gebhart/patrepeval huggingface dataset:
Deletion of the Helical Motif in the Intestinal Fatty Acid-Binding Protein Reduces Its Interactions with Membrane Monolayers:  Brewster Angle Microscopy, IR Reflection-Absorption Spectroscopy, and Surface Pressure Studies (2001)

Intestinal fatty acid binding protein (IFABP) appears to interact directly with membranes during fatty acid transfer [Hsu, K. T., and Storch, J. (1996) J. Biol. Chem. 271, 13317-13323]. The largely alpha-helical "portal" domain of IFABP was critical for these protein--membrane interactions. In the present studies, the binding of IFABP and a helixless variant of IFABP (IFABP-HL) to acidic monolayers of 1,2-dimyristoylphosphatidic acid (DMPA) has been monitored by surface pressure measurements, Brewster angle microscopy (BAM), and infrared reflection-absorption spectroscopy (IRRAS). Protein adsorption to DMPA exhibited a two phase kinetic process consisting of an initial slow phase, arising from protein binding to the monolayer and/or direct interfacial adsorption, and a more rapid phase that parallels formation of lipid-containing domains. IFABP exhibited more rapid changes in both phases than IFABP-HL. The second phase was absent when IFABP interacted with zwitterionic monolayers of 1,2-dipalmitoylphosphatidylcholine, revealing the important role of electrostatics at this stage. BAM images of DMPA monolayers with either protein revealed the formation of domains leading eventually to rigid films. Domains of DMPA/IFABP-HL formed more slowly and were less rigid than with the wild-type protein. Overall, the IRRAS studies revealed a protein-induced conformational ordering of the lipid acyl chains with a substantially stronger ordering effect induced by IFABP. The physical measurements thus suggested differing degrees of direct interaction between the proteins and DMPA monolayers with the IFABP/DMPA interaction being somewhat stronger. These data provide a molecular structure rationale for previous kinetic measurements indicating that the helical domain is essential for a collision-based mechanism of fatty acid transfer to phospholipid membranes [Corsico, B., Cistola, D. P., Frieden, C. and Storch, J. (1998) Proc. Natl. Acad. Sci. U.S.A. 95, 12174-12178].
Introduction (2016)

Abstract This chapter introduces the concepts that are needed to demonstrate how evolutionary principles enable a more integrated understanding of human biology and medicine and thus provide new insights into human health and disease. Evolution acts primarily by selection on heritable variation among a population of organisms. Selection maximizes fitness (lifetime reproductive success), not necessarily health or longevity. Selection is not the only evolutionary process. Health and disease are influenced by an individual’s evolutionary and developmental background in the context of their current environment. Consideration of ultimate causation provides additional insights to understandings of the proximate mechanisms of health and disease. Concepts of health and disease are altered by taking an evolutionary perspective.
Photocatalytically Generated Pt∕C–TiO[sub 2] Electrocatalysts with Enhanced Catalyst Dispersion for Improved Membrane Durability in Polymer Electrolyte Fuel Cells (2008)

Platinum/carbon/titanium oxide electrocatalysts were prepared by a heterogeneous photocatalysis method wherein the semiconductor optoelectronic properties of were exploited to facilitate photoreduction of a platinum precursor on the surface of the composite whole yielding excellent platinum dispersion. The loading in the electrocatalyst was varied in the ranges: and the Pt content was varied from . The physical and electrochemical characteristics of these new-generation electrocatalysts were benchmarked against commercial samples. Membrane electrode assemblies were prepared using these composite electrocatalysts and tested with hydrogen as fuel and oxygen/air as oxidants. The fluoride emission rate (in units of ) was estimated by condensate water analyses and found to be reduced by approximately an order of magnitude upon addition of . Implicatiońs of these data for optimization of polymer electrolyte fuel cells in terms of durability and performance are presented.
Left ventricle segmentation using graph searching on intensity and gradient and a priori knowledge (lvGIGA) for short‐axis cardiac magnetic resonance imaging (2008)

The lvGIGA algorithm substantially improves the robustness of LV segmentation automation over the commercial MASS software, agrees well with clinical manual tracing, and may be a useful tool for clinical practice.
Ketamine Disrupts Theta Modulation of Gamma in a Computer Model of Hippocampus (2011)

