gebhart/patrepeval huggingface dataset:
Syntheses of Highly Functionalized Spirocyclohexenes by Formal [4+2] Annulation of Arylidene Azlactones with Allenoates (2018)

A straightforward phosphine-catalyzed formal [4+2] annulation between α-branched allenoates and arylidene azlactones has been developed to access highly functionalized spirocyclohexenes. This cyclization favors the γ-addition of the phosphine-activated allenoates over a β'-addition pathway. Detailed computational studies support the proposed mechanism and provide a reasonable explanation for the observed regioselectivity and the noted effect of the catalyst.
<i>Bifidobacterium longum </i><scp>NCC</scp>3001 inhibits <scp>AH</scp> neuron excitability (2013)

The probiotic B. longum reduces excitability of AH sensory neurons likely via opening of potassium channels and closing of hyperpolarization-activated cation channels.
Visualization and Measurement of Dynamic Water Behavior in PEFC by Neutron Radiography (2007)

Hydrogen gas and air are supplied in saturated moist condition to keep a membrane wet in a PEFC. Condensation may occur in the cathode by the FC reaction, since air is saturated moist condition. The condensed water may affect on the fuel cell performance. It is very important for the design to know the water behaviors. In this study, in-situ visualization of an operating PEFC was carried by neutron radiography with the cell voltage measurements. A JARI standard cell was improved for the visualization with the same performance. Water distribution in the fuel cell could be quantitatively measured from visualized images via some image processing methods. The relationships between the water distributions and cell voltage fluctuations were clearly shown from the visualization and measurement results. The difference in water distribution for three types of gas supply channel was clearly shown.
Efficacy of imatinib mesylate in the treatment of idiopathic hypereosinophilic syndrome (2003)

Idiopathic hypereosinophilic syndrome (HES) is a myeloproliferative disorder characterized by persistent eosinophilia and organ involvement. Different treatments have been investigated in HES with modest success. It has been suggested that imatinib is active in HES. We treated 9 patients with HES with 100 mg imatinib daily. Doses for patients without response after 4 weeks were increased to 400 mg daily. Prior therapy had failed for 7 patients. Five patients responded: 4 achieved sustained complete remission lasting a median of 12+ weeks (range, 9+ to 36+ weeks), and 1 had a transient response. One patient died in complete remission. Responses occurred within 4 weeks of therapy; only 1 responder required an increase in dose to 400 mg daily. Three of 4 nonresponders failed to respond to an increase in dose. Toxicity was minimal. We conclude that imatinib therapy is effective for HES.
Gaze-based interaction with public displays using off-the-shelf components (2010)

Eye gaze can be used to interact with high-density information presented on large displays. We have built a system employing off-the-shelf hardware components and open-source gaze tracking software that enables users to interact with an interface displayed on a 55" screen using their eye movements. The system works at a viewing distance of 1 to 1.5 meters and requires a 30 second calibration procedure for every user. We demonstrate how it can be used to navigate a digital bulletin board display with several notes on top of each other. There are some technical challenges detecting the eyes when people are wearing glasses and when external light sources are present.
The transcription factor MITF is a critical regulator of GPNMB expression in dendritic cells (2015)

In summary, imatinib, nilotinib or IL-10 congruently inhibit the PI3K/Akt signaling pathway thereby activating MITF in moDC, resulting in a tolerogenic phenotype. These findings extend current knowledge on the molecular mechanisms balancing activating and inhibitory signals in human DC and may facilitate the targeted manipulation of T cell responses in the context of DC-based immunotherapeutic interventions.
Conformational Analysis of Non-terpenoid Juvenile Hormone Analogs and Steric Resemblance in Their Stable Conformations (1987)

強力なIGR活性を有する propionaldoxime O-2-(4-phenoxyphenoxy) ethyl ether と ethyl N-(4-phenoxyphenoxy) ethylcarbamate (Ro 13-5223) に関し, MNDO法に基づく安定コンホメーションにおける立体形状比較を行なった. 前者ではオキシムエーテル部のN-O結合での回転が著しく阻害されており, この結合に関しては, 事実上一つのコンホーマーのみが許され, これが活性コンホメーションと推察されること, さらに, 後者では, カーバメート部のN-C結合に関して二つの局所安定コンホメーションが存在することが判明した. 前者における安定コンホメーションでのN-O結合に基づくねじれ角が, 後者における二つの局所安定コンホメーション中, より安定なコンホメーションでのN-C結合に基づくねじれ角ときわめてよく一致することから, Ro 13-5223に関しては, このものが活性コンホメーションに対応していると推測された.
Optimization driven data mining and credit scoring (2002)

