gebhart/patrepeval huggingface dataset:
Q&A: Expansion microscopy (2017)

Expansion microscopy (ExM) is a recently invented technology that uses swellable charged polymers, synthesized densely and with appropriate topology throughout a preserved biological specimen, to physically magnify the specimen 100-fold in volume, or more, in an isotropic fashion. ExM enables nanoscale resolution imaging of preserved samples on inexpensive, fast, conventional microscopes. How does ExM work? How good is its performance? How do you get going on using it? In this Q&A, we provide the answers to these and other questions about this new and rapidly spreading toolbox.
Potent inhibition of Epstein-Barr virus by phosphorothioate oligodeoxynucleotides without sequence specification (1993)

We found that 28-mer phosphorothioate oligodeoxynucleotides (S-oligos) with and without sequence specificity complementary to Epstein-Barr virus (EBV) genes are potent inhibitors of EBV replication in cell culture. The decrease in the amount of EBV DNA, the activity of intracellular viral DNA polymerase, and virus production were dose dependent, with a 90% inhibitory dose of approximately 0.5 microM. No inhibition of cell growth was observed with the S-oligos at concentrations up to 20 microM. The mechanism of action appears to be the inhibition of EBV DNA synthesis. The reversibility of anti-EBV action is dependent on the dose and duration of drug exposure. S-oligos should be considered a new class of anti-EBV agents.
A new sensitive chemical actinometer - II. Potassium ferrioxalate as a standard chemical actinometer (1956)

Abstract The earlier experiments with potassium ferrioxalate have been extended and a detailed study has been made of the photolysis of the acidified solutions previously recommended for chemical actinometry (Parker 1953). Accurate values of quantum efficiency have been determined at twelve wavelengths between 254 and 578 mμ, and the effect of temperature, light intensity and of photolyte composition have been investigated. At some wavelengths independent values of quantum efficiency have been obtained by comparison with uranyl oxalate and by direct comparison with a calibrated thermopile. The results indicate that potassium ferrioxalate provides a very valuable new chemical actinometer, and its use is recommended in place of uranyl oxalate for many purposes. Full working details for the use of the actinometer are provided.
The Bivens Constitutional Tort: An Unfulfilled Promise (1989)

In the landmark Bivens decision the Supreme Court inferred from the Constitution the right to seek damages for the infringement of one's constitutional rights by a federal official
Alterations in serum phosphatidylcholine fatty acyl species by eicosapentaenoic and docosahexaenoic ethyl esters in patients with severe hypertriglyceridemia (1997)

A new and sensitive method has been developed to analyze the molecular species of glycerophospholipids. This method was used to examine the effects of hypolipidemic intervention with n-3 fatty acids on the serum phosphatidylcholine species in severely hypertriglyceridemic patients. The drug treated group (n = 19) received 4 g/day of an 85% concentrate of the ethyl esters of eicosapentenoic and docosahexaenoic acids for 6 weeks. Control patients (n = 21) received 4 g/day of ethyl esters of corn oil fatty acids. To evaluate the effects of n-3 fatty acids upon serum phosphatidylcholines (PCs), sera from treated and control patients were analyzed before and after 6 weeks of intervention. PCs isolated from sera were digested with phospholipase C to diglycerides, derivatized with 7-methoxycoumarin-3-carbonyl azide, and analyzed by reverse phase high performance liquid chromatography (HPLC) with fluorescence detection. Pre-intervention serum PC species were, in order of decreasing concentration C16:0,18:2, C16:0,18:1, C18:0,18:2, C16:0,20:1, C16:0,22:0, C18:0,20:4, C16:0,16:0, C18:0,18:1, C18:1,18:2, C16:0,20:5, and C18:1,20:5. In the treated patients, mean increases of 300% in C16:0,20:5 and of 160% in C16:0,22:6 species were observed. There were no significant changes in the molecular species of the serum phosphatidylcholines in the group receiving the corn oil ethyl esters. The cumulative relative percentages for each of the individual fatty acids measured by HPLC were comparable to those determined by gas-liquid chromatography (GLC). In the treated group plasma triglycerides were reduced 26%, while they were increased by 7% in the placebo group. Our data showed that incorporation of eicosapentaenoic and docosahexaenoic acid into the serum PCs occurred within 6 weeks primarily in the C16:0,20:5 and C16:0,22:6 species and were usually accompanied by a reduction in plasma triglyceride.
In vivo biomicroscopy and photography of meibomian glands in a rabbit model of meibomian gland dysfunction. (1982)

