bluuebunny/crossref_metadata_2025_split huggingface dataset:
Novel Trifunctional Xylanolytic Enzyme Axy43A from Paenibacillus curdlanolyticus Strain B-6 Exhibiting Endo-Xylanase, β-
d
-Xylosidase, and Arabinoxylan Arabinofuranohydrolase Activities
Authors: Teeravivattanakit Thitiporn , Baramee Sirilak , Phitsuwan Paripok , Waeonukul Rattiya , Pason Patthra , Tachaapaikoon Chakrit , Sakka Kazuo , Ratanakhanokchai Khanok 
Published: September 2016

ABSTRACT

The
axy43A
gene encoding the intracellular trifunctional xylanolytic enzyme from
Paenibacillus curdlanolyticus
B-6 was cloned and expressed in
Escherichia coli
. Recombinant PcAxy43A consisting of a glycoside hydrolase family 43 and a family 6 carbohydrate-binding module exhibited endo-xylanase, β-xylosidase, and arabinoxylan arabinofuranohydrolase activities. PcAxy43A hydrolyzed xylohexaose and birch wood xylan to release a series of xylooligosaccharides, indicating that PcAxy43A contained endo-xylanase activity. PcAxy43A exhibited β-xylosidase activity toward a chromogenic substrate,
p
-nitrophenyl-β-
d
-xylopyranoside, and xylobiose, while it preferred to hydrolyze long-chain xylooligosaccharides rather than xylobiose. In addition, surprisingly, PcAxy43A showed arabinoxylan arabinofuranohydrolase activity; that is, it released arabinose from both singly and doubly arabinosylated xylose, α-
l
-Ara
f
-(1→2)-
d
-Xyl
p
or α-
l
-Ara
f
-(1→3)-
d
-Xyl
p
and α-
l
-Ara
f
-(1→2)-[α-
l
-Ara
f
-(1→3)]-β-
d
-Xyl
p
. Moreover, the combination of PcAxy43A and
P. curdlanolyticus
B-6 endo-xylanase Xyn10C greatly improved the efficiency of xylose and arabinose production from the highly substituted rye arabinoxylan, suggesting that these two enzymes function synergistically to depolymerize arabinoxylan. Therefore, PcAxy43A has the potential for the saccharification of arabinoxylan into simple sugars for many applications.

IMPORTANCE
In this study, the glycoside hydrolase 43 (GH43) intracellular multifunctional endo-xylanase, β-xylosidase, and arabinoxylan arabinofuranohydrolase (AXH) from
P. curdlanolyticus
B-6 were characterized. Interestingly, PcAxy43A AXH showed a new property that acted on both the C(O)-2 and C(O)-3 positions of xylose residues doubly substituted with arabinosyl, which usually obstruct the action of xylanolytic enzymes. Furthermore, the studies here show interesting properties for the processing of xylans from cereal grains, particularly rye arabinoxylan, and show a novel relationship between PcAxy43A and endo-xylanase Xyn10C from strain B-6, providing novel metabolic potential for processing arabinoxylans into xylose and arabinose.
Response of Germfree Mice to Colonization by Oxalobacter formigenes and Altered Schaedler Flora
Authors: Li Xingsheng , Ellis Melissa L. , Dowell Alexander E. , Kumar Ranjit , Morrow Casey D. , Schoeb Trenton R. , Knight John 
Published: September 2016

ABSTRACT

Colonization with
Oxalobacter formigenes
may reduce the risk of calcium oxalate kidney stone disease. To improve our limited understanding of host-
O. formigenes
and microbe-
O. formigenes
interactions, germfree mice and mice with altered Schaedler flora (ASF) were colonized with
O. formigenes
. Germfree mice were stably colonized with
O. formigenes
, which suggests that
O. formigenes
does not require other organisms to sustain its survival. Examination of intestinal material indicated no viable
O. formigenes
in the small intestine and ∼4 × 10
6
CFU
O. formigenes
per 100 mg contents in the cecum and proximal colon, with ∼0.02% of total cecal
O. formigenes
cells being tightly associated with the mucosa.
O. formigenes
did not alter the overall microbial composition of ASF, and ASF did not affect the capacity of
O. formigenes
to degrade dietary oxalate in the cecum. Twenty-four-hour collections of urine and feces in metabolic cages in semirigid isolators demonstrated that the introduction of ASF into germfree mice significantly reduced urinary oxalate excretion. These experiments also showed that
O. formigenes
-monocolonized mice excreted significantly more urinary calcium than did germfree mice, which may be due to degradation of calcium oxalate crystals by
O. formigenes
and subsequent intestinal absorption of free calcium. In conclusion, the successful establishment of mouse models with defined flora and
O. formigenes
should improve our understanding of
O. formigenes
-host and
O. formigenes
-microbe interactions. These data support the use of
O. formigenes
as a probiotic that has limited impact on the composition of the resident microbiota but provides an efficient oxalate-degrading function.

