gebhart/patrepeval huggingface dataset:
Cytidine Deaminase Complexed to 3-Deazacytidine:  A “Valence Buffer” in Zinc Enzyme Catalysis (1996)

The cytidine deaminase substrate analog inhibitor 3-deazacytidine binds with its 4-amino group inserted into a site previously identified as a probable binding site for the leaving ammonia group. Binding to this site shifts the pyrimidine ring significantly further from the activated water molecule than the position it occupies in either of two complexes with compounds capable of hydrogen bonding at the 3-position of the ring [Xiang et al. (1995) Biochemistry 34, 4516-4523]. Difference Fourier maps between the deazacytidine, dihydrozebularine, and zebularine--hydrate inhibitor complexes suggest that the ring itself moves successively toward the activated water, leaving the amino group behind in this site as the substrate complex approaches the transition state. They also reveal systematic changes in a single zinc-sulfur bond distance. These correlate with chemical changes expected as the substrate approaches the tetrahedral transition state, in which the zinc-activated hydroxyl group develops maximal negative charge and forms a short hydrogen bond to the neighboring carboxylate group of Glu 104. Empirical bond valence relationships suggest that the Zn-S gamma 132 bond functions throughout the reaction as a "valence buffer" that accommodates changing negative charge on the hydroxyl group. Similar structural features in alcohol dehydrogenase suggest that analogous mechanisms may be a general feature of catalysis by zinc enzymes.
Gene Therapy and Stem Cell Therapy to Improve the Outcome of Human Islet Transplantation (2013)

Since its first introduction in 1990s, the Edmonton Protocol for human islet transplantation has helped more than 500 patients with type 1 diabetes worldwide and met great success from bench to bedside. The Edmonton Protocol involves isolating islets from a cadaveric donor pancreas by enzymatic digestion and infusing into the patient's portal vein. Each recipient usually receives islets from two or three donors for an optimal outcome and is dosed with two immunosuppressive drugs, sirolimus and tacrolimus and a monoclonal antibody drug daclizumab to prevent the graft rejection. However, despite the administration of immunosuppressive drugs and the recent improvement in islet isolation, preparation and transplantation, insulin independence is rarely sustained for long term after islet transplantation. It was reported that by a year after transplant, 50-68% of patients do not need to receive additional insulin, but by five years after the procedure, few than 10% of total patients are free of daily insulin injection.
Effect of lipid extracts of Nigella sativa L. seeds on the liver ATP reduction and alpha-glucosidase inhibition. (2016)

Various extracts from the seeds of Nigella sativa have been used in traditional folk medicine to treat inflammation, liver disorders and arthritis. These seeds have been experimentally shown to possess antioxidant and hepatoprotective properties. Beside the hypoglycaemic and hypolipidemic effects, this study was carried out to evaluate, in vitro, toxicological effect of lipid extracts from the Nigella sativa seeds. The tested fractions were: (i) defatted methanolic extract, (ii) total lipid extract obtained by hexane extraction from methanolic extract and (iii) neutral and polar lipid fractions. The fractions were assessed, in vitro, for their inhibitory activity potential on the enzyme alpha-glucosidase as suppressing the enzyme activity is one among the therapeutic approaches to attenuate postprandial hyperglycemia. High inhibition of alpha-glucosidase by the two polar lipid fractions (F6 and F7) was reflected by their IC50 (0.51±0.04mg/ml and 0.55±0.09mg/ml, respectively), compared to acarbose (0.53±0.06mg/ml) and thymoquinone (0.65±0.05mg/ml). The hypoglycaemic effect of the polar lipid fraction of Nigella sativa could be explained by the inhibition of alpha-glucosidase, which is one of early steps of carbohydrate metabolism. Toxicological evaluation was investigated on precision-cut rat liver slices (PCLS). On PCLS, lipid extracts reduced ATP levels by 27 to 35%. Results indicate suggest that Nigella sativa extracts don't show a hepatoprotective effect against acetaminophen, but don't exhibit a major hepatotoxicity when tested alone.
P‐8: A Novel Feedback‐Type AMOLEDs Driving Method for Large‐Size Panel Applications (2005)

