bluuebunny/crossref_metadata_2025 huggingface dataset:
Not all predators are equal: a continent‐scale analysis of the effects of predator control on Australian mammals
Authors: Hunter Daniel O. , Lagisz Malgorzata , Leo Viyanna , Nakagawa Shinichi , Letnic Mike
Published: January 2018

Introduced predators pose threats to biodiversity and are implicated in the extinction of many native species. In Australia, considerable effort is spent controlling populations of introduced predators, including the dingo Canis dingo and the red fox Vulpes vulpes, to reduce their effects on native species and livestock. Studies describe different outcomes of controlling dingo and fox populations on native species, making biodiversity management decisions difficult for conservation managers.

We conduct a meta‐analysis to compare the impacts that control programmes targeted towards dingoes and foxes in Australia have on introduced predators and on other mammal species, including native species and prey species.

Our results provide evidence that lethal control of dingoes and foxes has different outcomes for different mammalian species. Dingo removal had a negative effect on the abundance of native mammals weighing less than the critical weight range (CWR) of 30–5500 g, and a positive effect on the abundance of mammals above the CWR. Fox abundance increased in response to dingo control, but confidence intervals were large. Fox removal had strong positive effects on ground‐dwelling and arboreal mammals. Lethal control of dingoes did not have a significant effect on cats, but where dingoes were removed there was a tendency for foxes to increase, and where foxes were removed there was a tendency for cats to increase.

Our results highlight unintended and perverse outcomes of lethal predator control on Australian mammals. Lethal control of dingoes significantly increases abundances of above CWR mammals and significantly decreases abundances of under CWR mammals. Lethal control of foxes significantly increases the abundances of CWR mammals. These findings show how removing dingoes and foxes alters mammal assemblages and provide comprehensive and objective information for conservation managers.

We recommend that land management agencies take the results of this study into consideration when planning lethal control programmes targeting dingoes and foxes because, depending on the target canid, these programmes result in different outcomes for other mammal species. Removal programmes targeting dingoes and/or foxes can result in increased abundances of introduced predators and, ultimately, have far‐reaching effects on many mammal species.
Kangaroo Mother Care in Colombia: A Subaltern Health Innovation against For‐profit Biomedicine
Authors: Abadía‐Barrero César Ernesto
Published: January 2018

This ethnographic study presents the origins, growth, and collapse of the first Kangaroo Mother Care (KMC) program, a well‐established practice for neonatal care created in 1978 in Colombia. The WHO and UNICEF praised this zero‐cost revolutionary technique for its promotion of skin‐to‐skin contact between premature and low‐birth‐weight newborns and family members. KMC facilitates early hospital discharge, brings many clinical and psychological benefits, and constitutes an excellent alternative to placing babies in incubators. However, these benefits and political potential against biomedical interventions were undermined after being relabeled as a “reverse innovation,” a business concept that encourages corporate investments in low‐income countries to develop technologies that can both solve global health problems and boost multinational corporations profits. In response, I propose “subaltern health innovations” as a label for KMC that accounts for the power dynamics in global health between health care initiatives that originate in the Global South and neoliberal configurations of for‐profit biomedicine.
A novel two‐component system modulates quorum sensing and pathogenicity in Burkholderia cenocepacia
Authors: Cui Chaoyu , Yang Chunxi , Song Shihao , Fu Shuna , Sun Xiuyun , Yang Liang , He Fei , Zhang Lian‐Hui , Zhang Yongliang , Deng Yinyue
Published: January 2018

Quorum sensing (QS) is widely utilized by bacterial pathogens to regulate biological functions and pathogenicity. Recent evidence has shown that QS is subject to regulatory cascades, especially two‐component systems that often respond to environmental stimulation. At least two different types of QS systems regulate pathogenesis in Burkholderia cenocepacia. However, it remains unclear how this bacterial pathogen controls these QS systems. Here, we demonstrate a novel two‐component system RqpSR (Regulating Quorum sensing and Pathogenicity), which plays an important role in modulating QS and pathogenesis in B. cenocepacia. We demonstrate strong protein‐protein binding affinity between RqpS and RqpR. Mutations in rqpS and rqpR exerted overlapping effects on B. cenocepacia transcriptomes and phenotypes, including motility, biofilm formation and virulence. In trans expression of rqpR rescued the defective phenotypes in the rqpS mutant. RqpR controls target gene expression by direct binding to DNA promoters, including the cis‐2‐dodecenoic acid (BDSF) and N‐acylhomoserine lactone (AHL) signal synthase gene promoters. These findings suggest that the RqpSR system strongly modulates physiology by forming a complicated hierarchy with QS systems. This type of two‐component system appears to be widely distributed and coexists with the BDSF QS system in various bacterial species.
Spatiotemporally regulated proteolysis to dissect the role of vegetative proteins during Bacillus subtilis sporulation: cell‐specific requirement of σH and σA
Authors: Riley Eammon P. , Trinquier Aude , Reilly Madeline L. , Durchon Marine , Perera Varahenage R. , Pogliano Kit , Lopez‐Garrido Javier
Published: January 2018

