bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tracing the sources and spatial distribution of organic carbon in subsoils using a multi-biomarker approach
Authors: Angst Gerrit , John Stephan , Mueller Carsten W. , Kögel-Knabner Ingrid , Rethemeyer Janet 
Published: July 2016

AbstractSoil organic carbon (SOC) from aboveground and belowground sources has rarely been differentiated although it may drive SOC turnover and stabilization due to a presumed differing source dependent degradability. It is thus crucial to better identify the location of SOC from different sources for the parameterization of SOC models, especially in the less investigated subsoils. The aim of this study was to spatially assess contributions of organic carbon from aboveground and belowground parts of beech trees to subsoil organic carbon in a Dystric Cambisol. Different sources of SOC were distinguished by solvent-extractable and hydrolysable lipid biomarkers aided by 14C analyses of soil compartments <63 μm. We found no effect of the distance to the trees on the investigated parameters. Instead, a vertical zonation of the subsoil was detected. A high contribution of fresh leaf- and root-derived organic carbon to the upper subsoil (leaf- and root-affected zone) indicate that supposedly fast-cycling, leaf-derived SOC may still be of considerable importance below the A-horizon. In the deeper subsoil (root-affected zone), roots were an important source of fresh SOC. Simultaneously, strongly increasing apparent 14C ages (3860 yrs BP) indicate considerable contribution of SOC that may be inherited from the Pleistocene parent material.
4-aminopyridine reverses ataxia and cerebellar firing deficiency in a mouse model of spinocerebellar ataxia type 6
Authors: Jayabal Sriram , Chang Hui Ho Vanessa , Cullen Kathleen E. , Watt Alanna J. 
Published: July 2016

AbstractSpinocerebellar ataxia type 6 (SCA6) is a devastating midlife-onset autosomal dominant motor control disease with no known treatment. Using a hyper-expanded polyglutamine (84Q) knock-in mouse, we found that cerebellar Purkinje cell firing precision was degraded in heterozygous (SCA684Q/+) mice at 19 months when motor deficits are observed. Similar alterations in firing precision and motor control were observed at disease onset at 7 months in homozygous (SCA684Q/84Q) mice, as well as a reduction in firing rate. We further found that chronic administration of the FDA-approved drug 4-aminopyridine (4-AP), which targets potassium channels, alleviated motor coordination deficits and restored cerebellar Purkinje cell firing precision to wildtype (WT) levels in SCA684Q/84Q mice both in acute slices and in vivo. These results provide a novel therapeutic approach for treating ataxic symptoms associated with SCA6.
Evolutionary pressures on microbial metabolic strategies in the chemostat
Authors: Wortel Meike T. , Bosdriesz Evert , Teusink Bas , Bruggeman Frank J. 
Published: July 2016

AbstractProtein expression is shaped by evolutionary processes that tune microbial fitness. The limited biosynthetic capacity of a cell constrains protein expression and forces the cell to carefully manage its protein economy. In a chemostat, the physiology of the cell feeds back on the growth conditions, hindering intuitive understanding of how changes in protein concentration affect fitness. Here, we aim to provide a theoretical framework that addresses the selective pressures and optimal evolutionary-strategies in the chemostat. We show that the optimal enzyme levels are the result of a trade-off between the cost of their production and the benefit of their catalytic function. We also show that deviations from optimal enzyme levels are directly related to selection coefficients. The maximal fitness strategy for an organism in the chemostat is to express a well-defined metabolic subsystem known as an elementary flux mode. Using a coarse-grained, kinetic model of Saccharomyces cerevisiae’s metabolism and growth, we illustrate that the dynamics and outcome of evolution in a chemostat can be very counter-intuitive: Strictly-respiring and strictly-fermenting strains can evolve from a common ancestor. This work provides a theoretical framework that relates a kinetic, mechanistic view on metabolism with cellular physiology and evolutionary dynamics in the chemostat.
Quantum memristors
Authors: Pfeiffer P. , Egusquiza I. L. , Di Ventra M. , Sanz M. , Solano E. 
Published: July 2016

