gebhart/patrepeval huggingface dataset:
Beta-sheet Prediction Using Inter-strand Residue Pairs and Refinement with Hopfield Neural Network (1996)

Many secondary prediction methods have been studied, but the prediction accuracy is still unsatisfactory, since beta-sheet prediction is difficult. In this research, we gathered statistics of pairs of three residue sub-sequences in beta-sheets, calculated propensities for them. When a sequence is given, all possible three residue sub-sequences are examined whether they form beta-sheets. A short coming is that many false predictions are made. To exclude false predictions and improve the prediction, we employed a Hopfield neural network, in which the natural limitations on protein tertiary structure and preference of chemically stable long beta-sheet are expressed in a form of energy functions. To clarify the prediction for heads and tails of beta-sheets, special variables are introduced, which are similar to the line process proposed by Geman.
Intraoperative Management of Penile Erection with Intracorporeal Phenylephrine During Endoscopic Surgery (1987)

Intraoperative penile tumescence during endoscopic surgery is a troublesome complication that often is refractory to recommended methods of management. We report a new approach of pharmacological management with intracorporeal penile injections of phenylephrine (total dose of 0.1 mg.), which was successful in 3 successive patients. This approach is prompt, safe and reproducible, and it provides sustained resolution of erection without systemic side effects. It is concluded that local intracorporeal penile administration of this sympathomimetic agent appears to be a potent new tool in the armamentarium of the endoscopic surgeon dealing with this frustrating clinical situation, which merits further clinical trial.
Histamine induces microglia activation and dopaminergic neuronal toxicity via H1 receptor activation (2016)

Overall, our results highlight the relevance of histamine in the modulation of microglial activity that ultimately may interfere with neuronal survival in the context of Parkinson's disease (PD) and, eventually, other neurodegenerative diseases which are accompanied by microglia-induced neuroinflammation. Importantly, our results also open promising new perspectives for the therapeutic use of H1R antagonists to treat or ameliorate neurodegenerative processes.
Microbial Mannanases: Substrates, Production, and Applications (2000)

Mannans and xylans are the main components of woods beside cellulose and lignin and thus they belong to the most abundant polymers in the biosphere. Biodegradation of β-mannans occurs by the synergistic action of endo-1,4-β-mannanases, β-D-mannosidases, β-D-glucosidases, α-D-galactosidases and acetyl mannan esterases. Mannan degrading enzymes are widespread in nature and play an important role in the hydrolysis of hemicellulose containing biomass. They are produced by various microorganisms, including bacteria, yeasts and fungi, and also occur in germinating seeds of terrestrial plants, marine algae and animals. Mannanase activities secreted by microorganisms into the extracellular environment vary between 0.02 IU ml-1 and 800 IU ml-1. Mannanases cleave polymeric mannans as well as mannooligosaccharides, usually with a degree of polymerization greater than three to yield mannobiose, mannotriose and various mixed oligosaccharides. The activities of the individual enzymes can vary depending on the structure and substitution pattern of the heteromannans and many mannanases show transglycosylation activity. Mannan degrading enzymes have found applications including the food, feed, pharmaceutical, and pulp/paper industry as well as for oil and gas well stimulation.
The Effect of Epinephrine on the in Vivo Concentration of Erythrocyte Glycolytic Intermediates (1976)

Erythrocyte adenosine triphos-phate (ATP) concentration was found to increase in adult rhesus monkeys which have been injected with 3.5 mg of epinephrine. The average increase in red cell ATP concentration was 19.5% (significant at the 1% probability level). Epinephrine injection also increased the concentration of the early red cell glycolytic intermediates, glucose 6-phosphate (G6P), fructose 6-phos-phate (F6P), and dihydroxyacetone phosphate (DHAP). Respiratory alkalosis, which might have been induced by the epinephrine, is not responsible for the glycolytic changes. This effect of epinephrine on rhesus red cell glycolysis is compatible with an in vivo stimulation of red cell hexokinase by epinephrine or some substance elicited by epinephrine and suggests the possibility that such a stimulation may have a physiologic role in the mammalian erythrocyte.
Light‐Addressable Capsules as Caged Compound Matrix for Controlled Triggering of Cytosolic Reactions (2012)