The usefulness of transillumination and biomicroscopy of the lid margin in assessing meibomian gland dysfunction was studied in a rabbit model. Transillumination of rabbit lids treated with topical epinephrine for 2 to 3 months revealed plugging of the meibomian gland orifice. Plugging appeared to be correlated histopathologically with increased thickness and hyperkeratinization of the ductal epithelium at the orifice. Continued treatment resulted in microcystic changes within the duct, which were not easily discernible by routine examination without the aid of a transilluminator. Cystic changes were correlated with dilation of the duct by retained desquamated cornified cells. Biomicroscopy proved valuable in identifying and documenting early lesions associated with epinephrine-induced meibomian gland dysfunction.
The Multi-organ Chip - A Microfluidic Platform for Long-term Multi-tissue Coculture (2015)

The ever growing amount of new substances released onto the market and the limited predictability of current in vitro test systems has led to a high need for new solutions for substance testing. Many drugs that have been removed from the market due to drug-induced liver injury released their toxic potential only after several doses of chronic testing in humans. However, a controlled microenvironment is pivotal for long-term multiple dosing experiments, as even minor alterations in extracellular conditions may greatly influence the cell physiology. We focused within our research program on the generation of a microengineered bioreactor, which can be dynamically perfused by an on-chip pump and combines at least two culture spaces for multi-organ applications. This circulatory system mimics the in vivo conditions of primary cell cultures better and assures a steadier, more quantifiable extracellular relay of signals to the cells. For demonstration purposes, human liver equivalents, generated by aggregating differentiated HepaRG cells with human hepatic stellate cells in hanging drop plates, were cocultured with human skin punch biopsies for up to 28 days inside the microbioreactor. The use of cell culture inserts enables the skin to be cultured at an air-liquid interface, allowing topical substance exposure. The microbioreactor system is capable of supporting these cocultures at near physiologic fluid flow and volume-to-liquid ratios, ensuring stable and organotypic culture conditions. The possibility of long-term cultures enables the repeated exposure to substances. Furthermore, a vascularization of the microfluidic channel circuit using human dermal microvascular endothelial cells yields a physiologically more relevant vascular model.
A retinoic acid-responsive element is present in the 5' flanking region of the laminin B1 gene. (1989)

The retinoic acid (RA)-associated differentiation of murine F9 teratocarcinoma stem cells results in dramatic changes in gene expression. The cellular gene encoding the B1 subunit of the extracellular matrix protein laminin is transcriptionally activated by RA, and its transcription is further enhanced by N6,O2'-dibutyryladenosine 3',5'-cyclic monophosphate (Bt2cAMP) during the differentiation of F9 stem cells into extraembryonic parietal endoderm cells. We now report that expression vectors encoding the human RA receptors RAR-alpha, RAR-beta, and RAR-gamma can activate chloramphenicol acetyltransferase (CAT) expression from laminin B1 promoter/CAT expression vectors (e.g., p1.6LAMCAT) in RA-treated F9 cells, as measured in a transient transfection assay. Bt2cAMP does not further enhance the RA-associated increase in CAT activity. Through the use of deletion and mutation analyses, the RA-responsive element (RARE) of the murine laminin B1 gene has been defined as a 46-base-pair element between -477 and -432 of the laminin B1 5' flanking region. Insertion of a region of DNA containing this RARE in either orientation into a thymidine kinase promoter/CAT expression vector causes CAT expression to be activated 5- to 9-fold by the cotransfected human RAR-alpha or RAR-beta constructs in RA-treated F9 cells, and this RARE also functions in human HeLa cells. In contrast, this RARE in the p1.6LAMCAT vector does not activate CAT expression when cotransfected into F9 stem cells with the c-erbA gene in the presence of thyroid hormone. This suggests that the laminin B1 gene is activated by RA but not by thyroid hormone in vivo.
Atomic Layer Deposited Lithium Silicates as Solid-State Electrolytes for All-Solid-State Batteries (2017)

