Miracle-dz/UniFAR-FTUs huggingface dataset:
Preparation and Characterization of Stealth Archaeosomes Based on a Synthetic PEGylated Archaeal Tetraether Lipid

The present studies were focused on the formation and characterization of sterically stabilized archaeosomes made from a synthetic PEGylated archaeal lipid. In a first step, a synthetic archaeal tetraether bipolar lipid was functionalized with a poly(ethylene glycol), PEG, and (PEG45-Tetraether) with the aim of coating the archaeosome surface with a sterically stabilizing hydrophilic polymer. In a second step, Egg-PC/PEG45-Tetraether (90/10 wt%) archaeosomes were prepared, and their physicochemical characteristics were determined by dynamic light scattering (size, polydispersity), cryo-TEM (morphology), and by high-performance thin layer chromatography (lipid composition), in comparison with standard Egg-PC/PEG45-DSPE formulations. Further, a fluorescent dye, the carboxyfluorescein, was encapsulated into the prepared archaeosomes in order to evaluate the potential of such nanostructures as drug carriers. Release studies have shown that the stability of Egg-PC/PEG45-Tetraether-based archaeosomes is significantly higher at 37°C than the one of Egg-PC/PEG45-DSPE-based liposomes, as evidenced by the slower release of the dye encapsulated into PEGylated archaeosomes. This enhanced stability could be related to the membrane spanning properties of the archaeal bipolar lipid as already described with natural or synthetic tetraether lipids.
Fecal microbiota related to postoperative endoscopic recurrence in patients with Crohn's disease

Abstract Background Postoperative recurrence (POR) remains a major challenge for patients with Crohn’s disease (CD). Gut microbial dysbiosis has been reported to be involved in the pathogenesis of POR. This study aims to investigate the relationship between fecal microbiome and endoscopic recurrence in patients with CD after ileocolonic resection. Methods This is a cross-sectional study. Fecal samples were collected from 52 patients with CD after surgical intervention from 6 to 12 months before endoscopic examination. Endoscopic recurrence was defined as Rutgeerts score ≥ i2. The microbiome was analyzed by sequencing the V3–V4 hypervariable regions of the 16S rRNA gene. Results A total of 52 patients were included and classified into POR (n = 27) and non-POR (n = 25) groups. Compared with the non-POR group, the POR group had a significantly lower community richness (Chao1 index: 106.5 vs 124, P = 0.013) and separated microbial community (P = 0.007 for Adonis, P = 0.032 for Anosim), combined with different distribution of 16 gut microbiotas and decrease of 11 predicted metabolic pathways (P < 0.05). Lactobacillus and Streptococcus were identified to closely correlate to non-POR (P < 0.05) after controlling for confounding factors. Kaplan-Meier analysis indicated that the patients with higher abundance of Streptococcus experienced longer remission periods (P < 0.01), but this was not for Lactobacillus. The predicted ethylmalonyl-coA pathway related to increased amount of succinate was positively correlated with Streptococcus (r > 0.5, P < 0.05). Conclusions The characteristic alterations of fecal microbiota are associated with postoperative endoscopic recurrence in patients with CD; particularly, high abundance of Streptococcus may be closely related to endoscopic remission.
The Effect of Non-equispaced Sampling Instants, Sub-period Record Epochs, and Timebase Gain on the Information Content of Discretized Replicas of Periodic Signals

The effect of non-equispaced sampling instants and timebase gain on the information content of the discretized replica of a periodic signal is examined. The effect of the duration of record epochs that are not equal to an integer number of signal periods on the information content of the discretized replica is also explored. A general model describing sampled and windowed data is provided and compared to related models developed by other researchers.
Development and evaluation of three immunofluorometric assays that measure different forms of osteocalcin in serum.

