gebhart/patrepeval huggingface dataset:
The Neuronal Cytoskeleton as a Potential Therapeutical Target in Neurodegenerative Diseases and Schizophrenia (2004)

The cytoskeleton plays a key role in maintaining the highly asymmetrical shape and structural polarity of neurons that are essential for neuronal physiology. Cytoskeletal reorganization plays a key role in neuritogenesis. In neurodegenerative diseases, the cytoskeleton is abnormally assembled and impairment of neurotransmission occurs. In Alzheimer's disease, abundant amyloid plaques and neurofibrillary tangles constitute the two major neuropathologic alterations present in the brain. Neurofibrillary tangles are formed of paired helical filaments consisting nearly entirely of the microtubule-associated protein tau. Under normal conditions tau binds to microtubules, stabilizing neuron structure and integrity. Hyperphosphorylation of tau is assumed to be the cause of formation of paired helical filaments. Another example of cytoskeletal abnormalities present in neurodegenerative diseases are the Lewy bodies considered as cytopathologic markers of Parkinson's disease. Lewy bodies are constituted of tubulin, MAP1, and MAP2. Neuronal shape, loss of dendrites and spines, as well as irregular distribution of neuronal elongations occur in specific brain areas of schizophrenic patients. Increase in non-phosphorylated MAP2 and MAP1B at hippocampus has been suggested as responsible for somatodendritic and cytoarchitectural abnormalities found in schizophrenia. In addition, neurofibrillary tangles are more frequent among schizophrenic patients who received pharmacologic antipsychotic treatment. Cumulative evidence suggests that neurodegenerative diseases and psychiatric illnesses are associated with cytoskeletal alterations in neurons that, in turn, loose synaptic connectivity and the ability to transmit incoming axonal information to the somatodendritic domain. We will review evidence supporting that the neuronal cytoskeleton is disrupted in neurodegenerative and some psychiatric diseases, and therefore could be a target for drug therapy. In addition, current data indicating that melatonin, a hormone secreted by the pineal gland, promotes neuritogenesis through cytoskeletal rearrangements and in addition to the potential therapeutic use of melatonin in neurodegenerative diseases will be discussed.
GTLAB: Grid Tag Libraries Supporting Workflows within Science Gateways (2007)

Portlet-based grid portals have become a crucial part of the cyberinfrastructure by providing component-based problem solving environments for scientists. Although portals aim to provide user-friendly environments with easy-to-use interfaces, the development of portals and their portlet components is time consuming. We aim to provide reusable components for rapid portlet development. Our approach grid tag libraries and beans (GTLAB), encapsulates common grid operations with reusable XML tags. GTLAB also provides a way for creating composite tasks that models the requirements of computational science portals. In previous work, we have introduced grid tags libraries for the Globus toolkit. In this study, we extend GTLAB to support widely used Condor DAGMan and Taverna workflows for the grid community. These extended tags demonstrate that large workflows can be integrated within grid portlets without burdening of developers.
Development and experimental evaluation of a thermography measurement system for real-time monitoring of comfort and heat rate exchange in the built environment (2012)

A measurement system based on infrared (IR) thermovision technique (ITT) is developed for real-time estimation of room thermal variations and comfort conditions in office-type environment as a part of a feasibility study in the EU FP7 project 'INTUBE'. An IR camera installed on the ceiling allows thermal image acquisition and post-processing is performed to derive mean surface temperatures, number of occupants and presence of other heat sources (e.g. computer) through detecting algorithms. A lumped parameter model of the room, developed in the Matlab/Simulink environment, receives as input the information extracted from image processing to compute room exchanged heat rate, air temperature and thermal comfort (PMV). The aim is to provide in real time the room thermal balance and comfort information for energy-saving purposes in an improved way with respect to traditional thermostats. Instantaneous information can be displayed for the users or eventually used for automatic HVAC control. The system is based on custom adaptation of a surveillance low-cost IR system with dedicated radiometric calibration. Experimental results show average absolute discrepancies in the order of 0.4 °C between calculated and measured air temperature during a time period of a day. A sensitivity analysis is performed in order to identify main uncertainty sources.
Unmasking a hyaluronan‐binding site of the BX<sub>7</sub>B type in the H3 heavy chain of the inter‐α‐inhibitor family (2001)

