julilili42/papers huggingface dataset:
Controlled heparinase‐catalyzed degradation of polyelectrolyte multilayer capsules with heparin as responsive layer
2017-02-07

ABSTRACT This work describes the enzymatic degradation of combined hollow capsules via layer‐by‐layer (LbL) self‐assembly technique. They previously showed the build‐up and characterization of capsules composed of synthetic [Poly(sodium 4‐styrene‐sulfonate)/Poly(allylamine hydrochloride)] and biodegradable (Heparin/Chitosan) polyelectrolytes. Biocatalytic response of assembled multilayer capsules provides a more functional and oriented approach in controlled release of encapsulated molecules: in this case multilayer capsule was disassembled by heparinase. Morphological change of individual capsule was assessed with Atomic Force Microscopy and Confocal Laser Scanning Microscopy. The sustained release of encapsulated FITC‐Dextran model was realized under enzymatic degradation of the capsule shells by heparinase. The release profile of FITC‐Dextran indicated the successful control in a concentration‐dependent manner, which shows the applicability as smart drug delivery system. © 2017 Wiley Periodicals, Inc. J. Appl. Polym. Sci. 2017 , 134 , 44916.
Determinants of BH3 Sequence Specificity for the Disruption of Bcl-xL/cBid Complexes in Membranes
2017-02-07

The prosurvival Bcl-2 proteins exhibit a specific pattern of interactions with BH3-only proteins that determines the cellular dependence on apoptotic stress. This specificity is crucial for the development of BH3 mimetics, a class of anticancer molecules based on the BH3 domain with promising activity in clinical trials. Although complex formation mainly takes place in the mitochondrial outer membrane, most studies so far addressed the interaction between BH3 peptides and truncated Bcl-2 proteins in solution. As a consequence, quantitative understanding of the sequence specificity determinants of BH3 peptides in the membrane environment is missing. Here, we tackle this issue by systematically quantifying the ability of BH3 peptides to compete for the complexes between cBid and Bcl-xL in giant unilamellar vesicles and compare it with solution and mitochondria. We show that the BH3 peptides derived from Hrk, Bim, Bid, and Bad are the most efficient in disrupting cBid/Bcl-xL complexes in the membrane, which correlates with their activity in mitochondria. Our findings support the targeting to the membrane of small molecules that bind Bcl-2 proteins as a strategy to improve their efficiency.
Delayed phase separation in growth of organic semiconductor blends with limited intermixing
2017-02-07

Binary mixed thin films of picene (C22H14, PIC) and pentacene (C22H14, PEN) consist of crystallites with a statistical occupation of the lattice sites by either PEN or PIC and unit cell parameters continuously changing with the mixing ratio. For high PIC ratios a PIC phase forms which corresponds to a limited intermixing of the two compounds. The growth behavior of these mixtures is investigated in situ and in real-time using grazing incidence X-ray diffraction. We observe a delayed phase separation in PIC-rich blends, i.e. complete intermixing in the monolayer range and the nucleation of a pure PIC-phase in addition to the intermixed phase starting from the second monolayer. Growth scenario of picene-rich pentacene-picene blends.
Toric Geometry
2017-02-07

Toric geometry is a subfield of algebraic geometry with deep intersections with combinatorics. This workshop brought together researchers working in toric geometry, applying toric geometry elsewhere in algebraic geometry, and applying toric geometry elsewhere inside and outside mathematics.
Toxic Mixtures in Time—The Sequence Makes the Poison
2017-02-08

"The dose makes the poison". This principle assumes that once a chemical is cleared out of the organism (toxicokinetic recovery), it no longer has any effect. However, it overlooks the other process of re-establishing homeostasis, toxicodynamic recovery, which can be fast or slow depending on the chemical. Therefore, when organisms are exposed to two toxicants in sequence, the toxicity can differ if their order is reversed. We test this hypothesis with the freshwater crustacean Gammarus pulex and four toxicants that act on different targets (diazinon, propiconazole, 4,6-dinitro-o-cresol, 4-nitrobenzyl chloride). We found clearly different toxicity when the exposure order of two toxicants was reversed, while maintaining the same dose. Slow toxicodynamic recovery caused carry-over toxicity in subsequent exposures, thereby resulting in a sequence effect-but only when toxicodynamic recovery was slow relative to the interval between exposures. This suggests that carry-over toxicity is a useful proxy for organism fitness and that risk assessment methods should be revised as they currently could underestimate risk. We provide the first evidence that carry-over toxicity occurs among chemicals acting on different targets and when exposure is several days apart. It is therefore not only the dose that makes the poison but also the exposure sequence.
Salmonella entericagenomes recovered from victims of a major 16th century epidemic in Mexico
2017-02-08

