gebhart/patrepeval huggingface dataset:
Entropy Effects on Protein Hinges:  The Reaction Catalyzed by Triosephosphate Isomerase (2004)

Many proteins utilize segmental motions to catalyze a specific reaction. The Omega loop of triosephosphate isomerase (TIM) is important for preventing the loss of the reactive enediol(ate) intermediate. The loop opens and closes even in the absence of the ligand, and the loop itself does not change conformation during movement. The conformational changes are localized to two hinges at the loop termini. Glycine is never observed in native TIM hinge sequences. In this paper, the hypothesis that limited access to conformational space is a requirement for protein hinges involved in catalysis was tested. The N-terminal hinge was mutated to P166/V167G/W168G (PGG), and the C-terminal hinge was mutated to K174G/T175G/A176G (GGG) in chicken TIM. The single-hinge mutants PGG and GGG had k(cat) values 200-fold lower than that of the wild type and K(m) values 10-fold higher. The k(cat) of double-hinge mutant P166/V167G/W168G/K174G/T175G/A176G was reduced 2500-fold; the K(m) was 10-fold higher. A combination of primary kinetic isotope effect measurements, isothermal calorimetric measurements, and (31)P NMR spectroscopic titration with the inhibitor 2-phosphoglycolate revealed that the mutants have a different ligand-binding mode than that of the wild-type enzyme. The predominant conformations of the mutants even in the presence of the inhibitor are loop-open conformations. In conclusion, mutation of the hinge residues to glycine resulted in the sampling of many more hinge conformations with the consequence that the population of the active-closed conformation is reduced. This reduced population results in a reduced catalytic activity.
H2O2-mediated permeability: role of MAPK and occludin (2000)

H(2)O(2)-mediated elevation in endothelial solute permeability is associated with pathological events such as ischemia-reperfusion and inflammation. To understand how H(2)O(2) mediates increased permeability, we investigated the effects of H(2)O(2) administration on vascular endothelial barrier properties and tight junction organization and function. We report that H(2)O(2) exposure caused an increase in endothelial solute permeability in a time-dependent manner through extracellularly regulated kinase 1 and 2 (ERK1/ERK2) signal pathways. H(2)O(2) exposure caused the tight junctional protein occludin to be rearranged from endothelial cell-cell junctions. Occludin rearrangement involved redistribution of occludin on the cell surface and dissociation of occludin from ZO-1. Occludin also was heavily phosphorylated on serine residues upon H(2)O(2) administration. H(2)O(2) mediates changes in ERK1/ERK2 phosphorylation, increases endothelial solute permeability, and alters occludin localization and phosphorylation were all blocked by PD-98059, a specific mitogen-activated protein (MAP) or ERK kinase 1 inhibitor. These data strongly suggest that H(2)O(2)-mediated increased endothelial solute permeability involves the loss of endothelial tight junction integrity through increased ERK1/ERK2 activation.
Congenital Diaphragmatic Hernia: Perinatal Prognostic Factors and Short-Term Outcomes in a Single-Center Series (2023)

<b>Background</b>: Many prognostic factors for CDH patients are described and validated in the current literature: the size of diaphragmatic defects, need for patch repair, pulmonary hypertension and left ventricular dysfunction are recognized as the most influencing outcomes. The aim of this study is to analyze the influence of these parameters in the outcome of CDH patients in our department and identify any further prognostic factors. <b>Methods</b>: An observational retrospective single-center study was conducted including all patients treated at our centre with posterolateral CDH between 01.01.1997 and 12.31.2019. The main outcomes evaluated were mortality and length of hospital stay. A univariate and multivariate analysis was performed. <b>Results</b>: We identified 140 patients with posterolateral CDH; 34.8% died before discharge. The overall median length of stay was 24 days. A univariate analysis confirmed that both outcomes are associated with the size of diaphragmatic defects, need for patch repair and presence of spleen-up (<i>p</i> < 0.05). A multivariate analysis identified that the need for patch repair and maximum dopamine dose used for cardiac dysfunction are independent parameters associated with the length of stay only (<i>p</i> < 0.001). <b>Conclusions</b>: In our series, the duration of hospitalization is longer for newborns with CDH treated with higher doses of dopamine for left ventricular dysfunction or needing patch repair in large diaphragmatic defects.
Characterization of a monoclonal antibody recognizing a novel leucocyte adhesion molecule (1990)

