bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genome Sequence of Fowl Aviadenovirus A Strain JM1/1, Which Caused Gizzard Erosions in Japan
Authors: Thanasut Khompakorn , Fujino Kan , Taharaguchi Motoko , Taharaguchi Satoshi , Shimokawa Fumie , Murakami Masaru , Takase Kozo 
Published: October 2017

ABSTRACT
This study reports the complete genome sequence of fowl aviadenovirus A strain JM1/1, which caused gizzard erosions in broilers occurring in Japan. The JM1/1 genome is 43,809 bp in length and most closely related to the strain chicken embryo lethal orphan (CELO); moreover, multiple site insertions and deletions were found.
Draft Genome Sequence of Lactobacillus plantarum Strain A6, a Strong Acid Producer Isolated from a Vietnamese Fermented Sausage (Nem Chua)
Authors: Golneshin Aida , Gor Mian-Chee , Van Thi Thu Hao , May Bee , Moore Rob J. , Smith Andrew T. 
Published: October 2017

ABSTRACT

Lactobacillus plantarum
strain A6, a strong acid producer, was isolated from a Vietnamese fermented sausage (nem chua). Here, we report the genome sequence of this strain (3,368,579 bp).
Whole-Genome Sequence of Bifidobacterium longum Strain Indica, Isolated from the Gut of a Healthy Indian Adult
Authors: Bag Satyabrata , Ghosh Tarini Shankar , Das Bhabatosh 
Published: October 2017

ABSTRACT

Bifidobacterium longum
, a Gram-positive rod-shaped anaerobic bacterium, inhabits the human gastrointestinal tract and contributes significantly to oligosaccharide production, amino acid metabolism, and protection against intestinal inflammation. Here, we report the whole-genome sequence of
B. longum
, which was isolated from the gastrointestinal tract of a healthy Indian adult.
Draft Genome Sequence of a Picorna-Like Virus Associated with Gill Tissue in Clinically Normal Brook Trout,
Salvelinus fontinalis
Authors: Iwanowicz Luke R. , Iwanowicz Deborah D. , Adams Cynthia R. , Galbraith Heather , Aunins Aaron , Cornman Robert S. 
Published: October 2017

ABSTRACT

Here, we report a draft genome sequence of a picorna-like virus associated with brook trout,
Salvelinus fontinalis
, gill tissue. The draft genome comprises 8,681 nucleotides, excluding the poly(A) tract, and contains two open reading frames. It is most similar to picorna-like viruses that infect invertebrates.
Draft Genome Sequence of
Romboutsia maritimum
sp. nov. Strain CCRI-22766
T
, Isolated from Coastal Estuarine Mud
Authors: Maheux Andrée F. , Boudreau Dominique K. , Bérubé Ève , Boissinot Maurice , Raymond Frédéric , Brodeur Stéphanie , Corbeil Jacques , Brightwell Gale , Broda Dorota , Omar Rabeea F. , Bergeron Michel G. 
Published: October 2017

ABSTRACT

The
Romboutsia maritimum
sp. nov. CCRI-22766
T
strain was isolated from coastal estuarine mud in New Zealand. The genome assembly comprised 2,854,352 bp, with 27.1% G+C content. This is the first documentation that reports the genome sequence of
R. maritimum
.
Complete Genome Sequence of Peste des Petits Ruminants Virus from Georgia, 2016
Authors: Rajko-Nenow Paulina Z. , Cunliffe Tabitha G. , Flannery John T. , Ropiak Honorata M. , Avaliani Lasha , Donduashvili Marina , Baron Michael D. , Batten Carrie A. 
Published: October 2017

ABSTRACT
We report here the complete genome sequence of a peste des petits ruminants virus (PPRV) from the first outbreak of the disease in Georgia in January 2016. Genome sequencing was performed using Illumina next-generation sequencing technology in conjunction with Sanger sequencing. This PPRV/Georgia/Tbilisi/2016 genome sequence clustered within lineage IV PPRV viruses.
Genome Sequences of Coxsackievirus B5 Isolates from Two Children with Meningitis in Australia
Authors: Huang Bixing , Harrower Bruce , Burtonclay Peter , Constantino Tanya , Warrilow David 
Published: October 2017

ABSTRACT
Two coxsackievirus B5 (CVB5) strains were isolated from two children with aseptic meningitis in Australia. Their genomes were sequenced and found to be divergent from the previously reported CVB5 genome sequences, with both having 84% and 97% identities to the closest strains at the nucleotide and amino acid levels, respectively.
3D structural and thermal modelling of Mesozoic petroleum systems in the Po Valley Basin, northern Italy
Authors: Turrini Claudio , Bosica Barbara , Ryan Paul , Shiner Peter , Lacombe Olivier , Roure François 
Published: October 2017