Abstract Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Using a metagenomic tool called MALT to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked to the 1545-1550 CE epidemic locally known as “ cocoliztli ”, the cause of which has been debated for over a century. Here we present two reconstructed ancient genomes for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C contributed to the population decline during the 1545 cocoliztli outbreak in Mexico. One Sentence Summary Genomic evidence of enteric fever identified in an indigenous population from early contact period Mexico.
Mitogenome Diversity in Sardinians: A Genetic Window onto an Island's Past
2017-02-08

Sardinians are "outliers" in the European genetic landscape and, according to paleogenomic nuclear data, the closest to early European Neolithic farmers. To learn more about their genetic ancestry, we analyzed 3,491 modern and 21 ancient mitogenomes from Sardinia. We observed that 78.4% of modern mitogenomes cluster into 89 haplogroups that most likely arose in situ. For each Sardinian-specific haplogroup (SSH), we also identified the upstream node in the phylogeny, from which non-Sardinian mitogenomes radiate. This provided minimum and maximum time estimates for the presence of each SSH on the island. In agreement with demographic evidence, almost all SSHs coalesce in the post-Nuragic, Nuragic and Neolithic-Copper Age periods. For some rare SSHs, however, we could not dismiss the possibility that they might have been on the island prior to the Neolithic, a scenario that would be in agreement with archeological evidence of a Mesolithic occupation of Sardinia.
Anisotropic hydrodynamic turbulence in accretion disks
2017-02-08

\\n Recently, the vertical shear instability (VSI) has become an attractive purely hydrodynamic candidate for the anomalous angular momentum transport required for weakly ionized accretion disks. In direct three-dimensional numerical simulations of VSI turbulence in disks, a meridional circulation pattern was observed that is opposite to the usual viscous flow behavior. Here, we investigate whether this feature can possibly be explained by an anisotropy of the VSI turbulence. Using three-dimensional hydrodynamical simulations, we calculate the turbulent Reynolds stresses relevant for angular momentum transport for a representative section of a disk. We find that the vertical stress is significantly stronger than the radial stress. Using our results in viscous disk simulations with different viscosity coefficients for the radial and vertical direction, we find good agreement with the VSI turbulence for the stresses and meridional flow; this provides additional evidence for the anisotropy. The results are important with respect to the transport of small embedded particles in disks.\\n
Proprioceptive Feedback Facilitates Motor Imagery-Related Operant Learning of Sensorimotor β-Band Modulation
2017-02-08

Motor imagery (MI) activates the sensorimotor system independent of actual movements and might be facilitated by neurofeedback. Knowledge on the interaction between feedback modality and the involved frequency bands during MI-related brain self-regulation is still scarce. Previous studies compared the cortical activity during the MI task with concurrent feedback (MI <i>with</i> feedback condition) to cortical activity during the relaxation task where no feedback was provided (relaxation <i>without</i> feedback condition). The observed differences might, therefore, be related to either the task or the feedback. A proper comparison would necessitate studying a relaxation condition with feedback and a MI task condition without feedback as well. Right-handed healthy subjects performed two tasks, i.e., MI and relaxation, in alternating order. Each of the tasks (MI vs. relaxation) was studied with and without feedback. The respective event-driven oscillatory activity, i.e., sensorimotor desynchronization (during MI) or synchronization (during relaxation), was rewarded with contingent feedback. Importantly, feedback onset was delayed to study the task-related cortical activity in the absence of feedback provision during the delay period. The reward modality was alternated every 15 trials between proprioceptive and visual feedback. Proprioceptive input was superior to visual input to increase the range of task-related spectral perturbations in the α- and β-band, and was necessary to consistently achieve MI-related sensorimotor desynchronization (ERD) significantly below baseline. These effects occurred in task periods without feedback as well. The increased accuracy and duration of learned brain self-regulation achieved in the proprioceptive condition was specific to the β-band. MI-related operant learning of brain self-regulation is facilitated by proprioceptive feedback and mediated in the sensorimotor β-band.
Comparative drilling predation on time-averaged phosphatized and nonphosphatized assemblages of the minute clypeasteroid echinoidEchinocyamus stellatusfrom Miocene offshore sediments (Globigerina Limestone Formation, Malta)
2017-02-08

