bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparative genomic and functional analyses: unearthing the diversity and specificity of nematicidal factors in Pseudomonas putida strain 1A00316
Authors: Guo Jing , Jing Xueping , Peng Wen-Lei , Nie Qiyu , Zhai Yile , Shao Zongze , Zheng Longyu , Cai Minmin , Li Guangyu , Zuo Huaiyu , Zhang Zhitao , Wang Rui-Ru , Huang Dian , Cheng Wanli , Yu Ziniu , Chen Ling-Ling , Zhang Jibin 
Published: July 2016

AbstractWe isolated Pseudomonas putida (P. putida) strain 1A00316 from Antarctica. This bacterium has a high efficiency against Meloidogyne incognita (M. incognita) in vitro and under greenhouse conditions. The complete genome of P. putida 1A00316 was sequenced using PacBio single molecule real-time (SMRT) technology. A comparative genomic analysis of 16 Pseudomonas strains revealed that although P. putida 1A00316 belonged to P. putida, it was phenotypically more similar to nematicidal Pseudomonas fluorescens (P. fluorescens) strains. We characterized the diversity and specificity of nematicidal factors in P. putida 1A00316 with comparative genomics and functional analysis and found that P. putida 1A00316 has diverse nematicidal factors including protein alkaline metalloproteinase AprA and two secondary metabolites, hydrogen cyanide and cyclo-(l-isoleucyl-l-proline). We show for the first time that cyclo-(l-isoleucyl-l-proline) exhibit nematicidal activity in P. putida. Interestingly, our study had not detected common nematicidal factors such as 2,4-diacetylphloroglucinol (2,4-DAPG) and pyrrolnitrin in P. putida 1A00316. The results of the present study reveal the diversity and specificity of nematicidal factors in P. putida strain 1A00316.
Protease activated receptor 1 (PAR1) enhances Src-mediated tyrosine phosphorylation of NMDA receptor in intracerebral hemorrhage (ICH)
Authors: Duan Zhen-Zhen , Zhang Feng , Li Feng-Ying , Luan Yi-Fei , Guo Peng , Li Yi-Hang , Liu Yong , Qi Su-Hua 
Published: July 2016

AbstractIt has been demonstrated that Src could modulate NMDA receptor, and PAR1 could also affect NMDAR signaling. However, whether PAR1 could regulate NMDAR through Src under ICH has not yet been investigated. In this study, we demonstrated the role of Src-PSD95-GluN2A signaling cascades in rat ICH model and in vitro thrombin challenged model. Using the PAR1 agonist SFLLR, antagonist RLLFS and Src inhibitor PP2, electrophysiological analysis showed that PAR1 regulated NMDA-induced whole-cell currents (INMDA) though Src in primary cultured neurons. Both in vivo and in vitro results showed the elevated phosphorylation of tyrosine in Src and GluN2A and enhanced interaction of the Src-PSD95-GluN2A under model conditions. Treatment with the PAR1 antagonist RLLFS, AS-PSD95 (Antisense oligonucleotide against PSD95) and Src inhibitor PP2 inhibited the interaction among Src-PSD95-GluN2A, and p-Src, p-GluN2A. Co-application of SFLLR and AS-PSD95, PP2, or MK801 (NMDAR inhibitor) abolished the effect of SF. In conclusion, our results demonstrated that activated thrombin receptor PAR1 induced Src activation, enhanced the interaction among Src-PSD95-GluN2A signaling modules, and up-regulated GluN2A phosphorylation after ICH injury. Elucidation of such signaling cascades would possibly provide novel targets for ICH treatment.
Ionoacoustic tomography of the proton Bragg peak in combination with ultrasound and optoacoustic imaging
Authors: Kellnberger Stephan , Assmann Walter , Lehrack Sebastian , Reinhardt Sabine , Thirolf Peter , Queirós Daniel , Sergiadis George , Dollinger Günther , Parodi Katia , Ntziachristos Vasilis 
Published: July 2016

