bluuebunny/crossref_metadata_2025_split huggingface dataset:
Quasimetagenomics-Based and Real-Time-Sequencing-Aided Detection and Subtyping of Salmonella enterica from Food Samples
Authors: Hyeon Ji-Yeon , Li Shaoting , Mann David A. , Zhang Shaokang , Li Zhen , Chen Yi , Deng Xiangyu 
Published: December 2017

ABSTRACT

Metagenomics analysis of food samples promises isolation-independent detection and subtyping of foodborne bacterial pathogens in a single workflow. The selective concentration of
Salmonella
genomic DNA by immunomagnetic separation (IMS) and multiple displacement amplification (MDA) shortened the time for culture enrichment of
Salmonella
-spiked raw chicken breast samples by over 12 h while permitting serotyping and high-fidelity single nucleotide polymorphism (SNP) typing of the pathogen using short shotgun sequencing reads. The herein-termed quasimetagenomics approach was evaluated on
Salmonella
-spiked lettuce and black peppercorn samples as well as retail chicken parts naturally contaminated with different serotypes of
Salmonella
. Culture enrichment of between 8 and 24 h was required for detecting and subtyping naturally occurring
Salmonella
from unspiked chicken parts compared with 4- to 12-h culture enrichment when
Salmonella
-spiked food samples were analyzed, indicating the likely need for longer culture enrichment to revive low levels of stressed or injured
Salmonella
cells in food. A further acceleration of the workflow was achieved by real-time nanopore sequencing. After 1.5 h of analysis on a potable sequencer, sufficient data were generated from sequencing the IMS-MDA products of a cultured-enriched lettuce sample to enable serotyping and robust phylogenetic placement of the inoculated isolate.

IMPORTANCE
Both culture enrichment and next-generation sequencing remain time-consuming processes for food testing, whereas rapid methods for pathogen detection are widely available. Our study demonstrated a substantial acceleration of these processes by the use of immunomagnetic separation (IMS) with multiple displacement amplification (MDA) and real-time nanopore sequencing. In one example, the combined use of the two methods delivered a less than 24-h turnaround time from the collection of a
Salmonella
-contaminated lettuce sample to the phylogenetic identification of the pathogen. An improved efficiency such as this is important for further expanding the use of whole-genome and metagenomics sequencing in the microbial analysis of food. Our results suggest the potential of the quasimetagenomics approach in areas where rapid detection and subtyping of foodborne pathogens are important, such as for foodborne outbreak response and the precision tracking and monitoring of foodborne pathogens in production environments and supply chains.
Poly-3-Hydroxybutyrate Functionalization with BioF-Tagged Recombinant Proteins
Authors: Bello-Gil Daniel , Maestro Beatriz , Fonseca Jennifer , Dinjaski Nina , Prieto M. Auxiliadora , Sanz Jesús M. 
Published: December 2017

ABSTRACT

Polyhydroxyalkanoates (PHAs) are biodegradable polyesters that accumulate in the cytoplasm of certain bacteria. One promising biotechnological application utilizes these biopolymers as supports for protein immobilization. Here, the PHA-binding domain of the
Pseudomonas putida
KT2440 PhaF phasin (BioF polypeptide) was investigated as an affinity tag for the
in vitro
functionalization of poly-3-hydroxybutyrate (PHB) particles with recombinant proteins, namely, full-length PhaF and two fusion proteins tagged to BioF (BioF–C-LytA and BioF–β-galactosidase, containing the choline-binding module C-LytA and the β-galactosidase enzyme, respectively). The protein-biopolyester interaction was strong and stable at a wide range of pHs and temperatures, and the bound protein was highly protected from self-degradation, while the binding strength could be modulated by coating with amphiphilic compounds. Finally, BioF–β-galactosidase displayed very stable enzymatic activity after several continuous activity-plus-washing cycles when immobilized in a minibioreactor. Our results demonstrate the potentialities of PHA and the BioF tag for the construction of novel bioactive materials.

