bluuebunny/crossref_metadata_2025_split huggingface dataset:
An unusual strategy for the anoxic biodegradation of phthalate
Authors: Ebenau-Jehle Christa , Mergelsberg Mario , Fischer Stefanie , Brüls Thomas , Jehmlich Nico , von Bergen Martin , Boll Matthias 
Published: July 2016

Abstract
In the past two decades, the study of oxygen-independent degradation of widely abundant aromatic compounds in anaerobic bacteria has revealed numerous unprecedented enzymatic principles. Surprisingly, the organisms, metabolites and enzymes involved in the degradation of o-phthalate (1,2-dicarboxybenzene), mainly derived from phthalate esters that are annually produced at the million ton scale, are sparsely known. Here, we demonstrate a previously unknown capacity of complete phthalate degradation in established aromatic compound-degrading, denitrifying model organisms of the genera Thauera, Azoarcus and ‘Aromatoleum’. Differential proteome analyses revealed phthalate-induced gene clusters involved in uptake and conversion of phthalate to the central intermediate benzoyl-CoA. Enzyme assays provided in vitro evidence for the formation of phthaloyl-CoA by a succinyl-CoA- and phthalate-specific CoA transferase, which is essential for the subsequent oxygen-sensitive decarboxylation to benzoyl-CoA. The extreme instability of the phthaloyl-CoA intermediate requires highly balanced CoA transferase and decarboxylase activities to avoid its cellular accumulation. Phylogenetic analysis revealed phthaloyl-CoA decarboxylase as a novel member of the UbiD-like, (de)carboxylase enzyme family. Homologs of the encoding gene form a phylogenetic cluster and are found in soil, freshwater and marine bacteria; an ongoing global distribution of a possibly only recently evolved degradation pathway is suggested.
Speciation and ecological success in dimly lit waters: horizontal gene transfer in a green sulfur bacteria bloom unveiled by metagenomic assembly
Authors: Llorens-Marès Tomàs , Liu Zhenfeng , Allen Lisa Zeigler , Rusch Douglas B , Craig Matthew T , Dupont Chris L , Bryant Donald A , Casamayor Emilio O 
Published: July 2016

Abstract
A natural planktonic bloom of a brown-pigmented photosynthetic green sulfur bacteria (GSB) from the disphotic zone of karstic Lake Banyoles (NE Spain) was studied as a natural enrichment culture from which a nearly complete genome was obtained after metagenomic assembly. We showed in situ a case where horizontal gene transfer (HGT) explained the ecological success of a natural population unveiling ecosystem-specific adaptations. The uncultured brown-pigmented GSB was 99.7% identical in the 16S rRNA gene sequence to its green-pigmented cultured counterpart Chlorobium luteolum DSM 273T. Several differences were detected for ferrous iron acquisition potential, ATP synthesis and gas vesicle formation, although the most striking trait was related to pigment biosynthesis strategy. Chl. luteolum DSM 273T synthesizes bacteriochlorophyll (BChl) c, whereas Chl. luteolum CIII incorporated by HGT a 18-kbp cluster with the genes needed for BChl e and specific carotenoids biosynthesis that provided ecophysiological advantages to successfully colonize the dimly lit waters. We also genomically characterized what we believe to be the first described GSB phage, which based on the metagenomic coverage was likely in an active state of lytic infection. Overall, we observed spread HGT and we unveiled clear evidence for virus-mediated HGT in a natural population of photosynthetic GSB.
Bio-inspired sensitive and reversible mechanochromisms via strain-dependent cracks and folds
Authors: Zeng Songshan , Zhang Dianyun , Huang Wenhan , Wang Zhaofeng , Freire Stephan G. , Yu Xiaoyuan , Smith Andrew T. , Huang Emily Y. , Nguon Helen , Sun Luyi 
Published: July 2016