1D and 3D basin modelling was performed to investigate the Mesozoic carbonate petroleum systems of the Po Valley Basin (northern Italy), through integration of a recent 3D structural model of the study area with the distribution of potential Triassic source rocks, rock properties and heat flow models.
Results from standard 1D maturity models show significant overprediction of the thermal maturity of deep Triassic carbonates in the western Po Valley, unless the effect of the substantial overpressure observed in these sequences is incorporated into the model. In order to further test this observation, two thermal scenarios were applied to the Po Valley 3D geo-volume: one based on the actual geological heat flow and a second model based on a reduced heat flow as a proxy for the delaying effect of overpressure on hydrocarbon maturation. The predictions of these two models were then compared with the observed hydrocarbon distribution in the western Po Valley.
Both thermal scenarios are broadly consistent with the observed hydrocarbon distribution at the scale of the basin but, in detail, the overpressure model provides a better match between the predicted charge available from the kitchen area's post-critical moment and observed volumes of hydrocarbons initially in place within the traps, as well as with the observed and predicted hydrocarbon phases, as measured by the gas/oil ratio (GOR) of the fluids. Overpressure probably significantly delayed hydrocarbon maturation in the western domain of the basin, confirming results from previous studies.
Beyond regional implications, and despite its relative simplicity and inherent uncertainties, the adopted approach demonstrates the potential of a consistent 3D integration of the thermostructural history of sedimentary basins to constrain the geometry and structural evolution of hydrocarbon-bearing traps, as well as the generation and migration of hydrocarbons into these traps.
Practical initialization race detection for JavaScript web applications
Authors: Adamsen Christoffer Quist , Møller Anders , Tip Frank 
Published: October 2017

Event races are a common source of subtle errors in JavaScript web applications. Several automated tools for detecting event races have been developed, but experiments show that their accuracy is generally quite low. We present a new approach that focuses on three categories of event race errors that often appear during the initialization phase of web applications: form-input-overwritten errors, late-event-handler-registration errors, and access-before-definition errors. The approach is based on a dynamic analysis that uses a combination of adverse and approximate execution. Among the strengths of the approach are that it does not require browser modifications, expensive model checking, or static analysis.
In an evaluation on 100 widely used websites, our tool InitRacer reports 1085 initialization races, while providing informative explanations of their causes and effects. A manual study of 218 of these reports shows that 111 of them lead to uncaught exceptions and at least 47 indicate errors that affect the functionality of the websites.
Geo-distribution of actor-based services
Authors: Bernstein Philip A. , Burckhardt Sebastian , Bykov Sergey , Crooks Natacha , Faleiro Jose M. , Kliot Gabriel , Kumbhare Alok , Rahman Muntasir Raihan , Shah Vivek , Szekeres Adriana , Thelin Jorgen 
Published: October 2017

Many service applications use actors as a programming model for the middle tier, to simplify synchronization, fault-tolerance, and scalability. However, efficient operation of such actors in multiple, geographically distant datacenters is challenging, due to the very high communication latency. Caching and replication are essential to hide latency and exploit locality; but it is not a priori clear how to combine these techniques with the actor programming model.
We present Geo, an open-source geo-distributed actor system that improves performance by caching actor states in one or more datacenters, yet guarantees the existence of a single latest version by virtue of a distributed cache coherence protocol. Geo's programming model supports both volatile and persistent actors, and supports updates with a choice of linearizable and eventual consistency. Our evaluation on several workloads shows substantial performance benefits, and confirms the advantage of supporting both replicated and single-instance coherence protocols as configuration choices. For example, replication can provide fast, always-available reads and updates globally, while batching of linearizable storage accesses at a single location can boost the throughput of an order processing workload by 7x.
Project snowflake: non-blocking safe manual memory management in .NET
Authors: Parkinson Matthew , Vytiniotis Dimitrios , Vaswani Kapil , Costa Manuel , Deligiannis Pantazis , McDermott Dylan , Blankstein Aaron , Balkind Jonathan 
Published: October 2017