Release me: polyelectrolyte capsules with different cargo in their cavities and plasmonic and magnetic nanoparticles in their walls were synthesized. Enzymatic reactions were triggered inside cells by light-mediated opening of two individual capsules containing either an enzyme or its substrate, by using photothermal heating. Furthermore, this technique allows controlled release of mRNA from capsules, thereby resulting in synthesis of green fluorescent protein (GFP).
Computationally efficient solution of a compressor load sharing problem using the alternating direction method of multipliers (2015)

This article presents an efficient implementation of a compressor load sharing optimization problem. In a typical gas pipeline application several compressor units are interconnected and operated together to meet station set point requirements. Load sharing optimization solves the problem of distributing the load among several compressors while at the same time satisfying operational constraints, user constraints and minimizing the consumption of the station. The structure of the problem is special and can therefore be exploited by formulating and solving the problem using the alternating direction method of multipliers (ADMM). The potential of this approach is assessed through simulations using field data from a large compression station with variable-speed gas turbine driven gas compressors. Despite being based on code generation, the ADMM implementation is about ten times faster than a state-of-the-art active set method while at the same time having a much lower memory footprint.
A Novel Nonlinear Analytical Microwave Oscillator Design Approach Using Signal Space (1997)

The Signal Space approach [1],[2], which is an extension of Steer's [3] "Generalized Power Series" method, enables for a given nonlinearity, a direct calculation of the current spectrum given the voltage spectrum. This approach is suited to the implementation for harmonic balance which is today the most useful approach for nonlinear microwave network analysis [4],[5]. In this paper we propose analytical design tool for oscillators using the Signal Space approach. The expressions for oscillator parameters such as oscillation frequency, stability conditions, power output, injection locking bandwidth etc., were applied in the design of a X band Gunn microstrip oscillator in the MATLAB program. The stability condition expression is compatible with Kurakawa's results, and the injection locking bandwidth calculation includes Adler's expression as a limiting case. There is good agreement between the simulation and the measurement results.
Odds of Transfusion for Older Adults Compared With Younger Adults Undergoing Surgery (2014)

Brown, Charles H. IV*; Savage, William J.†; Masear, Courtney G.*; Walston, Jeremy D.‡; Tian, Jing§; Colantuoni, Elizabeth§; Hogue, Charles W.*; Frank, Steven M.* Author Information
Understanding the Interaction of Gluconamides and Gluconates with Amino Acids in Hair Care (2022)

A hair care mixture formed from a gluconamide derivative and 3-hydroxypropyl ammonium gluconate is known to strengthen hair fibers; however, the mechanism by which the mixture affects hair is unknown. To give insight into the aggregation of the target gluconamide and potential interactions between the gluconate-derived mixture and hair fibers, a range of systems were characterized by X-ray crystallography namely two polymorphic forms of the target gluconamide and three salts of 3-hydroxypropylammonium with sulfuric acid, methane sulfonic acid, and oxalic acid. The gluconamide proves to aggregate and becomes a supramolecular gelator in aniline and benzyl alcohol solution. The resulting gels were characterized by rheology, scanning electron microscopy, proton nuclear magnetic resonance, Fourier transform infrared spectroscopy, and powder X-ray diffraction.
Alternate Aggregation Pathways of the Alzheimer β-Amyloid Peptide (2000)

Deposition of amyloid-beta (Abeta) aggregates in the brain is a defining characteristic of Alzheimer's disease (AD). Fibrillar amyloid, found in the cores of senile plaques, is surrounded by dystrophic neurites. In contrast, the amorphous Abeta (also called preamyloid) in diffuse plaques is not associated with neurodegeneration. Depending on the conditions, Abeta will also form fibrillar or amorphous aggregates in vitro. In this present study, we sought to characterize the properties of the amorphous aggregate and determine whether we could establish an in vitro model for amorphous Abeta. CD data indicated that Abeta40 assembled to form either a beta-structured aggregate or an unfolded aggregate with the structured aggregate forming at high peptide concentrations and the unstructured aggregate forming at low Abeta40 levels. The critical concentration separating these two pathways was 10 microm. Fluorescence emission and polarization showed the structured aggregate was tightly packed containing peptides that were not accessible to water. Peptides in the unstructured aggregate were loosely packed, mobile, and accessible to water. When examined by electron microscopy, the structured aggregate appeared as protofibrillar structures and formed classic amyloid fibrils over a period of several weeks. The unstructured aggregate was not visible by electron microscopy and did not generate fibrils. These findings suggest that the unstructured aggregate shares many properties with the amorphous Abeta of AD and that conditions can be established to form amorphous Abeta in vitro. This would allow for investigations to better understand the relationship between fibrillar and amorphous Abeta and could have significant impact upon efforts to find therapies for AD.
Regeneration of pentasil zeolite catalysts using ozone and oxygen (1986)

