bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of Molds by Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry
Authors: Sanguinetti Maurizio , Posteraro Brunella 
Published: November 2016

ABSTRACT

Although to a lesser extent than diagnostic bacteriology, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has recently revolutionized the diagnostic mycology workflow. With regard to filamentous fungi (or molds), the precise recognition of pathogenic species is important for rapid diagnosis and appropriate treatment, especially for invasive diseases. This review summarizes the current experience with MALDI-TOF MS-based identification of common and uncommon mold species of
Aspergillus
,
Fusarium
, Mucorales, dimorphic fungi, and dermatophytes. This experience clearly shows that MALDI-TOF MS holds promise as a fast and accurate identification tool, particularly with common species or typical strains of filamentous fungi.
Evolution and Cryo-electron Microscopy Capsid Structure of a North American Bat Adenovirus and Its Relationship to Other Mastadenoviruses
Authors: Hackenbrack Nicole , Rogers Matthew B. , Ashley Robert E. , Keel M. Kevin , Kubiski Steven V. , Bryan John A. , Ghedin Elodie , Holmes Edward C. , Hafenstein Susan L. , Allison Andrew B. 
Published: November 2016

ABSTRACT

Since the first description of adenoviruses in bats in 2006, a number of micro- and megabat species in Europe, Africa, and Asia have been shown to carry a wide diversity of adenoviruses. Here, we report on the evolutionary, biological, and structural characterization of a novel bat adenovirus (BtAdV) recovered from a Rafinesque's big-eared bat (
Corynorhinus
rafinesquii
) in Kentucky, USA, which is the first adenovirus isolated from North American bats. This virus (BtAdV 250-A) exhibits a close phylogenetic relationship with
Canine mastadenovirus A
(CAdV A), as previously observed with other BtAdVs. To further investigate the relationships between BtAdVs and CAdVs, we conducted mass spectrometric analysis and single-particle cryo-electron microscopy reconstructions of the BtAdV 250-A capsid and also analyzed the
in vitro
host ranges of both viruses. Our results demonstrate that BtAdV 250-A represents a new mastadenovirus species that, in contrast to CAdV, has a unique capsid morphology that contains more prominent extensions of protein IX and can replicate efficiently in a phylogenetically diverse range of species. These findings, in addition to the recognition that both the genetic diversity of BtAdVs and the number of different bat species from disparate geographic regions infected with BtAdVs appears to be extensive, tentatively suggest that bats may have served as a potential reservoir for the cross-species transfer of adenoviruses to other hosts, as theorized for CAdV.

IMPORTANCE
Although many adenoviruses are host specific and likely codiverged with their hosts over millions of years, other adenoviruses appear to have emerged through successful cross-species transmission events on more recent time scales. The wide geographic distribution and genetic diversity of adenoviruses in bats and their close phylogenetic relationship to
Canine mastadenovirus
A
(CAdV A) has raised important questions about how CAdV A, and possibly other mammalian adenoviruses, may have emerged. Although most adenoviruses tend to cause limited disease in their natural hosts, CAdV A is unusual in that it may cause high morbidity and sometimes fatal infections in immunocompetent hosts and is thus an important pathogen of carnivores. Here, we performed a comparative evolutionary and structural study of representative bat and canine adenoviruses to better understand the relationship between these two viral groups.
Phosphorylation of the Bovine Papillomavirus E2 Protein on Tyrosine Regulates Its Transcription and Replication Functions
Authors: Culleton Sara P. , Kanginakudru Sriramana , DeSmet Marsha , Gilson Timra , Xie Fang , Wu Shwu-Yuan , Chiang Cheng-Ming , Qi Guihong , Wang Mu , Androphy Elliot J. 
Published: November 2016

ABSTRACT
Papillomaviruses are small, double-stranded DNA viruses that encode the E2 protein, which controls transcription, replication, and genome maintenance in infected cells. Posttranslational modifications (PTMs) affecting E2 function and stability have been demonstrated for multiple types of papillomaviruses. Here we describe the first phosphorylation event involving a conserved tyrosine (Y) in the bovine papillomavirus 1 (BPV-1) E2 protein at amino acid 102. While its phosphodeficient phenylalanine (F) mutant activated both transcription and replication in luciferase reporter assays, a mutant that may act as a phosphomimetic, with a Y102-to-glutamate (E) mutation, lost both activities. The E2 Y102F protein interacted with cellular E2-binding factors and the viral helicase E1; however, in contrast, the Y102E mutant associated with only a subset and was unable to bind to E1. While the Y102F mutant fully supported transient viral DNA replication, BPV genomes encoding this mutation as well as Y102E were not maintained as stable episomes in murine C127 cells. These data imply that phosphorylation at Y102 disrupts the helical fold of the N-terminal region of E2 and its interaction with key cellular and viral proteins. We hypothesize that the resulting inhibition of viral transcription and replication in basal epithelial cells prevents the development of a lytic infection.

