gebhart/patrepeval huggingface dataset:
Cell dynamics in fetal intestinal epithelium: implications for intestinal growth and morphogenesis (2011)

The cellular mechanisms that drive growth and remodeling of the early intestinal epithelium are poorly understood. Current dogma suggests that the murine fetal intestinal epithelium is stratified, that villi are formed by an epithelial remodeling process involving the de novo formation of apical surface at secondary lumina, and that radial intercalation of the stratified cells constitutes a major intestinal lengthening mechanism. Here, we investigate cell polarity, cell cycle dynamics and cell shape in the fetal murine intestine between E12.5 and E14.5. We show that, contrary to previous assumptions, this epithelium is pseudostratified. Furthermore, epithelial nuclei exhibit interkinetic nuclear migration, a process wherein nuclei move in concert with the cell cycle, from the basal side (where DNA is synthesized) to the apical surface (where mitosis takes place); such nuclear movements were previously misinterpreted as the radial intercalation of cells. We further demonstrate that growth of epithelial girth between E12.5 and E14.5 is driven by microtubule- and actinomyosin-dependent apicobasal elongation, rather than by progressive epithelial stratification as was previously thought. Finally, we show that the actin-binding protein Shroom3 is crucial for the maintenance of the single-layered pseudostratified epithelium. In mice lacking Shroom3, the epithelium is disorganized and temporarily stratified during villus emergence. These results favor an alternative model of intestinal morphogenesis in which the epithelium remains single layered and apicobasally polarized throughout early intestinal development.
Mode-coupling analysis of multipole symmetric resonant add/drop filters (1999)

Time-dependent mode-coupling theory is used to analyze a type of resonant add/drop filter based on the excitation of degenerate symmetric and antisymmetric modes. Flat-top transfer functions are achieved with higher order filters that utilize multiple resonator pairs, designed to satisfy the degeneracy conditions. The resulting analytic expressions lead to an equivalent circuit and the transfer characteristics of the filter are related to standard L-C circuit designs.
Hepatitis B virus envelope variation after transplantation with and without hepatitis B immune globulin prophylaxis (1996)

Hepatitis B virus (HBV) replicates via an intermediate RNA step. High frequency of polymerase errors with additional selection pressure leads to mutations in the HBV genome. We investigated the number, type, and antigenic effects of mutations in the coding region of the HBV surface antigen in eight patients who underwent orthotopic liver transplantation (OLT) for HBV-related end-stage liver disease and were experiencing infection of the graft and who received hepatitis B surface antigen antibody (anti-HBs) prophylaxis (hepatitis B immune globulin [HBIG]) after OLT. Controls were chronic HBV patients who underwent kidney transplantation and received the same immunosuppressive regime but no HBIG. The S-gene was amplified from serum before and after transplantation, sequenced, and changes in the genome were analyzed. In the five patients who experienced reinfection while receiving anti-HBs, clear mutations occurred in the S-gene. In the patient who did not receive HBIG and those who experienced reinfection only after termination of HBIG, no mutations were found in the S-gene. In the kidney recipients, mutations in the S-gene occurred in only one of eight patients. Because the a determinant contains neutralizing epitopes, this region was chosen for antibody binding to quantify antigenic effects of the mutations. The two patients who selected mutations in the a determinant and became reinfected while receiving HBIG had reduced antibody binding after OLT. Our results suggest that HBIG after OLT imposes a selection pressure on the S-gene, and that mutations are one mechanism for reinfection while receiving HBIG.
Performance evaluation of a secure MAC protocol for vehicular networks (2008)

The main benefit of vehicular communication is seen in active safety systems that increase passenger safety by exchanging warning messages between vehicles. Other applications and private services are also permitted in order to lower the cost and to encourage vehicular network deployment and adoption. The allocation of 75 MHz in the 5.9 GHz frequency band licensed for Dedicated Short Range Communications (DSRC), which supports seven separate channels, may also enable the future delivery of rich multimedia contents to vehicles at short- to medium-range via vehicular communications. There are many challenges that must be addressed before vehicular networks can be successfully deployed. Among these challenges is designing of security mechanisms to secure vehicular networks against abuse, and designing of efficient medium access control (MAC) protocols so that safety related and other application messages can be timely and reliably disseminated through vehicular networks. In this paper, we give an overview on a priority based secure MAC protocol for vehicular networks and present detailed security and performance analysis. We show that the MAC protocol can achieve both QoS and security requirements for vehicular network safety applications.
Temperature dependences of optical path length in fluorine-doped silica glass and bismuthate glass (2006)