AbstractIons provide a more advantageous dose distribution than photons for external beam radiotherapy, due to their so-called inverse depth dose deposition and, in particular a characteristic dose maximum at their end-of-range (Bragg peak). The favorable physical interaction properties enable selective treatment of tumors while sparing surrounding healthy tissue, but optimal clinical use requires accurate monitoring of Bragg peak positioning inside tissue. We introduce ionoacoustic tomography based on detection of ion induced ultrasound waves as a technique to provide feedback on the ion beam profile. We demonstrate for 20 MeV protons that ion range imaging is possible with submillimeter accuracy and can be combined with clinical ultrasound and optoacoustic tomography of similar precision. Our results indicate a simple and direct possibility to correlate, in-vivo and in real-time, the conventional ultrasound echo of the tumor region with ionoacoustic tomography. Combined with optoacoustic tomography it offers a well suited pre-clinical imaging system.
Novel Alleviation Mechanisms of Aluminum Phytotoxicity via Released Biosilicon from Rice Straw-Derived Biochars
Authors: Qian Linbo , Chen Baoliang , Chen Mengfang 
Published: July 2016

AbstractReplacing biosilicon and biocarbon in soil via biochar amendment is a novel approach for soil amelioration and pollution remediation. The unique roles of silicon (Si)-rich biochar in aluminum (Al) phytotoxicity alleviation have not been discovered. In this study, the alleviation of Al phytotoxicity to wheat plants (root tips cell death) by biochars fabricated from rice straw pyrolyzed at 400 and 700 °C (RS400 and RS700) and the feedstock (RS100) were studied using a slurry system containing typical acidic soils for a 15-day exposure experiment. The distributions of Al and Si in the slurry solution, soil and plant root tissue were monitored by staining methods, chemical extractions and SEM-EDS observations. We found that the biological sourced silicon in biochars served dual roles in Al phytotoxicity alleviation in acidic soil slurry. On one hand, the Si particles reduced the amount of soil exchangeable Al and prevented the migration of Al to the plant. More importantly, the Si released from biochars synchronously absorbed by the plants and coordinated with Al to form Al-Si compounds in the epidermis of wheat roots, which is a new mechanism for Al phytotoxicity alleviation in acidic soil slurry by biochar amendment. In addition, the steady release of Si from the rice straw-derived biochars was a sustainable Si source for aluminosilicate reconstruction in acidic soil.
Fabrication of water-soluble polymer-encapsulated As4S4 to increase oral bioavailability and chemotherapeutic efficacy in AML mice
Authors: Ma Qiang , Wang Chuan , Li Xiaojin , Guo Hua , Meng Jie , Liu Jian , Xu Haiyan 
Published: July 2016

AbstractRealgar (As4S4) has been demonstrated to be effective for the treatment of acute myeloid leukemia (AML); it has the advantages of no drug resistance and oral administration. Nevertheless, its poor solubility has been an obstacle to its bioavailability, requiring high-dose administration over a long period. We investigated whether crushing realgar crystals to the nanoscale and encapsulating the particles in a water-soluble polymer in one step using hot-melt extrusion would increase the bioavailability of As4S4. Raw As4S4 (r-As4S4) and water-soluble polymer were processed via co-rotating twin screw extrusion. The resulting product (e-As4S4) was characterized by SEM, XRD, and DLS. The cytotoxicity and therapeutic effects of e-As4S4 were evaluated in vivo and in vitro. The results show that e-As4S4 dissolved rapidly in water, forming a stable colloid solution. The average size of e-As4S4 particles was 680 nm, which was reduced by more than 40-fold compared with that of r-As4S4. The bioavailability of e-As4S4 was up to 12.6-fold higher than that of r-As4S4, and it inhibited the proliferation of HL-60 cells much more effectively than did r-As4S4, inducing apoptosis and significantly reducing the infiltration of HL-60 cells into the bone marrow, spleen, and liver. This in turn prolonged the survival of AML mice.
Efficient Inhibition of Hepatitis B Virus Infection by a preS1-binding Peptide
Authors: Ye Xiaoli , Zhou Ming , He Yonggang , Wan Yanmin , Bai Weiya , Tao Shuai , Ren Yanqin , Zhang Xinxin , Xu Jianqing , Liu Jing , Zhang Junqi , Hu Kanghong , Xie Youhua 
Published: July 2016