IMPORTANCE
Our results confirm the biotechnological potential of the BioF affinity tag as a versatile tool for functionalizing PHA supports with recombinant proteins, leading to novel bioactive materials. The wide substrate range of the BioF tag presumably enables protein immobilization
in vitro
of virtually all natural PHAs as well as blends, copolymers, or artificial chemically modified derivatives with novel physicochemical properties. Moreover, the strength of protein adsorption may be easily modulated by varying the coating of the support, providing new perspectives for the engineering of bioactive materials that require a tight control of protein loading.
Draft Genome Sequence of Leuconostoc citreum CW28 Isolated from Pozol, a Pre-Hispanic Fermented Corn Beverage
Authors: Olvera Clarita , Santamaría Rosa I. , Bustos Patricia , Vallejo Cristina , Montor Juan J. , Wacher Carmen , Lopez Munguia Agustín 
Published: December 2017

ABSTRACT

Leuconostoc citreum
CW28 was isolated from pozol, a Mayan fermented corn beverage. This strain produces a cell-associated inulosucrase, the first described in bacteria. Its draft genome sequence, announced here, has an estimated size of 1.98 Mb and harbors 1,915 coding genes, 12 rRNAs, 68 tRNAs, 17 putative pseudogenes, and 1 putative phage.
Genome Sequence of Bacillus velezensis S141, a New Strain of Plant Growth-Promoting Rhizobacterium Isolated from Soybean Rhizosphere
Authors: Sibponkrung Surachat , Kondo Takahiko , Tanaka Kosei , Tittabutr Panlada , Boonkerd Nantakorn , Teaumroong Neung , Yoshida Ken-ichi 
Published: December 2017

ABSTRACT

Bacillus velezensis
strain S141 is a plant growth-promoting rhizobacterium isolated from soybean (
Glycine max
) rhizosphere that enhances soybean growth, nodulation, and N
2
fixation efficiency by coinoculation with
Bradyrhizobium diazoefficiens
USDA110. The S141 genome was identified to comprise a 3,974,582-bp-long circular DNA sequence encoding at least 3,817 proteins.
Complete Chromosome Sequence of a Mycolactone-Producing Mycobacterium, Mycobacterium pseudoshottsii
Authors: Yoshida Mitsunori , Miyamoto Yuji , Ogura Yoshitoshi , Hayashi Tetsuya , Hoshino Yoshihiko 
Published: December 2017

ABSTRACT

Mycobacterium pseudoshottsii
is a fish pathogen that produces mycolactone. Here, we report the complete chromosome sequence of a type strain of
M. pseudoshottsii
(JCM 15466). The sequence will represent essential data for future phylogenetic and comparative genome studies of mycolactone-producing mycobacteria.
Complete Genome Sequence of Lactobacillus plantarum 10CH, a Potential Probiotic Lactic Acid Bacterium with Potent Antimicrobial Activity
Authors: El Halfawy Nancy M. , El-Naggar Moustafa Y. , Andrews Simon C. 
Published: December 2017

ABSTRACT

Lactobacillus plantarum
10CH is a bacteriocin-producing potential probiotic lactic acid bacterium (LAB) strain isolated from cheese. Its complete nucleotide sequence shows a single circular chromosome of 3.3 Mb, with a G+C content of 44.51%, a 25-gene plantaricin bacteriocin gene cluster, and the absence of recognized virulence factors.
Usage of unscheduled hospital care by homeless individuals in Dublin, Ireland: a cross-sectional study
Authors: Ní Cheallaigh Clíona , Cullivan Sarah , Sears Jess , Lawlee Ann Marie , Browne Joe , Kieran Jennifer , Segurado Ricardo , O’Carroll Austin , O’Reilly Fiona , Creagh Donnacha , Bergin Colm , Kenny Rose Anne , Byrne Declan 
Published: December 2017