AbstractTechnology based on memristors, resistors with memory whose resistance depends on the history of the crossing charges, has lately enhanced the classical paradigm of computation with neuromorphic architectures. However, in contrast to the known quantized models of passive circuit elements, such as inductors, capacitors or resistors, the design and realization of a quantum memristor is still missing. Here, we introduce the concept of a quantum memristor as a quantum dissipative device, whose decoherence mechanism is controlled by a continuous-measurement feedback scheme, which accounts for the memory. Indeed, we provide numerical simulations showing that memory effects actually persist in the quantum regime. Our quantization method, specifically designed for superconducting circuits, may be extended to other quantum platforms, allowing for memristor-type constructions in different quantum technologies. The proposed quantum memristor is then a building block for neuromorphic quantum computation and quantum simulations of non-Markovian systems.
High-Quality Crystal Growth and Characteristics of AlGaN-Based Solar-Blind Distributed Bragg Reflectors with a Tri-layer Period Structure
Authors: Chang Jianjun , Chen Dunjun , Yang Lianhong , Liu Yanli , Dong Kexiu , Lu Hai , Zhang Rong , Zheng Youdou 
Published: July 2016

AbstractTo realize AlGaN-based solar-blind ultraviolet distributed Bragg reflectors (DBRs), a novel tri-layer AlGaN/AlInN/AlInGaN periodical structure that differs from the traditional periodically alternating layers of high- and low-refractive-index materials was proposed and grown on an Al0.5Ga0.5N template via metal-organic chemical vapour deposition. Because of the intentional design of the AlInGaN strain transition layer, a state-of-the-art DBR structure with atomic-level-flatness interfaces was achieved using an AlGaN template. The fabricated DBR exhibits a peak reflectivity of 86% at the centre wavelength of 274 nm and a stopband with a full-width at half-maximum of 16 nm.
Spontaneous wettability patterning via creasing instability
Authors: Chen Dayong , McKinley Gareth H. , Cohen Robert E. 
Published: July 2016

SignificanceSurfaces with patterned wettability contrast are important in many applications. Traditional fabrication methods rely on microfabrication technologies, which are generally not cost effective and are difficult to implement on curved surfaces. We show that wettability contrast can be patterned spontaneously on both flat and curved surfaces in a single step process by taking advantage of a reversible creasing instability. Moreover, the domain size, morphology, and wettability contrast can be controlled independently, yielding heterogeneous surfaces that show potential for generating high-throughput parallel microreactors and for harvesting water from humid air. This mechanical self-assembly approach can also lead to other functional materials beyond wettability patterning.
Spectral discrimination in color blind animals via chromatic aberration and pupil shape
Authors: Stubbs Alexander L. , Stubbs Christopher W. 
Published: July 2016

Significance
We describe a means of obtaining spectral information using the principles of physical optics and an off-axis pupil shape without requiring spectrally distinct photoreceptor classes. The mechanism described here offers a possible solution to a long-standing puzzle in marine animals: cephalopods dramatically change color for both producing chromatically matched camouflage and signaling to conspecifics, despite having a single photoreceptor channel. The ability of these animals to achieve such excellent color matching to their surroundings, despite being “color blind” in the traditional sense, can be understood if they exploit chromatic aberration to deduce spectral information. The bizarre off-axis pupils of these animals can be understood as an adaptation that maximizes spectral information, even at the expense of image acuity.
Learning rational temporal eye movement strategies
Authors: Hoppe David , Rothkopf Constantin A. 
Published: July 2016

Significance
In a dynamic world humans not only have to decide where to look but also when to direct their gaze to potentially informative locations in the visual scene. Little is known about how timing of eye movements is related to environmental regularities and how gaze strategies are learned. Here we present behavioral data establishing that humans learn to adjust their temporal eye movements efficiently. Our computational model shows how established properties of the visual system determine the timing of gaze. Surprisingly, a Bayesian learner only incorporating the scalar law of biological timing can fully explain the course of learning these strategies. Thus, humans use temporal regularities learned from observations to adjust the scheduling of eye movements in a nearly optimal way.
Measurements of extinct fission products in nuclear bomb debris: Determination of the yield of the Trinity nuclear test 70 y later
Authors: Hanson Susan K. , Pollington Anthony D. , Waidmann Christopher R. , Kinman William S. , Wende Allison M. , Miller Jeffrey L. , Berger Jennifer A. , Oldham Warren J. , Selby Hugh D. 
Published: July 2016