IMPORTANCE
Papillomaviruses (PVs) are small, double-stranded DNA viruses that are responsible for cervical, oropharyngeal, and various genitourinary cancers. Although vaccines against the major oncogenic human PVs are available, there is no effective treatment for existing infections. One approach to better understand the viral replicative cycle, and potential therapies to target it, is to examine the posttranslational modification of viral proteins and its effect on function. Here we have discovered that the bovine papillomavirus 1 (BPV-1) transcription and replication regulator E2 is phosphorylated at residue Y102. While a phosphodeficient mutant at this site was fully functional, a phosphomimetic mutant displayed impaired transcription and replication activity as well as a lack of an association with certain E2-binding proteins. This study highlights the influence of posttranslational modifications on viral protein function and provides additional insight into the complex interplay between papillomaviruses and their hosts.
Molecular Architecture of the Cleavage-Dependent Mannose Patch on a Soluble HIV-1 Envelope Glycoprotein Trimer
Authors: Behrens Anna-Janina , Harvey David J. , Milne Emilia , Cupo Albert , Kumar Abhinav , Zitzmann Nicole , Struwe Weston B. , Moore John P. , Crispin Max 
Published: November 2016

ABSTRACT
The formation of a correctly folded and natively glycosylated HIV-1 viral spike is dependent on protease cleavage of the gp160 precursor protein in the Golgi apparatus. Cleavage induces a compact structure which not only renders the spike capable of fusion but also limits further maturation of its extensive glycosylation. The redirection of the glycosylation pathway to preserve underprocessed oligomannose-type glycans is an important feature in immunogen design, as glycans contribute to or influence the epitopes of numerous broadly neutralizing antibodies. Here we present a quantitative site-specific analysis of a recombinant, trimeric mimic of the native HIV-1 viral spike (BG505 SOSIP.664) compared to the corresponding uncleaved pseudotrimer and the matched gp120 monomer. We present a detailed molecular map of a trimer-associated glycan remodeling that forms a localized subdomain of the native mannose patch. The formation of native trimers is a critical design feature in shaping the glycan epitopes presented on recombinant vaccine candidates.

IMPORTANCE
The envelope spike of human immunodeficiency virus type 1 (HIV-1) is a target for antibody-based neutralization. For some patients infected with HIV-1, highly potent antibodies have been isolated that can neutralize a wide range of circulating viruses. It is a goal of HIV-1 vaccine research to elicit these antibodies by immunization with recombinant mimics of the viral spike. These antibodies have evolved to recognize the dense array of glycans that coat the surface of the viral molecule. We show how the structure of these glycans is shaped by steric constraints imposed upon them by the native folding of the viral spike. This information is important in guiding the development of vaccine candidates.
The dynamics of a very large intra-plate continental basaltic volcanic province, the Newer Volcanics Province, SE Australia, and implications for other provinces
Authors: Cas R. A. F. , van Otterloo J. , Blaikie T. N. , van den Hove J. 
Published: November 2016

Abstract

The Newer Volcanics Province of SE Australia is a very large continental basaltic province, with an area of >23 000 km
2
, a dense rock equivalent volume of <900 km
3
and >400 monogenetic volcanoes; it has been active since
c.
8 Ma. Lava fields, shields, scoria cones are common, and there are >40 maars and volcanic complexes. Maars occur dominantly in the south where magmas erupted through Tertiary sedimentary aquifers, whereas in the north, over Palaeozoic crust, there are few. Complex interactions of the magma volatile content, magma ascent rates, conduit characteristics and the availability and depth of aquifers caused diverse eruption styles. Volcanoes commonly occur close to major crustal faults, which acted as magma conduits. There is no simple age pattern of volcanism across the province. Volcanism was probably triggered by transtensional decompression in the crust where fault sets intersect, affecting hot, hydrated mantle that had welled up through edge-driven convection where the base of the lithosphere thins abruptly at the edge of the continent. Rock compositions range from picritic to basaltic andesitic. Some volcanoes are polymagmatic. Regional geophysical datasets have clarified the regional characteristics of the province, whereas detailed ground magnetic and gravity surveys resulted in new insights into the subsurface structure of maar-diatremes.
The Precambrian–Phanerozoic and Ediacaran–Cambrian boundaries: a historical approach to a dilemma
Authors: Geyer Gerd , Landing Ed 
Published: November 2016