Abstract A novel feedback‐type driving method for active matrix organic light diodes (AMOLEDs) is proposed for large‐size poly‐Si panel applications. The driver is composed of voltage and current DACs, current comparator, and feedback control circuits. We have performed the circuit simulations with 30‐inch HDTV panel conditions with both mobility and threshold variations of the driving TFT, and confirmed the pixel‐to‐pixel OLED‐current uniformity have been greatly improved compared to prior AMOLED pixels.
How Far Can a Molecule of Weak Acid Travel in the Apoplast or Xylem?  (2006)

The plant hormones auxin, abscisic acid (ABA), and the gibberellins (GAs) are all weak acids subject to the ion-trapping mechanism that tends to remove them from the extracellular space and concentrate them in the cytoplasm of plant cells. If a molecule of one of these compounds enters the
Host cell autophagy contributes to <i>Plasmodium</i> liver development (2015)

Autophagy plays an important role in the defence against intracellular pathogens. However, some microorganisms can manipulate this host cell pathway to their advantage. In this study, we addressed the role of host cell autophagy during Plasmodium berghei liver infection. We show that vesicles containing the autophagic marker LC3 surround parasites from early time-points after invasion and throughout infection and colocalize with the parasitophorous vacuole membrane. Moreover, we show that the LC3-positive vesicles that surround Plasmodium parasites are amphisomes that converge from the endocytic and autophagic pathways, because they contain markers of both pathways. When the host autophagic pathway was inhibited by silencing several of its key regulators such as LC3, Beclin1, Vps34 or Atg5, we observed a reduction in parasite size. We also found that LC3 surrounds parasites in vivo and that parasite load is diminished in a mouse model deficient for autophagy. Together, these results show the importance of the host autophagic pathway for parasite development during the liver stage of Plasmodium infection.
Fabrication of sharp silicon hollow microneedles by deep-reactive ion etching towards minimally invasive diagnostics (2019)

Microneedle technologies have the potential for expanding the capabilities of wearable health monitoring from physiology to biochemistry. This paper presents the fabrication of silicon hollow microneedles by a deep-reactive ion etching (DRIE) process, with the aim of exploring the feasibility of microneedle-based in-vivo monitoring of biomarkers in skin fluid. Such devices shall have the ability to allow the sensing elements to be integrated either within the needle borehole or on the backside of the device, relying on capillary filling of the borehole with dermal interstitial fluid (ISF) for transporting clinically relevant biomarkers to the sensor sites. The modified DRIE process was utilized for the anisotropic etching of circular holes with diameters as small as 30 μm to a depth of >300 μm by enhancing ion bombardment to efficiently remove the fluorocarbon passivation polymer. Afterward, isotropic wet and/or dry etching was utilized to sharpen the needle due to faster etching at the pillar top, achieving tip radii as small as 5 μm. Such sharp microneedles have been demonstrated to be sufficiently robust to penetrate porcine skin without needing any aids such as an impact-insertion applicator, with the needles remaining mechanically intact after repetitive penetrations. The capillary filling of DRIE-etched through-wafer holes with water has also been demonstrated, showing the feasibility of use to transport the analyte to the target sites.
A new charge pumping method for determining the spatial distribution of hot-carrier-induced fixed charge in p-MOSFETs (1993)

A charge pumping method is proposed for the direct measurement of the hot-carrier-induced fixed charge near the drain junction of p-MOSFETs. By holding the rising and falling slopes of the gate pulse constant and then varying the highest and lowest levels, the local threshold and local flatband voltages are readily obtained. The spatial distribution of fixed charges is directly calculated from the changes that occur in these curves after the application of stress. This method is quite simple and, specifically, requires no information about impurity concentrations in the substrate. The validity and reliability of the method have been supported by computer simulations.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
Herbacetin, A Constituent of Ephedrae herba, Suppresses the HGF-Induced Motility of Human Breast Cancer MDA-MB-231 Cells by Inhibiting c-Met and Akt Phosphorylation (2013)

