Miracle-dz/UniFAR-FTUs huggingface dataset:
Immunohistochemical Localization of Protein Gene Product 9.5, Ubiquitin, and Neuropeptide Y Immunoreactivities in Epithelial and Neuroendocrine Cells from Normal and Hyperplastic Human Prostate

This study was designed to investigate (a) the presence of protein gene product 9.5 (PGP 9.5), ubiquitin, and neuropeptide Y (NPY) in the neuroendocrine and secretory epithelium of the human normal prostate and its secretions, and (b) the changes in immunoreactivity to these proteins in men with benign prostatic hyperplasia. Western blotting and light microscopic immunohistochemistry techniques were used and the numerical density of immunoreactive neuroendocrine cells, and the volume fractions of immunostained secretory epithelium were evaluated. Western blotting revealed the presence of the three antigens in both tissue homogenates and prostate secretion. Some neuroendocrine cells immunoreacted to PGP 9.5 and NPY in all the prostate regions of control specimens. Ubiquitin immunoreactivity was detected in the nuclei from both basal cells and secretory epithelial cells. The cytoplasm of the secretory cells and the glandular lumen also showed immunostaining for the three proteins. The numerical densities of both PGP 9.5 and NPY neuroendocrine cells were lower in hyperplasia than in controls. No differences in the volume fraction occupied by epithelial immunostaining to both proteins was found between hyperplastic and control prostates. We concluded that (a) PGP 9.5 and NPY, but not ubiquitin, are common antigens in both neuroendocrine and secretory prostate cells, (b) the three immunoreactive proteins contribute to the prostate secretions, and (c) the secretion of ubiquitin is markedly diminished in the hyperplastic epithelium. (J Histochem Cytochem 48:1121–1130, 2000)
DISCOVERY OF A COMPANION CANDIDATE IN THE HD 169142 TRANSITION DISK AND THE POSSIBILITY OF MULTIPLE PLANET FORMATION

We present L′- and J-band high-contrast observations of HD 169142, obtained with the Very Large Telescope/NACO AGPM vector vortex coronagraph and the Gemini Planet Imager, respectively. A source located at 0. ″156 ± 0. ″032 north of the host star (P.A. = 7.°4 ± 11.°3) appears in the final reduced L′ image. At the distance of the star (∼145 pc), this angular separation corresponds to a physical separation of 22.7 ± 4.7 AU, locating the source within the recently resolved inner cavity of the transition disk. The source has a brightness of L′ = 12.2 ± 0.5 mag, whereas it is not detected in the J band (J >13.8 mag). If its L′ brightness arose solely from the photosphere of a companion and given the J − L′ color constraints, it would correspond to a 28–32 MJupiter object at the age of the star, according to the COND models. Ongoing accretion activity of the star suggests, however, that gas is left in the inner disk cavity from which the companion could also be accreting. In this case, the object could be lower in mass and its luminosity enhanced by the accretion process and by a circumplanetary disk. A lower-mass object is more consistent with the observed cavity width. Finally, the observations enable us to place an upper limit on the L′-band flux of a second companion candidate orbiting in the disk annular gap at ∼50 AU, as suggested by millimeter observations. If the second companion is also confirmed, HD 169142 might be forming a planetary system, with at least two companions opening gaps and possibly interacting with each other.
Mr perfusion studies with t1‐weighted echo planar imaging

The T1 perfusion model has worked well in brain functional studies where flow changes are measured. Using selective and nonselective inversion pulses, a new method has been developed to study steady‐state brain blood flow. The authors obtained flow‐sensitive images using selective inversion and flow‐insensitive images using nonselective inversion. Subtraction of flow‐insensitive images from flow‐sensitive images gave us flow‐weighted images with good gray‐white flow contrast in cortical gray matter as well as in the thalamus and basal ganglia. Fitting T1S of flow‐insensitive and flow‐sensitive images allowed us to obtain preliminary results of brain blood flow maps. Two specific problems can seriously affect the accuracy of the brain blood flow values and the gray‐white flow contrast of brain blood flow maps. These are the problems of the partial volume effect of CSF and gray matter, and the difference between blood T1 and white matter T1. The authors discuss in detail the character of these problems and present a number of approaches to manage such problems.
Effect of multiple-micronutrient supplementation on maternal nutrient status, infant birth weight and gestational age at birth in a low-income, multi-ethnic population

