bluuebunny/crossref_metadata_2025_split huggingface dataset:
Occurrence of acute renal failure on the same day as immune globulin product administrations during 2008 to 2014
Authors: Ekezue Bola F. , Sridhar Gayathri , Forshee Richard A. , Izurieta Hector S. , Selvam Nandini , Mintz Paul D. , Anderson Steven A. , Menis Mikhail D. 
Published: October 2017

BACKGROUNDAcute renal failure (ARF) is a rare serious adverse event after immune globulin (IG) use. Our large claims‐based study evaluated occurrence of same‐day ARF after administration of different IGs and ascertained potential risk factors, during the 2008 to 2014 study period.STUDY DESIGN AND METHODSA retrospective cohort study was conducted using a large commercial administrative database. The cohort included individuals exposed to IG products as identified by procedure codes. ARF was ascertained using ICD‐9‐CM diagnoses. Unadjusted same‐day ARF rates (per 1000 persons exposed) were estimated overall and by age, sex, and IG products. Regression analyses were conducted to control for confounding and assess potential risk factors.RESULTSOf 20,440 persons exposed, 163 (7.97 per 1000) had a recorded same‐day ARF. The unadjusted nonzero same‐day ARF rates (per 1000) ranged from 1.92 (95% confidence interval [CI], 0.05‐10.69) for Hizentra to 16.97 (95% CI, 11.36‐24.37) for Privigen and differed by sex. In multivariate analyses, compared to Gammagard Liquid, no significantly elevated ARF risks were identified with any IGs. A significantly lower odds ratio was identified with Gamunex, 0.53 (95% CI, 0.30‐0.93). Age 45 and over, prior renal impairment, hypertension, and other factors were associated with increased risk of same‐day ARF.CONCLUSIONThe study showed variation in the risk of IG‐related ARF by age, sex, and IG products. The study results suggest the importance of recipient factors, such as older age and underlying health conditions. Variations in ARF occurrence may also be explained by product dosage, administration route and rate, and manufacturing processes, which warrant further evaluation.
Sourcing patterns of export‐platform foreign affiliates: The case of Japanese affiliates in Mexico
Authors: Kondo Keisuke 
Published: October 2017

AbstractThis study investigates the sourcing patterns of Japanese export‐platform foreign affiliates in Mexico, which mainly export to the United States and Canada. We propose a novel approach to estimate intermediate input elasticities of exports by sourcing country. We find that, on average, Japanese export‐platform foreign affiliates in Mexico source intermediate inputs from third countries, including the United States and Canada, rather than from Japan and Mexico, suggesting that Japanese export‐platform foreign affiliates in Mexico are mainly integrated into the vertical production networks back and forth between Mexico, the United States and Canada. In turn, Japanese foreign affiliates selling domestically in Mexico source intermediate inputs not only within the North American Free Trade Agreement countries but also from Japan. In addition, we find that export‐platform foreign affiliates in Mexico use more labour‐intensive production than do foreign affiliates selling domestically in Mexico. This suggests that saving labour costs is one of the motives for export‐platform foreign direct investment in Mexico.
Single room versus open-bay design in neonatal intensive care units for improvement in infant outcomes: a systematic review protocol
Authors: Disher Timothy , Dol Justine , Richardson Brianna , Campbell-Yeo Marsha 
Published: October 2017

Review question/objective:
: The objective of this review is to identify the impact of single room neonatal intensive care unit (NICU) design on infant outcomes compared to alternative design.
The specific question is: what is the impact of single room design on outcomes of infants cared for in intensive care units compared to those in alternative designs?
The role of declining adaptive homeostasis in ageing
Authors: Pomatto Laura C. D. , Davies Kelvin J. A. 
Published: October 2017

