bluuebunny/crossref_metadata_2025 huggingface dataset:
Geographic Distribution of Providers With a DEA Waiver to Prescribe Buprenorphine for the Treatment of Opioid Use Disorder: A 5‐Year Update
Authors: Andrilla C. Holly A. , Moore Tessa E. , Patterson Davis G. , Larson Eric H.
Published: June 2018

Purpose

Opioid use disorder (OUD) is a substantial public health problem. Buprenorphine is an effective medication‐assisted treatment (MAT) for OUD, but access is difficult for patients, especially in rural locations. To improve access, the Comprehensive Addiction and Recovery Act of 2016 extended the ability to get a Drug Enforcement Administration (DEA) waiver to prescribe buprenorphine to treat OUD to nurse practitioners (NPs) and physician assistants (PAs). This study summarizes the geographic distribution of waivered physicians, NPs, and PAs at the end of 2017 and compares it to the distribution of waivered physicians 5 years earlier.

Methods

Using the DEA list of providers with a waiver to prescribe buprenorphine to treat OUD and the Area Health Resources File, we assigned waivered providers to counties in 1 of 4 geographic categories. We calculated the number of counties in each category that did not have a waivered provider and county provider to population ratios and then compared our results to the waivered workforce in 2012.

Findings

The availability of a physician with a DEA waiver to provide office‐based MAT has increased across all geographic categories since 2012. More than half of all rural counties (56.3%) still lack a provider, down from 67.1% in 2012. Almost one‐third (29.8%) of rural Americans compared to 2.2% of urban Americans live in a county without a buprenorphine provider. NPs and PAs add otherwise lacking treatment availability in 56 counties (43 rural).

Conclusions

Overall, MAT access has improved, but rural communities still experience treatment disparities.
Kleine‐Levin syndrome is associated with LMOD3 variants
Authors: Al Shareef Saad M. , Basit Sulman , Li Sha , Pfister Corinne , Pradervand Sylvain , Lecendreux Michel , Mayer Geert , Dauvilliers Yves , Salpietro Vincenzo , Houlden Henry , BaHammam Ahmed S. , Tafti Mehdi
Published: June 2018

Kleine‐Levin syndrome (KLS) is a rare periodic hypersomnia with associated behavioural abnormalities but with often favourable prognosis. There is excess risk of KLS in first‐degree relatives, suggesting a strong genetic contribution. So far, no mutation is identified in KLS and comprehensive genetic analysis of affected individuals is lacking. Here we performed whole genome single‐nucleotide polymorphism (SNP) genotyping and exome sequencing in a large family with seven affected members. The identified gene with a mutation was resequenced in 38 sporadic KLS patients and the expression of the gene product was mapped in the mouse brain. Linkage analysis mapped the disease locus to chromosome 3 and exome analysis identified a heterozygous missense variant in LMOD3 (p.E142D) in the linkage interval. The variant was found to segregate in all affected and one presumably unaffected member of the family. Resequencing LMOD3 in 38 other KLS patients and their families revealed three other low frequency or rare missense variants in seven cases that were inherited with incomplete penetrance. LMOD3 is expressed in the brain and colocalized with major structures involved in the regulation of vigilance states. LMOD proteins are structural proteins and seem to be developmentally regulated. Our findings suggest that KLS might be a structural/neurodevelopmental brain disease.
Vygotsky, Wittgenstein, and sociocultural theory
Authors: Newman Stephen
Published: June 2018

This paper considers the use made of Vygotsky's work by many who take a sociocultural perspective and, in particular, by those who use his work to advance a particular view of second language acquisition and the ‘silent period’. It is argued that Vygotsky's account as represented in Thought and Language (Vygotsky, ) needs to be thought of as consisting of two distinct aspects: first, the observations he made (or claimed to have made) and, second, the theoretical account he proposed to explain them. It is shown that some of Vygotsky's observations are problematic but that, even if they are accepted, Vygotsky's theoretical account suffers from fundamental difficulties. Thus the support claimed from Vygotsky in accounts of second language acquisition is misplaced, first because of those difficulties and, second, because many who claim support from Vygotsky, do not need or even use his theory but instead focus their attention on his empirical observations and assume incorrectly that if their own empirical observations match Vygotsky's, then Vygotsky's theory can be accepted. Wittgenstein's later philosophy is shown to provide a perspective which dispels confusions about, and gives us a clearer insight into, the issues.
The relative contributions of seed and pollen dispersal to gene flow and genetic diversity in seedlings of a tropical palm
Authors: Browne Luke , Ottewell Kym , Sork Victoria L. , Karubian Jordan
Published: June 2018

