gebhart/patrepeval huggingface dataset:
Holographic pixel super-resolution in portable lensless on-chip microscopy using a fiber-optic array (2011)

We report a portable lensless on-chip microscope that can achieve <1 µm resolution over a wide field-of-view of ∼ 24 mm(2) without the use of any mechanical scanning. This compact on-chip microscope weighs ∼ 95 g and is based on partially coherent digital in-line holography. Multiple fiber-optic waveguides are butt-coupled to light emitting diodes, which are controlled by a low-cost micro-controller to sequentially illuminate the sample. The resulting lensfree holograms are then captured by a digital sensor-array and are rapidly processed using a pixel super-resolution algorithm to generate much higher resolution holographic images (both phase and amplitude) of the objects. This wide-field and high-resolution on-chip microscope, being compact and light-weight, would be important for global health problems such as diagnosis of infectious diseases in remote locations. Toward this end, we validate the performance of this field-portable microscope by imaging human malaria parasites (Plasmodium falciparum) in thin blood smears. Our results constitute the first-time that a lensfree on-chip microscope has successfully imaged malaria parasites.
<title>High-Q whispering-gallery mode sensor in liquids</title> (2002)

Optical sensing of biomolecules on microfabricated glass surfaces requires surface coatings that minimize nonspecific binding while preserving the optical properties of the sensor. Microspheres with whispering-gallery (WG) modes can achieve quality factor (Q) levels many orders of magnitude greater than those of other WG-based microsensors: greater than 10<SUP>10</SUP> in air, and greater than 10<SUP>9</SUP> in a variety of solvents, including methanol, H<SUB>2</SUB>O and phosphate buffered saline (PBS). The presence of dyes that absorb in the wavelength of the WG excitation in the evanescent zone can cause this Q value to drop by almost 3 orders of magnitude. Silanization of the surface with mercapto-terminal silanes is compatible with high Q (&gt;10<SUP>9</SUP>), but chemical cross-linking of streptavidin reduces the Q to 10<SUP>5</SUP>-10<SUP>6</SUP> due to build-up of a thick, irregular layer of protein. However, linkage of biotin to the silane terminus preserves the Q at a ~2x10<SUP>7</SUP> and yields a reactive surface sensitive to avidin-containing ligands in a concentration-dependent manner. Improvements in the reliability of the surface chemistry show promise for construction of an ultrasensitive biosensor.
A relationship between proteinuria and acute tubulointerstitial disease in rats with experimental nephrotic syndrome. (1991)

The relationship between tubulointerstitial nephritis and proteinuria was characterized in experimental nephrosis in rats. In one group, proteinuria induced by aminonucleoside of puromycin (PAN) was reduced by using an 8% protein diet and adding the angiotensin I-converting enzyme (ACE) inhibitor enalapril to the drinking water. Two control groups were injected with saline and PAN, respectively, and fed a 27% protein diet. The first group had significantly reduced albuminuria and a definite attenuation of tubular cell injury. There was a strong positive correlation between the number of interstitial macrophages and albuminuria. The beneficial effect was reproduced by dietary-protein restriction alone, whereas ACE inhibition alone had an insignificant effect on the degree of proteinuria. Depletion of circulating T lymphocytes in one group of nephrotic rats eliminated interstitial lymphocytes but did not affect interstitial macrophage influx. Inhibition of the in situ proliferation of resident interstitial macrophages by unilateral kidney irradiation failed to change the intensity of the macrophage infiltration. Treatment of rats with sodium maleate produced proximal tubular cell toxicity but interstitial inflammation did not develop, suggesting that the latter is not a nonspecific response to tubular injury. These studies demonstrate a strong relationship between tubulointerstitial nephritis and the severity of proteinuria in experimental nephrosis.
Total Pancreatectomy and Islet Autotransplantation in Children for Chronic Pancreatitis (2014)

Total pancreatectomy and islet autotransplantation provides sustained pain relief and improved quality of life. The β-cell function is dependent on islet yield. Total pancreatectomy and islet autotransplantation is an effective therapy for children with painful pancreatitis that failed medical and/or endoscopic management.
A Comparison of Nefazodone, the Cognitive Behavioral-Analysis System of Psychotherapy, and Their Combination for the Treatment of Chronic Depression (2000)