AbstractEntry inhibitors are promising novel antivirals against hepatitis B virus (HBV) infection. The existing potential entry inhibitors have targeted the cellular receptor(s). In this study, we aim to develop the first entry inhibitor that inhibits HBV infection via targeting viral particles. The preS1 segment of the large envelope glycoprotein of HBV is essential for virion attachment and infection. Previously, we obtained a preS1-binding short peptide B10 by screening a phage display peptide library using the N-terminal half of preS1 (residues 1 to 60, genotype C). We report here that by means of concatenation of B10, we identified a quadruple concatemer 4B10 that displayed a markedly increased preS1-binding activity. The main binding site of 4B10 in preS1 was mapped to the receptor binding enhancing region. 4B10 blocked HBV attachment to hepatic cells and inhibited HBV infection of primary human and tupaia hepatocytes at low nanomolar concentrations. The 4B10-mediated inhibition of HBV infection is specific as it did not inhibit the infection of vesicular stomatitis virus glycoprotein pseudotyped lentivirus or human immunodeficiency virus type 1. Moreover, 4B10 showed no binding activity to hepatic cells. In conclusion, we have identified 4B10 as a promising candidate for a novel class of HBV entry inhibitors.
Global alternans instability and its effect on non-linear wave propagation: dynamical Wenckebach block and self terminating spiral waves
Authors: Vandersickel Nele , Defauw Arne , Dawyndt Peter , Panfilov Alexander V. 
Published: July 2016

AbstractThe main mechanism of formation of reentrant cardiac arrhythmias is via formation of waveblocks at heterogeneities of cardiac tissue. We report that heterogeneity and the area of waveblock can extend itself in space and can result formation of new additional sources, or termination of existing sources of arrhythmias. This effect is based on a new form of instability, which we coin as global alternans instability (GAI). GAI is closely related to the so-called (discordant) alternans instability, however its onset is determined by the global properties of the APD-restitution curve and not by its slope. The APD-restitution curve relates the duration of the cardiac pulse (APD) to the time interval between the pulses and can easily be measured in an experimental or even clinical setting. We formulate the conditions for the onset of GAI, study its manifestation in various 1D and 2D situations and discuss its importance for the onset of cardiac arrhythmias.
Solar irradiance dictates settlement timing and intensity of marine mussels
Authors: Fuentes-Santos Isabel , Labarta Uxío , Álvarez-Salgado X. Antón , Fernández-Reiriz Mª José 
Published: July 2016

AbstractIdentifying the environmental factors driving larval settlement processes is crucial to understand the population dynamics of marine invertebrates. This work aims to go a step ahead and predict larval presence and intensity. For this purpose we consider the influence of solar irradiance, wind regime and continental runoff on the settlement processes. For the first time, we conducted a 5-years weekly monitoring of Mytilus galloprovincialis settlement on artificial suspended substrates, which allowed us to search for interannual variability in the settlement patterns. Comparison between the seasonal pattern of larval settlement and solar irradiance, as well as the well-known effect of solar irradiance on water temperature and food availability, suggest that solar irradiance indirectly influences the settlement process, and support the use of this meteorological variable to predict settlement occurrence. Our results show that solar irradiance allows predicting the beginning and end of the settlement cycle a month in advance: Particularly we have observed that solar irradiance during late winter indirectly drives the timing and intensity of the settlement onset, Finally, a functional generalise additive model, which considers the influence of solar irradiance and continental runoff on the settlement process, provides an accurate prediction of settlement intensity a fortnight in advance.
Tumour sampling method can significantly influence gene expression profiles derived from neoadjuvant window studies
Authors: Pearce Dominic A. , Arthur Laura M. , Turnbull Arran K. , Renshaw Lorna , Sabine Vicky S. , Thomas Jeremy S. , Bartlett John M. S. , Dixon J. Michael , Sims Andrew H. 
Published: July 2016

AbstractPatient-matched transcriptomic studies using tumour samples before and after treatment allow inter-patient heterogeneity to be controlled, but tend not to include an untreated comparison. Here, Illumina BeadArray technology was used to measure dynamic changes in gene expression from thirty-seven paired diagnostic core and surgically excised breast cancer biopsies obtained from women receiving no treatment prior to surgery, to determine the impact of sampling method and tumour heterogeneity. Despite a lack of treatment and perhaps surprisingly, consistent changes in gene expression were identified during the diagnosis-surgery interval (48 up, 2 down; Siggenes FDR 0.05) in a manner independent of both subtype and sampling-interval length. Instead, tumour sampling method was seen to directly impact gene expression, with similar effects additionally identified in six published breast cancer datasets. In contrast with previous findings, our data does not support the concept of a significant wounding or immune response following biopsy in the absence of treatment and instead implicates a hypoxic response following the surgical biopsy. Whilst sampling-related gene expression changes are evident in treated samples, they are secondary to those associated with response to treatment. Nonetheless, sampling method remains a potential confounding factor for neoadjuvant study design.
mCSM-lig: quantifying the effects of mutations on protein-small molecule affinity in genetic disease and emergence of drug resistance
Authors: Pires Douglas E. V. , Blundell Tom L. , Ascher David B. 
Published: July 2016

