julilili42/papers huggingface dataset:
Hamiltonian approach to QCD in Coulomb gauge: Perturbative treatment of the quark sector
2015-06-15

We study the static gluon and quark propagator of the Hamiltonian approach to quantum chromodynamics in Coulomb gauge in one-loop Rayleigh–Schrödinger perturbation theory. We show that the results agree with the equal-time limit of the four-dimensional propagators evaluated in the functional integral (Lagrangian) approach.
10.1063/1.4922544.1
2015-06-15

Views Icon Views Article contents Figures & tables Video Audio Supplementary Data Peer Review Share Icon Share Twitter Facebook Reddit LinkedIn Tools Icon Tools Reprints and Permissions Cite Icon Cite Search Site Citation Heidi Stoll, Heiko Kiessling, Martin Stelzle, Hans Peter Wendel, Julia Schütte, Britta Hagmeyer, Meltem Avci-Adali; Microfluidic chip system for the selection and enrichment of cell binding aptamers. Biomicrofluidics 1 May 2015; 9 (3): 034111. https://doi.org/10.1063/1.4922544 Download citation file: Ris (Zotero) Reference Manager EasyBib Bookends Mendeley Papers EndNote RefWorks BibTex toolbar search Search Dropdown Menu toolbar search search input Search input auto suggest filter your search All ContentAIP Publishing PortfolioBiomicrofluidics Search Advanced Search |Citation Search
10.1063/1.4922544.2
2015-06-15

Aptamers are promising cell targeting ligands for several applications such as for the diagnosis, therapy, and drug delivery. Especially, in the field of regenerative medicine, stem cell specific aptamers have an enormous potential. Using the combinatorial chemistry process SELEX (Systematic Evolution of Ligands by Exponential enrichment), aptamers are selected from a huge oligonucleotide library consisting of approximately 1015 different oligonucleotides. Here, we developed a microfluidic chip system that can be used for the selection of cell specific aptamers. The major drawbacks of common cell-SELEX methods are the inefficient elimination of the unspecifically bound oligonucleotides from the cell surface and the unspecific binding/uptake of oligonucleotides by dead cells. To overcome these obstacles, a microfluidic device, which enables the simultaneous performance of dielectrophoresis and electrophoresis in the same device, was designed. Using this system, viable cells can be selectively assembled by dielectrophoresis between the electrodes and then incubated with the oligonucleotides. To reduce the rate of unspecifically bound sequences, electrophoretic fields can be applied in order to draw loosely bound oligonucleotides away from the cells. Furthermore, by increasing the flow rate in the chip during the iterative rounds of SELEX, the selection pressure can be improved and aptamers with higher affinities and specificities can be obtained. This new microfluidic device has a tremendous capability to improve the cell-SELEX procedure and to select highly specific aptamers.
On the evidence for human use and control of fire at Schöningen
2015-06-16

When and how humans began to control fire has been a central debate in Paleolithic archaeology for decades. Fire plays an important role in technology, social organization, subsistence, and manipulation of the environment and is widely seen as a necessary adaptation for the colonization of northern latitudes. Many researchers view purported hearths, burnt wooden implements, and heated flints from Schöningen as providing the best evidence for the control of fire in the Lower Paleolithic of Northern Europe. Here we present results of a multianalytical study of the purported hearths along with a critical examination of other possible evidence of human use or control of fire at Schöningen. We conclude that the analyzed features and artifacts present no convincing evidence for human use or control of fire. Our study also shows that a multianalytical, micro-contextual approach is the best methodology for evaluating claims of early evidence of human-controlled fire. We advise caution with macroscopic, qualitative identification of combustion features, burnt flint, and burnt wood without the application of such techniques as micromorphology, Fourier transform infrared (FTIR) spectroscopy, organic petrology, luminescence, and analysis of mineral magnetic parameters. The lack of evidence for the human control of fire at Schöningen raises the possibility that fire control was not a necessary adaptation for the human settlement of northern latitudes in the Lower Paleolithic.
Species-Specific Effects on Throughfall Kinetic Energy in Subtropical Forest Plantations Are Related to Leaf Traits and Tree Architecture
2015-06-16

