bluuebunny/crossref_metadata_2025_split huggingface dataset:
The NSIGHT1-randomized controlled trial: rapid whole-genome sequencing for accelerated etiologic diagnosis in critically ill infants
Authors: Petrikin Josh E. , Cakici Julie A. , Clark Michelle M. , Willig Laurel K. , Sweeney Nathaly M. , Farrow Emily G. , Saunders Carol J. , Thiffault Isabelle , Miller Neil A. , Zellmer Lee , Herd Suzanne M. , Holmes Anne M. , Batalov Serge , Veeraraghavan Narayanan , Smith Laurie D. , Dimmock David P. , Leeder J. Steven , Kingsmore Stephen F. 
Published: February 2018

AbstractGenetic disorders are a leading cause of morbidity and mortality in infants in neonatal and pediatric intensive care units (NICU/PICU). While genomic sequencing is useful for genetic disease diagnosis, results are usually reported too late to guide inpatient management. We performed an investigator-initiated, partially blinded, pragmatic, randomized, controlled trial to test the hypothesis that rapid whole-genome sequencing (rWGS) increased the proportion of NICU/PICU infants receiving a genetic diagnosis within 28 days. The participants were families with infants aged <4 months in a regional NICU and PICU, with illnesses of unknown etiology. The intervention was trio rWGS. Enrollment from October 2014 to June 2016, and follow-up until November 2016. Of all, 26 female infants, 37 male infants, and 2 infants of undetermined sex were randomized to receive rWGS plus standard genetic tests (n = 32, cases) or standard genetic tests alone (n = 33, controls). The study was terminated early due to loss of equipoise: 73% (24) controls received genomic sequencing as standard tests, and 15% (five) controls underwent compassionate cross-over to receive rWGS. Nevertheless, intention to treat analysis showed the rate of genetic diagnosis within 28 days of enrollment (the primary end-point) to be higher in cases (31%, 10 of 32) than controls (3%, 1 of 33; difference, 28% [95% CI, 10–46%]; p = 0.003). Among infants enrolled in the first 25 days of life, the rate of neonatal diagnosis was higher in cases (32%, 7 of 22) than controls (0%, 0 of 23; difference, 32% [95% CI, 11–53%];p = 0.004). Median age at diagnosis (25 days [range 14–90] in cases vs. 130 days [range 37–451] in controls) and median time to diagnosis (13 days [range 1–84] in cases, vs. 107 days [range 21–429] in controls) were significantly less in cases than controls (p = 0.04). In conclusion, rWGS increased the proportion of NICU/PICU infants who received timely diagnoses of genetic diseases.
Rice matrix metalloproteinase OsMMP1 plays pleiotropic roles in plant development and symplastic-apoplastic transport by modulating cellulose and callose depositions
Authors: Das Prabir Kumar , Biswas Rupam , Anjum Nazma , Das Amit Kumar , Maiti Mrinal K. 
Published: February 2018

AbstractMatrix metalloproteinases (MMPs) are well-known proteolytic enzymes in animal systems and play roles in tissue differentiation, growth, and defence. Although a few plant MMPs have been reported, their exact functions in development and growth remain elusive. In this study, we characterized the promoter and coding sequence of OsMMP1, one of the putative MMP genes in rice (Oryza sativa). The OsMMP1 catalytic domain is structurally similar to human MMPs with respect to cofactor orientation as predicted by homology modeling. Bacterially expressed recombinant OsMMP1 showed protease activity with bovine serum albumin and gelatin as substrates. Analyses of transcript accumulation and promoter-reporter gene expression revealed that OsMMP1 is spatio-temporally expressed in vegetative and reproductive parts of plants. The plasma membrane-localized OsMMP1 protease affected plant development upon heterologous expression in tobacco and endogenous gene silencing in rice. Transgenic tobacco plants expressing OsMMP1 showed enhanced deposition of cellulose and callose, leading to impairment of symplastic and apoplastic translocations. Moreover, transgenic tobacco tissues exhibited tolerance to oxidative stress-inducing agent by confining the area of tissue death owing to callose lining. Collectively, these findings demonstrate the involvement of a plant MMP in growth, organ differentiation, and development in relation to cell wall modification.
Altered DNA methylation indicates an oscillatory flow mediated epithelial-to-mesenchymal transition signature in ascending aorta of patients with bicuspid aortic valve
Authors: Björck Hanna M. , Du Lei , Pulignani Silvia , Paloschi Valentina , Lundströmer Karin , Kostina Alexandra S. , Österholm Cecilia , Malashicheva Anna , Kostareva Anna , Evangelista Arturo , Teixidó-Tura Gisela , Maleki Shohreh , Franco-Cereceda Anders , Eriksson Per ,   Mechanistic Interrogation of Bicuspid Aortic Valve associated Aortopathy (MIBAVA) Leducq Consortium, Dietz Harry C. , Loeys Bart , Van Laer Lut , McCallion Andrew S. , Mertens Luc , Mital Seema , Mohamed Salah A. , Andelfinger Gregor 
Published: February 2018

