gebhart/patrepeval huggingface dataset:
Proteoglycans and Amyloidogenic Proteins in Peripheral Amyloidosis (2003)

Amyloidogenic proteins have the characteristic of adopting a β-sheet conformation and assembling into fibrils. Although similar in fibrillar appearance, each type of peripheral amyloid deposits differs in the nature of the amyloidogenic protein forming fibrils. Other elements, known as the common structural elements of the amyloid deposits, also contribute to amyloidogenic process in vivo. Among these elements, heparan sulfate proteoglycans (HSPGs) have been shown to bind to different types of amyloidogenic proteins and to promote the formation of β-sheet secondary structure. Once fibrils are formed, HSPGs protect the fibrils from proteolytic degradation, which lead to the accumulation of the deposits in the targeted organs. Understanding the regulation of protein folding by proteoglycans can lead to the development of low molecular weight compounds, which bind to the amyloidogenic proteins prior to their organization as fibrils. Such binding would interfere with the natural association of amyloidogenic protein with HSPGs and maintain the amyloid protein in a non-fibrillar structure (either random coil or a mix of α-helix and β-sheet structure). It would also favor their clearance, and thereby inhibit or completely block the formation of amyloid deposits. Since HSPGs interact with several types of amyloidogenic proteins, such an approach may be beneficial for the treatment of systemic and localized types of amyloidosis. Keywords: Amyloidogenic, HSPGs, proteins, proteolytic
Design analysis of thin-body silicide source/drain devices (2002)

The use of complementary low-barrier silicides is investigated for reducing the series resistance of thin-body silicon-on-insulator (SOI) devices. Two different thin-body device types are simulated, one in which the source/drain regions are formed by the silicide without doping, and another in which the silicide source/drains are terminated by a doped extension region.
Luminescent barometry in wind tunnels (1990)

A flexible and relatively inexpensive method and apparatus are described for continuous pressure mapping of aerodynamic surfaces using photoluminescence and imaging techniques. Platinum octaethylporphyrin (PtOEP) has a phosphorescence known to be quenched by oxygen. When dissolved in a silicone matrix, PtOEP may be distributed over a surface as a thin, uniform film. When the film is irradiated with ultraviolet light, the luminescence intensity provides a readily detectable, qualitative surface flow visualization. Moreover, since the luminescence intensity is found to be inversely proportional to the partial pressure of oxygen, a quantitative measure of pressure change may be obtained using a silicon target vidicon or a charge-coupled device video sensor to measure intensity. Luminescent images are captured by a commercial frame buffer board. Images taken in wind tunnels during airflow are ratioed to images taken under ambient ‘‘wind-off’’ conditions. The resulting intensity ratio information is converted to pressure using calibration curves of I0/I vs p/p0, where I0 is the intensity at ambient pressure p0 and I is the intensity at any other pressure p. The result is a two-dimensional static pressure plot for the surface of interest. It is shown that the pressure plots predicted by luminescence intensity compare favorably with pressure plots made by conventional pressure measuring devices.
Library Design Practices for Success in Lead Generation With Small Molecule Libraries (2003)

The generation of novel structures amenable to rapid and efficient lead optimization comprises an emerging strategy for success in modern drug discovery. Small molecule libraries of sufficient size and diversity to increase the chances of discovery of novel structures make the high throughput synthesis approach the method of choice for lead generation. Despite an industry trend for smaller, more focused libraries, the need to generate novel lead structures makes larger libraries a necessary strategy. For libraries of a several thousand or more members, solid phase synthesis approaches are the most suitable. While the technology and chemistry necessary for small molecule library synthesis continue to advance, success in lead generation requires rigorous consideration in the library design process to ensure the synthesis of molecules possessing the proper characteristics for subsequent lead optimization. Without proper selection of library templates and building blocks, solid phase synthesis methods often generate molecules which are too heavy, too lipophilic and too complex to be useful for lead optimization. The appropriate filtering of virtual library designs with multiple computational tools allows the generation of information-rich libraries within a drug-like molecular property space. An understanding of the hit-to-lead process provides a practical guide to molecular design characteristics. Examples of leads generated from library approaches also provide a benchmarking of successes as well as aspects for continued development of library design practices.
Oral ingestion of egg yolk immunoglobulin from hens immunized with an enterotoxigenic Escherichia coli strain prevents diarrhea in rabbits challenged with the same strain (1992)

