bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constant light enhances synchrony among circadian clock cells and promotes behavioral rhythms in VPAC2-signaling deficient mice
Authors: Hughes Alun T.L. , Croft Cara. L. , Samuels Rayna E. , Myung Jihwan , Takumi Toru , Piggins Hugh D. 
Published: September 2015

AbstractIndividual neurons in the suprachiasmatic nuclei (SCN) contain an intracellular molecular clock and use intercellular signaling to synchronize their timekeeping activities so that the SCN can coordinate brain physiology and behavior. The neuropeptide vasoactive intestinal polypeptide (VIP) and its VPAC2 receptor form a key component of intercellular signaling systems in the SCN and critically control cellular coupling. Targeted mutations in either the intracellular clock or intercellular neuropeptide signaling mechanisms, such as VIP-VPAC2 signaling, can lead to desynchronization of SCN neuronal clocks and loss of behavioral rhythms. An important goal in chronobiology is to develop interventions to correct deficiencies in circadian timekeeping. Here we show that extended exposure to constant light promotes synchrony among SCN clock cells and the expression of ~24 h rhythms in behavior in mice in which intercellular signaling is disrupted through loss of VIP-VPAC2 signaling. This study highlights the importance of SCN synchrony for the expression of rhythms in behavior and reveals how non-invasive manipulations in the external environment can be used to overcome neurochemical communication deficits in this important brain system.
Photoelectron diffraction from laser-aligned molecules with X-ray free-electron laser pulses
Authors: Nakajima Kyo , Teramoto Takahiro , Akagi Hiroshi , Fujikawa Takashi , Majima Takuya , Minemoto Shinichirou , Ogawa Kanade , Sakai Hirofumi , Togashi Tadashi , Tono Kensuke , Tsuru Shota , Wada Ken , Yabashi Makina , Yagishita Akira 
Published: September 2015

AbstractWe report on the measurement of deep inner-shell 2p X-ray photoelectron diffraction (XPD) patterns from laser-aligned I2 molecules using X-ray free-electron laser (XFEL) pulses. The XPD patterns of the I2 molecules, aligned parallel to the polarization vector of the XFEL, were well matched with our theoretical calculations. Further, we propose a criterion for applying our molecular-structure-determination methodology to the experimental XPD data. In turn, we have demonstrated that this approach is a significant step toward the time-resolved imaging of molecular structures.
Imbalance between the expression dosages of X-chromosome and autosomal genes in mammalian oocytes
Authors: Fukuda Atsushi , Tanino Motohiko , Matoba Ryo , Umezawa Akihiro , Akutsu Hidenori 
Published: September 2015

AbstractOocytes have unique characteristics compared with other cell types. In mouse and human oocytes, two X chromosomes are maintained in the active state. Previous microarray studies have shown that the balance of the expression state is maintained in haploid oocytes. Here, we investigated transcripts using RNA-sequence technology in mouse and human oocytes. The median expression ratio between X chromosome and autosomal genes (X:A) in immature mouse oocytes increased as the gene expression levels increased, reaching a value of 1. However, the ratio in mature oocytes was under 1 for all expression categories. Moreover, we observed a markedly low ratio resulting from the bimodal expression patterns of X–linked genes. The low X:A expression ratio in mature oocyte was independent of DNA methylation. While mature human oocytes exhibited a slightly low X:A expression ratio, this was the result of the skewed high frequency of lowly expressed X-linked genes rather than the bimodal state. We propose that this imbalance between the expression dosages of X-chromosome and autosomal genes is a feature of transcripts in mammalian oocytes lacking X-chromosome inactivation.
Comparative genome-based identification of a cell wall-anchored protein from Lactobacillus plantarum increases adhesion of Lactococcus lactis to human epithelial cells
Authors: Zhang Bo , Zuo Fanglei , Yu Rui , Zeng Zhu , Ma Huiqin , Chen Shangwu 
Published: September 2015