Soil erosion is a key threat to many ecosystems, especially in subtropical China where high erosion rates occur. While the mechanisms that induce soil erosion on agricultural land are well understood, soil erosion processes in forests have rarely been studied. Throughfall kinetic energy (TKE) is influenced in manifold ways and often determined by the tree's leaf and architectural traits. We investigated the role of species identity in mono-specific stands on TKE by asking to what extent TKE is species-specific and which leaf and architectural traits account for variation in TKE. We measured TKE of 11 different tree species planted in monocultures in a biodiversity-ecosystem-functioning experiment in subtropical China, using sand-filled splash cups during five natural rainfall events in summer 2013. In addition, 14 leaf and tree architectural traits were measured and linked to TKE. Our results showed that TKE was highly species-specific. Highest TKE was found below Choerospondias axillaris and Sapindus saponaria, while Schima superba showed lowest TKE. These species-specific effects were mediated by leaf habit, leaf area (LA), leaf pinnation, leaf margin, stem diameter at ground level (GD), crown base height (CBH), tree height, number of branches and leaf area index (LAI) as biotic factors and throughfall as abiotic factor. Among these, leaf habit, tree height and LA showed the highest effect sizes on TKE and can be considered as major drivers of TKE. TKE was positively influenced by LA, GD, CBH, tree height, LAI, and throughfall amount while it was negatively influenced by the number of branches. TKE was lower in evergreen, simple leaved and dentate leaved than in deciduous, pinnated or entire leaved species. Our results clearly showed that soil erosion in forest plantations can be mitigated by the appropriate choice of tree species.
JSBML 1.0: providing a smorgasbord of options to encode systems biology models
2015-06-16

Abstract Summary: JSBML, the official pure Java programming library for the Systems Biology Markup Language (SBML) format, has evolved with the advent of different modeling formalisms in systems biology and their ability to be exchanged and represented via extensions of SBML. JSBML has matured into a major, active open-source project with contributions from a growing, international team of developers who not only maintain compatibility with SBML, but also drive steady improvements to the Java interface and promote ease-of-use with end users. Availability and implementation: Source code, binaries and documentation for JSBML can be freely obtained under the terms of the LGPL 2.1 from the website http://sbml.org/Software/JSBML. More information about JSBML can be found in the user guide at http://sbml.org/Software/JSBML/docs/. Contact: jsbml-development@googlegroups.com or andraeger@eng.ucsd.edu Supplementary information: Supplementary data are available at Bioinformatics online.
Beta/gamma and alpha backgrounds in CRESST-II Phase 2
2015-06-16

The experiment CRESST-II aims at the detection of dark matter with\\nscintillating CaWO crystals operated as cryogenic detectors. Recent results\\non spin-independent WIMP-nucleon scattering from the CRESST-II Phase 2 allowed\\nto probe a new region of parameter space for WIMP masses below 3 GeV/c .\\nThis sensitivity was achieved after background levels were reduced\\nsignificantly. We present extensive background studies of a CaWO crystal,\\ncalled TUM40, grown at the Technische Universit\\\\"at M\\\\"unchen. The average\\nbeta/gamma rate of 3.51/[kg keV day] (1-40 keV) and the total intrinsic alpha\\nactivity from natural decay chains of mBq/kg are the lowest\\nreported for CaWO detectors. Contributions from cosmogenic activation,\\nsurface-alpha decays, external radiation and intrinsic alpha/beta emitters are\\ninvestigated in detail. A Monte-Carlo based background decomposition allows to\\nidentify the origin of the majority of beta/gamma events in the energy region\\nrelevant for dark matter search.\\n
The νSaα Specific Lipoprotein Like Cluster (lpl) of S. aureus USA300 Contributes to Immune Stimulation and Invasion in Human Cells
2015-06-17