White Leghorn hens were immunized with enterotoxigenic Escherichia coli B16-4 with heat-labile enterotoxin and colonization factor antigen I in Freund's adjuvant. Specific antibodies were detected by an enzyme-linked immunosorbent assay in the serum after 8 days and in eggs after 10 days, with levels reaching peaks at 15 and 20 days after the first immunization, respectively. The protective effects of the egg yolk antibodies were tested in the rabbit reversible ileal tie model of diarrhea. Five control rabbits developed severe diarrhea within 72 h after inoculation with enterotoxigenic E. coli B16-4. Oral ingestion of egg yolks from immunized hens for 4 days prior to inoculation protected five rabbits from diarrhea after challenge with the same strain of E. coli. The rabbits showed no adverse effects from the ingestion of the egg yolks. Four rabbits fed control eggs were also afforded some protection in that three rabbits developed mild diarrhea and one rabbit remained entirely well. In vitro experiments showed that immunoglobulin from egg yolks interfered with the binding of E. coli to purified small bowel mucins; immunoglobulin from immunized hens reduced binding more than immunoglobulin from nonimmunized hens. These findings indicate that eggs from hens immunized with appropriate antigens have potential as a useful source of passive immunity.
Coding between mouse and keyboard, part I (2002)

In the first part of this two-part article, Jung provides a working example of building GUI apps with Qt.
Controlled fabrication of metallic electrodes with atomic separation (1999)

We report a technique for fabricating metallic electrodes on insulating substrates with separations on the 1 nm scale. The fabrication technique, which combines lithographic and electrochemical methods, provides atomic resolution without requiring sophisticated instrumentation. The process is simple, controllable, reversible, and robust, allowing rapid fabrication of electrode pairs with high yield. We expect the method to prove useful in interfacing molecular-scale structures to macroscopic probes and electronic devices.
Dendrimers: From Generations and Functional Groups to Functions (1995)

Not just the size but also the multiplication of functions possible through branching is at the forefront of dendrimer chemistry. Owing to the numerous recent key publications by Newkome, Fréchet, Moore, Majoral, Meijer, and others, this Highlight has the dimensions of a minireview.
Embryonic Sex Induces Differential Expression of Proteins in Bovine Uterine Fluid (2013)

The bovine endometrium recognizes early embryos and reacts differently depending on the developmental potential of the embryo. However, it is unknown whether the endometrium can distinguish embryonic sex. Our objective was to analyze sexual dimorphism in the uterus in response to male and female embryos. Differentially expressed (DE) proteins, different levels of hexoses, and other embryotrophic differences were analyzed in uterine fluid (UF). Proteomic analysis of day-8 UF recovered from heifers after the transfer of day-5 male or female embryos identified 23 DE proteins. Regulated proteasome/immunoproteasome protein subunits indicated differences in antigen processing between UF carrying male embryos (male-UF) or female embryos (female-UF). Several enzymes involved in glycolysis/gluconeogenesis and antioxidative/antistress responses were up-regulated in female-UF. Fructose concentration was increased in female-UF versus male-UF, while glucose levels were similar. In vitro cultures with molecules isolated from male-UF were found to improve male embryo development compared to female embryos cultured with molecules isolated from female-UF. We postulated that, in vivo, male embryos induce changes in the endometrium to help ensure their survival. In contrast, female embryos do not appear to induce these changes.
Effect of low‐level laser therapy on bone repair: Histological study in rats (2007)

The use of infrared LLLT directly to the injured tissue showed a biostimulating effect on bone remodeling by stimulating the modulation of the initial inflammatory response and anticipating the resolution to normal conditions at the earlier periods. However, there were no differences between the groups at 60 days.
Apoptosis and autophagy: BIM as a mediator of tumour cell death in response to oncogene‐targeted therapeutics (2009)

