bluuebunny/crossref_metadata_2025_split huggingface dataset:
Comparison CCEM-K4.2017 of 10 pF and 100 pF capacitance standards
Authors: Gournay P , Rolland B , Chayramy R , Overney F , Yang Y , Huang L , Lu Z , Wang Y , Koffman A , Johnson L , Xie R , Belliss J , Giblin S , Thornton B , Schurr J , Lee J , Semenov Y 
Published: November 2018

In 2017 the Consultative Committee for Electricity and Magnetism (CCEM) commissioned a key comparison of electrical capacitance standards, the second time this quantity has been compared since the implementation of the Mutual Recognition Agreement by the Comité International des Poids et Mesures (CIPM—MRA) in 1999. This comparison—CCEM-K4.2017—was piloted by the Bureau International des Poids et Mesures (BIPM) and included seven National Metrology Institutes (NMI) belonging to four Regional Metrology Organizations.
The measuring scheme adopted for the comparison was that of a star comparison consisting of a set of bilateral comparisons between the participating NMIs and the BIPM, whose capacitance reference base served as a common reference. For each of the bilateral comparisons, the measurands were the capacitance values of 10 pF travelling standard capacitors belonging to the NMIs and, optionally, the values of 100 pF standards.
All the participants have been chosen from those able to realize and maintain a representation of the farad at the best known level of accuracy. Four of them, including the BIPM, were taking their traceability from dc or ac quantum Hall effect standards and, the four others, from a calculable capacitor.
The comparison results analysis have evidenced an agreement within about ±5 parts in 108 for the mandatory 10 pF measurements and within about ±10 parts in 108 for the optional 100 pF measurements. Also, excepted for one of the participants, a good agreement has been found for the ratio 100 pF:10 pF (within ±5 parts in 108).
In addition to the comparison, it has been possible to evaluate the difference between the value of R
K (von Klitzing constant) measured by electrical means from calculable capacitors and its last CODATA recommended value (CODATA 2014 adjustment). A difference of (43 ± 23) parts in 109 (k = 1) has been found which is consistent with the difference that can be computed from the experimental data used in the CODATA 2014 adjustment of fundamental constants.
This report presents the details of the measurements and analysis having led to these results.

Main text

To reach the main text of this paper, click on Final Report. Note that this text is that which appears in Appendix B of the BIPM key comparison database kcdb.bipm.org/.
The final report has been peer-reviewed and approved for publication by the CCEM, according to the provisions of the CIPM Mutual Recognition Arrangement (CIPM MRA).
DiTaxa: nucleotide-pair encoding of 16S rRNA for host phenotype and biomarker detection
Authors: Asgari Ehsaneddin , Münch Philipp C , Lesker Till R , McHardy Alice C , Mofrad Mohammad R K 
Published: November 2018

Abstract

Summary
Identifying distinctive taxa for micro-biome-related diseases is considered key to the establishment of diagnosis and therapy options in precision medicine and imposes high demands on the accuracy of micro-biome analysis techniques. We propose an alignment- and reference- free subsequence based 16S rRNA data analysis, as a new paradigm for micro-biome phenotype and biomarker detection. Our method, called DiTaxa, substitutes standard operational taxonomic unit (OTU)-clustering by segmenting 16S rRNA reads into the most frequent variable-length subsequences. We compared the performance of DiTaxa to the state-of-the-art methods in phenotype and biomarker detection, using human-associated 16S rRNA samples for periodontal disease, rheumatoid arthritis and inflammatory bowel diseases, as well as a synthetic benchmark dataset. DiTaxa performed competitively to the k-mer based state-of-the-art approach in phenotype prediction while outperforming the OTU-based state-of-the-art approach in finding biomarkers in both resolution and coverage evaluated over known links from literature and synthetic benchmark datasets.

Availability and implementation
DiTaxa is available under the Apache 2 license at http://llp.berkeley.edu/ditaxa.

