julilili42/papers huggingface dataset:
Stimulus Contrast and Retinogeniculate Signal Processing
2016-02-19

Neuronal signals conveying luminance contrast play a key role in nearly all aspects of perception, including depth perception, texture discrimination, and motion perception. Although much is known about the retinal mechanisms responsible for encoding contrast information, relatively little is known about the relationship between stimulus contrast and the processing of neuronal signals between visual structures. Here, we describe simultaneous recordings from monosynaptically connected retinal ganglion cells and lateral geniculate nucleus (LGN) neurons in the cat to determine how stimulus contrast affects the communication of visual signals between the two structures. Our results indicate that: (1) LGN neurons typically reach their half-maximal response at lower contrasts than their individual retinal inputs and (2) LGN neurons exhibit greater contrast-dependent phase advance (CDPA) than their retinal inputs. Further analyses suggests that increased sensitivity relies on spatial convergence of multiple retinal inputs, while increased CDPA is achieved, in part, on temporal summation of arriving signals.
Trophic niche ontogeny and palaeoecology of earlyToarcianStenopterygius(Reptilia:Ichthyosauria)
2016-02-19

Abstract Reconstructing ecological niche shifts during ontogeny in extinct animals with no living analogues is difficult without exceptional fossil collections. Here we demonstrate how a previously identified ontogenetic shift in the size and shape of the dentition in the early T oarcian ichthyosaur S tenopterygius quadriscissus accurately predicts a particular dietary shift. The smallest S . quadriscissus fed on small, burst‐swimming fishes, with a steady shift towards faster moving fish and cephalopods with increasing body size. Larger adult specimens appear to have been completely reliant on cephalopods, with fish completely absent from gut contents shortly after onset of sexual maturity. This is consistent with a previously proposed ontogenetic niche shift based on tooth shape and body size, corroborating the idea that dental ontogeny may be a useful predictor of dietary shifts in marine reptiles. Applying the theoretical framework used here to other extinct species will improve the resolution of palaeoecological reconstructions, where appropriate sample sizes exist.
Toxic effects of melphalan, topotecan and carboplatin on retinal pigment epithelial cells
2016-02-19

Abstract Purpose Clinical evidence of retinal pigment epithelium ( RPE ) alterations after intra‐arterial ( IAC ) and intravitreal chemotherapy ( IV iC) of retinoblastoma has been reported. We, therefore, investigated the cellular toxic effects of melphalan, topotecan and carboplatin on the RPE in a cell culture model. Methods The effects of melphalan, carboplatin and topotecan on ARPE 19 cell morphology were examined by phase contrast microscopy. Cell proliferation was quantified by BrdU incorporation, cell viability studied via MTS assays, and cell densities were estimated by Crystal Violet staining, and apoptosis induction studied via caspase 3/7‐activity assays after a 24‐hr incubation period. Staurosporine, media without fetal bovine serum, diluents of melphalan, carboplatin and topotecan were applied as positive and negative controls, respectively. Results We observed a concentration‐dependent increase in the number and size of gaps in the ARPE 19 cell layer with each drug. There was a significant decrease in proliferative activity and cell viability of RPE cells as well as an increase in apoptosis after 24 hrs culture in media supplemented with melphalan and topotecan. Carboplatin had comparable effects on cell proliferation and cell viability; however, no significant apoptotic impacts were observed. The three cytostatic drugs had insignificant effects on cell density measurements. Conclusions Morphological monitoring and toxicity assays indicate a direct toxic effect of melphalan and the other two cytostatic drugs on ARPE 19 cells. Thus, a direct toxic effect of melphalan in vivo after IAC or IV iC on the RPE seems probable and may explain the clinical and angiographic RPE alterations observed in some retinoblastoma patients.
Substantia nigra hyperechogenicity and Parkinson's disease risk in patients with essential tremor
2016-02-19

ABSTRACT Background Several studies have reported an increased risk for patients with essential tremor to develop Parkinson's disease. In addition, hyperechogenicity in the area of the substantia nigra has been associated with a markedly increased risk for Parkinson's disease. The objective of this study was to evaluate the validity of substantia nigra hyperechogenicity in patients with essential tremor as a risk marker for Parkinson's disease. Methods Transcranial sonography was performed in 70 patients suffering from essential tremor. Fifty‐four of these patients were available for follow‐up after a mean of 6.16 ± 2.05 years and were assessed for the incidence of new‐onset Parkinson's disease. Results The relative risk for developing Parkinson's disease in patients with essential tremor who had hyperechogenicity at baseline versus those without this hyperechogenicity was 7.00 (95% confidence interval, 1.62–30.34; sensitivity, 77.8%; specificity, 75.6%). Conclusions Substantia nigra hyperechogenicity is also associated with an increased risk for Parkinson's disease in patients with essential tremor. These findings further support the potential role of this echofeature as a risk marker for Parkinson's disease. © 2016 Movement Disorder Society
Cross-Sectional Survey on Bronchoscopy in Germany – The Current Status of Clinical Practice
2016-02-19