All Staphylococcus aureus genomes contain a genomic island, which is termed νSaα and characterized by two clusters of tandem repeat sequences, i.e. the exotoxin (set) and 'lipoprotein-like' genes (lpl). Based on their structural similarities the νSaα islands have been classified as type I to IV. The genomes of highly pathogenic and particularly epidemic S. aureus strains (USA300, N315, Mu50, NCTC8325, Newman, COL, JH1 or JH9) belonging to the clonal complexes CC5 and CC8 bear a type I νSaα island. Since the contribution of the lpl gene cluster encoded in the νSaα island to virulence is unclear to date, we deleted the entire lpl gene cluster in S. aureus USA300. The results showed that the mutant was deficient in the stimulation of pro-inflammatory cytokines in human monocytes, macrophages and keratinocytes. Purified lipoprotein Lpl1 was further shown to elicit a TLR2-dependent response. Furthermore, heterologous expression of the USA300 lpl cluster in other S. aureus strains enhanced their immune stimulatory activity. Most importantly, the lpl cluster contributed to invasion of S. aureus into human keratinocytes and mouse skin and the non-invasive S. carnosus expressing the lpl gene cluster became invasive. Additionally, in a murine kidney abscess model the bacterial burden in the kidneys was higher in wild type than in mutant mice. In this infection model the lpl cluster, thus, contributes to virulence. The present report is one of the first studies addressing the role of the νSaα encoded lpl gene cluster in staphylococcal virulence. The finding that the lpl gene cluster contributes to internalization into non-professional antigen presenting cells such as keratinocytes highlights the lpl as a new cell surface component that triggers host cell invasion by S. aureus. Increased invasion in murine skin and an increased bacterial burden in a murine kidney abscess model suggest that the lpl gene cluster serves as an important virulence factor.
Anti-infective Natural Products from Cyanobacteria
2015-06-17

Cyanobacteria are a promising yet underexplored source for novel natural products with potent biological activities. While predominantly cytotoxic compounds have been isolated from cyanobacteria in the past, there are also a significant number of compounds known that possess anti-infective activities. As the need for novel anti-infective lead compounds is high, this manuscript aims at giving a concise overview on the current knowledge about anti-infective secondary metabolites isolated from cyanobacteria. Antibacterial, antifungal, antiviral, antiprotozoal, and molluscicidal activities are discussed. Covering up to February 2015.
Salt-Induced Universal Slowing Down of the Short-Time Self-Diffusion of a Globular Protein in Aqueous Solution
2015-06-17

The short-time self-diffusion D of the globular model protein bovine serum albumin in aqueous (D2O) solutions has been measured comprehensively as a function of the protein and trivalent salt (YCl3) concentration, noted cp and cs, respectively. We observe that D follows a universal master curve D(cs,cp) = D(cs = 0,cp) g(cs/cp), where D(cs = 0,cp) is the diffusion coefficient in the absence of salt and g(cs/cp) is a scalar function solely depending on the ratio of the salt and protein concentration. This observation is consistent with a universal scaling of the bonding probability in a picture of cluster formation of patchy particles. The finding corroborates the predictive power of the description of proteins as colloids with distinct attractive ion-activated surface patches.
Pitfalls in Echocardiography: Coarctation of the Aorta Presenting as Dilated Cardiomyopathy (DCM)
2015-06-17

<b>Purpose:</b> The morphologic spectrum of aortic coarctation extends from discrete isthmic obstruction to tubular hypoplasia of the entire aortic arch. Neonates with coarctation frequently present with congestive heart failure and critically reduced perfusion of the descending aorta following ductal closure. During the recent years we observed several infants with coarctation who presented beyond the neonatal period with dilated cardiomyopathy (DCM). We reviewed our patients with coarctation to determine whether this presentation represents an exception or is relevant for the differential diagnosis of children with DCM. <b>Materials and Methods:</b> From 1/2001 to 12/2013 74 babies with isolated coarctation were diagnosed in our institution. 50 patients presented in the neonatal period and 24 patients beyond the first month. <b>Results:</b> 5/74 infants presented after the neonatal period with poorly contractile, dilated left ventricles. Echocardiographic detection of the coarctation was facilitated by application of the ductal view and by Doppler interrogation of the celiac artery revealing a significantly diminished systolic flow velocity. All patients underwent resection of the coarctation and end-to-end anastomosis of the aorta. Postoperative normalization of left ventricular function was observed within a median interval of 2 months. <b>Conclusion:</b> Coarctation of the aorta presenting as DCM accounted for 21 % of our infants with coarctation who presented beyond the neonatal period and 7 % of those in the first year of life. The stenosis was difficult to detect because of its distal location and normal configuration of the aortic arch. Isthmic coarctation should be included in the differential diagnosis of infants with DCM and requires careful examination of the isthmic region in these children.
Compiling the Uralic Dataset for NorthEuraLex, a Lexicostatistical Database of Northern Eurasia
2015-06-17

