bluuebunny/crossref_metadata_2025_split huggingface dataset:
Modeling microbial communities from atrazine contaminated soils promotes the development of biostimulation solutions
Authors: Xu Xihui , Zarecki Raphy , Medina Shlomit , Ofaim Shany , Liu Xiaowei , Chen Chen , Hu Shunli , Brom Dan , Gat Daniella , Porob Seema , Eizenberg Hanan , Ronen Zeev , Jiang Jiandong , Freilich Shiri 
Published: October 2018

Abstract
Microbial communities play a vital role in biogeochemical cycles, allowing the biodegradation of a wide range of pollutants. The composition of the community and the interactions between its members affect degradation rate and determine the identity of the final products. Here, we demonstrate the application of sequencing technologies and metabolic modeling approaches towards enhancing biodegradation of atrazine—a herbicide causing environmental pollution. Treatment of agriculture soil with atrazine is shown to induce significant changes in community structure and functional performances. Genome-scale metabolic models were constructed for Arthrobacter, the atrazine degrader, and four other non-atrazine degrading species whose relative abundance in soil was changed following exposure to the herbicide. By modeling community function we show that consortia including the direct degrader and non-degrader differentially abundant species perform better than Arthrobacter alone. Simulations predict that growth/degradation enhancement is derived by metabolic exchanges between community members. Based on simulations we designed endogenous consortia optimized for enhanced degradation whose performances were validated in vitro and biostimulation strategies that were tested in pot experiments. Overall, our analysis demonstrates that understanding community function in its wider context, beyond the single direct degrader perspective, promotes the design of biostimulation strategies.
A novel rat model of comorbid PTSD and addiction reveals intersections between stress susceptibility and enhanced cocaine seeking with a role for mGlu5 receptors
Authors: Schwendt Marek , Shallcross John , Hadad Natalie A. , Namba Mark D. , Hiller Helmut , Wu Lizhen , Krause Eric G. , Knackstedt Lori A. 
Published: October 2018

Abstract
PTSD is highly comorbid with cocaine use disorder (CUD), and cocaine users with PTSD + CUD are more resistant to treatment. Here we sought to develop a rat model of PTSD + CUD in order to identify the neurobiological changes underlying such comorbidity and screen potential medications for reducing cocaine seeking in the PTSD population. We utilized a predator scent stress model of PTSD, wherein rats received a single exposure to the fox pheromone 2,5-dihydro-2,4,5-trimethylthiazoline (TMT). One week after TMT exposure, stress-susceptible (susceptible), intermediate, and resilient phenotypes were detected and were consistent with behavioral, corticosterone, and gene expression profiles 3 weeks post TMT. We assessed phenotypic differences in cocaine self-administration, extinction, and cue-primed reinstatement. Susceptible rats exhibited deficits in extinction learning and increased cue-primed reinstatement that was not prevented by Ceftriaxone, an antibiotic that consistently attenuates the reinstatement of cocaine seeking. TMT-exposed resilient rats displayed increased mGlu5 gene expression in the amygdala and medial prefrontal cortex and did not display the enhanced cocaine seeking observed in susceptible rats. Combined treatment with the mGlu5 positive allosteric modulator 3-Cyano-N-(1,3-diphenyl-1 H-pyrazol-5-yl)benzamide (CDPPB), fear extinction, and ceftriaxone prevented the reinstatement of cocaine seeking in susceptible rats with fear extinction an important mediating condition. These results highlight the need for animal models of PTSD to consider stress-responsivity, as only a subset of trauma-exposed individuals develop PTSD and these individuals likely exhibit distinct neurobiological changes compared with trauma-exposed populations who are resilient to stress. This work further identifies glutamate homeostasis and mGlu5 as a target for treating relapse in comorbid PTSD-cocaine addiction.
Tetratricopeptide repeat domain 7A is a nuclear factor that modulates transcription and chromatin structure
Authors: El-Daher Marie-Therese , Cagnard Nicolas , Gil Marine , Da Cruz Marie Chansel , Leveau Claire , Sepulveda Fernando , Zarhrate Mohammed , Tores Frédéric , Legoix Patricia , Baulande Sylvain , de Villartay Jean Pierre , Almouzni Geneviève , Quivy Jean-Pierre , Fischer Alain , de Saint Basile Geneviève 
Published: October 2018

