gebhart/patrepeval huggingface dataset:
Application of High Resolution Micro-CT Imaging and Pore Network Modeling (PNM) for the Petrophysical Characterization of Tight Gas Reservoirs - A Case History from a Deep Clastic Tight Gas Reservoir in Oman (2011)

Abstract The paper provides a case history of the application of 3D imaging and Pore Network Modeling (PNM) technology to establish a direct relationship between rock micro-structure parameters from 3D via micro-tomographic images, and the simulation of petrophysical properties of clastic tight gas reservoir rocks in Oman. Tight gas reservoirs exhibit storage and flow characteristics that are intimately tied to the depositional and diagenetic processes. In particular, cores have significant primary and secondary porosity often dominated by clays and slot like pores. Accurately mapping the pore and grain structure and mineralogy in 3D and the interconnectivity of primary and secondary porosity illustrates the role 3D imaging plays in a comprehensive reservoir characterization program. The computed petrophysical properties (e.g. porosity, permeability, formation resistivity factor, hydraulic radii and drainage capillary pressure) are compared with routine and special core analysis results measured on conventional core samples. The use of 3D micro-tomograms at different scales and PNM provides a quick complimentary method to characterize the distribution and nature of different pore types and matrix components to characterize the static, elastic and dynamic rock properties even on rock fragments (2mm to 1cm diameter) that are not suitable for conventional core analysis techniques. The presented case history demonstrates that the new 3D PNM technologies can also be successfully applied to the challenging tight gas reservoirs with low porosities and very low permeabilities for comprehensive reservoir characterization to optimize the development scenarios.
Anchored CCD for Gas Turbine Combustor Design and Data Correlation (1997)

Correlations based on design database, combined with multidimensional computational combustion dynamics (CCD) models are used in the combustion design process. However, because of limitations in the current turbulent combustion models, numerics, and boundary conditions, CCD has provided mainly qualitative trends for aerothermal performance, emissions, and liner wall temperature levels and gradients. To overcome these deficiencies, hybrid modeling approaches have been proposed to analyze existing combustors. A typical hybrid modeling approach combines empirical and semianalytical correlations with CCD to give quantitatively accurate predictions of NOx, CO, HC, smoke, lean blowout, ignition, pattern factor, and liner wall temperatures. An alternate approach, anchored CCD, is described in this paper. First, the models were anchored with one of the five modern turbopropulsion engine combustors. The anchored models were then run for the other four combustors. The predicted results correlated well with measured NOx, CO, HC, LEO, and exit temperature quality data, demonstrating a broader applicability of the anchored method. The models were also used for designing a new combustion concept. The pretest prediction agreed well with sector rig data from development hardware, showing the feasibility of using the anchored methodology as a design tool.
Superior muscle reinnervation after autologous nerve graft or poly-L-lactide-?-caprolactone (PLC) tube implantation in comparison to silicone tube repair (2001)

Recovery after peripheral nerve injury depends not only on the amount of reinnervation, but also on its accuracy. The rat sciatic nerve was subjected to an 8 mm long gap lesion repaired either by autograft (AG, n = 6) or tubulization with impermeable silicone tube (SIL, n = 6) or permeable tube of poly-L-lactide-epsilon-caprolactone (PLC, n = 8). Recordings of the compound muscle action potential (CMAP) from gastrocnemius (mGC), tibialis anterior (mTA) and plantar (mPL) muscles were performed 90 days after injury to assess the amount of muscle reinnervation. The CMAP amplitude achieved in mGC, mTA and mPL was similar in after nerve autograft (39%, 42%, 22% of control values) and PLC tube implantation (37%, 36%, 24%) but lower with SIL tube (29%, 30%, 14%). The nerve fascicles projecting into each of these muscles were then transected and retrograde tracers (Fluoro Gold, Fast Blue, DiI) were applied to quantify the percentage of motoneurons with single or multiple branches to different targets. The total number of labeled motoneurons for the three muscles did not differ in autografted rats (1186 +/- 56; mean +/- SEM) with respect to controls (1238 +/- 82), but was reduced with PLC tube (802 +/- 101) and SIL tube (935 +/- 213). The percentage of neurons with multiple projections was lower after autograft and PLC tube (6%) than with SIL tube (10%). Considering the higher CMAP amplitude and lower number of neurons with multiple projections, PLC nerve conduits seem superior to SIL tubes and a suitable alternative to autografts for the repair of long gaps.
Liquid‐liquid phase separation in acetone solutions of palm olein: Implications for solvent fractionation (2007)