Supplementary information
Supplementary data are available at Bioinformatics online.
CRISPR-Local: a local single-guide RNA (sgRNA) design tool for non-reference plant genomes
Authors: Sun Jiamin , Liu Hao , Liu Jianxiao , Cheng Shikun , Peng Yong , Zhang Qinghua , Yan Jianbing , Liu Hai-Jun , Chen Ling-Ling 
Published: November 2018

Abstract

Summary
CRISPR-Local is a high-throughput local tool for designing single-guide RNAs (sgRNAs) in plants and other organisms that factors in genetic variation and is optimized to generate genome-wide sgRNAs. CRISPR-Local outperforms other sgRNA design tools in the following respects: (i) designing sgRNAs suitable for non-reference varieties; (ii) screening for sgRNAs that are capable of simultaneously targeting multiple genes; (iii) saving computational resources by avoiding repeated calculations from multiple submissions and (iv) running offline, with both command-line and graphical user interface modes and the ability to export multiple formats for further batch analysis or visualization. We have applied CRISPR-Local to 71 public plant genomes, using both CRISPR/Cas9 and CRISPR/cpf1 systems.

Availability and implementation
CRISPR-Local can be freely downloaded from http://crispr.hzau.edu.cn/CRISPR-Local/.

Supplementary information
Supplementary data are available at Bioinformatics online.
Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters
Authors: Casto Amanda M , Adler Amanda L , Makhsous Negar , Crawford Kristen , Qin Xuan , Kuypers Jane M , Huang Meei-Li , Zerr Danielle M , Greninger Alexander L 
Published: November 2018

Abstract

Background
Norovirus outbreaks in hospital settings are a common challenge for infection prevention teams. Given the high burden of norovirus in most communities, it can be difficult to distinguish between ongoing in-hospital transmission of the virus and new introductions from the community, and it is challenging to understand the long-term impacts of outbreak-associated viruses within medical systems using traditional epidemiological approaches alone.

Methods
Real-time metagenomic sequencing during an ongoing norovirus outbreak associated with a retrospective cohort study.

Results
We describe a hospital-associated norovirus outbreak that affected 13 patients over a 27-day period in a large, tertiary, pediatric hospital. The outbreak was chronologically associated with a spike in self-reported gastrointestinal symptoms among staff. Real-time metagenomic next-generation sequencing (mNGS) of norovirus genomes demonstrated that 10 chronologically overlapping, hospital-acquired norovirus cases were partitioned into 3 discrete transmission clusters. Sequencing data also revealed close genetic relationships between some hospital-acquired and some community-acquired cases. Finally, this data was used to demonstrate chronic viral shedding by an immunocompromised, hospital-acquired case patient. An analysis of serial samples from this patient provided novel insights into the evolution of norovirus within an immunocompromised host.

Conclusions
This study documents one of the first applications of real-time mNGS during a hospital-associated viral outbreak. Given its demonstrated ability to detect transmission patterns within outbreaks and elucidate the long-term impacts of outbreak-associated viral strains on patients and medical systems, mNGS constitutes a powerful resource to help infection control teams understand, prevent, and respond to viral outbreaks.
SMRT long reads and Direct Label and Stain optical maps allow the generation of a high-quality genome assembly for the European barn swallow (Hirundo rustica rustica)
Authors: Formenti Giulio , Chiara Matteo , Poveda Lucy , Francoijs Kees-Jan , Bonisoli-Alquati Andrea , Canova Luca , Gianfranceschi Luca , Horner David Stephen , Saino Nicola 
Published: November 2018

Abstract

Background
The barn swallow (Hirundo rustica) is a migratory bird that has been the focus of a large number of ecological, behavioral, and genetic studies. To facilitate further population genetics and genomic studies, we present a reference genome assembly for the European subspecies (H. r. rustica).

Findings
As part of the Genome10K effort on generating high-quality vertebrate genomes (Vertebrate Genomes Project), we have assembled a highly contiguous genome assembly using single molecule real-time (SMRT) DNA sequencing and several Bionano optical map technologies. We compared and integrated optical maps derived from both the Nick, Label, Repair, and Stain technology and from the Direct Label and Stain (DLS) technology. As proposed by Bionano, DLS more than doubled the scaffold N50 with respect to the nickase. The dual enzyme hybrid scaffold led to a further marginal increase in scaffold N50 and an overall increase of confidence in the scaffolds. After removal of haplotigs, the final assembly is approximately 1.21 Gbp in size, with a scaffold N50 value of more than 25.95 Mbp.