ObjectivesHomeless people lack a secure, stable place to live and experience higher rates of serious illness than the housed population. Studies, mainly from the USA, have reported increased use of unscheduled healthcare by homeless individuals.We sought to compare the use of unscheduled emergency department (ED) and inpatient care between housed and homeless hospital patients in a high-income European setting in Dublin, Ireland.SettingA large university teaching hospital serving the south inner city in Dublin, Ireland. Patient data are collected on an electronic patient record within the hospital.ParticipantsWe carried out an observational cross-sectional study using data on all ED visits (n=47 174) and all unscheduled admissions under the general medical take (n=7031) in 2015.Primary and secondary outcome measuresThe address field of the hospital’s electronic patient record was used to identify patients living in emergency accommodation or rough sleeping (hereafter referred to as homeless). Data on demographic details, length of stay and diagnoses were extracted.ResultsIn comparison with housed individuals in the hospital catchment area, homeless individuals had higher rates of ED attendance (0.16 attendances per person/annum vs 3.0 attendances per person/annum, respectively) and inpatient bed days (0.3 vs 4.4 bed days/person/annum). The rate of leaving ED before assessment was higher in homeless individuals (40% of ED attendances vs 15% of ED attendances in housed individuals). The mean age of homeless medical inpatients was 44.19 years (95% CI 42.98 to 45.40), whereas that of housed patients was 61.20 years (95% CI 60.72 to 61.68). Homeless patients were more likely to terminate an inpatient admission against medical advice (15% of admissions vs 2% of admissions in homeless individuals).ConclusionHomeless patients represent a significant proportion of ED attendees and medical inpatients. In contrast to housed patients, the bulk of usage of unscheduled care by homeless people occurs in individuals aged 25–65 years.
Is the admission test for a course in medicine a good predictor of academic performance? A case−control experience at the school of medicine of Turin
Authors: Migliaretti Giuseppe , Bozzaro Salvatore , Siliquini Roberta , Stura Ilaria , Costa Giuseppe , Cavallo Franco 
Published: December 2017

ObjectivesThe usefulness of university admission tests to medical schools has been discussed in recent years. In the academic year 2014–15 in Italy, several students who failed the admission test appealed to the regional administrative court (‘Tribunale Amministrativo Regionale’—TAR) requesting to be included, despite their test results, and all were admitted to their respective courses. The existence of this population of students generated a control group, in order to evaluate the predictive capacity of the admission test. The aim of the present work is to discuss the ability of university admission tests to predict subsequent academic success.Setting and participantsThe study involved 683 students who enrolled onto the first year of the degree course in medicine in the academic year 2014–15 at the University of Turin (Molinette and San Luigi Gonzaga colleges). The students were separated into two categories: those who passed the admission test (n1=531) and those who did not pass the admission test but won their appeal in the TAR (n2=152).OutcomesThe validity of the admission test was analysed using specificity, sensitivity, positive and negative likelihood ratios (LH+, LH−), receiver operating characteristic (ROC) curves, area under the ROC curve (AUC), and relative (95% CI).ResultsThe results showed that the admission test appeared to be a good tool for predicting the academic performances in the first year of the course (AUC=0.70, 95% CI 0.64 to 0.76). Moreover, some subject areas seemed to have a greater discriminating capacity than others. In general, students who obtained a high score in scientific questions were more likely to obtain the required standards during the first year (LH+ 1.22, 95% CI 1.14 to 1.25).ConclusionsBased on a consistent statistical approach, our study seems to confirm the ability of the admission test to predict academic success in the first year at the school of medicine of Turin.
Garbage collection and efficiency in dynamic metacircular runtimes: an experience report
Authors: Pimás Javier , Burroni Javier , Arnaud Jean Baptiste , Marr Stefan 
Published: December 2017

In dynamic object-oriented languages, low-level mechanisms such as just-in-time compilation, object allocation, garbage collection (GC) and method dispatch are often handled by virtual machines (VMs). VMs are typically implemented using static languages, allowing only few changes at run time. In such systems, the VM is not part of the language and interfaces to memory management or method dispatch are fixed, not allowing for arbitrary adaptation. Furthermore, the implementation can typically not be inspected or debugged with standard tools used to work on application code.
This paper reports on our experience building Bee, a dynamic Smalltalk runtime, written in Smalltalk. Bee is a Dynamic Metacircular Runtime (DMR) and seamlessly integrates the VM into the application and thereby overcomes many restrictions of classic VMs, for instance by allowing arbitrary code modifications of the VM at run time. Furthermore, the approach enables developers to use their standard tools for application code also for the VM, allowing them to inspect, debug, understand, and modify a DMR seamlessly.
We detail our experience of implementing GC, compilation, and optimizations in a DMR. We discuss examples where we found that DMRs can improve understanding of the system, provide tighter control of the software stack, and facilitate research. We also show that the Bee DMR matches and surpass the performance of a widely used Smalltalk VM.
Quoted staged rewriting: a practical approach to library-defined optimizations
Authors: Parreaux Lionel , Shaikhha Amir , Koch Christoph E. 
Published: December 2017