SignificanceThis work describes an approach to postdetonation nuclear forensics involving isotopic measurements that allows for characterization of a nuclear detonation at any time. By performing high-precision measurements of stable isotope perturbations in nuclear bomb debris, it is possible to quantify short-lived fission products long after they have decayed below radiometric detection limits and become extinct. The extinct fission product concentrations can be used to reconstruct details of the nuclear device months to years after the detonation occurred. The approach is demonstrated by analysis of debris from the Trinity nuclear test and new estimates of the efficiency and yield of the historic test are presented.
Stochastic cycle selection in active flow networks
Authors: Woodhouse Francis G. , Forrow Aden , Fawcett Joanna B. , Dunkel Jörn 
Published: July 2016

Significance
Nature often uses interlinked networks to transport matter or information. In many cases, the physical or virtual flows between network nodes are actively driven, consuming energy to achieve transport along different links. However, there are currently very few elementary principles known to predict the behavior of this broad class of nonequilibrium systems. Our work develops a generic foundational understanding of mass-conserving active flow networks. By merging previously disparate concepts from mathematical graph theory and physicochemical reaction rate theory, we relate the self-organizing behavior of actively driven flows to the fundamental topological symmetries of the underlying network, resulting in a class of predictive models with applicability across many biological scales.
A study of interstellar aldehydes and enols as tracers of a cosmic ray-driven nonequilibrium synthesis of complex organic molecules
Authors: Abplanalp Matthew J. , Gozem Samer , Krylov Anna I. , Shingledecker Christopher N. , Herbst Eric , Kaiser Ralf I. 
Published: July 2016

Significance
Since the detection of the methylidyne radical (CH) in the interstellar medium nearly 80 y ago, about 200 molecules ranging from molecular hydrogen to fullerenes have been identified in interstellar and circumstellar environments, but the synthesis of complex organic molecules (COMs)––organics containing several atoms of carbon, hydrogen, nitrogen, and oxygen––has remained elusive to date. Here, we provide compelling evidence via laboratory experiments, computations, and modeling that the synthesis of COMs is driven by a cosmic-ray-triggered nonequilibrium chemistry within interstellar ices at temperatures as low as 10 K. These fundamental reaction mechanisms are of major significance to facilitate an understanding of the origin and evolution of the molecular universe.
Vagus nerve stimulation inhibits cytokine production and attenuates disease severity in rheumatoid arthritis
Authors: Koopman Frieda A. , Chavan Sangeeta S. , Miljko Sanda , Grazio Simeon , Sokolovic Sekib , Schuurman P. Richard , Mehta Ashesh D. , Levine Yaakov A. , Faltys Michael , Zitnik Ralph , Tracey Kevin J. , Tak Paul P. 
Published: July 2016

SignificanceRheumatoid arthritis (RA) is a chronic, prevalent, and disabling autoimmune disease that occurs when inflammation damages joints. Recent advances in neuroscience and immunology have mapped neural circuits that regulate the onset and resolution of inflammation. In one circuit, termed “the inflammatory reflex,” action potentials transmitted in the vagus nerve inhibit the production of tumor necrosis factor (TNF), an inflammatory molecule that is a major therapeutic target in RA. Although studied in animal models of arthritis and other inflammatory diseases, whether electrical stimulation of the vagus nerve can inhibit TNF production in humans has remained unknown. The positive mechanistic results reported here extend the preclinical data to the clinic and reveal that vagus nerve stimulation inhibits TNF and attenuates disease severity in RA patients.
Generalized nucleation and looping model for epigenetic memory of histone modifications
Authors: Erdel Fabian , Greene Eric C. 
Published: July 2016