A novel procedure for the removal of carbonaceous deposits from zeolites using ozone-enriched oxygen is described. Pentasil zeolites (SiO2/Al2O3 mole ratios 35, 70) were studied and deactivated using methanol conversion to hydrocarbons and o-xylene isomerisation. Low temperature ozone reactivation was found to restore the catalyst activity for these reactions and hence can be considered as an alternative procedure to high temperature oxygen reactivation currently utilised industrially. Ozone reactivation was found to increase slightly the catalyst lifetime and also to reduce the initial methane yield when compared with oxygen reactivation.
Supplementary Figure 4 from Nuclear–Cytoplasmic Transport Is a Therapeutic Target in Myelofibrosis (2023)

&lt;p&gt;Supplementary Figure 4&lt;/p&gt;
Mode of Delivery and Neonatal Outcomes in Preterm, Small-for-Gestational-Age Newborns (2012)

Cesarean delivery was not associated with improved neonatal outcomes in preterm SGA newborns and was associated with an increased risk of respiratory distress syndrome.
Burst Emergence of Intracellular Ca2+Waves Evokes Arrhythmogenic Oscillatory Depolarization via the Na+–Ca2+Exchanger (2008)

Intracellular Ca(2+) waves (CaWs) of cardiomyocytes are spontaneous events of Ca(2+) release from the sarcoplasmic reticulum that are regarded as an important substrate for triggered arrhythmias and delayed afterdepolarizations. However, little is known regarding whether or how CaWs within the heart actually produce arrhythmogenic membrane oscillation because of the lack of data confirming direct correlation between CaWs and membrane potentials (V(m)) in the heart. On the hypothesis that CaWs evoke arrhythmogenic oscillatory depolarization when they emerge synchronously and intensively in the heart, we conducted simultaneous fluorescence recording of intracellular Ca(2+) ([Ca(2+)](i)) dynamics and V(m) of ventricular myocytes on subepicardial surfaces of Langendorff-perfused rat hearts using in situ dual-view, rapid-scanning confocal microscopy. In intact hearts loaded with fluo4/acetoxymethyl ester and RH237 under perfusion with cytochalasin D at room temperature, individual myocytes exhibited Ca(2+) transients and action potentials uniformly on ventricular excitation, whereas low-K(+)-perfused (2.4 mmol/L) hearts exhibited CaWs sporadically between Ca(2+) transients without discernible membrane depolarization. Further [Ca(2+)](i) loading of the heart, produced by rapid pacing and addition of isoproterenol, evoked triggered activity and subsequent oscillatory V(m), which are caused by burst emergence of CaWs in individual myocytes. Such arrhythmogenic membrane oscillation was abolished by ryanodine or the Na(+)-Ca(2+) exchanger inhibitor SEA0400, indicating an essential role of CaWs and resultant Na(+)-Ca(2+) exchanger-mediated depolarization in triggered activity. In summary, we demonstrate a mechanistic link between intracellular CaWs and arrhythmogenic oscillatory depolarizations in the heart. Our findings provide a cellular perspective on abnormal [Ca(2+)](i) handling in the genesis of triggered arrhythmias in the heart.
Supplementary Materials and Methods from CUE-101, a Novel E7-pHLA-IL2-Fc Fusion Protein, Enhances Tumor Antigen-Specific T-Cell Activation for the Treatment of HPV16-Driven Malignancies (2023)

&lt;p&gt;Supplementary Materials and Methods&lt;/p&gt;
MeshSDF: Differentiable Iso-Surface Extraction (2020)