The BCL-2 homology domain 3 (BH3)-only protein, B-cell lymphoma 2 interacting mediator of cell death (BIM) is a potent pro-apoptotic protein belonging to the B-cell lymphoma 2 protein family. In recent years, advances in basic biology have provided a clearer picture of how BIM kills cells and how BIM expression and activity are repressed by growth factor signalling pathways, especially the extracellular signal-regulated kinase 1/2 and protein kinase B pathways. In tumour cells these oncogene-regulated pathways are used to counter the effects of BIM, thereby promoting tumour cell survival. In parallel, a new generation of targeted therapeutics has been developed, which show remarkable specificity and efficacy in tumour cells that are addicted to particular oncogenes. It is now apparent that the expression and activation of BIM is a common response to these new therapeutics. Indeed, BIM has emerged from this marriage of basic and applied biology as an important mediator of tumour cell death in response to such drugs. The induction of BIM alone may not be sufficient for significant tumour cell death, as BIM is more likely to act in concert with other BH3-only proteins, or other death pathways, when new targeted therapeutics are used in combination with traditional chemotherapy agents. Here we discuss recent advances in understanding BIM regulation and review the role of BIM as a mediator of tumour cell death in response to novel oncogene-targeted therapeutics.
An Audio-based Real-time Beat Tracking System for Music With or Without Drum-sounds (2001)

This paper describes a real-time beat tracking system that recognizes a hierarchical beat structure comprising the quarter-note, half-note, and measure levels in real-world audio signals sampled from popular-music compact discs. Most previous beat-tracking systems dealt with MIDI signals and had difficulty in processing, in real time, audio signals containing sounds of various instruments and in tracking beats above the quarter-note level. The system described here can process music with drums and music without drums and can recognize the hierarchical beat structure by using three kinds of musical knowledge: of onset times, of chord changes, and of drum patterns. This paper also describes several applications of beat tracking, such as beat-driven real-time computer graphics and lighting control.
Interleukin-17A induces glucocorticoid insensitivity in human bronchial epithelial cells (2011)

A subset of asthma patients suffer from glucocorticoid (GC) insensitivity. T-helper cell type 17 cells have an emerging role in GC insensitivity, although the mechanisms are still poorly understood. We investigated whether interleukin (IL)-17A induces GC insensitivity in airway epithelium by studying its effects on responsiveness of tumour necrosis factor (TNF)-α-induced IL-8 production to budesonide in human bronchial epithelial 16HBE cells. We unravelled the underlying mechanism by the use of specific pathway inhibitors, reporter and overexpression constructs and a histone deacetylase (HDAC) activity assay. We demonstrated that IL-17A-induced IL-8 production is normally sensitive to GCs, while IL-17A pre-treatment significantly reduced the sensitivity of TNF-α-induced IL-8 production to budesonide. IL-17A activated the p38, extracellular signal-related kinase (ERK) and phosphoinositide-3-kinase (PI3K) pathways, and the latter appeared to be involved in IL-17A-induced GC insensitivity. Furthermore, IL-17A reduced HDAC activity, and overexpression of HDAC2 reversed IL-17A-induced GC insensitivity. In contrast, IL-17A did not affect budesonide-induced transcriptional activity of the GC receptor, suggesting that IL-17A does not impair the actions of the ligated GC receptor. In conclusion, we have shown for the first time that IL-17A induces GC insensitivity in airway epithelium, which is probably mediated by PI3K activation and subsequent reduction of HDAC2 activity. Thus, blockade of IL-17A or downstream signalling molecule PI3K may offer new strategies for therapeutic intervention in GC-insensitive asthma.
Membrane Topology of the Human Dipeptide Transporter, hPEPT1, Determined by Epitope Insertions (1998)

