Miracle-dz/UniFAR-FTUs huggingface dataset:
Surfactant protein C: a review of its unique properties and metabolism.

Traditionally, our thinking about surfactant proteins has centered around their effects on the biophysical properties of surfactant phospholipids. It is now apparent that the three major surfactant proteins (SP-A, SP-B, and SP-C) are a biochemically and functionally diverse group of mammalian peptides. Accumulated data suggest that they have roles beyond modulation of alveolar surface tension. SP-C is a 33-35 amino acid peptide found in organic extracts of pulmonary surfactant. In part, because of its extreme hydrophobicity, a full understanding of SP-C is presently incomplete. Progress to date has included evaluation of the biophysical properties and investigations of the SP-C gene, including studies of the SP-C promoter. This review describes the unique structural and functional properties of the SP-C molecule and summarizes available data on its molecular biology and metabolism. Studies from literature show that SP-C represents a physiologically important peptide with novel structural properties; namely, extreme hydrophobicity, an alpha-helical membrane spanning region, and a unique posttranslational modification: palmitoylation. From data on similarly modified proteins, we propose that the properties of SP-C, including the covalent addition of palmitic acid, render it capable of being targeted to and interacting with specific cell membranes. A complete understanding of SP-C, especially with regard to its metabolism and function, may require a reorientation of our thinking to consider SP-C as a membrane peptide and not just as a "surfactant protein. "
Supervised Deep Features for Software Functional Clone Detection by Exploiting Lexical and Syntactical Information in Source Code

Software clone detection, aiming at identifying out code fragments with similar functionalities, has played an important role in software maintenance and evolution. Many clone detection approaches have been proposed. However, most of them rep-resent source codes with hand-crafted features using lexical or syntactical information, or unsupervised deep features, which makes it difﬁcult to detect the functional clone pairs, i.e., pieces of codes with similar functionality but differing in both syntactical and lexical level. In this paper, we address the software functional clone detection problem by learning supervised deep features. We formulate the clone detection as a supervised learning to hash problem and propose an end-to-end deep feature learning framework called CDLH for functional clone detection. Such framework learns hash codes by exploiting the lexical and syntactical information for fast computation of functional similarity between code fragments. Experiments on software clone detection benchmarks indicate that the CDLH approach is effective and outperforms the state-of-the-art approaches in software functional clone detection.
The Salmonella enterica Serovar Typhi tsx Gene, Encoding a Nucleoside-Specific Porin, Is Essential for Prototrophic Growth in the Absence of Nucleosides

ABSTRACT The Salmonella enterica serovar Typhi tsx gene encodes a porin that facilitates the import of nucleosides. When serovar Typhi is grown under anaerobic conditions, Tsx is among the outer membrane proteins whose expression increases dramatically. This increase in expression is due, at least in part, to increased transcription and is dependent on Fnr but not on ArcA. A mutant derivative of serovar Typhi strain STH2370 with a deletion of the tsx gene is an auxotroph that requires either adenosine or thymidine for growth on minimal medium. In contrast, an otherwise isogenic nupG nupC double mutant, defective in the inner membrane nucleoside permeases, is a prototroph. Because anaerobic growth enhances the virulence of serovar Typhi in vitro, we assessed the role that the tsx gene plays in pathogenicity and found that the serovar Typhi STH2370 Δtsx mutant is defective in survival within human macrophage-like U937 cells. To understand why the Δtsx mutant is an auxotroph, we selected for insertions of minitransposon T-POP in the Δtsx genetic background that restored prototrophy. One T-POP insertion that suppressed the Δtsx mutation in the presence of the inducer tetracycline was located upstream of the pyrD gene. The results of reverse transcription-PCR analysis showed that addition of the inducer decreased the rate of pyrD transcription. These results suggest that the Tsx porin and the balance of products of the tsx and pyrD genes play critical roles in membrane assembly and integrity and thus in the virulence of serovar Typhi.
Spondylodiskitic abscesses: CT-guided percutaneous catheter drainage.