AbstractDisturbed flow has been suggested to contribute to aneurysm susceptibility in bicuspid aortic valve (BAV) patients. Lately, flow has emerged as an important modulator of DNA methylation. Hear we combined global methylation analysis with in vitro studies of flow-sensitive methylation to identify biological processes associated with BAV-aortopathy and the potential contribution of flow. Biopsies from non-dilated and dilated ascending aortas were collected from BAV (n = 21) and tricuspid aortic valve (TAV) patients (n = 23). DNA methylation and gene expression was measured in aortic intima-media tissue samples, and in EA.hy926 and primary aortic endothelial cells (ECs) isolated from BAV and TAV exposed to oscillatory (±12 dynes/cm2) or laminar (12 dynes/cm2) flow. We show methylation changes related to epithelial-mesenchymal-transition (EMT) in the non-dilated BAV aorta, associated with oscillatory flow related to endocytosis. The results indicate that the flow-response in BAV ECs involves hypomethylation and increased expression of WNT/β-catenin genes, as opposed to an angiogenic profile in TAV ECs. The EMT-signature was exasperated in dilated BAV aortas. Aberrant EMT in BAV aortic walls could contribute to increased aneurysm susceptibility, and may be due to disturbed flow-exposure. Perturbations during the spatiotemporally related embryonic development of ascending aorta and semilunar valves can however not be excluded.
The impact of reconstructed soils following oil sands exploitation on aspen and its associated belowground microbiome
Authors: Stefani Franck , Isabel Nathalie , Morency Marie-Josée , Lamothe Manuel , Nadeau Simon , Lachance Denis , Li Edith H. Y. , Greer Charles , Yergeau Étienne , Pinno Bradley D. , Séguin Armand 
Published: February 2018

AbstractThe objective of this study was to investigate the impact of different soil covers used to reclaim decommissioned oil sands mining sites on the genetic diversity of aspen and their associated belowground microbiota. Aspen genotyping showed that trees mostly originated from sexual reproduction on sites reclaimed with soil covers made of upland forest floor-mineral mix (FFMM) and lowland peat-mineral mix (PMM). In contrast, most individuals in mature and burned stands sampled as benchmarks for natural disturbances originated from vegetative reproduction. Nonetheless, aspen populations in the FFMM and PMM sites were not genetically different from those in mature and burned stands. DNA metabarcoding of bacteria and fungi in root and soil samples revealed that the diversity of the belowground microbiota associated with aspen and the relative abundance of putative symbiotic taxa in PMM were significantly lower than for FFMM and naturally disturbed sites. Despite similar aspen genetic diversity between FFMM and PMM sites, trees were not associated with the same belowground microbiota. Because the soil microbiome and more specifically the mycorrhizal communities are variable both in space and time, long-term monitoring is particularly important to better understand the ecological trajectory of these novel ecosystems.
Comparative genomics reveals new single-nucleotide polymorphisms that can assist in identification of adherent-invasive Escherichia coli
Authors: Camprubí-Font Carla , Lopez-Siles Mireia , Ferrer-Guixeras Meritxell , Niubó-Carulla Laura , Abellà-Ametller Carles , Garcia-Gil Librado Jesús , Martinez-Medina Margarita 
Published: February 2018

AbstractAdherent-invasive Escherichia coli (AIEC) have been involved in Crohn’s disease (CD). Currently, AIEC are identified by time-consuming techniques based on in vitro infection of cell lines to determine their ability to adhere to and invade intestinal epithelial cells as well as to survive and replicate within macrophages. Our aim was to find signature sequences that can be used to identify the AIEC pathotype. Comparative genomics was performed between three E. coli strain pairs, each pair comprised one AIEC and one non-AIEC with identical pulsotype, sequence type and virulence gene carriage. Genetic differences were further analysed in 22 AIEC and 28 non-AIEC isolated from CD patients and controls. The strain pairs showed similar genome structures, and no gene was specific to AIEC. Three single nucleotide polymorphisms displayed different nucleotide distributions between AIEC and non-AIEC, and four correlated with increased adhesion and/or invasion indices. Here, we present a classification algorithm based on the identification of three allelic variants that can predict the AIEC phenotype with 84% accuracy. Our study corroborates the absence of an AIEC-specific genetic marker distributed across all AIEC strains. Nonetheless, point mutations putatively involved in the AIEC phenotype can be used for the molecular identification of the AIEC pathotype.
Drivers of spatio-temporal changes in paddy soil pH in Jiangxi Province, China from 1980 to 2010
Authors: Guo Xi , Li Hongyi , Yu Huimin , Li Weifeng , Ye Yingcong , Biswas Asim 
Published: February 2018