Staging has proved a successful technique for programmatically removing code abstractions, thereby allowing for faster program execution while retaining a high-level interface for the programmer. Unfortunately, techniques based on staging suffer from a number of problems — ranging from practicalities to fundamental limitations — which have prevented their widespread adoption. We introduce Quoted Staged Rewriting (QSR), an approach that uses type-safe, pattern matching-enabled quasiquotes to define optimizations. The approach is “staged” in two ways: first, rewrite rules can execute arbitrary code during pattern matching and code reconstruction, leveraging the power and flexibility of staging; second, library designers can orchestrate the application of successive rewriting phases (stages). The advantages of using quasiquote-based rewriting are that library designers never have to deal directly with the intermediate representation (IR), and that it allows for non-intrusive optimizations — in contrast with staging, it is not necessary to adapt the entire library and user programs to accommodate optimizations.
We show how Squid, a Scala macro-based framework, enables QSR and renders library-defined optimizations more practical than ever before: library designers write domain-specific optimizers that users invoke transparently on delimited portions of their code base. As a motivating example we describe an implementation of stream fusion (a well-known deforestation technique) that is both simpler and more powerful than the state of the art, and can readily be used by Scala programmers with no knowledge of metaprogramming.
Type qualifiers as composable language extensions
Authors: Carlson Travis , Van Wyk Eric 
Published: December 2017

This paper reformulates type qualifiers as language extensions that can be automatically and reliably composed. Type qualifiers annotate type expressions to introduce new subtyping relations and are powerful enough to detect many kinds of errors. Type qualifiers, as illustrated in our ableC extensible language framework for C, can introduce rich forms of concrete syntax, can generate dynamic checks on data when static checks are infeasible or not appropriate, and inject code that affects the program's behavior, for example for conversions of data or logging.
ableC language extensions to C are implemented as attribute grammar fragments and provide an expressive mechanism for type qualifier implementations to check for additional errors, e.g. dereferences to pointers not qualified by a "nonnull" qualifier, and report custom error messages. Our approach distinguishes language extension users from developers and provides modular analyses to developers to ensure that when users select a set of extensions to use, they will automatically compose to form a working compiler.
Oral Microbiome Composition Reflects Prospective Risk for Esophageal Cancers
Authors: Peters Brandilyn A. , Wu Jing , Pei Zhiheng , Yang Liying , Purdue Mark P. , Freedman Neal D. , Jacobs Eric J. , Gapstur Susan M. , Hayes Richard B. , Ahn Jiyoung 
Published: December 2017

Abstract
Bacteria may play a role in esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), although evidence is limited to cross-sectional studies. In this study, we examined the relationship of oral microbiota with EAC and ESCC risk in a prospective study nested in two cohorts. Oral bacteria were assessed using 16S rRNA gene sequencing in prediagnostic mouthwash samples from n = 81/160 EAC and n = 25/50 ESCC cases/matched controls. Findings were largely consistent across both cohorts. Metagenome content was predicted using PiCRUST. We examined associations between centered log-ratio transformed taxon or functional pathway abundances and risk using conditional logistic regression adjusting for BMI, smoking, and alcohol. We found the periodontal pathogen Tannerella forsythia to be associated with higher risk of EAC. Furthermore, we found that depletion of the commensal genus Neisseria and the species Streptococcus pneumoniae was associated with lower EAC risk. Bacterial biosynthesis of carotenoids was also associated with protection against EAC. Finally, the abundance of the periodontal pathogen Porphyromonas gingivalis trended with higher risk of ESCC. Overall, our findings have potential implications for the early detection and prevention of EAC and ESCC. Cancer Res; 77(23); 6777–87. ©2017 AACR.
Comparative Transcriptome Profiling Reveals Coding and Noncoding RNA Differences in NSCLC from African Americans and European Americans
Authors: Mitchell Khadijah A. , Zingone Adriana , Toulabi Leila , Boeckelman Jacob , Ryan Bríd M. 
Published: December 2017