An optimization tree approach to the mining of very extensive and complex databases for performance optimizing opportunities is described. This methodology is based on a combination of three innovations: a data management system designed explicitly for data intensive computing; a distributed algorithm for growing classification and regression trees (CART); and a tree based stochastic programming paradigm for the selection of control attributes to optimize a specified objective function. This methodology provides a general technique for optimization in financial applications that is scalable as the number of objects in the database and as the number of attributes per object grow. This scalability allows for a complete data driven analysis of large scale data sets, without the need to restrict attention to sparsely sampled data sets that limits previous methods.
Structural Features of HIV Envelope Defined by Antibody Escape Mutant Analysis (2001)

Two neutralizing antibodies specific for the V3 sequence of HIV envelope were used to generate escape variants from the HTLV(IIIB) founder virus. The full gp120 sequence of each variant was then analyzed to identify mutations responsible for immune escape. As predicted, most escape variants harbored amino acid changes in the V3 crown sequence. However, one variant differed from its founder only within the conserved C2 region. These findings, when analyzed in conjunction with crystallographic data, suggest a new three-dimensional model for HIV envelope folding, in which the V3 loop extends across the CD4-binding face of gp120 to associate with discontinuous C2 residues. This envelope configuration may provide an effective immune defense mechanism for HIV, as the highly variable residues of the V3 loop may shield conserved amino acids pertinent to viral infection.
Use of Polyamine Derivatives as Selective Histone Deacetylase Inhibitors (2011)

Histone acetylation and deacetylation, mediated by histone acetyltransferase and the 11 isoforms of histone deacetylase, play an important role in gene expression. Histone deacetylase inhibitors have found utility in the treatment of cancer by promoting the reexpression of aberrantly silenced genes that code for tumor suppressor factors. It is unclear which of the 11 histone deacetylase isoforms are important in human cancer. We have designed a series of polyaminohydroxamic acid (PAHA) and polyaminobenzamide (PABA) histone deacetylase inhibitors that exhibit selectivity among four histone deacetylase isoforms. Although all of the active inhibitors promote reexpression of tumor suppressor factors, they produce variable cellular effects ranging from stimulation of growth to cytostasis and cytotoxicity. This chapter describes the procedures used to quantify the global and isoform-specific inhibition caused by these inhibitors, and techniques used to measure cellular effects such as reexpression of tumor suppressor proteins and hyperacetylation of histones H3 and H4. Procedures are also described to examine the ability of PAHAs and PABAs to utilize the polyamine transport system and to induce overexpression of the early apoptotic factor annexin A1.
Voltage-induced broad-spectrum reflectivity change with surface-plasmon waves (2004)

Voltage-induced broad-spectrum reflectivity change with surface-plasmon waves is reported. When white light is incident at a metal/electro-optical material interface, surface-plasmon waves can be excited under phase match conditions. This surface-plasmon resonance depends on the dielectric constants of both the metal and the electro-optical material. Photons in the surface-plasmon resonance wavelength range are absorbed by the interface. Since metals have large imaginary parts of their dielectric constants, the surface-plasmon resonances are broad and may cover all visible wavelengths. Applying voltage to the electro-optical material to change its dielectric constant can result in a change in the reflectivity at the interface. Experimental results showed a reflectivity change from almost 0% to about 40% under an applied voltage using a liquid-crystal and nickel film structure, and the results had good agreement with theoretical calculations. The theoretical calculations also predicted a 90% reflectivity recovery by exciting surface-plasmon waves at a Rh–Al/electro-optical material interface. These results demonstrate that a high efficiency white light modulator can be built using surface-plasmon excitations.
Microfluidic skin chip with vasculature for recapitulating the immune response of the skin tissue (2020)