AbstractAdhesion to host cells is considered important for Lactobacillus plantarum as well as other lactic acid bacteria (LAB) to persist in human gut and thus exert probiotic effects. Here, we sequenced the genome of Lt. plantarum strain NL42 originating from a traditional Chinese dairy product, performed comparative genomic analysis and characterized a novel adhesion factor. The genome of NL42 was highly divergent from its closest neighbors, especially in six large genomic regions. NL42 harbors a total of 42 genes encoding adhesion-associated proteins; among them, cwaA encodes a protein containing multiple domains, including five cell wall surface anchor repeat domains and an LPxTG-like cell wall anchor motif. Expression of cwaA in Lactococcus lactis significantly increased its autoaggregation and hydrophobicity and conferred the new ability to adhere to human colonic epithelial HT-29 cells by targeting cellular surface proteins and not carbohydrate moieties, for CwaA adhesion. In addition, the recombinant Lc. lactis inhibited adhesion of Staphylococcus aureus and Escherichia coli to HT-29 cells, mainly by exclusion. We conclude that CwaA is a novel adhesion factor in Lt. plantarum and a potential candidate for improving the adhesion ability of probiotics or other bacteria of interest.
Determination of magnetic anisotropy constants and domain wall pinning energy of Fe/MgO(001) ultrathin film by anisotropic magnetoresistance
Authors: Hu Bo , He Wei , Ye Jun , Tang Jin , Zhang Yong-Sheng , Ahmad Syed Sheraz , Zhang Xiang-Qun , Cheng Zhao-Hua 
Published: September 2015

AbstractIt is challenging to determine domain wall pinning energy and magnetic anisotropy since both coherent rotation and domain wall displacement coexist during magnetization switching process. Here, angular dependence anisotropic magnetoresistance (AMR) measurements at different magnetic fields were employed to determine magnetic anisotropy constants and domain wall pinning energy of Fe/MgO(001) ultrathin film. The AMR curves at magnetic fields which are high enough to ensure the coherent rotation of magnetization indicate a smooth behavior without hysteresis between clockwise (CW) and counter-clockwise (CCW) rotations. By analyzing magnetic torque, the magnetic anisotropy constants can be obtained. On the other hand, the AMR curves at low fields show abrupt transitions with hysteresis between CW and CCW rotations, suggesting the presence of multi-domain structures. The domain wall pinning energy can be obtained by analyzing different behaviors of AMR. Our work suggests that AMR measurements can be employed to figure out precisely the contributions of magnetic anisotropy and domain wall pinning energy, which is still a critical issue for spintronics.
Bioaccumulation and biological effects of cigarette litter in marine worms
Authors: Wright Stephanie L. , Rowe Darren , Reid Malcolm J. , Thomas Kevin V. , Galloway Tamara S. 
Published: September 2015

AbstractMarine debris is a global environmental issue. Smoked cigarette filters are the predominant coastal litter item; 4.5 trillion are littered annually, presenting a source of bioplastic microfibres (cellulose acetate) and harmful toxicants to marine environments. Despite the human health risks associated with smoking, little is known of the hazards cigarette filters present to marine life. Here we studied the impacts of smoked cigarette filter toxicants and microfibres on the polychaete worm Hediste diversicolor (ragworm), a widespread inhabitant of coastal sediments. Ragworms exposed to smoked cigarette filter toxicants in seawater at concentrations 60 fold lower than those reported for urban run-off exhibited significantly longer burrowing times, >30% weight loss and >2-fold increase in DNA damage compared to ragworms maintained in control conditions. In contrast, ragworms exposed to smoked cigarette filter microfibres in marine sediment showed no significant effects. Bioconcentration factors for nicotine were 500 fold higher from seawater than from sediment. Our results illustrate the vulnerability of organisms in the water column to smoking debris and associated toxicants and highlight the risks posed by smoked cigarette filter debris to aquatic life.
Activation of acid-sensing ion channels by localized proton transient reveals their role in proton signaling
Authors: Zeng Wei-Zheng , Liu Di-Shi , Liu Lu , She Liang , Wu Long-Jun , Xu Tian-Le 
Published: September 2015