Abstract

The Cambrian was originally defined as a rock interval with a trilobite-dominated fauna that overlay a presumed biologically barren Precambrian epoch. Work to formally define the Cambrian base arose after the discovery of Precambrian macrofossils in South Australia. The Working Group on the Precambrian–Cambrian Boundary (set up in 1972) promoted an emphasis on an extended pre-trilobitic interval with mineralized skeletal elements (small shelly fossils or early skeletal fossils). The study of early skeletal fossils made the Ulakhan-Sulugur (Siberia) and Meishucun (South China) sections candidates for the basal Cambrian Global Stratotype Section and Point (GSSP), but difficulties in correlation and the taxonomy of early skeletal fossils did not allow the selection of a reliably correlative horizon. Bilaterian ichnofaunas below the first diverse early skeletal fossils suggested the definition of a Cambrian base GSSP below the early skeletal fossils. Work on the thick, stratigraphically continuous and fairly unifacial sections in the Burin Peninsula, southeastern Newfoundland led in 1992 to an ichnofossil-defined GSSP at Fortune Head. Despite arguments for a revision and redefinition of the lower boundary of the Cambrian System, the best definition of the basal Cambrian GSSP is at Fortune Head and does not rely on the
Treptichnus/Trichophycus pedum
(abbreviated below as
T. pedum
) first appearance datum, but rather on the base of the
T. pedum
Assemblage Zone at the highest occurrence of Ediacaran taxa and in the lower range of
T. pedum
.
X-ray microtomography as a tool for investigating the petrological context of Precambrian cellular remains
Authors: Hickman-Lewis Keyron , Garwood Russell J. , Withers Philip J. , Wacey David 
Published: November 2016

Abstract
A wide spectrum of tomographic techniques now exists for studying palaeontological specimens, but the suitability of these methods for assessing Earth's oldest prokaryotic life has not been comprehensively investigated. We evaluated the ability of X-ray computed tomography – specifically X-ray microtomography – to reveal the morphology and petrological context of Precambrian microfossils, pseudofossils and biosedimentary structures, all of which are important in the origin and early evolution of life of Earth. The materials tested came from the Pilbara Craton of Western Australia (the 3.49 Ga Dresser Formation, the 3.46 Ga Apex chert and the 3.43 Ga Strelley Pool Formation) and the 1.88 Ga Gunflint Formation of Ontario, Canada. These units chart key developments in palaeobiology. The oldest formations contain profoundly controversial microfossil-like objects and microbially-induced sedimentary structures, whereas definitive prokaryotes are found in the youngest formations. We demonstrate that the imaging of individual microfossils and pseudofossils currently lies at the limits of the capabilities of laboratory-based X-ray microtomography and requires beneficial taphonomy. However, microtomography does provide a good overview of their petrological context at flexible spatial scales, although the quality of the data obtained from mesoscopic microbially-induced sedimentary structures and stromatolites depends largely on their style of preservation.

Supplementary material:
A zipped Drishti volume for all CT scans, a 0.7z split zip file of one Drishti volume and a HDMI supplementary movie showing digital visualizations for all of the scans are available at
https://doi.org/10.5281/zenodo.58161
Martin Brasier's contribution to the palaeobiology of the Ediacaran–Cambrian transition
Authors: Liu Alexander G. , Menon Latha R. , Shields Graham A. , Callow Richard H. T. , McIlroy Duncan 
Published: November 2016