Ephedrae herba suppresses hepatocyte growth factor-induced cancer cell motility by inhibiting tyrosine phosphorylation of the hepatocyte growth factor receptor, c-Met, and the PI3K/Akt pathway. Moreover, Ephedrae herba directly inhibits the tyrosine-kinase activity of c-Met. Ephedrine-type alkaloids, which are the active component of Ephedrae herba, do not affect hepatocyte growth factor-c-Met-Akt signalling, prompting us to study other active molecules in the herb. We recently discovered herbacetin glycosides and found that their aglycon, herbacetin, inhibits hepatocyte growth factor-c-Met-Akt signalling. This study revealed a novel biological activity of herbacetin. Herbacetin suppressed hepatocyte growth factor-induced motility in human breast cancer MDA-MB-231 cells by inhibiting c-Met and Akt phosphorylation and directly inhibiting c-Met tyrosine kinase activity. The effects of herbacetin were compared to those of kaempferol, apigenin, and isoscutellarein, all of which have similar structures. Herbacetin inhibition of hepatocyte growth factor-induced motility was the strongest of those for the tested flavonols, and only herbacetin inhibited the hepatocyte growth factor-induced phosphorylation of c-Met. These data suggest that herbacetin is a novel Met inhibitor with a potential utility in cancer therapeutics.
Solar flower power (2017)

Bumblebees use invisible temperature patterns on flowers to make foraging decisions.
PI3 kinase signaling is involved in Aβ-induced memory loss in <i>Drosophila</i> (2010)

Multiple intracellular signals are altered in Alzheimer's disease brain tissues, including the PI3K/Akt pathway. However, the pathological relevance of such alterations is poorly understood. In vitro studies yield results that seem to be consistent with the conventional perception in which an up-regulation of the cell survival pathway, PI3K pathway, is protective in Alzheimer's disease pathogenesis. The current in vivo genetic approach, however, reveals that inhibition of the PI3K pathway leads to rescuing of the beta-amyloid peptide (Abeta)-induced memory loss in the Drosophila brain. We began our inquiry into the molecular basis of this memory loss by studying Abeta42-induced enhancement of long-term depression. We found that long-term depression is restored to a normal level through inhibition of PI3K activity. Abeta42-induced PI3K hyperactivity is directly confirmed by immunostaining of the PI3K phosphorylation targets, phospholipids. Such observations lead to the following demonstration that Abeta42-induced memory loss can be rescued through genetic silencing or pharmacological inhibition of PI3K functions. Our data suggest that Abeta42 stimulates PI3K, which in turn causes memory loss in association with an increase in accumulation of Abeta42 aggregates.
Low Power Smartdust Receiver with Novel Applications and Improvements of an RF Power Harvesting Circuit (2009)

Smartdust is the evolution of wireless sensor networks to cubic centimeter dimensions or less. Smartdust systems have advantages in cost, flexibility, and rapid deployment that make them ideal for many military, medical, and industrial applications. This work addresses the limitations of prior works of research to provide sufficient lifetime and performance for Smartdust sensor networks through the design, fabrication and testing of a novel low power receiver for use in a Smartdust transceiver. Through the novel optimization of a multi-stage LNA design and novel application of a power matched Villard voltage doubler circuit, a 1.0 V, 1.6 mW low power On-Off Key (OOK) receiver operating at 2.2 GHz is fabricated using 0.13 um CMOS technology. To facilitate data transfer in adverse RF propagation environments (1/r^3 loss), the chip receives a 1 Mbps data signal with a sensitivity of -90 dBm while consuming just 1.6 nJ/bit. The receiver operates without the addition of any external passives facilitating its application in Smartdust scale (mm^3) wireless sensor networks. This represents an order of magnitude decrease in power consumption over receiver designs of comparable sensitivity. In an effort to further extend the lifetime of the Smartdust transceiver, RF power harvesting is explored as a power source. The small scale of Smartdust sensor networks poses unique challenges in the design of RF power scavenging systems. To meet these challenges, novel design improvements to an RF power scavenging circuit integrated directly onto CMOS are presented. These improvements include a reduction in the threshold voltage of diode connected MOSFET and sources of circuit parasitics that are unique to integrated circuits. Utilizing these improvements, the voltage necessary to drive Smartdust circuitry (1 V) with a greater than 20% RF to DC conversion efficiency was generated from RF energy levels measured in the environment (66 uW). This represents better than double the RF to DC conversion efficiency of the conventional power matched RF energy harvesting circuit. The circuit is integrated directly onto a 130 nm CMOS process with no external passives and measures only 300 um by 600 um, meeting the strict form factor requirement of Smartdust systems.
Capacitor voltage balance limits in a multilevel-converter-based energy storage system (2011)