AbstractA loss-of-function mutation in tetratricopeptide repeat domain 7A (TTC7A) is a recently identified cause of human intestinal and immune disorders. However, clues to related underlying molecular dysfunctions remain elusive. It is now shown based on the study of TTC7A-deficient and wild-type cells that TTC7A is an essential nuclear protein. It binds to chromatin, preferentially at actively transcribed regions. Its depletion results in broad range of epigenomic changes at proximal and distal transcriptional regulatory elements and in altered control of the transcriptional program. Loss of WT_TTC7A induces general decrease in chromatin compaction, unbalanced cellular distribution of histones, higher nucleosome accessibility to nuclease digestion along with genome instability, and reduced cell viability. Our observations characterize for the first time unreported functions for TTC7A in the nucleus that exert a critical role in chromatin organization and gene regulation to safeguard healthy immune and intestinal status.
Identifying triplet pathways in dilute pentacene films
Authors: Lubert-Perquel Daphné , Salvadori Enrico , Dyson Matthew , Stavrinou Paul N. , Montis Riccardo , Nagashima Hiroki , Kobori Yasuhiro , Heutz Sandrine , Kay Christopher W. M. 
Published: October 2018

AbstractBuilding efficient triplet-harvesting layers for photovoltaic applications requires a deep understanding of the microscopic properties of the components involved and their dynamics. Singlet fission is a particularly appealing mechanism as it generates two excitons from a single photon. However, the pathways of the coupled triplets into free species, and their dependence on the intermolecular geometry, has not been fully explored. In this work, we produce highly ordered dilute pentacene films with distinct parallel and herringbone dimers and aggregates. Using electron paramagnetic resonance spectroscopy, we provide compelling evidence for the formation of distinct quintet excitons in ambient conditions, with intrinsically distinctive electronic and kinetic properties. We find that the ability of quintets to separate into free triplets is promoted in the parallel dimers and this provides molecular design rules to control the triplets, favouring either enhanced photovoltaic efficiency (parallel) or strongly bound pairs that could be exploited for logic applications (herringbone).
Charging dynamics of an individual nanopore
Authors: Tivony Ran , Safran Sam , Pincus Philip , Silbert Gilad , Klein Jacob 
Published: October 2018

AbstractMeso-porous electrodes (pore width « 1 µm) are a central component in electrochemical energy storage devices and related technologies, based on the capacitive nature of electric double-layers at their surfaces. This requires that such charging, limited by ion transport within the pores, is attained over the device operation time. Here we measure directly electric double layer charging within individual nano-slits, formed between gold and mica surfaces in a surface force balance, by monitoring transient surface forces in response to an applied electric potential. We find that the nano-slit charging time is of order 1 s (far slower than the time of order 3 × 10−2 s characteristic of charging an unconfined surface in our configuration), increasing at smaller slit thickness, and decreasing with solution ion concentration. The results enable us to examine critically the nanopore charging dynamics, and indicate how to probe such charging in different conditions and aqueous environments.
Spectral field mapping in plasmonic nanostructures with nanometer resolution
Authors: Krehl J. , Guzzinati G. , Schultz J. , Potapov P. , Pohl D. , Martin Jérôme , Verbeeck J. , Fery A. , Büchner B. , Lubk A. 
Published: October 2018

AbstractPlasmonic nanostructures and -devices are rapidly transforming light manipulation technology by allowing to modify and enhance optical fields on sub-wavelength scales. Advances in this field rely heavily on the development of new characterization methods for the fundamental nanoscale interactions. However, the direct and quantitative mapping of transient electric and magnetic fields characterizing the plasmonic coupling has been proven elusive to date. Here we demonstrate how to directly measure the inelastic momentum transfer of surface plasmon modes via the energy-loss filtered deflection of a focused electron beam in a transmission electron microscope. By scanning the beam over the sample we obtain a spatially and spectrally resolved deflection map and we further show how this deflection is related quantitatively to the spectral component of the induced electric and magnetic fields pertaining to the mode. In some regards this technique is an extension to the established differential phase contrast into the dynamic regime.
Spatially-resolved fluorescence-detected two-dimensional electronic spectroscopy probes varying excitonic structure in photosynthetic bacteria
Authors: Tiwari Vivek , Matutes Yassel Acosta , Gardiner Alastair T. , Jansen Thomas L. C. , Cogdell Richard J. , Ogilvie Jennifer P. 
Published: October 2018