Conference Article| April 01 1990 Characterization of a monoclonal antibody recognizing a novel leucocyte adhesion molecule LYNDA J. PARTRIDGE; LYNDA J. PARTRIDGE *Biochemistry Section, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN Search for other works by this author on: This Site PubMed Google Scholar IAN DRANSFIELD; IAN DRANSFIELD †Imperial Cancer Research Fund, Lincoln's Inn Fields, London WC2A 3PX, U.K. Search for other works by this author on: This Site PubMed Google Scholar DENNIS BURTON DENNIS BURTON *Biochemistry Section, Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN Search for other works by this author on: This Site PubMed Google Scholar Biochem Soc Trans (1990) 18 (2): 274–275. https://doi.org/10.1042/bst0180274a Article history Received: September 14 1989 Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter LinkedIn Cite Icon Cite Get Permissions Citation LYNDA J. PARTRIDGE, IAN DRANSFIELD, DENNIS BURTON; Characterization of a monoclonal antibody recognizing a novel leucocyte adhesion molecule. Biochem Soc Trans 1 April 1990; 18 (2): 274–275. doi: https://doi.org/10.1042/bst0180274a Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search nav search search input Search input auto suggest search filter All ContentAll JournalsBiochemical Society Transactions Search Advanced Search Keywords: FACS, flourescence-activated cell sorting This content is only available as a PDF. © 1990 Biochemical Society1990 Article PDF first page preview Close Modal You do not currently have access to this content.
Optimizing DRX configuration to improve battery power saving and latency of active mobile applications over LTE-A network (2013)

In LTE networks, mobile applications and their higher data rate requirements are the latest phenomenon causing a tremendous need in power saving for mobile devices. Discontinuous reception (DRX) is one of the key power saving mechanisms in LTE. Since DRX saves battery power of user equipment usually at the expense of potential increase in latency, an optimization is needed to find the best tradeoff between latency and power saving. In this paper, we first develop an analytical model to estimate power saving achieved and latency incurred by DRX operation. Then, a tradeoff scheme is formulated to maintain a balance between these two performance parameters based on operator's preference for power saving. We validate analytical model using system level simulation results obtained from OPNET Modeler. The results show that the proposed tradeoff scheme is highly efficient in keeping a balance between power saving and latency. We have shown that proposed scheme can achieve a significant delay improvement with a small decrease in power saving. The results also indicate that short DRX cycles are very effective in reducing latency for active traffic.
[X-ray phase imaging using a X-ray tube with a small focal spot -improvement of image quality in mammography-]. (2002)

Phase contrast X-ray imaging has been studied intensively using X-rays from synchrotron radiation and micro-focus X-ray tubes. However, these studies have revealed the difficulty of this technique's application to practical medical imaging. We have created a phase contrast imaging technique using a molybdenum X-ray tube with a small focal spot size for mammography. We identified the radiographic conditions in phase contrast magnification mammography with a screen-film system, where edge effect due to phase contrast overcomes geometrical unsharpness caused by the 0.1mm-focal spot of a molybdenum X-ray tube. The edge enhancement due to phase imaging was observed in an image of a plastic tube, and then geometrical configuration of the X-ray tube, the object and the screen-film system was determined for phase imaging of mammography. In order to investigate a potential for medical application of this method, we conducted evaluation of the images of ACR 156 mammography phantom. We obtained higher scores for phase imaging using high speed screen-film systems without any increase of X-ray dose than the score for contact imaging using a standard speed screen-film system.
Rabbit genome analysis reveals a polygenic basis for phenotypic change during domestication (2014)