The inter-alpha-inhibitor (I alpha I) family gathers together several plasma protease inhibitors such as I alpha I and pre-alpha-inhibitor (P alpha I) that are variously assembled from a set of polypeptide chain precursors designated H1P to H3P. In addition to their protease inhibitory activity, a major physiological function of I alpha I family members is hyaluronan (HA) binding and HA-dependent stabilization of the extracellular matrix surrounding various cell types. Also, binding of HA to these molecules has been shown to be an important event in tumor cell proliferation and rheumatoid arthritis. However, how HA and I alpha I family members first recognize each other has so far remained elusive. The so-called BX7B domain found in some HA-binding proteins is an HA-binding site in which B represents a basic amino-acid residue and X represents any nonacidic residue. This domain has now been identified in the N-terminal end of H3P that is a precursor of P alpha I. A series of wild-type or mutant recombinant H3P chains produced with a mouse cDNA expressed in Escherichia coli allowed us to demonstrate that this domain binds HA in a noncovalent fashion. Furthermore, unmasking this HA-binding activity required most of H3P to be trimmed off at its C-terminal end. The latter observation was confirmed with a natural, mature H3 chain purified from human plasma. Indeed, a thermolysin-generated, N-terminal fragment of this H3 chain strongly bound HA whereas the intact H3 chain did not. Therefore, in vivo, the HA-binding activity of the mature H3 chain within P alpha I may vary with the folding and/or fragmentation of this protein.
Attenuation of Leukocyte Sequestration by Selective Blockade of PECAM-1 or VCAM-1 in Murine Endotoxemia (2004)

These data show that both PECAM-1 and VCAM-1 are involved in endotoxin-induced leukocyte sequestration in the lung, liver and muscle, presumably through interference with arteriolar and/or venular leukocyte sticking.
Cloning of rat 92‐kDa type IV collagenase and expression of an active recombinant catalytic domain (1996)

A full-length cDNA for rat 92-kDa type IV collagenase was isolated and sequenced. RNase protection assay revealed tissue specific differential expression of the 92-kDa type IV collagenase in the rat during development. Natural and modified forms of the 92-kDa type IV collagenase were expressed. One active protein, 92-CD, contained only the putative catalytic domain. Large quantities of the 92-CD were expressed in Escherichia coli, extracted from inclusion bodies, purified, and refolded to an active form. This recombinant protein was able to cleave denatured and native collagen and was inactivated by known MMP inhibitors.
Buccal cells DNA extraction to obtain high quality human genomic DNA suitable for polymorphism genotyping by PCR-RFLP and Real-Time PCR (2012)

We demonstrated that the method described herein is simple and low cost, and that DNA can be extracted and pcr amplified after storage in mouthwash solution at room temperature.
Integration of high‐risk human papillomavirus: a key event in cervical carcinogenesis? (2007)

An important occurrence in cervical carcinogenesis is deregulated expression of the high-risk human papillomavirus (HR-HPV) oncogenes E6 and E7. Several risk factors for cervical neoplastic progression are likely to contribute to viral oncogene deregulation, particularly integration of HR-HPV into the host genome. Integration represents a by-product of viral infection that is detected in almost 90% of cervical carcinomas. The mechanism of integration is not fully understood, although there is a clear predilection for chromosomal common fragile sites, most likely due to their accessibility for insertion of foreign DNA. Recent work has suggested that an important intermediate stage in cervical carcinogenesis is characterized by transcriptionally silent HR-HPV integrants, which co-exist with viral episomes in infected cells. As episome-derived E2 protein inhibits integrant transcription, clearance of episomes (eg by host innate immunity) is associated with loss of integrant silencing and integrant selection. The process of integration and subsequent clonal selection of integrants can therefore be considered as two independent and biologically distinct events. Indeed, integrated HPV may be viewed as selectable because it represents a form of the virus that is resistant to host mechanisms of viral clearance, enabling infected cells to maintain viral oncogene expression and avoid cell death. Care should be taken in interpreting studies of HPV integration frequency in clinical samples, as the techniques used have assessed either the presence of integrated viral DNA or evidence of transcriptional activity from integrants, but not both.
Stimulus and Potassium-Induced Epileptiform Activity in the Human Dentate Gyrus from Patients with and without Hippocampal Sclerosis (2004)