Compared to preceding surveys, the experience of bronchoscopists, especially regarding interventional procedures, has increased. Endobronchial ultrasound has become a standard of care, as has patient sedation with propofol.
Metagenomic Analyses of the Autotrophic Fe(II)-Oxidizing, Nitrate-Reducing Enrichment Culture KS
2016-02-20

ABSTRACT Nitrate-dependent ferrous iron [Fe(II)] oxidation (NDFO) is a well-recognized chemolithotrophic pathway in anoxic sediments. The neutrophilic chemolithoautotrophic enrichment culture KS originally obtained from a freshwater sediment (K. L. Straub, M. Benz, B. Schink, and F. Widdel, Appl Environ Microbiol 62:1458–1460, 1996) has been used as a model system to study NDFO. However, the primary Fe(II) oxidizer in this culture has not been isolated, despite extensive efforts to do so. Here, we present a metagenomic analysis of this enrichment culture in order to gain insight into electron transfer pathways and the roles of different bacteria in the culture. We obtained a near-complete genome of the primary Fe(II) oxidizer, a species in the family Gallionellaceae , and draft genomes from its flanking community members. A search of the putative extracellular electron transfer pathways in these genomes led to the identification of a homolog of the MtoAB complex [a porin-multiheme cytochrome c system identified in neutrophilic microaerobic Fe(II)-oxidizing Sideroxydans lithotrophicus ES-1] in a Gallionellaceae sp., and findings of other putative genes involving cytochrome c and multicopper oxidases, such as Cyc2 and OmpB. Genome-enabled metabolic reconstruction revealed that this Gallionellaceae sp. lacks nitric oxide and nitrous oxide reductase genes and may partner with flanking populations capable of complete denitrification to avoid toxic metabolite accumulation, which may explain its resistance to growth in pure culture. This and other revealed interspecies interactions and metabolic interdependencies in nitrogen and carbon metabolisms may allow these organisms to cooperate effectively to achieve robust chemolithoautotrophic NDFO. Overall, the results significantly expand our knowledge of NDFO and suggest a range of genetic targets for further exploration.
Influence of Sae-regulated and Agr-regulated factors on the escape ofStaphylococcus aureusfrom human macrophages
2016-02-20

Although Staphylococcus aureus is not a classical intracellular pathogen, it can survive within phagocytes and many other cell types. However, the pathogen is also able to escape from cells by mechanisms that are only partially understood. We analysed a series of isogenic S. aureus mutants of the USA300 derivative JE2 for their capacity to destroy human macrophages from within. Intracellular S. aureus JE2 caused severe cell damage in human macrophages and could efficiently escape from within the cells. To obtain this full escape phenotype including an intermittent residency in the cytoplasm, the combined action of the regulatory systems Sae and Agr is required. Mutants in Sae or mutants deficient in the Sae target genes lukAB and pvl remained in high numbers within the macrophages causing reduced cell damage. Mutants in the regulatory system Agr or in the Agr target gene psmα were largely similar to wild-type bacteria concerning cell damage and escape efficiency. However, these strains were rarely detectable in the cytoplasm, emphasizing the role of phenol-soluble modulins (PSMs) for phagosomal escape. Thus, Sae-regulated toxins largely determine damage and escape from within macrophages, whereas PSMs are mainly responsible for the escape from the phagosome into the cytoplasm. Damage of macrophages induced by intracellular bacteria was linked neither to activation of apoptosis-related caspase 3, 7 or 8 nor to NLRP3-dependent inflammasome activation.
Solution-Processed Two-Dimensional Ultrathin InSe Nanosheets
2016-02-21

The rise of two-dimensional (2D) graphene-cognated crystals with nonzero band gaps like transition metal dichalcogenides has led to a rapidly increasing interest in their dimensionality-dependent anisotropic properties, which bear high potential for ultrathin electronics. 2D crystals of the III–VI metal chalcogenide InSe represent a new kind of material class predestined for the use in optoelectronic applications as highly responsive photodetectors and field-effect transistors. We present a solution-processable method for 2D ultrathin InSe nanosheets (≤5 nm with ligands, lateral sizes up to ∼800 μm) with a detailed characterization of the sheet formation by a lamellar ligand templated growth. Optical and electrical transport properties, as well as in depth analysis of the crystal structure and stoichiometry of the colloidal nanosheets by electron and atomic force microscopy, X-ray photoelectron spectroscopy, and scattering methods complete this comprehensive study on a wet-chemical alternative to produce ultrathin InSe nanosheets.
Determination of the Stoichiometry of the Complete Bacterial Type III Secretion Needle Complex Using a Combined Quantitative Proteomic Approach
2016-02-21