Conclusions
This high-quality genome assembly represents a valuable resource for future studies of population genetics and genomics in the barn swallow and for studies concerning the evolution of avian genomes. It also represents one of the very first genomes assembled by combining SMRT long-read sequencing with the new Bionano DLS technology for scaffolding. The quality of this assembly demonstrates the potential of this methodology to substantially increase the contiguity of genome assemblies.
Forcing and satisfaction in Kripke models of intuitionistic arithmetic
Authors: Abiri Maryam , Moniri Morteza , Zaare Mostafa 
Published: November 2018

Abstract
We define a class of first-order formulas $\mathsf{P}^{\ast }$ which exactly contains formulas $\varphi$ such that satisfaction of $\varphi$ in any classical structure attached to a node of a Kripke model of intuitionistic predicate logic deciding atomic formulas implies its forcing in that node. We also define a class of $\mathsf{E}$-formulas with the property that their forcing coincides with their classical satisfiability in Kripke models which decide atomic formulas. We also prove that any formula with this property is an $\mathsf{E}$-formula. Kripke models of intuitionistic arithmetical theories usually have this property. As a consequence, we prove a new conservativity result for Peano arithmetic over Heyting arithmetic.
Two-Tier Lyme Disease Serology Test Results Can Vary According to the Specific First-Tier Test Used
Authors: Maulden Alexandra B , Garro Aris C , Balamuth Fran , Levas Michael N , Bennett Jonathan E , Neville Desiree N , Branda John A , Nigrovic Lise E 
Published: November 2018

Abstract

Background
Variability in 2-tier Lyme disease test results according to the specific first-tier enzyme immunoassay (EIA) in children has not been examined rigorously. In this study, we compared paired results of clinical 2-tier Lyme disease tests to those of the C6 peptide EIA followed by supplemental immunoblotting (C6 2-tier test).

Methods
We performed a prospective cohort study of children aged ≥1 to ≤21 years who were undergoing evaluation for Lyme disease in the emergency department at 1 of 6 centers located in regions in which Lyme disease is endemic. The clinical first-tier test and a C6 EIA were performed on the same serum sample with supplemental immunoblotting if the first-tier test result was either positive or equivocal. We compared the results of the paired clinical and C6 2-tier Lyme disease test results using the McNemar test.

Results
Of the 1714 children enrolled, we collected a research serum sample from 1584 (92.4%). The clinical 2-tier EIA result was positive in 316 (19.9%) children, and the C6 2-tier test result was positive or equivocal in 295 (18.6%) children. The clinical and C6 2-tier test results disagreed more often than they would have by chance alone (P = .002). Of the 39 children with either a positive clinical or C6 2-tier test result alone, 2 children had an erythema migrans (EM) lesion, and 29 had symptoms compatible with early disseminated Lyme disease.

Conclusions
Two-tier Lyme disease test results differed for a substantial number of children on the basis of the specific first-tier test used. In children for whom there is a high clinical suspicion for Lyme disease and who have an initially negative test result, clinicians should consider retesting for Lyme disease.
Function words in statistical machine-translated Chinese and original Chinese: A study into the translationese of machine translation systems
Authors: Kuo Chen-li 
Published: November 2018

AbstractStatistical approaches have become the mainstream in machine translation (MT), for their potential in producing less rigid and more natural translations than rule-based approaches. However, on closer examination, the uses of function words between statistical machine-translated Chinese and the original Chinese are different, and such differences may be associated with translationese as discussed in translation studies. This article examines the distribution of Chinese function words in a comparable corpus consisting of MTs and the original Chinese texts extracted from Wikipedia. An attribute selection technique is used to investigate which types of function words are significant in discriminating between statistical machine-translated Chinese and the original texts. The results show that statistical MT overuses the most frequent function words, even when alternatives exist. To improve the quality of the end product, developers of MT should pay close attention to modelling Chinese conjunctions and adverbial function words. The results also suggest that machine-translated Chinese shares some characteristics with human-translated texts, including normalization and being influenced by the source language; however, machine-translated texts do not exhibit other characteristics of translationese such as explicitation.
Tenofovir Alafenamide in Multimorbid HIV-Infected Patients With Prior Tenofovir-Associated Renal Toxicity
Authors: Walti Laura N , Steinrücken Julia , Rauch Andri , Wandeler Gilles 
Published: November 2018

AbstractAlthough the use of tenofovir alafenamide (TAF), a new prodrug of tenofovir, was safe and efficacious in clinical trials, real-world data from multimorbid individuals are scarce. Among 10 persons living with HIV with previous tenofovir disoproxil fumarate–induced nephrotoxicity, renal function remained stable, and proteinuria decreased in several patients after the switch to TAF.
Running in the Family? Structural Brain Abnormalities and IQ in Offspring, Siblings, Parents, and Co-twins of Patients with Schizophrenia
Authors: de Zwarte Sonja M C , Brouwer Rachel M , Tsouli Andromachi , Cahn Wiepke , Hillegers Manon H J , Hulshoff Pol Hilleke E , Kahn René S , van Haren Neeltje E M 
Published: November 2018