AbstractExtracellular transients of pH alterations likely mediate signal transduction in the nervous system. Neuronal acid-sensing ion channels (ASICs) act as sensors for extracellular protons, but the mechanism underlying ASIC activation remains largely unknown. Here, we show that, following activation of a light-activated proton pump, Archaerhodopsin-3 (Arch), proton transients induced ASIC currents in both neurons and HEK293T cells co-expressing ASIC1a channels. Using chimera proteins that bridge Arch and ASIC1a by a glycine/serine linker, we found that successful coupling occurred within 15 nm distance. Furthermore, two-cell sniffer patch recording revealed that regulated release of protons through either Arch or voltage-gated proton channel Hv1 activated neighbouring cells expressing ASIC1a channels. Finally, computational modelling predicted the peak proton concentration at the intercellular interface to be at pH 6.7, which is acidic enough to activate ASICs in vivo. Our results highlight the pathophysiological role of proton signalling in the nervous system.
Quantum interference based Boolean gates in dangling bond loops on Si(100):H surfaces
Authors: Kleshchonok Andrii , Gutierrez Rafael , Joachim Christian , Cuniberti Gianaurelio 
Published: September 2015

AbstractImplementing atomic and molecular scale electronic functionalities represents one of the major challenges in current nano-electronic developments. Engineered dangling bond nanostructures on Silicon or Germanium surfaces posses the potential to provide novel routes towards the development of non-conventional electronic circuits. These structures are built by selectively removing hydrogen atoms from an otherwise fully passivated Si(100) or Ge(100) substrate. In this theoretical study, we demonstrate how dangling bond loops can be used to implement different Boolean logic gates. Our approach exploits quantum interference effects in such ring-like structures combined with an appropriate design of the interfacing of the dangling bond system with mesoscopic electrodes. We show how OR, AND and NOR gates can be realized by tuning either the global symmetry of the system in a multi-terminal setup—by arranging the position of the input and output electrodes—or, alternatively, by selectively applying electrostatic gates in a two-terminal configuration.
Post-dispersal seed removal by ground-feeding rodents in tropical peatlands, Central Kalimantan, Indonesia
Authors: Blackham Grace V. , Corlett Richard T. 
Published: September 2015

AbstractForested tropical peatlands in Southeast Asia are being rapidly converted to agriculture or degraded into non-forest vegetation. Although large areas have been abandoned, there is little evidence for subsequent forest recovery. As part of a study of forest degradation and recovery, we used seed removal experiments and rodent surveys to investigate the potential role of post-dispersal seed predation in limiting the regeneration of woody plants. Two 14-day seed removal trials were done in deforested and forested peatland habitat in Central Kalimantan, Indonesia. Seeds of Nephelium lappaceum, Syzygium muelleri, Artocarpus heterophyllus (all animal-dispersed) and Combretocarpus rotundatus (wind-dispersed) were tested. Significantly more seeds (82.8%) were removed in forest than non-forest (38.1%) and Combretocarpus had the lowest removal in both habitats. Most handled seeds were eaten in situ and little caching was observed. Six species of rodents were captured in forest and five in non-forest. The most trapped taxa were three Maxomys spp. in forest (85.5% of individuals) and Rattus tiomanicus in non-forest (74.8%). Camera traps confirmed that rodents were responsible for seed removal. Seed predation in deforested areas, which have a much lower seed rain than forest, may contribute to the low density and diversity of regenerating forest.
BMI Affects the Relationship between Long Chain N-3 Polyunsaturated Fatty Acid Intake and Stroke Risk: a Meta-Analysis
Authors: Cheng Pengfei , Huang Wen , Bai Shunjie , Wu Yu , Yu Jia , Zhu Xiaofeng , Qi Zhiguo , Shao Weihua , Xie Peng 
Published: September 2015

AbstractWe performed a meta-analysis to clarify the relationship between long chain n-3 polyunsaturated fatty acid (PUFA) intake and stroke risk. Relevant studies were identified by searching online databases through May 2015. Log relative risks (RRs) of the highest versus the lowest for cohort studies were weighed by the inverse variance method to obtain pooled RRs. Fourteen prospective cohort studies including 514,483 individuals and 9,065 strokes were included. The pooled RR of overall stroke risk for long chain n-3 PUFA intake was 0.87 [95% confidence interval (CI), 0.79–0.95]. Stratification analysis showed that higher long chain n-3 PUFAs intake was associated with reduced fatal stroke risk (RR = 0.84; 95% CI, 0.73–0.97), reduced stroke risk for BMI < 24 (RR = 0.86; 95% CI, 0.75–0.98) and reduced stroke risk for females (RR = 0.81; 95% CI, 0.71–0.92), but was not associated with stroke risk for either BMI ≥ 24 or men. This meta-analysis reveals that higher long chain n-3 PUFA intake is inversely associated with risk of stroke morbidity and mortality with BMI and sex as key factors influencing this risk. Individuals should be encouraged to manage their body weight while increasing their intake of long chain n-3 PUFAs.
A structural dissection of large protein-protein crystal packing contacts
Authors: Luo Jiesi , Liu Zhongyu , Guo Yanzhi , Li Menglong 
Published: September 2015