BACKGROUND Circulating human osteocalcin (hOC) has been used as a marker of bone formation. Our aim was to validate three immunofluorometric assays (IFMAs), measuring different forms of hOC. METHODS The two-site IFMAs were based on previously characterized monoclonal antibodies. Assay 2 recognized intact hOC, assays 4 and 9 measured the NH(2)-terminal mid-fragment and the intact hOC. In addition, assay 9 required hOC to be gamma-carboxylated. RESULTS A 76-79% increase of serum immunoreactive hOC was found in the postmenopausal group compared with the premenopausal group with all IFMAs. With EDTA-plasma samples, the observed increases were lower (49-65%). The hOC concentration in the postmenopausal group receiving hormone replacement therapy was 42-44% lower than that in the postmenopausal control group in both serum and EDTA-plasma samples. The depressed carboxylation in warfarin-treated patients was accompanied by lower results in assay 9. The ratio of assay 9 to assay 4 totally discriminated the warfarin-treated patients from the controls. Assay 9 showed the smallest decreases in measured hOC after storage of serum or plasma for 4 weeks at 4 degrees C, followed by assay 4 and assay 2. Results from the last assay were <17% of their initial values after 4 weeks of storage. No diurnal variation was observed with assay 9 as opposed to the two other IFMAs. CONCLUSION The three assays with their distinct specificity profiles (intact vs fragmented and carboxylated vs decarboxylated hOC) may provide valuable tools for investigating the significance of different hOC forms in various bone-related diseases.
Edinburgh Research Explorer Characterization of Erysipelothrix species isolates from clinically affected pigs, environmental samples, and vaccine strains from six recent swine erysipelas outbreaks in the United States

The aim of this study was to characterize Erysipelothrix sp. isolates from clinically affected pigs and their environment and compare them to the Erysipelothrix sp. vaccines used at the sites. Samples were collected during swine erysipelas outbreaks in vaccinated pigs in six Midwest United States swine operations from 2007 to 2009. Pig tissue samples were collected from 1 to 3 pigs from each site. Environmental samples (manure, feed, central-line water, oral ﬂuids, and swabs collected from walls, feed lines, air inlets, exhaust fans, and nipple drinkers) and live vaccine samples were collected following the isolation of Erysipelothrix spp. from clinically affected pigs. All Erysipelothrix sp. isolates obtained were further characterized by serotyping. Selected isolates were further characterized by PCR assays for genotype ( E. rhusiopathiae , E. tonsillarum , Erysipelothrix sp. strain 1, and Erysipelothrix sp. strain 2) and surface protective antigen ( spa ) type (A, B1, B2, and C). All 26 isolates obtained from affected pigs were E. rhusiopathiae , speciﬁcally, serotypes 1a, 1b, 2, and 21. From environmental samples, 56 isolates were obtained and 52/56 were E. rhusiopathiae (serotypes 1a,
Reinnervation of Vastus lateralis is increased significantly in seniors (70-years old) with a lifelong history of high-level exercise

It has long been recognized that histological changes observed in aging muscle suggest that denervation contributes to muscle deterioration and that disuse accelerates the process while running activity, sustained for decades, protects against age-related loss of motor units. Here we show at the histological level that lifelong increased physical activity promotes reinnervation of muscle fibers. In muscle biopsies from 70-year old men with a lifelong history of high-level physical activity, we observed a considerable increase in fiber-type groupings (almost exclusively of the slow type) in comparison to sedentary seniors, revealing a large population of reinnervated muscle fibers in the sportsmen. Slow-type transformation by reinnervation in senior sportsmen seems to be a clinically relevant mechanism: the muscle biopsies fluctuate from those with scarce fiber-type transformation and groupings to almost fully transformed muscle, going through a process in which isolated fibers co-expressing fast and slow MHCs seems to fill the gaps. Taken together, our results suggest that, beyond the direct effects of aging on the muscle fibers, changes occurring in skeletal muscle tissue appear to be largely, although not solely, a result of sparse denervation. Our data suggest that lifelong exercise allows the body to adapt to the consequences of the age-related denervation and to preserve muscle structure and function by saving otherwise lost muscle fibers through recruitment to different, mainly slow, motor units. These beneficial effects on motoneurons and, subsequently on muscle fibers, serve to maintain size, structure and function of muscle fibers, delaying the functional decline and loss of independence that are commonly seen in late aging.
Socioeconomic differentials in mortality among men within Great Britain: time trends and contributory causes.