Sporulation in Bacillus subtilis is a paradigm of bacterial development, which involves the interaction between a larger mother cell and a smaller forespore. The mother cell and the forespore activate different genetic programs, leading to the production of sporulation‐specific proteins. A critical gap in our understanding of sporulation is how vegetative proteins, made before sporulation initiation, contribute to spore formation. Here we present a system, spatiotemporally regulated proteolysis (STRP), which enables the rapid, developmentally regulated degradation of target proteins, thereby providing a suitable method to dissect the cell‐ and developmental stage‐specific role of vegetative proteins. STRP has been used to dissect the role of two major vegetative sigma factors, σH and σA, during sporulation. The results suggest that σH is only required in predivisional cells, where it is essential for sporulation initiation, but that it is dispensable during subsequent steps of spore formation. However, evidence has been provided that σA plays different roles in the mother cell, where it replenishes housekeeping functions, and in the forespore, where it plays an unexpected role in promoting spore germination and outgrowth. Altogether, the results demonstrate that STRP has the potential to provide a comprehensive molecular dissection of every stage of sporulation, germination and outgrowth.
The investment case for folic acid fortification in developing countries
Authors: Hoddinott John
Published: January 2018

There is compelling evidence that neural tube defects can be prevented through mandatory folic acid fortification. Why, then, is an investment case needed? At the core of the answer to this question is the notion that governments and individuals have limited resources for which there are many competing claims. An investment case compares the costs and benefits of folic acid fortification relative to alternative life‐saving investments and informs estimates of the financing required for implementation. Our best estimate is that the cost per death averted through mandatory folic acid fortification is $957 and the cost per disability‐adjusted life year is $14.90. Both compare favorably to recommended life‐saving interventions, such as the rotavirus vaccine and insecticide‐treated bed nets. Thus, there is a strong economic argument for mandatory folic acid fortification. Further improvements to these estimates will require better data on the costs of implementing fortification and on the costs of improving compliance where regulations are already in place.
Obliterative portal venopathy: A histopathologic finding associated with chronic antibody‐mediated rejection in pediatric liver allografts
Authors: Guerra Marjorie‐Anne R. , Naini Bita V. , Scapa Jason V. , Reed Elaine F. , Busuttil Ronald W. , Cheng Elaine Y. , Farmer Douglas G. , Vargas Jorge H. , Venick Robert S. , McDiarmid Sue V. , Wozniak Laura J.
Published: January 2018

The significance of post‐transplant HLA DSA and chronic AMR in LT is an emerging field of study. Although OPV has previously been described as a histopathologic finding in DSA‐positive adult LT recipients, it was not included in the recent Banff criteria for chronic AMR. Our aim was to describe the association between OPV and chronic AMR in pediatric LT recipients. A retrospective review of 67 liver biopsies performed between November 2014 and April 2016 in 45 pediatric LT recipients identified four patients with OPV. Clinical status, liver biochemistry, the presence of DSA, and available non‐HLA antibody testing, as well as histopathologic features of chronic AMR, were assessed. All four patients with OPV had class II DSA and histopathologic features of chronic AMR based on the Banff criteria. Two patients were noted to have non‐HLA antibodies. Three patients are undergoing treatment with IVIG but have persistent DSA. Two patients have graft failure and are awaiting retransplantation. In conclusion, OPV is a histopathologic finding associated with chronic AMR in pediatric LT recipients. Further studies are needed to elucidate whether OPV is reversible and/or amenable to medical therapy.
Phylogenetic, expression and functional characterizations of the maize NLP transcription factor family reveal a role in nitrate assimilation and signaling
Authors: Wang Zhangkui , Zhang Lei , Sun Ci , Gu Riliang , Mi Guohua , Yuan Lixing
Published: January 2018

Although nitrate represents an important nitrogen (N) source for maize, a major crop of dryland areas, the molecular mechanisms of nitrate uptake and assimilation remain poorly understood. Here, we identified nine maize NIN‐like protein (ZmNLP) genes and analyzed the function of one member, ZmNLP3.1, in nitrate nutrition and signaling. The NLP family genes were clustered into three clades in a phylogenic tree. Comparative genomic analysis showed that most ZmNLP genes had collinear relationships to the corresponding NLPs in rice, and that the expansion of the ZmNLP family resulted from segmental duplications in the maize genome. Quantitative PCR analysis revealed the expression of ZmNLP2.1, ZmNLP2.2, ZmNLP3.1, ZmNLP3.2, ZmNLP3.3 and ZmNLP3.4 was induced by nitrate in maize roots. The function of ZmNLP3.1 was investigated by overexpressing it in the Arabidopsis nlp7‐1 mutant, which is defective in the AtNLP7 gene for nitrate signaling and assimilation. Ectopic expression of ZmNLP3.1 restored the N‐deficient phenotypes of nlp7‐1 under nitrate‐replete conditions in terms of shoot biomass, root morphology and nitrate assimilation. Furthermore, the nitrate induction of NRT2.1, NIA1, and NiR1 gene expression was recovered in the 35S::ZmNLP3.1/nlp7‐1 transgenic lines, indicating that ZmNLP3.1 plays essential roles in nitrate signaling. Taken together, these results suggest that ZmNLP3.1 plays an essential role in regulating nitrate signaling and assimilation processes, and represents a valuable candidate for developing transgenic maize cultivars with high N‐use efficiency.
Seborrheic keratoses mimicking melanoma unveiled by in vivo reflectance confocal microscopy
Authors: Pezzini C. , Mandel V. D. , Persechino F. , Ciardo S. , Kaleci S. , Chester J. , De Carvalho N. , Persechino S. , Pellacani G. , Farnetani F.
Published: January 2018

Background

Seborrheic keratoses (SebK) with atypical dermoscopy presentation are increasingly reported. These lesions do not exhibit typical dermoscopy features of SebK and sometimes mimic melanoma, thus complicating the differential diagnosis. Reflectance confocal microscopy (RCM) is a non‐invasive tool, which allows an in vivo imaging of the skin. The study objectives were to evaluate the agreement between RCM classification and histological diagnoses, and the reliability of well‐known RCM criteria for SebK in the identification of SebK with atypical dermoscopy presentation.