This paper studies an energy storage system based on a three-level DC-DC converter and a gridconnected\nneutral-point-clamped inverter. The main advantages of this multilevel power conversion\nsystem are highlighted and the neutral-point voltage oscillations are analyzed. A modulation algorithm\nfor the DC-DC converter which includes the neutral-point voltage balance control is used to improve\nthe voltage balancing capabilities of the inverter. Some figures are presented to show the extended\noperating areas without neutral-point voltage oscillations thanks to the contribution of the DC-DC\nconverter to the voltage balance. Finally, some guidelines to size the DC-link capacitors are given for\na practical application.
Vertically emitting annular Bragg lasers using polymer epitaxial transfer (2004)

Fabrication of a planar semiconductor microcavity, composed of cylindrical Bragg reflectors surrounding a radial defect, is demonstrated. A versatile polymer bonding process is used to transfer active InGaAsP resonators to a low-index transfer substrate. Vertical emission of in-plane modes lasing at telecom wavelengths is observed under pulsed optical excitation with a submilliwatt threshold.
Microwave-Assisted Base-Catalyzed Cyclization and Nucleophilic Substitution of<i>O</i>-Azidobenzanilides to Synthesize 1,2-Disubstituted Indazol-3-ones (2009)

Abstract A series of 1,2-disubstituted indazol-3-ones were synthesized by microwave-assisted base-catalyzed cyclization and nucleophilic substitution of o-azidobenzanilides. Among five tested reaction conditions, the cyclization of o-azidobenzanilides catalyzed by sodium hydride in DMF, sequentially followed by the nucleophilic substitution under microwave irradiation, exhibited the optimal results. Moreover, compared to the counterparts prepared by conventional heat, this method demonstrated a more expeditious and efficient process to establish a diversified 1,2-disubstituted indazol-3-one library for high-throughput biological screening.
Investigation of magnesium oxychloride cement at the initial hardening stage (2018)

The paper investigates the process of variation of magnesium oxychloride cement deformations at the initial hardening stage depending on the activity of magnesium oxide powder which is determined by the parameters of the source material burning. Investigation is focused on magnesium cements obtained from pure magnesium hydroxide. Source materials were burnt at various temperatures with the purpose to obtain magnesium oxide powder with different activity. Regular content of hydrated phases was determined in hardened magnesium cement prepared on the basis of binders with different activity. The study reveals the influence of magnesium oxide powder activity on the process of deformation occurrence in hardened magnesium cement and its tendency to crack formation.
Surface modifications introduced to a polytetrafluorethylene‐filled polycarbonate compound by dry sliding against steel as revealed by imaging XPS (1992)

Abstract Imaging XPS has been used to study surface modifications in a polytetrafluoroethylene (PTFE)‐filled polycarbonate compound as a result of dry sliding wear testing. The novel observation of the formation of a PTFE film over the polymer compound surface (in addition to a transfer film on the steel counterface) will be of significance to the understanding of friction and wear mechanisms and to the performance of polymer systems in tribological applications.
Stabilizing Nanosized Si Anodes with the Synergetic Usage of Atomic Layer Deposition and Electrolyte Additives for Li-Ion Batteries (2015)

A substantial increase in charging capacity over long cycle periods was made possible by the formation of a flexible weblike network via the combination of Al2O3 atomic layer deposition (ALD) and the electrolyte additive vinylene carbonate (VC). Transmission electron microscopy shows that a weblike network forms after cycling when ALD and VC were used in combination that dramatically increases the cycle stability for the Si composite anode. The ALD-VC combination also showed reduced reactions with the lithium salt, forming a more stable solid electrolyte interface (SEI) absent of fluorinated silicon species, as evidenced by X-ray photoelectron spectroscopy. Although the bare Si composite anode showed only an improvement from a 56% to a 45% loss after 50 cycles, when VC was introduced, the ALD-coated Si anode showed an improvement from a 73% to a 11% capacity loss. Furthermore, the anode with the ALD coating and VC had a capacity of 630 mAh g(-1) after 200 cycles running at 200 mA g(-1), and the bare anode without VC showed a capacity of 400 mAh g(-1) after only 50 cycles. This approach can be extended to other Si systems, and the formation of this SEI is dependent on the thickness of the ALD that affects both capacity and stability.
Current advances in biomarkers for targeted therapy in triple-negative breast cancer (2016)

