gebhart/patrepeval huggingface dataset:
Mutation of the His ligand in mitoNEET stabilizes the 2Fe–2S cluster despite conformational heterogeneity in the ligand environment (2011)

MitoNEET is the only identified Fe-S protein localized to the outer mitochondrial membrane and a 1.5 Å resolution X-ray analysis has revealed a unique structure [Paddock et al. (2007), Proc. Natl Acad. Sci. USA, 104, 14342-14347]. The 2Fe-2S cluster is bound with a 3Cys-1His coordination which defines a new class of 2Fe-2S proteins. The hallmark feature of this class is the single noncysteine ligand His87, which when replaced by Cys decreases the redox potential (E(m)) by ∼300 mV and increases the stability of the cluster by around sixfold. Unexpectedly, the pH dependence of the lifetime of the 2Fe-2S cluster remains the same as in the wild-type protein. Here, the crystal structure of H87C mitoNEET was determined to 1.7 Å resolution (R factor = 18%) to investigate the structural basis of the changes in the properties of the 2Fe-2S cluster. In comparison to the wild type, structural changes are localized to the immediate vicinity of the cluster-binding region. Despite the increased stability, Cys87 displays two distinct conformations, with distances of 2.3 and 3.2 Å between the S(γ) and the outer Fe of the 2Fe-2S cluster. In addition, Lys55 exhibits multiple conformations in the H87C mutant protein. The structure and distinct characteristics of the H87C mutant provide a framework for further studies investigating the effects of mutation on the properties of the 2Fe-2S cluster in this new class of proteins.
Influence of food matrix on absorption of flavour compounds by linear low-density polyethylene: proteins and carbohydrates (2000)

The effects of differences in food matrices on the absorption of four flavour compounds (limonene, decanal, linalool and ethyl 2-methyl butyrate) into linear low-density polyethylene (LLDPE) were studied using a large volume injection GC ‘in vial’ extraction method. Food components investigated included β-lactoglobulin (β-lg), casein, pectin, carboxymethylcellulose (CMC), lactose and saccharose. β-lg interacted irreversibly with decanal (P < 0.01) and suppressed absorption of the latter by LLDPE by more than 50% after 14 days of exposure. Casein was capable of binding limonene and decanal (p < 0.05) by hydrophobic and covalent interactions, resulting in decreased absorption of 40% and 90%, respectively. The absorption rates of limonene, and to a leaser extent decanal, were decreased in presence of pectin and CMC. Increasing viscosity slowed down diffusion of flavour compounds from the matrix to LLDPE. An increase of absorption (p < 0.01) was observed for linalool and ethyl 2-methyl butyrate, due to a ‘salting out’ effect caused by lactose and saccharose. The absorption of decanal was decreased (p < 0.01) after 14 days of exposure in the presence of lactose, saccharose and CMC. There might be an interactive effect between a sugar (residue) and decanal. Knowledge of the composition of a food matrix and packaging material is necessary to estimate the amount of flavour absorption. © 2000 Society of Chemical Industry
The Characterization of CdS Thin Film Prepared by CBD Method (2012)

CdS thin film was deposited onto glass substrates by the chemical bath deposition. The deposition temperature was maintained at 75 °C. The crystal structure, surface morphology, optical and electrical properties have investigated employing X-ray diffraction (XRD), scanning electron microscopy (SEM), spectrophotometer and seeback coefficient measurement, respectively. The XRD reveals CdS thin film grown at 75 °C has the mixed hexagonal and cubic structure. The optical band gap energy is 2.4 eV. The seeback coefficient is 197.3μV/k at room temperature. The electric resistivity of CdS thin film is in the order of 10000Ω•cm.
One-to-many interprocess communication in the V-system (1984)