Hippocampal specimens resected to cure medically intractable temporal lobe epilepsy (TLE) provide a unique possibility to study functional consequences of morphological alterations. One intriguing alteration predominantly observed in cases of hippocampal sclerosis is an uncommon network of granule cells monosynaptically interconnected via aberrant supragranular mossy fibers. We investigated whether granule cell populations in slices from sclerotic and nonsclerotic hippocampi would develop ictaform activity when challenged by low-frequency hilar stimulation in the presence of elevated extracellular potassium concentration (10 and 12 mm) and whether the experimental activity differs according to the presence of aberrant mossy fibers. We found that ictaform activity could be evoked in slices from sclerotic and nonsclerotic hippocampi (27 of 40 slices, 14 of 20 patients; and 11 of 22 slices, 6 of 12 patients, respectively). However, the two patient groups differed with respect to the pattern of ictaform discharges and the potassium concentration mandatory for its induction. Seizure-like events were already induced with 10 mm K+. They exclusively occurred in slices from sclerotic hippocampi, of which 80% displayed stimulus-induced oscillatory population responses (250-300 Hz). In slices from nonsclerotic hippocampi, atypical negative field potential shifts were predominantly evoked with 12 mm K+. In both groups, the ictaform activity was sensitive to ionotropic glutamate receptor antagonists and lowering of [Ca2+]o. Our results show that, in granule cell populations of hippocampal slices from TLE patients, high K+-induced seizure-like activity and ictal spiking coincide with basic electrophysiological abnormalities, hippocampal sclerosis, and mossy fiber sprouting, suggesting that network reorganization could play a crucial role in determining type and threshold of such activity.
A New Class of Fuel Cells Based on Ion Pair-Coordinated Proton Exchange Membranes (2017)

Low temperature proton exchange membrane (PEM) fuel cells that use perfluorinated sulfonic acid are at present being commercialized in fuel cell vehicles, but these cells can operate only at relatively low temperatures, ca. &lt; 100°C, and high hydration levels. High temperature PEM fuel cells that use phosphoric acid-doped polybenzimidazole can operate effectively up to 180°C; however, these are difficult to operate below 140°C without suffering loss of phosphoric acid when exposed to water. 1 In this presentation, we discuss a new class of fuel cells based on ion pair-coordinated proton exchange membranes. 2 In the ion pair-coordinated proton exchange membranes, quaternary ammonium functionalized membranes, also known as anion exchange membranes, are doped with phosphoric acid. Due to the high basicity of the quaternary ammonium hydroxide, the acidic proton of phosphoric acid is completely deprotonated to form a strong ionic interaction between quaternary ammonium and biphosphate. Our density functional theory calculation indicated that the ion-pair interaction is 8.5 times greater than the conventional acid base interaction in the phosphoric acid doped polybenzimidazole. The strong interaction between the ion pair enables fuel cell operation at lower temperatures with substantially higher water partial pressure than are possible for high-temperature phosphoric acid doped polybenimidazole fuel cells. In this presentation, the chemical structural difference between this new system and the conventional phosphoric acid-doped polybenzimidazole system will be compared. The benefits and challenges of the new system in fuel cell operations will be further discussed. Acknowledgment This work was supported by the US Department of energy, Energy Efficiency and Renewable Energy, Fuel Cell Technology Office (Program Manager: Dimitrios Papageorgopoulos). References G. Bendlamudi Systematic Characterization of HT PEMFCs Containing PBI/H 3 PO 4 Systems: Thermodynamic analysis and Experimental Investigations 104 (Logos Verlag Berlin GmbH, 2011). Kwan-Soo Lee, Jacob S. Spendelow, Yoong-Kee Choe, Cy Fujimoto, and Yu Seung Kim Nature Energy , 1, 16120 (2016).
Brain fatty acid synthase activates PPARα to maintain energy homeostasis (2007)