IMPORTANCE
Despite evidence suggesting that a lack of
Oxalobacter formigenes
colonization is a risk factor for calcium oxalate stone formation, little is known about
O. formigenes
biology. This study is the first to utilize germfree mice to examine the response to monocolonization with
O. formigenes
, as well as the impact of a defined bacterial cocktail (i.e., ASF) on
O. formigenes
colonization. This study demonstrated that germfree mice receiving their regular diet remained monocolonized with
O. formigenes
, and it suggests that further studies with
O. formigenes
gnotobiotic mouse models could improve our understanding of
O. formigenes
biology and host-
O. formigenes
and microbe-
O. formigenes
interactions.
The end of the Ediacaran: Two new exceptionally preserved body fossil assemblages from Mount Dunfee, Nevada, USA
Authors: Smith E.F. , Nelson L.L. , Strange M.A. , Eyster A.E. , Rowland S.M. , Schrag D.P. , Macdonald F.A. 
Published: September 2016

Abstract
Evaluation of hypotheses that relate environmental to evolutionary change across the Ediacaran-Cambrian transition has been hampered by a dearth of sections that preserve both the last appearance of Ediacaran body fossils and the first appearance of Treptichnus pedum within carbonate-rich strata suitable for chemostratigraphic studies. Here, we report two new exceptionally preserved latest Ediacaran fossil assemblages from the Deep Spring Formation at Mount Dunfee, Nevada (USA). Further, we report these occurrences in a high-resolution carbon isotope chemostratigraphic framework, permitting correlation on a regional and global scale. The lower of the two horizons, at the base of the Deep Spring Formation, hosts a body fossil assemblage that includes Gaojiashania, other vermiform body fossils, and possible Wutubus annularis interbedded with Cloudina shell beds. The upper of the two fossil horizons, in the Esmeralda Member of the Deep Spring Formation, contains Conotubus and occurs within the basal Cambrian negative carbon isotope excursion, establishing it as the youngest Ediacaran fossil assemblage discovered to date. This is the first report of Gaojiashania, Conotubus, and Wutubus in Laurentia, extending the known stratigraphic ranges and biogeographic distributions of these taxa to a global scale. These data refine the relative ages of defining characteristics of the Ediacaran-Cambrian boundary and confirm that a large perturbation to the carbon cycle and surface ocean conditions coincided with the extinction of Ediacaran organisms.
A continental arc tempo discovered in the Pacific-Gondwana margin mudpile?
Authors: Paulsen Timothy , Deering Chad , Sliwinski Jakub , Bachmann Olivier , Guillong Marcel 
Published: September 2016

Abstract
The integration of detrital zircon age and trace element analyses provides a powerful tool with which to reconstruct continental arc evolution. Detrital zircons from the Ross-Delamerian orogen along the Pacific-Gondwana margin in north Victoria Land in Antarctica yield a broad 700–500 Ma U-Pb age population that shows a prominent period of activity centered at ca. 630–550 Ma. This activity is well correlated with the highest zircon Th/U and U/Yb ratios, suggesting an increase in lithospheric contribution coincident with fluid input from oceanic slab subduction, respectively. A low Yb/Gd ratio over this same period also suggests crustal thickening. Determination of zircon parent rock types using trace element proxies reveals the presence of previously unrecognized distinct pulses of granitoid activity that occur over tens of millions of years. Lulls between granitoid flare-ups overlap with increases in mafic-carbonatite-alkaline magma production, suggesting an influx of mantle or lower crustal melts during syn-subduction extension. A concomitant increase in the number of metamorphic zircons (U/Th &gt; 10) and 40Ar/39Ar white mica cooling ages found during these extensional episodes suggest that significant thermal perturbations of the crust coincided with orogenic cooling, which was possibly influenced by uplift and exhumation.
The milling factory: Componentry-dependent fragmentation and fines production in pyroclastic flows
Authors: Bernard Julien , Le Pennec Jean-Luc 
Published: September 2016