Materials and Methods

We retrospectively analysed at RCM excised lesions presenting in dermoscopy ≥1 score at revisited 7‐point checklist. The study population consisted of cases showing no melanocytic RCM findings. Lesions were investigated for distinct non‐melanocytic RCM features, blinded from histopathology diagnoses. Histopathology matching was then performed before statistical analysis.

Results

The study consisted of 117 cases, classified at RCM as SebK (71 cases), dermatofibroma (18 cases), basal cell carcinoma (13 cases), squamous cell carcinoma (2 cases), and “non‐specific” (13 cases). Overall K strength of agreement at histopathology matching proved 0.76. Of the 71 cases classified at RCM with SebK, agreement was achieved in 97%.

Conclusion

Reflectance confocal microscopy classification proved high agreement with histopathology for SebK with atypical dermoscopy presentations, allowing an early differential diagnosis. RCM features in this group of lesions were similar to those described for typical cases of SebK, and may assist clinician therapy decision making, whilst avoiding unnecessary excisions.
High‐frequency ultrasound‐based differentiation between nodular dermal filler deposits and foreign body granulomas
Authors: Mlosek R. K. , Skrzypek E. , Skrzypek D. M. , Malinowska S.
Published: January 2018

Background

The number of procedures involving dermal filler injection is still on the rise. Although their safety is improving, not all complications can be avoided. The late complications manifesting as nodules or granulomas pose a particular diagnostic and therapeutic challenge, due to the lack of uniform standards or guidelines. High‐frequency, ultrasound imaging appears to be a useful method for distinguishing between granulomas and nodular dermal filler deposits.

Aim

The aim of the paper was to evaluate the utility of high frequency ultrasound imaging for distinguishing between foreign body granulomas and nodular dermal filler deposits.

Material and methods

Eleven females aged 21‐66 years (mean age of 43.6 years old) who had soft tissue fillers injected were enrolled. All patients had a high‐frequency ultrasound scan of the involved skin area performed. The shape, margins, area, location and echogenicity of the lesions were assessed. Additionally, the lesions were evaluated histologically and photographs were taken.

Results

The analysis indicated differences between the ultrasound image of granulomas and dermal filler deposits. Characteristic ultrasound features of granulomas include oval shape and blurred, irregular outer edges. Small hyperechoic areas were seen inside the granulomas. The deposits were anechogenic, with sharp, regular borders.

Conclusions

High‐frequency ultrasound imaging enables distinguishing between granulomas and nodules—dermal filler deposits, which form after dermal filler injections.
Next‐generation sequencing‐based typing of a new allele HLA‐DQB1*03:01:01:20 in a Chinese family
Authors: Wu R. , Li H. , Wang N. , Peng D. , Sun H.
Published: January 2018

DQB1*03:01:01:20 showed one nucleotide difference when compared to DQB1*03:01:01:01 at 224 (C>T).
HLA‐A*02:01:01:28, a novel HLA allele identified by next‐generation sequencing in a Chinese family
Authors: Wu R. , Peng D. , Li R. , Li H. , Sun H.
Published: January 2018

HLA‐A*02:01:01:28 differs from A*02:01:01:01 by one nucleotide transition, T>A 2952 in intron 6.
A role for Mitochondrial Rho GTPase 1 (MIRO1) in motility and membrane dynamics of peroxisomes
Authors: Castro Inês G. , Richards David M. , Metz Jeremy , Costello Joseph L. , Passmore Josiah B. , Schrader Tina A. , Gouveia Ana , Ribeiro Daniela , Schrader Michael
Published: January 2018

Peroxisomes are dynamic organelles which fulfil essential roles in lipid and ROS metabolism. Peroxisome movement and positioning allows interaction with other organelles and is crucial for their cellular function. In mammalian cells, such movement is microtubule‐dependent and mediated by kinesin and dynein motors. The mechanisms of motor recruitment to peroxisomes are largely unknown, as well as the role this plays in peroxisome membrane dynamics and proliferation. Here, using a combination of microscopy, live‐cell imaging analysis and mathematical modelling, we identify a role for Mitochondrial Rho GTPase 1 (MIRO1) as an adaptor for microtubule‐dependent peroxisome motility in mammalian cells. We show that MIRO1 is targeted to peroxisomes and alters their distribution and motility. Using a peroxisome‐targeted MIRO1 fusion protein, we demonstrate that MIRO1‐mediated pulling forces contribute to peroxisome membrane elongation and proliferation in cellular models of peroxisome disease. Our findings reveal a molecular mechanism for establishing peroxisome‐motor protein associations in mammalian cells and provide new insights into peroxisome membrane dynamics in health and disease.
Canine spinal meningiomas and nerve sheath tumours in 34 dogs (2008‐2016): Distribution and long‐term outcome based upon histopathology and treatment modality
Authors: Lacassagne K. , Hearon K. , Berg J. , Séguin B. , Hoyt L. , Byer B. , Selmic L. E.
Published: January 2018