AbstractA number of marine organisms use muscle-controlled surface structures to achieve rapid changes in colour and transparency with outstanding reversibility. Inspired by these display tactics, we develop analogous deformation-controlled surface-engineering approaches via strain-dependent cracks and folds to realize the following four mechanochromic devices: (1) transparency change mechanochromism (TCM), (2) luminescent mechanochromism (LM), (3) colour alteration mechanochromism (CAM) and (4) encryption mechanochromism (EM). These devices are based on a simple bilayer system that exhibits a broad range of mechanochromic behaviours with high sensitivity and reversibility. The TCM device can reversibly switch between transparent and opaque states. The LM can emit intensive fluorescence as stretched with very high strain sensitivity. The CAM can turn fluorescence from green to yellow to orange as stretched within 20% strain. The EM device can reversibly reveal and conceal any desirable patterns.
Essential role of autoactivation circuitry on Aurora B-mediated H2AX-pS121 in mitosis
Authors: Shimada Midori , Goshima Takahiro , Matsuo Hiromi , Johmura Yoshikazu , Haruta Mayumi , Murata Kazuhiro , Tanaka Hiromitsu , Ikawa Masahito , Nakanishi Keiko , Nakanishi Makoto 
Published: July 2016

AbstractProper deposition and activation of Aurora B at the centromere is critical for faithful chromosome segregation in mammals. However, the mechanistic basis for abrupt Aurora B kinase activation at the centromere has not yet been fully understood. We demonstrate here that Aurora B-mediated phosphorylation of histone H2AX at serine 121 (H2AX-pS121) promotes Aurora B autophosphorylation and is essential for proper chromosome segregation. Aurora B-mediated H2AX-pS121 is specifically detected at the centromere during mitosis. H2AX depletion results in a severe defect in activation and deposition of Aurora B at this locus. A phosphomimic mutant of H2AX at S121 interacts with activated Aurora B more efficiently than wild-type in vitro. Taken together, these results propose a model in which Aurora B-mediated H2AX-pS121 probably provide a platform for Aurora B autoactivation circuitry at centromeres and thus play a pivotal role in proper chromosome segregation.
Wars2 is a determinant of angiogenesis
Authors: Wang Mao , Sips Patrick , Khin Ester , Rotival Maxime , Sun Ximing , Ahmed Rizwan , Widjaja Anissa Anindya , Schafer Sebastian , Yusoff Permeen , Choksi Pervinder Kaur , Ko Nicole Shi Jie , Singh Manvendra K. , Epstein David , Guan Yuguang , Houštěk Josef , Mracek Tomas , Nuskova Hana , Mikell Brittney , Tan Jessie , Pesce Francesco , Kolar Frantisek , Bottolo Leonardo , Mancini Massimiliano , Hubner Norbert , Pravenec Michal , Petretto Enrico , MacRae Calum , Cook Stuart A 
Published: July 2016

AbstractCoronary flow (CF) measured ex vivo is largely determined by capillary density that reflects angiogenic vessel formation in the heart in vivo. Here we exploit this relationship and show that CF in the rat is influenced by a locus on rat chromosome 2 that is also associated with cardiac capillary density. Mitochondrial tryptophanyl-tRNA synthetase (Wars2), encoding an L53F protein variant within the ATP-binding motif, is prioritized as the candidate at the locus by integrating genomic data sets. WARS2(L53F) has low enzyme activity and inhibition of WARS2 in endothelial cells reduces angiogenesis. In the zebrafish, inhibition of wars2 results in trunk vessel deficiencies, disordered endocardial-myocardial contact and impaired heart function. Inhibition of Wars2 in the rat causes cardiac angiogenesis defects and diminished cardiac capillary density. Our data demonstrate a pro-angiogenic function for Wars2 both within and outside the heart that may have translational relevance given the association of WARS2 with common human diseases.
Effect of levodopa-carbidopa intestinal gel on resting tremors in patients with advanced Parkinson’s disease
Authors: Fernandez Hubert H , Robieson Weining Z , Chatamra Krai , Dubow Jordan , Eaton Susan , Benesh Janet A , Odin Per 
Published: July 2016