AbstractWith the rapid increase in crystal structures of protein-protein complexes deposited in the Protein Data Bank (PDB), more and more crystal contacts have been shown to have similar or even larger interface areas than biological interfaces. However, little attention has been paid to these large crystal packing contacts and their structural principles remain unknown. To address this issue, we used a comparative feature analysis to analyze the geometric and physicochemical properties of large crystal packing contacts by comparing two types of specific protein-protein interactions (PPIs), weak transient complexes and permanent homodimers. Our results show that although large crystal packing contacts have a similar interface area and contact size as permanent homodimers, they tend to be more planar, loosely packed and less hydrophobic than permanent homodimers and cannot form a central core region that is fully buried during interaction. However, the properties of large crystal packing contacts, except for the interface area and contact size, more closely resemble those of weak transient complexes. The large overlap between biological and large crystal packing contacts indicates that interface properties are not efficient indicators for classification of biological interfaces from large crystal packing contacts and finding other specific features urgently needed.
Soil N retention and nitrate leaching in three types of dunes in the Mu Us desert of China
Authors: Jin Zhao , Zhu Yajuan , Li Xiangru , Dong Yunshe , An Zhisheng 
Published: September 2015

AbstractA large reservoir of soil nitrate in desert subsoil zones has been demonstrated in previous studies; however, information on the subsoil nitrate reservoir and its distribution characteristics in the deserts of China is still limited. This study investigated the distribution patterns of soil total nitrogen (N), nitrate, ammonium and stable isotopic ratios of 15N (δ15N) in shallow (1 m) and subsoil (5 m) profiles in three types of dunes in the Mu Us desert of China. We found that soil N retention of the fixed and semi-fixed dunes followed a progressive nutrient depletion pattern in shallow soil profiles, whereas the subsoil nitrate of the fixed, semi-fixed and mobile dunes maintained a conservative accumulation pattern. The results indicate that the subsoil of the Mu Us desert may act as a reservoir of available nitrate. Furthermore, a soil δ15N analysis indicate that the nitrate content of the fixed dune is likely derived from soil nitrification, whereas the nitrate content in the mobile dune is derived from atmospheric nitrate deposition. Within the context of looming climate change and intensifying human activities, the subsoil nitrate content in the deserts of northern China could become mobilized and increase environmental risks to groundwater.
Termite mounds harness diurnal temperature oscillations for ventilation
Authors: King Hunter , Ocko Samuel , Mahadevan L. 
Published: September 2015

SignificanceTermite mounds are meter-sized structures built by millimeter-sized insects. These structures provide climate-controlled microhabitats that buffer the organisms from strong environmental fluctuations and allow them to exchange energy, information, and matter with the outside world. By directly measuring the flow inside a mound, we show that diurnal ambient temperature oscillations drive cyclic flows that flush out CO2from the nest and ventilate the mound. This swarm-built architecture demonstrates how work can be derived from the fluctuations of an intensive environmental parameter, and might serve as an inspiration and model for the design of passive, sustainable human architecture.
Targeted, activity-dependent spinal stimulation produces long-lasting motor recovery in chronic cervical spinal cord injury
Authors: McPherson Jacob G. , Miller Robert R. , Perlmutter Steve I. 
Published: September 2015

Significance
This study describes a new strategy for enhancing motor recovery after neurological injury. Using a recurrent neural–computer interface, we attempt to facilitate and direct functionally relevant activity-dependent neural plasticity, the mechanism thought to underlie the benefits of use-dependent physical therapy. We show that this approach can lead to meaningful functional gains that last for weeks after discontinuation of stimulation, a finding that is both unique and highly clinically relevant. Our results suggest that we have leveraged the nervous system’s intrinsic capacity for reorganization and repair to drive true neurological rehabilitation rather than enhancing performance through reanimation or replacement of function. This approach could also be adapted to other impairments, such as locomotion, bowel, bladder or sexual dysfunction, and pain.
Integration of high-content screening and untargeted metabolomics for comprehensive functional annotation of natural product libraries
Authors: Kurita Kenji L. , Glassey Emerson , Linington Roger G. 
Published: September 2015