STUDY OBJECTIVE: To assess the size of mortality differentials in men by social class in Scotland as compared with England and Wales, and to analyse the time trends in these differentials. SUBJECTS: Men from England and Wales and Scotland around each census from 1951 to 1981. METHODS: Poisson regression analysis was used to calculate relative indices of inequality for disease specific and all cause mortality as a measure of mortality differentials between social classes. This measure is not dependent on the size of the social class groups, so it can be used to compare the magnitude of differentials over time periods during which the relative sizes of social class groups change. MAIN RESULTS: While overall death rates were higher in Scotland than in England and Wales around the 1951, 1961, and 1971 censuses the relative indices of inequality indicated smaller mortality differences between social classes in Scotland. Inequality, as indexed by the relative index of inequality, increased over time in both Scotland and England and Wales, but to a greater degree in Scotland, resulting in greater social class mortality differentials for Scotland in 1981 (the relative index of inequality increased from 1.40 to 2.43 for England and Wales, and from 1.22 to 2.57 for Scotland between 1951 and 1981). This greater increase in the magnitude of inequalities in all cause mortality in Scotland seemed to result from increasing social class differentials in cardiovascular disease, accidents and external causes, and "all other causes of death". Examining the trends in overall death rates, it seems that the greater increase in social class differences in Scotland occurred because of the greater decrease in death rates among the privileged social groups, in combination with a smaller decrease (or a greater increase) in the death rates in the lower social class groups. CONCLUSIONS: This study has shown that trends in mortality and in inequalities in mortality differ within Great Britain. Although death rates were higher in Scotland than in England and Wales, smaller mortality differentials by social class were found in Scotland over the period 1951 to 1971. By 1981, however, social class mortality differentials were greater in Scotland than in England and Wales. The greater increase in the social class differentials over time in Scotland, may have contributed to the worsening overall mortality profile in Scotland as compared with England and Wales that occurred between 1971 and 1981.
Maximum Power of Thermally and Electrically Coupled Thermoelectric Generators

In a recent work, we have reported a study on the figure of merit of a thermoelectric system composed by thermoelectric generators connected electrically and thermally in different configurations. In this work, we are interested in analyzing the output power delivered by a thermoelectric system for different arrays of thermoelectric materials in each configuration. Our study shows the impact of the array of thermoelectric materials in the output power of the composite system. We evaluate numerically the corresponding maximum output power for each configuration and determine the optimum array and configuration for maximum power. We compare our results with other recently reported studies.
The c-kit ligand suppresses apoptosis of human natural killer cells through the upregulation of bcl-2.

The bcl-2 protein plays a central role in the regulation of programmed cell death in a variety of tissues and is pivotal to the survival of lymphocytes in vivo. The growth factors responsible for survival of normal lymphocytes are unknown but are likely to maintain viability in part through the regulation of bcl-2 expression. A subset of human natural killer (NK) cells (CD3-CD56bright) are unique among lymphocytes in their constitutive expression of c-kit, a tyrosine kinase cell surface receptor that binds c-kit ligand (KL). Alone, KL does not promote proliferation or further differentiation of CD56bright NK cells. We now report that, in the absence of serum or additional growth factors, KL prevents apoptosis of cultured CD56bright NK cells, as assessed by DNA fragmentation studies, and maintains viability, as measured by biologic responses (i.e., proliferation and cytotoxicity) to the subsequent addition of other cytokines. Furthermore, we demonstrate that KL induces CD56bright NK cells to express the bcl-2 protein. In the presence of anti-c-kit antibody, the tyrosine kinase inhibitor genistein, or bcl-2 antisense oligonucleotide, the protective effect of KL on the survival of CD56bright NK cells is dramatically reduced. These data demonstrate that the binding of KL to its tyrosine kinase receptor results in the upregulation of bcl-2, thereby preventing apoptosis in this subset of normal human lymphocytes. As soluble KL is plentiful in normal human serum, this survival mechanism may be operative for CD56bright NK cells in vivo.
Human papillomavirus infections and upper aero-digestive tract cancers: the ARCAGE study.

