gebhart/patrepeval huggingface dataset:
Solution Structure of Oxidized Horse Heart Cytochrome c, (1997)

The solution structure of oxidized horse heart cytochrome c was obtained at pH 7.0 in 100 mM phosphate buffer from 2278 NOEs and 241 pseudocontact shift constraints. The final structure was refined through restrained energy minimization. A 35-member family, with RMSD values with respect to the average structure of 0.70 +/- 0.11 A and 1.21 +/- 0.14 A for the backbone and all heavy atoms, respectively, and with an average penalty function of 130 +/- 4.0 kJ/mol and 84 +/- 3.7 kJ/mol for NOE and pseudocontact shift constraints, respectively (corresponding to a target function of 0.9 A2 and 0.2 A2), was obtained. The solution structure is somewhat different from that recently reported (Qi et al., 1996) and appears to be similar to the X-ray structure of the same oxidation state (Bushnell et al., 1990). A noticeable difference is a rotation of 17 +/- 8 degrees of the imidazole plane between solid and solution structure. Detailed and accurate structural determinations are important within the frame of the current debate of the structural rearrangements occurring upon oxidation or reduction. From the obtained magnetic susceptibility tensor a separation of the hyperfine shifts into their contact and pseudocontact contributions is derived and compared to that of the analogous isoenzyme from S. cerevisiae and to previous results.
Tissue engineering of regenerative cardiovascular patch material based on decellularized pericardium (2014)

Objectives: Autologous pericardium is often used to substitute small or medium sized vascular or myocardial lesions. However, its use is restricted due to its limited availability. Hence, glutaraldehyde-fixed bovine pericardium is currently being employed more extensively despite potential impact of the xenogenic tissue on the host, possible toxicity of residual fixing solution within the graft, and absence of any regenerative and growing potential. We therefore developed a new biological and viable matrix, based on decellularized and reseeded pericardium.
Control of colonic motility using electrical stimulation to modulate enteric neural activity (2021)

Electrical stimulation of the enteric nervous system (ENS) is an attractive approach to modify gastrointestinal transit. Colonic motor complexes (CMCs) occur with a periodic rhythm, but the ability to elicit a premature CMC depends, at least in part, upon the intrinsic refractory properties of the ENS, which are presently unknown. The objectives of this study were to record myoelectric complexes (MCs, the electrical correlates of CMCs) in the smooth muscle and <i>1</i>) determine the refractory periods of MCs, <i>2</i>) inform and evaluate closed-loop stimulation to repetitively evoke MCs, and <i>3</i>) identify stimulation methods to suppress MC propagation. We dissected the colon from male and female C57BL/6 mice, preserving the integrity of intrinsic circuitry while removing the extrinsic nerves, and measured properties of spontaneous and evoked MCs in vitro. Hexamethonium abolished spontaneous and evoked MCs, confirming the necessary involvement of the ENS for electrically evoked MCs. Electrical stimulation reduced the mean interval between evoked and spontaneous CMCs (24.6 ± 3.5 vs. 70.6 ± 15.7 s, <i>P</i> = 0.0002, <i>n</i> = 7). The absolute refractory period was 4.3 s (95% confidence interval (CI) = 2.8-5.7 s, <i>R<sup>2</sup></i> = 0.7315, <i>n</i> = 8). Electrical stimulation applied during fluid distention-evoked MCs led to an arrest of MC propagation, and following stimulation, MC propagation resumed at an increased velocity (<i>n</i> = 9). The timing parameters of electrical stimulation increased the rate of evoked MCs and the duration of entrainment of MCs, and the refractory period provides insight into timing considerations for designing neuromodulation strategies to treat colonic dysmotility.<b>NEW & NOTEWORTHY</b> Maintained physiological distension of the isolated mouse colon induces rhythmic cyclic myoelectric complexes (MCs). MCs evoked repeatedly by closed-loop electrical stimulation entrain MCs more frequently than spontaneously occurring MCs. Electrical stimulation delivered at the onset of a contraction temporarily suppresses the propagation of MC contractions. Controlled electrical stimulation can either evoke MCs or temporarily delay MCs in the isolated mouse colon, depending on timing relative to ongoing activity.
Hematology patient reported symptom screen to assess quality of life for AL amyloidosis (2017)