Abstract Fossilized tests of 1,053 Echinocyamus stellatus (Capeder, 1906) from the Miocene Globigerina Limestone Formation exposed on the northern coast of Gozo (Maltese Islands) were analyzed for predation traces. Specimens mixed by time-averaging processes can be clearly separated into two distinct samples according to their preservation as phosphatized or nonphosphatized individuals. Overall, 11.1% of the tests reveal holes that are referred to the ichnospecies Oichnus simplex (Bromley, 1981). Because of the hole morphology and diameter, the holes are interpreted as predatory drill holes, most likely produced by cassid gastropods. Redeposited phosphatized echinoids derived from an earlier period of reduced sedimentation rates show drilling frequencies of 20.5%. Younger, autochthonous, nonphosphatized echinoids show drilling frequencies of 8.1%. In both samples, predators predominantly targeted the aboral side of the echinoid test, particularly on the petalodium.
High intraspecific phenotypic variation, but little evidence for local adaptation in Geum reptans populations in the Central Swiss Alps
2017-02-08

The Alpine landscape is characterized by high spatiotemporal heterogeneity in environmental variables, such as climate and soil characteristics. This may lead to divergent selection pressures across plant populations and to local adaptation. Geum reptans, a widespread high-alpine clonal herb, has been the subject of several studies investigating phenotypic variation in populations across the Swiss Alps, yet so far, there is only little knowledge about local adaptation in this species from reciprocal transplantations across original field sites. Here, we reciprocally transplanted three populations of Geum reptans in the Central Swiss Alps, growing at close or far geographical distance from each other, and compared growth- and reproduction-related traits to investigate patterns of local adaptation. We further measured leaf morphological traits to assess potential selection at field sites, and quantified the relative importance of genetic vs. environmental variation (i.e., phenotypic plasticity) for all traits. Additionally, among and within population genetic differentiation was analyzed using microsatellite markers. Molecular diversity was high within populations, and molecular differentiation increased with geographic distance among populations, suggesting that gene flow is maintained at close range, but decreased with distance. Although extensive phenotypic variation was found across site × population transplant combinations, our study revealed little evidence for local adaptation in G. reptans populations. Plant traits also showed strong plasticity, as revealed by pronounced site effects, yet no direct linear selection was detected on leaf trait values within field sites. We suggest that the glacier forelands studied here, which are representative of the habitat of large G. reptans populations, are too similar in environmental conditions to lead to among population intraspecific differentiation in line with local adaptation. As G. reptans showed a great capacity to respond plastically to environmental conditions, we cautiously advocate that the evolution of phenotypic plasticity might have prevailed over genetic differentiation for the adaptation to the relatively narrow niche of this species.
Intralesional anti‐CD20 antibody for low‐grade primary cutaneous B‐cell lymphoma: Adverse reactions correlate with favorable clinical outcome
2017-02-08