BACKGROUND Human papillomavirus (HPV) is causally implicated in a subset of cancers of the upper aero-digestive tract (UADT). METHODS Associations between type-specific HPV antibodies were examined among 1496 UADT cancer case subjects and 1425 control subjects by estimating odds ratios (ORs) in logistic regression analyses adjusted for potential confounders. The agreement between serology and tumor markers of HPV infection, including presence of HPV DNA and p16 expression, were examined in a subset of tumors. RESULTS HPV16 L1 seropositivity was associated with increased risk of oral cavity and oropharyngeal cancer (OR = 1.94, 95% confidence interval [CI] = 1.03 to 3.65; OR = 8.60, 95% CI = 5.21 to 14.20, respectively). HPV16 E6 antibodies were present in 30.2% of oropharyngeal case subjects and only 0.8% of control subjects (OR = 132.0, 95% CI = 65.29 to 266.86). Combined seropositivity to HPV16 E6 and E7 was rare (n = 1 of 1425 control subjects). An agreement of 67% was observed between HPV16 E6 serology and the corresponding presence of an HPV-related cancer: four of six HPV DNA-positive/p16-overexpressing tumors were HPV16 E6 antibody positive. An HPV16 independent association was observed for HPV18 and oropharyngeal cancer (OR = 8.14, 95% CI = 2.21 to 29.99 for HPV18 E6 seropositivity) and HPV6 and laryngeal cancer (OR = 3.25, 95% CI = 1.46 to 7.24 for HPV6 E7 seropositivity). CONCLUSIONS These results confirm an important role for HPV16 infection in oropharyngeal cancer. HPV16 E6 antibodies are strongly associated with HPV16-related oropharyngeal cancers. Continuing efforts are needed to consider both HPV serology and p16 staining as biomarkers relevant to the etiology and natural history of HPV16-related oropharyngeal tumors. These results also support a marginal role for HPV18 in oropharyngeal cancer and HPV6 in laryngeal cancer.
Linear antenna array synthesis using fitness-adaptive differential evolution algorithm

Design of non-uniform linear antenna arrays is one of the most important electromagnetic optimization problems of current interest. In this article, an adaptive Differential Evolution (DE) algorithm has been used to optimize the spacing between the elements of the linear array to produce a radiation pattern with minimum side lobe level and null placement control. DE is arguably one of the best real parameter optimizers of current interest takes very few control parameters and is easy to implement in any programming language. In this study two very simple adaptation schemes are used to regulate the control parameters F and Cr, upon which the performance of DE is critically dependent. The adaptation schemes are based on the objective function values of the target vectors and donor vectors. The adaptive DE-variant has been used to solve three difficult instances of the design problem and the optimization goal in each example is easily achieved. The results of the proposed algorithm have been shown to meet or beat the recently published results obtained using other state-of-the-art metaheuristics like the Genetic Algorithm (GA), Particle Swarm Optimization (PSO), Memetic Algorithms (MA), and Tabu Search (TS) in a statistically meaningful way.
Edinburgh Research Explorer Identification of two sequences in the cytoplasmic tail of the human immunodeficiency virus type 1 envelope glycoprotein that inhibit cell surface expression

During synthesis and export of protein, the majority of the human immunodeﬁciency virus type 1 (HIV-1) Env glycoprotein gp160 is retained in the endoplasmic reticulum (ER) and subsequently ubiquitinated and degraded by proteasomes. Only a small fraction of gp160 appears to be correctly folded and processed and is transported to the cell surface, which makes it difﬁcult to identify negative sequence elements regulating steady-state surface expression of Env at the post-ER level. Moreover, poorly localized mRNA retention sequences inhibiting the nucleocytoplasmic transport of viral transcripts interfere with the identiﬁcation of these sequence elements. Using two heterologous systems with CD4 or immunoglobulin extracellular/trans-membrane domains in combination with the gp160 cytoplasmic domain, we were able to identify two mem-brane-distal, neighboring motifs, is1 (amino acids 750 to 763) and is2 (amino acids 764 to 785), which inhibited surface expression and induced Golgi localization of the chimeric proteins. To prove that these two elements act similarly in the homologous context of the Env glycoprotein, we generated a synthetic gp160 gene with synonymous codons, the transcripts of which are not retained within
Sloan School of Management Working Paper Factors That Influence Technical Communication in Distributed Product Development: an Empirical Study in the Telecommunications Industry Factors That Influence Technical Communication in Distributed Product Development: an Empirical Study in the Telecommunica