PURPOSE To determine whether computed tomographically (CT) guided percutaneous catheter drainage of spondylodiskitic abscesses is an appropriate and effective alternative to surgery. MATERIALS AND METHODS CT-guided percutaneous catheter drainage was performed in 21 patients (16 men, five women; age range, 24-81 years) with 33 spondylodiskitic abscesses. Nine intradiskal, 12 paravertebral, and 12 psoas abscesses were drained with 5.6-14.0-F catheters. In 29 cases, the catheter was inserted by using the Seldinger technique in four cases, a trocar technique was used. All patients underwent follow-up CT or magnetic resonance imaging examinations for 6 months. RESULTS Successful placement of the drainage catheter was achieved in each patient without procedural complications. The duration of drainage was 4-56 days (average duration, 26.8 days). Three of 33 catheters were changed because of insufficient drainage; one of the 33 catheters had to be reinserted because of dislocation. Two patients underwent surgery for stabilization of the spine with the drainage catheter in place. In 16 of the 21 patients, specific organisms were isolated; thus, definitive medical therapy was possible. Complete evacuation of all abscesses was achieved initially, with no evidence of recurrence during the follow-up. CONCLUSION CT-guided percutaneous catheter drainage is an efficient and safe procedure in the management of spondylodiskitic abscesses.
Phenotypic distinctiveness of Staphylococcus aureus strains associated with toxic shock syndrome

Twenty Staphylococcus aureus strains from patients with toxic shock syndrome (TSS) and 20 from control patients (non-TSS) with infection but no clinical evidence of TSS were compared phenotypically in a collaborative, blinded, randomized study. TSS strains were significantly (P less than 0.05) more likely than non-TSS strains to produce various previously described but related toxic shock-associated proteins (pyrogenic exotoxin C, enterotoxin F, and TSS marker protein), as well as differing in other distinctive phenotypic characteristics, such as hemolysis, bacteriocin susceptibility, arsenate resistance, pigment production, and casein proteolysis. TSS strains were significantly less likely to carry plasmids than control strains. A combination of two variables--proteolysis and toxic shock-associated protein production--statistically accounted for all other phenotypic variations between TSS and non-TSS strains. Only proteolysis covaried with all other significant variables, suggesting a primary role in the phenotypic distinctiveness of TSS S. aureus strains and possibly in the pathogenesis of TSS.
Differential regulation of the progesterone receptor A and B in the human uterine cervix at parturition

The concept of a blockade of progesterone during human pregnancy and withdrawal of this blockade at parturition remains controversial There is no sharp fall in serum progesterone before parturition, but treatment with an antiprogestin is successful for labor induction at term pregnancy. The human progesterone receptor (PR) exists in two isoforms (PR-A and PR-B), mediating different biological responses. Here, the hypothesis of a progesterone withdrawal at parturition in terms of a change in PR isoforms was tested. Cervical biopsies were obtained at term before the onset of labor, immediately after parturition and from non-pregnant women. Solution hybridization showed a tendency for the PR mRNA level to be decreased at parturition. Immunohistochemistry displayed decreased PR(A+B) and PR-B levels (p<0.05) immediately after parturition. The relative importance of PR-A seemed higher immediately after parturition as compared to its importance in non-pregnant and term pregnant women. Our results are consistent with the concept of a functional progesterone blockade at the receptor level at term pregnancy, and withdrawal of this blockade at parturition. These observations may have important clinical and therapeutic implications.
Transmural pH gradient in canine myocardial ischemia.

The subendocardium is more susceptible to ischemia than the subepicardium. Studies during critical coronary stenosis have demonstrated subendocardial hypoperfusion relative to the subepicardium and transmural gradients in certain tissue metabolites. Although ischemia causes acidosis, the existence of a transmural pH gradient has never been demonstrated or quantitated. Thus we reduced coronary blood flow to 20 +/- 5% of normal in eight open chest anesthetized (morphine sulfate and pentobarbital) dogs and to 45 +/- 5% in two dogs. We implanted specially designed miniature fiber-optic pH probes in normal and ischemic subendocardium (depth 5.5-8 mm) and subepicardium (depth 3-4 mm). Separate experiments validated use of the fiber-optic pH probe system to measure tissue pH. Although both probes were located in the ischemic zone, there was a large transmural gradient, i.e., from normal pH values (7.36) in the subepicardium to severely acidotic (pH 6.94) 2 mm deeper in the subendocardium. This marked difference in pH between nearby transmural layers may have important implications regarding arrhythmogenesis in the setting of acute myocardial ischemia.
Evaluation of 13‐Week Inhalation Toxicity Study on Methyl t‐Butyl Ether (MTBE) in Fischer 344 Rats

