julilili42/papers huggingface dataset:
A COMMON EARTH RELIGION: WORLD RELIGIONS FROM AN ECOLOGICAL PERSPECTIVE
2013-06-12

Is globalization making modern world religions out of local beliefs? What changes are required of the world religions in the light of the new ecological perspective on the earth? In this article, I will begin by critically taking stock of a globalization that takes no care of the globe, and modern world religions that have no thought for the world. I will then explain how the earth sustains the life of every religion on it. My question is this: Do we need an earth religion as the overarching framework in which world religions can encounter one another and live side by side in harmony?
Increased Cell Wall Teichoic Acid Production and D-alanylation Are Common Phenotypes among Daptomycin-Resistant Methicillin-Resistant Staphylococcus aureus (MRSA) Clinical Isolates
2013-06-13

Multiple mechanisms have been correlated with daptomycin-resistance (DAP-R) in Staphylococcus aureus. However, one common phenotype observed in many DAP-R S. Aureus strains is a thickened cell wall (CW). The first evidence for an impact of CW-linked glycopolymers on this phenotype was recently demonstrated in a single, well-characterized DAP-R methicillin-susceptible S. aureus (MSSA) strain. In this isolate the thickened CW phenotype was linked to an increased production and D-alanylation of wall teichoic acids (WTA). In the current report, we extended these observations to methicillin-resistant daptomycin-sensitive/daptomyin-resistant (DAP-S/DAP-R) strain-pairs. These pairs included methicillin-resistant S. aureus (MRSA) isolates with and without single nucleotide polymorphisms (SNPs) in mprF (a genetic locus linked to DAP-R phenotype). We found increased CW dry mass in all DAP-R vs DAP-S isolates. This correlated with an increased expression of the WTA biosynthesis gene tagA, as well as an increased amount of WTA in the DAP-R vs DAP-S isolates. In addition, all DAP-R isolates showed a higher proportion of WTA D-alanylation vs their corresponding DAP-S isolate. We also detected an increased positive surface charge amongst the DAP-R strains (presumably related to the enhanced D-alanylation). In comparing the detailed CW composition of all isolate pairs, substantive differences were only detected in one DAP-S/DAP-R pair. The thickened CW phenotype, together with an increased surface charge most likely contributes to either: i) a charge-dependent repulsion of calcium complexed-DAP; and/or ii) steric-limited access of DAP to the bacterial cell envelope target. Taken together well-defined perturbations of CW structural and functional metrics contribute to the DAP-R phenotype and are common phenotypes in DAP-R S. Aureus isolates, both MSSA and MRSA. Note: Although "daptomycin-nonsusceptibility" is the generally accepted terminology, we have utilized the term "daptomycin resistance" for ease of presentation in this manuscript.
Low Osteogenic Differentiation Potential of Placenta-Derived Mesenchymal Stromal Cells Correlates with Low Expression of the Transcription Factors Runx2 and Twist2
2013-06-13

Recent studies indicated that mesenchymal stromal cells from bone marrow (bmMSC) differ in their osteogenic differentiation capacity compared to MSC from term placenta (pMSC). We extended these studies and investigated the expression of factors involved in regulation of bone metabolism in both cell types. To this end, MSC were expanded in vitro and characterized. The total transcriptome was investigated by microarrays, and for selected genes, the differences in gene expression were explored by quantitative reverse transcriptase-polymerase chain reaction, immunocytochemistry, and flow cytometry. We report that bmMSC and pMSC share expression of typical lineage surface markers, including CD73, CD90, CD105, and lack of CD14, CD34, and CD45. However, according to transcriptome analyses, they differ significantly in their expression of more than 590 genes. Factors involved in bone metabolism, including alkaline phosphatase (P<0.05), osteoglycin (P<0.05), osteomodulin (P<0.05), runt-related transcription factor 2 (Runx2) (P<0.04), and WISP2 (P<0.05), were expressed at significantly lower levels in pMSC, but twist-related protein 2 (Twist2) (P<0.0002) was expressed at significantly higher levels. The osteogenic differentiation capacity of pMSC was very low. The adipogenic differentiation was somewhat more prominent in bmMSC, while the chondrogenic differentiation seemed not to differ between bmMSC and pMSC, as determined by histochemical staining. However, expression and induction of peroxisome proliferator-activated receptor gamma-2 (PPARγ2) and Sox9, factors involved in early adipogenesis and chondrogenesis, respectively, were higher in bmMSC. We conclude that despite many similarities between bmMSC and pMSC, when expanded under identical conditions, they vary considerably with respect to their in vitro differentiation potential. For regenerative purposes, the choice of MSC may therefore influence the outcome of a treatment considerably.
Measuring wearing times of glasses and ocular patches using a thermosensor device from orthodontics
2013-06-13