Patients with light chain amyloidosis (AL) often have delayed diagnosis and present with significant symptomatology; this may result in decreased quality of life (QOL). We prospectively employ a "Hematology Patient Reported Symptom Screen" (HPRSS), which is three questions about fatigue, pain, and QOL, scored 0-10. The aim of this study is to better understand QOL and determine if HPRSS parameters predict for clinical outcomes. From 2009 to 2014, 302 newly diagnosed AL patients were included. Baseline median scores [interquartile range] for fatigue, pain, and QOL were 6 [3,7], 2 [0,5], 5 [3,8], respectively. Median overall survival was 53 months, with 102 (34%) deaths in the first year. There were significant differences in baseline HPRSS between those that lived longer than one year and early death patients in the domains of fatigue (5 [IQR 3, 7] vs. 7 [IQR 5, 8], P < 0.0001) and QOL (6 [IQR 4, 8] vs. 5 [IQR 3, 7], P = 0.006). On univariate analysis fatigue, QOL, physician-reported performance status, autologous stem cell transplant (ASCT), and Mayo stage were prognostic for survival. On multivariate analysis Mayo stage, ASCT, and baseline fatigue remained independently prognostic. When analyses were restricted to the 125 patients with HPRSS measurements at 12 months, we found that over time QOL scores improved significantly 6 [IQR 3.5, 8] → 7 [IQR 5, 8] (P = 0.01). Asking AL patients to rate their fatigue and QOL has predictive value. Baseline patient reported fatigue is an independent prognostic factor for survival. Survival at one year was associated with significant improvement in QOL.
The Imperative of Psychiatric Neurosurgery (2000)

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Fate of Distal Lung Epithelium Cultured in a Decellularized Lung Extracellular Matrix (2020)

Type II cells are the defenders of the alveolus. They produce surfactant to prevent alveolar collapse, they actively transport water to prevent filling of the air sacs that would otherwise prevent gas exchange, and they differentiate to type I epithelial cells. They are an indispensable component of functional lung tissue. To understand the functionality of type II cells in isolation, we sought to track their fate in decellularized matrices and to assess their ability to contribute to barrier function by differentiation to type I alveolar epithelial cells. Rat type II cells were isolated from neonatal rat lungs by labeling with the RTII-70 surface marker and separation using a magnetic column. This produced a population of ∼50% RTII-70-positive cells accompanied by few type I epithelial cells or α-actin-positive mesenchymal cells. This population was seeded into decellularized rat lung matrices and cultured for 1 or 7 days. Culture in Dulbecco's modified Eagle's medium +10% fetal bovine serum (FBS) resulted in reduced expression of epithelial markers and increased expression of mesenchymal markers. By 7 days, no epithelial markers were visible by immunostaining; nearly all cells were α-actin positive. Gene expression for the mesenchymal markers, α-actin, vimentin, and TGF-βR, was significantly upregulated on day 1 (p=0.0005, 0.0005, and 2.342E-5, respectively). Transcript levels of α-actin and TGF-βR remained high at 7 days (p=1.364E-10 and 0.0002). Interestingly, human type II cells cultured under the same conditions showed a similar trend in the loss of epithelial markers, but did not display high expression of mesenchymal markers. Rat cells additionally showed the ability to produce and degrade the basement membrane and extracellular matrix components, such as fibronectin, collagen IV, and collagen I. Quantitative real-time reverse transcription polymerase chain reaction (RT-PCR) showed significant increases in expression of the fibronectin and matrix metalloprotease-2 (MMP-2) genes after 1 day in culture (p=0.0135 and 0.0128, respectively) and elevated collagen I expression at 7 days (p=0.0016). These data suggest that the original type II-enriched population underwent a transition to increased expression of mesenchymal markers, perhaps as part of a survival or wound-healing program. These results suggest that additional medium components and/or the application of physiologically appropriate stimuli such as ventilation may be required to promote lung-specific epithelial phenotypes.
NMR Mapping of the IFNAR1-EC Binding Site on IFNα2 Reveals Allosteric Changes in the IFNAR2-EC Binding Site (2010)

