bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cross‐contamination of the human salivary gland HSG cell line with HeLa cells: A STR analysis study
Authors: Lin Li‐Chieh , Elkashty Osama , Ramamoorthi Murali , Trinh Nathalie , Liu Younan , Sunavala‐Dossabhoy Gulshan , Pranzatelli Thomas , Michael Drew G. , Chivasso Clara , Perret Jason , Chiorini John A. , Delporte Christine , Tran Simon D. 
Published: June 2018

AbstractObjectivesThe human salivary gland (HSG) cell line, labeled as a submandibular ductal cell line, is commonly used as in vitro models to study radiation therapy, Sjögren's syndrome, pleomorphic adenoma, mucocele, epithelial‐to‐mesenchymal transition, and epigenetics. However, the American Type Culture Collection (ATCC) has recently released a list of cross‐contaminated cell lines that included HSG. Despite this notice, some research laboratories still use HSG as a salivary cell model. Therefore, this study examined the authenticity of HSG sampled from three different laboratories.MethodsDNA was extracted from HSG and additional salivary cell lines (NS‐SV‐AC, NS‐SV‐DC, A253, HSY) and submitted for cell line authentication with short tandem repeat (STR) analysis.ResultsAll HSG samples had STR profiles indicating >80% match with HeLa in both the ATCC and Deutsche Sammlung von Mikroorganismen und Zellkulturen (DSMZ) databases. This confirmed that HSG sampled from three different laboratories and HSY shared a common ancestry (host) with HeLa, whereas NS‐SV‐AC, NS‐SV‐DC, and A253 had unique STR profiles.ConclusionShort tandem repeat analysis revealed that HSG was contaminated by the HeLa cell line. Furthermore, because genotyping of the original HSG cell line was not performed during its establishment, it will be difficult to authenticate an uncontaminated sample of HSG.
Areas for improvement in community optometry: flashes and floaters take priority
Authors: Duncan Eilidh M. , Cassie Heather , Pooley Janet , Elouafakoui Paula , Prior Maria , Gibb Elizabeth , Ramsay Craig , Young Linda 
Published: June 2018

AbstractPurposeA common response to rising demand for healthcare is to extend the role of health professionals and the range of their service provision. Community optometry in Scotland is a recent example of this. Within this context of innovation and change there are challenges to ensuring quality in optometry practice. The purpose of this research is to establish what the priorities are for practice improvement within community optometry and to start a programme to inform strategies to improve practice.MethodsA four stage study was conducted: (1) a service‐driven topic prioritisation exercise to identify priorities for optometry practice improvement; (2) a review of national and international guidance and UK protocols relating to the identified priority topic; (3) a national theory‐based survey identifying current practice and the barriers and facilitators to the target behaviour; and (4) the identification of theory‐based intervention options to improve practice. The Behaviour Change Wheel approach to behaviour change intervention development and Theoretical Domains Framework (TDF) provided the underlying theoretical framework.ResultsStakeholders identified ‘patients presenting with flashes and floaters’ as an important priority for practice improvement. The decision about whether or not to refer patients on to secondary care for further examination is the target behaviour. Guidance for optometrists on this topic is lacking. Six TDF domains were related to the decision about whether or not to refer patients with flashes and floaters to secondary care – ‘social influences’, ‘emotion’, ‘beliefs about capabilities’, ‘beliefs about consequences’, ‘behavioural regulation’ and ‘reinforcement’.ConclusionsThis study has examined current practice in relation to the management of patients with flashes and floaters, identified the most salient targets for future strategies to improve optometry practice and highlighted what form these strategies may take. It demonstrates the use of a flexible, theory‐informed approach, which can be used to engage with stakeholders and professionals to inform the design and development of efforts to improve practice in a variety of healthcare settings.
Cecum perforation induced by mycophenolate mofetil after hematopoietic stem cell transplantation: A case report and review of literature
Authors: Karagun Barbaros Sahin , Akbas Tugana , Arpaci Taner , Antmen Bulent 
Published: June 2018

