gebhart/patrepeval huggingface dataset:
Recellularization of Well-Preserved Acellular Kidney Scaffold Using Embryonic Stem Cells (2013)

For chronic kidney diseases, there is little chance that the vast majority of world's population will have access to renal replacement therapy with dialysis or transplantation. Tissue engineering would help to address this shortcoming by regeneration of damaged kidney using naturally occurring scaffolds seeded with precursor renal cells. The aims of the present study were to optimize the production of three-dimensional (3D) rat whole-kidney scaffolds by shortening the duration of organ decellularization process using detergents that avoid nonionic compounds, to investigate integrity of extracellular matrix (ECM) structure and to enhance the efficacy of scaffold cellularization using physiological perfusion method. Intact rat kidneys were successfully decellularized after 17 h perfusion with sodium dodecyl sulfate. The whole-kidney scaffolds preserved the 3D architecture of blood vessels, glomeruli, and tubuli as shown by transmission and scanning electron microscopy. Micro-computerized tomography (micro-CT) scan confirmed integrity, patency, and connection of the vascular network. Collagen IV, laminin, and fibronectin staining of decellularized scaffolds were similar to those of native kidney tissues. After infusion of whole-kidney scaffolds with murine embryonic stem (mES) cells through the renal artery, and pressure-controlled perfusion with recirculating cell medium for 24 and 72 h, seeded cells were almost completely retained into the organ and uniformly distributed in the vascular network and glomerular capillaries without major signs of apoptosis. Occasionally, mES cells reached peritubular capillary and tubular compartment. We observed the loss of cell pluripotency and the start of differentiation toward meso-endodermal lineage. Our findings indicate that, with the proposed optimized protocol, rat kidneys can be efficiently decellularized to produce renal ECM scaffolds in a relatively short time, and rapid recellularization of vascular structures and glomeruli. This experimental setup may open the possibility to obtain differentiation of stem cells with long lasting in vitro perfusion.
Interferon standardization and designations. (1997)

A large number of different human and nonhuman interferon (IFN) preparations are now available for either research purposes or commercial use. Consistency of results can be achieved only through rigorous application of biologic standards and individual species designation. International standards for the potency determinations of these preparations have been produced in accordance with World Health Organization (WHO) guidelines and are available for calibrating assays. Until recently, potency has been assessed purely as a measure of antiviral activity expressed in international units. Other biologic properties are now also being considered, including antiproliferation and immunomodulation. Indirect methods of measuring IFN, such as radioimmunoassay or enzyme immunoassay, if fully validated, may also provide useful estimates of function. Reference antisera are useful for characterizing IFN preparations and for monitoring neutralization assays for detecting anti-IFN antibodies but should not have a function in assay calibration. Factors to be considered when referring to specific designations for pure IFN species include distinctions for the species of origin, any mutant or hybrid forms, the method of production, and the presence of additional glycosylation.
From Plasmon Spectra of Metallic to Vibron Spectra of Dielectric Nanoparticles (2012)

Light interacts surprisingly differently with small particles than with bulk or gas phase materials. This can cause rare phenomena such as the occurence of a "blue moon". Spectroscopic particle phenomena of similar physical origin have also spawned countless applications ranging from remote sensing to medicine. Despite the broad interest in particle spectra, their interpretation still poses many challenges. In this Account, we discuss the challenges associated with the analysis of infrared, or vibron, extinction spectra of small dielectric particles. The comparison with the more widely studied plasmon spectra of metallic nano-particles reveals many common features. The shape, size, and architecture of particles influence the band profiles in vibron and plasmon spectra in similar ways. However, the molecular structure of dielectric particles produces infrared spectral features that are more diverse and detailed or even unique to vibron spectra. More complexity means higher information content, but that also makes the spectra more difficult to interpret. Conventional models such as classical electromagnetic theory with a continuum description of the wavelength-dependent optical constants are often no longer applicable to these spectra. In cases where accurate optical constants are not available and for ultrafine particles, where the molecular structure and quantum effects become essential, researchers must resort to molecular models for light-particle interaction that do not require the prior knowledge of optical constants. In this Account, we illustrate how vibrational exciton approaches combined with molecular dynamics simulations and solid-state density functional calculations provide a viable solution to these challenges. Molecular models reveal two important characteristics of vibron spectra of small molecularly structured particles. The band profiles in vibron spectra are largely determined by transition dipole coupling between the molecules in a particle. Below a specific particle size limit, conventional models fail. Molecular models explain many other phenomena in particle spectra, such as size, shape, and mixing effects, providing the foundation for a better understanding of the interaction of solar radiation with aerosols and clouds and for the design of dielectric nanomaterials.
An Ethical Debate: Elective ventilation of potential organ donors (1995)