Abstract
Martin Brasier's work spanned almost the entire geological column, but the origin of animals and the nature of the Cambrian explosion were areas of particular interest to him. Martin adopted a holistic approach to the study of these topics that considered the interplay between multiple geological and biological phenomena and he sought to interpret the fossil record within the broad context of geological, biogeochemical and ecological changes in the Earth system. Here we summarize Martin's main contributions to this area of research and assess the impact of his findings on the development of this field.
PROTOCADHERIN 7 Acts through SET and PP2A to Potentiate MAPK Signaling by EGFR and KRAS during Lung Tumorigenesis
Authors: Zhou Xiaorong , Updegraff Barrett L. , Guo Yabin , Peyton Michael , Girard Luc , Larsen Jill E. , Xie Xian-Jin , Zhou Yunyun , Hwang Tae Hyun , Xie Yang , Rodriguez-Canales Jaime , Villalobos Pamela , Behrens Carmen , Wistuba Ignacio I. , Minna John D. , O'Donnell Kathryn A. 
Published: November 2016

Abstract
Non–small cell lung cancer (NSCLC) is the leading cause of cancer-associated deaths worldwide. Given the efficacy of membrane proteins as therapeutic targets in human malignancies, we examined cell-surface receptors that may act as drivers of lung tumorigenesis. Here, we report that the PROTOCADHERIN PCDH7 is overexpressed frequently in NSCLC tumors where this event is associated with poor clinical outcome. PCDH7 overexpression synergized with EGFR and KRAS to induce MAPK signaling and tumorigenesis. Conversely, PCDH7 depletion suppressed ERK activation, sensitized cells to MEK inhibitors, and reduced tumor growth. PCDH7 potentiated ERK signaling by facilitating interaction of protein phosphatase PP2A with its potent inhibitor, the SET oncoprotein. By establishing an oncogenic role for PCDH7 in lung tumorigenesis, our results provide a rationale to develop novel PCDH7 targeting therapies that act at the cell surface of NSCLC cells to compromise their growth. Cancer Res; 77(1); 187–97. ©2016 AACR.
Dietary Emulsifier–Induced Low-Grade Inflammation Promotes Colon Carcinogenesis
Authors: Viennois Emilie , Merlin Didier , Gewirtz Andrew T. , Chassaing Benoit 
Published: November 2016

Abstract
The increased risks conferred by inflammatory bowel disease (IBD) to the development of colorectal cancer gave rise to the term “colitis-associated cancer” and the concept that inflammation promotes colon tumorigenesis. A condition more common than IBD is low-grade inflammation, which correlates with altered gut microbiota composition and metabolic syndrome, both present in many cases of colorectal cancer. Recent findings suggest that low-grade inflammation in the intestine is promoted by consumption of dietary emulsifiers, a ubiquitous component of processed foods, which alter the composition of gut microbiota. Here, we demonstrate in a preclinical model of colitis-induced colorectal cancer that regular consumption of dietary emulsifiers, carboxymethylcellulose or polysorbate-80, exacerbated tumor development. Enhanced tumor development was associated with an altered microbiota metagenome characterized by elevated levels of lipopolysaccharide and flagellin. We found that emulsifier-induced alterations in the microbiome were necessary and sufficient to drive alterations in major proliferation and apoptosis signaling pathways thought to govern tumor development. Overall, our findings support the concept that perturbations in host–microbiota interactions that cause low-grade gut inflammation can promote colon carcinogenesis. Cancer Res; 77(1); 27–40. ©2016 AACR.
A Transcriptional Signature Identifies LKB1 Functional Status as a Novel Determinant of MEK Sensitivity in Lung Adenocarcinoma
Authors: Kaufman Jacob M. , Yamada Tadaaki , Park Kyungho , Timmers Cynthia D. , Amann Joseph M. , Carbone David P. 
Published: November 2016

Abstract
LKB1 is a commonly mutated tumor suppressor in non–small cell lung cancer that exerts complex effects on signal transduction and transcriptional regulation. To better understand the downstream impact of loss of functional LKB1, we developed a transcriptional fingerprint assay representing this phenotype. This assay was predictive of LKB1 functional loss in cell lines and clinical specimens, even those without detected sequence alterations in the gene. In silico screening of drug sensitivity data identified putative LKB1-selective drug candidates, revealing novel associations not apparent from analysis of LKB1 mutations alone. Among the candidates, MEK inhibitors showed robust association with signature expression in both training and testing datasets independent of RAS/RAF mutations. This susceptibility phenotype is directly altered by RNA interference–mediated LKB1 knockdown or by LKB1 re-expression into mutant cell lines and is readily observed in vivo using a xenograft model. MEK sensitivity is dependent on LKB1-induced changes in AKT and FOXO3 activation, consistent with genomic and proteomic analyses of LKB1-deficient lung adenocarcinomas. Our findings implicate the MEK pathway as a potential therapeutic target for LKB1-deficient cancers and define a practical NanoString biomarker to identify functional LKB1 loss. Cancer Res; 77(1); 153–63. ©2016 AACR.
ДЕФІЦИТ ВІТАМІНУ D І ВАГІТНІСТЬ.
Authors: Boychuk A. V. , Budnik T. O. 
Published: November 2016