AbstractGI perforation after stem cell transplantation is extremely rare and is associated with poor prognosis. In addition, the clinical limitations of MMF are associated with GI intolerance and hematologic suppression. However, the exact mechanism whereby MMF induces changes in GI mucosa is unknown. Currently, there is no definite method to distinguish between GI toxicity associated with MMF and GVHD. It is important to recognize association between MMF and the histologic changes mimicking GVHD, given that GVHD is a significant differential diagnosis in stem cell transplant patients. MMF‐induced colitis and GI perforation are extremely rare but should be considered in patients presenting with diarrhea and abdominal pain. Histology and clinical features are helpful to distinguish this condition from ischemic colitis. Early recognition of GI perforation is necessary for proper diagnosis and subsequent intervention. Emergency medical treatment and laparotomy have been shown to reduce the risk of fatal complications in patients presenting with GI symptoms suspected of GI perforation.
Comparison of survival outcome between donor types or stem cell sources for childhood acute myeloid leukemia after allogenic hematopoietic stem cell transplantation: A multicenter retrospective study of Study Alliance of Yeungnam Pediatric Hematology‐oncology
Authors: Shim Ye Jee , Lee Jae Min , Kim Heung Sik , Jung Nani , Lim Young Tak , Yang Eu Jeen , Hah Jeong Ok , Lee Young‐Ho , Chueh Hee Won , Lim Jae Young , Park Eun Sil , Park Jeong A , Park Ji Kyoung , Park Sang Kyu ,   Study Alliance of Yeungnam Pediatric Hematology‐oncology (SAYPH)
Published: June 2018

AbstractWe compared transplant outcomes between donor types and stem cell sources for childhood acute myeloid leukemia (AML). The medical records of children with AML in the Yeungnam region of Korea from January 2000 to June 2017 were reviewed. In all, 76 children with AML (male‐to‐female ratio = 46:30) received allogenic hematopoietic stem cell transplantation (allo‐HSCT). In total, 29 patients received HSCT from either a matched‐related donor or a mismatched‐related donor, 32 patients received an unrelated donor, and 15 patients received umbilical cord blood. In term of stem cell sources, bone marrow was used in 15 patients and peripheral blood in 46 patients. For all HSCT cases, the 5‐year overall survival (OS) was 73.1% (95% CI: 62.7‐83.5) and the 5‐year event‐free survival (EFS) was 66.1% (95% CI: 54.5‐77.7). There was no statistical difference in 5‐year OS according to the donor types or stem cell sources (P = .869 and P = .911). There was no statistical difference in 5‐year EFS between donor types or stem cell sources (P = .526 and P = .478). For all HSCT cases, the 5‐year relapse rate was 16.1% (95% CI: 7.3‐24.9) and the 5‐year non‐relapse mortality (NRM) was 13.3% (95% CI: 5.1‐21.5). There was no statistical difference in the 5‐year relapse rate according to the donor types or stem cell sources (P = .971 and P = .965). There was no statistical difference in the 5‐year NRM between donor types or stem cell sources (P = .461 and P = .470).
Current controversies in the stepping up and stepping down of inhaled therapies for COPD at the patient level
Authors: Lopez‐Campos Jose Luis , Carrasco Hernández Laura , Muñoz Xavier , Bustamante Víctor , Barreiro Esther 
Published: June 2018

ABSTRACTThe implementation of potential new step‐up or step‐down treatment recommendations in response to current guidelines is one of the main challenges currently faced in actual daily practice settings. In the present narrative review, we aim to discuss the relevance of these step‐up and step‐down proposals at the patient level in daily clinical practice. In particular, we aim to review the challenges associated with inhaled maintenance therapy for chronic obstructive pulmonary disease (COPD) in four clinical scenarios. First, we discuss the step up from single to double bronchodilation, including current controversies regarding the addition of a second bronchodilator versus initial treatment with two bronchodilators. Second, we discuss the step up from double bronchodilation to triple therapy while challenging current indications for inhaled steroid therapy and discussing triple therapy designs. Third, we discuss the step down from triple therapy to double bronchodilation while evaluating the effect of this downshift in risk categories on the patient according to the new classifications. Finally, we discuss the step down from double to single bronchodilation, with a special focus on safety. We believe this review will help to highlight the most relevant discussion points regarding the treatment of COPD in a manner that will stimulate and guide related clinical research.
Integrative Interdisciplinary Approaches to Critical Infrastructure Interdependency Analysis
Authors: Mitsova Diana 
Published: June 2018