The genetic changes underlying the initial steps of animal domestication are still poorly understood. We generated a high-quality reference genome for the rabbit and compared it to resequencing data from populations of wild and domestic rabbits. We identified more than 100 selective sweeps specific to domestic rabbits but only a relatively small number of fixed (or nearly fixed) single-nucleotide polymorphisms (SNPs) for derived alleles. SNPs with marked allele frequency differences between wild and domestic rabbits were enriched for conserved noncoding sites. Enrichment analyses suggest that genes affecting brain and neuronal development have often been targeted during domestication. We propose that because of a truly complex genetic background, tame behavior in rabbits and other domestic animals evolved by shifts in allele frequencies at many loci, rather than by critical changes at only a few domestication loci.
Spatio‐energetic cross talk in photon counting detectors: Detector model and correlated Poisson data generator (2016)

The authors have developed a novel, computationally efficient PCD model that takes into account double-counting and resulting spatio-energetic correlation between PCD pixels. The MC simulation validated the accuracy.
Jenseits von Sauerstoff: Die Neonatale Sepsis ist ein unabhängiger Risikofaktor für die Entwicklung einer ROP bei sehr unreifen Frühgeborenen (2023)

Hintergrund Die Frühgeborenenretinopathie (ROP) ist eine den Visus gefährdende Erkrankung von unveränderter Bedeutung. Regelmäßige Screening-Untersuchungen und eine frühzeitige Therapie sind essenziell. Dennoch ist die Prognose der hochgradigen ROP auch bei adäquater Therapie ungünstig, und ist die Prävention unerlässlich. Jüngere Studien deuten darauf hin, dass die neonatale Sepsis einen unabhängigen ROP-Risikofaktor darstellt.
Communicating Quality of Service Requirements to an Object-Based Storage Device (2005)

Obtaining consistent bandwidth with predictable latency from disk-based storage systems has proven difficult due to the storage system's inability to understand quality of service (QoS) requirements. In this paper, we present a feasibility study of QoS with the object-based storage device (OSD) specification. We look at OSD's ability to provide QoS guarantees for consistent bandwidth with predictable latency. Included in this paper is a description of QoS requirements of a sample application and how these requirements are translated into parameters that are then communicated to, and interpreted by, the OSD. Implementation problems lead to the failure of a hard real-time QoS model, but this failure is not due to the OSD protocol. The paper concludes with a description of how well the revision 9 OSD standard (OSDR9) is able to accommodate QoS. We provide suggestions for improving the OSD specification and its ability to communicate QoS requirements.
Asymmetries between the production of D− and D+ mesons from 500 GeV/c π− nucleon interaction as functions of x and p2 (1997)

We present measurements of the production of Ds− mesons relative to Ds+ mesons as functions of xF and of pt2 for a sample of 2445 Ds decays to φπ. The Ds mesons were produced in Fermilab experiment E791 with 500 GeV/c π− mesons incident on one platinum and four carbon foil targets. The acceptance-corrected integrated asymmetry in the xF range −0.1 to 0.5 for Ds± mesons is 0.032 ± 0.022 ± 0.022, consistent with no net asymmetry. We compare the results as functions of xF and pt2 to predictions and to the large production asymmetry observed for D± mesons in the same experiment. These comparisons support the hypothesis that production asymmetries come from the fragmentation process and not from the charm quark production itself.
Isolated Large Cell Calcifying Sertoli Cell Tumor in a Young Boy, not Associated with Peutz-Jeghers Syndrome or Carney Complex (2015)

LCCSCT is a rare testicular neoplasm, and may present in isolated rather than in more typical association with syndromes such as CNC and PJS.
Combustor assembly for use in a turbine engine and methods of assembling same (2023)

A fuel nozzle assembly for use with a turbine engine is described herein. The fuel nozzle assembly includes a plurality of fuel nozzles positioned within an air plenum defined by a casing. Each of the plurality of fuel nozzles is coupled to a combustion liner defining a combustion chamber. Each of the plurality of fuel nozzles includes a housing that includes an inner surface that defines a cooling fluid plenum and a fuel plenum therein, and a plurality of mixing tubes extending through the housing. Each of the mixing tubes includes an inner surface defining a flow channel extending between the air plenum and the combustion chamber. At least one mixing tube of the plurality of mixing tubes including at least one cooling fluid aperture for channeling a flow of cooling fluid from the cooling fluid plenum to the flow channel.
[Mast-cell rosettes in the immunized rat]. (1976)