AbstractThe spatio-temporal distribution soil pH is critical for understanding the productivity and long-term sustainability of our agri-ecosystem. This study quantified the spatio-temporal distribution of paddy soil pH in Jiangxi province, China, and the potential driver of the change between 1980 and 2010. Data from the Soil Survey Information of Jiangxi province (1980s) and Jiangxi Soil Testing and Fertilizer Recommendation study (2010s) were collected and categorized into six pH ranges from strongly-acidic to strongly-alkaline with unit pH differences. Changes were calculated from the maps developed using the Pedological Knowledge base for 1980s data (without geolocation) and geostatistical methods for the 2010s data (geolocated). An overall 0.6-unit decrease and a major shift of soil pH from weakly-acidic (54% → 18%) to acidic (35% → 74%) was observed over the province in a scattered fashion with concentration in the central part and the Poyang Lake area. About half of the area under paddy cultivation went through acidification by at least one pH unit and 7% by at least 2 pH units, while 40% of the area remained unchanged. Excessive fertilizer application and acid-rain intensity contributed to the acidification. Thus, a more knowledge-based and comprehensive fertilizer management should be adopted to make paddy production sustainable in the province.
African ancestry of New World, Bemisia tabaci-whitefly species
Authors: Mugerwa Habibu , Seal Susan , Wang Hua-Ling , Patel Mitulkumar V. , Kabaalu Richard , Omongo Christopher A. , Alicai Titus , Tairo Fred , Ndunguru Joseph , Sseruwagi Peter , Colvin John 
Published: February 2018

AbstractBemisia tabaci whitefly species are some of the world’s most devastating agricultural pests and plant-virus disease vectors. Elucidation of the phylogenetic relationships in the group is the basis for understanding their evolution, biogeography, gene-functions and development of novel control technologies. We report here the discovery of five new Sub-Saharan Africa (SSA) B. tabaci putative species, using the partial mitochondrial cytochrome oxidase 1 gene: SSA9, SSA10, SSA11, SSA12 and SSA13. Two of them, SSA10 and SSA11 clustered with the New World species and shared 84.8‒86.5% sequence identities. SSA10 and SSA11 provide new evidence for a close evolutionary link between the Old and New World species. Re-analysis of the evolutionary history of B. tabaci species group indicates that the new African species (SSA10 and SSA11) diverged from the New World clade c. 25 million years ago. The new putative species enable us to: (i) re-evaluate current models of B. tabaci evolution, (ii) recognise increased diversity within this cryptic species group and (iii) re-estimate divergence dates in evolutionary time.
Open-Label Placebo Treatment for Cancer-Related Fatigue: A Randomized-Controlled Clinical Trial
Authors: Hoenemeyer Teri W. , Kaptchuk Ted J. , Mehta Tapan S. , Fontaine Kevin R. 
Published: February 2018

AbstractThe purpose of this 21-day assessor blinded, randomized-controlled trial was to compare an open-label placebo (OLP) to treatment as usual (TAU) for cancer survivors with fatigue. This was followed by an exploratory 21-day study in which TAU participants received OLPs while OLP participants in the main study were followed after discontinuing placebos. Cancer survivors (N = 74) who completed cancer treatment 6 months to 10 years prior to enrollment reporting at least moderate fatigue (i.e., ≥4 on a 0–10 scale) were randomized to OLP or TAU. Those randomized to OLP took 2 placebo pills twice a day for 21 days. Compared to those randomized to TAU, OLP participants reported a 29% improvement in fatigue severity (average difference in the mean change scores (MD) 12.47, 95% CI 3.32, 21.61; P = 0.008), medium effect (d = 0.63), and a 39% improvement in fatigue-disrupted quality of life (MD = 11.76, 95% CI 4.65, 18.86; P = 0.002), a large effect (d = 0.76). TAU participants who elected to try OLP for 21-days after the main study reported reductions in fatigue of a similar magnitude for fatigue severity and fatigue-disrupted quality of life (23% and 35%, respectively). OLP may reduce fatigue symptom severity and fatigue-related quality of life disruption in cancer survivors.
Gene-Specific Genetic Complementation between Brca1 and Cobra1 During Mouse Mammary Gland Development
Authors: Chiang Huai-Chin , Zhang Xiaowen , Zhao Xiayan , Zhang Chi , Chen Jerry , Garza Paula , Smith Sabrina , Ludwig Thomas , Baer Richard J. , Li Rong , Hu Yanfen 
Published: February 2018