AbstractThere is a growing understanding that cross‐sector risks faced by critical infrastructure assets in natural disasters require a collaborative foresight from multiple disciplines. However, current contributions to infrastructure interdependency analysis remain centered in discipline‐specific methodologies often constrained by underlying theories and assumptions. This perspective article contributes to ongoing discussions about the uses, challenges, and opportunities provided by interdisciplinary research in critical infrastructure interdependency analysis. In doing so, several modes of integration of computational modeling with contributions from the social sciences and other disciplines are explored to advance knowledge that can improve the infrastructure system resilience under extreme events. Three basic modes of method integration are identified and discussed: (a) integrating engineering models and social science research, (b) engaging communities in participative and collaborative forms of social learning and problem solving using simulation models to facilitate synthesis, exploration, and evaluation of scenarios, and (c) developing interactive simulations where IT systems and humans act as “peers” leveraging the capacity of distributed networked platforms and human‐in‐the‐loop architectures for improving situational awareness, real‐time decision making, and response capabilities in natural disasters. Depending on the conceptualization of the issues under investigation, these broadly defined modes of integration can coalesce to address key issues in promoting interdisciplinary research by outlining potential areas of future inquiry that would be most beneficial to the critical infrastructure protection communities.
Multiphotonic staging of chronic wounds and evaluation of sterile, optical transparent bacterial nanocellulose covering: A diagnostic window into human skin
Authors: Springer S. , Zieger M. , Hipler U. C. , Lademann J. , Albrecht V. , Bueckle R. , Meß C. , Kaatz M. , Huck V. 
Published: June 2018

AbstractBackgroundDiagnostics of healing, infection, and inflammation in chronic wounds in comparison with physiological wound healing in acute wounds may help for therapy decisions toward individualized therapy management. With emerging new optical techniques the coupling of optical diagnostic devices with tissue provides a great challenge. Traditional coupling with cover slips is used since the early days of microscopy. In modern health care, hygienic covering of surfaces is necessary to avoid infections and cross‐contaminations.MethodsMeasurements in chronic wounds were performed at three different areas including the center of the wound, the border of the wound and healthy skin as comparison area. For each measurement area, three vertical stacks were taken by MPT.Additionally, three different optical measuring procedures (MPT, OCT, CLSM) were used for the examination of BNC foil. Examinations of BNC foil were carried out at two different areas of healthy skin compared to a standard setup as control.ResultsThe MPT evaluation revealed a distinct difference in the second harmonic generation‐to‐autofluorescence aging index of dermis (SAAID) behavior between the vertical stacks taken at central wound areas and wound margins as well as unaffected skin. Through BNC foil covers, MPT CLSM and OCT images were captured with good quantitative and qualitative results.ConclusionsPhases in chronic wounds could be matched with physiologically healing in acute wounds according to SAAID and MPT imaging. BNC provided an alternative covering for MPT, OCT, and CLSM with clear morphological images.
JMJ30‐mediated demethylation of H3K9me3 drives tissue identity changes to promote callus formation in Arabidopsis
Authors: Lee Kyounghee , Park Ok‐Sun , Seo Pil Joon 
Published: June 2018

SummaryPlant somatic cells can be reprogrammed by in vitro tissue culture methods, and massive genome‐wide chromatin remodeling occurs, particularly during callus formation. Since callus tissue resembles root primordium, conversion of tissue identity is essentially required when leaf explants are used. Consistent with the fact that the differentiation state is defined by chromatin structure, which permits limited gene profiles, epigenetic changes underlie cellular reprogramming for changes to tissue identity. Although a histone methylation process suppressing leaf identity during leaf‐to‐callus transition has been demonstrated, the epigenetic factor involved in activation of root identity remains elusive. Here, we report that JUMONJI C DOMAIN‐CONTAINING PROTEIN 30 (JMJ30) stimulates callus formation by promoting expression of a subset of LATERAL ORGAN BOUNDARIES‐DOMAIN (LBD) genes that establish root primordia. The JMJ30 protein binds to promoters of the LBD16 and LBD29 genes along with AUXIN RESPONSE FACTOR 7 (ARF7) and ARF19 and activates LBD expression. Consistently, the JMJ30‐deficient mutant displays reduced callus formation with low LBD transcript levels. The ARF–JMJ30 complex catalyzes the removal of methyl groups from H3K9me3, especially at the LBD16 and LBD29 loci to activate their expression during leaf‐to‐callus transition. Moreover, the ARF–JMJ30 complex further recruits ARABIDOPSIS TRITHORAX‐RELATED 2 (ATXR2), which promotes deposition of H3K36me3 at the LBD16 and LBD29 promoters, and the tripartite complex ensures stable LBD activation during callus formation. These results indicate that the coordinated epigenetic modifications promote callus formation by establishing root primordium identity.
The Effects of Implicit Team Identification (iTeam ID) on Revisit and WOM Intentions: A Moderated Mediation of Emotions and Flow
Authors: Chang Yonghwan , Wann Daniel L. , Inoue Yuhei 
Published: June 2018