Garbage collection greatly improves programmer productivity and ensures memory safety. Manual memory management on the other hand often delivers better performance but is typically unsafe and can lead to system crashes or security vulnerabilities. We propose integrating safe manual memory management with garbage collection in the .NET runtime to get the best of both worlds. In our design, programmers can choose between allocating objects in the garbage collected heap or the manual heap. All existing applications run unmodified, and without any performance degradation, using the garbage collected heap.
Our programming model for manual memory management is flexible: although objects in the manual heap can have a single owning pointer, we allow deallocation at any program point and concurrent sharing of these objects amongst all the threads in the program. Experimental results from our .NET CoreCLR implementation on real-world applications show substantial performance gains especially in multithreaded scenarios: up to 3x savings in peak working sets and 2x improvements in runtime.
Dietary copper-fructose interactions alter gut microbial activity in male rats
Authors: Song Ming , Li Xiaohong , Zhang Xiang , Shi Hongxue , Vos Miriam B. , Wei Xiaoli , Wang Yuhua , Gao Hong , Rouchka Eric C. , Yin Xinmin , Zhou Zhanxiang , Prough Russell A. , Cave Matthew C. , McClain Craig J. 
Published: October 2017

Dietary copper-fructose interactions contribute to the development of nonalcoholic fatty liver disease (NAFLD). Gut microbiota play critical roles in the pathogenesis of NAFLD. The aim of this study was to determine the effect of different dietary doses of copper and their interactions with high fructose on gut microbiome. Male weanling Sprague-Dawley rats were fed diets with adequate copper (6 ppm CuA), marginal copper (1.5 ppm CuM) (low copper), or supplemented copper (20 ppm CuS) (high copper) for 4 wk. Deionized water or deionized water containing 30% fructose (wt/vol) was given ad libitum. Copper status, liver enzymes, gut barrier function, and gut microbiome were evaluated. Both low- and high-copper diets led to liver injury in high-fructose-fed rats, and this was associated with gut barrier dysfunction, as shown by the markedly decreased tight junction proteins and increased gut permeability. 16S rDNA sequencing analysis revealed distinct alterations of the gut microbiome associated with dietary low- and high-copper/high-fructose feeding. The common features of the alterations of the gut microbiome were the increased abundance of Firmicutes and the depletion of Akkermansia. However, they differed mainly within the phylum Firmicutes. Our data demonstrated that a complex interplay among host, microbes, and dietary copper-fructose interaction regulates gut microbial metabolic activity, which may contribute to the development of liver injury and hepatic steatosis. The distinct alterations of gut microbial activity, which were associated with the different dietary doses of copper and fructose, imply that separate mechanism(s) may be involved.NEW & NOTEWORTHY First, dietary low- and high-copper/high-fructose-induced liver injury are associated with distinct alterations of gut microbiome. Second, dietary copper level plays a critical role in maintaining the gut barrier integrity, likely by acting on the intestinal tight junction proteins and the protective commensal bacteria Akkermansia. Third, the alterations of gut microbiome induced by dietary low and high copper with or without fructose differ mainly within the phylum Firmicutes.
microRNA-206 correlates with left ventricular function after transcatheter aortic valve implantation
Authors: Kleeberger J. A. , Neuser J. , de Gonzalo-Calvo D. , Kempf T. , Bauersachs J. , Thum T. , Widder J. D. 
Published: October 2017

Transcatheter aortic valve implantation (TAVI) is the method of choice in patients with high risk or contraindications for conventional aortic valve replacement. However, it is not well understood which parameters predict the overall cardiac function postprocedurally. miRNAs are small noncoding RNA molecules that repress gene expression by different mechanisms and can also be detected in the blood. Recent studies have shown that miRNAs detected in the blood may serve as sensitive and specific biomarkers in various diseases; therefore, we examined the levels of different microRNAs in the serum of patients undergoing TAVI. We thereby intended to find potential predictors for cardiac function after TAVI. Serum from patients with aortic valve disease was obtained at five different points: before the TAVI procedure, at days 1 and 3 after the TAVI procedure, and the day of dischargement and after a period of 3 mo. We next performed quantitative real-time PCRs to examine the samples for changes in the level of miRNAs previously described as cardiac enriched. Our results show that the level of miR-206 in the serum of patients after TAVI correlated negatively with the left ventricular ejection fraction of individual patients. We found left ventricular function to be better in patients with lower levels of miR-206 after implantation of the new valve. A decrease in the serum level of miR-206 may be linked to changes in cardiac function of patients after TAVI. Further studies are necessary to test the miRNA for its potential value as a prognostic marker. NEW & NOTEWORTHY This study is the first to investigate novel miRNA-based biomarkers within the context of transcatheter aortic valve implantation. miRNA-206 proved to correlate inversely with the postprocedural left ventricular ejection fraction of patients.
Sex-specific impact of aging on the blood pressure response to exercise
Authors: Trinity Joel D. , Layec Gwenael , Hart Corey R. , Richardson Russell S. 
Published: October 2017