Geometric Deep Learning has recently made striking progress with the advent of continuous Deep Implicit Fields. They allow for detailed modeling of watertight surfaces of arbitrary topology while not relying on a 3D Euclidean grid, resulting in a learnable parameterization that is not limited in resolution. Unfortunately, these methods are often not suitable for applications that require an explicit mesh-based surface representation because converting an implicit field to such a representation relies on the Marching Cubes algorithm, which cannot be differentiated with respect to the underlying implicit field. In this work, we remove this limitation and introduce a differentiable way to produce explicit surface mesh representations from Deep Signed Distance Functions. Our key insight is that by reasoning on how implicit field perturbations impact local surface geometry, one can ultimately differentiate the 3D location of surface samples with respect to the underlying deep implicit field. We exploit this to define MeshSDF, an end-to-end differentiable mesh representation which can vary its topology. We use two different applications to validate our theoretical insight: Single-View Reconstruction via Differentiable Rendering and Physically-Driven Shape Optimization. In both cases our differentiable parameterization gives us an edge over state-of-the-art algorithms.
Optimal sizing of energy storage system and their impacts in hybrid microgrid environment (2017)

Large-scale deployment and integration of renewable energy sources (RES) such as wind turbine generators and photovoltaics are important in a Hybrid Microgrid (HMG) environment, an immense challenge considering their intermittent power generation. Energy storage resources play a vital role in enhancing intermittency issues in RES and when integrated into a HMG, also enable other benefits, such as power quality improvement, short-term power supply, ancillary service and arbitrage [1]. However, economics of large-scale energy storage systems (ESS) are high considering their present status of technology maturity [2]. A trade-off on optimal sizing of ESS to the cost of its implementation in a HMG is imperative for its successful operation. This paper presents a thorough analysis on appropriate HMG architecture design based on location and load requirements, optimal sizing of ESS resources and ESS characteristics in serving various degree of power needs. In addition, thorough sensitivity analysis on component sizing in HMG environment is performed and knowledge gained from the simulation studies is utilized to propose a control philosophy for the operation of battery energy storage in HMG.
Designing a robust high-speed CMOS-MEMS capacitive humidity sensor (2012)

In our previous work (Lazarus and Fedder 2011 J. Micromech. Microeng. 21 0650281), we demonstrated a CMOS-MEMS capacitive humidity sensor with a 72% improvement in sensitivity over the highest previously integrated on a CMOS die. This paper explores a series of methods for creating a faster and more manufacturable high-sensitivity capacitive humidity sensor. These techniques include adding oxide pillars to hold the plates apart, spin coating polymer to allow sensors to be fabricated more cheaply, adding a polysilicon heater and etching away excess polymer in the release holes. In most cases a tradeoff was found between sensitivity and other factors such as response time or robustness. A robust high-speed sensor was designed with a sensitivity of 0.21% change in capacitance per per cent relative humidity, while dropping the response time constant from 70 to 4s. Although less sensitive than our design, the sensor remains 17% more sensitive than the most sensitive interdigitated designs successfully integrated with CMOS.
Paper: An improved optimization method for finding a color filter to make a camera more colorimetric (2020)

Recently, an iterative optimization method was proposed that determines the spectral transmittance of a color filter which, when placed in front of a camera, makes the camera more colorimetric [1]. However, the performance of this method depends strongly on the filter (guess) that initializes the optimization. In this paper, we develop a simple extension to the optimization where we systematically sample the set of possible initial filters and for each initialization solve for the best refinement. Experiments demonstrate that improving the initialization step can result in the effective ‘camera+filter’ imaging system being much more colorimetric. Moreover, the filters we design are smoother than previously reported (which makes them easier to manufacture).
Two-stage blind identification of SIMO systems with common zeros (2006)

Blind identification of SIMO systems is dependent on identi-fiability conditions which include the requirement that there are no common zeros between multiple channels. We demonstrate that common zeros are likely to exist for long channels, such as acoustic impulse responses and we illus-trate the performance degradation due to common zeros in blind system identification. Subsequently, we propose a new scheme where the characteristic zeros components of the transfer functions are identified using a blind multichannel method and the common zeros component is obtained with a single channel approach. 1.
Genomic analysis identifies frequent deletions of Dystrophin in olfactory neuroblastoma (2018)