Although about half of patients with chronic forms of major depression have a response to short-term treatment with either nefazodone or a cognitive behavioral-analysis system of psychotherapy, the combination of the two is significantly more efficacious than either treatment alone.
Coding of Elevation in Acoustic Image of Space (2005)

Spectral features of sound are believed to be the primary cues for the human perception of spatial sound elevation. It has also been observed that people connect higher frequencies of sound with a higher elevation of the sound source and lower frequencies with lower elevations. The most common approach to creating an acoustic image delivered by headphones is to use Head Related Transfer Functions (HRTFs). Unfortunately, satisfactory perception of elevation can only be achieved with personalized HRTFs which are impractical to measure. This paper describes an alternative method of sound coding for representation of the virtual sound source elevation in an acoustic image. Our method is based on coding particular elevations with sound stimuli which differ in spectral content. Sound stimuli were created by various signal processing techniques (e.g. filtration, modulation). Experiments show that, in certain cases, test subjects were able to perceive up to 60 different elevations in the range of –40 ° to 90°.
A New System, the LipiFlow, for the Treatment of Meibomian Gland Dysfunction (2012)

The LipiFlow System was significantly more effective than iHeat WC. These results support its safety and effectiveness in the treatment of MGD and dry eye symptoms.
End-Cap Stabilized Oligoynes: Model Compounds for the Linear sp Carbon Allotrope Carbyne (2002)

Three series of differently 3,5-disubstituted alpha,omega-diphenylpolyynes Ar-(C[triple bond]C)n-Ar (n=2, 4, 6, 8, 10) were synthesized under optimized Cadiot-Chodkiewicz conditions, isolated and completely characterized. These compounds can be considered as model substances for the hypothetical one-dimensional carbon allotrope carbyne Cx. The longest sp-carbon chain contains 20 atoms and is therefore the longest, purely organic polyyne studied with NMR techniques. Extinction coefficients over 600,000 M(-1) cm(-1) represent the highest measured quantitative values for that compound class so far. Comparisons with previous investigations and electrochemical studies allow the assignment of absorption for both wavelength regions structuring the UV/Vis spectra. Based on the trends in the spectroscopic behaviour of those molecules with increasing chain length, electronic as well as the NMR properties of carbyne are predicted, in line with our previously reported results. The observed stability properties promise the synthesis of even longer polyynes.
Multiple, disparate roles for calcium signaling in apoptosis of human prostate and cervical cancer cells exposed to diindolylmethane (2006)

Diindolylmethane (DIM), derived from indole-3-carbinol in cruciferous vegetables, causes growth arrest and apoptosis of cancer cells in vitro. DIM also induces endoplasmic reticulum (ER) stress, and thapsigargin, a specific inhibitor of the sarcoplasmic reticulum/ER calcium-dependent ATPase, enhances this effect. We asked whether elevated cytosolic free calcium [Ca2+]i is required for cytotoxicity of DIM and thapsigargin in two cancer cells lines (C33A, from cervix, and DU145, from prostate). [Ca2+]i was measured in real-time by FURA-2 fluorescence. We tested whether DIM, thapsigargin, and DIM + thapsigargin cause apoptosis, measured by nucleosome release, under conditions that prevented elevation of [Ca2+]i, using both cell-permeable and cell-impermeable forms of the specific calcium chelator BAPTA. DIM, like thapsigargin, rapidly mobilized ER calcium. C33A and DU145 responded differently to perturbations in Ca2+ homeostasis, suggesting that DIM induces apoptosis by different mechanisms in these two cell lines and/or that calcium mobilization also activates different survival pathways in C33A and DU145. Apoptosis in C33A was independent of increased [Ca2+]i, suggesting that depletion of ER Ca2+ stores may be sufficient for cell killing, whereas apoptosis in DU145 required elevated [Ca2+]i for full response. Inhibitor studies using cyclosporin A and KN93 showed that Ca2+ signaling is important for cell survival but the characteristics of this response also differed in the two cell lines. Our results underscore the complex and variable nature of cellular responses to disrupted Ca2+ homeostasis and suggest that alteration Ca2+ homeostasis in the ER can induce cellular apoptosis by both calcium-dependent and calcium-independent mechanisms.
Glucosamine-derived phospholipids in Escherichia coli. Structure and chemical modification of a triacyl glucosamine 1-phosphate found in a phosphatidylglycerol-deficient mutant. (1983)