The TheraMon(®) microsensor can reliably measure wearing times of glasses and ocular patches without making the wearer uncomfortable, although the data are not unquestionable, especially in higher surrounding temperatures. Further studies on a larger number of individuals with different wearing profiles are needed.
Quaternary paleolake nutrient evolution and climatic change in the western Qaidam Basin deduced from phosphorus geochemistry record of deep drilling core SG-1
2013-06-13

Phosphorus (P) provides an important biologically limiting nutrient in lake ecosystems, and its concentrations furnish significant information on lake nutrient status, climatic change, and landscape development within a drainage area. This study explores the potential of calcium-bound P and iron-bound P in calcareous lacustrine sediments to reveal variations of the paleolake nutrient status and its related climatic changes. Data come from the nearly 1000-m long core (SG-1) from the western Qaidam Basin (NE Tibetan Plateau), which has been well-dated by paleomagnetism to between 2.77 and 0.1 Ma. Calcium-bound P and iron-bound P make up the two most frequent phases of inorganic phosphorus pools in the calcareous sediment. This study compares the variations of calcium-bound P and iron-bound P with the independent proxy for biologic production proxy Total Organic Carbon (TOC) as well as a climatic proxy for lake level fluctuation from the borehole. Those results indicate that calcium-bound P responds sensitively to paleolake nutrients and climatic changes, while the iron-bound P responds to more complex factors, more specific, to the content of iron oxides. Variations of the calcium-bound P in the core SG-1 show a long-term, stepwise decrease, with shifts at similar to 2.5 Ma, 1.8 Ma, 12 Ma, and 0.6 Ma, indicating a long-term stepwise decrease of the paleolake nutrient supply in the drainage. This suggests that the ecologic systems experienced a long-term deterioration, and the climate in central Asia became increasingly arid since after the late Pliocene. (C) 2013 Elsevier Ltd and INQUA. All rights reserved.
Histological and ultrastructural findings of corneal tissue after failed descemet membrane endothelial keratoplasty
2013-06-13

Abstract. Purpose: To investigate in a retrospective review the histological and ultrastructural findings after failed primary and early Descemet membrane endothelial keratoplasty (DMEK), propose possible pathomechanisms of graft failure and give clinical implications. Methods: The explanted grafts underwent light‐ and electromicroscopical investigations in eight failed DMEK cases. Haematoxylin – Eosin, periodic acid Schiff and Alcian blue stainings were performed. Special note was given to any residual stromal remnants, absence of endothelial cells, lamellar structure and ‘activation’ of keratocytes. Results: Of the eight cases, six were re‐DMEKs and two penetrating keratoplasties. Partial graft separation was seen in six and no graft separation in two of the cases. The average time – interval to the re‐DMEK or penetrating keratoplasty was 4.6 months. Light and electron microscopy of the two explanted stromal specimens showed varying degrees of keratocyte activation. Endothelial cell loss was observed in essentially all explants with varying degrees and positive correlation with intraoperative difficulty. Assumed upside‐down situations showed large areas of intact endothelial cells. In addition, a new layer, situated between the endothelial cell layer and the posterior nonbanded layer, was observed with loose intercellular structure. Conclusion: A loss of the endothelial cell layer of varying degrees and positive correlation with intraoperative difficulty are the prominent feature of primary and early DMEK graft failure. Of note is the upside‐down situation, in which in some cases, the endothelial cell layer not only remains intact but also demonstrates metabolical activity in forming a novel cellular layer.
Extraction of otoacoustic distortion product sources using pulse basis functions
2013-06-13