Summary Background and Objectives Intralesional injection of anti‐CD20 antibody (rituximab) has been described as effective therapeutic option for patients with indolent primary cutaneous B‐cell lymphoma (PCBL). To date, no parameters that reproducibly predict favorable clinical outcome of this treatment have been identified. The study aims to evaluate the clinical response and adverse effects as well as patients’ self‐perception of intralesional injection of anti‐CD20 antibody for treatment of indolent PCBL compared to other treatment modalities. Patients and Methods Eleven patients with PCBL, namely primary cutaneous follicle center lymphoma (n = 9) and primary cutaneous marginal zone lymphoma (n = 2), treated with intralesional anti‐CD20 antibody were retrospectively evaluated for response rate and adverse events as well as their self‐perception of anti‐CD20 antibody therapy and other therapies of PCBL. Results Patients treated with intralesional anti‐CD20 antibody for PCBL showed complete response or partial response in 45 % or 27 % of patients, respectively. Particularly, patients with marked flu‐like symptoms after intralesional injection of rituximab responded very well to rituximab. The majority of patients considered rituximab as best therapy compared to other therapies such as excision or radiotherapy. Conclusions Intralesional rituximab is an effective therapy with high patient satisfaction. Strong therapy induced side effects of fever, chills and headache after administration of rituximab might be used as indicator for favorable response.
Benford and the Internal Capital Market: A Useful Indicator of Managerial Engagement
2017-02-08

Abstract We propose the application of digit analysis using the Benford law to indicate managerial engagement in the capital allocation process. First, we motivate the potential of the Benford digit analysis to identify allocation outcomes that are shaped by human engagement instead of fixed decision rules. Second, we provide a case study to illustrate how the Benford digit analysis can be used to detect allocations affected by managerial interventions. We are unaware of any study applying the Benford test to internal capital markets, while this approach appears very useful in this context. It is commonly used in the auditing, financial accounting, and fraud detection literature.
High vacuum compatible fiber feedthrough for hot alkali vapor cells
2017-02-08

We demonstrate a method to produce vacuum tight, metal free, bakeable and\\nalkali compatible feedthroughs for optical fibers. The manufacturing process\\nmainly relies on encasing fibers made of fused silica with glass materials with\\nlower melting points by heating. We analyze the vacuum and optical performance\\nof the devices by various methods including helium leak checking and several\\nspectroscopic schemes, among others electromagnetically induced transparency\\ninvolving Rydberg states.\\n
Echinoderm ichnology: bioturbation, bioerosion and related processes
2017-02-09

Abstract Among invertebrates and both in modern and ancient marine environments, certain echinoderms have been and are some of the most active and widespread bioturbators and bioeroders. Bioturbation and/or bioerosion of regular and irregular echinoids, starfish, brittle stars, sea cucumbers and crinoids are known from modern settings, and some of the resulting traces have their counterparts in the fossil record. By contrast, surficial trails or trackways produced by other modern echinoderms, e.g., sand dollars, exhibit a lower preservation rate and have not yet been identified in the fossil record. In addition, the unique features of the echinoderm skeleton (e.g., composition, rapid growth, multi-element architecture, etc.) may promote the production of related traces produced by the reutilization of echinoderm ossicles (e.g., burrow lining), predation (e.g., borings), or parasitism (e.g., swellings or cysts). Finally, the skeletal robustness of some echinoids may promote their post mortum use as benthic islands for the settlement of hard-substrate dwellers.
Long-term observation reveals high-frequency engraftment of human acute myeloid leukemia in immunodeficient mice
2017-02-09

Repopulation of immunodeficient mice remains the primary method for functional assessment of human acute myeloid leukemia. Published data report engraftment in ~40-66% of cases, mostly of intermediate- or poor-risk subtypes. Here we report that extending follow-up beyond the standard analysis endpoints of 10 to 16 weeks after transplantation permitted leukemic engraftment from nearly every case of xenotransplanted acute myeloid leukemia (18/19, ~95%). Xenogeneic leukemic cells showed conserved immune pheno-types and genetic signatures when compared to corresponding pre-transplant cells and, furthermore, were able to induce leukemia in re-transplantation assays. Importantly, bone marrow biopsies taken at standardized time points failed to detect leukemic cells in 11/18 of cases that later showed robust engraftment (61%, termed "long-latency engrafters"), indicating that leukemic cells can persist over months at undetectable levels without losing disease-initiating properties. Cells from favorable-risk leukemia subtypes required longer to become detectable in NOD/SCID/IL2Rγ<sup>null</sup> mice (27.5±9.4 weeks) than did cells from intermediate-risk (21.9±9.4 weeks, <i>P</i><0.01) or adverse-risk (17±7.6 weeks; <i>P</i><0.0001) subtypes, explaining why the engraftment of the first was missed with previous protocols. Mechanistically, leukemic cells engrafting after a prolonged latency showed inferior homing to the bone marrow. Finally, we applied our model to favorable-risk acute myeloid leukemia with inv(16); here, we showed that CD34<sup>+</sup> (but not CD34<sup>-</sup>) blasts induced robust, long-latency engraftment and expressed enhanced levels of stem cell genes. In conclusion, we provide a model that allows <i>in vivo</i> mouse studies with a wide range of molecular subtypes of acute myeloid leukemia subtypes which were previously considered not able to engraft, thus enabling novel insights into leukemogenesis.
AGOS: A Plug-and-Play Method for the Assembly of Artificial Gene Operons into Functional Biosynthetic Gene Clusters
2017-02-09