AbstractConventional implementations of two-dimensional electronic spectroscopy typically spatially average over ~1010 chromophores spread over ~104 micron square area, limiting their ability to characterize spatially heterogeneous samples. Here we present a variation of two-dimensional electronic spectroscopy that is capable of mapping spatially varying differences in excitonic structure, with sensitivity orders of magnitude better than conventional spatially-averaged electronic spectroscopies. The approach performs fluorescence-detection-based fully collinear two-dimensional electronic spectroscopy in a microscope, combining femtosecond time-resolution, sub-micron spatial resolution, and the sensitivity of fluorescence detection. We demonstrate the approach on a mixture of photosynthetic bacteria that are known to exhibit variations in electronic structure with growth conditions. Spatial variations in the constitution of mixed bacterial colonies manifests as spatially varying peak intensities in the measured two-dimensional contour maps, which exhibit distinct diagonal and cross-peaks that reflect differences in the excitonic structure of the bacterial proteins.
Rifampicin can induce antibiotic tolerance in mycobacteria via paradoxical changes in rpoB transcription
Authors: Zhu Jun-Hao , Wang Bi-Wei , Pan Miaomiao , Zeng Yu-Na , Rego Hesper , Javid Babak 
Published: October 2018

AbstractMetrics commonly used to describe antibiotic efficacy rely on measurements performed on bacterial populations. However, certain cells in a bacterial population can continue to grow and divide, even at antibiotic concentrations that kill the majority of cells, in a phenomenon known as antibiotic tolerance. Here, we describe a form of semi-heritable tolerance to the key anti-mycobacterial agent rifampicin, which is known to inhibit transcription by targeting the β subunit of the RNA polymerase (RpoB). We show that rifampicin exposure results in rpoB upregulation in a sub-population of cells, followed by growth. More specifically, rifampicin preferentially inhibits one of the two rpoB promoters (promoter I), allowing increased rpoB expression from a second promoter (promoter II), and thus triggering growth. Disruption of promoter architecture leads to differences in rifampicin susceptibility of the population, confirming the contribution of rifampicin-induced rpoB expression to tolerance.
State-recycling and time-resolved imaging in topological photonic lattices
Authors: Mukherjee Sebabrata , Chandrasekharan Harikumar K. , Öhberg Patrik , Goldman Nathan , Thomson Robert R. 
Published: October 2018

AbstractPhotonic lattices—arrays of optical waveguides—are powerful platforms for simulating a range of phenomena, including topological phases. While probing dynamics is possible in these systems, by reinterpreting the propagation direction as time, accessing long timescales constitutes a severe experimental challenge. Here, we overcome this limitation by placing the photonic lattice in a cavity, which allows the optical state to evolve through the lattice multiple times. The accompanying detection method, which exploits a multi-pixel single-photon detector array, offers quasi-real time-resolved measurements after each round trip. We apply the state-recycling scheme to intriguing photonic lattices emulating Dirac fermions and Floquet topological phases. We also realise a synthetic pulsed electric field, which can be used to drive transport within photonic lattices. This work opens an exciting route towards the detection of long timescale effects in engineered photonic lattices and the realisation of hybrid analogue-digital simulators.
The quantum-confined Stark effect in layered hybrid perovskites mediated by orientational polarizability of confined dipoles
Authors: Walters G. , Wei M. , Voznyy O. , Quintero-Bermudez R. , Kiani A. , Smilgies D.-M. , Munir R. , Amassian A. , Hoogland S. , Sargent E. 
Published: October 2018