Abstract
Purpose: To determine whether racial differences in gene and miRNA expression translates to differences in lung tumor biology with clinical relevance in African Americans (AAs) and European Americans (EAs).
Experimental Design: The NCI-Maryland Case Control Study includes seven Baltimore City hospitals and is overrepresented with AA patients (∼40%). Patients that underwent curative NSCLC surgery between 1998 and 2014 were enrolled. Comparative molecular profiling used mRNA (n = 22 AAs and 19 EAs) and miRNA (n = 42 AAs and 55 EAs) expression arrays to track differences in paired fresh frozen normal tissues and lung tumor specimens from AAs and EAs. Pathway enrichment, predicted drug response, tumor microenvironment infiltration, cancer immunotherapy antigen profiling, and miRNA target enrichment were assessed.
Results: AA-enriched differential gene expression was characterized by stem cell and invasion pathways. Differential gene expression in lung tumors from EAs was primarily characterized by cell proliferation pathways. Population-specific gene expression was partly driven by population-specific miRNA expression profiles. Drug susceptibility predictions revealed a strong inverse correlation between AA resistance and EA sensitivity to the same panel of drugs. Statistically significant differences in M1 and M2 macrophage infiltration were observed in AAs (P &lt; 0.05); however, PD-L1, PD-L2 expression was similar between both.
Conclusions: Comparative transcriptomic profiling revealed clear differences in lung tumor biology between AAs and EAs. Increased participation by AAs in lung cancer clinical trials are needed to integrate, and leverage, transcriptomic differences with other clinical information to maximize therapeutic benefit in both AAs and EAs. Clin Cancer Res; 23(23); 7412–25. ©2017 AACR.
Faith and Defiance (信仰与反抗：毛泽东统治时期的基督徒囚犯)
Authors: Lee (李榭熙) Joseph Tse-Hei 
Published: December 2017

The persecution of Chinese Christians after the outbreak of the Korean War raised important questions about faith and politics in a state-centric society. This article examines the experience and memory of three Protestant religious prisoners in the Maoist era: Watchman Nee (Ni Tuosheng 倪柝声), who founded the Christian Assembly (jidutu juhuichu基督徒聚会处) or Little Flock (xiaoqun小群) in early twentieth-century China; Epaphras Wu (Wu Weizun 吳维僔), an active Little Flock member; and Robert Huang (Huang Zhaojian 黃兆坚), who organized Seventh-Day Adventist activities in 1950s Shanghai. The persecution stories of these religious leaders entered Chinese Christian hagiography, providing Chinese Christians with a shared cultural resource that transcended denominational and theological differences. Central to my investigation are questions about how Christians reacted to Maoism, how they came to terms with the traumatizing experience of incarceration as part of a broader life struggle, and how Chinese churches made sense of these persecution narratives to assert their faith and agency. A closer look at the history of these religious prisoners enables us to capture faith-based resistance at an individual level, and to contextualize the particularities of each persecution in the Maoist period.朝鲜战争爆发之后，对基督徒的迫害在中国这样一个国家主导的社会里是一个严重的信仰与政治问题。本文探究了毛泽东时代三位基督新教徒囚犯的经历与回忆。第一位是倪柝声，二十世纪早期中国基督徒聚会处或小群的创始人；吴维僔，一位活跃的小群信徒；以及黄兆坚，50年代上海基督复临安息日会活动的组织者。这三位基督徒领袖受迫害的故事纳入了中国基督徒的圣人史，为中国基督徒提供了超越宗派神学差异的共享文化资源。本文的核心问题是，这些基督徒如何应对毛泽东思想，他们如何忍受漫长的囚禁生涯，以及中国教会如何理解这些事迹以维护其信仰与教会。深入分析这些被囚基督徒的历史能帮助我们捕捉个人层面以信仰为根基的反抗，以及理解毛时期每个逼迫案例的独特性。
On the Drivers of Wintertime Temperature Extremes in the High Arctic
Authors: Messori Gabriele , Woods Cian , Caballero Rodrigo 
Published: December 2017

Abstract
The salient features and drivers of wintertime warm and cold spells in the high Arctic are investigated. The analysis is based on the European Centre for Medium-Range Weather Forecasts interim reanalysis dataset. It is found that the warm spells are systematically associated with an intense sea level pressure and geopotential height anomaly dipole, displaying a low over the Arctic basin and a high over northern Eurasia. This configuration creates a natural pathway for extreme moisture influx episodes from the Atlantic sector into the Arctic (herein termed moisture intrusions). Anomalous cyclone frequency at the pole (largely attributable to local cyclogenesis) then favors a deep penetration of these intrusions across the Arctic basin. The large-scale circulation pattern associated with the warm spells further favors the advection of cold air across Siberia, leading to the so-called warm Arctic–cold Eurasia pattern previously discussed in the literature. On the contrary, cold Arctic extremes are associated with a severely reduced frequency of moisture intrusions and a persistent low pressure system over the pole. This effectively isolates the high latitudes from midlatitude air masses, favoring an intense radiative cooling of the polar region.