Through this study, attempts were made to (a) define the concept of implicit team identification (iTeam ID), (b) examine the effects the interactions between iTeam ID and emotions exert on flow, and (c) examine the behavioral consequences of flow in the context of spectator sports. The opponent process and implicit memory theories served as the study’s main theoretical frameworks. An experiment was conducted in which we developed the team identification implicit association test (Team ID IAT) as a measure of iTeam ID and manipulated spectators’ emotions based on their retrospective spectating experiences. We conclude from the findings that anger, fear, and sadness paradoxically enhanced flow experiences and subsequent consumption behaviors for spectators with stronger iTeam ID, whereas happiness was universally appealing regardless of the level of iTeam ID. A recommendation is to strategically create experiences that elicit both positive and negative emotions in spectators to encourage flow.
Genome Sequences of 12 Mycobacteriophages Recovered from Archival Stocks in Japan
Authors: Uchiyama Jumpei , Mizukami Keijiro , Yahara Koji , Kato Shin-ichiro , Murakami Hironobu , Nasukawa Tadahiro , Ohara Naoya , Ogawa Midori , Yamazaki Toshio , Matsuzaki Shigenobu , Sakaguchi Masahiro 
Published: June 2018

ABSTRACT

Using
Mycobacterium smegmatis
mc
2
155, 12 siphoviruses were recovered from long-term archival stocks stored in Japan. Their genome sequences were 46.0 to 61.3 kbp with 63 to 68% G+C contents, which allowed them to be categorized within cluster W and subclusters A1, A2, B3, A7, I1, and K4.
Complete Genome Sequence of Broad-Host-Range Shiga Toxin-Converting Bacteriophage SH2026Stx1, Isolated from Escherichia coli O157:H7
Authors: Duan Mingrui , Hunter Samuel S. , Minnich Scott A. , Fagnan Matthew W. , New Daniel D. , Hovde Carolyn J. , Sheng Haiqing 
Published: June 2018

ABSTRACT

The Shiga toxin-encoding phage SH2026Stx1 was isolated from
Escherichia coli
O157:H7 strain 2026. SH2026Stx1 and its detoxified derivative can infect a broad range of
E. coli
strains, including commensal, enteropathogenic, and enteroaggregative strains. We report here the complete genome sequence of phage SH2026Stx1 and its important features.
Complete Genome Sequences of HonestAbe, Anthony, and Taffo16, Three Cluster C Bacillus cereus Group Bacteriophages
Authors: Lee Martin , Puglisi Kayla M. ,   UMBC STEM-BUILD Cohort 1, Erill Ivan , Caruso Steven M. 
Published: June 2018

ABSTRACT

Three cluster C
Myoviridae
bacteriophages that infect
Bacillus cereus
group bacteria were isolated from soil collected in the mid-Atlantic region using
B. thuringiensis
subsp.
kurstaki
as a host.
Bacillus
phages HonestAbe, Anthony, and Taffo16 each shared 90% or higher average nucleotide identities within their subclusters.
Complete Genome Sequence of Escherichia coli ME8067, an Azide-Resistant Laboratory Strain Used for Conjugation Experiments
Authors: Matsumura Yasufumi , Yamamoto Masaki , Nakano Satoshi , Nagao Miki 
Published: June 2018

ABSTRACT

We report here the complete genome sequence of
Escherichia coli
ME8067, an azide-resistant laboratory strain used for conjugation experiments. The ME8067 genome was closely related to
E. coli
strain K-12 substrain W3110. This genome sequence will support further genetic analysis of conjugative elements.
Whole-Genome Sequences of Listeria monocytogenes Sequence Type 6 Isolates Associated with a Large Foodborne Outbreak in South Africa, 2017 to 2018
Authors: Allam Mushal , Tau Nomsa , Smouse Shannon L. , Mtshali Phillip S. , Mnyameni Florah , Khumalo Zamantungwa T. H. , Ismail Arshad , Govender Nevashan , Thomas Juno , Smith Anthony M. 
Published: June 2018

ABSTRACT

We report whole-genome sequences for 10
Listeria monocytogenes
sequence type 6 isolates associated with a large listeriosis outbreak in South Africa, which occurred over the period of 2017 to 2018. The possibility of listeriosis spreading beyond South Africa’s borders as a result of exported contaminated food products prompted us to make the genome sequences publicly available.
Draft Genome Sequences of Two Natural Isolates of the Yeast Barnettozyma californica from Ireland, UCD09 and UCD89
Authors: Mullen Alisha A. , Lynch Ciara D. , Hill Shannon M. , Holohan Cian P. , Ó Cróinín Tadhg , Wolfe Kenneth H. , O’Brien Caoimhe E. , Butler Geraldine 
Published: June 2018