Significance
The genome-wide distribution of histone modifications influences cellular processes that involve access to the DNA. How cells establish and maintain these patterns is currently under debate. Understanding the underlying mechanisms is a prerequisite for predicting the cellular response to epigenetic drugs or programmed epigenetic editing. Here we simulated linear and looping-driven propagation mechanisms and compared the results to the spatiotemporal methylation profiles recently observed in fission yeast. We found that looping-driven spreading, which arises from productive collisions among nucleosomes and chromatin-bound histone modifiers, explains several key observations on engineered methylation domains. These findings point to important roles of chromatin-bound enzymes and chromatin dynamics in controlling modification patterns and epigenetic memory, which might not be restricted to repressive histone methylation.
DNA binding triggers tetramerization of the glucocorticoid receptor in live cells
Authors: Presman Diego M. , Ganguly Sourav , Schiltz R. Louis , Johnson Thomas A. , Karpova Tatiana S. , Hager Gordon L. 
Published: July 2016

Significance
The glucocorticoid receptor (GR) is a ligand-regulated transcription factor and one of the most targeted proteins in the pharmaceutical industry due to its powerful antiinflammatory actions. The search for side effects-free glucocorticoids relies exclusively on a model wherein the GR oligomerization state, whether a monomer or a dimer, dictates its transcriptional output. Here, we use an experimental approach where the GR–DNA interaction is observed in real time with a technique that allows the quantification of the oligomeric state of proteins in living cells. Unexpectedly, we find that DNA binding triggers tetramerization of the GR, which would be the truly activated form of the receptor. Our findings reveal a previously unidentified step in the glucocorticoid activation pathway.
SIFORM: shared informative factor models for integration of multi-platform bioinformatic data
Authors: An Xuebei , Hu Jianhua , Do Kim-Anh 
Published: July 2016

AbstractMotivation: High-dimensional omic data derived from different technological platforms have been extensively used to facilitate comprehensive understanding of disease mechanisms and to determine personalized health treatments. Numerous studies have integrated multi-platform omic data; however, few have efficiently and simultaneously addressed the problems that arise from high dimensionality and complex correlations.Results: We propose a statistical framework of shared informative factor models that can jointly analyze multi-platform omic data and explore their associations with a disease phenotype. The common disease-associated sample characteristics across different data types can be captured through the shared structure space, while the corresponding weights of genetic variables directly index the strengths of their association with the phenotype. Extensive simulation studies demonstrate the performance of the proposed method in terms of biomarker detection accuracy via comparisons with three popular regularized regression methods. We also apply the proposed method to The Cancer Genome Atlas lung adenocarcinoma dataset to jointly explore associations of mRNA expression and protein expression with smoking status. Many of the identified biomarkers belong to key pathways for lung tumorigenesis, some of which are known to show differential expression across smoking levels. We discover potential biomarkers that reveal different mechanisms of lung tumorigenesis between light smokers and heavy smokers.Availability and Implementation: R code to implement the new method can be downloaded from http://odin.mdacc.tmc.edu/jhhu/Contact: jhu@mdanderson.org
Whole-pelvic radiotherapy with spot-scanning proton beams for uterine cervical cancer: a planning study
Authors: Hashimoto Shingo , Shibamoto Yuta , Iwata Hiromitsu , Ogino Hiroyuki , Shibata Hiroki , Toshito Toshiyuki , Sugie Chikao , Mizoe Jun-etsu 
Published: July 2016