We have used epitope insertion to analyze the transmembrane topology of the human H+-dipeptide symporter hPEPT1. An epitope tag, EYMPME (EE), was inserted into different locations at amino acids 39, 78, 106, 412, and 708 of hPEPT1 by site-directed mutagenesis. The functional integrity of the tagged protein was tested by measuring its dipeptide transport activity in transfected Cos7 cells. Further, cells expressing hPEPT1 or EE-tagged hPEPT1 derivatives were labeled with an anti-EE-monoclonal antibody (anti-EE-mAb) or an antiserum raised against the carboxyl terminus of hPEPT1 (anti-hPEPT1) and examined by immunofluorescence confocal microscopy. EE106-, 412-, and 708-hPEPT1 transported the dipeptide tracer as well as wild-type hPEPT1. Tags at position 106 and 412 were shown to be extracellular because they were accessible to anti-epitope antibody in nonpermeabilized cells. In contrast, the carboxyl-terminal domain and EE708 were shown to be intracellular since they were only accessible to the antibodies in permeabilized cells. These results are consistent with a 12-transmembrane domain (TMD) topological model of PEPT1. Epitope insertions at regions linking the putative TMD1 and TMD2, and TMD2 and TMD3 (EE39- and EE78-hPEPT1), abolished the dipeptide transport into the cells. In transfected Cos7 cells, these tagged proteins remained largely intracellular rather than at the plasma membrane. These results suggest that the integrity of these regions is essential for transporter trafficking and/or function. Thus, the topology of the amino-terminal portion, including putative TMD1 and -2, remains to be clarified.
Comparison of the Ocular Hypotensive Lipid AGN 192024 With Timolol (2001)

Of the 3 concentrations tested, 0.03% AGN 192024 once daily had the best therapeutic profile. AGN 192024 was safe and well tolerated, and it provided superior ocular hypotensive efficacy and diurnal IOP control compared with timolol in patients with ocular hypertension and glaucoma.
A Gold Standard Evaluation of the “Discogenic Pain” Diagnosis as Determined by Provocative Discography (2006)

Positive discography was not highly predictive in identifying bona fide isolated intradiscal lesions primarily causing chronic serious LBP illness in this first study comparing discography results to a gold standard.
Metal organic vapour-phase epitaxy growth of GaN wires on Si (111) for light-emitting diode applications (2013)

GaN wires are grown on a Si (111) substrate by metal organic vapour-phase epitaxy on a thin deposited AlN blanket and through a thin SiNx layer formed spontaneously at the AlN/Si interface. N-doped wires are used as templates for the growth of core-shell InGaN/GaN multiple quantum wells coated by a p-doped shell. Standing single-wire heterostructures are connected using a metallic tip and a Si substrate backside contact, and the electroluminescence at room temperature and forward bias is demonstrated at 420 nm. This result points out the feasibility of lower cost nitride-based wires for light-emitting diode applications.
Color change following vital bleaching of tetracycline-stained teeth. (1985)

A technique currently used to bleach intrinsically stained vital teeth in humans was studied to quantify the amount of color alteration attained by the process. The components of the bleaching technique, 35% hydrogen peroxide at I42°F, were applied to the labial surfaces of the canine teeth of 5 dogs. These experimental teeth, which were vital and tetracyline stained, were divided into 4 groups with respect to duration of application of the bleaching technique: 0 (control), 15, 30, and 45 min. The teeth were treated at their respective duration times every other week for a total of 4 sessions. Observation times for assessing stability of color removal were at 13, 62, 92 days after the final bleaching. Four examiners rated the teeth for color density, before and after each bleaching and at the follow-up sessions, by comparing the teeth to a custom-made porcelain shade guide. The control teeth did not change color significantly. The teeth treated for 15 and 30 min became significantly and progressively lighter through the 4 bleachings. The teeth treated for 45 min lightened significantly and progressively through the second bleaching, and then did not significantly lighten further. The color change of all teeth was stable at the follow-up times.
Energy-Aware TDMA-Based MAC for Sensor Networks (2005)

Networking unattended sensors is expected to have a significant impact on the efficiency of many military and civil applications. Sensors in such systems are typically disposable and expected to last until their energy drains. Therefore, energy is a very scarce resource for such sensor systems and has to be managed wisely in order to extend the life of the sensors for the duration of a particular mission. In this chapter, we present a novel approach for energy-aware management of sensor networks that maximizes the lifetime of the sensors while maintaining desired quality of service attributes related to sensed data delivery. The approach is to dynamically set routes and arbitrate medium access to minimize energy consumption and maximize sensor life. We give a brief overview of the energy-aware routing and a description of a Time-Division-Multiple-Access (TDMA) -based Medium AccessControl (MAC) protocol. We discuss algorithms for assigning time slots for the communicating sensor nodes. The approach is evaluated through simulation. Simulation results have confirmed the effectiveness of our new approach.
Fabrication of the SnS/ZnO heterojunction for PV applications using electrodeposited ZnO films (2009)

