close relationship. Teleomorphs of these Malbranchea species are members of the Onygenaceae (Order, Onygenales). This family also includes teleomorphs of two human respiratory pathogens, Histoplasma capsulatum and Blastomyces dermatitidis. Although the 18S rRNA gene sequences (1713 bp) of these two pathogenic forms differ from that of C. immitis by only 35 and 33 substitutions, respectively, their mode of conidiogenesis is characterized by production of solitary aleurioconidia rather than alternate arthroconidia. In this study we have used characters derived from biochemical, immunological and molecular analyses to compare relatedness between C. immitis, H. capsulatum, B. dermatitidis, and six non-pathogenic species of Malbranchea (the Malbranchea states of Uncinocarpus reesii and Auxarthron zuffianum, as well as M. albolutea, M. dendritica, M. filamentosa and M. gypsea). Evidence is presented which supports inclusion of C. immitis in the Onygenaceae, and indicates that a close phylogenetic relationship exists between the Malbranchea state of U. reesii and this respiratory pathogen.
Hydrogen peroxide generated by xanthine/xanthine oxidase system represses the proliferation of colorectal cancer cell line Caco-2 (2014)

The twin character of reactive oxygen species is substantiated by a growing body of evidence that reactive oxygen species within cells act as inducers and accelerators of the oncogenic phenotype of cancer cells, while reactive oxygen species can also induce cancer cell death and can therefore function as anti-tumorigenic species. The aim of this study was to assess a possible influence of xanthine/xanthine oxidase on the proliferation of colorectal cancer cell line Caco-2. xanthine/xanthine oxidase (2.5 µM/0.25 mU/ml-25 µM/2.5 mU/ml) dose-dependently inhibited the proliferation of Caco-2 cells. Experiments utilizing reactive oxygen species scavengers (superoxide dismutase, catalase and mannitol) and exogenous hydrogen peroxide revealed a major role of hydrogen peroxide in the xanthine/xanthine oxidase effect. Investigations utilizing annexin V-fluorescein/PI assay using flow cytometry, and the lactate dehydrogenase extracellular release assay indicated that hydrogen peroxide induced necrosis, but not apoptosis, in Caco-2 cells. These results suggest that hydrogen peroxide generated by xanthine/xanthine oxidase has the potential to suppress colorectal cancer cell proliferation.
An efficient one-pot approach to the synthesis of symmetric trithiocarbonates from carbon disulfide and alkyl halides using imidazole (2014)

A novel method is reported for the synthesis of symmetric dialkyl and cyclic (5, 6 and 7 member) trithiocarbonates from alkyl halides and carbon disulfide in the presence of imidazole and water in DMSO under mild reaction conditions. Imidazole is used as an inexpensive, non-toxic and readily available catalyst in this procedure.
Genetic and epigenetic control of gene expression by CRISPR–Cas systems (2017)

The discovery and adaption of bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems has revolutionized the way researchers edit genomes. Engineering of catalytically inactivated Cas variants (nuclease-deficient or nuclease-deactivated [dCas]) combined with transcriptional repressors, activators, or epigenetic modifiers enable sequence-specific regulation of gene expression and chromatin state. These CRISPR-Cas-based technologies have contributed to the rapid development of disease models and functional genomics screening approaches, which can facilitate genetic target identification and drug discovery. In this short review, we will cover recent advances of CRISPR-dCas9 systems and their use for transcriptional repression and activation, epigenome editing, and engineered synthetic circuits for complex control of the mammalian genome.
Fibulins in development and heritable disease (2004)

Fibulins are a family of five extracellular glycoproteins found in a variety of tissues in association with diverse supramolecular structures, including elastic fibers, basement membrane networks, fibronectin microfibrils, and proteoglycan aggregates. Studies of the developmental expression patterns have indicated that several fibulins are prominently expressed at sites of epithelial-mesenchymal transformations during embryogenesis; among these sites, the cardiovascular system has been analyzed in more detail. Gene targeting of fibulins in mice has provided important insights into their biological roles, and has led to the identification of gene mutations in a congenital disorder of humans, cutis laxa. Genetic linkage and molecular studies have also associated several fibulin genes with various human heritable disorders that affect a wide range of organs, including limb, eye, blood, and arteries. In this review, we discuss the role of fibulins in development, with an emphasis on the cardiovascular system, and their involvement in human genetic disease.
Coadministration of IL-12 or IL-10 Expression Cassettes Drives Immune Responses Toward a Thl Phenotype (1998)

Cytokines are important regulators of the immune response. They influence immune expression, the development of immunologic memory, and regulation of antigen-specific and nonspecific immune activation as well as allergic responses. In a model system in mice, we have studied the effect of plasmids expressing interleukin (IL)-10 or IL-12 on the modulation of antigen-specific responses. Coadministration of IL-12 or IL-10 genes with DNA immunogens directed the antigen-specific immune response toward a T helper (Th1)-type immunity. In addition to the modulation of antigen-specific immune responses, we studied the induction of delayed-type hypersensitivity (DTH) to contact allergens as an in vivo model of the Th1 response. We found that IL-12 and IL-10 gene-containing plasmids, and not the bacterial plasmid alone, upregulate this response. Our cytokine gene delivery technique demonstrates an important level of control of the magnitude and direction of induced immune responses and could be advantageous in a wide variety of immunotherapeutic strategies.
The Australian chemistry enhanced laboratory learning project (2006)