The purpose of this retrospective, multicentre case series was to describe the outcome following surgery and/or radiation of spinal meningiomas and nerve sheath tumours (NSTs) based upon treatment modality, with a specific aim to evaluate the survival times and time to recurrence following treatment for each histopathological diagnosis. Our hypothesis was that the addition of radiation therapy modalities to treatment will yield longer time to recurrence of clinical signs and survival time. Thirty‐four dogs met the inclusion criteria of histopathologically diagnosed extramedullary spinal meningioma or NST. Sixteen extramedullary spinal meningiomas and 18 NSTs were diagnosed. A diagnosis of meningioma was associated with a significantly longer survival time compared with NSTs, with median survival times (MST) of 508 days (95% confidence interval [CI]: 66‐881) vs 187 days (95% CI: 76‐433; P = .02). Dogs (seven) treated with stereotactic radiation therapy (SRT) for recurrence after surgery alone or SRT alone as their initial treatment gained an additional 125 to 346 days survival time.
Ultrasonographic and computed tomographic features of rice bodies in an Arabian horse with atlantal bursitis
Authors: Hohu Kyle K. , Lim Chee Kin , Adams Stephen B. , Heng Hock Gan , Ramos‐Vara José A.
Published: January 2018

A 19‐year‐old castrated Arabian male horse presented for evaluation of a firm mass at the dorsal cervical region. Ultrasonography and computed tomography revealed multiple well defined fusiform structures within the atlantal bursa. Multiple glossy smooth, white to yellowish, flattened fusiform structures were removed surgically. These structures were composed of dense fibrin with some leukocytes and red blood cells. The imaging and histopathological features of these structures were similar to chronic ‘rice bodies’ reported in humans with bursitis or tenosynovitis. This is the first veterinary report describing the imaging features of ‘rice bodies’ in a horse with atlantal bursitis.
Plant species composition and potential feed value of permanent grasslands in the Sýkořská hornatina Upland
Authors: Nerušil Pavel , Komárek Petr , Křivánková Zuzana , Menšík Ladislav
Published: January 2018

In multifunctional agriculture, permanent grasslands (PG) present an important culture which keeps the soil in the continuous production status while helping to shape the landscape and protecting biodiversity, plus it has a number of other non-productive functions. The aim of the study was to evaluate, using the “Inventory and Classification of PG” method, species composition and the feed value of fodder in permanent grasslands in a specific farming company (ZEAS Lysice, a. s.) located in the area of the Sýkořská hornatina Upland. Multivariate analysis of PCA identified three categories of sites in the area: (1) PG with a low proportion of grass species and a high proportion of other herbs (47–55 %); (2) PG with a high proportion of grass species (68–81 %); (3) PG with a medium-high proportion of grass species (50–60 %), legumes (1 %) and other herbs. Most of PG are completely lacking legumes which supply nitrogen to the vegetation and are a major improvement for fodder production and its quality. Additional seeding of grass-clover mixtures seems to be a useful way to improve the botanical composition of meadows and pastures in the area of interest.
Preface
Authors: Atangana Abdon , Bulut Hasan , Hammouch Zakia , Baskonus Haci Mehmet
Published: January 2018

In the last decade, it has been proven in several research papers that, mathematical tools are rather power in describing real world problem in all fields of science, technology and engineering. Various mathematical models that examine real world problems have been studied and developed with the aim of predicting the future. Due to the wider applicability of these tools, research observes that the field of applied sciences is a rapidly growing discipline and has engaged the minds of researchers. The recently developed mathematical models bear certain kinds of complexities. Therefore new methods have been elaborated for observing the properties of intricated models accurately. Moreover, comprehensive information about the models have been found by modifiying the existing methods in literature. By means of the outstanding increase in information, such findings uncover new aspects and properties of real world problems. In addition, structural changes of models and technical improvements in practices brought out novel challenging issues. Such challenges have resulted in new and modified methods. Therefore, the studies in such fields are essential and meaningful in understanding the diverse aspects of the models.This special issue aims at addressing these interesting research matters in the field of applied and engineering sicences. The main source of the articles in this special issue were the selected papers from those presented at the Second International Conference on Computational Mathematics and Engineering Sciences (CMES2017), which was held on May 20-22, 2017, in Istanbul, Turkey. During CMES2017, several various papers related to applied and engineering sicence have been presented. In this special issue, we have received 12 manuscripts based on rigorous reviews. This special issue has greatly benefited from the cooperation among the authors, reviewers, and editors.We would like to express our sincere gratitude to Moulay Ismail University and Firat University for organizing CMES2017 Conference and all the authors for their contributions, which has made this special issue possible.
Residual Force Enhancement in Humans: A Systematic Review
Authors: Chapman Neil , Whitting John , Broadbent Suzanne , Crowley-McHattan Zachary , Meir Rudi
Published: January 2018