Olfactory neuroblastoma (ONB) is a rare malignant neoplasm arising in the upper portion of the sinonasal cavity. To better understand the genetic bases for ONB, here we perform whole exome and whole genome sequencing as well as single nucleotide polymorphism array analyses in a series of ONB patient samples. Deletions involving the dystrophin (DMD) locus are found in 12 of 14 (86%) tumors. Interestingly, one of the remaining tumors has a deletion in LAMA2, bringing the number of ONBs with deletions of genes involved in the development of muscular dystrophies to 13 or 93%. This high prevalence implicates an unexpected functional role for genes causing hereditary muscular dystrophies in ONB.
Neonatal Maternal Separation Increases Brain-Derived Neurotrophic Factor and Tyrosine Kinase Receptor B Expression in the Descending Pain Modulatory System (2009)

Neonatal maternal separation (NMS) could trigger long-term changes in the central neuronal responses to nociceptive stimuli in rats. Stress-induced visceral hyperalgesia is closely associated with the dysfunction of descending pain modulatory systems. Brain-derived neurotrophic factor (BDNF) not only has an important role in long-term synaptic plasticity but also in facilitating descending pain. The present study aimed to investigate changes in the expression of BDNF and its receptor tyrosine kinase receptor B (TrkB) in the amygdala and the rostral ventromedial medulla (RVM) after NMS and colorectal distention (CRD) stimulation in rats. Male Wistar rat pups were subjected to 180 min of daily NMS or not handled for 13 consecutive days. Expression of BDNF and TrkB following NMS and CRD stimulation was determined using immunohistochemistry. The results revealed an increase in the expression of BDNF and TrkB in the amygdala after NMS. An interactive effect of NMS and CRD on the expression of TrkB, but not BDNF, was found in the RVM. Furthermore, a significant interactive effect of NMS and CRD on the colocalization coefficient of TrkB and phospho-extracellular signal-regulated kinase expression in both the amygdala and RVM were found. These data demonstrate that NMS increases BDNF and TrkB expression in the descending pain systems, which may contribute to the development of NMS-induced visceral hyperalgesia.
ChemInform Abstract: Polyoxometalate‐Diphosphate Complexes. Part 5. Cigar‐Shaped 30‐Molybdobispyrophosphate: Structure of (N(C4H9)4)2H9 [{(P2O7)Mo15O45}2] [PMo12O40]. (2000)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Carrier Transport Across Metal-Polymer Barriers (1993)

The electrical transport properties of aluminium-poly(3-octylthiophene) are investigated using current-voltage ( I - V ) measurement. The theoretical analysis of the I - V spectra measured at various temperatures shows that at relatively high forward voltage the forward current is dominated by the diffusion of charge carriers, while at lower forward bias and low temperature it is the tunneling current that dominates.
Inhibiting Metalloproteases with PD 166793 in Heart Failure: Impact on Cardiac Remodeling and Beyond (2008)

Metalloproteinases (MMPs, also called matrixins) are extracellular proteolytic enzymes involved in the degradation of both matrix and nonmatrix proteins. Currently, 25 MMPs have been identified in humans, and the overexpression of one or more MMPs has been implicated in several pathologies, spanning from cancer to rheumathoid arthritis to cardiovascular disease. While research over the past 20 years has focused on understanding MMP biology and selectively inhibiting MMP activity, key issues that remain to be addressed include MMP roles in the context of normal versus pathological conditions and whether globally inhibiting MMPs improves or deteriorates overall organ function. In terms of cardiovascular disease, increased MMP expression has been demonstrated in the setting of myocardial ischemia, reperfusion injury, and during the progression to congestive heart failure. MMPs are also major contributors to the progression of atherosclerotic lesions. In this review, we focus on cardiovascular effects produced by PD 166793, a wide-broad spectrum MMP inhibitor, originally developed by Parke-Davis (now Pfizer). We will briefly review its structure, mechanism of action, and inhibitory capacity. Finally, we will illustrate the cardiac contexts, both in vivo and in vitro, in which PD166793 administration has proven beneficial.