AbstractThe ability to predict how a mutation affects ligand binding is an essential step in understanding, anticipating and improving the design of new treatments for drug resistance and in understanding genetic diseases. Here we present mCSM-lig, a structure-guided computational approach for quantifying the effects of single-point missense mutations on affinities of small molecules for proteins. mCSM-lig uses graph-based signatures to represent the wild-type environment of mutations and small-molecule chemical features and changes in protein stability as evidence to train a predictive model using a representative set of protein-ligand complexes from the Platinum database. We show our method provides a very good correlation with experimental data (up to ρ = 0.67) and is effective in predicting a range of chemotherapeutic, antiviral and antibiotic resistance mutations, providing useful insights for genotypic screening and to guide drug development. mCSM-lig also provides insights into understanding Mendelian disease mutations and as a tool for guiding protein design. mCSM-lig is freely available as a web server at http://structure.bioc.cam.ac.uk/mcsm_lig.
Source–sink plasmid transfer dynamics maintain gene mobility in soil bacterial communities
Authors: Hall James P. J. , Wood A. Jamie , Harrison Ellie , Brockhurst Michael A. 
Published: July 2016

Significance
Bacterial adaptation through horizontal gene transfer is central to microbial evolution and, in the context of antibiotic resistance, represents a growing clinical threat. Conjugative plasmids are key mediators of genetic exchange both within and between species. Experimental studies have mostly focused on plasmid population dynamics in single-species populations, but between-species transfer could counteract purifying selection and maintain plasmids in hosts that would otherwise lose them. We show that plasmids can be lost from single-species populations, even when their genes are under selection, because beneficial genes are captured by the chromosome. In contrast, experiments and models show that, in a two-species community, between-species transfer maintains community-wide access to plasmids, promoting the spread of the ecologically and clinically important genes they carry.
Rationalizing spatial exploration patterns of wild animals and humans through a temporal discounting framework
Authors: Namboodiri Vijay Mohan K. , Levy Joshua M. , Mihalas Stefan , Sims David W. , Hussain Shuler Marshall G. 
Published: July 2016

Significance
Understanding the movement patterns of wild animals is a fundamental question in ecology with implications for wildlife conservation. It has recently been hypothesized that random search patterns known as Lévy walks are optimal and underlie the observed power law movement patterns of wild foragers. However, as Lévy walk models assume that foragers do not learn from experience, they may not apply generally to cognitive animals. Here, we present a decision-theoretic framework wherein animals attempting to optimally learn from their environments will show near power law-distributed path lengths due to temporal discounting. We then provide experimental support for this framework in human exploration in a controlled laboratory setting and in animals foraging in the wild.
CCR7 expression alters memory CD8 T-cell homeostasis by regulating occupancy in IL-7– and IL-15–dependent niches
Authors: Jung Yong Woo , Kim Hyun Gyung , Perry Curtis J. , Kaech Susan M. 
Published: July 2016

SignificanceIL-7 and IL-15 have been shown to play crucial roles in maintaining the population of memory T cells, which are important in fighting against secondary infections, but how effector and memory T cells receive these cytokines is incompletely understood. We investigated the role of C-C receptor 7 (CCR7) in the development of memory T cells using CCR7-deficient mice. CCR7-deficient memory T cells showed an abnormal migratory pattern and increased survival, especially in the lungs and bone marrow, in an IL-15–dependent fashion compared with wild type memory cells. We conclude that the localization of memory T cells is important to “see” these cytokines for homeostasis.
Numerous proteins with unique characteristics are degraded by the 26S proteasome following monoubiquitination
Authors: Braten Ori , Livneh Ido , Ziv Tamar , Admon Arie , Kehat Izhak , Caspi Lilac H. , Gonen Hedva , Bercovich Beatrice , Godzik Adam , Jahandideh Samad , Jaroszewski Lukasz , Sommer Thomas , Kwon Yong Tae , Guharoy Mainak , Tompa Peter , Ciechanover Aaron 
Published: July 2016