Temperature dependences of optical path length (<i>dS</i>/<i>dT</i>; calculated using the equation, <i>dS</i>/<i>dT</i> = <i>dn</i>/<i>dT</i> + <i>na</i>, where <i>a</i> is coefficient of thermal expansion, <i>n</i> is refractive index and <i>dn</i>/<i>dT</i> is temperature coefficient of refractive index) in various oxide glasses were investigated. The <i>dS</i>/<i>dT</i> is generally difficult to adjust by change of glass composition because <i>dn</i>/<i>dT</i> and <i>a</i> are interrelated. However, low <i>dS</i>/<i>dT</i> materials are desired for optical applications such as athermal devices, and high <i>dS</i>/<i>dT</i> materials can be used for thermo-optic devices. Pure silica glass is well-known as a typical low <i>dS</i>/<i>dT</i> material but still not sufficient. Fluorine-doped silica glass showed a lower <i>dS</i>/<i>dT</i> than that of pure silica glass. By fluorine-doping in silica glass, refractive index and <i>dn</i>/<i>dT</i> decreased but a near room temperature stayed at the same level. As a result, the <i>dS</i>/<i>dT</i> decreased with increasing fluorine concentration. On the other hand, bismuthate glass showed the highest <i>dS</i>/<i>dT</i> in this study. Most glasses having high <i>a</i> such as tellurite glass showed negative <i>dn</i>/<i>dT</i>. However, bismuthate glasses showed positive dn/dT in spite of high <i>a</i>. As a result, bismuthate glasses showed quite high <i>dS</i>/<i>dT</i>. These results indicate that dS/dT of the glass can be controllable and that fluorine doped silica glass and bismuthate glass are appropriate candidate materials for optical applications.
Potential roles of abundant extracellular chaperones in the control of amyloid formation and toxicity (2007)

The in vivo formation of fibrillar proteinaceous deposits called amyloid is associated with more than 40 serious human diseases, collectively referred to as protein deposition diseases. In many cases the amyloid deposits are extracellular and are found associated with newly identified abundant extracellular chaperones (ECs). Evidence is presented suggesting an important regulatory role for ECs in amyloid formation and disposal in the body. A model is presented which proposes that, under normal conditions, ECs stabilize extracellular misfolded proteins by binding to them, and then guide them to specific cell receptors for uptake and subsequent degradation. Thus ECs and their receptors may be critical parts of a quality control system to protect the body against dangerously hydrophobic proteins/peptides. However, it also appears possible that in the presence of a high molar excess of misfolded protein, such as might occur during disease, the limited amounts of ECs available may actually exacerbate pathology. Further advances in understanding of the mechanisms that control extracellular protein folding are likely to identify new strategies for effective disease therapies.
Tardive Dyskinesia (1986)

Department of Neurological Sciences, Rush-Presbyterian-St. Luke's Medical Center, Chicago, Illinois, U.S.A.
Realizing InGaN monolithic solar-photoelectrochemical cells for artificial photosynthesis (2014)

InGaN alloys are very promising for solar water splitting because they have direct bandgaps that cover almost the whole solar spectrum. The demonstration of direct solar-to-fuel conversion without external bias with the sunlight being the only energy input would pave the way for realizing photoelectrochemical (PEC) production of hydrogen by using InGaN. A monolithic solar-PEC cell based on InGaN/GaN multiple quantum wells capable to directly generate hydrogen gas under zero bias via solar water splitting is reported. Under the irradiation by a simulated sunlight (1-sun with 100 mW/cm2), a 1.5% solar-to-fuel conversion efficiency has been achieved under zero bias, setting a fresh benchmark of employing III-nitrides for artificial photosynthesis. Time dependent hydrogen gas production photocurrent measured over a prolonged period (measured for 7 days) revealed an excellent chemical stability of InGaN in aqueous solution of hydrobromic acid. The results provide insights into the architecture design of using InGaN for artificial photosynthesis to provide usable clean fuel (hydrogen gas) with the sunlight being the only energy input.
Conditional inactivation ofHas2reveals a crucial role for hyaluronan in skeletal growth, patterning, chondrocyte maturation and joint formation in the developing limb (2009)