Methyl‐t‐butyl ether (MTBE) is widely used as an octane enhancing agent in gasoline. A 13‐week inhalation study was conducted in Fischer 344 rats to provide information on potential target organs and toxicity of MTBE, and to ascertain a no‐observed‐adverse‐effect level (NOAEL) for MTBE. Male and female Fischer 344 rats were exposed to target doses of MTBE vapor of 0, 800, 4000 and 8000 ppm for 6 h a day, 5 days per week for 13 weeks: MTBE produced no mortalities. At 8000 ppm, males and females showed a decrease in body weights compared to controls. The only notable effect on clinical observation was ataxia at 8000 ppm, which was apparent during the first 4 weeks of treatment. Mild hematological and clinical chemistry changes were observed in the 8000 ppm group. At 8000 ppm, animals showed increased serum levels of corticosteroids, which suggest some stress‐like effect. At necropsy, there were no treatment‐related gross lesions. Absolute and relative organ weights (liver, adrenals and kidneys) were increased in both sexes at 4000 and 8000 ppm, but there were no microscopic lesions in these tissues with the exception of the kidney. Microscopic examination of other tissues revealed no effects with the exception that at 8000 ppm, male rats showed: mild increased size of hyaline droplets within the kidney, mild increase in hemosiderosis in the spleen and higher incidence of hyperplasia in the lymph nodes. The highest NOAEL was judged at 800 ppm. © 1997 by John Wiley & Sons, Ltd.
Recent advances in diffuse optical imaging

We review the current state-of-the-art of diffuse optical imaging, which is an emerging technique for functional imaging of biological tissue. It involves generating images using measurements of visible or near-infrared light scattered across large (greater than several centimetres) thicknesses of tissue. We discuss recent advances in experimental methods and instrumentation, and examine new theoretical techniques applied to modelling and image reconstruction. We review recent work on in vivo applications including imaging the breast and brain, and examine future challenges.
Demokratisierung der EU durch Online-Konsultationen?

Online-Konsultationen sind ein zentrales, regelmäßig genutztes Instrument der Europäischen Kommission zur Einbindung nicht-staatlicher Akteure in europäische Politikprozesse. Sie verfolgt damit zwei Ziele: Die Informationsbasis ihrer politischen Entscheidungen soll sich durch erweiterte Einbindung verbessern und die demokratische Qualität erhöhen (und beides zusammen soll die Legitimität der europäischen politischen Ordnung steigern). Diese Vorstellungen gehen auf das Weißbuch über „Europäisches Regieren" (Kommission 2001) zurück, welches vor allem im Hinblick auf das Demokratieziel eine Veränderung der Erwartungen der Kommission an die Leistungen zivilgesellschaftlicher Einbindung darstellt (Kohler-Koch/Finke 2007). Inwieweit die Demokratisierungserwartungen berechtigt sind, wird in diesem Aufsatz überprüft. Mit Online-Konsultationen sind hier diejenigen Angebote zur politischen Beteiligung gemeint, die die Kommission über ihre Internetseite . Ihre Stimme in Europa' und den entsprechenden Seiten ihrer Generaldirektionen ankündigt. Hier können Bürger, zivilgesellschaftliche Organisationen, aber auch staatliche Körperschaften in einem Zeitraum von zumeist mindestens acht Wochen Stellung zu den konkreten Vorhaben der EU beziehen. Online-Konsultationen können sich entweder an bestimmte, von der Kommission ausgewählte Adressaten richten (beschränkte Konsultationen) oder an alle möglicherweise Betroffene (offene Konsultationen). Online-Konsultationen sind bei weitem nicht das einzige Instrument der Kommission zur Einbindung zivilgesellschaftlicher Organisationen (für einen Überblick siehe Fazi/Smith 2006 und den Beitrag von Christine Quittkat in diesem Heft). In der Praxis bestehen nebeneinander informelle Kontakte zwischen einzelnen Vertretern zivilgesellschaftlicher Organisationen und Kommissionsmitarbeitern, restriktive und nicht unbedingt transparente formelle Beteiligungsverfahren und schließlich offene Online-Konsultationen. Letztere können wohl für ,best démocratie practice' unter den unterschiedlichen vorhandenen Zugängen für zivilgesellschaftliche Akteure genommen werden, weil sie sich durch das Offenheitskriterium zumindest dem Prinzip formaler Chancengleichheit (in der Konsultation) verschrieben haben und auch eine hinreichende Transparenz entsprechend behandelter Regelungsgegenstände anzunehmen ist. Zudem bietet das Internet Partizipationswilligen einen vergleichsweise aufwandsarmen Zugang an. Doch wird das selbst gesetzte Ziel der Kommission, die Demokratisierung, durch das Einführen und die Nutzung von offenen OnlineKonsultationen tatsächlich befördert? Bevor diese Frage im zweiten Schritt geklärt werden kann, braucht es einen Maßstab für Demokratisierung. Zunächst geht es also um die Frage: Woran erkennen wir Demokratie/Demokratisierung?
Dysregulation of the Cytokine Network in the Uterus of the Diabetic Rat