Development of solid-state electrolyte (SSE) thin films is a key toward the fabrication of all-solid-state batteries (ASSBs). However, it is challenging for conventional deposition techniques to deposit uniform and conformal SSE thin films in a well-controlled fashion. In this study, atomic layer deposition (ALD) was used to fabricate lithium silicate thin films as a potential SSE for ASSBs. Lithium silicates thin films were deposited by combining ALD Li<sub>2</sub>O and SiO<sub>2</sub> subcycles using lithium tert-butoxide, tetraethylorthosilane, and H<sub>2</sub>O as precursors. Uniform and self-limiting growth was achieved at temperatures between 225 and 300 °C. X-ray absorption spectroscopy analysis disclosed that the as-deposited lithium silicates were composed of SiO<sub>4</sub> tetrahedron structure and lithium oxide as the network modifier. X-ray photoelectron spectroscopy confirmed the chemical states of Li in the thin films were the same with that in standard lithium silicate. With one to one subcycle of Li<sub>2</sub>O and SiO<sub>2</sub> the thin films had a composition close to Li<sub>4</sub>SiO<sub>4</sub> whereas one more subcycle of Li<sub>2</sub>O delivered a higher lithium content. The lithium silicate thin film prepared at 250 °C exhibited an ionic conductivity of 1.45× 10<sup>-6</sup> S cm<sup>-1</sup> at 373 K. The high ionic conductivity of lithium silicate was due to the higher lithium concentration and lower activation energy.
Stress and wafer bending of a-plane GaN layers on r-plane sapphire substrates (2006)

The stress and wafer bending of (112¯0) a-plane GaN layers of different thicknesses grown on (11¯02) r-plane sapphire substrates by hydride vapor phase epitaxy were studied by high-resolution x-ray diffraction and photoluminescence and photoreflectance spectroscopies. The layers are found to be under compression in the growth plane and under tension in the growth direction. The elastic and thermal anisotropies of the GaN and the sapphire crystal result in an in-plane stress and a wafer curvature, both of which are different in the two in-plane directions parallel and perpendicular to the GaN c axis. The GaN unit cell is no longer hexagonal but orthorhombic. The stress relaxes with increasing GaN layer thickness while the curvature of the wafer increases. Different stress relief mechanisms are considered, and the stresses in the layer and the curvature of the wafer are calculated using standard models on wafer bending. The results suggest that the wafer bending is the dominant stress relief mechanism. In addition, the redshift of the near-band-edge photoluminescence and the free exciton photoreflectance peaks with increasing layer thickness is correlated with the strain data determined by x-ray diffraction.
Nutrition Principles for the Management off Diabetes and Related Complications (1994)

Health professionals and people with diabetes recognize nutrition therapy as one of the most challenging aspects of diabetes care and education (1). Adherence to meal planning principles requires the person with diabetes to learn specific nutrition recommendations. It may require altering previous patterns of eating and implementing new eating behaviors, which requires motivation for a healthy lifestyle and may also require participation in exercise programs. Finally, individuals must be able to evaluate the effectiveness of these lifestyle changes. Despite these challenges, nutrition is an essential component of successful diabetes management.
Integrated Photoacoustic Microscopy and Fiber-Optic Confocal Microscopy Using Signal Laser Source (2010)

The back-reflected photons from samples in optical-resolution photoacoustic microscopy are usually discarded and the optical scattering information carried by these photons is therefore ignored. By employing a 2×2 single-mode fiber optical coupler in a laser-scanning optical-resolution photoacoustic microscope for delivering the illuminating laser light and collecting the back reflected photons, a fiber-optic confocal microscope is integrated with the photoacoustic microscope. Hence, simultaneous multimodal imaging can be achieved with a single light source and images from the two modalities are intrinsically registered. Such capabilities are demonstrated in imaging both phantoms and small animals in vivo.
Effect of epinephrine on cerebral and myocardial perfusion in an infant animal preparation of cardiopulmonary resuscitation. (1986)