AbstractResting tremors occur in more than 70% of patients with advanced Parkinson’s disease (PD). PD patients with resting tremors are typically treated with oral dopaminergic therapy or non-dopaminergic agents. However, treatment response with these medications is inconsistent and often unsatisfactory. Levodopa-carbidopa intestinal gel (LCIG, also known in the United States as carbidopa-levodopa enteral suspension (CLES)), administered continuously by a portable pump via a percutaneous endoscopic gastrojejunostomy (PEG-J) tube, significantly improves motor complications in patients with advanced PD. This was a post hoc analysis of a large phase 3, 12-month, open-label study evaluating long-term safety and efficacy of LCIG via PEG-J tube (NCT00335153). Unified Parkinson’s Disease Rating Scale Part III Question 20 total scores at baseline, measuring resting tremors, were used to stratify patients into three subgroups (none, mild, or significant baseline resting tremors). Out of 354 enrolled patients, 286 had baseline and post-PEG-J assessments of resting tremors and were included in this analysis. At baseline the majority of patients (69%) had no resting tremors, whereas 13% had mild resting tremors, and 18% had significant resting tremors. A complete resolution in resting tremors after 12 months of LCIG treatment was reported for 78% and 70% of patients with mild and significant baseline resting tremors, respectively. Improvements in motor complications and quality of life occurred regardless of degree of baseline resting tremors. LCIG may provide more consistent and sustained improvements in resting tremors that were not well-controlled with optimized oral medication among patients with advanced PD.
Integrated network-diversity analyses suggest suppressive effect of Hodgkin’s lymphoma and slightly relieving effect of chemotherapy on human milk microbiome
Authors: Ma Zhanshan , Li Lianwei , Li Wendy , Li Jie , Chen Hongju 
Published: July 2016

AbstractWe aim to investigate the effects of Hodgkin’s lymphoma and the chemotherapy for treating the disease on the human milk microbiome through integrated network and community diversity analyses. Our analyses suggest that Hodgkin’s lymphoma seems to have a suppressing effect on the milk microbiome by lowering the milk microbial community diversity, as measured by the Hill numbers profiles. Although the diversity analysis did not reveal an effect of chemotherapy on community diversity, bacterial species interaction network analysis shows that chemotherapy may help to slightly restore the milk microbiome impacted by Hodgkin’s lymphoma through its influence on the interactions among species (or OTUs). We further constructed diversity-metabolites network, which suggests that the milk microbial diversity is positively correlated with some beneficial milk metabolites such as DHA (DocosaHexaenoic Acid), and that the diversity is negatively correlated with some potentially harmful metabolites such as Butanal. We hence postulate that higher milk microbial diversity should be a signature of healthy mothers and beneficial to infants. Finally, we constructed metabolites OTU correlation networks, from which we identified some special OTUs. These OTUs deserve further investigations given their apparent involvements in regulating the levels of critical milk metabolites such as DHA, Inositol and Butanal.
Effects of Water on Structure and Dynamics of Trehalose Glasses at Low Water Contents and its Relationship to Preservation Outcomes
Authors: Weng Lindong , Ziaei Shima , Elliott Gloria D. 
Published: July 2016

AbstractDry preservation of biologics in sugar glasses is regarded as a promising alternative to conventional cryopreservation. Evidence from various studies has suggested that there is a critical range of water content beyond which the viability of preserved biologics can be greatly compromised. In this study the viability of T-cells was determined as a function of end water content after microwave-assisted drying in trehalose solutions. Hydrogen-bonding and clustering phenomena in trehalose solutions of the same moisture content were also evaluated using molecular dynamics simulation. Post-rehydration viability decreased dramatically within the range of 0.1–1 gH2O/gdw. Molecular modeling revealed that as the water content approached 0.1 gH2O/gdw the matrix formed a large interconnected trehalose skeleton with a minimal number of bound water molecules scattered in the bulk. The diffusion coefficients of trehalose oxygen atoms most distant from the glycosidic linkage fluctuated around 7.5 × 10−14 m2/s within the range of 0.02–0.1 gH2O/gdw and increased again to ~1.13 × 10−13 m2/s at 0.01 gH2O/gdw and below due to the loss of water in the free volume between trehalose molecules. These insights can guide the optimal selection of final moisture contents to advance dry preservation methods.
Effect of caesarean section on maternal and foetal outcomes in acute fatty liver of pregnancy: a systematic review and meta-analysis
Authors: Wang Hong-Yan , Jiang Qing , Shi Hao , Xu Yun-Qing , Shi Ai-Chao , Sun Yuan-Li , Li Jian , Ning Qin , Shen Guan-Xin 
Published: July 2016