Elective ventilation describes the procedure of transferring selected patients dying from rapidly progressive intracranial haemorrhage from general medical wards to intensive care units for a brief period of ventilation before confirmation of brain stem death and harvesting of organs. This approach in Exeter has led to a rate of kidney retrieval and transplant higher than has been achieved elsewhere in the United Kingdom, with a stabilisation of numbers on patients on dialysis. Recently doubt has been cast on the legality of our practice of elective ventilation on the grounds that relatives are not permitted to consent to treatment of an incompetent person when that treatment is not in the patient's best interests. We are thus faced with the dilemma of a protocol that is ethical, practical, and operates for the greater good but which may be illegal. This article explores various objections to the protocol and calls for public, medical, and legal debate on the issues.
Real-time compensation of the refractive index of air in distance measurement (2015)

A two-color scheme of heterodyne laser interferometer is devised for distance measurements with the capability of real-time compensation of the refractive index of the ambient air. A fundamental wavelength of 1555 nm and its second harmonic wavelength of 777.5 nm are generated, with stabilization to the frequency comb of a femtosecond laser, to provide fractional stability of the order of 3.0 × 10(-12) at 1 s averaging. Achieved uncertainty is of the order of 10(-8) in measuring distances of 2.5 m without sensing the refractive index of air in adverse environmental conditions.
The IQGAP1-Rac1 and IQGAP1-Cdc42 Interactions (2007)

IQGAP1 contains a domain related to the catalytic portion of the GTPase-activating proteins (GAPs) for the Ras small G proteins, yet it has no RasGAP activity and binds to the Rho family small G proteins Cdc42 and Rac1. It is thought that IQGAP1 is an effector of Rac1 and Cdc42, regulating cell-cell adhesion through the E-cadherin-catenin complex, which controls formation and maintenance of adherens junctions. This study investigates the binding interfaces of the Rac1-IQGAP1 and Cdc42-IQGAP1 complexes. We mutated Rac1 and Cdc42 and measured the effects of mutations on their affinity for IQGAP1. We have identified similarities and differences in the relative importance of residues used by Rac1 and Cdc42 to bind IQGAP1. Furthermore, the residues involved in the complexes formed with IQGAP1 differ from those formed with other effector proteins and GAPs. Relatively few mutations in switch I of Cdc42 or Rac1 affect IQGAP1 binding; only mutations in residues 32 and 36 significantly decrease affinity for IQGAP1. Switch II mutations also affect binding to IQGAP1 although the effects differ between Rac1 and Cdc42; mutation of either Asp-63, Arg-68, or Leu-70 abrogate Rac1 binding, whereas no switch II mutations affect Cdc42 binding to IQGAP1. The Rho family "insert loop" does not contribute to the binding affinity of Rac1/Cdc42 for IQGAP1. We also present thermodynamic data pertaining to the Rac1/Cdc42-RhoGAP complexes. Switch II contributes a large portion of the total binding energy to these complexes, whereas switch I mutations also affect binding. In addition we identify "cold spots" in the Rac1/Cdc42-RhoGAP/IQGAP1 interfaces. Competition data reveal that the binding sites for IQGAP1 and RhoGAP on the small G proteins overlap only partially. Overall, the data presented here suggest that, despite their 71% identity, Cdc42 and Rac1 appear to have only partially overlapping binding sites on IQGAP1, and each uses different determinants to achieve high affinity binding.
Etching of GaN Using Phosphoric Acid (1976)