Abstract
Structural brain abnormalities and cognitive deficits have been reported in patients with schizophrenia and to a lesser extent in their first-degree relatives (FDRs). Here we investigated whether brain abnormalities in nonpsychotic relatives differ per type of FDR and how these abnormalities are related to intelligent quotient (IQ). Nine hundred eighty individuals from 5 schizophrenia family cohorts (330 FDRs, 432 controls, 218 patients) were included. Effect sizes were calculated to compare brain measures of FDRs and patients with controls, and between each type of FDR. Analyses were repeated with a correction for IQ, having a nonpsychotic diagnosis, and intracranial volume (ICV). FDRs had significantly smaller ICV, surface area, total brain, cortical gray matter, cerebral white matter, cerebellar gray and white matter, thalamus, putamen, amygdala, and accumbens volumes as compared with controls (ds < −0.19, q < 0.05 corrected). Offspring showed the largest effect sizes relative to the other FDRs; however, none of the effects in the different relative types survived correction for multiple comparisons. After IQ correction, all effects disappeared in the FDRs after correction for multiple comparisons. The findings in FDRs were not explained by having a nonpsychotic disorder and were only partly explained by ICV. FDRs show brain abnormalities that are strongly covarying with IQ. On the basis of consistent evidence of genetic overlap between schizophrenia, IQ, and brain measures, we suggest that the brain abnormalities in FDRs are at least partly explained by genes predisposing to both schizophrenia risk and IQ.
Examining the external validity of the CRUZA study, a randomized trial to promote implementation of evidence-based cancer control programs by faith-based organizations
Authors: Allen Jennifer Dacey , Shelton Rachel C , Kephart Lindsay , Tom Laura S , Leyva Bryan , Ospino Hosffman , Cuevas Adolfo G 
Published: November 2018

Abstract
The CRUZA trial tested the efficacy of an organizational-level intervention to increase capacity among Catholic parishes to implement evidence-based interventions (EBIs) for cancer control. This paper examines the external generalizability of the CRUZA study findings by comparing characteristics of parishes that agreed to participate in the intervention trial versus those that declined participation. Sixty-five Roman Catholic parishes that offered Spanish-language mass in Massachusetts were invited to complete a four-part survey assessing organization-level characteristics that, based on the Consolidated Framework for Implementation Research (CFIR), may be associated with EBI implementation. Forty-nine parishes (75%) completed the survey and were invited to participate in the CRUZA trial, which randomized parishes to either a “capacity enhancement intervention” or a “standard dissemination” group. Of these 49 parishes, 31 (63%) agreed to participate in the trial, whereas 18 parishes (37%) declined participation. Parishes that participated in the CRUZA intervention trial were similar to those that did not participate with respect to “inner organizational setting” characteristics of the CFIR, including innovation and values fit, implementation climate, and organizational culture. Change commitment, a submeasure of organizational readiness that reflects the shared resolve of organizational members to implement an innovation, was significantly higher among the participating parishes (mean = 3.93, SD = 1.08) as compared to nonparticipating parishes (mean = 3.27, SD = 1.08) (Z = −2.16, p = .03). Parishes that agreed to participate in the CRUZA intervention trial were similar to those that declined participation with regard to organizational characteristics that may predict implementation of EBIs. Pragmatic tools to assess external generalizability in community-based implementation trials and to promote readiness among faith-based organizations to implement EBIs are needed to enhance the reach and impact of public health research.
Clinical Trial information: The CRUZA trial identifier number with clinicaltrials.gov is NCT01740219.
Transient Receptor Potential Ion Channels Mediate Adherens Junctions Dysfunction in a Toluene Diisocyanate-Induced Murine Asthma Model
Authors: Yao Lihong , Chen Shuyu , Tang Haixiong , Huang Peikai , Wei Shushan , Liang Zhenyu , Chen Xin , Wang Hongyu , Tao Ailin , Chen Rongchang , Zhang Qingling 
Published: November 2018