After stimulation by ovalbumin + Bordetella pertussis, rat peritoneal mast cells can form rosettes with antigen-coated erythrocytes. This phenomenon is inhibited by previous incubation of mast cells with antigen; it is attributed to apparition of membrane-bound anaphylactic antibody. The variations of percentage of rosette forming mast cells during the course of immunization are reported and compared with P.C.A. titers.
From Newspaper Substrate to Nanotubes—Analysis of Carbonized Soot Grown on Kaolin Sized Newsprint (2019)

Herein, we report the successful use of newspaper as a substrate for the growth of single-walled carbon nanotubes (SWCNTs) by chemical vapor deposition (CVD) with intriguing results demonstrating that (a) the large surface area of newspaper stock allows for SWCNT growth and (b) only newspaper produced with kaolin clay sizing allowed for SWCNT growth. Kaolin newsprint was impregnated with Al2O3 and Fe(NO3)3·9H2O (as precursors to FexOy nanoparticles), and calcined (30 min at 400 °C). The subsequent char residue was loaded into a CVD chamber and used as a substrate for SWCNT growth at 750 °C, using H2, C2H2, and water vapor as the growth gas. Samples of raw carbon soot exhibiting fluorescence spectra, indicative of SWCNTs, were further evaluated by resonant Raman spectroscopy, and by transmission electron microscopy (TEM). The calcinated substrate remnants were evaluated by scanning electron microscopy (SEM) and energy dispersive X-ray spectroscopy (EDS). Experiments utilizing paper substrates produced with kaolin filler resulted in hybridized sp2–sp3 bonded carbon species. The soot was found to consist primarily of carbon nanotubes and bi-layer graphene in the form of collapsed nanotubes, also known as graphene nanoribbons (GNR).
Functional and technological definition of BIM-aware services to assess, predict and optimize energy performance of buildings (2013)

There are a number of important elements in designing of building energy management systems – when data collection, aggregation and management is usually well addressed by existing building management systems, actual analytical components allowing to diagnose a behavior leading to excessive energy consumption and/or compromised occupants’ comfort are far less mature. It is not only about developing algorithms for such tools, but also proper design of a hosting platform and its viability – it should not only enable access to sensor readings, but also provide access to other building data like Building Information Models and allow collaboration and interconnection of such analytics. BaaS project calls such tools Assess, Predict and Optimize services. Developing a smart platform supporting these services naturally leads to a concept of the building as a service eco-system (BaaS) where any new tool can be plugged in the system and can benefit from already existing components. In the present work, the high level architecture of the BaaS platform is presented and the ability of BaaS system to act as a platform enabling the building contextual data as well as dynamic data (sensor readings) to software modules is demonstrated through a use-case example on a simple one zone office building.
The Unusual Phylogenetic Distribution of Retrotransposons: A Hypothesis (2003)

Retrotransposons have proliferated extensively in eukaryotic lineages; the genomes of many animals and plants comprise 50% or more retrotransposon sequences by weight. There are several persuasive arguments that the enzymatic lynchpin of retrotransposon replication, reverse transcriptase (RT), is an ancient enzyme. Moreover, the direct progenitors of retrotransposons are thought to be mobile self-splicing introns that actively propagate themselves via reverse transcription, the group II introns, also known as retrointrons. Retrointrons are represented in modern genomes in very modest numbers, and thus far, only in certain eubacterial and organellar genomes. Archaeal genomes are nearly devoid of RT in any form. In this study, I propose a model to explain this unusual distribution, and rationalize it with the proposed ancient origin of the RT gene. A cap and tail hypothesis is proposed. By this hypothesis, the specialized terminal structures of eukaryotic mRNA provide the ideal molecular environment for the lengthening, evolution, and subsequent massive expansion of highly mobile retrotransposons, leading directly to the retrotransposon-cluttered structure that typifies modern metazoan genomes and the eventual emergence of retroviruses.
Enzymatic Microreactor-on-a-Chip:  Protein Mapping Using Trypsin Immobilized on Porous Polymer Monoliths Molded in Channels of Microfluidic Devices (2002)