Significance
Compound Activity Mapping provides an alternative approach to natural products drug discovery by integrating high-content biological screening and untargeted metabolomics to directly reveal the identities and biological functions of individual bioactive compounds in complex natural product libraries. This accelerated discovery pipeline addresses many of the issues that have contributed to the decline of natural products research in some areas by improving dereplication and lead prioritization strategies. The detailed structural and functional annotation offered by this tool may help to improve the integration of natural products with modern high-content, high-throughput screening and provide an additional strategy for the discovery of the next generation of natural product-inspired drug leads and chemical probes.
Protecting group-free, selective cross-coupling of alkyltrifluoroborates with borylated aryl bromides via photoredox/nickel dual catalysis
Authors: Yamashita Yohei , Tellis John C. , Molander Gary A. 
Published: September 2015

Significance
Efficient assembly of small-molecule scaffolds is among the most fundamental goals of organic synthesis. Iterative synthesis, wherein predefined building blocks are unified in an “assembly line” fashion using only a small number of reaction types, is an attractive means for achieving this ideal. These methods are particularly well-suited for applications in drug discovery, agrochemistry, and materials science, where rapid generation of structural diversity is a central objective. A strategy is described in which two reactive sites are differentiated by their preferred mode of reactivity (single vs. two electron). This unique platform allows discrimination between the two sites without artificial blocking of reactivity, streamlining the iterative process by removing the need for deprotection or interconversion of functional groups.
Musical expertise is related to altered functional connectivity during audiovisual integration
Authors: Paraskevopoulos Evangelos , Kraneburg Anja , Herholz Sibylle Cornelia , Bamidis Panagiotis D. , Pantev Christo 
Published: September 2015

Significance
Multisensory integration engages distributed cortical areas and is thought to emerge from their dynamic interplay. Nevertheless, large-scale cortical networks underpinning audiovisual perception have remained undiscovered. The present study uses magnetoencephalography and a methodological approach to perform whole-brain connectivity analysis and reveals, for the first time to our knowledge, the cortical network related to multisensory perception. The long-term training-related reorganization of this network was investigated by comparing musicians to nonmusicians. Results indicate that nonmusicians rely on processing visual clues for the integration of audiovisual information, whereas musicians use a denser cortical network that relies mostly on the corresponding auditory information. These data provide strong evidence that cortical connectivity is reorganized due to expertise in a relevant cognitive domain, indicating training-related neuroplasticity.
Erosion in southern Tibet shut down at ∼10 Ma due to enhanced rock uplift within the Himalaya
Authors: Tremblay Marissa M. , Fox Matthew , Schmidt Jennifer L. , Tripathy-Lang Alka , Wielicki Matthew M. , Harrison T. Mark , Zeitler Peter K. , Shuster David L. 
Published: September 2015

SignificanceThe Himalaya–Tibet plateau system formed by collision between India and Asia that began ca. 50 Ma and is still ongoing today. Despite being the most studied example of continent–continent collision, the evolution of topography in the Himalaya and Tibetan plateau remains an area of vigorous debate and active research. We present geochemical data on the cooling history of granites from the southern Tibetan plateau, which indicate that exhumation of these granites and therefore erosion rates in this region decreased significantly by ∼10 Ma after ∼5 Ma of rapid erosion. We hypothesize that this change in erosion rate reflects a tectonically imposed shift of the topographic and drainage divides south to their current positions within the Himalaya.
Creation of a histone deacetylase 6 inhibitor and its biological effects
Authors: Lee Ju-Hee , Yao Yuanshan , Mahendran Adaickapillai , Ngo Lang , Venta-Perez Gisela , Choy Megan L. , Breslow Ronald , Marks Paul A. 
Published: September 2015

Significance
We discovered an improved hydroxamic acid-based small-molecule N-hydroxy-4-[(N(2-hydroxyethyl)-2-phenylacetamido)methyl)benzamide)] that selectively inhibits histone deacetylase 6 catalytic activity in vivo and in vitro. This can have important anticancer activity.