Distortion product otoacoustic emissions (DPOAEs) acquired in normal-hearing subjects show considerable variation in amplitude with varying frequency. This is known as DPOAE fine structure. It is widely accepted that fine structure results from wave interference from two DPOAE sources, a non-linear generation component and a coherent reflection component. Here a method is presented that decomposes short-pulse DPOAE recordings into pulse basis functions and enables the quantification of both source components in the time domain, independent of their relative phase and at low cost of measurement time. Input-output functions utilizing the extracted primary-source component are analyzed.
Genome-Wide Comparison of Medieval and Modern Mycobacterium leprae
2013-06-14

Leprosy: Ancient and Modern In medieval Europe, leprosy was greatly feared: Sufferers had to wear bells and were shunned and kept isolated from society. Although leprosy largely disappeared from Europe in the 16th century, elsewhere in the world almost a quarter of a million cases are still reported annually, despite the availability of effective drugs. Schuenemann et al. (p. 179 , published online 13 June; see the 14 June News story by Gibbons , p. 1278 ) probed the origins of leprosy bacilli by using a genomic capture-based approach on DNA obtained from skeletal remains from the 10th to 14th centuries. Because the unique mycolic acids of this mycobacterium protect its DNA, for one Danish sample over 100-fold, coverage of the genome was possible. Sequencing suggests a link between the middle-eastern and medieval European strains, which falls in line with social historical expectations that the returning expeditionary forces of antiquity originally spread the pathogen. Subsequently, Europeans took the bacterium westward to the Americas. Overall, ancient and modern strains remain remarkably similar, with no apparent loss of virulence genes, indicating it was most probably improvements in social conditions that led to leprosy's demise in Europe.
Prohibition or Coffee Shops: Regulation of Amphetamine and Methylphenidate for Enhancement Use by Healthy Adults
2013-06-14

This article analyzes appropriate public policies for enhancement use of two most important stimulant drugs: Ritalin (methylphenidate) and Adderall (mixed amphetamine salts). The author argues that appropriate regulation of cognition enhancement drugs cannot be a result of a general discussion on cognitive enhancements as such, but has to be made on a case-by-case basis. Starting from the recently proposed taxation approach to cognition enhancement drugs, the author analyzes available, moderately permissive models of regulation. After a thorough analysis of relevant characteristics of methylphenidate and amphetamine, the author concludes that a moderately liberal permissive regulation of enhancement use by healthy adults might be appropriate for extended release forms of methylphenidate. However, due to their danger profile, amphetamine and instant release forms of methylphenidate should not be made readily available to healthy adults and would need to be prohibited.
Long-Term Stabilization Effects of Leptin on Brain Functions in a Leptin-Deficient Patient
2013-06-14

This follow-up study shows that the long lasting benefit of metreleptin therapy is also associated with activation changes in homeostatic, hedonic and frontal control regions in congenital leptin deficiency.
Assessing parental impact on the sports participation of children: A socio‐economic analysis of the UK
2013-06-14

Abstract This study examines the effects of parental attitudes on children's physical activity. A measure of parental attitude (their sport participation when being young) that is independent of the child's behaviour is needed. Using data from the sixth wave of the Taking Part Survey ( n = 14,002 adults and n = 1116 children), a matching estimator analysis is conducted. The results reveal that there are substantial intergenerational transfers of behaviours, in particular for male adults and male children. Furthermore, while an effect is observed for female adults and male children, female children's sport participation is only marginally influenced by female adult's physical activity when growing up. The results imply that promoting sport to the younger generation seems to be a fruitful strategy in creating a sporting habit and promoting sport participation when being older. However, there are challenges to be overcome in promoting female participation.
Parental anxiety and concern for children undergoing dermatological surgery
2013-06-14