There is a considerable need for cell-based in vitro skin models for studying dermatological diseases and testing cosmetic products, but current in vitro skin models lack physiological relevance compared to human skin tissue. For example, many dermatological disorders involve complex immune responses, but current skin models are not capable of recapitulating the phenomena. Previously, we reported development of a microfluidic skin chip with a vessel structure and vascular endothelial cells. In this study, we cocultured dermal fibroblasts and keratinocytes with vascular endothelial cells, human umbilical vascular endothelial cells. We verified the formation of a vascular endothelium in the presence of the dermis and epidermis layers by examining the expression of tissue-specific markers. As the vascular endothelium plays a critical role in the migration of leukocytes to inflammation sites, we incorporated leukocytes in the circulating media and attempted to mimic the migration of neutrophils in response to external stimuli. Increased secretion of cytokines and migration of neutrophils was observed when the skin chip was exposed to ultraviolet irradiation, showing that the microfluidic skin chip may be useful for studying the immune response of the human tissue.
2P2-Q10 Realization of Hula Hooping by a Robot for an Example of a Movement using Flexible Spine in the Torso(Informative Motion &amp; Motion Media) (2011)

Many types of humanoid robots have been developed, but it is hard to find one with supple spine structure. To act in a proper manner with natural, human-like motions, we believe that humanoid robots should have and use their spines effectively. To find out how to use the spine flexibly and elegantly, we focused on dancing, the art of beautiful movements. Dancing demands you to develop flexible and well coordinated movements of the torso, so we decided to pick up a movement of the sort and realize it by a robot, in order to understand the basics of dancing. This paper describes a way of realizing hula hooping by an exclusive hula-hooping robot as the first step toward dancing humanoids.
Study of the Phosphoryl‐Transfer Mechanism of Shikimate Kinase by NMR Spectroscopy (2016)

The phosphoryl-transfer mechanism of shikimate kinase from Mycobacterium tuberculosis and Helicobacter pylori, which is an attractive target for antibiotic drug discovery, has been studied by 1D (1)H and (31)P NMR spectroscopy. Metaphosphoric acid proved to be a good mimetic of the metaphosphate intermediate and facilitated the ready and rapid evaluation by NMR spectroscopic analysis of a dissociative mechanism. The required closed form of the active site for catalysis was achieved by the use of ADP (product) or two synthetic ADP analogues (AMPNP, AMPCP). Molecular dynamics simulation studies reported here also revealed that the essential arginine (Arg116/Arg117 in H. pylori and M. tuberculosis, respectively), which activates the γ-phosphate group of ATP for catalysis and triggers the release of the product for turnover, would also be involved in the stabilisation of the metaphosphate intermediate during catalysis. We believe that the studies reported here will be helpful for future structure-based design of inhibitors of this attractive target. The approach is also expected be useful for studies on the possible dissociative mechanism of other kinase enzymes.
Preventing the Airborne Spread of<i>Staphylococcus aureus</i>by Persons With the Common Cold: Effect of Surgical Scrubs, Gowns, and Masks (2007)

Scrubs reduced the spread of airborne S. aureus, independent of the presence of a rhinovirus-induced cold. Airborne dispersal of S. aureus during sessions in which participants wore surgical scrubs was not significantly different from that during sessions in which gowns and gowns plus masks were also worn.
Nucleotide Sequence of the Genes Coding for the Membrane Glycoproteins E1 and E2 of Rubella Virus (1987)

The complete nucleotide sequence of the genes coding for the two membrane glycoproteins E1 and E2 of rubella virus has been determined from cloned cDNA derived from the 40S genomic RNA. A sequence of 2451 nucleotides extending from the poly(A) tract towards the 5' end is presented. Within one continuous open reading frame E2 is located amino-terminally followed by E1 and a 58 residue long untranslated 3' region preceding the poly(A) tract. The coding regions of E2 and E1 are unusually G/C rich, 71.4% and 66.4% respectively. At the carboxy-terminal end of the coding region of E1, there is an inverted complementary nucleotide sequence, which could form a 13 base pair hairpin structure. Mature E2 and E1 are both preceded by a stretch of uncharged mainly non-polar amino acids, 21 and 20 residues in length, respectively. These could serve as signal peptides that mediate the membrane translocation of the proteins. At the carboxy termini of both proteins there are stretches of hydrophobic amino acids, 19 and 27 residues in length, which probably represent the transmembrane anchors of the proteins. The size of mature E1 is 481 amino acids (mol. wt. 51,502), whereas the exact size of mature E2 could not be established as its carboxy-terminal end could not be located in the sequence. A maximum size of 262 amino acids (mol. wt. 28,277) is, however, suggested. Between the E2 and E1 genes, there is a stretch of seven amino acids, five of which are arginines, which may serve as cleavage sites for a trypsin-like protease. E1 contains three and E2 four potential sites for asparagine-linked glycosylation. Both proteins are cysteine-rich (5%). Comparison of the rubella virus amino acid sequence to those of several alphaviruses indicated no sequence homology.
Leveraging a Big Dataset to Develop a Recurrent Neural Network to Predict Adverse Glycemic Events in Type 1 Diabetes (2019)