All type I interferons (IFNs) bind to a common cell-surface receptor consisting of two subunits. IFNs initiate intracellular signal transduction cascades by simultaneous interaction with the extracellular domains of its receptor subunits, IFNAR1 and IFNAR2. In this study, we mapped the surface of IFNalpha2 interacting with the extracellular domain of IFNAR1 (IFNAR1-EC) by following changes in or the disappearance of the (1)H-(15)N TROSY-HSQC cross peaks of IFNalpha2 caused by the binding of the extracellular domain of IFNAR1 (IFNAR1-EC) to the binary complex of IFNalpha2 with IFNAR2-EC. The NMR study of the 89 kDa complex was conducted at pH 8 and 308 K using an 800 MHz spectrometer. IFNAR1 binding affected a total of 47 of 165 IFNalpha2 residues contained in two large patches on the face of the protein opposing the binding site for IFNAR2 and in a third patch located on the face containing the IFNAR2 binding site. The first two patches form the IFNAR1 binding site, and one of these matches the IFNAR1 binding site previously identified by site-directed mutagenesis. The third patch partially matches the IFNalpha2 binding site for IFNAR2-EC, indicating allosteric communication between the binding sites for the two receptor subunits.
Congestion Control in ISDN Frame-Relay Networks (1988)

Like X.25 packet networks, ISDN frame-relay networks require effective congestion control mechanisms to cope with unanticipated network component failures and overloads. Unlike X.25 packet networks, ISDN frame-relay networks perform the requisite packet-switching function without terminating the link and network layer data-transfer protocols. They therefore cannot use delayed acknowledgment and/or receiver-not-ready indications embedded in these protocols for congestion control. This paper reviews the measures that can be used to control congestion effectively in ISDN frame-relay networks.
An Assessment of the Role of Polymers for Drug Delivery in Tissue Engineering (2006)

The field of tissue engineering was born out of the need to reduce both the loss of life and debilitating effects resulting from the damage to, or malfunction of, human organs and tissues. It is a relatively new field that involves the repair and regeneration of biological tissue that can be guided through the application and control of cells, materials and growth factors. Several strategies have been developed in order to regenerate functional tissue, the majority of which involve the use of polymer scaffolds specifically designed to direct tissue growth. The cell transplantation method is one of the most commonly used in cartilage and bone formation. Collagen is a naturally occurring structural protein that binds to and surrounds the cells to form the extracellular matrix of cartilage (ECM). The role of the ECM is to provide the necessary physical and biological support to the cells during tissue formation.
Recent development in stereochemical control of heterogeneous Ziegler‐Natta catalysts (1992)

Abstract A completely aspecific catalyst was prepared by supporting TiCl 3 on MgCl 2 . The catalyst isospecificity could be drastically converted from aspecific into isospecific either by adding ethyl benzoate or by changing the cocatalyst from Al(C 2 H 5 ) 3 to Cp 2 Ti(CH 3 ) 2 . On the other hand, the catalyst system composed of SiO 2 ‐supported CpTiCl 3 and methylaluminoxane (MAO) gave atactic polypropylene as well as a random copolymer of ethylene and propylene with frequent chemical inversion of propylene units. It was also found that the CpTiCl 3 /SiO 2 ‐MAO catalyst system can afford poly(ethylene‐co‐1‐hexadecene) containing a large amount of 1‐hexadecene. The mechanisms of stereochemical control(isospecificity and regiospecificity) are discussed from these results.
Milk casein-based diet containing TGF-beta controls the inflammatory reaction in the HLA-B27 transgenic rat model (2005)

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Special Section Guest Editorial: Nanoengineering: Fabrication, Properties, Optics, and Devices (2011)