A systematic literature search was conducted to review the evidence of residual force enhancement (RFE) in vivo human muscle. The search, adhered to the PRISMA statement, of CINAHL, EBSCO, Embase, MEDLINE, and Scopus (inception—July 2017) was conducted. Full-text English articles that assessed at least 1 measure of RFE in vivo voluntarily contracted human skeletal muscle were selected. The methodologies of included articles were assessed against the Downs and Black checklist. Twenty-four studies were included (N = 424). Pooled Downs and Black scores ranked “fair” ([2.26]). RFE was observed in all muscles tested. Joint range of motion varied from 15° to 60°. Contraction intensities ranged from 10% to >95% maximum. Although transient force enhancement during the stretch phase may change with angular velocity, RFE in the subsequent isometric phase is independent of velocity. The magnitude of RFE was influenced by smaller stretch amplitudes and greatest at joint angles indicative of longer muscle lengths. Contraction and activation intensity influenced RFE, particularly during the initial isometric contraction phase of a poststretch isometric contraction. RFE resulted in increased torque production, reduced muscular activation, and enhanced torque production when the neuromuscular system is weakened seen in an aged population.
The Self-Regulatory and Task-Specific Strategies of Elite-Level Amateur Golfers in Tournament Preparation
Authors: Pilgrim Jarred , Kremer Peter , Robertson Sam
Published: January 2018

Little is known regarding the factors that are important for tournament preparation in golf. Eighteen elite amateur golfers and 12 expert coaches/practitioners were interviewed to identify the self-regulatory and task-specific strategies important for tournament preparation. Thematic analysis revealed four themes: understanding tournament preparation, planning, tournament preparation strategies, and self-reflection. Players used specific strategies to optimize their physiological and psychological state, develop course strategy, and structure and implement preparatory routines. The findings of this study have implications for coaches and players in developing a system for preparation, and could provide a framework to improve coaching curricula and guide further research.
Guanabenz inhibits TLR9 signaling through a pathway that is independent of eIF2α dephosphorylation by the GADD34/PP1c complex
Authors: Perego Jessica , Mendes Andreia , Bourbon Clarisse , Camosseto Voahirana , Combes Alexis , Liu Hong , Manh Thien-Phong Vu , Dalet Alexandre , Chasson Lionel , Spinelli Lionel , Bardin Nathalie , Chiche Laurent , Santos Manuel A. S. , Gatti Evelina , Pierre Philippe
Published: January 2018

Guanabenz attenuates autoimmune inflammation by preventing TLR9 from reaching endosomes and becoming fully activated.
Integrin α
4
β
7
expression on peripheral blood CD4
+
T cells predicts HIV acquisition and disease progression outcomes
Authors: Sivro Aida , Schuetz Alexandra , Sheward Daniel , Joag Vineet , Yegorov Sergey , Liebenberg Lenine J. , Yende-Zuma Nonhlanhla , Stalker Andrew , Mwatelah Ruth S. , Selhorst Philippe , Garrett Nigel , Samsunder Natasha , Balgobin Anisha , Nawaz Fatima , Cicala Claudia , Arthos James , Fauci Anthony S. , Anzala Aggrey Omu , Kimani Joshua , Bagaya Bernard S. , Kiwanuka Noah , Williamson Carolyn , Kaul Rupert , Passmore Jo-Ann S. , Phanuphak Nittaya , Ananworanich Jintanat , Ansari Aftab , Abdool Karim Quarraisha , Abdool Karim Salim S. , McKinnon Lyle R. ,   on behalf of the CAPRISA004 and RV254 study groups
Published: January 2018

CD4
+
T cells expressing α
4
β
7
play an important role in HIV pathogenesis.
Miniaturized neural system for chronic, local intracerebral drug delivery
Authors: Dagdeviren Canan , Ramadi Khalil B. , Joe Pauline , Spencer Kevin , Schwerdt Helen N. , Shimazu Hideki , Delcasso Sebastien , Amemori Ken-ichi , Nunez-Lopez Carlos , Graybiel Ann M. , Cima Michael J. , Langer Robert
Published: January 2018

An implantable, remotely controllable, miniaturized drug delivery system permits dynamic adjustment of therapy with a pinpoint spatial accuracy in the brain.
Genome Sequence of
Pseudomonas plecoglossicida
Strain NZBD9
Authors: Huang Lixing , Zhao Lingmin , Su Yongquan , Yan Qingpi
Published: January 2018

Pseudomonas plecoglossicida
NZBD9 is the causative agent of white nodules in cultured large yellow croaker in Fujian Province, China. We sequenced the genome of NZBD9 to gain a better understanding of the etiological agent. The genome sequence of the bacterium consists of 5.44 million bp, with a G+C content of 61.9%.
Complete Genome Sequence of a
Lily virus X
Isolate from Japan
Authors: Nijo Takamichi , Okano Yukari , Kondo Masayoshi , Okuhara Hiroaki , Sekimura Hiroyo , Fujimoto Yuji , Hosoe Naoi , Maejima Kensaku , Yamaji Yasuyuki , Namba Shigetou
Published: January 2018

The complete genome sequence of
Lily virus X
(LVX), which infects lilies, was determined for the first time from lilies in Japan. As with previous reports, the genome of the Japanese LVX isolate lacked an AUG start codon for the triple gene block protein 3-like region.
First Insights into the Draft Genome Sequence of the Endophyte
Paenibacillus amylolyticus
Strain GM1FR, Isolated from
Festuca rubra
L
Authors: Poehlein Anja , Hollensteiner Jacqueline , Granzow Sandra , Wemheuer Bernd , Vidal Stefan , Wemheuer Franziska
Published: January 2018