Poor nutrient intake during pregnancy can adversely affect both infant and maternal health. The aim was to investigate the efficacy of multiple-micronutrient supplementation during pregnancy in a socially deprived population in the developed world. We conducted a randomised, double-blind, placebo-controlled trial of multiple-micronutrient supplementation including 20 mg Fe and 400 μg folic acid, from the first trimester of pregnancy in 402 mothers, in East London, UK. Nutrient status was measured at recruitment, and at 26 and 34 weeks of gestation. Infants were weighed at birth. At recruitment the prevalence of anaemia was 13 %, vitamin D insufficiency 72 %, thiamin deficiency 12 % and folate deficiency 5 %, with no differences between groups. Only 39 % of women completed the study; rates of non-compliance were similar in both groups. Intention-to-treat analysis showed that participants receiving treatment had higher mean Hb at 26 weeks of gestation (110 (sd 10) v.108 (sd 10) g/l; P = 0·041) and 34 weeks of gestation (113 (sd 12) v.109 (sd 10) g/l; P = 0·003) and packed cell volume concentrations at 26 weeks of gestation (0·330 (sd 0·025) v. 0·323 (sd 0·026) l/l; P = 0·011) and 34 weeks of gestation (0·338 (sd 0·029) v. 0·330 (sd 0·028) l/l; P = 0·014) compared with controls. Analysis of compliant women showed supplemented women had higher median concentrations of serum ferritin, erythrocyte folate and 25-hydroxyvitamin D later in gestation than controls. In the compliant subset (n 149), placebo mothers had more small-for-gestational age (SGA) infants (eight SGA v. thirteen; P = 0·042) than treatment mothers. Baseline micronutrient deficiencies were common; the multiple-micronutrient supplement was well-tolerated and improved nutrient status. Multiple-micronutrient supplements from early pregnancy may be beneficial and larger studies are required to assess impact on birth outcomes and infant development.
X-RAY IONIZATION OF HEAVY ELEMENTS APPLIED TO PROTOPLANETARY DISKS

The consequences of the Auger effect on the population of heavy-element ions are analyzed for the case of relatively cool gas irradiated by keV X-rays with intended applications to the accretion disks of young stellar objects. Highly charged ions are rapidly reduced to the doubly charged state in neutral gas, so the aim here is to derive the production rates for these singly and doubly charged ions and to specify their transformation by recombination, charge transfer, and molecular reactions. The theory is illustrated by calculations of the abundances of 11 of the most cosmically abundant heavy elements in a model of a typical T Tauri star disk. The physical properties of the gas are determined with an X-ray irradiated thermal–chemical model, which shows that the disk atmosphere consists of a hot atmosphere overlaying the mainly cool body of the disk. There is a warm transition layer where hydrogen, carbon, and oxygen are transformed from atomic to molecular species and the ionization drops by several orders of magnitude. The doubly charged ions are then largely confined to the hot outer layers of the disk. The nature of the dominant ions below the transition depends sensitively on the poorly constrained abundances of the heavy elements. Observational consequences and connections with the active layers of the magnetorotational instability are briefly discussed.
Rac3 inhibits adhesion and differentiation of neuronal cells by modifying GIT1 downstream signaling

Rac1 and Rac3 are highly homologous regulatory proteins that belong to the small GTPases of the Rho family. Previously, we showed that Rac3 induces cell rounding and prevents neuronal differentiation, in contrast to its close relative Rac1, which stimulates cell spreading and neuritogenesis. To explain these opposing effects, we investigated whether Rac1 and Rac3 interact with different proteins. Here, we show that both Rac1 and Rac3 interact with GIT1, a multifunctional Arf-GAP protein, which regulates cell-matrix adhesion, cell spreading and endocytosis. However, in contrast to Rac1, the Rac3-GIT1 interaction is not mediated by βPix. Interestingly, Rac3 expression severely attenuates the interaction between GIT1 and paxillin, accompanied by defective paxillin distribution, focal adhesion formation and disturbed cell spreading. Moreover, in Rac3-expressing cells, Arf6 activity is strongly reduced and the Arf6-GAP activity of GIT1 is required for Rac3 downstream signaling. Indeed, expression of wild-type Arf6 or the Arf6-GEF ARNO induced cell spreading in the otherwise rounded Rac3-expressing cells. Our data suggest that Rac3 and Rac1 oppose each other's function by differently modulating GIT1 signaling. Rac1 induces adhesion and differentiation by activating PAK1 and stimulating the GIT1-paxillin interaction, whereas Rac3 blocks this interaction and inactivates Arf6 by stimulating the GAP function of GIT1, thereby preventing cell spreading and differentiation.
An augmented reality system to guide radio‐frequency tumour ablation