Certain Escherichia coli mutants defective in phosphatidylglycerol biosynthesis accumulate novel glucosamine-derived phospholipids. We previously demonstrated that the simplest of these substance (lipid X) is a diacylglucosamine 1-phosphate bearing beta-hydroxymyristoyl groups at positions 2 and 3 (Takayama, K., Qureshi, N., Mascagni, P., Nashed, M. A., Anderson, L., and Raetz, C. R. H. (1983) J. Biol. Chem. 258, 7379-7385). We now report the structural characterization of a triacylglucosamine 1-phosphate (designated lipid Y) that is also found in these mutants. Hydrolyzates of Y contain 2 mol of beta-hydroxymyristate and 1 mol of palmitate/mol of glucosamine. In the lipid, one of the beta-hydroxymyristates is amide-linked at position 2, while the two other fatty acyl groups are ester-linked. Fast atom bombardment mass spectrometry is used to confirm that Y is a monosaccharide derivative and that the molecular weight of Y as the free acid (C50H96NO13P) is 950.29. Analysis of Y by proton NMR spectroscopy at 200 MHz reveals that the anomeric configuration is alpha. Further, one of the esterified fatty acid residues is attached to the 3 OH of the sugar, while the second is linked to an OH moiety of a hydroxymyristate. The 4 and 6 OH groups of the sugar are unsubstituted, as in E. coli lipid X. To establish the precise location of each esterified fatty acyl residue, we subjected Y to a very mild alkaline hydrolysis in the presence of triethylamine. This resulted in the selective removal of a single hydroxymyristoyl group. The triethylamine-treated derivative (lipid Y) has a molecular weight of 723. NMR spectroscopy of Y shows that the 3 OH of the sugar is no longer substituted, while the beta OH of the remaining amide-linked hydroxymyristate is still esterified with palmitate. On the basis of these findings, we propose that lipid Y has the same fundamental structure as lipid X, except for the additional presence of a palmitoyl moiety on the N-linked hydroxymyristate. Presumably, lipid Y is synthesized from X by a selective acylation reaction.
The 5-HT deficiency theory of depression: perspectives from a naturalistic 5-HT deficiency model, the tryptophan hydroxylase 2Arg439Hisknockin mouse (2012)

A decreased level of brain 5-hydroxytryptamine (5-HT) has been theorized to be a core pathogenic factor in depression for half a century. The theory arose from clinical observations that drugs enhancing extracellular levels of 5-HT (5-HT(Ext)) have antidepressant effects in many patients. However, whether such drugs indeed correct a primary deficit remains unresolved. Still, a number of anomalies in putative biomarkers of central 5-HT function have been repeatedly reported in depression patients over the past 40 years, collectively indicating that 5-HT deficiency could be present in depression, particularly in severely ill and/or suicidal patients. This body of literature on putative 5-HT biomarker anomalies and depression has recently been corroborated by data demonstrating that such anomalies indeed occur consequent to severely reduced 5-HT(Ext) levels in a mouse model of naturalistic 5-HT deficiency, the tryptophan hydroxylase 2 His(439) knockin (Tph2KI) mouse. In this review, we will critically assess the evidence for 5-HT deficiency in depression and the possible role of polymorphisms in the Tph2 gene as a causal factor in 5-HT deficiency, the latter investigated from a clinical as well as preclinical angle.
Autochthonous T cells to the rescue: IL-10 directly activates tumor-resident CD8+T cells (2012)

Successful cancer immunotherapy is thought to require de novo priming of tumor specific CD8(+) T cells in lymphatic organs. Contrasting these beliefs, cancer therapy based on interleukin-10 (IL-10) results in tumor rejection without a requirement for T-cell trafficking from lymphatic organs. Rather, IL-10 directly activates autochthonous, tumor-resident CD8(+) T cells.
Inherent-opening-controlled pattern formation in carbon nanotube arrays (2007)