Interprocess communication (IPC) normally allows one process to communicate with only one other process at a time. One-to-many IPC allows one process to communicate simultaneously with a group of processes., possibly of unknown membership. While the broadcast and multicast facilities of local networks support efficient one-to-many communication between hosts, its use between processes has been limited by the lack of support in the distributed operating system. This paper describes the integration of one-to-many communication into V interprocess communication system. We discuss the different models of use and the reliability and present some initial applications.
Apical Membrane Expression of Distinct Sulfated Glycans Is a Characteristic Feature of Ductules and Their Reactive and Neoplastic Counterparts (2021)

Intrahepatic bile ducts transport bile between bile canaliculi and the extrahepatic bile duct. The luminal surface of this tract is lined by a layer of biliary epithelial cells, or cholangiocytes, which secrete mucins consisting of scaffold proteins and <i>O</i>-glycosidically linked carbohydrate side chains. Although mucin core proteins have been extensively investigated, the structure and function of carbohydrate side chains have not. Here, we demonstrate that distinct sulfated glycans positive for MECA-79, R-10G, and 297-11A, but not 5D4, monoclonal antibodies are expressed in the cytoplasm of cells of large-sized ducts and in the apical membrane of cells in ductules, and that R-10G immunolabeling is partially eliminated by endo-β-galactosidase digestion, supporting the presence of <i>N</i>-acetylglucosamine-6-<i>O</i>-sulfated <i>N</i>-acetyllactosamine structures. We observed comparable apical membrane-predominant staining in ductular reactions seen during regeneration that occurs in various liver diseases and in cholangiolocarcinoma, a subtype of small duct-type intrahepatic cholangiocarcinoma (iCCA). Apical membrane expression of distinct sulfated glycans in large duct-type iCCA was negligible. Intriguingly, under pathological conditions, endo-β-galactosidase digestion almost completely eliminated R-10G immunoreactivity. These findings suggest that apical membrane expression of distinct sulfated glycans is a characteristic feature of ductules and their reactive and neoplastic counterparts.
Principal Component Models for Generating Large GARCH Covariance Matrices (2002)

The implementation of multivariate GARCH models in more than a few dimensions is extremely difficult: because the model has many parameters, the likelihood function becomes very flat, and consequently the optimization of the likelihood becomes practicably impossible. There is simply no way that full multivariate GARCH models can be used to estimate directly the very large covariance matrices that are required to net all the risks in a large trading book. This paper begins by describing the principal component GARCH or ‘orthogonal GARCH’ (O‐GARCH) model for generating large GARCH covariance matrices that was first introduced in Alexander and Chibumba (1996) and subsequently developed in Alexander (2000, 2001b). The O‐GARCH model is an accurate and efficient method for generating large covariance matrices that only requires the estimation of univariate GARCH models. Hence, it has many practical advantages, for example in value–at–risk models. It works best in highly correlated systems, such as term structures. The purpose of this paper is to show that, if sufficient care is taken with the initial calibration of the model, equities and foreign exchange rates can also be included in one large covariance matrix. Simple conditions for the final covariance matrix to be positive semi‐definite are derived. (J.E.L.: C32, C53, G19, G21, G28).
Bifunctional Coating with Sustained Release of 4-Amide-piperidine-C12 for Long-Term Prevention of Bacterial Colonization on Silicone (2015)