Radio‐frequency ablation is a difficult operative task that requires a precise needle positioning in the centre of the pathology. This article presents an augmented reality system for hepatic therapy guidance that superimposes in real‐time 3D reconstructions (from CT acquisition) and a virtual model of the needle on external views of a patient. The superimposition of reconstructed models is performed with a 3D/2D registration based on radio‐opaque markers stuck on to the patient's skin. The characteristics of the problem (accuracy, robustness and time processing) led us to develop automatic procedures to extract and match the markers and to track the needle in real time. Experimental studies confirmed that our algorithms are robust and reliable. Preliminary experiments conducted on a human abdomen phantom showed that our system is highly accurate (needle positioning error within 3 mm) and enables the surgeon to reach a target in less than 1 minute on average. Our next step will be to perform an in vivo evaluation. Copyright © 2005 John Wiley & Sons, Ltd.
Does the ID-MS traceable MDRD equation work and is it suitable for use with compensated Jaffe and enzymatic creatinine assays?

BACKGROUND International recommendations suggest that measurement of serum creatinine should be supplemented with an estimate of glomerular filtration rate (GFR) using the Modification of Diet in Renal Disease (MDRD) study equation. One problem has been the lack of standardization of commercially available creatinine assays resulting in varying estimates of GFR. A revision of the MDRD equation offers traceability to a reference method. This study evaluates the use of isotope dilution mass spectrometry (ID-MS), the compensated Jaffe and enzymatic creatinine methods compared with the Beckman CX3 Jaffe assay used to derive the MDRD equation and investigates their impact on GFR estimation using both the original and ID-MS-traceable MDRD equations. METHODS Serum creatinine was measured in 277 patients by (i) ID-MS, (ii) a Roche enzymatic assay, (iii) a Roche compensated kinetic Jaffe assay and (iv) a Beckman CX3 kinetic Jaffe assay. Estimated GFR was calculated using the MDRD equations. RESULTS The ID-MS (-7.5%), Roche enzymatic (-8.6%) and compensated kinetic Jaffe (-11.9%) assays were all negatively biased (P < 0.0001) compared with the Beckman CX3 assay, causing predictable, clinically significant, overestimation of GFR when the original MDRD equation is used. This positive bias was reduced (ID-MS 6.7 to 0.4%; enzymatic 8.8 to 3.4%; compensated kinetic Jaffe 13.7 to 7.1%) when GFRs were calculated using the ID-MS-traceable MDRD equation. CONCLUSIONS Compensated assays that account for non-creatinine chromogen interference produce significantly higher estimates of GFR when using the original MDRD equation. Use of the ID-MS-traceable MDRD equation ameliorates this effect. There is good agreement between estimated GFR derived from the original MDRD equation using Beckman Astra CX3 data and estimated GFR derived from the new ID-MS-traceable MDRD equation using a local ID-MS creatinine assay. This suggests that the ID-MS-traceable MDRD equation may be reliably used with both ID-MS and true ID-MS-traceable creatinine assays without the requirement for standardization to the MDRD laboratory.
Human immunodeficiency virus type 1–infected monocytic cells can destroy human neural cells after cell‐to‐cell adhesion