Patients with type 1 diabetes (T1D) do not produce their own insulin. They must continuously monitor their glucose and make decisions about insulin dosing to avoid the consequences of adverse glucose excursions. Continuous glucose monitoring (CGM) systems and insulin pumps are state-of-the-art systems that can help people with T1D manage their glucose. Accurate glucose prediction algorithms are becoming critical components of CGM systems that can help people with T1D proactively avoid the occurrence of impending hyperglycemia and hypoglycemia events. We present Glucop30, a robust data-driven glucose prediction model that is trained on a big dataset (27,466 days) to forecast glucose concentration along a short-term prediction horizon of 30 minutes. Our proposed prediction method is composed of (i) a recurrent neural network with long-short-term-memory (LSTM) units that predicts the general trend of future glucose levels, followed by (ii) a patient-specific smoothing error correction step that accounts for inter- and intra-patient glucose variability. We retrospectively test our proposed method on a clinical dataset obtained from 10 T1D insulin pump users who were continuously monitored during a 4-week trial under free-living conditions (255 days), and assess the impact of the size of the training set on the accuracy of the proposed model. In addition, we report on the accuracy of our method when both CGM and insulin data are used for prediction; however we discovered that adding insulin as an additional input feature improves prediction accuracy by only 1%. Glucop30 achieves leading performance as measured by the RMSE of 7.55 (SD = 2.20 mg/dL) and MAE of 4.89 (SD = 1.43 mg/dL) for an effective prediction horizon of 27.50 (SD = 2.64) minutes. Moreover, Glucop30 accurately anticipates the occurrence of 97.79 (SD = 5.35)% of hyperglycemia events (glucose > 180 mg/dL), and 90.87 (SD = 6.79)% of hypoglycemia events (glucose < 70 mg/dL) with remarkably few false alerts (1 and 2 false alarms per week for hypoglycemia and hyperglycemia events, respectively).
Neonatal life support during magnetic resonance imaging (2002)

Magnetic resonance techniques are required frequently for the assessment of the brain of ill neonates. In the present study, the effects of a 1.5 T MR scanner on devices for life support were assessed. A ventilator (Dräger Babylog 2000) was tested in the 1.5 T magnet, using a neonatal ventilation tester and 1.5-5 m tubes. In a special MR incubator, temperature and humidity were measured at 1-min intervals. Infusion was tested with the pump outside the magnet room: infusion rates and time to alarm were tested with 7-m tubes. The ventilator performed normally at a magnetic field line of 2 mT, although the alarms failed. The incubator created a temperature of 35.9 degrees C and humidity of 40.7%, which was acceptable for examinations of 45 min. The alarm limits of the infusion pump placed outside the magnet at 7 m were within company limits. The study indicates that magnetic resonance examinations can be performed safely in ill preterm neonates who require life-support devices.
GABAergic signaling promotes early-life seizures in epileptic SYNGAP1 <sup>+/-</sup> mice (2020)