This paper presents a large comparative lexical database which covers about a thousand concepts across twenty Uralic languages. The dataset will be releasedas the first part of NorthEuraLex, a lexicostatistical database of Northern Eurasia which is being compiled within the EVOLAEMP project.The chief purpose of the lexical database is to serve as a basis of benchmarks for different tasks within computational historical linguistics, but it might also be valuable to researchers who work on the application of computational methods to open research questions within the language family.The paper describes and motivates the decisions taken concerning data collection methodology, also discussing some of the problems involved in compiling and unifying data from lexical resources in six different gloss languages.The dataset is already publicly available in various PDF formats for inspection and review, and is scheduled for release in machine-readable form in early 2015.
Cortical information flow during flexible sensorimotor decisions
2015-06-18

Signal flow during sensorimotor choices Little is known about the flow of task signals across the brain. Siegel et al. simultaneously recorded from multiple units in the sensory, parietal, prefrontal, and motor cortex while monkeys were cued to perform one among two possible simple tasks. The proportion of neurons coding for stimuli, cues, tasks, and choices, and their response latency, varied across regions. Parietal and prefrontal brain regions encoded task information and choices with the same latency. Interestingly, all brain areas encoded all types of information. However, they differed functionally according to the proportions of neurons and their response latency. Science , this issue p. 1352
Detection and Characterization of Compounds in the Mn‐W‐Cl System through a Combined Thermal Scanning ‐ XRD Approach
2015-06-18

Abstract A procedure combining thermal analyses and XRD powder diffraction is used to scan and detect a series of new compounds in the Mn‐W‐Cl system. Four new ternary Mn‐W‐Cl compounds are formed in a progressive reaction of tungsten hexachloride (WCl 6 ) with manganese powder, in which tungsten is gradually reduced from W 6+ to W 2+ . Among several DSC signals, the new compounds Mn x WCl 6 , MnW 2 Cl 10 , (Mn, W) 1– x Cl 2 , and MnW 6 Cl 14 are detected and their crystal structures are assigned or identified by X‐ray diffraction techniques. Magnetic properties are reported for MnW 2 Cl 10 and MnW 6 Cl 14 .
Hospital admission for diabetic ketoacidosis or severe hypoglycemia in 31 330 young patients with type 1 diabetes
2015-06-19

Objective To investigate rates and risk factors of hospital admission for diabetic ketoacidosis (DKA) or severe hypoglycemia in young patients with established type 1 diabetes. Design In total, 31 330 patients with type 1 diabetes (median age 12.7 years) from the Diabetes Patienten Verlaufsdokumentation (DPV) Prospective Diabetes Registry treated between 2011 and 2013 in Germany were included. Methods Admission rates for DKA (pH &lt;7.3 or bicarbonate &lt;15 mmol/l) and severe hypoglycemia (requiring assistance from another person) were calculated by negative binomial regression analysis. Associations of DKA or hypoglycemia with patient and treatment characteristics were assessed by multivariable regression analysis. Results The mean admission rate for DKA was 4.81/100 patient-years (95% CI, 4.51–5.14). The highest DKA rates were observed in patients with HbA1c ≥9.0% (15.83 (14.44–17.36)), age 15–20 years (6.21 (5.61–6.88)) and diabetes duration of 2–4.9 years (5.60 (5.00–6.27)). DKA rate was higher in girls than in boys (5.35 (4.88–5.86) vs 4.34 (3.95–4.77), P =0.002), and more frequent in migrants than in non-migrants (5.65 (4.92–6.49) vs 4.57 (4.23–4.93), P =0.008). The mean admission rate for severe hypoglycemia was 1.45/100 patient-years (1.30–1.61). Rates were higher in migrants compared to non-migrants (2.13 (1.72–2.65) vs 1.28 (1.12–1.47), P &lt;0.001), and highest in individuals with severe hypoglycemia within the preceding year (17.69 (15.63–20.03) vs patients without preceding hypoglycemia 0.42 (0.35–0.52), P &lt;0.001). Differences remained significant after multivariable adjustment. Conclusions The identification of at-risk individuals for DKA (patients with high HbA1c, longer diabetes duration, adolescents, girls) and for severe hypoglycemia (patients with preceding severe hypoglycemia, migrants) may facilitate targeted diabetes counselling in order to prevent these complications.
Treatment of Primary Hypophysitis in Germany
2015-06-19