Bacterial colonization by nosocomial pathogens on medical device surface can cause serious and life-threatening infections. We showed that 4-amide-piperidine-C12 (4AP12), the base form of 4-dodecaneamidepiperidine HCl, has broad-spectrum antimicrobial activity against both Gram-negative and Gram-positive bacteria and fungi. Resistance assay confirmed that prolonged exposure of bacteria to subinhibitory concentrations of 4AP12 did not induce resistance to 4AP12. The possible antimicrobial mechanism of 4AP12 was investigated, and attributed to the disruption of the cell membrane of microorganisms and subsequent cell lysis. The hydrophobic 4AP12 was incorporated in Pluronic F127 diacrylate (F127DA) micelles, which were then graft-copolymerized with acrylic acid and cross-linked onto ozonized silicone surface. Sulfobetaine methacrylate and F127DA were then graft-copolymerized as an antifouling layer on top of the F127DA-AA hydrogel containing the 4AP12, thus forming a microscale two-layer bifunctional coating. Sustained release of 4AP12 at a rate of up to 1 μg/day per cm<sup>2</sup> of hydrogel-coated silicone surface was achieved and this was sufficient to inhibit ∼97% of bacterial colonization by <i>Acinetobacter baumannii</i> in artificial urine medium under static condition over a 14-day period. Bacterial colonization by <i>Escherichia coli</i> and <i>Pseudomonas aeruginosa</i> under similar conditions was also significantly reduced. In addition, after 96 h exposure to flowing artificial urine (0.7 mL/min), <i>Escherichia coli</i> colonization on the 4AP12-loaded hydrogel-coated surface was reduced by ∼89% compared to the pristine surface. The concentration of 4AP12 that was released and was effective in inhibiting bacterial colonization did not result in significant cytotoxicity to human epithelial cells.
ChemInform Abstract: Asymmetric Catalysis at Chiral Metal Surfaces (2008)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Application of a New Vertical Profiling Tool (ESASS) for Sampling Groundwater Quality During Hollow‐Stem Auger Drilling (2011)

A new tool called ESASS ( E nhanced S creen A uger S ampling S ystem) was developed by the U.S. Geological Survey. The use of ESASS, because of its unique U.S. patent design (U.S. patent no. 7,631,705 B1), allows for the collection of representative, depth‐specific groundwater samples (vertical profiling) in a quick and efficient manner using a 0.305‐m long screen auger during hollow‐stem auger drilling. With ESASS, the water column in the flights above the screen auger is separated from the water in the screen auger by a specially designed removable plug and collar. The tool fits inside an auger of standard inner diameter (82.55 mm). The novel design of the system constituted by the plug, collar, and A‐rod allows the plug to be retrieved using conventional drilling A‐rods. After retrieval, standard‐diameter (50.8 mm) observation wells can be installed within the hollow‐stem augers. Testing of ESASS was conducted at one waste‐disposal site with tetrachloroethylene (PCE) contamination and at two reference sites with no known waste‐disposal history. All three sites have similar geology and are underlain by glacial, stratified‐drift deposits. For the applications tested, ESASS proved to be a useful tool in vertical profiling of groundwater quality. At the waste site, PCE concentrations measured with ESASS profiling at several depths were comparable (relative percent difference &lt;25%) to PCE concentrations sampled from wells. Vertical profiling with ESASS at the reference sites illustrated the vertical resolution achievable in the profile system; shallow groundwater quality varied by a factor of five in concentration of some constituents (nitrate and nitrite) over short (0.61 m) distances.
Extended field of view soft x-ray Fourier transform holography: toward imaging ultrafast evolution in a single shot (2007)

Panoramic full-field imaging is demonstrated by applying spatial multiplexing to Fourier transform holography. Multiple object and reference waves extend the effective field of view for lensless imaging without compromising the spatial resolution. In this way, local regions of interest distributed throughout a sample can be simultaneously imaged with high spatial resolution. A method is proposed for capturing multiple ultrafast images of a sample with a single x-ray pulse.
Diabetes and Hypertension: Experimental Models for Pharmacological Studies (1999)

Since hypertensive and diabetes-mellitus frequently occur simultaneously there exists a requirement for animal models where both pathological entities are combined. The streptozotocin (STZ)-spontaneously hypertensive rat (STZ-SHR) and the obese Zucker rat are examples of animal models where hypertension and diabetes occur simultaneously. STZ-SHR develop a hyperglycaemic syndrome, associated with other biochemical and morphological changes that to some extent approach IDDM (type I diabetes) combined with hypertension. The obese Zucker rat is characterised by the simultaneous occurrence of obesity, hyperglycaemia, hyperinsulinaemia, hyperlipidaemia and moderate hypertension. As such it approaches the patient with NIDDM (type II diabetes) who is simultaneously hypertensive. Lean Zucker rats are suitable controls with respect to the obese animals. Both animal models (STZ-SHR and obese Zucker rats) were characterised with respect to their biochemical, morphometric and haemodynamic characteristics of their cardiovascular system. The resemblance of this model with human NIDDM with hypertension syndrome indicates that the obese Zucker rat deserves special attention in pharmacological research.
Structural basis for regulation of rhizobial nodulation and symbiosis gene expression by the regulatory protein NolR (2014)