AbstractSeveral studies have reported a positive association between caesarean section for expeditious pregnancy termination and perinatal outcomes in acute fatty liver of pregnancy (AFLP); however, the risks remain unclear and independent studies have reported conflicting findings. In this meta-analysis, we aimed to confirm the relationship between caesarean section and perinatal outcomes in AFLP. The PubMed, Embase, and China National Knowledge Infrastructure databases were searched (until July 17, 2015) for observational clinical studies focusing on the association between caesarean section and perinatal outcomes in AFLP. Data were extracted and processed independently by 2 authors. We also compared caesarean section with vaginal delivery to further investigate this relationship. We observed that 2 of the 3 primary outcomes in caesarean section exhibited positive effects—the maternal mortality rate was 44% lower (relative risk [RR], 0.56 [0.41–0.76]) and perinatal mortality rate was also reduced (RR, 0.52 [0.38–0.71]), compared to those for vaginal delivery. We did not find any associations between caesarean section and perinatal outcomes in AFLP in terms of neonatal mortality type and maternal multiple organ complications. These findings emphasise the significant prognostic value and clinical implications of caesarean section in AFLP, and suggest that the adverse outcomes should be reduced.
Aero-Thermo-Dynamic Mass Analysis
Authors: Shiba Kota , Yoshikawa Genki 
Published: July 2016

AbstractEach gas molecule has its own molecular weight, while such a microscopic characteristic is generally inaccessible, and thus, it is measured indirectly through e.g. ionization in conventional mass analysis. Here, we present a novel approach to the direct measurement of molecular weight through a nanoarchitectonic combination of aerodynamics, thermodynamics, and mechanics, transducing microscopic events into macroscopic phenomena. It is confirmed that this approach can provide molecular weight of virtually any gas or vaporizable liquid sample in real-time without ionization. Demonstrations through analytical calculations, numerical simulations, and experiments verify the validity and versatility of the novel mass analysis realized by a simple setup with a flexible object (e.g. with a bare cantilever and even with a business card) placed in a laminar jet. Owing to its unique and simple working principle, this aero-thermo-dynamic mass analysis (AMA) can be integrated into various analytical devices, production lines, and consumer mobile platforms, opening new chapters in aerodynamics, thermodynamics, mechanics, and mass analysis.
Effects of shrub encroachment on soil organic carbon in global grasslands
Authors: Li He , Shen Haihua , Chen Leiyi , Liu Taoyu , Hu Huifeng , Zhao Xia , Zhou Luhong , Zhang Pujin , Fang Jingyun 
Published: July 2016

AbstractThis study aimed to evaluate the effect of shrub encroachment on soil organic carbon (SOC) content at broad scales and its controls. We conducted a meta-analysis using paired control data of shrub-encroached grassland (SEG) vs. non-SEG collected from 142 studies worldwide. SOC contents (0–50 cm) were altered by shrub encroachment, with changes ranging from −50% to + 300%, with an effect size of 0.15 (p < 0.01). The SOC contents increased in semi-arid and humid regions, and showed a greater rate of increase in grassland encroached by leguminous shrubs than by non-legumes. The SOC content decreased in silty and clay soils but increased in sand, sandy loam and sandy clay loam. The SOC content increment was significantly positively correlated with precipitation and temperature as well as with soil bulk density but significantly negatively correlated with soil total nitrogen. We conclude the main effects of shrub encroachment would be to increase topsoil organic carbon content. As structural equation model revealed, soils properties seem to be the primary factors responsible for the extent of the changes, coarse textured soils having a greater capacity than fine textured soils to increase the SOC content. This increased effect appears to be secondarily enhanced by climate and plant elements.
Controllable light capsules employing modified Bessel-Gauss beams
Authors: Gong Lei , Liu Weiwei , Zhao Qian , Ren Yuxuan , Qiu Xingze , Zhong Mincheng , Li Yinmei 
Published: July 2016

AbstractWe report, in theory and experiment, on a novel class of controlled light capsules with nearly perfect darkness, directly employing intrinsic properties of modified Bessel-Gauss beams. These beams are able to naturally create three-dimensional bottle-shaped region during propagation as long as the parameters are properly chosen. Remarkably, the optical bottle can be controlled to demonstrate various geometries through tuning the beam parameters, thereby leading to an adjustable light capsule. We provide a detailed insight into the theoretical origin and characteristics of the light capsule derived from modified Bessel-Gauss beams. Moreover, a binary digital micromirror device (DMD) based scheme is first employed to shape the bottle beams by precise amplitude and phase manipulation. Further, we demonstrate their ability for optical trapping of core-shell magnetic microparticles, which play a particular role in biomedical research, with holographic optical tweezers. Therefore, our observations provide a new route for generating and controlling bottle beams and will widen the potentials for micromanipulation of absorbing particles, aerosols or even individual atoms.
Direct radiocarbon dating and genetic analyses on the purported Neanderthal mandible from the Monti Lessini (Italy)
Authors: Talamo Sahra , Hajdinjak Mateja , Mannino Marcello A. , Fasani Leone , Welker Frido , Martini Fabio , Romagnoli Francesca , Zorzin Roberto , Meyer Matthias , Hublin Jean-Jacques 
Published: July 2016