The Australian Chemistry Enhanced Laboratory Learning (ACELL) project aims to build a database of educationally sound, peer-reviewed and student-tested undergraduate laboratory exercises. These exercises will be available to everyone on the Internet, and should help to promote effective laboratory learning in universities in Australia, New Zealand and throughout the world.
PULMONARY CONTUSION INDUCES ALVEOLAR TYPE 2 EPITHELIAL CELL APOPTOSIS (2008)

Alveolar type 2 (AT-2) cell apoptosis is an important mechanism during lung inflammation, lung injury, and regeneration. Blunt chest trauma has been shown to activate inflammatory cells such as alveolar macrophages (AMs) or neutrophils (polymorphonuclear granulocytes [PMNs]), resulting in an inflammatory response. The present study was performed to determine the capacity of different components/cells of the alveolar compartment (AMs, PMNs, or bronchoalveolar lavage [BAL] fluids) to induce apoptosis in AT-2 cells following blunt chest trauma. To study this, male Sprague-Dawley rats were subjected to either sham procedure or blunt chest trauma induced by a single blast wave. Various time points after injury (6 h to 7 d), the lungs were analyzed by immunohistochemistry, for AT-2 cells, or with antibodies directed against caspase 3, caspase 8, Fas, Fas ligand (FasL), BAX, and BCL-2. Bronchoalveolar lavage concentrations of TNF-alpha, IL-1beta, and soluble FasL were determined by enzyme-linked immunosorbent assay. Furthermore, cultures of AT-2 cells isolated from healthy rats were incubated with supernatants of AMs, PMNs, or BAL fluids obtained from either trauma or sham-operated animals in the presence or absence of oxidative stress. Annexin V staining or TUNEL (terminal deoxynucleotidyl transferase) assay was used to detect apoptotic AT-2 cells. Histological evaluation revealed that the total number of AT-2 cells was significantly reduced at 48 h following trauma. Fas, FasL, active caspase 8, and active caspase 3 were markedly up-regulated in AT-2 cells after chest trauma. BAX and BCL-2 did not show any significant changes between sham and trauma. IL-1beta, but not TNF-alpha, levels were markedly increased at 24 h after the injury, and soluble FasL concentrations were significantly enhanced at 6, 12, 24, and 48 h after the insult. Apoptosis of AT-2 cells incubated with supernatants from cultured AMs, isolated at 48 h following chest trauma was markedly increased when compared with shams. In contrast, no apoptosis was induced in AT-2 cells incubated with supernatants of activated PMNs or BAL fluids of traumatized animals. In summary, blunt chest trauma induced apoptosis in AT-2 cells, possibly involving the extrinsic death receptor pathway. Furthermore, mediators released by AMs appeared to be involved in the induction of AT-2 cell apoptosis.
The Curative Outcome of Radioimmunotherapy in a Mouse Breast Cancer Model Relies on mTOR Signaling (2014)

Radiotherapy is a successful treatment modality for localized cancer. Our group has been exploring radiotherapy in combination with immunotherapy (radioimmunotherapy) to enhance systemic antitumor responses. Previously, we have shown that when local radiotherapy was combined with monoclonal antibodies (mAbs) (that enable T-cell responses by engaging costimulation [anti (α)-CD137] and blocking coinhibition [α-PD-1] [corrected], up to 100% of mice bearing established syngeneic AT-3 mammary tumors were cured, but single modality treatments were not curative. Here, we investigated the molecular mechanisms underlying responses to this radioimmunotherapy approach. We observed that inhibition of signaling through the mammalian target of rapamycin (mTOR) pathway during the first 10 days of treatment severely impaired the curative effect of radioimmunotherapy, at least in part by reducing MHC class I expression on tumor cells, reducing dendritic cell (DC) activation status and CD8+ T-cell function. This data indicates that the efficacy of this type of radioimmunotherapy approach involves mTOR signaling and therefore, mTOR inhibitory drugs may impede the efficacy of similar radioimmunotherapy approaches in humans.
Metamaterials for perpetual cooling at large scales (2017)

A glass-polymer film can cool structures by radiating heat, even under direct sunlight
Application of Lamination Theory to Study Warpage Across PWB and PWBA During Convective Reflow Process (2012)

Out-of-plane displacement (warpage) has been a major reliability concern for board-level electronic packaging. Printed wiring board (PWB) and component warpage results principally from coefficient of thermal expansion (CTE) mismatch among the materials that make up the PWB assembly (PWBA). Warpage occurring during surface-mount assembly processes and normal operations may lead to severe solder bump failures. In this paper, the classical laminated plate theory was applied to study the warpage behavior of PWBs and PWBAs during the thermal reflow process. The rule of mixtures was used to estimate the effective material properties of PWBA composites. Closed form solutions of the differential equations for the PWB and PWBA deformation were generated from the classical lamination theory to evaluate the sample warpage. The board support conditions and thermal gradients through the assembly thickness were considered in the theoretical model. The calculated warpage results were compared with experimental results using the projection moiré measurement system in a simulated convective reflow process to evaluate the accuracy of the model. Finite element modeling was applied to estimate the sample warpage values under the same thermal loading and boundary constraints. The warpage values obtained from the theoretical models show high sensitivity to the thermal loads, through-the-thickness temperature gradients of the test samples, and CTE values of the composite materials. The relative warpage results obtained from the theoretical models and numerical models agreed well with the experimental measurement results during the thermal reflow process.