Insulin‐dependent (type 1) diabetes is an auto‐immune disorder that produces secondary complications in numerous non‐immunological systems. Changes in the synthesis and action pattern of several cytokines have been associated with the development of these alterations. Based on the clinical facts that the pregnant and non‐pregnant functions of the reproductive system are also disrupted by diabetes, our laboratory has decided to concentrate its research activities on the hypothesis that cytokines may be implicated in the uteropathy and embryopathy associated with the metabolic disorder. This review article summarizes our major findings concerning the synthesis of TNF‐α and IL‐1β in the uterus of diabetic rats, and in cultures of rodent uterine cells upon their exposure to high concentrations of glucose. The paper also reviews evidence that both the peri‐implanting embryo and the epithelial cell layer lining the uterine lumen are targets for the deleterious influence of excess TNF‐α. If confirmed in the uterus of diabetic patients, these observations may explain how cytokines contribute to the dysregulation of crucial reproductive events like menstruation and embryo implantation in humans.
Liver Triglyceride Content in HIV-1-Infected Patients on Combination Antiretroviral Therapy Studied with 1H-MR Spectroscopy

Objective To carry out an exploratory evaluation of liver triglyceride content in HIV-1-infected patients receiving highly active antiretroviral therapy (HAART) using proton magnetic resonance spectroscopy and to study how both the treatment itself and the biochemical and physiological variables in which the treatment causes alterations are related to liver fat content. Methods Intracellular hepatic triglyceride content was determined in 29 HIV-1-infected patients on their first HAART regime by means of localized water-unsuppressed single voxel proton spectra. Other measurements were body mass index, waist-to-hip ratio, lipodystrophy assessment and a detailed blood biochemical analysis. The relationship between intracellular hepatic triglycerides and relevant descriptive, treatment and biochemical variables was studied by correlation and regression analysis. Results Intrahepatic triglycerides were detected in 58.6% of the patients and 13.8% showed a triglyceride content compatible with liver steatosis. Many variables (body mass index, waist-to-hip ratio, cumulative exposure to PIs, lactate, insulin, insulin resistance measured by the homeostasis model assessment method [HOMA-R index], pH, total triglycerides, high density lipoprotein cholesterol and very low density lipoprotein [VLDL] cholesterol) correlated individually with the amount of triglycerides. Stepwise multiple regression analysis showed that the combination of insulin or HOMA-R index and VLDL cholesterol accounted for up to 50.2% of the triglyceride liver variance. A positive relationship was found between the concomitant presence of the metabolic syndrome components (insulin resistance, dyslipidaemia and central obesity) and intrahepatic triglyceride content. Conclusions The study showed that intrahepatic triglyceride deposit appears to be a frequent feature of HIV-1-infected patients receiving HAART. A coherent multifactorial combination of biochemical and physiological factors associated with the deposit suggested that cumulative exposure to PIs might be a possible trigger event.
A Novel Zone Division Approach for Power System Fault Detection Using ANN-Based Pattern Recognition Technique