AbstractAdaptive homeostasis is “the transient expansion or contraction of the homeostatic range for any given physiological parameter in response to exposure to sub‐toxic, non‐damaging, signalling molecules or events, or the removal or cessation of such molecules or events” (Davies, 2016). Adaptive homeostasis enables biological systems to make continuous short‐term adjustments for optimal functioning despite ever‐changing internal and external environments. Initiation of adaptation in response to an appropriate signal allows organisms to successfully cope with much greater, normally toxic, stresses. These short‐term responses are initiated following effective signals, including hypoxia, cold shock, heat shock, oxidative stress, exercise‐induced adaptation, caloric restriction, osmotic stress, mechanical stress, immune response, and even emotional stress. There is now substantial literature detailing a decline in adaptive homeostasis that, unfortunately, appears to manifest with ageing, especially in the last third of the lifespan. In this review, we present the hypothesis that one hallmark of the ageing process is a significant decline in adaptive homeostasis capacity. We discuss the mechanistic importance of diminished capacity for short‐term (reversible) adaptive responses (both biochemical and signal transduction/gene expression‐based) to changing internal and external conditions, for short‐term survival and for lifespan and healthspan. Studies of cultured mammalian cells, worms, flies, rodents, simians, apes, and even humans, all indicate declining adaptive homeostasis as a potential contributor to age‐dependent senescence, increased risk of disease, and even mortality. Emerging work points to Nrf2‐Keap1 signal transduction pathway inhibitors, including Bach1 and c‐Myc, both of whose tissue concentrations increase with age, as possible major causes for age‐dependent loss of adaptive homeostasis.
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Chloroplast Genome Sequences of Seven Strains of the Bloom-Forming Raphidophyte Heterosigma akashiwo
Authors: Seoane Sergio , Hyodo Kiwamu , Ueki Shoko 
Published: October 2017

ABSTRACT

We report here the complete chloroplast genome sequences of seven strains of the bloom-forming raphidophyte
Heterosigma akashiwo
. These ~160-kb sequences contain 124 protein-, 6 rRNA-, and 34 tRNA-coding sequences. Notable sequence variations were observed among these seven sequenced and two previously characterized strains.
Complete Genome Sequences of Four
Brucella
Strains Isolated from China
Authors: Yang Xiaowen , Cao Xiaofang , Wang Ning , Wang Jiawei , Bie Pengfei , Lyu Yanli , Wu Qingmin 
Published: October 2017

ABSTRACT

Brucella
spp. are facultative intracellular pathogens that cause a contagious zoonotic disease. Twelve different species are currently identified. This study presents the complete genome sequences of four
Brucella
strains. These complete genomes were annotated and the contents compared to those of other strains isolated from China.
Two Complete Sequences for Genomes of Human Respiratory Syncytial Virus Genotype ON1 Field Strains from Beijing, China
Authors: Cui Guanglin , Zhu Runan , Deng Jie , Qian Yuan 
Published: October 2017

ABSTRACT
Here, we report the complete sequences for genomes of two human respiratory syncytial virus field strains. It was determined by sequence alignment and phylogenetics that they belong to genotype ON1, characterized by a 72-nucleotide duplication in the C termini of the attachment protein G genes.
Complete Genome Sequence of Super Biofilm-Elaborating Staphylococcus aureus Isolated in Japan
Authors: Yu Liansheng , Hisatsune Junzo , Hirakawa Hideki , Mizumachi Emiri , Toyoda Atsushi , Yahara Koji , Sugai Motoyuki 
Published: October 2017

ABSTRACT

Staphylococcus aureus
JP080, previously named TF2758, is a clinical isolate from an atheroma and a super biofilm-elaborating strain whose biofilm elaboration is dependent solely on polysaccharide poly-
N
-acetylglucosamine/polysaccharide intercellular adhesin (PNAG/PIA). Here, we report the complete genome sequence of strain JP080, which consists of one chromosome and one circular plasmid.
Draft Genome Sequences of Two Novel Sub-Antarctic
Williamsia
Species
Authors: Nahar Akhikun , Baker Anthony L. , Charleston Michael A. , Bowman John P. , Britz Margaret L. 
Published: October 2017

ABSTRACT

Illumina MiSeq shotgun sequencing technology was used to sequence the genomes of two novel sub-Antarctic
Williamsia
species, designated strains 1135 and 1138. The estimated genome sizes for strains 1135 and 1138 are 5.99 Mb and 6.08 Mb, respectively. This genome sequence information will aid in understanding the lipid metabolic pathways of cold-tolerant
Williamsia
species.
Draft Genome Sequence of Bacillus aryabhattai Strain PHB10, a Poly(3-Hydroxybutyrate)-Accumulating Bacterium Isolated from Domestic Sewerage
Authors: Balakrishna Pillai Aneesh , Jaya Kumar Arjun , Thulasi Kavitha , Reghunathan Dinesh , Prasannakumar Manoj , Kumarapillai Harikrishnan 
Published: October 2017