Paenibacillus amylolyticus
strain GM1FR is an endophyte isolated from aerial plant tissues of
Festuca rubra
L. Here, we report the draft genome sequence (7.3 Mb) of GM1FR containing 6,241 protein-coding genes, some of which are potentially involved in plant growth promotion and biocontrol.
Whole-Genome Sequences of Zika Virus FLR Strains after Passage in Vero or C6/36 Cells
Authors: Moser Lindsey A. , Oldfield Lauren M. , Fedorova Nadia , Puri Vinita , Shrivastava Susmita , Amedeo Paolo , Isom Richard , Hu Lihui , Durbin Alan , Rocchi Iara , Williams Torrey , Tan Gene S. , Shabman Reed S. , Bernard Kristen A. , Pickett Brett E.
Published: January 2018

We report 26 complete genomes of Zika virus (ZIKV) isolated after passaging the Zika virus strain FLR in mosquito (C6/36) and mammalian (Vero) cell lines. The consensus ZIKV genomes we recovered show greater than 99% nucleotide identify with each other and with the FLR strain used as input.
Complete Genome Sequence of
Bacillus velezensis
CN026 Exhibiting Antagonistic Activity against Gram-Negative Foodborne Pathogens
Authors: Nannan Catherine , Gillis Annika , Caulier Simon , Mahillon Jacques
Published: January 2018

We report here the complete genome sequence of
Bacillus velezensis
strain CN026, a member of the
B. subtilis
group, which is known for its many industrial applications. The genome contains 3,995,812 bp and displays six gene clusters potentially involved in strain CN026’s activity against Gram-negative foodborne pathogens.
Draft Genome Sequences of Four
Salmonella enterica
subsp.
enterica
Serovar Enteritidis Strains Implicated in Infections of Avian and Human Hosts
Authors: An Ran , Lin Pengpeng , Bougouffa Salim , Essack Magbubah , Boxrud David , Bajic Vladimir B. , Vidovic Sinisa
Published: January 2018

Salmonella enterica
subsp.
enterica
serovar Enteritidis is a wide-host-range pathogen. Occasionally, it is involved in invasive infections, leading to a high mortality rate. Here, we present the draft genome sequences of four
S
. Enteritidis strains obtained from human and avian hosts that had been involved in bacteremia, gastroenteritis, and primary infections.
Complete Genome Sequence of an
Escherichia coli
O121:H19 Strain from an Outbreak in Canada Associated with Flour
Authors: Robertson James , Lin Janet , Levett Paul N. , Nadon Celine , Nash John , Berry Chrystal
Published: January 2018

Here, we present the first complete genome sequence of an
Escherichia coli
non-O157 Shiga-toxin producing isolate, 16-9255, from serotype O121:H19. This strain is notable as a clinical case recovered from a recent Canadian flour-associated outbreak event.
Complete Genome Sequence of
Mycobacterium
sp. Strain 3519A
Authors: Bouam Amar , Levasseur Anthony , Bonnet Maryline , Borand Laurence , Van Goethem Charles , Drancourt Michel , Godreuil Sylvain
Published: January 2018

Mycobacterium
sp. strain 3519A is a nontuberculous mycobacterium isolated from sputum from a Cambodian patient with a pulmonary infection. We report here the first complete 7.3-Mbp-long genome sequence of
Mycobacterium
sp. 3519A with 66.35% GC content, encoding 7,029 protein-coding genes, 50 tRNAs, and 5 rRNA genes.
Draft Genome Sequences of Two Psychrotolerant Strains,
Colwellia polaris
MCCC 1C00015
T
and
Colwellia chukchiensis
CGMCC 1.9127
T
Authors: Zhang Cong , Guo Wenbin , Wang Yuguang , Chen Xinhua
Published: January 2018

Colwellia polaris
MCCC 1C00015
T
and
Colwellia chukchiensis
CGMCC 1.9127
T
are psychrotolerant bacteria isolated from the Canadian Basin and Chukchi Sea, respectively. Here, we report the draft genome sequences of
C. polaris
MCCC 1C00015
T
and
C. chukchiensis
CGMCC 1.9127
T
, which will help reveal how they adapt to cold environments.
Mimicry of Cellular A Kinase-Anchoring Proteins Is a Conserved and Critical Function of E1A across Various Human Adenovirus Species
Authors: King Cason R. , Gameiro Steven F. , Tessier Tanner M. , Zhang Ali , Mymryk Joe S.
Published: January 2018

The E1A proteins of the various human adenovirus (HAdV) species perform the critical task of converting an infected cell into a setting primed for virus replication. While E1A proteins differ in both sequence and mechanism, the evolutionary pressure on viruses with limited coding capacity ensures that these proteins often have significant overlap in critical functions. HAdV-5 E1A is known to use mimicry to rewire cyclic AMP (cAMP) signaling by decoupling protein kinase A (PKA) from cellular A kinase-anchoring proteins (AKAPs) and utilizing PKA to its own advantage. We show here that E1As from other species of HAdV also possess this viral AKAP (vAKAP) function and examine how they manipulate PKA. E1A from most species of HAdV examined contain a small AKAP-like motif in their N terminus which targets the docking-dimerization domain of PKA as the binding interface for a conserved protein-protein interaction. This motif is also responsible for an E1A-mediated relocalization of PKA regulatory subunits from the cytoplasm into the nucleus, with species-specific E1A proteins having preference for one particular isoform of PKA subunit over another. Importantly, we showed that these newly characterized vAKAPs can integrate into cAMP-responsive transcription as well as contribute to viral genome replication and infectious progeny production for several distinct HAdV species.