This paper presents a waveform analysis-based approach for detection and classification of short-circuit faults in large power networks. To reduce the computational burden in dealing with a large volume of waveform data, a novel zone detection method has been used where a large power network is divided into optimal number of zones with manageable number of buses and lines. A first module of the artificial neural network-based classifier has been developed to perform an “exploratory global search” to find the faulty zone, which is then refined to a “local search” within a zone, by a second module of classifier for determination of exact fault location and fault type. The elementary waveform data are being captured by disturbance recorders placed at strategic buses, termed as “monitoring locations. ” Feature extraction, which is typically the underlying principle of any waveform analysis-based fault detection approach, is implemented by the extended Kalman filter. The proposed method has been successfully tested on the IEEE 57 bus network with encouraging results.
Enhanced Flux Pinning in YBCO+YSZ Composite Films Grown by TFA-MOD Method

More attention was paid to the fact that columnar defects generated by introducing nano-particles into YBCO films can improve the in-field superconducting properties of YBCO as pinning centers. Epitaxial YBCO films with self-assembled Yttrium-stabilized Zirconia (YSZ) nano-particles have been successfully prepared by TFA-MOD based on different solutions and the effect of nano-particle dopants on the field properties of YBCO films was investigated by analyzing the results obtained by PPMS according to the Bean Model. The critical current densities (Jc) of YBCO films with YSZ nano-particle were found to be improved with respect to pure YBCO films in range of 0-5 T. The Jc value of YBCO film with YSZ dopant was 0.2 MA/cm2 at 50 K and 4 T field, which is 4 times higher than that of pure YBCO film. Furthermore, an optimized property was observed for YBCO films doped by 6 mol. % YSZ nano-particle shown by the dependence relationship between Jc value and field for YBCO films with different amount of YSZ dopants.
Rho-dependent Rho Kinase Activation Increases CD44 Surface Expression and Bone Resorption in Osteoclasts*

Osteoclasts from osteopontin-efficient mice exhibit decreased CD44 surface expression. Osteopontin (OPN)/αvβ3 generated Rho signaling pathway is required for the surface expression of CD44. In this work we show the Rho effector, Rho kinase (ROK-α), to be a potent activator of CD44 surface expression. ROK-α activation was associated with autophosphorylation, leading to its translocation to the plasma membrane, as well as its association with CD44. ROK-α promoted CD44 surface expression through phosphorylation of CD44 and ezrin-radixin-moesin (ERM) proteins and CD44·ERM·actin complex formation. Osteoclasts from OPN–/– mice exhibited an ∼55–60% decrease in basal level ROK-α phosphorylation as compared with wild type osteoclasts. Furthermore, RhoVal-14 transduction was only partially effective in stimulating ROK-α/CD44 phosphorylation, as well as CD44 surface expression, in these osteoclasts. Studies on the inhibition of Rho by C3 transferase or ROK-α by the specific inhibitor, Y-27632, showed a decrease in the phosphorylation mediated by ROK-α and CD44 surface expression. Neutralizing antibodies to αv, β3, or CD44 inhibited the migration and bone resorption of wild type osteoclasts. However, only anti-αv or -β3 antibodies blocked OPN-induced phosphorylation of ROK-α, CD44, and the ERM proteins. Our results strongly suggest a role for ROK-α in αvβ3-mediated Rho signaling, which is required for the phosphorylation events and CD44 surface expression. The functional deficiencies in the Rho effector(s) because of the lack of OPN were associated with decreased CD44 surface expression and hypomotility in the OPN–/– osteoclasts. Finally, we find that cooperativity exists between αvβ3 and CD44 for osteoclast motility and bone resorption.
Equity Mutual Funds: A Risk-adjusted Performance Analysis of Loads vs. No-loads

This thesis applies Sharpe Ratios (1966) and alphas from the Carhart four-factor model (1997) to determine whether no-load mutual funds outperformed load mutual funds over a ten year period, December 2002 through December 2012, using U.S. equity mutual fund data. In total, 36 mutual funds were chosen for the sample, 18 no-load funds and 18 load funds. The load funds, which consist of 12 front-end loads and 6 back-end loads, were adjusted for their respective load fees throughout the study based on the investment time period under consideration. After computing 10-year, 5-year, 2-year, and recession period Sharpe Ratios and four-factor alphas, it was determined that no-load mutual funds consistently outperformed load mutual funds in every time period considered. Based on these results, it can be concluded that managers of load funds did not reward their investors with superior returns relative to no-load funds. On average, investors would have been better off investing in no-load funds rather than load funds from December 2002 through December 2012.