Primary cultures of human embryonic neurons and astrocytes have been used to test the interactions between neural cells and either human immunodeficiency virus type 1 (HIV‐1) or HIV‐1–infected monocytes. After direct infection with HIV‐1, neither morphological alteration of neurons and astrocytes nor signs of viral replication were observed. Similarly, cultured human neurons and astrocytes were resistant to incubation with the supernatant of HIV‐1–infected U937 cells, a human monoblastoid cell line. In contrast, HIV‐1–infected U937 monocytic cells adhered to neural cells and induced large plaques of necrosis surrounding them. This cytopathic effect began at the time of viral replication (day 16 after infection). Its intensity depended on that of viral replication, and its range was identical to the region of diffusion of viral antigens, as judged by immunocytochemistry. The cytopathic effect was not dependent on the release of free radicals. It could not be induced by cytokines or cytokine‐stimulated U937 cells. It is likely that this cytopathic effect depends on the release of viral antigens either within the site of adherence itself or within close range of the astrocyte membrane.
Impact of long external fiber cavities on the pulse train stabilization of a passively mode-locked quantum dot laser emitting at 1250 nm

Passively mode-locked (PML) semiconductor lasers are compact photonic sources delivering a train of picosecond short optical pulses for optical clock distribution, high bit-rate optical time division multiplexing and compact microwave/millimeter-wave signal generation. The pulse train can exhibit considerable timing jitter (TJ). We extend the recently studied impact of dual long-cavity optical feedback (DLC OFB) by investigating the impact of two long external fiber cavities on the timing and amplitude stability as well as the pulse repetition rate (RR). Modeling results by a simple time-domain model allow to reproduce the experiments with good agreement.
Expansion of the target of rapamycin (TOR) kinase family and function in Leishmania shows that TOR3 is required for acidocalcisome biogenesis and animal infectivity

Target of rapamycin (TOR) kinases are key regulators of cell growth, proliferation, and structure in eukaryotes, processes that are highly coordinated during the infectious cycle of eukaryotic pathogens. Database mining revealed three TOR kinases in the trypanosomatid parasite Leishmania major, as defined by homology to the phosphoinositide 3-kinase–related kinase (PIKK) family and a signature conserved FKBP12/rapamycin-binding domain. Consistent with the essential roles of TOR complexes in other organisms, we were unable to generate null TOR1 or TOR2 mutants in cultured L. major promastigotes. In contrast, tor3− null mutants were readily obtained; while exhibiting somewhat slower growth, tor3− maintained normal morphology, rapamycin sensitivity, and differentiation into the animal-infective metacyclic stage. Significantly, tor3− mutants were unable to survive or replicate in macrophages in vitro, or to induce pathology or establish infections in mice in vivo. The loss of virulence was associated with a defect in acidocalcisome formation, as this unique organelle was grossly altered in tor3- mutants and no longer accumulated polyphosphates. Correspondingly, tor3- mutants showed defects in osmoregulation and were sensitive to starvation for glucose but not amino acids, glucose being a limiting nutrient in the parasitophorous vacuole. Thus, in Leishmania, the TOR kinase family has expanded to encompass a unique role in AC function and biology, one that is essential for parasite survival in the mammalian infective stage. Given their important roles in cell survival and virulence, inhibition of TOR kinase function in trypanosomatids offers an attractive target for chemotherapy.
Centripetal Forces in China's Economic Takeoff

This paper uses provincial time series data from the People's Republic of China to empirically investigate two propositions relating to economic development: (i) that economic takeoff – or an acceleration in economic growth – is associated with inflows of foreign direct investment (FDI), possibly through technological transfer; and (ii) that takeoff is accompanied, at least in the short term, by widening income inequality. The results indicate that FDI flows have increased the rate of convergence in per capita incomes across China's provinces. However, the pattern of FDI, which has gone mainly to the relatively wealthy provinces, has caused different provinces to converge toward different steady states.
Clinical applications of image fusion for electrophysiology procedures

Cardiac electrophysiology procedures are routinely used to treat patients with rhythm disorders. The success rates of ablation procedures and cardiac resynchronization therapy are still sub-optimal. Recent advances in medical imaging, image processing and cardiac biophysical modeling have the potential to improve patient outcome. This manuscript provides an overview of how these advances have been translated into the clinical environment.
Consistent variation across soil types in salinity resistance of a diverse range of chickpea (Cicer arietinum L.) genotypes