Abnormalities in oscillations have been suggested to play a role in schizophrenia. We studied theta-modulated gamma oscillations in a computer model of hippocampal CA3 in vivo with and without simulated application of ketamine, an NMDA receptor antagonist and psychotomimetic. Networks of 1200 multicompartment neurons [pyramidal, basket, and oriens-lacunosum moleculare (OLM) cells] generated theta and gamma oscillations from intrinsic network dynamics: basket cells primarily generated gamma and amplified theta, while OLM cells strongly contributed to theta. Extrinsic medial septal inputs paced theta and amplified both theta and gamma oscillations. Exploration of NMDA receptor reduction across all location combinations demonstrated that the experimentally observed ketamine effect occurred only with isolated reduction of NMDA receptors on OLMs. In the ketamine simulations, lower OLM activity reduced theta power and disinhibited pyramidal cells, resulting in increased basket cell activation and gamma power. Our simulations predict the following: (1) ketamine increases firing rates; (2) oscillations can be generated by intrinsic hippocampal circuits; (3) medial-septum inputs pace and augment oscillations; (4) pyramidal cells lead basket cells at the gamma peak but lag at trough; (5) basket cells amplify theta rhythms; (6) ketamine alters oscillations due to primary blockade at OLM NMDA receptors; (7) ketamine alters phase relationships of cell firing; (8) ketamine reduces network responsivity to the environment; (9) ketamine effect could be reversed by providing a continuous inward current to OLM cells. We suggest that this last prediction has implications for a possible novel treatment for cognitive deficits of schizophrenia by targeting OLM cells.
The stress field near the tip of a plane stress crack in a gel consisting of chemical and physical cross-links (2019)

We study the time-dependent asymptotic stress fields near the tip of a mode I plane stress crack in a hydrogel. The analysis is based on a three-dimensional continuum model which describes the viscoelastic behaviour of a hydrogel gel with permanent and transient cross-links. The viscoelasticity results from the breaking and healing of the transient cross-links in the gel network. We show that the crack tip fields satisfy a local correspondence principle-that is, the spatial singularities of these fields are identical to a hyperelastic cracked body with the same but undamaged networks. Asymptotic results compare very well with finite-element simulations on a single-edge crack specimen loaded under constant stretch rate. We also compare the theoretical results (crack opening profile and crack tip strain field) with experiments and find excellent agreement.
Comparison of the Pharmacokinetics, Safety, and Tolerability of Two Empagliflozin Formulations in Healthy Korean Subjects (2023)

The two formulations of empagliflozin showed similar PK characteristics and were generally well tolerated in healthy subjects.
Highly Efficient Ethylene Tetramerization Using Cr Catalysts Constructed with Trifluoromethyl-Substituted <i>N</i>-Aryl PNP Ligands (2022)

Tetramerization of ethylene by chromium catalysts stabilized with functionalized <i>N</i>-aryl phosphineamine ligands C<sub>6</sub>H<sub>4</sub>(<i>m</i>-CF<sub>3</sub>)N(PPh<sub>2</sub>)<sub>2</sub> (<b>1</b>), C<sub>6</sub>H<sub>4</sub>(<i>p</i>-CF<sub>3</sub>)N(PPh<sub>2</sub>)<sub>2</sub> (<b>2</b>), C<sub>6</sub>H<sub>4</sub>(<i>o</i>-CF<sub>3</sub>)N=PPh<sub>2</sub>-PPh<sub>2</sub> (<b>3</b>), and C<sub>6</sub>H<sub>3</sub>(3,5-bis(CF<sub>3</sub>))N(PPh<sub>2</sub>)<sub>2</sub> (<b>4</b>) was evaluated. The parameter optimization includes temperature, co-catalyst, and solvent. Upon activation with MMAO-3A, the new catalyst system especially with <i>m</i>-functional PNP ligand (<b>1</b>) exhibited high 1-octene selectivity and productivity while giving minimum undesirable polyethylene and C<sub>10</sub> <sup>+</sup> olefin by-products. Using PhCl as a solvent at 75 °C led to a remarkable α-olefin (1-C<sub>6</sub> + 1-C<sub>8</sub>) selectivity (>90 wt %) at a reaction rate of 2000 kg·g<sub>Cr</sub> <sup>-1</sup>·h<sup>-1</sup>. Under identical conditions, analogous PNP ligands bearing -CH<sub>3</sub>, -Et, and -Cl functional moieties at the meta position of the <i>N</i>-phenyl ring displayed significantly lower reactivity. The catalyst with <i>p</i>-functional ligand (<b>2</b>) exhibited lower activity and comparable selectivities, while the Cr/PPN (with ligand <b>3</b>) system gave no noticeable reactivity. The molecular structure of the precatalyst (<b>1</b>-Cr), exhibiting a monomeric structural feature, was elucidated with the aid of single-crystal X-ray diffraction study.
Beet western yellows virus-associated RNA: an independently replicating RNA that stimulates virus accumulation. (1993)