У статті наведені дані щодо сучасних поглядів на роль вітаміну D у забезпеченні різноманітних функцій організму і, зокрема, ролі дефіциту вітаміну D у розвитку ускладнень вагітності. Показано багатогранність функцій вітаміну D та вплив його дефіциту на низку акушерських і перинатальних ускладнень. Вказано на необхідність скринінгового цілеспрямованого обстеження вагітних на вміст вітаміну D у сироватці крові, що дозволить проводити вчасну корекцію та попередити ускладнення.
Ischemic Stroke and Risk of Venous Thromboembolism in the General Population: The Tromsø Study
Authors: Rinde Ludvig B. , Småbrekke Birgit , Mathiesen Ellisiv B. , Løchen Maja‐Lisa , Njølstad Inger , Hald Erin M. , Wilsgaard Tom , Brækkan Sigrid K. , Hansen John‐Bjarne 
Published: November 2016

Background

Even though clinical data support a relation between ischemic stroke and venous thromboembolism (
VTE
), the strength and time dependence of the association remain to be settled at the population level. We therefore aimed to investigate the association between ischemic stroke and
VTE
in a prospective population‐based cohort.

Methods and Results

Participants (n=30 002) were recruited from 3 surveys of the Tromsø study (conducted in 1994–1995, 2001, and 2007–2008) and followed through 2010. All incident events of ischemic stroke and
VTE
during follow‐up were recorded. Cox‐regression models with age as time scale and ischemic stroke as a time‐dependent variable were used to calculate hazard ratios (
HR
) of
VTE
adjusted for cardiovascular risk factors. During a median follow‐up time of 15.7 years, 1360 participants developed ischemic stroke and 722 had a
VTE
. The risk of
VTE
was highest the first month (
HR
19.7; 95%
CI
, 10.1–38.5) and from 1 to 3 months after the stroke (
HR
10.6; 95%
CI
5.0–22.5), but declined rapidly thereafter. The risk estimates were approximately the same for deep vein thrombosis (
HR
19.1; 95%
CI
, 7.8–38.5), and pulmonary embolism (
HR
20.2; 95%
CI
, 7.4–55.1). Stroke was associated with higher risk for provoked (
HR
22.6; 95%
CI
, 12.5–40.9) than unprovoked
VTE
(
HR
7.4; 95%
CI
, 2.7–20.1) the first 3 months.

Conclusions

The risk of
VTE
increased during the first 3 months after an ischemic stroke. The particularly high risk of provoked
VTE
suggests that additional predisposing factors, such as immobilization, potentiate the
VTE
risk in patients with ischemic stroke.
Discontinuities and the Maintenance of Chinese Cemeteries in Kolkata (India) (印度加尔各答华人墓地的间断与维持)
Authors: Guéguen Catherine 
Published: November 2016

In India, where migrations from mainland China are not constantly renewed, the Chinese cemeteries constitute the perennial elements of cultural transmission. As they build cemeteries for their community, these overseas-Chinese people inscribe the concrete references that they hold sacred in India, and no longer look to mainland China. We shall see that there are multiple reasons that explain the Chinese cemeteries’ location on the margins of the city. However, the places for the dead are the result of a long process, cultural and spatial, specific to how they were established in Kolkata and its suburbs. The cemetery constitutes in itself a space of adaptation and a space of practice; it reflects the anchoring of the Chinese in India.
在印度，来自中国大陆的移民浪潮经历了长久的间断，而华人墓地却不因中国移民的间断而逐渐消亡，反而成为华族文化传承的不间断载体。当海外华人为自己的社区建立墓地时，意味着他们决定扎根于印度而不再遥望中国作为落叶归根的想象家乡。华人将墓地设在城市边缘的原因众多。但是，地点的选择是一个冗长的、文化与空间局限交织作用的过程，尤其是如何将墓地设于加尔各答及其郊区内。墓地本身便是一个包含不断适应和实践的空间，它反映了华人在印度扎根繁衍的历史现象。
This article is in English.