Precisely knowing the stoichiometry of their components is critical for investigating structure, assembly, and function of macromolecular machines. This has remained a technical challenge in particular for large, hydrophobic membrane-spanning protein complexes. Here, we determined the stoichiometry of a type III secretion system of Salmonella enterica serovar Typhimurium using two complementary protocols of gentle complex purification combined with peptide concatenated standard and synthetic stable isotope-labeled peptide-based mass spectrometry. Bacterial type III secretion systems are cell envelope-spanning effector protein-delivery machines essential for colonization and survival of many Gram-negative pathogens and symbionts. The membrane-embedded core unit of these secretion systems, termed the needle complex, is composed of a base that anchors the machinery to the inner and outer membranes, a hollow filament formed by inner rod and needle subunits that serves as conduit for substrate proteins, and a membrane-embedded export apparatus facilitating substrate translocation. Structural analyses have revealed the stoichiometry of the components of the base, but the stoichiometry of the essential hydrophobic export apparatus components and of the inner rod protein remain unknown. Here, we provide evidence that the export apparatus of type III secretion systems contains five SpaP, one SpaQ, one SpaR, and one SpaS. We confirmed that the previously suggested stoichiometry of nine InvA is valid for assembled needle complexes and describe a loose association of InvA with other needle complex components that may reflect its function. Furthermore, we present evidence that not more than six PrgJ form the inner rod of the needle complex. Providing this structural information will facilitate efforts to obtain an atomic view of type III secretion systems and foster our understanding of the function of these and related flagellar machines. Given that other virulence-associated bacterial secretion systems are similar in their overall buildup and complexity, the presented approach may also enable their stoichiometry elucidation.
Silicon thin film photodetectors for multi‐channel fluorescence detection in a microfluidic point‐of‐care testing device
2016-02-22

Fluorescence spectroscopy is a highly sensitive detection method widely used in analytical chemistry, bioanalytics, and medicine. The here presented amorphous silicon (a‐Si:H) based thin film photodetector arrays contribute to the miniaturization of this measurement method and thereby enable integration of a point‐of‐care testing (POCT) device. Revealed from photocurrent decay measurements, the limit of detection of the photodiodes with an active area A = 36.3 mm 2 is in the 100 fA‐range. Dark current analysis at zero bias voltage yields a standard deviation σ = 4.4 fA for the thermally generated noise of the nip photodiodes. In the context of the desired application, a minimum detectable fluorescence radiation intensity U min = 4.5 pW cm −2 with a dynamic range DNR = 78 dB is estimated. At the emission peak wavelength λ em = 667 nm and with a bandwidth Δ f = 0.25 Hz the photodiodes reach a noise equivalent power NEP = 54.6 fW Hz −1/2 and therewith a specific detectivity D * = 1.1 × 10 13 Jones. Fluorescence measurements with the dye DY‐636 diluted in pure water with a molar concentration c = 1.31 μM demonstrate the suitability of the multi‐channel photodetectors for high‐sensitivity fluorescence spectroscopy. Low‐signal a‐Si:H photodetector multi‐channel chips in different geometrical layouts with an active area of up to 36.3 mm 2 per diode.
Combining brain stimulation and video game to promote long-term transfer of learning and cognitive enhancement
2016-02-23

Abstract Cognitive training offers the potential for individualised learning, prevention of cognitive decline and rehabilitation. However, key research challenges include ecological validity (training design), transfer of learning and long-term effects. Given that cognitive training and neuromodulation affect neuroplasticity, their combination could promote greater, synergistic effects. We investigated whether combining transcranial direct current stimulation (tDCS) with cognitive training could further enhance cognitive performance compared to training alone and promote transfer within a short period of time. Healthy adults received real or sham tDCS over their dorsolateral prefrontal cortices during two 30-minute mathematics training sessions involving body movements. To examine the role of training, an active control group received tDCS during a non-mathematical task. Those who received real tDCS performed significantly better in the game than the sham group and showed transfer effects to working memory, a related but non-numerical cognitive domain. This transfer effect was absent in active and sham control groups. Furthermore, training gains were more pronounced amongst those with lower baseline cognitive abilities, suggesting the potential for reducing cognitive inequalities. All effects associated with real tDCS remained 2 months post-training. Our study demonstrates the potential benefit of this approach for long-term enhancement of human learning and cognition.
Transient elasticity and polymeric fluids: Small-amplitude deformations
2016-02-23