Enzymatic microreactors have been prepared in capillaries and on microfluidic chips by immobilizing trypsin on porous polymer monoliths consisting of 2-vinyl-4,4-dimethylazlactone, ethylene dimethacrylate, and acrylamide or 2-hydroxyethyl methacrylate. The azlactone functionalities react readily with amine and thiol groups of the enzyme to form stable covalent bonds. The optimized porous properties of the monoliths lead to very low back pressures enabling the use of simple mechanical pumping to carry out both the immobilization of the enzyme from its solution and the subsequent analyses of substrate solutions. The Michealis-Menten kinetic characteristics of the reactors were probed using a low molecular weight substrate: N-alpha-benzoyl-L-arginine ethyl ester. The effects of immobilization variables such as the concentration of trypsin in solution and percentage of azlactone functionalities in the monolith, as well as the effect of reaction time on the enzymatic activity, and of process variables such as substrate flow velocity and residence time in the reactor, were studied in detail. The proteolytic activity of the enzymatic microreactor on chip was demonstrated at different flow rates with the cleavage of fluorescently labeled casein used as a substrate. The excellent performance of the monolithic microreactor was also demonstrated with the digestion of myoglobin at the fast flow rate of 0.5 microL/min, which affords a residence time of only 11.7 s. The digest was then characterized using MALDI-TOF MS, and 102 out of 153 possible peptide fragments were identified giving a sequence coverage of 67%.
Fast data-derived fundamental spheroidal excitation models with application to UXO discrimination (2005)

Current idealized forward models for electromagnetic induction (EMI) response can be defeated by the characteristic material and geometrical heterogeneity of realistic unexploded ordnance (UXO). A new, physically complete modeling system was developed that includes all effects of these heterogeneities and their interactions within the object, in both near and far fields. The model is fast enough for implementation in inversion processing algorithms. A method is demonstrated for extracting the model parameters by straightforward processing of data from a defined measurement protocol. Depending on the EMI sensor used for measurements, the process of inferring model parameters is more or less ill-posed. More complete data can alleviate the problem. For a given set of data, special numerical treatment is introduced to take the best advantage of the data and obtain reliable model parameters. The resulting fast model is implemented in a pattern matching treatment of measurements by which signals from a UXO are identified within a series of those from unknown targets. Preliminary results show that this fast model is promising for use in processing of this kind. The inherent difficulties of target identification are examined, and solutions for resolving these difficulties are discussed.
Coronectomy of Deeply Impacted Lower Third Molar: Incidence of Outcomes and Complications after One Year Follow-Up (2015)

The results indicate that coronectomy can be considered a reasonable and safe treatment alternative for patients who demonstrate elevated risk for injury to the inferior alveolar nerve with removal of the third molars. Coronectomy did not increase the incidence of damage to the inferior alveolar nerve and would be safer than complete extraction in situations in which the root of the mandibular third molar overlaps or is in close proximity to the mandibular canal.
Automatic respiratory gating for perfusion quantification of DCEUS (2013)

A novel automatic respiratory gating (ARG) algorithm for ultrasound is presented. The ARG algorithm was applied on dual contrast imaging (contrast/tissue) loops in order to remove respiratory motion artifacts from dynamic contrast enhanced ultrasound (DCEUS) of liver lesion images. The ARG algorithm is fully automated and it only requires the operator to define the breathing cycle phase to be extracted. The ARG algorithm was applied on the tissue side of the dual contrast acquisition. Motion was detected using frame subtraction; frequency domain analysis identified the contribution of respiration in the motion. A respiratory kinetics curve was extracted based on the motion detection and frequency analyses. Gating was performed by detecting the signal envelope of the respiratory kinetics curve and applying a threshold in order to remove frames that are out of synchronization with the trigger frame. DCEUS images from fourteen liver metastasis patients were extracted with and without the use of ARG. The lesion DCEUS data were fitted onto the lognormal indicator dilution model and the goodness of fit was evaluated. Significant improvement to the goodness of fit of the liver lesion DCEUS data onto the lognormal model was demonstrated with the use of ARG.