ABSTRACT

Bacillus aryabhattai
PHB10 is a poly(3-hydroxybutyrate) (PHB)-accumulating bacterium isolated from domestic sewerage. Here, we report the 4.19-Mb draft genome sequence, with 4,050 protein-coding genes and a G+C content of 37.5%. This sequence will be helpful in the study of the high-level PHB accumulation mechanism of the strain.
Draft Genome Sequences of Nine Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 5 Isolates Obtained from Humans after Short-Term Swine Contact
Authors: Hau Samantha J. , Bayles Darrell O. , Alt David P. , Frana Timothy S. , Nicholson Tracy L. 
Published: October 2017

ABSTRACT

Livestock-associated methicillin-resistant
Staphylococcus aureus
(LA-MRSA) sequence type 5 (ST5) has raised concerns surrounding the potential for these isolates to colonize or cause disease in humans with swine contact. Here, we report draft genome sequences for nine LA-MRSA ST5 isolates obtained from humans after short term swine contact.
Genome Sequence of Saccharomyces cerevisiae Strain Kagoshima No. 2, Used for Brewing the Japanese Distilled Spirit Shōchū
Authors: Mori Kazuki , Kadooka Chihiro , Masuda Chika , Muto Ai , Okutsu Kayu , Yoshizaki Yumiko , Takamine Kazunori , Futagami Taiki , Tamaki Hisanori 
Published: October 2017

ABSTRACT

Here, we report a draft genome sequence of
Saccharomyces cerevisiae
strain Kagoshima no. 2, which is used for brewing shōchū, a traditional distilled spirit in Japan. The genome data will facilitate an understanding of the evolutional traits and genetic background related to the characteristic features of strain Kagoshima no. 2.
Genome Sequence of Pseudomonas putida Strain ASAD, an Acetylsalicylic Acid-Degrading Bacterium
Authors: Parales Rebecca E. , Navara Rachita , Gettys Rebecca , Huang Jean J. 
Published: October 2017

ABSTRACT

Pseudomonas putida
strain ASAD was isolated from compost because of its ability to utilize aspirin (acetylsalicylic acid) as a carbon and energy source. We report the draft genome sequence of strain ASAD, with an estimated length of 6.9 Mb. Study of this isolate will provide insight into the aspirin biodegradation pathway.
Synergistic divergence: case series and literature review
Authors: Awadein Ahmed , Zedan Rasha Hamdallah 
Published: October 2017

BackgroundTo present the data of a series of patients with synergistic divergence, to propose a different modality of surgical correction and to perform a literature review of such a rare entity.MethodsA retrospective study was performed on all patients who presented with unilateral or bilateral synergistic divergence to the Ophthalmology Department, Cairo University, during the period from January 2007 to July 2016. The demographic data, the results of sensorimotor examination, the surgical procedures performed and the ophthalmological as well as the systemic findings of all patients were collected and tabulated. PubMed was searched for patients with features of synergistic divergence.ResultsThirteen patients with features of synergistic divergence were identified. The mean age of the patients was 8.9±10.1 years (range 1–40 years). Only one case was orthotropic in the primary position. Lateral rectus orbital wall fixation combined with 8–10 mm medial rectus resection was done in 10 patients. The mean follow-up was 6.6±7.7 months. Exotropia was significantly reduced in all patients. All patients had complete disappearance of synergistic divergence after surgery. A total of 78 patients with features of synergistic divergence were identified from PubMed. Surgery was done for 37 patients. Synergistic divergence disappeared in patients who had lateral rectus extirpation or orbital wall fixation.ConclusionSynergistic divergence is a challenging rare condition. We propose that lateral rectus orbital wall fixation combined with medial rectus resection both improves the alignment in primary position and eliminates the synergistic divergence in such patients.
Global shortage of neonatal and paediatric antibiotic trials: rapid review
Authors: Thompson Georgina , Barker Charlotte I , Folgori Laura , Bielicki Julia A , Bradley John S , Lutsar Irja , Sharland Mike 
Published: October 2017