Nanoengineering is the controlled placement or removal of material on the atomic, molecular, or small granular scale. The term has typically encompassed the engineering of materials at dimensions of 100 nm or less. The beginning of nanoscience, or nanoengineering, is not really clear. Metallurgists and glass formers have been making specially engineered sintered and nanocrystalline materials for many decades. Chemists have also synthesized molecular clusters and enzymes for many years. Watson and Crick proposed molecular templating in "Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid" (Nature, 1953). However the emergence of the fields of nanoscience and nanoengineering is widely attributed to the famous speech by Richard Feymann, "There is plenty of room at the bottom," given at the American Physical Society Meeting, December 29, 1959.
Optimized phase coding to enhance discrimination in digital word recognition (1999)

Optical pattern recognition is widely considered a key operation in any hypothesis of optical computer or communication network fabric, in which it is necessary to identify at very high speed streams of digital data. Several correlators [1,2] have been investigated and can be considered good mainly in recognition of very different 2-D images [3,4,5].
HIV Rev-dependent binding of SF2/ASF to the Rev response element: Possible role in Rev-mediated inhibition of HIV RNA splicing (1997)

Production of the structural and enzymatic proteins of type 1 human immunodeficiency virus (HIV-1) is controlled by the rev regulatory gene product. The 116-amino acid Rev protein acts by binding to the Rev response element (RRE), a complex RNA stem-loop structure located within the env gene of HIV. Rev exerts a series of posttranscriptional effects, including the inhibition of viral RNA splicing, the activation of nuclear export of incompletely spliced viral RNAs, and the enhancement of translation of RRE-containing RNAs. Our studies now demonstrate that at least one member of the SR family of splicing factors, SF2/ASF, specifically binds to a subregion of the RRE in vitro in a Rev-dependent manner. Furthermore, expression of high levels of SF2/ASF inhibits Rev function and impairs HIV replication in vivo. Both the in vitro binding of SF2/ASF to the Rev/RRE complex and the in vivo inhibition of Rev action by SF2/ASF are abrogated by mutation of the N-terminal RNA recognition motif but are not affected by mutation of the C-terminal arginine-serine-rich domain. These findings suggest that Rev inhibition of HIV splicing likely involves recruitment of the essential splicing factor SF2/ASF to the Rev/RRE complex. However, these inhibitory effects of Rev on viral RNA splicing are apparently overcome by augmenting the intracellular levels of SF2/ASF expression.
Computational predictions of corroles as a class of Hsp90 inhibitors (2015)

Corroles have been shown experimentally to cause cell cycle arrest, and there is some evidence that this might be attributed to an inhibitory effect of corroles on Heat shock protein 90 (Hsp90), which is known to play a vital role in cancer cell proliferation. In this study, we used molecular dynamics to examine the interaction of gallium corroles with Hsp90, and found that they can bind preferentially to the ATP-binding N-terminal site. We also found that structural variations of the corrole ring can influence the binding energies and affinities of the corrole to Hsp90. We predict that both the bis-carboxylated corrole (4-Ga) and a proposed 3,17-bis-sulfonated corrole (7-Ga) are promising alternatives to Ga(III) 5,10,15-tris(pentafluorophenyl)-2,17-bis(sulfonic acid)-corrole (1-Ga) as anti-cancer agents.
C60 fullerene decoration of carbon nanotubes (2016)

A new fully carbon nanocomposite material is synthesized by the immersion of carbon nanotubes in a fullerene solution in carbon disulfide. The presence of a dense layer of fullerene molecules on the outer nanotube surface is demonstrated by TEM and XPS. Fullerenes are redistributed on the nanotube surface during a long-term action of an electron beam, which points to the existence of a molecular bond between a nanotube and fullerenes. Theoretical calculations show that the formation of a fullerene shell begins with the attachment of one C60 molecule to a defect on the nanotube surface.
Soft fluctuating surfactant membranes in supercritical CO2-microemulsions (2010)

The bending rigidity of surfactant membranes in novel bicontinuous CO(2)-microemulsions of the type H(2)O/NaCl-scCO(2)-Zonyl FSH/Zonyl FSN 100 was determined using both high pressure small angle neutron scattering and neutron-spin echo spectroscopy. As an important result it was found, that the stiffness of the membrane increases solely by an increase of the pressure.
A dynamic frequency selective surface using addressable metamaterials (2009)