The symbiosis between rhizobial microbes and host plants involves the coordinated expression of multiple genes, which leads to nodule formation and nitrogen fixation. As part of the transcriptional machinery for nodulation and symbiosis across a range of Rhizobium, NolR serves as a global regulatory protein. Here, we present the X-ray crystal structures of NolR in the unliganded form and complexed with two different 22-base pair (bp) double-stranded operator sequences (oligos AT and AA). Structural and biochemical analysis of NolR reveals protein-DNA interactions with an asymmetric operator site and defines a mechanism for conformational switching of a key residue (Gln56) to accommodate variation in target DNA sequences from diverse rhizobial genes for nodulation and symbiosis. This conformational switching alters the energetic contributions to DNA binding without changes in affinity for the target sequence. Two possible models for the role of NolR in the regulation of different nodulation and symbiosis genes are proposed. To our knowledge, these studies provide the first structural insight on the regulation of genes involved in the agriculturally and ecologically important symbiosis of microbes and plants that leads to nodule formation and nitrogen fixation.
A supercapacitor agent for providing real-time power services to the grid (2015)

Supercapacitors-based storage systems are expected to play a key role in microgrids in view of their capability to compensate high-power imbalances. We define an agent for the control of supercapacitor arrays within the context of the novel control framework Commelec, proposed by the Authors as a composable method for real-time control of active distribution networks with explicit power setpoints. An important function of such an agent is to advertise the real-time power capabilities and operational preferences of the supercapacitor array based on local information. Given the small energy capacity of such a device, its internal state can largely vary from one setpoint implementation to the next one. For this reason, the use of an accurate model is crucial in the agent definition. We show that it is possible to infer the real-time power capabilities of the device by using simple measurements on the supercapacitor array suitably coupled with an accurate representation of the cells composing the array. Results show that the agent is able to speak for the resource, thus allowing its use from an external controller.
CO2 Capture and H2 Recovery Using a Hollow Fiber Membrane Contactor (2023)

In this study, hydrogen was recovered and purified by using a membrane contactor unit from CO2-rich gas without the use of any basic chemicals such as amines. The membrane operational parameters were adjusted to achieve high CO2 removal and H2 recovery. The effects of gas flow rate, pressure, gas composition (CO2/H2 ratio), pressure difference between liquid and gas, and gas/liquid ratio on CO2 removal and H2 recovery were investigated. Depending on the gas flow rate, the contact time between gas and liquid could be controlled, changing the absorption amounts of CO2 and H2. Regarding gas composition, an increase in the CO2/H2 ratio from 0.25 to 1 boosted H2 recovery. Furthermore, increasing the CO2/H2 ratio above 1 (from 1 to 3) generally reduced H2 recovery from 98.7% to 83%. Additionally, supplementation with the optimal amount of additive enhanced CO2 removal and H2 recovery. Thus, using a membrane contactor system results in high CO2 removal (82.7–93.5%) and H2 recovery (91.5–98.7%). Moreover, H2 production and separation can be performed in one system, implying that CO2 removal can be performed more efficiently by the membrane contactor. This study offers a new and promising route for producing high-purity H2 while removing CO2.
Changes in Quality of Life over Time in Patients Registered on the Mayo Clinic Esophageal Adenocarcinoma and Barrettʼs Esophagus Registry (2007)