We assessed the efficacy of conventional cardiopulmonary resuscitation (CPR) in 2-week-old piglets. We determined intrathoracic vascular pressures, cerebral (CBF) and myocardial blood flows (MBF), and cerebral oxygen uptake during conventional CPR in this infant animal preparation and contrasted these results with those of previous work on adult animals. We further examined the effects of the infusion of epinephrine on these pressures and flows and on cerebral oxygen uptake, which has not been previously evaluated in adult preparations. Conventional CPR was performed on pentobarbital-anesthetized piglets with a 20% sternal displacement with the use of a pneumatic piston compressor. Chest recoil was incomplete, leading to an 18% to 27% reduction in anteroposterior diameter during the relaxation phase. Aortic and right atrial pressures in excess of 80 mm Hg were generated. These pressures are greater than those generally obtained in adult animals with similar percent pulsatile displacements. CBF and MBF were also initially greater than those reported in adult animals undergoing conventional CPR. However, when CPR was prolonged beyond 20 min, aortic pressure fell and CBF and MBF declined to the near-zero levels seen in adult preparations. At 5 min of CPR, CBF and MBF were 24 +/- 7 and 27 +/- 7 ml . min-1 x 100 g-1 (50% and 17% of the values during cardiac arrest), respectively. With the continuous infusion of epinephrine (4 micrograms/kg/min) in another group of animals, MBF was significantly greater at 20 min of CPR and CBF and cerebral O2 uptake were greater at 35 min of CPR as a result of higher perfusion pressures.(ABSTRACT TRUNCATED AT 250 WORDS)
Enzyme‐assisted Cell Photosensitization: A Proposal for an Efficient Approach to Tumor Therapy and Diagnosis. The Rose Bengal Fluorogenic Substrate (1997)

Rose bengal, a xanthene derivative among the most efficient producer of singlet oxygen, was submitted to a chemical modification consisting in the introduction of an acetate group into the aromatic ring fluorophore structure. The acetate group acts as a quencher, thus inactivating both fluorescence and photosensitization properties of the molecule. In the modified structure, rose bengal acts as a fluorogenic substrate giving rise to the cellular reaction termed fluorochromasia. The acetate group is recognized by a carboxylic esterase activity that splits it. Removal of the quencher group results in restoring the native structure of photosensitizer inside the cells. The intracellular turnover of rose bengal acetate was studied in rat glioma-derived cultures cells, in terms of the balance of the processes of influx and enzyme hydrolysis of the fluorogenic substrate, and of the efflux of the fluorescent product. A large intracellular accumulation of photosensitizer is obtained when treatments are performed with the fluorogenic substrate, even at the drug concentration at which rose bengal does not enter the cells. The intracellular localization allows rose bengal to exert a more effective photosensitization effect. Provided that the quencher group is selected according to the metabolic properties of the tumor cells, the use of fluorogenic substrates as photosensitizer precursors could improve fluorescence diagnosis and the photodynamic therapy of tumors, exploiting the biological properties that distinguish pathological from normal conditions.
Physiological implications of the substrate specificities of acetohydroxy acid synthases from varied organisms (1990)

Acetohydroxy acid synthase (AHAS; EC 4.1.3.18) catalyzes the following two parallel, physiologically important reactions: condensation of two molecules of pyruvate to form acetolactate (AL), in the pathway to valine and leucine, and condensation of pyruvate plus 2-ketobutyrate to form acetohydroxybutyrate (AHB), in the pathway to isoleucine. We have determined the specificity ratio R with regard to these two reactions (where VAHB and VAL are rates of formation of the respective products) as follows: VAHB/VAL = R [2-ketobutyrate]/[pyruvate] for 14 enzymes from 10 procaryotic and eucaryotic organisms. Each organism considered has at least one AHAS of R greater than 20, and some appear to contain but a single biosynthetic AHAS. The implications of this for the design of the pathway are discussed. The selective pressure for high specificity for 2-ketobutyrate versus pyruvate implies that the 2-ketobutyrate concentration is much lower than the pyruvate concentration in all these organisms. It seems important for 2-ketobutyrate levels to be relatively low to avoid a variety of metabolic interferences. These results also reinforce the conclusion that biosynthetic AHAS isozymes of low R (1 to 2) are a special adaptation for heterotrophic growth on certain poor carbon sources. Two catabolic "pH 6 AL-synthesizing enzymes" are shown to be highly specific for AL formation only (R less than 0.1).
Si single-electron MOS memory with nanoscale floating-gate and narrow channel (2002)

Floating-gate MOS memories based on single electron effect are very attractive, because of the potential quantized threshold voltage shift, quantized charging voltage to create the shift, small device size and fast charging time. However, to relax the challenges in fabricating such devices, previous single-electron MOS memories (SEMMs) had to have nonconventional structures (e.g. a polysilicon channel or a floating gate consisting of many isolated silicon nanocrystals), causing large fluctuation in device dimension and performance and making them unsuitable to ULSI. Here we present the first SEMMs having a narrow crystalline Si channel and a nanoscale poly-Si floating gate of a well controlled dimension. We report that charging of a single electron to the floating gate will lead to, at room temperature, quantized threshold voltage shift, discrete charging voltage, and self-limiting charging process.
Reduced adipose tissue triglyceride synthesis and increased muscle fatty acid oxidation in C5L2 knockout mice (2007)