In the perspectives of fabricating a nontoxic and low-cost photovoltaic system, SnS has recently received considerable interest as a potential solar cell material. However, doped or undoped CdS has been extensively studied as a window material with p-SnS for the fabrication of a heterojunction solar cell. Because of the carcinogenic character of CdS, there is a prevailing need to search for an alternative window layer and scrutinize the performance of the heterojunction with p-SnS. In this work ZnO thin films were fabricated onto ITO using a galvanostatic electrodeposition approach from the dimethyl sulfoxide bath. The as-deposited ZnO films were subsequently annealed at 400 °C in argon ambiance to reduce the intermediate trap states and effective sintering. Finally, SnS thin films were grown onto the ZnO layer by thermally evaporating high-purity SnS powder. The photovoltaic properties of the SnS/ZnO heterojunction were investigated.
Hybridization dynamics of surface immobilized DNA (2004)

We model the hybridization kinetics of surface attached DNA oligomers with solubilized targets. Using both master equation and rate equation formalisms, we show that, for surface coverages at which the surface immobilized molecules interact, barriers to penetration create a distribution of target molecule concentrations within the adsorbed layer. By approximately enumerating probe and target conformations, we estimate the probability of overlap between complementary probe and target regions as a function of probe density and chain length. In agreement with experiments, we find that as probe molecules interact more strongly, fewer nucleation sites become accessible and binding rates are diminished relative to those in solution. Nucleation sites near the grafted end of the probes are least accessible; thus targets which preferentially bind to this region show more drastic rate reductions than those that bind near the free end of the probe. The implications of these results for DNA-based biosensors are discussed.
Intravenous Zoledronic Acid in Postmenopausal Women with Low Bone Mineral Density (2002)

Zoledronic acid infusions given at intervals of up to one year produce effects on bone turnover and bone density as great as those achieved with daily oral dosing with bisphosphonates with proven efficacy against fractures, suggesting that an annual infusion of zoledronic acid might be an effective treatment for postmenopausal osteoporosis.
Chemokine-induced recruitment of genetically modified bone marrow cells into the CNS of GM1-gangliosidosis mice corrects neuronal pathology (2005)

Bone marrow cells (BMCs) could correct some pathologic conditions of the central nervous system (CNS) if these cells would effectively repopulate the brain. One such condition is G(M1)-gangliosidosis, a neurodegenerative glycosphingolipidosis due to deficiency of lysosomal beta-galactosidase (beta-gal). In this disease, abnormal build up of G(M1)-ganglioside in the endoplasmic reticulum of brain cells results in calcium imbalance, induction of an unfolded protein response (UPR), and neuronal apoptosis. These processes are accompanied by the activation/proliferation of microglia and the production of inflammatory cytokines. Here we demonstrate that local neuroinflammation promotes the selective activation of chemokines, such as stromal-cell-derived factor 1 (SDF-1), macrophage inflammatory protein 1-alpha (MIP-1alpha), and MIP-1beta, which chemoattract genetically modified BMCs into the CNS. Mice that underwent bone marrow transplantation showed increased beta-gal activity in different brain regions and reduced lysosomal storage. Decreased production of chemokines and effectors of the UPR as well as restoration of neurologic functions accompanied this phenotypic reversion. Our results suggest that beta-gal-expressing bone marrow (BM)-derived cells selectively migrate to the CNS under a gradient of chemokines and become a source of correcting enzyme to deficient neurons. Thus, a disease condition such as G(M1)-gangliosidosis, which is characterized by neurodegeneration and neuroinflammation, may influence the response of the CNS to ex vivo gene therapy.
Outpatient Insulin Therapy in Type 1 and Type 2 Diabetes Mellitus (2003)

Many options for insulin therapy are now available. Physiologic insulin therapy with insulin analogues is now relatively simple to use and is associated with fewer episodes of hypoglycemia.