We have introduced inherent openings into densely packed carbon nanotube arrays to study self-organized pattern formation when the arrays undergo a wetting-dewetting treatment from nanotube tips. These inherent openings, made of circular or elongated hollows in nanotube mats, serve as dewetting centres, from where liquid recedes from. As the dewetting centres initiate dry zones and the dry zones expand, surrounding nanotubes are pulled away from the dewetting centres by liquid surface tension. Among short nanotubes, the self-organized patterns are consistent with the shape of the inherent openings, i.e. slender openings lead to elongated trench-like structures, and circular holes result in relatively round nest-like arrangements. Nanotubes in a relatively high mat are more connected, like in an elastic body, than those in a short mat. Small cracks often initialize themselves in a relatively high mat, along two or more adjacent round openings; each of the cracks evolves into a trench as liquid dries up. Self-organized pattern control with inherent openings needs to initiate the dewetting process above the nanotube tips. If there is no liquid on top, inherent openings barely enlarge themselves after the wetting-dewetting treatment.
Antigen-induced Mediator Release in Primates (1991)

We examined the release of bronchoactive mediators into the airways of allergic primates during the acute response to specific antigen inhalation. Twelve adult male cynomolgus monkeys (Macaca fascicularis) with a naturally occurring respiratory sensitivity to inhaled Ascaris suum extract were anesthetized and intubated for each study. Respiratory system resistance (Rrs) and dynamic lung compliance (CLdyn) were measured before and after antigen inhalation, and the release of mediators into the airways was assessed by bronchoalveolar lavage (BAL). BAL samples were concentrated approximately 5-fold before quantitation of LTC4 and PGD2 by RP-HPLC and radioimmunoassay and histamine by a fluorometric assay. Antigen inhalation resulted in a 40-fold increase in BAL levels of i-LTC4 (1.5 +/- 0.7 to 41.6 +/- 12.7 ng, p less than 0.01), a 10-fold increase in i-PGD2 (2.4 +/- 0.9 to 25.9 +/- 5.5 ng, p less than 0.01), and a 20-fold increase in BAL histamine (1.0 +/- 1.5 to 21.4 +/- 2.3 micrograms, p less than 0.01). Dexamethasone (n = 7) inhibited the antigen-induced increase in BAL i-LTC4 (71 +/- 6%, p less than 0.01) and i-PGD2 (52 +/- 8%, p less than 0.05) while weakly inhibiting histamine release (43 +/- 10%). Indomethacin (n = 7) had a variable effect on i-LTC4 levels (6 +/- 51%), strongly inhibited i-PGD2 (88 +/- 9%, p less than 0.01), and had no effect on histamine release (25 +/- 8%). Pretreatment with iodoxamide tromethamine significantly blocked the release of each mediator, but mepyramine, an H1 antagonist, had no effect on mediator release.(ABSTRACT TRUNCATED AT 250 WORDS)
Characterization of the major hydroperoxide-reducing activity of human plasma. Purification and properties of a selenium-dependent glutathione peroxidase. (1987)

We have recently characterized the major hydroperoxide-reducing enzyme of human plasma as a glutathione peroxidase (Maddipati, K. R., Gasparski, C., and Marnett, L. J. (1987) Arch. Biochem. Biophys. 254, 9-17). We now report the purification and kinetic characterization of this enzyme. The purification steps involved ammonium sulfate precipitation, hydrophobic interaction chromatography on phenyl-Sepharose, anion exchange chromatography, and gel filtration. The purified peroxidase has a specific activity of 26-29 mumol/min/mg with hydrogen peroxide as substrate. The human plasma glutathione peroxidase is a tetramer of identical subunits of 21.5 kDa molecular mass as determined by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and is different from human erythrocyte glutathione peroxidase. The plasma peroxidase is a selenoprotein containing one selenium per subunit. Unlike several other glutathione peroxidases this enzyme exhibits saturation kinetics with respect to glutathione (Km for glutathione = 4.3 mM). The peroxidase exhibits high affinity for hydroperoxides with Km values ranging from 2.3 microM for 13-hydroperoxy-9,11-octadecadienoic acid to 13.3 microM for hydrogen peroxide at saturating glutathione concentration. These kinetic parameters are suggestive of the potential of human plasma glutathione peroxidase as an important regulator of plasma hydroperoxide levels.
A Differential Effect of Bone Morphogenetic Protein-2 and Vascular Endothelial Growth Factor Release Timing on Osteogenesis at Ectopic and Orthotopic Sites in a Large-Animal Model (2012)