Abstract The quality of palm mid fractions (PMF) obtained by dry fractionation has increased, but the best‐quality PMF for application in many confectionery fats are still produced by solvent fractionation. In the present study, liquid‐liquid phase separation has been observed in acetone solutions both for pure triacylglycerols and for palm olein. The temperature at which phase separation occurs increases as the oil concentration is increased and linearly as the water content of the system is increased. The triacylglycerol compositions of the two liquid phases that form do not differ. However, the oil‐rich phase is depleted with respect to the polar components. The temperature at which liquid‐liquid phase separation occurs is reduced by about 0.2 and 0.4 °C per percent of free fatty acids and diacylglycerols, respectively. When oil‐rich droplets appear, crystallisation occurs within them rather than in the oil‐depleted phase, due to the higher oil concentration. Thus, liquid‐liquid phase separation prior to crystallisation raises the nucleation temperature but may lead to a greater concentration of entrained olein in the filter cake, leading to a poorer‐quality PMF.
RNA therapeutics inactivate PCSK9 by inducing a unique intracellular retention form (2015)

Hypercholesterolemia is a medical condition often characterized by high levels of low-density lipoprotein cholesterol (LDL-C) in the blood. Despite the available therapies, not all patients show sufficient responses, especially those with very high levels of LDL-C or those with familial hypercholesterolemia. Regulation of plasma cholesterol levels is very complex and several proteins are involved (both receptors and enzymes). From these, the proprotein convertase subtilisin/kexin type 9 (PCSK9) has emerged as a promising pharmacologic target. The objective of this work is to develop a new approach to inactivate PCSK9 by splice-switching oligonucleotides (SSOs), converting the normal splice form to a natural, less abundant and inactive, splice variant. For this purpose, a new RNA therapeutic approach for hypercholesterolemia based on SSOs was developed for modulation of the splice pattern of human PCSK9 pre-mRNA. Our results show an increase of the selected splice form at both the mRNA and protein level when compared to non-treated Huh7 and HepG2 cell lines, with concomitant increase of the protein level of the low-density lipoprotein receptor (LDLR) demonstrating the specificity and efficiency of the system. In vivo, full conversion to the splice form was achieved in a reporter system when mice were treated with the specific oligonucleotide, thus further indicating the therapeutic potential of the approach. In conclusion, PCSK9 activity can be modulated by splice-switching through an RNA therapeutic approach. The tuning of the natural active to non-active isoforms represents a physiological way of regulating the cholesterol metabolism, by controlling the amount of LDL receptor available and the rate of LDL-cholesterol clearance.
Hypernet: A Communication-Efficient Architecture for Constructing Massively Parallel Computers (1987)

A new class of modular networks is proposed for hierarchically constructing massively parallel computer systems for distributed supercomputing and AI applications. These networks are called hypernets. They are constructed incrementally with identical cubelets, treelets, or buslets that are well suited for VLSI implementation. Hypernets integrate positive features of both hypercubes and tree-based topologies, and maintain a constant node degree when the network size increases. This paper presents the principles of constructing hypernets and analyzes their architectural potentials in terms of message routing complexity, cost-effective support for global as well as localized communication, I/O capabilities, and fault tolerance. Several algorithms are mapped onto hypernets to illustrate their ability to support parallel processing in a hierarchically structured or data-dependent environment. The emulation of hypercube connections using less hardware is shown. The potential of hypernets for efficient support of connectionist models of computation is also explored.
Carbon source control of the phosphorylation state of the Bacillus subtilis carbon-flux regulator Crh in vivo (2011)