Glucocorticoid pulse therapy is associated with a high recurrence rate. Evidence suggests that surgery is not able to prevent recurrence. Considering the favorable results of observation, conservative management is recommended in PrHy unless symptoms are severe or progressive.
The Radiative Lifetime in Near‐IR‐Luminescent Ytterbium Cryptates: The Key to Extremely High Quantum Yields
2015-06-19

Abstract A powerful strategy for the improvement of near‐IR lanthanoid luminescence has been successfully employed for the first time, which involves the rational and deliberate shortening of the radiative luminescence lifetimes τ rad in molecular ytterbium complexes. In this context, the bidentate chelating unit 2,2′‐bipyridine‐ N , N ′‐dioxide has been identified as being responsible for decreasing τ rad substantially in macrobicyclic Yb cryptates. This strategy, when combined with conventional approaches, yields unprecedented absolute near‐IR quantum yields of up to 12 %. This extraordinary efficiency represents the highest value measured for any molecular lanthanoid near‐IR emitter. The proof‐of‐concept for the implementation of the new strategy opens up entirely new prospects for the field of lanthanoid luminescence.
Hydraulic Tomography: Continuity and Discontinuity of High‐ K and Low‐ K Zones
2015-06-19

Abstract Hydraulic tomography is an emerging field and modeling method that provides a continuous hydraulic conductivity ( K ) distribution for an investigated region. Characterization approaches that rely on interpolation between one‐dimensional ( 1D ) profiles have limited ability to accurately identify high‐ K channels, juxtapositions of lenses with high K contrast, and breaches in layers or channels between such profiles. However, locating these features is especially important for groundwater flow and transport modeling, and for design and operation of in situ remediation in complex hydrogeologic environments. We use transient hydraulic tomography to estimate 3D K in a volume of 15‐m diameter by 20‐m saturated thickness in a highly heterogeneous unconfined alluvial (clay to sand‐and‐gravel) aquifer with a K range of approximately seven orders of magnitude at an active industrial site in Assemini, Sardinia, Italy. A modified Levenberg‐Marquardt algorithm was used for geostatistical inversion to deal with the nonlinear nature of the highly heterogeneous system. The imaging results are validated with pumping tests not used in the tomographic inversion. These tests were conducted from three of five clusters of continuous multichannel tubing ( CMTs ) installed for observation in the tomographic testing. Locations of high‐ K continuity and discontinuity, juxtaposition of very high‐ K and very low‐ K lenses, and low‐ K “plugs” are evident in regions of the investigated volume where they likely would not have been identified with interpolation from 1D profiles at the positions of the pumping well and five CMT clusters. Quality assessment methods identified a suspect high‐ K feature between the tested volume and a lateral boundary of the model.
Bacillus subtilis SalA is a phosphorylation‐dependent transcription regulator that represses scoC and activates the production of the exoprotease AprE
2015-06-19

Summary B acillus subtilis M rp family protein SalA has been shown to indirectly promote the production of the exoprotease AprE by inhibiting the expression of scoC , which codes for a repressor of aprE . The exact mechanism by which SalA influences scoC expression has not been clarified previously. We demonstrate that SalA possesses a DNA ‐binding domain (residues 1–60), which binds to the promoter region of scoC . The binding of SalA to its target DNA depends on the presence of ATP and is stimulated by phosphorylation of SalA at tyrosine 327. The B . subtilis protein‐tyrosine kinase PtkA interacts specifically with the C ‐terminal domain of SalA in vivo and in vitro and is responsible for activating its DNA binding via phosphorylation of tyrosine 327. In vivo , a mutant mimicking phosphorylation of SalA ( SalA Y327E ) exhibited a strong repression of scoC and consequently overproduction of AprE . By contrast, the non‐phosphorylatable SalA Y327F and the Δ ptkA exhibited the opposite effect, stronger expression of scoC and lower production of the exoprotease. Interestingly, both SalA and PtkA contain the same ATP ‐binding Walker domain and have thus presumably arisen from the common ancestral protein. Their regulatory interplay seems to be conserved in other bacteria.