Parents experience anxiety and concern about their children's anesthesia and surgeries, which can adversely affect the children's outcomes. Therefore, it is important to identify the factors that influence parental fear. Because dermatological surgery is often performed in young children, we examined how a child's age and the size of the dermatological surgical area affected the levels of parental anxiety and concern. The parents' levels of anxiety and concern were accessed by parental self-reports in a prospective observational study of 106 children undergoing dermatological surgery. Correlation analysis showed that the level of parental anxiety decreased with the child's age. In contrast, the level of parental anxiety increased with the size of the surgical area. Our findings thus indicate that parents whose children undergo large-sized surgeries at a young age are at high risk. This result should be considered when performing dermatological surgery in children.
Optical Properties of Blends: Influence of Mixing-Induced Disorder in Pentacene:Diindenoperylene versus Perfluoropentacene:Diindenoperylene
2013-06-14

The optical properties of mixed films of pentacene:diindenoperylene and perfluoropentacene:diindenoperylene in various mixing ratios are studied using spectroscopic ellipsometry and polarization dependent transmission spectroscopy. Compared to the spectra of films of the pure compounds, the absorption spectra of the blends are found to be significantly influenced by interactions of the comixed compounds and the mixing-induced disorder. On the basis of the comparison of the two mixed systems, we address the effects of mixing and ordering behavior on the specific optical transitions of the different blends by analyzing the line shape of the spectra and the energy positions and widths of the characteristic peaks. The results are important for a fundamental understanding of organic semiconductor blends and possible charge transfer effects in these systems relevant for device applications.
α-Fucosidase as a novel convenient biomarker for cellular senescence
2013-06-15

Due to its role in aging and antitumor defense, cellular senescence has recently attracted increasing interest. However, there is currently no single specific marker that can unequivocally detect senescent cells. Here, we identified α-L-fucosidase (α-Fuc) as a novel sensitive biomarker for cellular senescence. Regardless of the stress stimulus and cell type, α-Fuc activity was induced in all canonical types of cellular senescence, including replicative, DNA damage- and oncogene-induced senescence. Strikingly, in most models the degree of α-Fuc upregulation was higher than the induction of senescence-associated β-galactosidase (SA-β-Gal), the current gold standard for senescence detection. As α-Fuc is convenient and easy to measure, we suggest its utility as a valuable marker, in particular in cells with low SA-β-Gal activity.
The Kinesin-3, Unc-104 Regulates Dendrite Morphogenesis and Synaptic Development in Drosophila
2013-06-15

Abstract Kinesin-based transport is important for synaptogenesis, neuroplasticity, and maintaining synaptic function. In an anatomical screen of neurodevelopmental mutants, we identified the exchange of a conserved residue (R561H) in the forkhead-associated domain of the kinesin-3 family member Unc-104/KIF1A as the genetic cause for defects in synaptic terminal- and dendrite morphogenesis. Previous structure-based analysis suggested that the corresponding residue in KIF1A might be involved in stabilizing the activated state of kinesin-3 dimers. Herein we provide the first in vivo evidence for the functional importance of R561. The R561H allele (unc-104bris) is not embryonic lethal, which allowed us to investigate consequences of disturbed Unc-104 function on postembryonic synapse development and larval behavior. We demonstrate that Unc-104 regulates the reliable apposition of active zones and postsynaptic densities, possibly by controlling site-specific delivery of its cargo. Next, we identified a role for Unc-104 in restraining neuromuscular junction growth and coordinating dendrite branch morphogenesis, suggesting that Unc-104 is also involved in dendritic transport. Mutations in KIF1A/unc-104 have been associated with hereditary spastic paraplegia and hereditary sensory and autonomic neuropathy type 2. However, we did not observe synapse retraction or dystonic posterior paralysis. Overall, our study demonstrates the specificity of defects caused by selective impairments of distinct molecular motors and highlights the critical importance of Unc-104 for the maturation of neuronal structures during embryonic development, larval synaptic terminal outgrowth, and dendrite morphogenesis.
Genetic screening for Niemann-Pick disease type C in adults with neurological and psychiatric symptoms: findings from the ZOOM study
2013-06-16