Bacillus subtilis possesses carbon-flux regulating histidine protein (Crh), a paralog of the histidine protein (HPr) of the phosphotransferase system (PTS). Like HPr, Crh becomes (de)phosphorylated in vitro at residue Ser46 by the metabolite-controlled HPr kinase/phosphorylase HPrK/P. Depending on its phosphorylation state, Crh exerts regulatory functions in connection with carbohydrate metabolism. So far, knowledge on phosphorylation of Crh in vivo has been limited and derived from indirect evidence. Here, we studied the dynamics of Crh phosphorylation directly by non-denaturing gel electrophoresis followed by Western analysis. The results confirm that HPrK/P is the single kinase catalyzing phosphorylation of Crh in vivo. Accordingly, phosphorylation of Crh is triggered by the carbon source as observed previously for HPr, but with some differences. Phosphorylation of both proteins occurred during exponential growth and disappeared upon exhaustion of the carbon source. During exponential growth, ~80% of the Crh molecules were phosphorylated when cells utilized a preferred carbon source. The reverse distribution, i.e. around 20% of Crh molecules phosphorylated, was obtained upon utilization of less favorable substrates. This clear-cut classification of the substrates into two groups has not previously been observed for HPr(Ser)~P formation. The likely reason for this difference is the additional PTS-dependent phosphorylation of HPr at His15, which limits accumulation of HPr(Ser)~P.
In-Search Assignment of Monoisotopic Peaks Improves the Identification of Cross-Linked Peptides (2018)

ABSTRACT Cross-linking/mass spectrometry (CLMS) has undergone a maturation process akin to standard proteomics by adapting key methods such as false discovery rate control and quantification. A seldom-used search setting in proteomics is the consideration of multiple (lighter) alternative values for the monoisotopic precursor mass to compensate for possible misassignments of the monoisotopic peak. Here, we show that monoisotopic peak assignment is a major weakness of current data handling approaches in cross-linking. Cross-linked peptides often have high precursor masses, which reduces the presence of the monoisotopic peak in the isotope envelope. Paired with generally low peak intensity, this generates a challenge that may not be completely solvable by precursor mass assignment routines. We therefore took an alternative route by ‘in-search assignment of the monoisotopic peak’ in Xi (Xi-MPA), which considers multiple precursor masses during database search. We compare and evaluate the performance of established preprocessing workflows that partly correct the monoisotopic peak and Xi-MPA on three publicly available datasets. Xi-MPA always delivered the highest number of identifications with ~2 to 4-fold increase of PSMs without compromising identification accuracy as determined by FDR estimation and comparison to crystallographic models.
Influence of Artificial Soft Tissue on Intra-Operative Vibration Analysis Method for Primary Fixation Monitoring in Cementless Total Hip Arthroplasty (2022)

In cementless Total Hip Arthroplasty (THA), achieving high primary implant fixation is crucial for the long-term survivorship of the femoral stem. While orthopedic surgeons traditionally assess fixation based on their subjective judgement, novel vibration-analysis fixation-monitoring techniques show promising potential in providing the surgeon with objective and quantifiable fixation measurements. This study presents a dynamic response measurement protocol for implant endpoint insertion and evaluates this protocol in the presence of artificial soft tissue. After the artificial femur was prepared in accordance with the THA protocol, the implant was inserted and progressively hammered into the cavity. The Pearson Correlation Coefficient (PCC) and Frequency Response Assurance Criterion (FRAC) corresponding to each insertion hammer hit were derived from the Frequency Response Functions (FRF) corresponding to each insertion step. The protocol was repeated with the artificial femur submerged in artificial soft tissue to imitate the influence of anatomical soft tissue. The FRAC appeared overall more sensitive than the PCC. In the presence of the artificial soft tissue the technique yielded higher PCC and FRAC values earlier in the insertion process. The measurements with artificial soft tissue produced FRFs with fewer peaks, lower resonance frequencies, and overall higher damping factors. The soft tissue appears to limit the fixation-change detection capabilities of the system and a promising potential remedy to this limitation is suggested.
A Photo-Crosslinking Approach to Identify Class II SUMO-1 Binders (2022)