In this paper, we have presented the design and experiment of a frequency selective metamaterial surface that controls the scattering of incident electromagnetic radiation. The surface consists of digitally addressable CELC metamaterials tuned to realize a spatial gradient in the reflection coefficient phase angle, resulting in a scattered field distribution that matched very closely with theoretical predictions. We showed measurements of the scattered electric field for two different potentiometer configurations, and showed peak deflection 10deg and 25deg away from the specular direction.
The Phormidolide Biosynthetic Gene Cluster: A trans‐AT PKS Pathway Encoding a Toxic Macrocyclic Polyketide (2015)

Phormidolide is a polyketide produced by a cultured filamentous marine cyanobacterium and incorporates a 16-membered macrolactone. Its complex structure is recognizably derived from a polyketide synthase pathway, but possesses unique and intriguing structural features that prompted interest in investigating its biosynthetic origin. Stable isotope incorporation experiments confirmed the polyketide nature of this compound. We further characterized the phormidolide gene cluster (phm) through genome sequencing followed by bioinformatic analysis. Two discrete trans-type acyltransferase (trans-AT) ORFs along with KS-AT adaptor regions (ATd) within the polyketide synthase (PKS) megasynthases, suggest that the phormidolide gene cluster is a trans-AT PKS. Insights gained from analysis of the mode of acetate incorporation and ensuing keto reduction prompted our reevaluation of the stereochemistry of phormidolide hydroxy groups located along the linear polyketide chain.
Translation of Bacteriophage Qβ Messenger RNA in a Murine Krebs 2 Ascites Tumor Cell-Free System (1972)

Qbeta is a small bacterial virus whose three genes are encoded in a single-stranded molecule of RNA. This RNA serves directly as the Qbeta message. Here we describe conditions under which RNA corresponding to the coat cistron of this bacterial virus is translated in a system derived from mammalian cells. Translation of the bacterial virus messenger RNA is less effective than that of mammalian globin messenger RNA, but is somewhat enhanced by mild alkali treatment of the messenger. The synthesized product when subjected to electrophoresis migrates with authentic Qbeta coat protein and yields tryptic peptides that correspond to those derived from the Qbeta coat protein.
Deep Policy Gradient for Reactive Power Control in Distribution Systems (2020)

Pronounced variability due to the growth of renewable energy sources, flexible loads, and distributed generation is challenging residential distribution systems. This context, motivates well fast, efficient, and robust reactive power control. Optimal reactive power control is possible in theory by solving a non-convex optimization problem based on the exact model of distribution flow. However, lack of high-precision instrumentation and reliable communications, as well as the heavy computational burden of non-convex optimization solvers render computing and implementing the optimal control challenging in practice. Taking a statistical learning viewpoint, the input-output relationship between each grid state and the corresponding optimal reactive power control (a.k.a., policy) is parameterized in the present work by a deep neural network, whose unknown weights are updated by minimizing the accumulated power loss over a number of historical and simulated training pairs, using the policy gradient method. In the inference phase, one just feeds the real-time state vector into the learned neural network to obtain the `optimal' reactive power control decision with only several matrix-vector multiplications. The merits of this novel deep policy gradient approach include its computational efficiency as well as robustness to random input perturbations. Numerical tests on a 47-bus distribution network using real solar and consumption data corroborate these practical merits.
An Experimental Assessment of Numerical Predictive Accuracy for Electronic Component Heat Transfer in Forced Convection—Part I: Experimental Methods and Numerical Modeling (2003)

Numerical predictive accuracy is assessed for component-printed circuit board (PCB) heat transfer in forced convection using a computational fluid dynamics (CFD) software for the thermal analysis of electronic equipment. This is achieved by comparing numerical predictions with experimental benchmark data for three different components, mounted individually on single-component PCBs, and collectively on a multi-component PCB. Benchmark criteria are based on measured steady-state component junction temperature and component-PCB surface temperature profiles. The benchmark strategy applied permits the impact of both aerodynamic conditions and component thermal interaction on predictive accuracy to be quantified. In the accompanying Part II of this paper, the experimental measurements are reported and numerical predictive accuracy is assessed.