Understanding the communication process in product development organizations has been recognized as a key element to improve product development performance. It is particularly interesting to study information exchanges in geographically distributed product development teams because of the highly interdependent nature of design organizations. Additionally, the use of electronic-based communication media has changed how development teams communicate. By studying the way product development teams use various communication media (face-to-face, telephone and email), we assess how the process of exchanging technical information is influenced by factors such as geographic dispersion, organizational bonds, and degree of team interdependence. We develop a theoretical framework that allows us to formulate several hypotheses about how these factors influence both communication frequency and media choice. We use empirical evidence from the telecommunications industry to test our hypotheses. We confirm previous results about the obstructive influence of distance on technical communication. However, we found that such negative effects may be mitigated by other factors such as the recognizing of highly interdependent team members, the existence of strong organizational bonds, and the use of electronic communication media.
Technologies for sub-ns pulse coherent mm-wave radar

Pulse coherent radar and pulsed magnetic resonance spectrometry are closely related techniques which share similar design constraints and technological difficulties, despite the obvious differences in application. Millimetre wave pulsed electron spin resonance (ESR) spectrometry is a rapidly developing scientific technique which is at the forefront of pulse coherent mm-wave instrumentation. Our work in developing technologies for sub-nanosecond pulsed ESR may be directly applied to radar, where extremely short pulse lengths offer very high range resolution and clutter suppression. Sub-ns ESR has been made possible by the careful design of the transmit/receive electronics and the use of quasi-optical (QO) techniques for signal transport and control. We present results for a low phase noise sub-ns pulse generator, high performance isolators, ultra low return loss QO loads, and a demonstration of ns coherent pulse demodulation
Factors of selection and quality of wood used for woodcraft in medieval Polish strongholds and early urban centres

Abstract This paper discusses various aspects of the use of wood for crafts in the Middle Ages, based on xylological analyses of 4211 crafted items of everyday use discovered at 62 archaeological sites in Poland. Over 1500 items were identified in the authors’ own analyses, and the remaining taxonomic data were taken from the literature. The research showed that the main types of wood used at the time were Pinus sylvestris, Quercus sp. , Fraxinus excelsior, Picea sp. vel Larix sp. , Taxus baccata, Alnus sp. , Abies alba and Euonymus sp. Nineteen other taxa were used to make a much smaller pool of objects. At most of the analysed sites a similar set of materials was used to produce the items, regardless of their age and location. The choice of wood was selective and was based on the characteristics of particular tree and shrub species. Large coopered vessels were primarily made of wood from Quercus sp. , Pinus sylvestris and Taxus baccata. The manufacture of turned utensils usually involved Fraxinus excelsior, while stave bowls were made using only Pinus sylvestris and Picea/Larix (mainly Picea abies). To verify the local availability of the source taxa, we used pollen sequences from natural and anthropogenic sites in the vicinity of the places where the examined artefacts were found. The choice of wood was limited by the availability of the trees and shrubs. In north-western Poland the most important taxa used for woodworking in the Middle Ages were Pinus sylvestris, Quercus sp. , Fraxinus excelsior and Fagus sylvatica; in the south, Picea/Larix and Abies alba were used most frequently. Some items made of Abies alba, Picea and Larix were imported from other parts of the country. We inferred two stages of the use of wood by medieval Polish craftsmen. In the first stage, from the mid-10th century to the late 12th century, they largely used deciduous taxa; the second stage, from the 13th to the 15th centuries, saw the increased use of conifers. We found that the medieval craftsmen chose high-quality wood without defects. Radial wood with the best technical parameters was preferred. Its share increased in the late Middle Ages; this can be attributed to the craftsmen’s increasing familiarity with carpentry techniques.