Transient elasticity (TE) is a concept useful for a systematic generalization of viscoelasticity. Due to its thermodynamic consistency, it naturally leads to a simple description of non-Newtonian effects displayed by polymeric fluids, granular media, and other soft matter. We employ a continuum-mechanical theory that is derived from TE and tailored to polymeric fluids, showing how it captures a surprisingly large number of phenomena in shear and elongational flows, including stationary, oscillatory, and transient ones, as well as the flow down an inclined channel. Even the Weissenberg effect is well accounted for. This theory is applicable for small- as well as large-amplitude deformations. We concentrate on the former in the present article, leaving the latter to a companion article.
The Ancient Rural Settlement Structure in the Hinterland of Pompeii Inferred from Spatial Analysis and Predictive Modeling of Villae Rusticae
2016-02-23

Pompeii, buried by the explosive A.D. 79 eruption of Somma‐Vesuvius, is one of the most studied ancient cities in the Roman world. However, until very recently, the rural settlement in its hinterland had been largely ignored by systematic archaeological research. The ancient landscape around Pompeii consisted of a dense network of Roman farms ( villae rusticae ). They are believed to have played a vital role in ancient rural life and economy and thus represented the interactive rural–urban relationship in the Sarno River plain. The systematic investigation of published work combined with new fieldwork has yielded a data set of 140 villae rusticae in the Sarno River plain. Geographic information system based spatial statistics as well as predictive modeling were applied to gain a more detailed understanding of the ancient rural settlement structure in relation to the underlying paleoenvironmental and socioeconomic conditions. A high‐resolution pre‐A.D. 79 paleolandscape model of the Sarno River plain was utilized. The aim of this paper is to address theoretical considerations, the methodological implementation, and the archaeological discussion of the analysis of the ancient rural settlements and agriculture around Pompeii.
Transient elasticity and the rheology of polymeric fluids with large amplitude deformations
2016-02-23

Transient elasticity is a systematic generalization of viscoelasticity. Its purpose is to give a coherent description of non-Newtonian effects displayed by soft-matter systems, especially polymer melts and solutions. Using the concept of transient elasticity we describe here a hydrodynamic model for polymeric fluids, which is applicable for large amplitude deformations. We present an energy density with only two independent parameters, which is compatible with all thermodynamic requirements and which reduces for small deformations to models studied previously. The expression discussed is simple enough to allow full analytic treatment and shows semiquantitative agreement with experimental data. This model is used to capture many of the interesting effects thought to be characteristic of polymer rheology for large deformations including viscosity overshoot near the onset of shear flow, the onset of elongational flows in situations for which there is no stationary solution as well as shear thinning and normal stress differences for a large range of shear rates. In addition, we analyze how well our model accounts for empirical relations including the Cox-Merz rule, the Yamamoto relation, and Gleißle's mirror relations.
Human Vision–Motivated Algorithm Allows Consistent Retinal Vessel Classification Based on Local Color Contrast for Advancing General Diagnostic Exams
2016-02-23

Our study demonstrates that vessel classification based on local color contrast can cope with inter- or intraimage lightness variability and allows consistent AVR calculation. We offer an open-source implementation of this method upon request, which can be integrated into existing tool sets and applied to general diagnostic exams.
Climatic niche groups: A novel application of a common assumption predicting plant community response to climate change
2016-02-24

Defining species by their climatic niche is the simple and intuitive principle underlying Bioclimatic Envelope Model (BEM) predictions for climate change effects. However, these correlative models are often criticised for neglecting many ecological processes. Here, we apply the same niche principle to entire communities within a medium/long-term climate manipulation study, where ecological processes are inherently included. In a nine generation study in Israel, we manipulated rainfall (Drought −30%; Irrigation +30%; Control natural rainfall) at two sites which differ chiefly in rainfall quantity and variability. We analysed community responses to the manipulations by grouping species based on their climatic rainfall niche. These responses were compared to analyses based on single species, total densities, and commonly used taxonomic groupings. Climate Niche Groups yielded clear and consistent results: within communities, those species distributed in drier regions performed relatively better in the drought treatment, and those from wetter climates performed better when irrigated. In contrast, analyses based on other principles revealed little insight into community dynamics. Notably, most relationships were weaker at the drier, more variable site, suggesting that enhanced adaptation to variability may buffer climate change impacts. We provide robust experimental evidence that using climatic niches – commonly applied in BEMs – is a valid approach for eliciting community changes in response to climate change. However, we also argue that additional empirical information needs to be gathered using experiments in situ to correctly assess community vulnerability. Climatic Niche Groups used in this way, may therefore provide a powerful tool and directional testing framework to generalise and compare climate change impacts across habitats.