ObjectivesThere have been few clinical trials (CTs) on antibiotics that inform neonatal and paediatric drug labelling. The rate of unlicensed and off-label prescribing in paediatrics remains high. It is unclear whether the current neonatal and paediatric antibiotic research pipeline is adequate to inform optimal drug dosing. Using the ClinicalTrials.gov registry, this review aims to establish the current global status of antibiotic CTs in children up to 18 years of age.MethodsStudies were identified using key word searches of the ClinicalTrials.gov registry and were manually filtered using prespecified inclusion/exclusion criteria.Results76 registered open CTs of antibiotics in children were identified globally; 23 (30%) were recruiting newborns (only 8 (11%) included preterm neonates), 52 (68%) infants and toddlers, 58 (76%) children and 54 (71%) adolescents. The majority of registered trials were late phase (10 (15%) phase 3 and 23 (35%) phase 4/pharmacovigilance). Two-thirds were sponsored by non-profit organisations, compared with pharmaceutical companies (50 (66%) vs 26 (34%), respectively). A greater proportion of non-profit funded trials were efficacy-based strategic trials (n=34, 68%), in comparison with industry-led trials, which were most often focused on safety or pharmacokinetic data (n=17, 65%). Only 2 of the 37 antibiotics listed on the May 2016 Pew Charitable Trusts antibiotic development pipeline, currently being studied in adults, appear to be currently recruiting in open paediatric CTs.ConclusionsThis review highlights that very few paediatric antibiotic CTs are being conducted globally, especially in neonates. There is a striking disparity noted between antibiotic drug development programmes in adults and children.
Pre-emptive ice cube cryotherapy for reducing pain from local anaesthetic injections for simple lacerations: a randomised controlled trial
Authors: Song JaeWoo , Kim HyukHoon , Park EunJung , Ahn Jung Hwan , Yoon Eunhui , Lampotang Samsun , Gravenstein Nikolaus , Choi SangChun 
Published: October 2017

ObjectiveSubcutaneous local anaesthetic injection can be painful to patients in the ED. We evaluated the effect of cryotherapy by application of an ice cube to the injection site prior to injection in patients with simple lacerations.MethodsWe conducted a prospective, randomised, controlled trial in consented patients with simple lacerations needing primary repair at a single emergency centre from April to July 2016. We randomly assigned patients undergoing repair for simple lacerations to either the cryotherapy group or the control group (standard care; no cryotherapy or other pretreatment of the injection site). In cryotherapy group subjects, we applied an ice cube (size: 1.5×1.5×1.5 cm) placed inside a sterile glove on the wound at the anticipated subcutaneous lidocaine injection site for 2 min prior to injection. The primary outcome was a subjective numeric rating (0–10 scale) of the perceived pain from the subcutaneous local anaesthetic injections. Secondary outcomes were (a) perceived pain on a numeric scale for cryotherapy itself, that is, pain from contact of the ice cube/glove with the skin and (b) the rate of complications after primary laceration repair.ResultsFifty patients were enrolled, consented and randomised, with 25 in the cryotherapy group and 25 in the control group. The numeric rating scale for subcutaneous anaesthetic injections was median, IQR, 95% CI 2.0 (1 to 3.5), 1.81 to 3.47, respectively, in the cryotherapy group and 5.0 (3 to 7), 3.91 to 6.05 in the control group (Mann-Whitney U=147.50, p=0.001). No wound complications occurred in either group. The numeric rating scale for cryotherapy itself was median, IQR, 95% CI: 2.0 (1 to 3.5), 1.90 to 3.70.ConclusionPre-emptive topical injection site cryotherapy lasting 2 min before subcutaneous local anaesthetic injections can significantly reduce perceived pain from subcutaneous local anaesthetic injections in patients presenting for simple laceration repair.Trial registration numberKCT0001990.
Boxelder tree (Acer negundo) intoxication in fallow deer (Dama dama) and Dutch Landrace goats (Capra aegagrus hircus)
Authors: Bos Jan Herman , Kik Marja JL , van der Kolk Johannes H , IJzer Jooske 
Published: October 2017

Within 10 days of ingesting boxelder tree (Acer negundo) cuttings, seven fallow deer (Dama dama) died (n=2) or were euthanased (n=5) after showing signs of colic, anorexia and severe depression. Another fallow deer and two Dutch Landrace goats (Capra aegagrus hircus) simultaneously displayed colic signs but survived. Therapy included intramuscular flunixine meglumine. Postmortem investigation revealed subacute renal tubular necrosis and extensive lung oedema in all animals, and three deer had liver degeneration. The combination of clinical history and postmortem findings lead to the presumptive diagnosis of maple leaf intoxication as described in equids. This is the first report of likely boxelder tree (A negundo) intoxication in animals and the first report of maple leaf intoxication in fallow deer and goats.
A simple soundness proof for dependent object types
Authors: Rapoport Marianna , Kabir Ifaz , He Paul , Lhoták Ondřej 
Published: October 2017