The glycosaminoglycan hyaluronan (HA) is a structural component of extracellular matrices and also interacts with cell surface receptors to directly influence cell behavior. To explore functions of HA in limb skeletal development, we conditionally inactivated the gene for HA synthase 2, Has2, in limb bud mesoderm using mice that harbor a floxed allele of Has2 and mice carrying a limb mesoderm-specific Prx1-Cre transgene. The skeletal elements of Has2-deficient limbs are severely shortened, indicating that HA is essential for normal longitudinal growth of all limb skeletal elements. Proximal phalanges are duplicated in Has2 mutant limbs indicating an involvement of HA in patterning specific portions of the digits. The growth plates of Has2-deficient skeletal elements are severely abnormal and disorganized, with a decrease in the deposition of aggrecan in the matrix and a disruption in normal columnar cellular relationships. Furthermore, there is a striking reduction in the number of hypertrophic chondrocytes and in the expression domains of markers of hypertrophic differentiation in the mutant growth plates, indicating that HA is necessary for the normal progression of chondrocyte maturation. In addition, secondary ossification centers do not form in the central regions of Has2 mutant growth plates owing to a failure of hypertrophic differentiation. In addition to skeletal defects, the formation of synovial joint cavities is defective in Has2-deficient limbs. Taken together, our results demonstrate that HA has a crucial role in skeletal growth, patterning, chondrocyte maturation and synovial joint formation in the developing limb.
Identification of New Functional Inhibitors of Acid Sphingomyelinase Using a Structure−Property−Activity Relation Model (2007)

Some organic weak bases induce a detachment from inner lysosomal membranes and subsequent inactivation of acid sphingomyelinase (ASM) and thus work as functional ASM inhibitors. The aim of the present investigation was to develop a structure-property-activity relation (SPAR) model in order to specify the structural and physicochemical characteristics of probes capable of functionally inhibiting ASM. High p K a and high log P values are necessary but not sufficient preconditions for functional inhibition of ASM. The experimental data supported the requirement of an additional factor, which is necessary for functional inhibition of ASM. This factor k is related to the steric hindrance of the most basic nitrogen atom and presumably modulates the free presentation of a protonated nitrogen atom at the inner lysosomal surface. During the course of the study, we characterized 26 new functional ASM inhibitors, including doxepine 63, fluoxetine 104, maprotiline 109, nortriptyline 114, paroxetine 118, sertraline 124, suloctidil 125, and terfenadine 127.
Polymorphic Internal Transcribed Spacer Region 1 DNA Sequences Identify Medically Important Yeasts (2001)

Species-specific polymorphisms in the noncoding internal transcribed spacer 2 (ITS2) region of the rRNA operon provide accurate identification of clinically significant yeasts. In this study, we tested the hypothesis that ITS1 noncoding regions contain diagnostically useful alleles. The length of ITS1 region PCR products amplified from 40 species (106 clinical strains, 5 reference strains, and 30 type strains) was rapidly determined with single-base precision by automated capillary electrophoresis. Polymorphisms in the PCR product length permitted 19 species to be distinguished by ITS1 alone, compared with 16 species distinguished by using only ITS2. However, combination of both ITS alleles permitted identification of 30 species (98% of clinical isolates). The remaining 10 species with PCR products of similar sizes contained unique ITS alleles distinguishable by restriction enzyme analysis. DNA sequence analysis of amplified ITS1 region DNA from 79 isolates revealed species-specific ITS1 alleles for each of the 40 pathogenic species examined. This provided identification of unusual clinical isolates, and 53 diagnostic ITS1 sequences were deposited in GenBank. Phylogenetic analyses based on ITS sequences showed a similar overall topology to 26S rRNA gene-based trees. However, different species with identical 26S sequences contained distinct ITS alleles that provided species identification with strong statistical support. Together, these data indicate that the analysis of ITS polymorphisms can reliably identify 40 species of clinically significant yeasts and that the capacity for identifying potentially new pathogenic species by using this database holds significant promise.
Reconstitution of Opsonizing Activity by Infusion of Mannan‐Binding Lectin (MBL) to MBL‐Deficient Humans (1998)