The small ubiquitin-like modifier (SUMO) is involved in various cellular processes and mediates known non-covalent protein-protein interactions by three distinct binding surfaces, whose interactions are termed class I to class III. While interactors for the class I interaction, which involves binding of a SUMO-interacting motif (SIM) to a hydrophobic groove in SUMO-1 and SUMO-2/3, are widely abundant, only a couple of examples have been reported for the other two types of interactions. Class II binding is conveyed by the E67 loop region on SUMO-1. Many previous studies to identify SUMO binders using pull-down or microarray approaches did not strategize on the SUMO binding mode. Identification of SUMO binding partners is further complicated due to the typically transient and low affinity interactions with the modifier. Here we aimed to identify SUMO-1 binders selectively enriched for class II binding. Using a genetically encoded photo-crosslinker approach, we have designed SUMO-1 probes to covalently capture class II SUMO-1 interactors by strategically positioning the photo-crosslinking moiety on the SUMO-1 surface. The probes were validated using known class II and class I binding partners. We utilized the probe with p-benzoyl-phenylalanine (BzF, also termed BpF or Bpa) at the position of Gln69 to identify binding proteins from mammalian cell extracts using mass spectrometry. By comparison with results obtained with a similarly designed SUMO-1 probe to target SIM-mediated binders of the class I type, we identified 192 and 96 proteins specifically enriched by either probe, respectively. The implicated preferential class I or class II binding modes of these proteins will further contribute to unveiling the complex interplay of SUMO-1-mediated interactions.
ARPACK Users' Guide (1998)

List of figures List of tables Preface 1. Introduction to ARPACK. Important features Getting started Reverse communication interface Availability Installation Documentation Dependence on LAPACK and BLAS Expected performance P_ARPACK Contributed additions Trouble shooting and problems 2. Getting started with ARPACK. Directory structure and contents Getting started An example for a symmetric Eigenvalue problem 3. General use of ARPACK. Naming conventions, Precisions, and types Shift and invert spectral transformation mode Reverse communication structure for shift-Invert Using the computational modes Computational modes for real symmetric problems Postprocessing for Eigenvectors using dseupd Computational modes for real nonsymmetric problems Postprocessing for Eigenvectors Using dneupd Computational modes for complex problems Postprocessing for Eigenvectors Using zneupd 4. The implicitly restarted Arnoldi method: structure of the Eigenvalue problem Krylov subspaces and projection methods The Arnoldi factorization Restarting the Arnoldi method The generalized Eigenvalue problem Stopping Criterion 5. Computational routines. ARPACK subroutines LAPACK routines used by ARPACK BLAS routines used by ARPACK Appendix A. Templates and driver routines Symmetric drivers Real Nonsymmetric drivers Complex drivers Band drivers The singular value decomposition Appendix B. Tracking the progress of ARPACK. Obtaining trace output Check-pointing ARPACK Appendix C. The XYaupd ARPACK Routines. DSAUPD DNAUPD ZNAUPD Bibliography Index.
Effect of Oxygen Coverage on Electron Emission from Boron-Doped Polycrystalline Diamond (2001)

The relationship between the electron emission properties of a boron-doped chemical vapor deposited polycrystalline diamond thin film and the oxygen coverage on the diamond surface is systematically investigated. The threshold voltage of electron emission becomes higher with increasing oxygen coverage on the surface. The change of emission barrier height estimated from the slopes of Fowler-Nordheim plots and from the coverage of adsorbed oxygen atoms is evaluated. From the results, it was speculated that the emission barrier height was changed by the surface dipole layer that was formed by oxygen atoms on the diamond surface and led to the changes in the electron emission properties.
A method of efficient data transmission over Evolved Packet System (2014)

Even though Evolved Packet System (EPS) features flat-IP architecture, it is essentially a connection oriented system and establishes logical bearers between the User Equipment (UE) and the core network entities for any user data transmission. EPS was designed assuming high speed real-time bulk multimedia data transfer; so initial cost of bearer setup signaling for user plane data is justified. However, this basic assumption is changed due to very small and infrequent background data transfer by the smartphone's always-on applications most of the time when smartphone is not in active use. To transmit this background data, UE incurs frequent idle to connected state transitions and require costly disproportionate signaling overhead for EPS bearer and Radio Resource Control (RRC) connection setup/release procedure. This paper presents a connectionless transmission (CLT) scheme for efficient exchange of background data without establishing the EPS bearer and RRC connection. In the proposed CLT scheme, the data packets are made self-sustainable by carrying routing information in the packet's header. These self-sustained packets are carried through modified Random Access Channel (RACH) procedure between the UE and the eNodeB. Further, another novel aspect of the CLT scheme is to establish common user plane bearers between the radio access network and packet gateways in the core network, to forward self-sustain data packets using the routing information. Our simulation results show CLT scheme reduces the signaling overhead significantly compared to the traditional connection oriented transmission.
Analysis and design of AlGaN/GaN HEMT resistive mixers (2007)