AbstractThe aim of this study was to compare the dosimetric parameters of whole-pelvic radiotherapy (WPRT) for cervical cancer among plans involving 3D conformal radiotherapy (3D-CRT), intensity-modulated radiotherapy (IMRT), or spot-scanning proton therapy (SSPT). The dose distributions of 3D-CRT-, IMRT-, and SSPT-based WPRT plans were compared in 10 patients with cervical cancer. All of the patients were treated with a prescribed dose of 50.4 Gy in 1.8-Gy daily fractions, and all of the plans involved the same planning target volume (PTV) constrictions. A 3D-CRT plan involving a four-field box, an IMRT plan involving seven coplanar fields, and an SSPT plan involving four fields were created. The median PTV D95% did not differ between the 3D-CRT, IMRT and SSPT plans. The median conformity index 95% and homogeneity index of the IMRT and SSPT were better than those of the 3D-CRT. The homogeneity index of the SSPT was better than that of the IMRT. SSPT resulted in lower median V20 values for the bladder wall, small intestine, colon, bilateral femoral heads, skin, and pelvic bone than IMRT. Comparing the Dmean values, SSPT spared the small intestine, colon, bilateral femoral heads, skin and pelvic bone to a greater extent than the other modalities. SSPT can reduce the irradiated volume of the organs at risk compared with 3D-CRT and IMRT, while maintaining excellent PTV coverage. Further investigations of SSPT are warranted to assess its role in the treatment of cervical cancer.
Spillovers in Local Banking Markets
Authors: Garmaise Mark J. , Natividad Gabriel 
Published: July 2016

AbstractHow are neighboring firms affected when a bank learns more about a given firm? We analyze exchange-rate-induced movements of Peruvian firms across a threshold that governs their regulatory treatment by banks. Firms that cross the threshold supply more information to their banks and experience a substantial increase in financing. We find positive spillover effects: the neighbors of the above-threshold firms also experience increased financing. These spillovers are confined to neighbors sharing a bank, and the performance of new loans to these neighbors improves, suggesting that the bank has become better informed about other local firms.Received October 15, 2015; accepted May 16, 2016 by Editor Efraim Benmelech.
Microglial Inhibition Influences XCL1/XCR1 Expression and Causes Analgesic Effects in a Mouse Model of Diabetic Neuropathy
Authors: Zychowska Magdalena , Rojewska Ewelina , Piotrowska Anna , Kreiner Grzegorz , Mika Joanna 
Published: July 2016

Abstract

Background
Recent studies indicated the involvement of some chemokines in the development of diabetic neuropathy; however, participation of the chemokine-C-motif ligand (XCL) subfamily remains unknown. The goal of this study was to examine how microglial inhibition by minocycline hydrochloride (MC) influences chemokine-C-motif ligand 1 (XCL1)–chemokine-C-motif receptor 1 (XCR1)/G protein–coupled receptor 5 expression and the development of allodynia/hyperalgesia in streptozotocin-induced diabetic neuropathy.

Methods
The studies were performed on streptozotocin (200 mg/kg, intraperitoneally)-induced mouse diabetic neuropathic pain model and primary glial cell cultures. The MC (30 mg/kg, intraperitoneally) was injected two times daily until day 21. XCL1 and its neutralizing antibody were injected intrathecally, and behavior was evaluated with von Frey and cold plate tests. Quantitative analysis of protein expression of glial markers, XCL1, and/or XCR1 was performed by Western blot and visualized by immunofluorescence.

Results
MC treatment diminished allodynia (0.9 ± 0.1 g; n = 7 vs. 3.8 ± 0.7 g; n = 7) and hyperalgesia (6.5 ± 0.6 s; n = 7 vs. 16.5 ± 1 s; n = 7) in the streptozotocin-induced diabetes. Repeated MC administration prevented microglial activation and inhibited the up-regulation of the XCL1/XCR1 levels. XCL1 administration (10 to 500 ng/5 μl; n = 9) in naive mice enhanced nociceptive transmission, and injections of neutralizing XCL1 (4 to 8 μg/5 μl; n = 10) antibody into the mice with diabetic neuropathic pain diminished allodynia/hyperalgesia. Microglia activation evoked in primary microglial cell cultures resulted in enhanced XCL1 release and XCR1 expression. Additionally, double immunofluorescence indicated the widespread coexpression of XCR1-expressing cells with spinal neurons.

Conclusions
In diabetic neuropathy, declining levels of XCL1 evoked by microglia inhibition result in the cause of analgesia. The putative mechanism corroborating this finding can be related to lower spinal expression of XCR1 together with the lack of stimulation of these XCR1 receptors, which are localized on neurons.