Niemann-Pick disease type C (NP-C) is a rare, autosomal-recessive, progressive neurological disease caused by mutations in either the NPC1 gene (in 95% of cases) or the NPC2 gene. This observational, multicentre genetic screening study evaluated the frequency and phenotypes of NP-C in consecutive adult patients with neurological and psychiatric symptoms. Diagnostic testing for NP-C involved NPC1 and NPC2 exonic gene sequencing and gene dosage analysis. When available, results of filipin staining, plasma cholestane-3β,5α,6β-triol assays and measurements of relevant sphingolipids were also collected. NPC1 and NPC2 gene sequencing was completed in 250/256 patients from 30 psychiatric and neurological reference centres across the EU and USA [median (range) age 38 (18-90) years]. Three patients had a confirmed diagnosis of NP-C; two based on gene sequencing alone (two known causal disease alleles) and one based on gene sequencing and positive filipin staining. A further 12 patients displayed either single mutant NP-C alleles (8 with NPC1 mutations and 3 with NPC2 mutations) or a known causal disease mutation and an unclassified NPC1 allele variant (1 patient). Notably, high plasma cholestane-3β,5α,6β-triol levels were observed for all NP-C cases (n = 3). Overall, the frequency of NP-C patients in this study [1.2% (95% CI; 0.3%, 3.5%)] suggests that there may be an underdiagnosed pool of NP-C patients among adults who share common neurological and psychiatric symptoms.
Neuronal correlates of a visual “sense of number” in primate parietal and prefrontal cortices
2013-06-17

“Sense of number” refers to the classical idea that we perceive the number of items (numerosity) intuitively. However, whether the brain signals numerosity spontaneously, in the absence of learning, remains unknown; therefore, we recorded from neurons in the ventral intraparietal sulcus and the dorsolateral prefrontal cortex of numerically naive monkeys. Neurons in both brain areas responded maximally to a given number of items, showing tuning to a preferred numerosity. Numerosity was encoded earlier in area ventral intraparietal area, suggesting that numerical information is conveyed from the parietal to the frontal lobe. Visual numerosity is thus spontaneously represented as a perceptual category in a dedicated parietofrontal network. This network may form the biological foundation of a spontaneous number sense, allowing primates to intuitively estimate the number of visual items.
Human colonic mucus is a reservoir for antimicrobial peptides
2013-06-17

These findings indicate that epithelial antimicrobial peptides are retained in the intestinal mucus layer without losing their efficacy. Thus, the mucus layer and its composition provide an attractive drug target to restore antimicrobial barrier function in intestinal diseases.
Memory cell based on a φ Josephson junction
2013-06-17

The φ Josephson junction has a doubly degenerate ground state with the Josephson phases ±φ. We demonstrate the use of such a φ Josephson junction as a memory cell (classical bit), where writing is done by applying a magnetic field and reading by applying a bias current. In the “store” state, the junction does not require any bias or magnetic field, but just needs to stay cooled for permanent storage of the logical bit. Straightforward integration with rapid single flux quantum logic is possible.
Nor-1, a novel incretin-responsive regulator of insulin genes and insulin secretion
2013-06-17

B-cell failure at the onset of type 2 diabetes is caused by a decline in Î2-cell function in the postprandial state and loss of pancreatic Î2-cell mass. Recently, we showed an association between increased insulin secretion and a single nucleotide polymorphism (SNP), SNP rs12686676, in the NR4A3 gene locus encoding the nuclear receptor Nor-1. Nor-1 is expressed in Î2-cells, however, not much is known about its function with regard to insulin gene expression and insulin secretion. Nor-1 is induced in a glucose-/incretin-dependent manner via the PKA pathway and directly induces insulin gene expression. Additionally, it stimulates insulin secretion possibly via regulation of potentially important genes in insulin exocytosis. Moreover, we show that the minor allele of NR4A3 SNP rs12686676 fully rescues incretin resistance provoked by a well-described polymorphism in TCF7L2. Thus, Nor-1 represents a promising new target for pharmacological intervention to fight diabetes.
PII signaling proteins of cyanobacteria and green algae. New features of conserved proteins
2013-06-17

The characteristics of signal PII proteins identified in bacteria, archaea, and plants are presented. Special attention is paid to the properties and functions of PII proteins in microorganisms with oxygenic photosynthesis type: cyanobacteria and unicellular green algae. The structure and regulation of PII proteins are reviewed. The mechanisms of interactions of PII proteins with effectors and cellular targets are analyzed in detail. The conservative properties and unique characteristics of proteins from representatives of pro-and eukaryotic phototrophs are discussed.