An exaggerated blood pressure (BP) response to exercise has been linked to cardiovascular disease, but little is known about the impact of age and sex on this response. Therefore, this study examined the hemodynamic and skeletal muscle metabolic response to dynamic plantar flexion exercise, at 40% of maximum plantar flexion work rate, in 40 physical activity-matched young (23 ± 1 yr, n = 20) and old (73 ± 2 yr, n = 20), equally distributed, male and female subjects. Central hemodynamics and BP (finometer), popliteal artery blood flow (Doppler ultrasound), and skeletal muscle metabolism (31P-magnetic resonance spectroscopy) were measured during 5 min of plantar flexion exercise. Popliteal artery blood flow and high-energy phosphate responses to exercise were not affected by age or sex, whereas aging, independent of sex, attenuated stroke volume and cardiac output responses. Systolic BP and mean arterial pressure responses were exaggerated in old women (Δ42 ± 4 and Δ28 ± 3 mmHg, respectively), with all other groups exhibiting similar increases in systolic BP (old men: Δ27 ± 8 mmHg, young men: Δ27 ± 3 mmHg, and young women: Δ22 ± 3 mmHg) and mean arterial pressure (old men: Δ15 ± 4 mmHg, young men: Δ19 ± 2 mmHg, and young women: Δ17 ± 2 mmHg). Interestingly, the exercise-induced change in systemic vascular resistance in old women (∆0.8 ± 1.0 mmHg·l−1·min−1) was augmented compared with young women and young and old men (∆−2.8 ± 0.5, ∆−1.6 ± 0.6, and ∆−3.18 ± 1.4 mmHg·l−1·min−1, respectively, P < 0.05). Thus, in combination, advancing age and female sex results in an exaggerated BP response to exercise, likely the result of a failure to reduce systemic vascular resistance. NEW & NOTEWORTHY An exaggerated blood pressure response to exercise has been linked to cardiovascular disease; however, little is known about how age and sex impact this response in healthy individuals. During dynamic exercise, older women exhibited an exaggerated blood pressure response driven by an inability to lower systemic vascular resistance.
Relative contributions of systemic hemodynamic variables to cerebral autoregulation during orthostatic stress
Authors: Yoshida Hisao , Hamner Jason W. , Ishibashi Keita , Tan Can Ozan 
Published: October 2017

Postural changes impair the ability of the cerebrovasculature to buffer against dynamic pressure fluctuations, but the mechanisms underlying this impairment have not been elucidated. We hypothesized that autoregulatory impairment may reflect the impact of static central volume shifts on hemodynamic factors other than arterial pressure (AP). In 14 young volunteers, we assessed the relation of fluctuations in cerebral blood flow (CBF) to those in AP, cardiac output, and CO2, during oscillatory lower body pressure (LBP) (±20 mmHg at 0.01 and 0.06 Hz) at three static levels (−20, 0, and +20 mmHg). Static and dynamic changes in AP, cardiac output, and CO2explained over 70% of the variation in CBF fluctuations. However, their contributions were different across frequencies and levels: dynamic AP changes explained a substantial proportion of the variation in faster CBF fluctuations (partial R2 = 0.75, standardized β = 0.83, P < 0.01), whereas those in CO2explained the largest portion of the variation in slow fluctuations (partial R2 = 0.43, β = 0.51, P < 0.01). There was, however, a major contribution of slow dynamic AP changes during negative (β = 0.43) but not neutral (β = 0.05) or positive (β = −0.07) LBP. This highlights the differences in contributions of systemic variables to dynamic and static autoregulation and has important implications for understanding orthostatic intolerance.NEW & NOTEWORTHY While fluctuations in blood pressure drive faster fluctuations in cerebral blood flow, overall level of CO2and the magnitude of its fluctuations, along with cardiac output, determine the magnitude of slow ones. The effect of slow blood pressure fluctuations on cerebrovascular responses becomes apparent only during pronounced central volume shifts (such as when standing). This underlines distinct but interacting contributions of static and dynamic changes in systemic hemodynamic variables to the cerebrovascular regulation.
Endothelial Activation and Blood–Brain Barrier Disruption in Neurotoxicity after Adoptive Immunotherapy with CD19 CAR-T Cells
Authors: Gust Juliane , Hay Kevin A. , Hanafi Laïla-Aïcha , Li Daniel , Myerson David , Gonzalez-Cuyar Luis F. , Yeung Cecilia , Liles W. Conrad , Wurfel Mark , Lopez Jose A. , Chen Junmei , Chung Dominic , Harju-Baker Susanna , Özpolat Tahsin , Fink Kathleen R. , Riddell Stanley R. , Maloney David G. , Turtle Cameron J. 
Published: October 2017