Dependent Object Types (DOT) is intended to be a core calculus for modelling Scala. Its distinguishing feature is abstract type members, fields in objects that hold types rather than values. Proving soundness of DOT has been surprisingly challenging, and existing proofs are complicated, and reason about multiple concepts at the same time (e.g. types, values, evaluation). To serve as a core calculus for Scala, DOT should be easy to experiment with and extend, and therefore its soundness proof needs to be easy to modify.
This paper presents a simple and modular proof strategy for reasoning in DOT. The strategy separates reasoning about types from other concerns. It is centred around a theorem that connects the full DOT type system to a restricted variant in which the challenges and paradoxes caused by abstract type members are eliminated. Almost all reasoning in the proof is done in the intuitive world of this restricted type system. Once we have the necessary results about types, we observe that the other aspects of DOT are mostly standard and can be incorporated into a soundness proof using familiar techniques known from other calculi.
A volatile-by-default JVM for server applications
Authors: Liu Lun , Millstein Todd , Musuvathi Madanlal 
Published: October 2017

A *memory consistency model* (or simply *memory model*) defines the possible values that a shared-memory read may return in a multithreaded programming language. Choosing a memory model involves an inherent performance-programmability tradeoff. The Java language has adopted a *relaxed* (or *weak*) memory model that is designed to admit most traditional compiler optimizations and obviate the need for hardware fences on most shared-memory accesses. The downside, however, is that programmers are exposed to a complex and unintuitive semantics and must carefully declare certain variables as `volatile` in order to enforce program orderings that are necessary for proper behavior.
This paper proposes a simpler and stronger memory model for Java through a conceptually small change: *every* variable has `volatile` semantics by default, but the language allows a programmer to tag certain variables, methods, or classes as `relaxed` and provides the current Java semantics for these portions of code. This *volatile-by-default* semantics provides *sequential consistency* (SC) for all programs by default. At the same time, expert programmers retain the freedom to build performance-critical libraries that violate the SC semantics.
At the outset, it is unclear if the `volatile`-by-default semantics is practical for Java, given the cost of memory fences on today's hardware platforms. The core contribution of this paper is to demonstrate, through comprehensive empirical evaluation, that the `volatile`-by-default semantics is arguably acceptable for a predominant use case for Java today -- server-side applications running on Intel x86 architectures. We present VBD-HotSpot, a modification to Oracle's widely used HotSpot JVM that implements the `volatile`-by-default semantics for x86. To our knowledge VBD-HotSpot is the first implementation of SC for Java in the context of a modern JVM. VBD-HotSpot incurs an average overhead versus the baseline HotSpot JVM of 28% for the Da Capo benchmarks, which is significant though perhaps less than commonly assumed. Further, VBD-HotSpot incurs average overheads of 12% and 19% respectively on standard benchmark suites for big-data analytics and machine learning in the widely used Spark framework.
Model checking copy phases of concurrent copying garbage collection with various memory models
Authors: Ugawa Tomoharu , Abe Tatsuya , Maeda Toshiyuki 
Published: October 2017

Modern concurrent copying garbage collection (GC), in particular, real-time GC, uses fine-grained synchronizations with a mutator, which is the application program that mutates memory, when it moves objects in its copy phase. It resolves a data race using a concurrent copying protocol, which is implemented as interactions between the collector threads and the read and write barriers that the mutator threads execute. The behavioral effects of the concurrent copying protocol rely on the memory model of the CPUs and the programming languages in which the GC is implemented. It is difficult, however, to formally investigate the behavioral properties of concurrent copying protocols against various memory models.
To address this problem, we studied the feasibility of the bounded model checking of concurrent copying protocols with memory models. We investigated a correctness-related behavioral property of copying protocols of various concurrent copying GC algorithms, including real-time GC Stopless, Clover, Chicken, Staccato, and Schism against six memory models, total store ordering (TSO), partial store ordering (PSO), relaxed memory ordering (RMO), and their variants, in addition to sequential consistency (SC) using bounded model checking. For each combination of a protocol and memory model, we conducted model checking with a model of a mutator. In this wide range of case studies, we found faults in two GC algorithms, one of which is relevant to the memory model. We fixed these faults with the great help of counterexamples. We also modified some protocols so that they work under some memory models weaker than those for which the original protocols were designed, and checked them using model checking. We believe that bounded model checking is a feasible approach to investigate behavioral properties of concurrent copying protocols under weak memory models.