Mannan-binding lectin (MBL, previously named mannan-binding protein, MBP) is a serum collectin, which activates complement upon binding to microbial carbohydrates. This results in opsonization of the microorganisms as well as direct complement-mediated killing. Clinical evidence indicates that MBL has an important role in the innate immune defence against various pathogens. Genetically determined MBL deficiency is associated with increased susceptibility to infections. We have infused two MBL-deficient individuals with clinical grade MBL, purified from pooled donor plasma, in doses sufficient to attain normal concentration of MBL in serum. This resulted in normalization of complement-mediated opsonization. An initial rapid decrease in the serum concentration of MBL was followed by a slower decline with an estimated half-life of about 6 days. No adverse effects were observed and anti-MBL antibodies could not be detected following several MBL infusions. One of the two MBL recipient, a two-year-old girl, who had been suffering from repeated infections from the age of 4 months, was given a total of six MBL infusions. She has subsequently remained healthy for more than three years.
Mixing Weak Learners in Semantic Parsin (2004)

Nine cases with a pneumonitis (alveolitis or interstitial lung disease) have been described so far. In all cases, including ours, HU medication was usually administered over a 3- to 12-week period, mostly for 4 weeks (five of eleven cases). All patients showed a uniform illness with fever (11/11), chills (6/11), reticular or nodular infiltrates on both sides (11/11), small pleural effusions (5/11), and lung symptoms (11/11) such as dyspnea (10/11) or cough (5/11). Due to the acute or subacute onset, all cases were first misinterpreted as bacterial pneumonia.
Molecular Basis for Membrane Selectivity of an Antimicrobial Peptide, Magainin 2 (1995)

Magainin peptides, isolated from Xenopus skin, kill bacteria by permeabilizing their cell membranes whereas they do not lyse erythrocytes. To elucidate the rationale for this membrane selectivity, we compared the effects of the membrane lipid composition and the transmembrane potential on the membrane-lytic power of magainin 2 with that of hemolytic melittin. The activity of magainin to zwitterionic phospholipids constituting the erythrocyte surface was extremely weak compared with that of melittin, and acidic phospholipids are necessary for effective action. The presence of sterols reduced the susceptibility of the membrane to magainin. The generation of an inside-negative transmembrane potential enhanced magainin-induced hemolysis. We can conclude that the absence of any acidic phospholipids on the outer monolayer and the abundant presence of cholesterol, combined with the lack of the transmembrane potential, contribute to the protection of erythrocytes from magainin's attack.
Androgen Stimulation of Nucleotide Pyrophosphatase during Mullerian Duct Regression* (1984)

Mullerian inhibiting substance (MIS) causes regression of the embryonic Mullerian duct. In the fetal rat urogenital ridge, extracellular nucleotide pyrophosphatase (NPPase) can be detected by histochemical staining on the regressing male Mullerian duct, with no corresponding enzyme localization on developing female Mullerian ducts. In vivo results in male embryos can be confirmed in vitro by incubating 14.5-day-gestation female urogenital ridges with MIS and testosterone for 72 h before enzyme localization. Since the addition of testosterone to MIS is obligatory to detect NPPase activity in vitro, and certain steroids enhance Mullerian duct regression, additional steroids were tested in vitro alone or in combination with MIS for their abilities to stimulate NPPase. NPPase induction occurred only with the combinations of MIS and testosterone or MIS and medroxyprogesterone acetate. Neither MIS alone nor any steroid used alone stimulated NPPase activity. The effect of exogenous NPPase added alone to the developing urogenital ridge was also assessed. Incubation of the female urogenital ridge for 72 h with exogenous NPPase caused marked hyperplasia of the Mullerian duct epithelial cells and early mesenchymal cell condensation, without the basement membrane breakdown normally seen in regression. Since NPPase activity is present in the Mullerian duct only during regression, these findings suggest that MIS and fetal androgens are synergistically modulating the activity of this enzyme. Its role in the Mullerian duct, as suggested by its cytological effects, may be to stimulate cellular responses before migration during regression.
Large area dense nanoscale patterning of arbitrary surfaces (2001)