AbstractThe quantum-confined Stark effect (QCSE) is an established optical modulation mechanism, yet top-performing modulators harnessing it rely on costly fabrication processes. Here, we present large modulation amplitudes for solution-processed layered hybrid perovskites and a modulation mechanism related to the orientational polarizability of dipolar cations confined within these self-assembled quantum wells. We report an anomalous (blue-shifting) QCSE for layers that contain methylammonium cations, in contrast with cesium-containing layers that show normal (red-shifting) behavior. We attribute the blue-shifts to an extraordinary diminution in the exciton binding energy that arises from an augmented separation of the electron and hole wavefunctions caused by the orientational response of the dipolar cations. The absorption coefficient changes, realized by either the red- or blue-shifts, are the strongest among solution-processed materials at room temperature and are comparable to those exhibited in the highest-performing epitaxial compound semiconductor heterostructures.
Single molecule localization microscopy coupled with touch preparation for the quantification of trastuzumab-bound HER2
Authors: Tobin Steven J. , Wakefield Devin L. , Jones Veronica , Liu Xueli , Schmolze Daniel , Jovanović-Talisman Tijana 
Published: October 2018

AbstractAll breast cancers are assessed for levels of human epidermal growth factor receptor 2 (HER2). Fluorescence in situ hybridization (FISH) and immunohistochemistry are currently used to determine if a patient is eligible for anti-HER2 therapy. Limitations of both tests include variability and relatively long processing times. Additionally, neither test determines whether HER2 contains the extracellular domain. While truncated in some tumors, this domain is required for binding of the therapeutic antibody trastuzumab. Here, trastuzumab was used to directly detect HER2 with quantitative single molecule localization microscopy (qSMLM). In proof of concept studies, our new method rapidly quantified both HER2 density and features of nano-organization. In cultured cells, the method was sensitive to subtle variations in HER2 expression. To assess patient samples, we combined qSMLM with tissue touch preparation (touch prep-qSMLM) and examined large areas of intact membranes. For cell lines and patient samples, HER2 copy numbers from FISH showed a significant positive correlation with detected densities from qSMLM and trended with HER2 cluster occupancy.
The CTLA-4 rs231775 GG genotype is associated with favorable 90-day survival in Caucasian patients with sepsis
Authors: Mewes Caspar , Büttner Benedikt , Hinz José , Alpert Ayelet , Popov Aron Frederik , Ghadimi Michael , Beissbarth Tim , Tzvetkov Mladen , Shen-Orr Shai , Bergmann Ingo , Mansur Ashham 
Published: October 2018

AbstractCytotoxic T-lymphocyte-associated protein 4 (CTLA-4) is a surface protein on T cells, that has an inhibitory effect on the host immune reaction and prevents overreaction of the immune system. Because the functional single-nucleotide polymorphism (SNP) rs231775 of the CTLA-4 gene is associated with autoimmune diseases and because of the critical role of the immune reaction in sepsis, we intended to examine the effect of this polymorphism on survival in patients with sepsis. 644 septic adult Caucasian patients were prospectively enrolled in this study. Patients were followed up for 90 days. Mortality risk within this period was defined as primary outcome parameter. Kaplan-Meier survival analysis revealed a significantly lower 90-day mortality risk among GG homozygous patients (n = 101) than among A allele carriers (n = 543; 22% and 32%, respectively; p = 0.03565). Furthermore, the CTLA-4 rs231775 GG genotype remained a significant covariate for 90-day mortality risk after controlling for confounders in the multivariate Cox regression analysis (hazard ratio: 0.624; 95% CI: 0.399–0.975; p = 0.03858). In conclusion, our study provides the first evidence for CTLA-4 rs231775 as a prognostic variable for the survival of patients with sepsis and emphasizes the need for further research to reveal potential functional associations between CTLA-4 and the immune pathophysiology of sepsis.
Genome-wide association identifies methane production level relation to genetic control of digestive tract development in dairy cows
Authors: Pszczola M. , Strabel T. , Mucha S. , Sell-Kubiak E. 
Published: October 2018