Hot phosphoric acid is found to be useful for etching and characterizing epitaxial crystals grown on (0001) sapphire substrates. The obtained etch rates are 0.2–1.0 μm/min and the activation energy is about 4.4 kcal/mole in the temperature region of 50°–200°C. Hydration of Ga ion is considered the rate‐determining step of the etching action. The x‐ray diffraction and the infrared spectrometric studies indicate that the ortho and meta phosphoric ions play an important role as attacking ions in etching. This phosphoric acid etching reveals crystal defects in undoped (n), Zn‐doped (i), and i‐n structure epitaxial crystals. Conical hexagonal pyramid pits and truncated hexagonal pits develop in the undoped layers, and they tend to be arranged along the slip direction and are attributed to certain dislocations. These hexagonal pits are densely generated near the interface of the epitaxial layer and the substrate. The density of the pits decreases exponentially with crystal growth. The pits are apt to increase in density and size when the carrier concentration is high (1019–1020 cm3). The rounded etch figures develop in Zn‐doped crystals and sometimes in the undoped crystals with a high carrier concentration (1019 cm−3). Etching also indicates that there is a significant difference in growth patterns between the Zn‐doped and the undoped crystals even if the Zn‐doped layer is continuously deposited on the undoped layer. This implies a difference in the crystal growth mechanism between these crystals.
Intense (18)F-FDG uptake in brown fat can be reduced pharmacologically. (2004)

This rodent study demonstrated that BAT can exhibit high (18)F-FDG uptake under stimulated conditions including exposure to cold and that propranolol or reserpine treatment can remarkably reduce the high (18)F-FDG uptake in BAT. The effect of these drugs on (18)F-FDG uptake in human BAT, as well as on tracer accumulation in other organs, should carefully be evaluated clinically to minimize the USA-Fat artifact.
Fibronectin 1 protein expression in clear cell renal cell carcinoma (2012)

Fibronectin 1 (FN1) is a glycoprotein that is involved in cell adhesion and migration processes including embryogenesis, wound healing, blood coagulation, host defenses and metastasis. The aim of this study was to elucidate the FN1 protein expression in renal cell carcinoma (RCC) and to determine its potential prognostic relevance. A total of 270 clear cell RCC tissue specimens were collected from patients undergoing surgery for renal tumors. Biomarker expression was determined by immunohistochemistry and correlated with clinical variables. Survival analysis was carried out for 153 patients with complete follow-up data and pathologically proven clear cell carcinoma of the kidney. The follow-up group had a mean follow-up period of 83.8 months (IQR 26.2-136.2 months). The calculated median 5-year overall and tumor-specific survival rate of all 153 evaluable patients was 66.6 and 71.0%, respectively. A higher disease-related mortality rate was observed among patients with cytoplasmic FN1 expression (41.3 vs. 24.7%, p=0.039, Fisher's exact test). No significant correlation was found between FN1 staining and patient characteristics such as age, gender, tumor differentiation and visceral metastasis. However, there was a trend for FN1 expression and correlation with tumor stage and lymph node metastasis (p=0.085 and p=0.203; respectively). The Kaplan-Meier analysis revealed significant differences in the 5-year tumor-specific survival for patients with and without cytoplasmic FN1 expression (64.8 vs. 77.7%; p=0.035, log-rank test). However, results of the multivariate Cox regression analysis showed that FN1 expression was not an independent marker of either overall or tumor-specific survival. In conclusion, FN1 protein expression in RCC is associated with a higher disease-related mortality rate, indicating a possible role in RCC progression. Therefore, our data on FN1 encourage further investigations to determine the role of FN1 in RCC.
Hair growth induction by ultraviolet radiation in the marsupial Monodelphis domestica (1987)

• Hair follicles in the telogen stage of the hair cycle were induced into anagen phase after the skin of the South American opossum,<i>Monodelphis domestica</i>, was exposed to levels of ultraviolet B radiation (280 to 320 nm), which induced desquamation. Post-ultraviolet B exposure to long-wavelength radiation (320 to 400 nm, ultraviolet A) suppressed the induction of edema and desquamation and the induction of hair growth. Hair growth induction was also observed in skin damaged either by mechanical abrasion or by exposure to methoxsalen and ultraviolet A. (<i>Arch Dermatol</i>1987;123:1032-1035)
Comparison of intravascular and conventional hypothermia after cardiac arrest. (2011)

The presented technique of intravascular hypothermia provides more precise temperature control in comparison with the traditional method.
Oxidant stress and constrictor reactivity impair cerebral artery dilation in obese Zucker rats (2004)