Central nervous system control of energy balance affects susceptibility to obesity and diabetes, but how fatty acids, malonyl-CoA, and other metabolites act at this site to alter metabolism is poorly understood. Pharmacological inhibition of fatty acid synthase (FAS), rate limiting for de novo lipogenesis, decreases appetite independently of leptin but also promotes weight loss through activities unrelated to FAS inhibition. Here we report that the conditional genetic inactivation of FAS in pancreatic beta cells and hypothalamus produced lean, hypophagic mice with increased physical activity and impaired hypothalamic PPARalpha signaling. Administration of a PPARalpha agonist into the hypothalamus increased PPARalpha target genes and normalized food intake. Inactivation of beta cell FAS enzyme activity had no effect on islet function in culture or in vivo. These results suggest a critical role for brain FAS in the regulation of not only feeding, but also physical activity, effects that appear to be mediated through the provision of ligands generated by FAS to PPARalpha. Thus, 2 diametrically opposed proteins, FAS (induced by feeding) and PPARalpha (induced by starvation), unexpectedly form an integrative sensory module in the central nervous system to orchestrate energy balance.
Enhancement Effect of Lauric Acid on the Rectal Absorption of Propranolol from Suppository in Rats. (1991)

In a previous paper, we have demonstrated that medium chain fatty acids significantly enhance the in vitro rectal absorption of propranolol (PL) and that the enhancement may be partly due to the formation of a complex with a fatty acid at a 1:1 molar ratio. To confirm in vivo the enhancement effect of lauric acid on PL absorption, PL suppositories with lauric acid at various molar ratios were administered to rat rectum. PL absorption from Witepsol and macrogol suppositories with lauric acid at a 1:1 molar ratio was much larger than that after PL alone and the 1:2 or 1:3 molar ratio ones. The bioavailability (BA) after administration of the 1:1 molar ratio suppository (PL, 4 mg/kg) was 1.6- and 2.1-fold for the Witepsol and macrogol formulations respectively, compared with that after PL alone. A similar result was obtained with the PL solid dispersion suppository with lauric acid at a 1:1 molar ratio, showing a 1.7-fold higher BA compared with PL alone. The release of PL from the macrogol suppository was significantly faster at a 1:1 molar ratio than that of other preparations, but not so in the solid dispersion suppository. There was not good agreement between the release rates of PL from the suppositories and the plasma levels after dosing. These results supported the concept that a portion of PL, by forming a 1:1 complex with lauric acid, would penetrate across the rectal mucosa more easily than PL alone.
Suppression of crack generation in GaN epitaxy on Si using cubic SiC as intermediate layers (2006)

We demonstrate suppression of crack generation in GaN epitaxy on Si using cubic SiC as intermediate layers. Crack-free GaN with a thickness of 2μm was obtained. Epilayers of SiC (0–1μm), thin AlN (50nm), and GaN (1–3μm) were prepared on 3in. (111)Si substrates (GaN∕AlN∕SiC∕Si) by metalorganic vapor-phase epitaxy. Cracking of GaN is suppressed with thicker SiC (1μm), whereas cracks are generated in GaN without SiC and with thinner SiC (50nm). Transmission electron microscopy analysis revealed monocrystalline wurzite structure of GaN. Current-voltage measurements showed breakdown voltage exceeding 250V, indicating its potential for high voltage application.
Cooperative Object Tracking and Composite Event Detection With Wireless Embedded Smart Cameras (2010)

Embedded smart cameras have limited processing power, memory, energy, and bandwidth. Thus, many system- and algorithm-wise challenges remain to be addressed to have operational, battery-powered wireless smart-camera networks. We present a wireless embedded smart-camera system for cooperative object tracking and detection of composite events spanning multiple camera views. Each camera is a CITRIC mote consisting of a camera board and wireless mote. Lightweight and robust foreground detection and tracking algorithms are implemented on the camera boards. Cameras exchange small-sized data wirelessly in a peer-to-peer manner. Instead of transferring or saving every frame or trajectory, events of interest are detected. Simpler events are combined in a time sequence to define semantically higher-level events. Event complexity can be increased by increasing the number of primitives and/or number of camera views they span. Examples of consistently tracking objects across different cameras, updating location of occluded/lost objects from other cameras, and detecting composite events spanning two or three camera views, are presented. All the processing is performed on camera boards. Operating current plots of smart cameras, obtained when performing different tasks, are also presented. Power consumption is analyzed based upon these measurements.
A simple method for rectified noise floor suppression: Phase‐corrected real data reconstruction with application to diffusion‐weighted imaging (2010)