IMPORTANCE
These data enhance the mechanistic knowledge on how HAdV E1A manipulates cellular PKA to benefit infection. The work establishes that mimicry of AKAPs and subversion of PKA-mediated cAMP signaling are conserved features for numerous human adenoviruses. This study also highlights the molecular determinants conferring selective protein-protein interactions between distinct PKA regulatory subunits and the different E1A proteins of these viruses. Additionally, it further emphasizes the utility of using viral proteins like E1A as tools for studying the molecular biology of cellular regulatory pathways.
Pre–mass extinction decline of latest Permian ammonoids
Authors: Kiessling Wolfgang , Schobben Martin , Ghaderi Abbas , Hairapetian Vachik , Leda Lucyna , Korn Dieter
Published: January 2018

The devastating end-Permian mass extinction is widely considered to have been caused by large-scale and rapid greenhouse gas release by Siberian magmatism. Although the proximate extinction mechanisms are disputed, there is widespread agreement that a major extinction pulse occurred immediately below the biostratigraphically defined Permian–Triassic boundary. Our statistical analyses of stratigraphic confidence intervals do not comply with a single end-Permian extinction pulse of ammonoids in Iran. High turnover rates and extinction pulses are observed over the last 700 k.y. of the Permian period in two widely separated sections representative of a larger area. Analyses of body sizes and morphological complexity support a gradual decline over the same interval. Similar pre–mass extinction declines and disturbances of the carbon cycle have sometimes been reported from other regions, suggesting a widespread, but often overlooked, environmental deterioration at a global scale, well before the traditional main extinction pulse.
External validity, generalisability, applicability and directness: a brief primer
Authors: Murad Mohammad H , Katabi Abdulrahman , Benkhadra Raed , Montori Victor M
Published: January 2018

External validity is a construct that attempts to answer the question of whether we can use the results of a study in patients other than those enrolled in the study. External validity consists of two unique underlying concepts, generalisability and applicability. When the concern is about extending the results from a sample to the population from which the sample was drawn, the problem is one of generalisability. When the concern is about using inferences drawn from study participants in the care of specific patients belonging to any population, the problem is one of applicability. Clinicians, guideline developers and policymakers do not struggle with generalisability, but often struggle with applicability. When applicability is deemed to be low for a certain population, certainty in the supporting evidence becomes low due to indirectness.
Catalogue of bias: attrition bias
Authors: Nunan David , Aronson Jeffrey , Bankhead Clare
Published: January 2018

This article is part of a series of articles featuring the Catalogue of Bias introduced in this volume ofBMJ Evidence-Based Medicinethat describes attrition bias and outlines its potential impact on research studies and the preventive steps to minimise its risk. Attrition bias is a type of selection bias due to systematic differences between study groups in the number and the way participants are lost from a study. Differences between people who leave a study and those who continue, particularly between study groups, can be the reason for any observed effect and not the intervention itself. Associations for mortality in trials of tranexamic acid and upper gastrointestinal bleeding were no longer apparent after studies with high or unclear risk of attrition bias were removed. Over-recruitment can help prevent important attrition bias. Sampling weights and tailored replenishment samples can help to compensate for the effects of attrition bias when present.
Comparative genome analysis to identify SNPs associated with high oleic acid and elevated protein content in soybean
Authors: Kulkarni Krishnanand P. , Patil Gunvant , Valliyodan Babu , Vuong Tri D. , Shannon J. Grover , Nguyen Henry T. , Lee Jeong-Dong
Published: January 2018

The objective of this study was to determine the genetic relationship between the oleic acid and protein content. The genotypes having high oleic acid and elevated protein (HOEP) content were crossed with five elite lines having normal oleic acid and average protein (NOAP) content. The selected accessions were grown at six environments in three different locations and phenotyped for protein, oil, and fatty acid components. The mean protein content of parents, HOEP, and NOAP lines was 34.6%, 38%, and 34.9%, respectively. The oleic acid concentration of parents, HOEP, and NOAP lines was 21.7%, 80.5%, and 20.8%, respectively. The HOEP plants carried both FAD2-1A (S117N) and FAD2-1B (P137R) mutant alleles contributing to the high oleic acid phenotype. Comparative genome analysis using whole-genome resequencing data identified six genes having single nucleotide polymorphism (SNP) significantly associated with the traits analyzed. A single SNP in the putative gene Glyma.10G275800 was associated with the elevated protein content, and palmitic, oleic, and linoleic acids. The genes from the marker intervals of previously identified QTL did not carry SNPs associated with protein content and fatty acid composition in the lines used in this study, indicating that all the genes except Glyma.10G278000 may be the new genes associated with the respective traits.
Tilted Kantowski–Sachs cosmological model in Brans–Dicke theory of gravitation
Authors: Pawar D. D. , Shahare S. P. , Dagwal V. J.
Published: January 2018

Tilted Kantowski–Sachs cosmological model in Brans–Dicke theory for perfect fluid has been investigated. The general solution of field equations in Brans–Dicke theory for the combined scalar and tensor field are obtained by using power law relation. Also, some physical and geometrical parameters are obtained and discussed.
Automatic Quantification of Endothelial Nitric Oxide Levels in a Microvessel with and without Tumor Cell Adhesion
Authors: Wei Jie , Zhang Lin , Fu Bingmei M.
Published: January 2018