We demonstrate a large-area fabrication of hexagonally ordered metal dot arrays with an area density of ∼1011/cm2. We produced 20 nm dots with a 40 nm period by combining block copolymer nanolithography and a trilayer resist technique. A self-assembled spherical-phase block copolymer top layer spontaneously generated the pattern, acting as a template. The pattern was first transferred to a silicon nitride middle layer by reactive ion etch, producing holes. The nitride layer was then used as a mask to further etch into a polyimide bottom layer. The metal dots were produced by an electron beam evaporation followed by a lift-off process. Our method provides a viable route for highly dense nanoscale patterning of different materials on arbitrary surfaces.
Self‐calibrating parallel imaging with automatic coil sensitivity extraction (2002)

Calibration of the spatial sensitivity functions of coil arrays is a crucial element in parallel magnetic resonance imaging (PMRI). The most common approach has been to measure coil sensitivities directly using one or more low-resolution images acquired before or after accelerated data acquisition. However, since it is difficult to ensure that the patient and coil array will be in exactly the same positions during both calibration scans and accelerated imaging, this approach can introduce sensitivity miscalibration errors into PMRI reconstructions. This work shows that it is possible to extract sensitivity calibration images directly from a fully sampled central region of a variable-density k-space acquisition. These images have all the features of traditional PMRI sensitivity calibrations and therefore may be used for any PMRI reconstruction technique without modification. Because these calibration data are acquired simultaneously with the data to be reconstructed, errors due to sensitivity miscalibration are eliminated. In vivo implementations of self-calibrating parallel imaging using a flexible coil array are demonstrated in abdominal imaging and in real-time cardiac imaging studies.
A simplified method of tumor imaging using 18F-FMAU with PET (2006)

513 Objectives: The kinetic measurements of [18F] FMAU (1-(2’-deoxy-2’-fluoro-beta-D-arabinofuranosyl) thymine) PET were studied to determine the most appropriate and simplest approaches to image acquisition and analysis. The rapid uptake and clearance of FMAU indicate that shortened imaging times and kinetic analysis may be suitable. Methods: Ten patients with brain (n= 4) or prostate tumors (n= 6) were imaged after injection of [18F]FMAU (mean 350 MBq) before therapy. Sixty minute dynamic images were obtained followed by whole body images. Regions of interest were placed on the three adjacent planes with the most visually active area of the tumor and isocontours used to delineate the edges. Mean Standard Uptake Values (SUVmean) and maximum SUV (SUVmax) were determined as the average over the 3 planes from the 5 to 11, 50 to 60, and 30 to 60 min images. For the kinetics analyses, blood activity was measured in 18 samples over 60 min by HPLC to determine tracer metabolism. Tumor retention was calculated as tumor uptake area under the curve (AUC)/ blood FMAU activity AUC. Tissue kinetics of FMAU were measured using a three compartment model. Results: SUVmean 30 to 60 min correlated with the measurements obtained from 5 to 11 and 50 to 60 min (r2=0.91, p Conclusions: Measurement of compartmental K can be replaced by tissue retention measurement in FMAU imaging. Measuring the whole blood activity in the first 11 min is sufficient to calculate the tissue kinetics in FMAU PET imaging. Five blood samples taken in the first 10 min are sufficient for tumor tissue kinetics measurements. The SUVmean and the SUVmax in 11 minute images correlated well with images obtained at 50 to 60 minutes, since the clearance of FMAU is so rapid. The quality of the images and tissue kinetics in 11 minutes of imaging makes it a simple imaging option. Research Support (if any): DOD W81XWH-04-1-0140, NIH CA39566, NCI CA22453
Life Cycle Inventory of Portland Cement Manufacture (2006)

This report is an update of Life Cycle Inventory of Portland Cement Manufacture published in 2002. The purpose of this update is to incorporate the most recent energy use data from the Portland Cement Association’s annual U.S. and Canadian Labor-Energy Input Survey. The results of the latest U.S. Environmental R&D Project Questionnaire also are included. This is a significant update because it includes high quality data on water usage, fuel and raw material consumption, and transportation modes and distances. The goal is to present the most accurate data on the inputs and emissions related to manufacturing portland cement. The LCI of portland cement is the basis of the LCI of concrete, concrete products, and concrete structures. These LCIs are used in turn to conduct life cycle assessments of concrete structures and other structures containing concrete.