Infections of plants by subviral RNA agents, alone or in association with virus genomic RNA molecules, are well known. The ST9 strain of beet western yellows virus encapsidates not only the 5.6-kilobase genomic RNA that is typical of luteoviruses, but also a 2.8-kilobase-associated RNA that has a distinct nucleotide sequence. The ST9-associated RNA has been postulated to be a satellite RNA, which by definition would be capable of replicating only in coinfections with beet western yellows virus or closely related viruses. To characterize the associated RNA, we inoculated protoplasts and leaves with in vitro transcripts of the virus genomic RNA and the ST9-associated RNA separately and in combination. Surprisingly, the ST9-associated RNA alone replicated efficiently in both protoplasts and leaves, and it stimulated accumulation of the virus genomic RNA in protoplasts. Thus, the ST9-associated RNA is a newly discovered type of plant infectious agent, which depends on its associated virus, beet western yellows virus, for encapsidation but not for replication.
Effects of Heat-Processed Ginseng and Its Active Component Ginsenoside 20(S)-Rg3 on the Progression of Renal Damage and Dysfunction in Type 2 Diabetic Otsuka Long-Evans Tokushima Fatty Rats (2010)

The effects of heat-processed ginseng (HPG) and ginsenoside 20(S)-Rg(3) on the progression of renal damage in type 2 diabetic rats were investigated. Twenty-two-week-old male Otsuka Long-Evans Tokushima Fatty (OLETF) rats were divided into 4 orally administered groups: vehicle (diabetic control), HPG water extract (100 mg/kg) and 20(S)-Rg(3) (5, 10 mg/kg). Non-diabetic Long-Evans Tokushima Otsuka (LETO) rats were used as a normal group. OLETF rats showed markedly higher blood glucose, triglyceride, and total cholesterol levels than those of LETO rats. The elevated blood glucose level of OLETF rats was significantly lowered by 20(S)-Rg(3) administration. The elevated serum triglyceride and total cholesterol levels were significantly reduced by the administrations of HPG and 20(S)-Rg(3). The serum levels of thiobarbituric acid-reactive substance, an index of lipid peroxidation, were markedly increased in OLETF compared to LETO rats, but it was significantly reduced by HPG and 20(S)-Rg(3) administrations. The urinary protein level, an indicator of advanced diabetic nephropathy, of OLETF rats was 4.4 times higher than in LETO rats, but it was reduced significantly by the administrations of HPG and 20(S)-Rg(3). Creatinine clearance of OLETF rats was significantly increased after HPG and 20(S)-Rg(3) administrations. The elevation of inducible nitric oxide synthase and N(epsilon)-(carboxymethyl)lysine protein expressions in renal tissues of OLETF rats was prevented by 20(S)-Rg(3) administration. This study provides scientific evidence that 20(S)-Rg(3) prevents the progression of renal damage and dysfunction in type 2 diabetic rats via inhibiting oxidative stress and advanced glycation endproduct formation.
Spray Dryer Parameters for Fruit Juice Drying (2007)

2 Abstract: Spray drying is one of the most complex methods for fruit juice drying. Fruit juice is very sensitive and affected the different drying parameters. These parameters should be tested and determined before the design of the dryers. With laboratory spray dryer the basic parameters for drying of orange juice with 65% concentration was studied. The investigated parameters include: drying agent material, feed flow rate inlet and outlet air temperature and sticky point temperature. Tests were performed without and with agent materials and studied the different operating condition of spray drying and the sticky point temperature for orange juice powder. The results of statistical analysis of experimental data show that the parameters of inlet air temperature and feed flow rate have significant effect on the dryer yield and wall deposit of spray dryer individually and jointly. Also with the addition of liquid glucose, the optimum conditions have been obtained with feed flow rate of 15 ml min , inlet air temperature of 130°C and outlet air temperature of 85°C. For the orange powder 1 containing 2% moisture, the sticky point temperature was 44°C.
Efficient image segmentation of walking hazards using IR illumination in wearable low vision (2003)

Pulsed IR illumination is used to segment near obstacles and hazards from the background from incoming video to a wearable low vision aid that displays icons.
The VpreB1 enhancer drives developmental stage‐specific gene expression <i>in vivo</i> (2003)