Elevated nitric oxide (NO) and endothelial nitric oxide synthase (eNOS) have been observed in cancer patients in malignancy state. We hypothesize that the higher NO production in the microvessels of these patients attracts more tumor cells (TCs) to adhere and accomplish their metastases. Since there are tens to hundreds of endothelial cells (ECs) forming on the microvessel walls, it is unsustainable to let human operators measure NO intensity levels by correlating TC maps with a multitude of microphotographs via manual labor and eyeballing. To achieve effective and scalable quantifications, we developed an automatic algorithm to quantify NO intensity for microphotographs taken from the experiments. Taking account of the special visual and geometric properties of microvessels in the study, the first step performs a novel Markov integrated dynamic programming procedure to single out the microvessel from the microphotograph. The next step applies image processing and morphological operations to identify ECs and TCs on the microvessel detected from the prior step. Finally, a normalized cross-correlation procedure is applied to register the TC map to the microvessel and evaluate the NO ratios in the ECs with and without TC adhesions. With a processing time reduced from hours to seconds, this algorithm evaluates NO ratios exceedingly similar to those by human operators.
The signature of undetected change: an exploratory electrotomographic investigation of gradual change blindness
Authors: Kiat John E. , Dodd Michael D. , Belli Robert F. , Cheadle Jacob E.
Published: January 2018

Neuroimaging-based investigations of change blindness, a phenomenon in which seemingly obvious changes in visual scenes fail to be detected, have significantly advanced our understanding of visual awareness. The vast majority of prior investigations, however, utilize paradigms involving visual disruptions (e.g., intervening blank screens, saccadic movements, “mudsplashes”), making it difficult to isolate neural responses toward visual changes cleanly. To address this issue in this present study, high-density EEG data (256 channel) were collected from 25 participants using a paradigm in which visual changes were progressively introduced into detailed real-world scenes without the use of visual disruption. Oscillatory activity associated with undetected changes was contrasted with activity linked to their absence using standardized low-resolution brain electromagnetic tomography (sLORETA). Although an insufficient number of detections were present to allow for analysis of actual change detection, increased beta-2 activity in the right inferior parietal lobule (rIPL), a region repeatedly associated with change blindness in disruption paradigms, followed by increased theta activity in the right superior temporal gyrus (rSTG) was noted in undetected visual change responses relative to the absence of change. We propose the rIPL beta-2 activity to be associated with orienting attention toward visual changes, with the subsequent rise in rSTG theta activity being potentially linked with updating preconscious perceptual memory representations.

NEW & NOTEWORTHY This study represents the first neuroimaging-based investigation of gradual change blindness, a visual phenomenon that has significant potential to shed light on the processes underlying visual detection and conscious perception. The use of gradual change materials is reflective of real-world visual phenomena and allows for cleaner isolation of signals associated with the neural registration of change relative to the use of abrupt change transients.
A Description of Pseudorapidity Distributions of Charged Particles Produced in Au+Au Collisions at RHIC Energies
Authors: Jiang Z. J. , Xu Dongfang , Huang Yan
Published: January 2018

In heavy ion collisions, charged particles come from two parts: the hot and dense matter and the leading particles. In this paper, the hot and dense matter is assumed to expand according to the hydrodynamic model including phase transition and decouples into particles via the prescription of Cooper-Frye. The leading particles are as usual supposed to have Gaussian rapidity distributions with the number equaling that of participants. The investigations of this paper show that, unlike low energy situations, the leading particles are essential in describing the pseudorapidity distributions of charged particles produced in high energy heavy ion collisions. This might be due to the different transparencies of nuclei at different energies.
Derivation and Identification of Motor Neurons from Human Urine-Derived Induced Pluripotent Stem Cells
Authors: Yi Huan , Xie Bingbing , Liu Ben , Wang Xuan , Xu Li , Liu Jia , Li Min , Zhong Xiufeng , Peng Fuhua
Published: January 2018

Induced pluripotent stem cells (iPSCs) have provided new opportunities for motor neuron disease (MND) modeling, drug screening, and cellular therapeutic development. Among the various types of iPSCs, urine-derived iPSCs have become a promising source of stem cells because they can be safely and noninvasively isolated and easily reprogrammed. Here, for the first time, we differentiated urine-derived iPSCs (urine-iPSCs) into motor neurons (MNs) and compared the capacity of urine-iPSCs and cord-blood-derived iPSCs (B-iPSCs) to differentiate into MNs. With the use of small molecules, mature MNs were generated from urine-iPSCs as early as 26 days in culture. Furthermore, in coculture with muscle cells, MNs projected long axons and formed neuromuscular junctions (NMJs). Immunofluorescence and PCR confirmed the expression levels of both MN and NMJ markers. The comparison of the ratios of positive labeling for MN markers between urine-iPSCs and B-iPSCs demonstrated that the differentiation potentials of these cells were not significantly different. The abovementioned results indicate that urine-iPSCs are a new, promising source of stem cells for MND modeling and further cellular therapeutic development.
Hybrid Synchronization of Uncertain Generalized Lorenz System by Adaptive Control
Authors: Zhou Xinlian , Xu Yuhua
Published: January 2018

This paper investigates hybrid synchronization of the uncertain generalized Lorenz system. Several useful criteria are given for synchronization of two generalized Lorenz systems, and the adaptive control law and the parameter update law are used. In comparison with those of existing synchronization methods, hybrid synchronization includes full-order synchronization, reduced-order synchronization, and modified projective synchronization. What is more, control of the stability point, complete synchronization, and antisynchronization can coexist in the same system. Numerical simulations show the effectiveness of this method in a class of chaotic systems.