ABSTRACT

No genome sequence of a species from
Barnettozyma
, a yeast genus in the family Phaffomycetaceae, is currently available. We isolated two
B. californica
strains from soils in Ireland and generated draft sequences of their 11.7-Mb genomes. Single nucleotide polymorphism (SNP) analysis showed 20,490 differences between the strains and suggests that
B. californica
is haploid.
Draft Genome Sequence of the Yeast Nadsonia starkeyi-henricii UCD142, Isolated from Forest Soil in Ireland
Authors: O’Boyle Sinéad , Bergin Sean A. , Hussey Éabha E. , McLaughlin Aaron D. , Riddell Luan R. , Byrne Kevin P. , Wolfe Kenneth H. , O’Brien Caoimhe E. , Butler Geraldine 
Published: June 2018

ABSTRACT

We report a draft genome sequence of a strain of the nonfermentative yeast
Nadsonia starkeyi-henricii
, isolated from soil in a forest in Ireland. Comparison to
Nadsonia fulvescens
shows few rearrangements and a level of divergence similar to that of
Saccharomyces cerevisiae
versus
Saccharomyces paradoxus
. Its mitochondrial genome lacks
NAD
genes.
Draft Genome Sequence of a Highly Heterozygous Yeast Strain from the Metschnikowia pulcherrima Subclade, UCD127
Authors: Venkatesh Anjan , Murray Anthony L. , Boyle Adrian B. , Quinn Farrington Lisa , Maher Timothy J. , Ó’Gaora Peadar , Wolfe Kenneth H. , O’Brien Caoimhe E. , Butler Geraldine 
Published: June 2018

ABSTRACT

Metschnikowia
strain UCD127 was isolated from soil in Ireland and sequenced. It is a highly heterozygous diploid strain with 385,000 single nucleotide polymorphisms (SNPs). Its ribosomal DNA has the highest similarity to that of
M. chrysoperlae
, but its
ACT1
and
TEF1
loci and mitochondrial genome show affinity to those of
M. fructicola
, whose genome is significantly larger.
Complete Genome Sequence of Mycobacterium shigaense
Authors: Yoshida Mitsunori , Fukano Hanako , Ogura Yoshitoshi , Kazumi Yuko , Mitarai Satoshi , Hayashi Tetsuya , Hoshino Yoshihiko 
Published: June 2018

ABSTRACT

Mycobacterium shigaense
is a slowly growing scotochromogenic species and a member of the
Mycobacterium simiae
complex group. Here, we report the complete sequence of its genome, comprising a 5.2-Mb chromosome. The sequence will represent the essential data for future phylogenetic and comparative genome studies of the
Mycobacterium simiae
complex group.
Draft Genome Sequence of a Dissimilatory U(VI)-Reducing Bacterium, Shewanella xiamenensis Strain DCB2-1, Isolated from Nitrate- and Radionuclide-Contaminated Groundwater in Russia
Authors: Grouzdev Denis S. , Safonov Alexey V. , Babich Tamara L. , Tourova Tatiyana P. , Krutkina Maria S. , Nazina Tamara N. 
Published: June 2018

ABSTRACT

Here, we describe the draft genome sequence of
Shewanella xiamenensis
strain DCB2-1, isolated from nitrate- and radionuclide-contaminated groundwater. This strain is able to reduce nitrate, Tc(VII), Cr(VI), Fe(III), and U(VI), and its genome sequence contains several gene sets encoding denitrification, resistance to heavy metals, and reduction of metals and metalloids.
Single Circular Chromosome Identified from the Genome Sequence of the Vibrio cholerae O1 bv. El Tor Ogawa Strain V060002
Authors: Yamamoto Shouji , Lee Ken-ichi , Morita Masatomo , Arakawa Eiji , Izumiya Hidemasa , Ohnishi Makoto 
Published: June 2018

ABSTRACT

We report here the complete genome sequence of the
Vibrio cholerae
O1 bv. El Tor Ogawa strain V060002, isolated in 1997. The data demonstrate that this clinical strain has a single chromosome resulting from recombination of two prototypical chromosomes.
Complete Genome Sequences of Three Bacillus amyloliquefaciens Strains That Inhibit the Growth of Listeria monocytogenes
In Vitro
Authors: Tran Thao D. , Huynh Steven , Parker Craig T. , Hnasko Robert , Gorski Lisa , McGarvey Jeffery A. 
Published: June 2018

ABSTRACT

Here, we report the complete genome sequences of three
Bacillus amyloliquefaciens
strains isolated from alfalfa, almond drupes, and grapes that inhibited the growth of
Listeria monocytogenes
strain 2011L-2857
in vitro
. We also report multiple gene clusters encoding secondary metabolites that may be responsible for the growth inhibition of
L. monocytogenes
.