The generation of novel secondary metabolites by reengineering or refactoring biochemical pathways is a rewarding but also challenging goal of synthetic biology. For this, the development of tools for the reconstruction of secondary metabolite gene clusters as well as the challenge of understanding the obstacles in this process is of great interest. The artificial gene operon assembly system (AGOS) is a plug-and-play method developed as a tool to consecutively assemble artificial gene operons into a destination vector and subsequently express them under the control of a de-repressed promoter in a Streptomyces host strain. AGOS was designed as a set of entry plasmids for the construction of artificial gene operons and a SuperCos1 based destination vector, into which the constructed operons can be assembled by Red/ET-mediated recombination. To provide a proof-of-concept of this method, we disassembled the well-known novobiocin biosynthetic gene cluster into four gene operons, encoding for the different moieties of novobiocin. We then genetically reorganized these gene operons with the help of AGOS to finally obtain the complete novobiocin gene cluster again. The production of novobiocin precursors and of novobiocin could successfully be detected by LC-MS and LC-MS/MS. Furthermore, we demonstrated that the omission of terminator sequences only had a minor impact on product formation in our system.
MR Imaging of Individual Perfusion Reorganization Using Superselective Pseudocontinuous Arterial Spin-Labeling in Patients with Complex Extracranial Steno-Occlusive Disease
2017-02-09

Superselective pseudocontinuous arterial spin-labeling is a robust technique for regional brain perfusion imaging, suitable for the noninvasive diagnostics of individual perfusion patterns in patients with complex cerebrovascular disease.
Hunted or Scavenged Neanderthals? Taphonomic Approach to Hominin Fossils with Carnivore Damage
2017-02-09

Abstract Carnivore damage on Neanderthal fossils is a much more common taphonomic modification than previously thought. Its presence could have different explanations, including predatory attacks or scavenging scenarios, which are both situations with important implications concerning Neanderthal behaviour. In the present paper, we analyse several Neanderthal hominin fossils from a taphonomic and forensic perspective in order to infer the nature of the modifications observed on the bone surfaces. Fossils displaying carnivore modifications from Spain, Germany, Belgium and Greece are evaluated from a taphonomic perspective for the first time in a significant sample of hominin specimens. Our results show that the materials analysed have been modified by small to large carnivores and that both attacks and strictly carnivore scavenging events can be inferred. This study also points out the importance of developing taphonomic approaches to the analysis of hominin bone surfaces, which can contribute significantly to knowledge of several aspects of Neanderthal behaviour. Copyright © 2017 John Wiley &amp; Sons, Ltd.
Simulation approach of atomic layer deposition in large 3D structures
2017-02-09

We present a new simulation method predicting thicknesses of thin films obtained by atomic layer deposition in high aspect ratio 3D geometries as they appear in MEMS manufacturing. The method features a Monte-Carlo computation of film deposition in free molecular flow, as well as in the Knudsen and diffusive gas regime, applicable for large structures. We compare our approach to analytic and simulation results from the literature. The capability of the method is demonstrated by a comparison to experimental film thicknesses in a large 3D structure. Finally, the feasability to extract process parameters, i.e. sticking coefficients is shown.