Abstract
In order to decipher the mobility of hazardous small-volume pyroclastic flows (PFs), we investigate here the role of clast fragmentation and production of fine particles (&lt;2 mm) in controlling PF dynamics. We report a high-resolution textural data set (i.e., grain size distribution, clast componentry, and clast morphology) of andesitic scoriaceous PF deposits from Tungurahua volcano (Ecuador) based on a unique method and data processing procedure. The strong relationship shown between clast size and componentry in PF deposits is quantified through a componentry versus size index (CSI), which varies between −1 and +1 (all components in the coarse or fine fractions, respectively). Our results show that the incorporated old lava clasts (CSI of −0.33) control early grinding of the pristine juvenile bombs (CSI of −1), which produce smaller scoriaceous andesitic fragments (CSI of 0.26). These latter interact in the granular assemblage and release fine particles through the abrasion processes, as supported by the morphological data. The textural maturity of the deposits reveals that the “milling factory” works before sedimentation begins (i.e., on steep upper slopes) and that there is some balance between fines production and loss. The process evident here tends to redistribute stress into the moving flow and produces fines that contribute to fluidization of it. The milling factory is thus likely to enhance the mobility of geophysical flows, which has strong implications for modeling and hazard assessment purposes.
Electroacupuncture Pretreatment Induces Rapid Tolerance to Bupivacaine Cardiotoxicity in Rats
Authors: Gao Jun-Long , Li Yu-Lan , Wang Xiu-Mei , Zhao Qian-Long , Zhang Hai-Jun , Han Fang-Fang , Li Xia-Xia , Zhang Dong-Hang 
Published: September 2016

Background Evidence suggests that electroacupuncture (EA) protects against arrhythmia and myocardial injury induced by myocardial ischaemia-reperfusion. However, to our knowledge, it remains unknown whether EA could alleviate bupivacaine-induced cardiotoxicity. Therefore, we aimed to explore the effect of EA pretreatment on bupivacaine-induced cardiac arrest and outcomes of cardiopulmonary resuscitation (CPR) in rats. Methods 24 adult male Sprague-Dawley rats were randomly divided into two groups: EA (n=12), and minimal acupuncture (MA) (n=12). Rats in both groups were needled at bilateral PC6, ST36, and ST40. Needles in the EA group were electrically stimulated for 60 min. ECG and invasive arterial blood pressure measurements were recorded. Two hours after EA or MA, 10 mg/kg bupivacaine was infused intravenously at a rate of 5 mg/kg/min in all rats. Rats suffering cardiac arrest were immediately subjected to CPR. At the end of the experiment, arterial blood samples were taken from surviving rats for blood gas analysis. Results The time from bupivacaine infusion until 20% prolongation of the QRS and QT interval, and the time to cardiac arrest, were notably increased among the rats pretreated with EA. Moreover, EA pretreatment significantly improved mean arterial pressure and heart rate at all monitored points after bupivacaine infusion. The proportion of animals surviving was higher in the EA group (9/12) than the MA group (3/12) at the end of experiment (p=0.039). Conclusions Tolerance to bupivacaine-induced cardiotoxicity appeared to be increased following EA pre-treatment. The mechanism of action underlying the effects of EA on bupivacaine-induced cardiotoxicity requires further investigation.
Does end-tidal capnography confirm tracheal intubation in fresh-frozen cadavers?
Authors: Reid Cliff , Ferguson Ian , Burns Brian , Habig Karel , Shareef Mohammed 
Published: September 2016

BackgroundLife-like end-tidal capnography (ETCO2) waveforms have been demonstrated in recently deceased and fresh-frozen cadavers following tracheal intubation, offering potential for high fidelity airway simulation training. As the mechanism for carbon dioxide production is not fully understood, it is possible that oesophageal intubation may also generate a capnograph. Our aim was to measure ETCO2levels following (1) oesophageal and (2) tracheal intubation in fresh-frozen cadavers, and to observe the size, shape and duration of any capnographic waveform.MethodsFour fresh frozen cadavers underwent oesophageal intubation by an emergency medicine specialist with confirmation by a second specialist. Hand ventilation with room air via a self-inflating resuscitation bag was provided at 12 breaths per minute for 2 min or until ETCO2was zero for 10 consecutive breaths. ETCO2and waveform morphology were examined and video recorded. The oesophagus was then extubated and the process was repeated for tracheal intubation.ResultsIn no case was oesophageal ETCO2detected. For two cadavers, life-like ETCO2waveforms were achieved immediately after tracheal intubation, with maximum ETCO2achieved by the second breath. In these cases waveform morphology was normal and persistent.ConclusionsCadaveric oesophageal intubation did not result in a capnography waveform, simulating live patients. When present, ETCO2following tracheal intubation showed normal morphology which was sustained for 2 min. However, ETCO2was not present following tracheal intubation in all cadavers. These results represent instrumentation on the cadavers for the first time after thawing and further work should assess the repeatability of the findings with subsequent intubations.
Stroke prevention by endovascular treatment of carotid and vertebral artery dissections
Authors: Moon Karam , Albuquerque Felipe C , Cole Tyler , Gross Bradley A , McDougall Cameron G 
Published: September 2016