Activation of C5L2, a G-protein-coupled receptor, by acylation-stimulating protein/complement C3adesArg (ASP/C3adesArg) has been shown to stimulate triglyceride (TG) synthesis in both mature adipocytes and preadipocytes. ASP is an adipocyte-derived hormone that acts by increasing diacylglycerol acyltransferase activity and glucose transport. ASP-deficient mice (C3KO, precursor protein) are lean, display delayed postprandial TG clearance, increased food intake, and increased energy expenditure. The present study shows that C5L2KO mice on a low fat diet are hyperphagic (~60% increase in total food intake) yet maintain the same body weight and adipose tissue mass as wild-type (WT) controls. However, on a high fat diet, average adipocyte size and adipose tissue TG/DNA content were significantly reduced and postprandial TG clearance was delayed in C5L2KO. Adipose tissue TG synthesis (WT: 47.2 +/- 5.6 versus C5L2KO: 7.8 +/- 1.8 pmol/microg protein, P < 0.001), TG lipolysis (WT: 227.6 +/- 36.4 versus C5L2KO: 45.8 +/- 5.0 nmol/microg protein, P < 0.001), and fatty acid re-esterification (WT: 85.3 +/- 2.4% versus C5L2KO: 59.5 +/- 6.8%, P < 0.001) were significantly reduced in C5L2KO mice. Indirect calorimetry measurements revealed C5L2KO mice have unchanged oxygen consumption levels yet reduced respiratory quotient value, suggesting preferential fatty acid utilization over carbohydrate. In agreement, fatty acid oxidation was elevated in heart and skeletal muscle tissue in C5L2KO mice and skeletal muscle levels of uncoupling protein 3 (425.5 +/- 86.3%, P < 0.0001), CD36 (277.6 +/- 49.5%, P < 0.05), cytochrome c (252.6 +/- 33.9%, P < 0.05), and phospho-acetyl CoA carboxylase (118.4 +/- 9.3%, P < 0.05) were significantly increased in C5L2KO mice versus WT (100%). The study shows that in response to reduced TG storage in white adipose tissue, C5L2KO mice have developed a compensatory mechanism of increased muscle fat oxidation.
Pathophysiology of the Clinical Manifestations of Preeclampsia (2007)

Five to 7% of all pregnancies are complicated by preeclampsia. Proteinuria and hypertension dominate the clinical picture, because the chief target organ is the kidney (glomerular endotheliosis). The pathogenesis of preeclampsia is complex; numerous genetic, immunologic, and environmental factors interact. It has been suggested that preeclampsia is a two-stage disease (1). The first stage is asymptomatic, characterized by abnormal placental development during the first trimester resulting in placental insufficiency and the release of excessive amounts of placental materials into the maternal circulation. This in turn leads to the second, symptomatic stage, wherein the pregnant woman develops characteristic hypertension, renal impairment, and proteinuria and is at risk for the HELLP syndrome (hemolysis, elevated liver function enzymes and low platelets), eclampsia, and other end-organ damage. This review focuses on the pathophysiology of stages 1 and 2 and then considers the potential that changes in soluble angiogenic factors may underlie much of the disease process.

On the basis of the observation that the only definitive cure for preeclampsia is delivery of the placenta and that women who experience a molar pregnancy, in which a placenta develops without a fetus, frequently develop severe preeclampsia, it is reasonable to assume that the placenta plays a central role in the pathogenesis of the disease. Pathologic examination of placentas from preeclamptic pregnancies generally reveals placental infarcts and sclerotic narrowing of arteries and arterioles, with characteristic diminished endovascular invasion by cytotrophoblasts and inadequate remodeling of the uterine spiral arterioles (2). Although gross pathologic changes are not always seen in the placentas of women with preeclampsia, placental profiles including abnormal uterine artery Doppler and placental morphology have been used to identify a subset from a cohort of high-risk women who go on to develop the syndrome (3). Uterine artery Doppler studies that assess the pulsatility index (PI) reveal increased …