Chickpea is considered sensitive to salinity, but the salinity resistance of chickpea germplasm has rarely been explored. This study aimed to (i) determine whether there is consistent genetic variation for salinity resistance in the chickpea minicore and reference collections; (ii) determine whether the range of salinity resistance is similar across two of the key soil types on which chickpea is grown; (iii) assess the strength of the relationship between the yield under saline conditions and that under non-saline conditions; and (iv) test whether salinity resistance is related to differences in seed set under saline conditions across soils and seasons. The seed yield of 265 chickpea genotypes in 2005– 2006 and 294 cultivated genotypes of the reference set in 2007–2008 were measured. This included 211 accessions of the minicore collection of chickpea germplasm from the International Crops Research Institute for the Semi-Arid Tropics (ICRISAT). The experiments were conducted in a partly controlled environment using a Vertisol soil in 2005–2006 and an Alfisol soil in 2007– 2008, with or without 80 mm sodium chloride (NaCl) added prior to planting. In a separate experiment in 2006–2007, 108 genotypes (common across 2005– 2006 and 2007–2008 evaluations) were grown under saline (80 mm NaCl) and non-saline conditions in a Vertisol and an Alfisol soil. In 2005–2006 in the Vertisol and 2007–2008 in the Alfisol, salinity delayed flowering and maturity, and reduced both shoot biomass and seed yield at maturity. There was a large variation in seed yield among the genotypes in the saline pots, and a small genotype by environment interaction for grain yield in both soil types. The non-saline control yields explained only 12–15 % of the variation of the saline yields indicating that evaluation for salinity resistance needs to be conducted under saline conditions. The reduction in yield in the saline soil compared with the non-saline soil was more severe in the Alfisol than in the Vertisol, but rank order was similar in both soil types with a few exceptions. Yield reductions due to salinity were closely associated with fewer pods and seeds per pot (61– 91 %) and to lesser extent from less plant biomass (12–27 %), but not seed size. Groups of consistently salinity resistant genotypes and the ones specifically resistant in Vertisols were identified for use as donor sources for crossing with existing chickpea cultivars.
Proteolytic cleavage of the Chlamydia pneumoniae major outer membrane protein in the absence of Pmp10

The genome of the obligate intracellular bacteria Chlamydia pneumoniae contains 21 genes encoding polymorphic membrane proteins (Pmp). While no function has yet been attributed to the Pmps, they may be involved in an antigenic variation of the Chlamydia surface. It has previously been demonstrated that Pmp10 is differentially expressed in the C. pneumoniae CWL029 isolate. To evaluate whether the absence of Pmp10 in the outer membrane causes further changes to the C. pneumoniae protein profile, we subcloned the CWL029 isolate and selected a clone with minimal Pmp10 expression. Subsequently, we compared the proteome of the CWL029 isolate with the proteome of the subcloned strain and identified a specific cleavage of the C‐terminal part of the major outer membrane protein (MOMP), which occurred only in the absence of Pmp10. In contrast, when Pmp10 was expressed we predominantly observed full‐length MOMP. No other proteins appeared to be regulated according to the presence or absence of Pmp10. These results suggest a close association between MOMP and Pmp10, where Pmp10 may protect the C‐terminal part of MOMP from proteolytic cleavage.
Effects of size of noncovalent complexes on their stability during collision-induced dissociation.

The size-dependent stability of noncovalent complexes under collision-induced dissociation (CID) conditions was studied on a quadrupole ion trap mass spectrometer. Complexes of heme, tetraphenylporphyrin iron(III) (TPP-Fe), and tetraphenylporphyrin manganese(III) (TPP-Mn) with several histidine-containing peptides and model compounds were formed by electrospray ionization (ESI) and their stability was probed by variable-energy CID. It was found that the stability of complexes with the same (or nearly the same) binding energy has a linear dependence on the complex size (or total number of degrees of freedom). This approach will allow comparisons of variable-energy CID data for noncovalent complexes with different binding energies and could be used to help in structural elucidation of some complexes formed by multidentate ligands. The linearity of size effects on the stability of the complexes was also tested in three crown ether/protonated primary amine systems.
Semantic and Pragmatic Conditions for the Dative Alternation

This paper has revisited the dative alternation in English, and defended the so-called polysemy view. The paper has argued for a particular format of lexical representation, one that allows reference to events. In addition to the semantic conditions, the paper has argued that the DO and PO constructions also allow for different information structures.