IntroductionEndovascular intervention for cervical carotid artery dissection (CAD) and vertebral artery dissection (VAD) may be indicated in specific circumstances.ObjectiveTo review our institutional experience with endovascular treatment of cervical dissections over the past 20 years to examine indications for treatment, interventional methods, and outcomes.MethodsRetrospective review of a prospectively maintained database to identify patients with extracranial dissection who underwent endovascular intervention between January 1996 and January 2016. Demographic data and details of procedures, outcomes, and complications were extracted.ResultsOf 116 patients [93 CAD, 23 VAD; mean age 44.9 years (range 5–76 years)], 104 underwent stent placement; 11, coil occlusion of the parent artery; and 1, stenting with contralateral vessel occlusion. The cohorts were well matched for age, sex, dissection etiology, and admission and follow-up modified Rankin Scale (mRS) scores. Patients with CAD had significantly more stent placements (p<0.001), failure of medical therapy (p=0.004), and interventions for enlarging pseudoaneurysms (p=0.01) or thromboembolic events (p=0.004). Patients with VAD had significantly more interventions for traumatic occlusion with recanalization (p<0.001). Dissections were spontaneous (n=67), traumatic (n=36), or iatrogenic (n=13). Traumatic dissections in patients with CAD were associated with poor admission mRS scores (p=0.01). Six of 67 (9.0%) patients with spontaneous dissection reported recent chiropractic manipulation. Mean follow-up was 3.5 years (range 1–146 months). Permanent morbidity/mortality was 3.4%, including two deaths. Over a follow-up period of 364 patient-years, 1 stroke occurred (0.27% per year). At last follow-up, 41 previously disabled patients [CAD, 31/93 (33.3%); VAD, 10/23 (43.5%)] were no longer disabled; no patient reported worsened disability.ConclusionsPatients with CAD and VAD differ significantly in presentation, indications for treatment, and treatment methods. Endovascular treatment of CAD and VAD has low procedural morbidity and is associated with a low incidence of future stroke.
Characteristics of retractions related to faked peer reviews: an overview
Authors: Qi Xingshun , Deng Han , Guo Xiaozhong 
Published: September 2016

ABSTRACTA faked peer review is a novel cause for retraction. We reviewed the characteristics of papers retracted due to a faked peer review. All papers retracted due to faked peer reviews were identified by searching the Retraction Watch website and by conducting a manual search. All identified papers were confirmed in published journals. The information of retracted papers was collected, which primarily included publisher, journal, journal impact factor, country, as well as publication and retraction year. Overall, 250 retracted papers were identified. They were published in 48 journals by six publishers. The top 5 journals included the Journal of Vibration and Control (24.8%), Molecular Biology Reports (11.6%), Immunopharmacology and Immunotoxicology (8.0%), Tumour Biology (6.8%) and European Journal of Medical Research (6.4%). The publishers included SAGE (31%), Springer (26%), BioMed Central (18%), Elsevier (13%), Informa (11%) and LWW (1%). A minority (4%) of retracted papers were published in Science Citation Index (SCI) journals with an impact factor of &gt;5. A majority (74.8%) of retracted papers were written by Chinese researchers. In terms of the publication year, the retracted papers were published since 2010, and the number of retracted papers peaked in 2014 (40.8%). In terms of the retraction year, the retractions started in 2012, and the number of retractions peaked in 2015 (59.6%). The number of papers retracted due to faked peer reviews differs largely among journals and countries. With the improvement of the peer review mechanism and increased education about publishing ethics, such academic misconduct may gradually disappear in future.
Monogenetic v. polygenetic kimberlite volcanism: in-depth examination of the Tango Extension Super Structure, Attawapiskat kimberlite field, Ontario, Canada
Authors: Fulop Alexandrina , Kurszlaukis Stephan 
Published: September 2016