Triple-negative breast cancer (TNBC) is a complex heterogeneous disease characterized by the absence of three hallmark receptors: human epidermal growth factor receptor 2, estrogen receptor, and progesterone receptor. Compared to other breast cancer subtypes, TNBC is more aggressive, has a higher prevalence in African-Americans, and more frequently affects younger patients. Currently, TNBC lacks clinically accepted targets for tailored therapy, warranting the need for candidate biomarkers. BiomarkerBase, an online platform used to find biomarkers reported in clinical trials, was utilized to screen all potential biomarkers for TNBC and select only the ones registered in completed TNBC trials through clinicaltrials.gov. The selected candidate biomarkers were classified as surrogate, prognostic, predictive, or pharmacodynamic (PD) and organized by location in the blood, on the cell surface, in the cytoplasm, or in the nucleus. Blood biomarkers include vascular endothelial growth factor/vascular endothelial growth factor receptor and interleukin-8 (IL-8); cell surface biomarkers include EGFR, insulin-like growth factor binding protein, c-Kit, c-Met, and PD-L1; cytoplasm biomarkers include PIK3CA, pAKT/S6/p4E-BP1, PTEN, ALDH1, and the PIK3CA/AKT/mTOR-related metabolites; and nucleus biomarkers include <i>BRCA1</i>, the gluco-corticoid receptor, <i>TP53</i>, and Ki67. Candidate biomarkers were further organized into a "cellular protein network" that demonstrates potential connectivity. This review provides an inventory and reference point for promising biomarkers for breakthrough targeted therapies in TNBC.
Effects of Fluoride and Chlorhexidine on the Microflora of Dental Root Surfaces and Progression of Root-surface Caries (1991)

The effects of fluoride and chlorhexidine varnishes on the microflora of dental root surfaces and on the progression of root-surface caries were studied. Forty-four patients, surgically treated for advanced periodontal disease, were distributed at random among three groups. All patients received a standardized preventive treatment. Furthermore, the dentition of the patients in the two experimental groups was treated, at three-month intervals, with chlorhexidine and fluoride varnish, respectively. Patients in the control group received no additional treatment. In the experimental groups, plaque samples were collected from selected sound and carious root surfaces at baseline and at three, six, and nine months after the onset of the study. The presence of root-surface caries was scored at baseline and after one year. In addition, the texture, depth, and color of the root-surface lesions were monitored. Mutans streptococci on root surfaces were suppressed significantly (p less than 0.05) during the whole experimental period in the chlorhexidine varnish group, but not in the fluoride varnish group. A non-significant increase in the number of Actinomyces viscosus/naeslundii was noted after treatment with chlorhexidine and fluoride varnish. The increase in the number of decayed and filled root surfaces after one year was significantly lower in the experimental groups than in the control group. After treatment with chlorhexidine varnish, significantly more initial root-surface lesions had hardened than in the other groups.
Fabrication and properties of cucurbit[6]uril induced thermo-responsive supramolecular hydrogels (2009)

Novel thermo-responsive supramolecular hydrogels consisting of cucurbit[6]uril(CB[6]) and butan-1-aminium 4-methylbenzenesulfonate (BAMB) were prepared, which were based on hydrophobic interaction, π–π stacking interaction and van der Walls interaction. Furthermore, hydrogels were not only sensitive to the thermal stimulation, but also showed an interesting property of the inducing action of CB[6] threaded in [2]pseudorotaxane. In this paper, the external morphology and sol–gel transition process of hydrogels were observed by polarized microscopy observation (PMO) and digital camera. DSC results show that the gel–sol transition temperature rose with increasing the concentration of either BMAB or CB[6]. The characteristics of the xerogels were determined by 1H NMR, FT-IR, SEM and TGA. It was found that the CB[6] was threaded in the butyl amine units of BAMB, and the inducing action of CB[6] threaded in [2]pseudorotaxane was essential for the hydrogel formation. Only when the concentrations of both BAMB and CB[6] reached certain values, hydrogels with three-dimensional network structure could be formed. And the viscosity changes for increasing the temperature of the hydrogel systems with different concentration of either CB[6] or BMAB were determined by the rheometer. A possible model was proposed to explain the driving forcing of the gelation.