AbstractAnatomically modern humans replaced Neanderthals in Europe around 40,000 years ago. The demise of the Neanderthals and the nature of the possible relationship with anatomically modern humans has captured our imagination and stimulated research for more than a century now. Recent chronological studies suggest a possible overlap between Neanderthals and anatomically modern humans of more than 5,000 years. Analyses of ancient genome sequences from both groups have shown that they interbred multiple times, including in Europe. A potential place of interbreeding is the notable Palaeolithic site of Riparo Mezzena in Northern Italy. In order to improve our understanding of prehistoric occupation at Mezzena, we analysed the human mandible and several cranial fragments from the site using radiocarbon dating, ancient DNA, ZooMS and isotope analyses. We also performed a more detailed investigation of the lithic assemblage of layer I. Surprisingly we found that the Riparo Mezzena mandible is not from a Neanderthal but belonged to an anatomically modern human. Furthermore, we found no evidence for the presence of Neanderthal remains among 11 of the 13 cranial and post-cranial fragments re-investigated in this study.
Cathepsin S attenuates endosomal EGFR signalling: A mechanical rationale for the combination of cathepsin S and EGFR tyrosine kinase inhibitors
Authors: Huang Chien-Chang , Lee Cheng-Che , Lin Hsiao-Han , Chang Jang-Yang 
Published: July 2016

AbstractEGF-mediated EGFR endocytosis plays a crucial role in the attenuation of EGFR activation by sorting from early endosomes to late endosomes and transporting them into lysosomes for the final proteolytic degradation. We previously observed that cathepsin S (CTSS) inhibition induces tumour cell autophagy through the EGFR-mediated signalling pathway. In this study, we further clarified the relationship between CTSS activities and EGFR signalling regulation. Our results revealed that CTSS can regulate EGFR signalling by facilitating EGF-mediated EGFR degradation. CTSS inhibition delayed the EGFR degradation process and caused EGFR accumulation in the late endosomes at the perinuclear region, which provides spatial compartments for prolonged EGFR and sustained downstream signal transducer and activator of transcription 3 and AKT signalling. Notably, cellular apoptosis was markedly enhanced by combining treatment with the EGFR inhibitor Iressa and CTSS inhibitor 6r. The data not only reveal a biological role of CTSS in EGFR signalling regulation but also evidence a rationale for its clinical evaluation in the combination of CTSS and EGFR tyrosine kinase inhibitors.
High-Resolution Group Quantization Phase Processing Method in Radio Frequency Measurement Range
Authors: Du Baoqiang , Feng Dazheng , Tang Yaohua , Geng Xin , Zhang Duo , Cai Chaofeng , Wan Maoquan , Yang Zhigang 
Published: July 2016

AbstractAiming at the more complex frequency translation, the longer response time and the limited measurement precision in the traditional phase processing, a high-resolution phase processing method by group quantization higher than 100 fs level is proposed in radio frequency measurement range. First, the phase quantization is used as a step value to quantize every phase difference in a group by using the fixed phase relationships between different frequencies signals. The group quantization is formed by the results of the quantized phase difference. In the light of frequency drift mainly caused by phase noise of measurement device, a regular phase shift of the group quantization is produced, which results in the phase coincidence of two comparing signals which obtain high-resolution measurement. Second, in order to achieve the best coincidences pulse, a subtle delay is initiatively used to reduce the width of the coincidences fuzzy area according to the transmission characteristics of the coincidences in the specific medium. Third, a series of feature coincidences pulses of fuzzy area can be captured by logic gate to achieve the best phase coincidences information for the improvement of the measurement precision. The method provides a novel way to precise time and frequency measurement.