Abstract
Disruption of epithelial cell-cell junctions is essential for the initiation and perpetuation of airway inflammation in asthma. We’ve previously reported compromised epithelial barrier integrity in a toluene diisocyanate (TDI)-induced occupational asthma model. This study is aimed to explore the role of transient receptor potential vanilloid 4 (TRPV4) and transient receptor potential ankyrin 1 (TRPA1) in the dysfunction of adherens junctions in TDI-induced asthma. Mice were sensitized and challenged with TDI for a chemical-induced asthma model. Selective blockers of TRPV4 glycogen synthase kinase (GSK)2193874, 5 and 10 mg/kg) and TRPA1 (HC030031, 10 and 20 mg/kg) were intraperitoneally given to the mice. Immunohistochemistry revealed different expression pattern of TRPV4 and TRPA1 in lung. TDI exposure increased TRPV4 expression in the airway, which can be suppressed by GSK2193874, while treatment with neither TDI alone nor TDI together with HC030031 led to changes of TRPA1 expression in the lung. Blocking either TRPV4 or TRPA1 blunted TDI-induced airway hyperreactivity, airway neutrophilia and eosinophilia, as well as Th2 responses in a dose-dependent manner. At the same time, membrane levels of E-cadherin and β-catenin were significantly decreased after TDI inhalation, which were inhibited by GSK2193874 or HC030031. Moreover, GSK2193874 and HC030031 also suppressed serine phosphorylation of glycogen synthase kinase 3β, tyrosine phosphorylation of β-catenin, as well as activation and nuclear transport of β-catenin in mice sensitized and challenged with TDI. Our study suggested that both TRPV4 and TRPA1 contribute critically to E-cadherin and β-catenin dysfunction in TDI-induced asthma, proposing novel therapeutic targets for asthma.
Histopathological and Molecular Signatures of a Mouse Model of Acute-on-Chronic Alcoholic Liver Injury Demonstrate Concordance With Human Alcoholic Hepatitis
Authors: Furuya Shinji , Cichocki Joseph A , Konganti Kranti , Dreval Kostiantyn , Uehara Takeki , Katou Yuuki , Fukushima Hisataka , Kono Hiroshi , Pogribny Igor P , Argemi Josepmaria , Bataller Ramon , Rusyn Ivan 
Published: November 2018

Abstract
Human alcoholic hepatitis (AH) carries a high mortality rate. AH is an acute-on-chronic form of liver injury characterized by hepatic steatosis, ballooned hepatocytes, neutrophil infiltration, and pericellular fibrosis. We aimed to study the pathogenesis of AH in an animal model which combines chronic hepatic fibrosis with intragastric alcohol administration. Adult male C57BL6/J mice were treated with CCl4 (0.2 ml/kg, 2×weekly by intraperitoneal injections for 6 weeks) to induce chronic liver fibrosis. Then, ethyl alcohol (up to 25 g/kg/day for 3 weeks) was administered continuously to mice via a gastric feeding tube, with or without one-half dose of CCl4. Liver and serum markers and liver transcriptome were evaluated to characterize acute-on-chronic-alcoholic liver disease in our model. CCl4 or alcohol treatment alone induced liver fibrosis or steatohepatitis, respectively, findings that were consistent with expected pathology. Combined treatment resulted in a marked exacerbation of liver injury, as evident by the development of inflammation, steatosis, and pericellular fibrosis, pathological features of human AH. E. coli and Candida were also detected in livers of mice cotreated with CCl4 and alcohol, indicating pathogen translocation from gut to liver, similar to human AH. Importantly, liver transcriptomic changes specific to combined treatment group demonstrated close concordance with pathways perturbed in patients with severe AH. Overall, mice treated with CCl4 and alcohol displayed key molecular and pathological characteristics of human AH—pericellular fibrosis, increased hepatic bacterial load, and dysregulation of the same molecular pathways. This model may be useful for developing therapeutics for AH.
Should we be targeting sleep architecture to more effectively treat schizophrenia?
Authors: Luu Brent , Rodway George W. , Rice Elizabeth 
Published: November 2018

ABSTRACT
The sleep architecture (or sleep kinetics) of schizophrenia is different from that of other mental illnesses, including major depressive disorder. However, clinicians rarely consider these parameters in clinical settings during treatment. This article discusses the use of polysomnography to characterize the sleeping patterns of patients diagnosed with schizophrenia and the positive influence of clozapine on sleep in patients with schizophrenia.