Abstract Objective SYNGAP1 encephalopathy is a developmental and epileptic encephalopathy caused by pathogenic loss of function variants. Syngap1 -heterozygous (Het +/- ) mice demonstrate progressive epilepsy with multiple seizure phenotypes in adulthood. Here, we investigate early-life seizures in Het +/- pups and explore of Syngap1 encephalopathy during development. Methods Post-natal day 7 (P7) and P12 mice were investigated by tethered video-electroencephalographic (vEEG). The effects of GABAergic drugs phenobarbital (PB) and pentylenetetrazol (PTZ) were investigated at P7 and P12, respectively. 24h tethered vEEG was performed at P24, and telemetric 24h vEEG with 6h sleep deprivation was performed at P35. The effect of perampanel (PMP), an AMPA receptor antagonist, was investigated at P24. Results Het +/- mice have spontaneous early-life seizures that lack an overt behavioral phenotype. These subclinical seizures are refractory to PB, but the GABA A receptor (GABA A R) antagonist PTZ significantly reduced seizure frequency suggesting that GABAergic signaling may promote seizure generation in Het +/- pups. At juvenile ages, Het +/- pups recapitulated the early emergence of high gamma (35-50Hz) during NREM and disruption of behavioral-state gamma homeostasis. This biomarker was significantly exacerbated in Het +/- pups after increasing sleep pressure with sleep deprivation. Significance Seizures during development have adverse effects on cognitive function. Therefore, an improved understanding of the SYNGAP1 epilepsy during developmental ages is necessary to delineate the deleterious interactions between aberrant synaptic function and recurrent seizures. The development of evidence-based therapies for early-life intervention will benefit from these insights.
Papain Catalyzed (co)Oligomerization of α-Amino Acids (2012)

Four hydrophobic amino acids (Leu, Tyr, Phe, Trp) were oligomerized by the protease papain in homo-oligomerization, binary co-oligomerization and ternary co-oligomerization. After 24 h, solid polydisperse reaction products of the homo-oligomerization were obtained in yields ranging from 30–80% by weight. A DPavg was calculated based on MALDI-ToF MS results using the ion counts for the chains in the product. Based on the DPavg and the yield of the homo-oligomerization it was determined that the amino acids can be ranked according to reactivity in the order: Tyr &gt; Leu &gt; Phe &gt; Trp. Thermal degradation of the homo-oligomers shows two degradation steps: at 178–239 °C and at 300–330 °C. All the products left a significant amount of char ranging from 18–57% by weight at 800 °C. Binary co-oligomers were obtained as a polydisperse precipitate with a compositional distribution of the chains. Both the compositional and chain length distribution are calculated from MALDI-ToF mass spectra. By comparing the amount of each amino acid present in the chains it was determined that the amino acids are incorporated with a preference: Leu &gt; Tyr &gt; Phe &gt; Trp. Ternary co-oligomers were also obtained as a precipitate and analyzed by MALDI-ToF MS. The compositional distribution and the chain length distribution were calculated from the MALDI-ToF data. The quantity of every amino acid in the chains was determined. Also determined was the influence on the DPavg when the oligomers were compared with corresponding binary co-oligomers. From the combined results it was concluded that in the co-oligomerization of three amino acids the reactivity preference is Leu &gt; Tyr &gt; Phe &gt; Trp. Thermal degradation of all the co-oligomers showed a weight loss of 2 wt% before the main oligomer degradation step at 300–325 °C.
Covert sensing using floodlight illumination (2019)

We present an active covert phase sensing scheme using floodlight illumination with an amplified spontaneous emission (ASE) source. We show that the performance of an ASE source is substantially superior compared to a laser source. © 2019 The Author(s)
The Ross procedure in children. (1996)

Although it has been almost 30 years since Ross described his technique for aortic valve replacement using the pulmonary autograft, only recently has there been widespread interest in the use of the Ross procedure for aortic valve replacement in children with congenital heart disease. Since July 1992 we have performed the Ross procedure in 46 patients, 40 of whom were < or = 18 years of age at the time of surgery. In 10 children the procedure was combined with Konno ventriculoplasty, and in 3 others a Ross-Konno procedure was used for biventricular repair of borderline hypoplastic left heart syndrome. The only early deaths were in two of the patients with borderline hypoplastic left heart syndrome. There has been no late mortality, and two patients have required reoperation: one for recurrent distal aortic arch obstruction, and one for moderate-severe autograft insufficiency. Freedom from reoperation at 30 months is 89%. Aside from one patient with moderate autograft insufficiency and eight with mild regurgitation, all patients have trace or no aortic insufficiency at follow-up ranging from 1 to 38 months (median 22 months). The Ross procedure is an important advance in the treatment of aortic valve disease in pediatric patients. It is the only available replacement for the aortic valve that has growth potential, and there is ample evidence that the pulmonary autograft holds up well in the systemic circulation.