Diffusion-weighted MRI is an intrinsically low signal-to-noise ratio application due to the application of diffusion-weighting gradients and the consequent longer echo times. The signal-to-noise ratio worsens with increasing image resolution and diffusion imaging methods that use multiple and higher b-values. At low signal-to-noise ratios, standard magnitude reconstructed diffusion-weighted images are confounded by the existence of a rectified noise floor, producing poor estimates of diffusion metrics. Herein, we present a simple method of rectified noise floor suppression that involves phase correction of the real data. This approach was evaluated for diffusion-weighted imaging data, obtained from ethanol and water phantoms and the brain of a healthy volunteer. The parameter fits from monoexponential, biexponential, and stretched-exponential diffusion models were computed using phase-corrected real data and magnitude data. The results demonstrate that this newly developed simple approach of using phase-corrected real images acts to reduce or even suppress the confounding effects of a rectified noise floor, thereby producing more accurate estimates of diffusion parameters.
Intein-Mediated Synthesis of Geranylgeranylated Rab7 Protein in Vitro (2002)

Production of recombinant proteins is an important prerequisite for biotechnology and life sciences in general. However, there is a paucity of methods for production of posttranslationally modified recombinant proteins or proteins with non-native functional groups, such as fluorophores, spin labels, and so forth. In this work we have used a combination of organic synthesis and in vitro protein ligation to construct monoprenylated Rab7 GTPase. The protein was prepared from a recombinant N-terminal portion and a peptide mimicking the C terminus of Rab7. For construction of a synthetic six-amino-acid-long fluorescent monoprenylated peptide, we used a block condensation strategy. Ligation was achieved with a yield of >70%. The resulting protein was purified from the unligated peptide by a combination of organic extraction and phase partitioning and refolding. The refolded monoprenylated semisynthetic Rab7 protein (Rab7GG) formed a stable complex with its natural chaperone REP-1 (Rab escort protein 1) and could serve as an acceptor of the second prenyl group in the enzymatic prenylation reaction. Using fluorescence spectroscopy, we characterized the interaction of the Rab7GG:REP-1 complex with Rab geranylgeranyl transferase and came to the conclusion that it functioned as a genuine intermediate of the prenylation reaction. Thus, we present the first example of the in vitro generation of a semisynthetic lipidated protein using the native chemical ligation method.
A rate-adaptive MAC protocol for multi-Hop wireless networks (2001)

Wireless local area networks (W-LANs) have become increasingly popular due to the recent availability of affordable devices that are capable of communicating at high data rates. These high rates are possible, in part, through new modulation schemes that are optimized for the channel conditions bringing about a dramatic increase in bandwidth efficiency. Since the choice of which modulation scheme to use depends on the current state of the transmission channel, newer wireless devices often support multiple modulation schemes, and hence multiple datarates, with mechanisms to switch between them Users are given the option to either select an operational datarate manually or to let the device automatically choose the appropriate modulation scheme (data rate) to match the prevailing conditions. Automatic rate selection protocols have been studied for cellular networks but there have been relatively few proposals for W-LANs. In this paper we present a rate adaptive MAC protocol called the Receiver-Based AutoRate (RBAR) protocol. The novelty of RBAR is that its rate adaptation mechanism is in the receiver instead of in the sender. This is in contrast to existing schemes in devices like the WaveLAN II [15]. We show that RBAR is better because it results in a more efficient channel quality estimation which is then reflected in a higher overall throughput Our protocol is based on the RTS/CTS mechanism and consequently it can be incorporated into many medium access control protocols including the widely popular IEEE 802.11 protocol. Simulation results of an implementation of RBAR inside IEEE 802.11 show that RBAR performs consistently well.