In adult mice, the VpreB genes are expressed in bone marrow progenitor (pro-) and precursor (pre-) B cells. As part of the pre-B cell receptor, the proteins are crucial for the proliferation of these cells and consequently normal B lymphocyte development. Using cell lines, we identified a lineage- and developmental-stage-specific VpreB1 enhancer. Here, we analyze its specificity in vivo by generating transgenic mice in which expression of a reporter gene (human CD122) is regulated by the VpreB1 enhancer in the context of its own promoter. All transgenic lines expressed the reporter gene in the bone marrow in a copy number-independent manner, whereas expression levels were integration site-dependent. While the enhancer is not tissue specific, within the B cell lineage the expression pattern of human CD122 mimicked that of endogenous VpreB1. Thus, low levels were detected in pro-B cells, high levels in pre-BI and slightly lower levels in pre-BII cells; no expression was detected in immature/mature B cells. Furthermore, when in vitro cultured transgenic pre-B cells differentiated into immature B cells there was concomitant down-regulation of human CD122 and endogenous VpreB1. Thus the VpreB1 enhancer is sufficient to ensure developmental stage-specific expression of a reporter gene in B lymphocytes in vivo.
New soft stack decoder for MIMO channel (2008)

In this paper, we investigate the use of soft output decoders for signals transmitted on linear channels when applied to multiple input multiple output (MIMO) systems. A new soft output MIMO decoder is proposed. It's an extension of the hard stack decoder. A straightforward idea was to exploit internal nodes still stored in the stack at the end of hard decoding process to calculate LLR. We show that the potential gain of such method is rather large then classical soft decoders.
Immune complexes (IC) down-regulate the basal and interferon-<i>γ</i>-induced expression of MHC Class II on human monocytes (2001)

The interaction of Fc receptors for IgG (FcgammaRs) on monocytes/macrophages with immune complexes (IC) triggers regulatory and effector functions. Previous studies have shown that FcgammaR-IC interactions inhibit the IFN-gamma-induced expression of MHC class II in murine macrophages. However, the mechanism(s) responsible for these effects have not been elucidated. In addition, whether this IC-dependent effect also occurs in human cells is not known. Taking into account the fact that IC and IFN-gamma are frequently found in infections and autoimmune disorders, together with the crucial role MHC class II molecules play in the regulation of immune response, we explored the effect and mechanism of IC-induced MHC class II down-regulation in human peripheral blood mononuclear cells (PBMC). This effect was studied either in the presence or absence of IFN-gamma. We demonstrate that IC exert a drastic inhibition of basal and IFN-gamma-induced expression of MHC class II on human monocytes. This effect was mediated through the interaction of IC with both FcgammaRI and FcgammaRII. Moreover, similar results were obtained using supernatants from IC-treated PBMC. The IC-induced down-regulation of MHC class II is abrogated by pepstatin and phosphoramidon, supporting the role of aspartic protease(s) and metalloprotease(s) in this process. In parallel with MHC class II expression, antigen presentation was markedly inhibited in the presence of IC.
Reduction of Aliphatic and Aromatic Nitro Compounds with Sodium Borohydride in THF using 10% Pd/C as Catalyst: a New and Efficient Method." (1987)

Aliphatic and aromatic nitro compounds are reduced to amino compounds in good yields with sodium borohydride in tetrahydrofuran using 10% palladium-on-carbon as catalyst.
Effect of Coherency Strains on Phase Separation in the AlN‐Al <sub>2</sub> OC Pseudobinary System (1993)

AlN and Al 2 OC, both of 2H structure, form a homogeneous solid solution at elevated temperatures. Annealing at lower temperatures leads to the formation of two solid solutions, one AlN‐rich and the other Al 2 OC‐rich. Samples of near equimolar composition form disk‐shaped precipitates upon annealing at temperatures below ∼1900°C. In the present work, samples of several compositions were fabricated by hot‐pressing mixtures of AlN, Al 4 C 3 and Al 2 O 3 . Lattice parameters of the resulting solid solutions were measured by X‐ray diffraction. Samples of an equimolar composition were annealed at 1500°C for various periods of time up to a maximum of 512 h. Disk‐shaped precipitates with their axes along the [0001] direction were initially coherent. In the coherent stage, the a lattice parameters of the precipitate and the matrix were identical because of coherent fitting of lattice planes. The shape of the precipitates and their orientation were in accord with predictions based on theoretical calculations of coherency strain energy. Using the experimentally measured values of the aspect ratios, the precipitate/matrix interfacial energy for coherent precipitates was estimated to be on the order of a few mJ/m 2 . Long‐term annealing led to the loss of coherency as manifested by the formation of interface dislocations.
Development of Real-Time PCR Assays for Detection of the <i>Streptococcus milleri</i> Group from Cystic Fibrosis Clinical Specimens by Targeting the <i>cpn60</i> and 16S rRNA Genes (2010)