AbstractThe global temperatures are increasing. This increase is partly due to methane (CH4) production from ruminants, including dairy cattle. Recent studies on dairy cattle have revealed the existence of a heritable variation in CH4 production that enables mitigation strategies based on selective breeding. We have exploited the available heritable variation to study the genetic architecture of CH4 production and detected genomic regions affecting CH4 production. Although the detected regions explained only a small proportion of the heritable variance, we showed that potential QTL regions affecting CH4 production were located within QTLs related to feed efficiency, milk-related traits, body size and health status. Five candidate genes were found: CYP51A1 on BTA 4, PPP1R16B on BTA 13, and NTHL1, TSC2, and PKD1 on BTA 25. These candidate genes were involved in a number of metabolic processes that are possibly related to CH4 production. One of the most promising candidate genes (PKD1) was related to the development of the digestive tract. The results indicate that CH4 production is a highly polygenic trait.
The role of Mean Platelet Volume/platelet count Ratio and Neutrophil to Lymphocyte Ratio on the risk of Febrile Seizure
Authors: Liu Zhigang , Li Xiangxin , Zhang Meipin , Huang Xiaofei , Bai Jun , Pan Zhiwei , Lin Xiuxian , Yu Dongni , Zeng Huaping , Wan Ruiping , Ye Xingguang 
Published: October 2018

AbstractSystemic inflammatory response has been implicated as a contributor to the onset of febrile seizures (FS). The four novel indices of the inflammatory response such as, neutrophil-to-lymphocyte ratio (NLR), mean platelet volume (MPV), platelet count (PLT) ratio and red blood cell distribution width (RDW) have been investigated in FS susceptibility and FS types (simple febrile seizure and complex febrile seizure). However, the potential role of these inflammatory markers and MPV/PLT ratio (MPR) in Chinese children with FS has yet to be fully determined. This study investigated the relevance of NLR, MPV, PLT, MPR and RDW in febrile children with and without seizures. 249 children with FS and 249 age matched controls were included in this study. NLR and MPR were calculated from complete blood cell counts prior to therapy. Differences in age, gender and these inflammatory markers between the FS group and the control group were evaluated using the chi-square test,t-test or logistic regression analysis. Receiver Operating Characteristic (ROC) curve was used to determine the optimal cut-off value of NLR and MPR for FS risk. Interactions between NLR and MPR on the additive scale were calculated by using the relative excess risk due to interaction (RERI), the proportion attributable to interaction (AP), and the synergy index (S). It has been shown that the elevated NLR and MPR levels were associated with increased risk of FS. The optimal cut-off values of NLR and MPR for FS risk were 1.13 and 0.0335 with an area under the curve (AUC) of 0.768 and 0.689, respectively. Additionally, a significant synergistic interaction between NLR and MPR was found on an additive scale. The mean levels of MPV were lower and NLR levels were higher in complex febrile seizure (CFS) than simple febrile seizure (SFS), and the differences were statistically significant. ROC analysis showed that the optimal cut-off value for NLR was 2.549 with 65.9% sensitivity and 57.5% specificity. However, no statistically significant differences were found regarding average values of MPR and RDW between CFS and SFS. In conclusion, elevated NLR and MPR add evidence to the implication of white cells subsets in FS risk, and our results confirmed that NLR is an independent, albeit limited, predictor in differentiating between CFS and SFS. Moreover, NLR and MPR may have a synergistic effect that can influence the occurrence of FS.
Atomic scale insight into the effects of Aluminum doped Sb2Te for phase change memory application
Authors: Wang Yong , Wang Tianbo , Zheng Yonghui , Liu Guangyu , Li Tao , Lv Shilong , Song Wenxiong , Song Sannian , Cheng Yan , Ren Kun , Song Zhitang 
Published: October 2018

AbstractTo date, the unpleasant trade-off between crystallization speed and thermal stability for most phase change materials is detrimental to achieve phase change memory (PCM) with both features of high-speed and good-retention. However, it is proved that Al doping in Sb2Te, served as storage media in PCM, favors both a high writing speed (6 ns) and a good retention (103 °C), as well as a low power consumption. Judging by experimental and theoretical investigations, doped Al atoms prefer to replace Sb in Sb2Te lattice, strongly bonded with 6 Te atoms, to form a homogeneous phase. While in amorphous Al doped Sb2Te (AST), Al atoms are in tetrahedral environment, firmly bonded with four Sb/Te atoms. The strong bonding in Al centered tetrahedron in amorphous AST can obstruct the collective motion of Sb atoms near the matrix boundary, leading to the improvement in thermal stability and the confinement in grain size.