Purpose: To explore the change in patient quality of life (QOL) over time in patients with esophageal adenocarcinoma (EA) or Barrett's esophagus (BE). Methods: Members of the Mayo Clinic EABE Registry completing two QOL assessments (baseline and 1 year (range 11–16 mos)) were selected to evaluate whether QOL changes occurred over time. Completed was the Linear Analogue Self Assessment (LASA) containing 12 questions relating to QOL (overall, social, spiritual, physical, mental, emotional, social support, financial, pain, fatigue and legal issues). Each LASA question has a value from 0 (worst) to 10 (best). The change from baseline was calculated for each question. Further, the change in each score was dichotomously categorized as being a positive (increase in QOL) or negative (decrease in QOL) change. Basic summary statistics were computed for baseline characteristics and QOL scores. Student's t-tests were used to determine significance in changes from baseline, Kruskal-Wallis tests were performed for the difference in continuous data between groups and Fischer-Exact tests were performed for differences in categorical data between groups. Results: Data from 372 patients was analyzed. Median age was 66 (range 30–93). 81% were male, 10% received treatment for EA prior to QOL assessment, 8% received treatment between assessments, and 82% received no treatment. Change in scores showed that the group had significant decreases in pain frequency ( < 0.001) and social support ( < 0.001) and a marginally significant decrease in pain severity (P= 0.06). Patients treated between assessments had a higher change in financial well-being score than the other two groups (mean 1.5 vs −0.1 vs −0.1, P-0.001) and a higher change in legal well-being (mean 0.9 vs −0.1 vs −0.1, P= 0.04). Treated patients reported higher pain severity (P= 0.048). There were no differences in the change from baseline scores between gender or age groups. The categorical change resulted in a difference in financial well-being (P= 0.03) and social support (P= 0.03). Differences in physical well-being were marginal (P= 0.06). Conclusion: Treated patients had less financial concerns and legal concerns but did experience higher pain severity. The significant change from baseline of social support was not evident upon subgroup analyses.
Sustainable Precast-Concrete-Block Structural System (2007)

The structural system herein described is comprised of oversized reinforced precast concrete blocks. These blocks can be placed rapidly, speeding construction of revetments, retaining walls, blast barriers, sound attenuation walls, quays, breakwaters, seawalls, and shore protection structures. The blocks can be made with a hollow core or alternatively encapsulate vehicle-tire-bundles (sustainable option). The system allows for the placement of continuity reinforcing and piles can be incorporated to increase foundation performance. The use of the system is particularly advantageous in marine construction by allowing precast manufacturers to competitively supply projects locally and globally through direct delivery of the blocks — via barge or ship — from a marine-side precast plant to a marine-side construction site. Public agencies are increasingly concerned about their project's contribution to sustainability. The system's potential maximization of discarded tire usage becomes highly significant as a method to reduce the amount of waste tires ending up in landfills or being burned.
High speed VCSELs for optical interconnects (2012)

This paper presents an overview of our recent work on high speed, oxide confined, 850 nm vertical cavity surface emitting lasers (VCSELs). With proper active region and cavity designs, and techniques for reducing capacitance and thermal impedance, we have reached a modulation bandwidth of 23 GHz and demonstrated 40 Gbps transmission. Using an integrated mode filter for reducing the spectral width we have extended the reach on multimode fiber at 25 Gbps from 100 to 500 m. Improved link capacity was also demonstrated using a more spectrally efficient multi-level modulation format (4-PAM). Finally, a MEMS-technology for wafer scale integration of tunable high speed VCSELs was developed, enabling a tuning range of 24 nm, a 6 GHz modulation bandwidth, and 5 Gbps transmission.
Development of a film thickness probe using capacitance for asymmetrical two-phase flow with heat addition (1992)

A film thickness probe based on capacitance measurements has been developed which is used to measure the liquid film thickness on both the upper and lower surface of a horizontal tube containing a two-phase mixture. Using appropriate nondimensionalization of the capacitance versus film thickness relationship, a new method has been developed in which the sensor may be used in temperature-dependent flow fields. The liquid film thickness probe was calibrated at room temperature and tested in a refrigerant R113 flow boiling facility over a 60 °C temperature span. Measurements made over a film thickness range of 25 mm using the capacitance probe are in close agreement with optical measurements made with a charge coupled device camera. In addition, spectral analysis of the probe signal allows for a trace of the low-frequency characteristics of the liquid film.