This study tested the hypothesis that evolution of the metabolic syndrome in obese Zucker rats (OZR) leads to impaired dilator reactivity of cerebral resistance arteries vs. responses determined in lean Zucker rats (LZR). Middle cerebral arteries (MCA) from 17-wk-old male LZR and OZR were isolated and cannulated with glass micropipettes. Vascular reactivity was assessed in response to challenge with ACh, sodium nitroprusside (SNP), reductions and elevations in Po2, 5-HT, and increased intralumenal pressure. Vessels were treated with the free radical scavenger 4-hydroxy-2,2,6,6-tetramethylpiperidine 1-oxyl (tempol) to assess the role of superoxide production in altering reactivity, and passive vascular wall mechanics was assessed in each vessel. Vascular superoxide production was assessed in isolated arteries using fluorescence microscopy. Vessel dilation to ACh and hypoxia was impaired in OZR vs. LZR, although responses to SNP were normal. Vessel constriction to 5-HT, elevated Po2, and elevated intralumenal pressure was enhanced in OZR vs. LZR. Fluorescence microscopy demonstrated an increased superoxide production in arteries of OZR vs. LZR, correctable by incubation with tempol. Although treatment of vessels from OZR with tempol improved dilation to ACh and hypoxia, constrictor responses to 5-HT, elevated Po2, and pressure were not altered by tempol treatment. Indexes of vessel wall mechanics were comparable between groups. These results suggest that vasodilator reactivity of MCA of OZR in response to endothelium-dependent dilator stimuli is impaired vs. LZR and that this may represent a reduced bioavailability of signaling molecules due to oxidant scavenging. However, oxidative stress-independent increases in myogenic tone and constrictor reactivity may contribute to blunted dilator responses of cerebral microvessels.
All-Printed and Roll-to-Roll-Printable 13.56-MHz-Operated 1-bit RF Tag on Plastic Foils (2010)

An all-printed rectifier that can provide at least 10 V dc from a 13.56-MHz radio frequency identification (RFID) reader and an all-printed ring oscillator that can generate at least 100 Hz of clock signal to read a 96-bit RFID tag in a second under the dc power provided by the rectifier should first be printable on plastic foils for the realization of roll-to-roll (R2R) printed ultralow cost RFID tags. Here, we describe a practical way to provide all-printed and R2R-printable antenna, rectifiers, and ring oscillators on plastic foils and demonstrate 13.56-MHz-operated 1-bit RF tags. The all-printed and R2R-printable 13.56-MHz 1-bit tags can generate 102.8 Hz of clock signal as the tag approaches the 13.56-MHz RFID reader.
Treatment of functional dyspepsia with serotonin agonists: A meta‐analysis of randomized controlled trials (2006)

Abstract Background: Functional dyspepsia (FD) is often treated with serotonin agonists; however, the efficacy of such agents has recently been questioned. The aim of this study was to perform a meta‐analysis of randomized controlled trials (RCTs) comparing serotonin agonists with other types of prokinetics in patients with FD. Methods: Included studies were RCTs that compared serotonin agonists, including cisapride and mosapride, with dopamine antagonists, including metoclopramide and domperidone, and an opiate agonist, trimebutine, in patients with FD. Studies were identified by searching the Medline database (January 1951 – January 2005) and Cochrane Library (Issue 4, 2004), and by manual searches. The difference in the probability of patients' responses between the serotonin agonists and control agents was used as a summary statistic for the treatment effect. Meta‐regression analysis was used to detect sources of heterogeneity. Results: Five studies were identified. In total, 467 subjects were assigned to a serotonin agonist arm, and 322 subjects were assigned to a control arm. In the overall analysis, the summary statistic was 0.019 (95% confidence interval [CI]: −0.055 to 0.093; P = 0.612), indicating that the patients' responses to serotonin agonists were similar to those to control agents. However, in the stratified meta‐analysis of cisapride and mosapride, mosapride had a 6.7% greater probability of producing a response compared with control agents (summary statistic: 0.067; 95% CI: 0.010–0.124; P = 0.021), whereas no significant effect was observed with cisapride. Conclusion: The data suggest that mosapride may be more effective than cisapride for the treatment of FD. Although FD is a chronic condition, efficacy was assessed over short periods in the studies used for the present meta‐analysis. Long‐term RCTs are needed to confirm the effect.
Cyclic Diguanylate Is a Ubiquitous Signaling Molecule in Bacteria: Insights into Biochemistry of the GGDEF Protein Domain (2005)