Significance
A substrate-conjugated polyubiquitin chain is accepted as the “canonical” proteasomal degradation signal. Using a cellular (human and yeast) proteomic screen in the exclusive presence of nonpolymerizable ubiquitin, we show that a large group of proteins is degraded by the proteasome following monoubiquitination. The screen also unraveled polyubiquitin-dependent substrates, as they are stabilized in the presence of this ubiquitin mutant. Notably, monoubiquitination- and polyubiquitination-dependent substrates display distinct important characteristics. Monoubiquitinated proteins are of lower molecular mass and of lesser structural disorder. The two groups can be assigned to defined cellular pathways. Furthermore, some of the characteristics are confined to either human or yeast cells, suggesting that the mechanism of action/recognition of the ubiquitin system in the two organisms are different somehow.
Graphene patterning by nanosecond laser ablation: the effect of the substrate interaction with graphene
Authors: Pérez-Mas Ana M , Álvarez Patricia , Campos Nuria , Gómez David , Menéndez Rosa 
Published: July 2016

Abstract
This paper focuses on the development of patterned graphene/substrate by means of green nanosecond pulse laser irradiation. Monolayer graphene samples supported on a Si/SiO2 substrate were patterned using 532 nm laser irradiation under fluence conditions ranging from 31 mJ cm−2 to 4240 mJ cm−2. Raman spectroscopy was used to investigate the effect of laser irradiation on the graphene. It was found that at 356 mJ cm−2 selective ablation of the graphene occurs. However, at fluence values above 1030 mJ cm−2 (when damage to the substrate is observed) no ablation of the graphene takes place. In contrast, its graphenic structure was found to have been modified. Only at fluence values where the ablation of the substrate occurs, is graphene eliminated in an area almost equivalent to that of the ablated substrate. In this case, additional damage to the graphene sheet edges is produced. The increment in the number of oxygenated functional groups in these regions, as measured by x-ray photoelectron spectroscopy (XPS), suggests that this damage is probably caused by thermal phenomena during the ablation of the substrate.
Extensor Digitorum Brevis Flap for the Coverage of Ankle and Dorsal Foot Wounds: A Technical Trick
Authors: Houdek Matthew T. , Wagner Eric R. , Pensy Raymond A. , Eglseder Walter A. 
Published: July 2016

Summary:
Soft tissue wounds overlying the dorsum of the foot and ankle are difficult to treat, and historically have been treated with free tissue transfer. Advances in surgical technique have expanded the use of pedicle perforator flaps to avoid free tissue transfer in certain situations. The authors describe a technique for using an extensor digitorum brevis flap to provide soft tissue coverage for wounds of the ankle and foot. In the senior authors’ experience, the use of this flap has achieved wound coverage in 100% of patients with smaller wounds (≤45 cm2) of the ankle.
Direct Measurement of Tissue Oxygenation as a Method of Diagnosis of Acute Compartment Syndrome
Authors: Weick Jack W. , Kang Heejae , Lee Lawrence , Kuether Justin , Liu Xuhui , Hansen Erik N. , Kandemir Utku , Rollins Mark D. , Mok James M. 
Published: July 2016

Objective:
The aim of this study was to investigate the utility of direct measurement of tissue oxygenation during compartment syndrome (CS) and tourniquet-induced ischemia in a large animal model. We hypothesize that as compartment pressure (CP) rises, circulation within the compartment will decrease resulting in a decreased level of oxygen in the muscle.

Methods:
This study used a dog model of both CS- and tourniquet-based ischemia. In 15 animals, CS was induced in 1 hind limb with varying degrees of severity using an infusion model. Tourniquet ischemia was induced in the contralateral hind limb for varying durations. The partial pressure of oxygen (PmO2) was continuously monitored using a polarographic oxygen probe in the muscle of both hind limbs. CP was monitored in the CS limb. PmO2 and CP were analyzed after fasciotomy, performed after approximately 7 hours of warm ischemia, or release of tourniquet.

Results:
With the application of tourniquet ischemia, PmO2 fell from 38.40 to 1.30 mm Hg (P < 0.001) and subsequently rose after release of the tourniquet to 39.81 mm Hg (P < 0.001). Elevated CP induced by infusion was relieved by fasciotomy (52.04–11.37 mm Hg postfasciotomy, P < 0.001). PmO2 readings in the infusion model were significantly higher in pre-CS than during CS (31.77 mm Hg vs. 3.88 mm Hg, P < 0.001) and rebounded after fasciotomy (50.24 mm Hg, P < 0.001), consistent with hyperemic response.

Conclusions:
Increased CP caused an observable decrease in PmO2 that was reversed by fasciotomy. PmO2 can be directly measured in real time with a polarographic tissue pO2 probe. This study is the first step of evaluating an alternative method for diagnosing acute CS.