Abstract
Lymphodepletion chemotherapy followed by infusion of CD19-targeted chimeric antigen receptor–modified T (CAR-T) cells can be complicated by neurologic adverse events (AE) in patients with refractory B-cell malignancies. In 133 adults treated with CD19 CAR-T cells, we found that acute lymphoblastic leukemia, high CD19+ cells in bone marrow, high CAR-T cell dose, cytokine release syndrome, and preexisting neurologic comorbidities were associated with increased risk of neurologic AEs. Patients with severe neurotoxicity demonstrated evidence of endothelial activation, including disseminated intravascular coagulation, capillary leak, and increased blood–brain barrier (BBB) permeability. The permeable BBB failed to protect the cerebrospinal fluid from high concentrations of systemic cytokines, including IFNγ, which induced brain vascular pericyte stress and their secretion of endothelium-activating cytokines. Endothelial activation and multifocal vascular disruption were found in the brain of a patient with fatal neurotoxicity. Biomarkers of endothelial activation were higher before treatment in patients who subsequently developed grade ≥4 neurotoxicity.
Significance: We provide a detailed clinical, radiologic, and pathologic characterization of neurotoxicity after CD19 CAR-T cells, and identify risk factors for neurotoxicity. We show endothelial dysfunction and increased BBB permeability in neurotoxicity and find that patients with evidence of endothelial activation before lymphodepletion may be at increased risk of neurotoxicity. Cancer Discov; 7(12); 1404–19. ©2017 AACR.
See related commentary by Mackall and Miklos, p. 1371.
This article is highlighted in the In This Issue feature, p. 1355
Reduction of In-Stent Restenosis by Cholesteryl Ester Transfer Protein Inhibition
Authors: Wu Ben J. , Li Yue , Ong Kwok L. , Sun Yidan , Shrestha Sudichhya , Hou Liming , Johns Douglas , Barter Philip J. , Rye Kerry-Anne 
Published: October 2017

Objective—
Angioplasty and stent implantation, the most common treatment for atherosclerotic lesions, have a significant failure rate because of restenosis. This study asks whether increasing plasma high-density lipoprotein (HDL) levels by inhibiting cholesteryl ester transfer protein activity with the anacetrapib analog, des-fluoro-anacetrapib, prevents stent-induced neointimal hyperplasia.

Approach and Results—

New Zealand White rabbits received normal chow or chow supplemented with 0.14% (wt/wt) des-fluoro-anacetrapib for 6 weeks. Iliac artery endothelial denudation and bare metal steel stent deployment were performed after 2 weeks of des-fluoro-anacetrapib treatment. The animals were euthanized 4 weeks poststent deployment. Relative to control, dietary supplementation with des-fluoro-anacetrapib reduced plasma cholesteryl ester transfer protein activity and increased plasma apolipoprotein A-I and HDL cholesterol levels by 53±6.3% and 120±19%, respectively. Non-HDL cholesterol levels were unaffected. Des-fluoro-anacetrapib treatment reduced the intimal area of the stented arteries by 43±5.6% (
P
<0.001), the media area was unchanged, and the arterial lumen area increased by 12±2.4% (
P
<0.05). Des-fluoro-anacetrapib treatment inhibited vascular smooth muscle cell proliferation by 41±4.5% (
P
<0.001). Incubation of isolated HDLs from des-fluoro-anacetrapib–treated animals with human aortic smooth muscle cells at apolipoprotein A-I concentrations comparable to their plasma levels inhibited cell proliferation and migration. These effects were dependent on scavenger receptor-B1, the adaptor protein PDZ domain-containing protein 1, and phosphatidylinositol-3-kinase/Akt activation. HDLs from des-fluoro-anacetrapib–treated animals also inhibited proinflammatory cytokine-induced human aortic smooth muscle cell proliferation and stent-induced vascular inflammation.

Conclusions—
Inhibiting cholesteryl ester transfer protein activity in New Zealand White rabbits with iliac artery balloon injury and stent deployment increases HDL levels, inhibits vascular smooth muscle cell proliferation, and reduces neointimal hyperplasia in an scavenger receptor-B1, PDZ domain-containing protein 1– and phosphatidylinositol-3-kinase/Akt-dependent manner.