Proteins containing GGDEF domains are encoded in the majority of sequenced bacterial genomes. In several species, these proteins have been implicated in biosynthesis of exopolysaccharides, formation of biofilms, establishment of a sessile lifestyle, surface motility, and regulation of gene expression. However, biochemical activities of only a few GGDEF domain proteins have been tested. These proteins were shown to be involved in either synthesis or hydrolysis of cyclic-bis(3'-->5') dimeric GMP (c-di-GMP) or in hydrolysis of cyclic AMP. To investigate specificity of the GGDEF domains in Bacteria, six GGDEF domain-encoding genes from randomly chosen representatives of diverse branches of the bacterial phylogenetic tree, i.e., Thermotoga, Deinococcus-Thermus, Cyanobacteria, spirochetes, and alpha and gamma divisions of the Proteobacteria, were cloned and overexpressed. All recombinant proteins were purified and found to possess diguanylate cyclase (DGC) activity involved in c-di-GMP synthesis. The individual GGDEF domains from two proteins were overexpressed, purified, and shown to possess a low level of DGC activity. The oligomeric states of full-length proteins and individual GGDEF domains were similar. This suggests that GGDEF domains are sufficient to encode DGC activity; however, enzymatic activity is highly regulated by the adjacent sensory protein domains. It is shown that DGC activity of the GGDEF domain protein Rrp1 from Borrelia burgdorferi is strictly dependent on phosphorylation status of its input receiver domain. This study establishes that majority of GGDEF domain proteins are c-di-GMP specific, that c-di-GMP synthesis is a wide-spread phenomenon in Bacteria, and that it is highly regulated.
Molecular basis of Sindbis virus neurovirulence in mice (1988)

We examined a variety of strains of Sindbis virus for the genetic changes responsible for differences in neurovirulence in mice. SV1A (a low passage of the AR339 strain of Sindbis virus), a neuroadapted Sindbis virus (NSV), and two laboratory strains of Sindbis virus (HRSP and Toto1101) were examined. NSV causes severe encephalomyelitis with hind-limb paralysis and high mortality after intracerebral inoculation in weanling mice. In contrast, SV1A causes only mild, nonfatal disease in weanling mice; however, in suckling mice, SV1A causes a fatal encephalomyelitis after either intracerebral or subcutaneous inoculation. The two laboratory strains used have a greatly reduced neurovirulence for suckling mice and are avirulent for weanling mice. The nucleotide sequences and encoded amino acid sequences of the structural glycoproteins of these four strains were compared. Hybrid genomes were constructed by replacing restriction fragments in a full-length cDNA clone of Sindbis virus, from which infectious RNA can be transcribed in vitro, with fragments from cDNA clones of the various strains. These recombinant viruses allowed us to test the importance of each amino acid difference between the various strains for neurovirulence in weanling and suckling mice. Glycoproteins E2 and E1 were of paramount importance for neurovirulence in adult mice. Recombinant viruses containing the nonstructural protein region and the capsid protein region from an avirulent strain and the E1 and E2 glycoprotein regions from NSV were virulent, although they were less virulent than NSV. Furthermore, changes in either E2 (His-55 in NSV to Gln in SV1A) or E1 (Ala-72 in NSV to Val in SV1A and Asp-313 in NSV to Gly in SV1A) reduced virulence. For virulence in suckling mice, we found that a number of changes in E2 and E1 can lead to decreased virulence and that in fact, a gradient of virulence exists.
Physiological effects of HIV infection on human intestinal epithelial cells (1994)

These results suggest that absorptive and secretory function of enterocytes may be altered by direct HIV infection and that additional physiologic experiments with this in vitro model may lead to a better understanding of the clinical syndrome of HIV enteropathy.
Ultra-compact Si-SiO2 microring resonator optical channel dropping filters (1998)

Compact optical channel dropping filters incorporating side-coupled ring resonators as small as 3 μm in radius are realized in silicon technology. Quality factors up to 250, and a free-spectral range (FSR) as large as 24 nm are measured. Such structures can be used as fundamental building blocks in more sophisticated optical signal processing devices.