AbstractGerm-line mutations in breast cancer susceptibility gene,BRCA1, result in familial predisposition to breast and ovarian cancers. The BRCA1 protein has multiple functional domains that interact with a variety of proteins in multiple cellular processes. Understanding the biological consequences of BRCA1 interactions with its binding partners is important for elucidating its tissue-specific tumor suppression function. The Cofactor of BRCA1 (COBRA1) is a BRCA1-binding protein that, as a component of negative elongation factor (NELF), regulates RNA polymerase II pausing during transcription elongation. We recently identified a genetic interaction between mouseBrca1andCobra1that antagonistically regulates mammary gland development. However, it remains unclear which of the myriad functions ofBrca1are required for its genetic interaction withCobra1. Here, we show that, unlike deletion ofBrca1exon 11, separation-of-function mutations that abrogate either the E3 ligase activity of its RING domain or the phospho-recognition property of its BRCT domain are not sufficient to rescue the mammary developmental defects inCobra1knockout mice. Furthermore, deletion of mousePalb2, another breast cancer susceptibility gene with functional similarities toBRCA1, does not rescueCobra1knockout-associated mammary defects. Thus, theBrca1/Cobra1genetic interaction is both domain- and gene-specific in the context of mammary gland development.
Evaluation of Serum CEA, CA19-9, CA72-4, CA125 and Ferritin as Diagnostic Markers and Factors of Clinical Parameters for Colorectal Cancer
Authors: Gao Yanfeng , Wang Jinping , Zhou Yue , Sheng Sen , Qian Steven Y. , Huo Xiongwei 
Published: February 2018

AbstractBlood-based protein biomarkers have recently shown as simpler diagnostic modalities for colorectal cancer, while their association with clinical pathological characteristics is largely unknown. In this study, we not only examined the sensitivity and reliability of single/multiple serum markers for diagnosis, but also assessed their connection with pathological parameters from a total of 279 colorectal cancer patients. Our study shown that glycoprotein carcinoembryonic antigen (CEA) owns the highest sensitivity among single marker in the order of CEA > cancer antigen 72-4 (CA72-4) > cancer antigen 19-9 9 (CA19-9) > ferritin > cancer antigen 125 (CA125), while the most sensitive combined-markers for two to five were: CEA + CA72-4; CEA + CA72-4 + CA125; CEA + CA19-9 + CA72-4 + CA125; and CEA + CA19-9 + CA72-4 + CA125 + ferritin, respectively. We also demonstrated that patients who had positive preoperative serum CEA, CA19-9, or CA72-4 were more likely with lymph node invasion, positive CA125 were prone to have vascular invasion, and positive CEA or CA125 were correlated with perineural invasion. In addition, positive CA19-9, CA72-4, or CA125 was associated with poorly differentiated tumor, while CEA, CA19-9, CA72-4, CA125 levels were positively correlated with pathological tumor-node-metastasis stages. We here conclude that combined serum markers can be used to not only diagnose colorectal cancer, but also appraise the tumor status for guiding treatment, evaluation of curative effect, and prognosis of patients.
Crystal structures of a bacterial dipeptidyl peptidase IV reveal a novel substrate recognition mechanism distinct from that of mammalian orthologues
Authors: Roppongi Saori , Suzuki Yoshiyuki , Tateoka Chika , Fujimoto Mayu , Morisawa Saori , Iizuka Ippei , Nakamura Akihiro , Honma Nobuyuki , Shida Yosuke , Ogasawara Wataru , Tanaka Nobutada , Sakamoto Yasumitsu , Nonaka Takamasa 
Published: February 2018