Abstract
Extensive drilling of the Tango Extension kimberlite pipe resulted in the construction of an emplacement model that revealed the complex architecture of two amalgamated pipes: an older pipe, the Tango Extension Deep, which is cut along its northern margin by the smaller Tango Extension pipe. The resulting volcano forms a complex pipe-in-pipe structure called the Tango Extension Super Structure. The emplacement of the Tango Extension Super Structure sequence indicates prolonged hiatuses, which, similar to other volcanoes classified as monogenetic, puts the classical monogenetic and polygenetic definitions of maar-diatreme volcanoes to the test. Although the Tango Extension and Tango Extension Deep volcanoes could be characterized individually as monogenetic volcanoes, the Tango Extension Super Structure shows evidence of the occurrence of the significant hiatuses typical of polygenetic volcanoes. We suggest that hiatuses that are long enough to consolidate earlier tephra unambiguously differentiate polygenetic from monogenetic maar-diatreme volcanoes.
Overexpression of Functional SLC6A3 in Clear Cell Renal Cell Carcinoma
Authors: Hansson Jennifer , Lindgren David , Nilsson Helén , Johansson Elinn , Johansson Martin , Gustavsson Lena , Axelson Håkan 
Published: September 2016

Abstract
Purpose: Renal cell carcinoma (RCC) is derived from a tissue with a remarkable capacity for vectorial transport. We therefore performed an unbiased exploration of transporter proteins in normal kidney and kidney cancer to discover novel clinical targets.
Experimental Design: Using The Cancer Genome Atlas (TCGA) database, we investigated differences in membrane transporter expression in clear cell RCC (ccRCC) and normal kidney. We identified the dopamine transporter SLC6A3 as a specific biomarker for ccRCC. To investigate the functionality of SLC6A3, we used a [3H]-dopamine uptake assay on ccRCC cells. We further explored the effect of hypoxia-inducible factor (HIF) proteins on SLC6A3 expression by introducing siRNA in ccRCC cells and by hypoxic treatment of nonmalignant cells.
Results: We show that ccRCC expresses very high transcript levels of SLC6A3 in contrast to normal kidney tissue and other tumor types, which do not express appreciable levels of this transporter. Importantly, we demonstrate that the elevated expression of SLC6A3 in ccRCC cells is associated with specific uptake of dopamine. By targeting the expression of HIF-1α and HIF-2α, we could show that SLC6A3 expression is primarily influenced by HIF-2α and that hypoxia can induce SLC6A3 expression in normal renal cells.
Conclusions: We conclude that the dopamine transporter SLC6A3 constitutes a novel biomarker that is highly specific for ccRCC. We further postulate that the protein can be exploited for diagnostic or therapeutic purposes for detection or treatment of ccRCC. Clin Cancer Res; 23(8); 2105–15. ©2016 AACR.
Selective Targeting of Cyclin E1-Amplified High-Grade Serous Ovarian Cancer by Cyclin-Dependent Kinase 2 and AKT Inhibition
Authors: Au-Yeung George , Lang Franziska , Azar Walid J. , Mitchell Chris , Jarman Kate E. , Lackovic Kurt , Aziz Diar , Cullinane Carleen , Pearson Richard B. , Mileshkin Linda , Rischin Danny , Karst Alison M. , Drapkin Ronny , Etemadmoghadam Dariush , Bowtell David D.L. 
Published: September 2016

AbstractPurpose: Cyclin E1 (CCNE1) amplification is associated with primary treatment resistance and poor outcome in high-grade serous ovarian cancer (HGSC). Here, we explore approaches to target CCNE1-amplified cancers and potential strategies to overcome resistance to targeted agents.Experimental Design: To examine dependency on CDK2 in CCNE1-amplified HGSC, we utilized siRNA and conditional shRNA gene suppression, and chemical inhibition using dinaciclib, a small-molecule CDK2 inhibitor. High-throughput compound screening was used to identify selective synergistic drug combinations, as well as combinations that may overcome drug resistance. An observed relationship between CCNE1 and the AKT pathway was further explored in genomic data from primary tumors, and functional studies in fallopian tube secretory cells.Results: We validate CDK2 as a therapeutic target by demonstrating selective sensitivity to gene suppression. However, we found that dinaciclib did not trigger amplicon-dependent sensitivity in a panel of HGSC cell lines. A high-throughput compound screen identified synergistic combinations in CCNE1-amplified HGSC, including dinaciclib and AKT inhibitors. Analysis of genomic data from TCGA demonstrated coamplification of CCNE1 and AKT2. Overexpression of Cyclin E1 and AKT isoforms, in addition to mutant TP53, imparted malignant characteristics in untransformed fallopian tube secretory cells, the dominant site of origin of HGSC.Conclusions: These findings suggest a specific dependency of CCNE1-amplified tumors for AKT activity, and point to a novel combination of dinaciclib and AKT inhibitors that may selectively target patients with CCNE1-amplified HGSC. Clin Cancer Res; 23(7); 1862–74. ©2016 AACR.