Abstract In this article, resistive mixers using AlGaN/GaN high electron‐mobility transistor (HEMT) devices are examined. Models of the GaN devices in linear region were created. Behavior of conversion loss with LO power is well predicted using the developed model. Three down‐conversion mixers were designed for RF frequency of 1.7 GHz and IF frequency of 200 MHz using LO frequency of 1.9 GHz. GaN HEMT devices with gate width of 300 μm, and gate lengths of 1.2, 1.0, and 0.75 μm were used in the mixers. © 2007 Wiley Periodicals, Inc. Microwave Opt Technol Lett 49: 1152–1154, 2007; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.22390
Toward Programmed Molecular Lanthanide Probes and Sensors (1996)

The peculiar spectroscopic properties of the lanthanide metal ions (4f-block, Lnlll), and particularly Eulll and Tblll, make them suitable for the design of chemical luminescent probes and analytical sensors when Lnlll is introduced into organized molecular architectures possessing controlled and protected coordination sites. The tridentate receptors 2,6-bis(1-alkylbenzimidazol-2-yl)pyridine (Li, i=2-7) play a crucial role since they react with Ln3+ to give mononuclear building blocks [Ln(Li)3]3+ where the metal ion is protected by the wrapping of the aromatic ligands. In these ultraviolet to visible light-converting devices (Ln=Eu, Tb), the size of the internal cavity is controlled by the three closely packed strands which produce i) a promising discrimination between Lnlll according to their sizes and ii) efficient light-harvesting resulting form the strong absoprtion of ultraviolet light by the ligands. These building blocks have been introduced into more sophisticated homodinuclear triple-helical complexes [Ln2(L8)3]6+ and statistical mixtures containing the heterodinuclear directional visible to visible light-converting device [EuTb(L8)3]6+. Improved molecular programming results form the use of acyclic segmental ligand possessing different binding units coded for one particular ion. The segmental ligands Li (i=9,10) discriminate Fell and AgI to give the heterodinuclear double helicate [FeAg(L10)2]3+ and the heterotrinuclear organometallic [2]-catenate [FeAg2(L9)2]4+ where each metal ion occupies a coordination site satisfying its stereochemical requirements. The receptor L11 recognizes 3d- and 4f-block metal ions to give the heterodinuclear d-f-triple-helical complexes [LnZn(L11)3]5+ where Znll occupies the pseudo-octahedral capping site and corresponds to a noncovalent tripod which properly organizes the strands for their coordination to Lnlll. In these new self-assembled lanthanide podates, predetermined structural and physical properties result form i) the judicious choice of the d-block ion associated with Lnlll and ii) the design of the tridentate unit bound to Lnlll. [LnFe(L11)3]5+ (Ln=La-Eu) display thermochromism and spin-crossover behavior while light emission can be increased by a factor 104 when going from [EuZn(L11)3]5+ to [EuZn(L12)3]5+. The design of tailored receptors for the preparation of stable lanthanide light-converting devices is discussed together with new characterization methods applied to complicated assembly processes in solution.
Non‐vital, prosthetic, and virtual reality models of microsurgical training (2001)

Many microsurgical training models exist. These can be broadly classified into living and non-living. The latter type can be further sub-classified into non-vital, prosthetic, and virtual reality models. We review each model within these sub-groups with reference to the ideal properties of a training model. The most important attribute of any model is that the skills acquired from it must translate efficiently into microsurgical skill in the clinical situation. We believe that non-vital and prosthetic models are an important complement to living ones in training and maintaining the skills of all microsurgeons. As virtual reality technology improves, virtual models may succeed the rat as the microsurgical training tool of choice.