Cystic fibrosis (CF) is a multiorgan disease, with the majority of mortalities resulting from pulmonary failure due to repeated pulmonary exacerbations. Recently, members of the Streptococcus anginosus group (S. anginosus, S. constellatus, and S. intermedius), herein referred to as the "Streptococcus milleri group" (SMG) have been implicated as important etiological pathogens contributing to pulmonary exacerbations in CF patients. This is partly due to better microbiological detection of the SMG species through the development of a novel specific medium termed "McKay agar." McKay agar demonstrated that SMG has been an underreported respiratory pathogen contributing to lung exacerbations. Our aim was to develop a real-time PCR assay to expedite the detection of SMG within diagnostic samples. The cpn60 gene was chosen as a target, with all three members amplified using a single hybridization probe set. SMG strain analysis showed that speciation based on melting curve analysis allowed for the majority of the S. constellatus (96%), S. intermedius (94%), and S. anginosus (60%) strains to be correctly identified. To increase specificity for S. anginosus, two 16S rRNA real-time PCR assays were developed targeting the 16S rRNA gene. The 16s_SA assay is specific for S. anginosus (100%), while the 16s_SCI assay is specific for S. constellatus and S. intermedius (100%). These assays can detect <10 genome equivalents in pure culture and >10(4) genome equivalents in sputum samples, making this a great tool for assessment of the presence of SMG in complex polymicrobial samples. Novel molecular methods were developed providing detection ability for SMG, an emerging opportunistic pathogen.
Compact Models and the Physics of Nanoscale FETs (2013)

The device physics of nanoscale MOSFETs is related to traditional compact models. Beginning with the virtual source model, a model for nanoscale MOSFETs expressed in traditional form, we show how the Landauer approach gives a clear physical interpretation to the parameters in the model. The analysis shows that transport in the channel is limited by diffusion near the virtual source both below and above threshold, that the current saturation is determined by velocity saturation near the source, not by the maximum velocity in the channel, and that the channel resistance approaches a finite value as the channel length approaches zero. These results help explain why traditional models continue to work well at the nanoscale, even though carrier transport is distinctly different from that at the microscale, and they identify the essential physics that physics-based compact models for nanoscale MOSFETs should comprehend.
Degrees-of-freedom of a robotic exoskeleton and human adaptation to new gait templates (2012)

This paper addresses an important question in the field of rehabilitation robotics that can help engineers to develop and optimize future gait training robotic exoskeletons. This question can be posed as follows: Do the exoskeleton's degrees-of-freedom at the pelvis affect human adaptation to new gait templates? More specifically, would additional degrees-of-freedom in the exoskeleton that allow the human trunk to translate and rotate, and the hips to abduct/adduct increase human gait adaptation with an exoskeleton?
Physical implementation of immersive boundary conditions in one dimension (2017)

Immersive boundary conditions (IBCs) are a novel approach to target-oriented numerical wavefield modeling. When implemented physically, IBCs allow the construction of anechoic chambers that actively suppress the reflection of wavefields from the boundaries of a physical domain, such as a wave propagation laboratory. Moreover, IBCs can be used for immersive wave propagation experimentation by linking the wave propagation in the physical domain with the propagation in a virtual domain enclosing the physical domain. In this case, the IBCs correctly account for all wavefield interactions between the two domains. The physical implementation of IBCs is achieved by densely populating the boundary surrounding the physical domain with transducers that enforce the necessary boundary conditions. To estimate the signals that need to be emitted at the injection boundary, a second surface of transducers slightly inside the physical domain records the propagating wavefield. The recorded wavefield is extrapolated to the injection boundary by evaluating a Kirchhoff-Helmholtz integral in real-time using an FPGA-enabled data acquisition and control system. A recently constructed one-dimensional acoustic wave propagation laboratory provides an ideal setup for the physical installation of IBCs in one dimension. In this work, we demonstrate the implementation of IBCs on one side of this laboratory.