AbstractDipeptidyl peptidase IV (DPP IV, DPP4, or DAP IV) preferentially cleaves substrate peptides with Pro or Ala at the P1 position. The substrate recognition mechanism has been fully elucidated for mammalian DPP IV by crystal structure analyses but not for bacterial orthologues. Here, we report the crystal structures of a bacterial DPP IV (PmDAP IV) in its free form and in complexes with two kinds of dipeptides as well as with a non-peptidyl inhibitor at 1.90 to 2.47 Å resolution. Acyl-enzyme intermediates were observed for the dipeptide complexes of PmDAP IV, whereas tetrahedral intermediates were reported for the oligopeptide complexes of mammalian DPP IVs. This variation reflects the different structural environments of the active site Arg residues, which are involved in the recognition of a substrate carbonyl group, of mammalian and bacterial enzymes. A phylogenetic analysis revealed that PmDAP IV is a closer relative of dipeptidyl peptidases 8 and 9 (DPP8 and DPP9, DPP IV-family enzymes) than DPP IV. These results provide new insights into the substrate recognition mechanism of bacterial DAP IVs and may assist in the development of selective inhibitors for DAP IVs from pathogenic asaccharolytic bacteria, which utilise proteins or peptides as an energy source.
Cerebral ischemia induces the aggregation of proteins linked to neurodegenerative diseases
Authors: Kahl Anja , Blanco Ismary , Jackman Katherine , Baskar Juhi , Milaganur Mohan Harihar , Rodney-Sandy Reunet , Zhang Sheng , Iadecola Costantino , Hochrainer Karin 
Published: February 2018

AbstractProtein aggregation critically affects cell viability in neurodegenerative diseases, but whether this also occurs in ischemic brain injury remains elusive. Prior studies report the post-ischemic aggregation of ubiquitin, small ubiquitin-related modifier (SUMO) and ribosomes, however whether other proteins are also affected is unknown. Here we employed a proteomic approach to identify the insoluble, aggregated proteome after cerebral ischemia. Mice underwent transient middle cerebral artery occlusion or sham-surgery. After 1-hour reperfusion, prior to apparent brain injury, mice were sacrificed and detergent-insoluble proteins were obtained and identified by nanoLC-MS/MS. Naturally existing insoluble proteins were determined in sham controls and aggregated proteins after cerebral ischemia/reperfusion were identified. Selected aggregated proteins found by proteomics were biochemically verified and aggregation propensities were studied during ischemia with or without reperfusion. We found that ischemia/reperfusion induces the aggregation of RNA-binding and heat-shock proteins, ubiquitin, SUMO and other proteins involved in cell signalling. RNA-binding proteins constitute the largest group of aggregating proteins in ischemia. These include TDP43, FUS, hnRNPA1, PSF/SFPQ and p54/NONO, all of which have been linked to neurodegeneration associated with amyotrophic lateral sclerosis and frontotemporal dementia. The aggregation of neurodegeneration-related disease proteins in cerebral ischemia unveils a previously unappreciated molecular overlap between neurodegenerative diseases and ischemic stroke.
Quantum Clique Gossiping
Authors: Li Bo , Li Shuang , Wu Junfeng , Qi Hongsheng 
Published: February 2018

AbstractThis paper establishes a framework of quantum clique gossiping by introducing local clique operations to networks of interconnected qubits. Cliques are local structures in complex networks being complete subgraphs, which can be used to accelerate classical gossip algorithms. Based on cyclic permutations, clique gossiping leads to collective multi-party qubit interactions. We show that at reduced states, these cliques have the same acceleration effects as their roles in accelerating classical gossip algorithms. For randomized selection of cliques, such improved rate of convergence is precisely characterized. On the other hand, the rate of convergence at the coherent states of the overall quantum network is proven to be decided by the spectrum of a mean-square error evolution matrix. Remarkably, the use of larger quantum cliques does not necessarily increase the speed of the network density aggregation, suggesting quantum network dynamics is not entirely decided by its classical topology.
Wavelength and pulse duration tunable ultrafast fiber laser mode-locked with carbon nanotubes
Authors: Li Diao , Jussila Henri , Wang Yadong , Hu Guohua , Albrow-Owen Tom , C. T. Howe Richard , Ren Zhaoyu , Bai Jintao , Hasan Tawfique , Sun Zhipei 
Published: February 2018

AbstractUltrafast lasers with tunable parameters in wavelength and time domains are the choice of light source for various applications such as spectroscopy and communication. Here, we report a wavelength and pulse-duration tunable mode-locked Erbium doped fiber laser with single wall carbon nanotube-based saturable absorber. An intra-cavity tunable filter is employed to continuously tune the output wavelength for 34 nm (from 1525 nm to 1559 nm) and pulse duration from 545 fs to 6.1 ps, respectively. Our results provide a novel light source for various applications requiring variable wavelength or pulse duration.