In bone tissue engineering, growth factors are widely used. Bone morphogenetic proteins (BMPs) and vascular endothelial growth factor (VEGF) are the most well-known regulators of osteogenesis and angiogenesis. We investigated whether the timing of dual release of VEGF and BMP-2 influences the amount of bone formation in a large-animal model. Poly(lactic-co-glycolic acid) (PLGA) microparticles (MPs) were loaded with BMP-2 or VEGF to create sustained-release profiles, and rapidly degrading gelatin was loaded with either growth factor for fast-release profiles. To study in vivo osteogenicity, the two delivery vehicles were combined with biphasic calcium phosphate (BCP) scaffolds and implanted in 10 Beagle dogs for 9 weeks, at both ectopic (paraspinal muscles) and orthotopic sites (critical-size ulnar defect). The 9 ectopic groups contained combined or single BMP/VEGF dosage, in sustained- or fast-release profiles. In the ulnae of 8 dogs, fast VEGF and sustained BMP-2 were applied to one leg, and the other received the opposite release profiles. The two remaining dogs received bilateral control scaffolds. Bone growth dynamics was analyzed by fluorochrome injection at weeks 3, 5, and 7. Postoperative and posteuthanization X-rays of the ulnar implants were taken. After 9 weeks of implantation, bone quantity and bone growth dynamics were studied by histology, histomorphometry, and fluorescence microscopy. The release of the growth factors resulted in both enhanced orthotopic and ectopic bone formation. Bone formation started before 3 weeks and continued beyond 7 weeks. The ectopic BMP-2 fast groups showed significantly more bone compared to sustained release, independent of the VEGF profile. The ulna implants revealed no significant differences in the amount of bone formed. This study shows that timing of BMP-2 release largely determines speed and amount of ectopic bone formation independent of VEGF release. Furthermore, at the orthotopic site, no significant effect on bone formation was found from a timed release of growth factors, implicating that timed-release effects are location dependent.
Humanized mice for the study of type 1 and type 2 diabetes (2011)

The availability of immunodeficient mice engrafted with functional human immune systems and islets permits in vivo study of human diabetes without putting patients at risk.
Ascorbate content of wheat leaves is not determined by maximal l‐galactono‐1,4‐lactone dehydrogenase (GalLDH) activity under drought stress (2005)

ABSTRACT Although ascorbic acid (AA) is a high‐abundance metabolite, relatively little is known about the factors controlling its accumulation in leaves. To address this issue, we examined the role of l ‐galactono‐1,4‐lactone dehydrogenase (GalLDH), the enzyme which catalyses the last step of this pathway, in the control of AA content under optimal and stress conditions. In a range of species, no clear relationship between AA content and leaf GalLDH protein and activity was found under optimal growth conditions. To explore the effect of drought stress on GalLDH activity and protein content, wheat ( Triticum aestivum L.) was selected for detailed analysis, using two cultivars that differ in their constitutive AA level. In well‐watered plants, the AA content of cv Buck Chambergo (BCH) was over twice that of cv Cooperativa Maipún (CM) but dehydroascorbic acid content was similar in both cv. In agreement with this, dehydroascorbate reductase and glutathione reductase activities were higher in cv BCH than in cv CM, indicating a higher capacity for AA regeneration. Neither leaf DHA content nor activities of AA regenerating enzymes were modified by drought. Although drought caused a substantial increase in GalLDH protein and activity in the low AA cv CM, this treatment had no effect on these parameters in cv BCH. Notably, leaf AA content was unaffected by drought in either cv. These results suggest that GalLDH protein and activity cannot be used as an indicator for changes in the capacity for ascorbate biosynthesis and that AA biosynthesis is constrained by other factors under stress. This can be explained by the importance of regeneration in maintaining AA levels and possibly also by redox regulation of GalLDH.