Seed and pollen dispersal shape patterns of gene flow and genetic diversity in plants. Pollen is generally thought to travel longer distances than seeds, but seeds determine the ultimate location of gametes. Resolving how interactions between these two dispersal processes shape microevolutionary processes is a long‐standing research priority. We unambiguously isolated the separate and combined contributions of these two dispersal processes in seedlings of the animal‐dispersed palm Oenocarpus bataua to address two questions. First, what is the spatial extent of pollen versus seed movement in a system characterized by long‐distance seed dispersal? Second, how does seed dispersal mediate seedling genetic diversity? Despite evidence of frequent long‐distance seed dispersal, we found that pollen moves much further than seeds. Nonetheless, seed dispersal ultimately mediates genetic diversity and fine‐scale spatial genetic structure. Compared to undispersed seedlings, seedlings dispersed by vertebrates were characterized by higher female gametic and diploid seedling diversity and weaker fine‐scale spatial genetic structure for female gametes, male gametes and diploid seedlings. Interestingly, the diversity of maternal seed sources at seed deposition sites (Nem) was associated with higher effective number of pollen sources (Nep), higher effective number of parents (Ne) and weaker spatial genetic structure, whereas seed dispersal distance had little impact on these or other parameters we measured. These findings highlight the importance maternal seed source diversity (Nem) at frugivore seed deposition sites in driving emergent patterns of fine‐scale genetic diversity and structure.
Kin discrimination and outer membrane exchange in Myxococcus xanthus: A comparative analysis among natural isolates
Authors: Wielgoss Sébastien , Fiegna Francesca , Rendueles Olaya , Yu Yuen‐Tsu N. , Velicer Gregory J.
Published: June 2018

Genetically similar cells of the soil bacterium Myxococcus xanthus cooperate at multiple social behaviours, including motility and multicellular development. Another social interaction in this species is outer membrane exchange (OME), a behaviour of unknown primary benefit in which cells displaying closely related variants of the outer membrane protein TraA transiently fuse and exchange membrane contents. Functionally incompatible TraA variants do not mediate OME, which led to the proposal that TraA incompatibilities determine patterns of intercellular cooperation in nature, but how this might occur remains unclear. Using natural isolates from a centimetre‐scale patch of soil, we analyse patterns of TraA diversity and ask whether relatedness at TraA is causally related to patterns of kin discrimination in the form of both colony‐merger incompatibilities (CMIs) and interstrain antagonisms. A large proportion of TraA functional diversity documented among global isolates is predicted to be contained within this cm‐scale population. We find evidence of balancing selection on the highly variable PA14‐portion of TraA and extensive transfer of traA alleles across genomic backgrounds. CMIs are shown to be common among strains identical at TraA, suggesting that CMIs are not generally caused by TraA dissimilarity. Finally, it has been proposed that interstrain antagonisms might be caused by OME‐mediated toxin transfer. However, we predict that most strain pairs previously shown to exhibit strong antagonisms are incapable of OME due to TraA dissimilarity. Overall, our results suggest that most documented patterns of kin discrimination in a natural population of M. xanthus are not causally related to the TraA sequences of interactants.
Functional plasticity of antibacterial EndoU toxins
Authors: Michalska Karolina , Quan Nhan Dinh , Willett Julia L. E. , Stols Lucy M. , Eschenfeldt William H. , Jones Allison M. , Nguyen Josephine Y. , Koskiniemi Sanna , Low David A. , Goulding Celia W. , Joachimiak Andrzej , Hayes Christopher S.
Published: June 2018

Bacteria use several different secretion systems to deliver toxic EndoU ribonucleases into neighboring cells. Here, we present the first structure of a prokaryotic EndoU toxin in complex with its cognate immunity protein. The contact‐dependent growth inhibition toxin CdiA‐CTSTECO31 from Escherichia coli STEC_O31 adopts the eukaryotic EndoU fold and shares greatest structural homology with the nuclease domain of coronavirus Nsp15. The toxin contains a canonical His‐His‐Lys catalytic triad in the same arrangement as eukaryotic EndoU domains, but lacks the uridylate‐specific ribonuclease activity that characterizes the superfamily. Comparative sequence analysis indicates that bacterial EndoU domains segregate into at least three major clades based on structural variations in the N‐terminal subdomain. Representative EndoU nucleases from clades I and II degrade tRNA molecules with little specificity. In contrast, CdiA‐CTSTECO31 and other clade III toxins are specific anticodon nucleases that cleave tRNAGlu between nucleotides C37 and m2A38. These findings suggest that the EndoU fold is a versatile scaffold for the evolution of novel substrate specificities. Such functional plasticity may account for the widespread use of EndoU effectors by diverse inter‐bacterial toxin delivery systems.
Assessment of the interaction between the flux‐signaling metabolite fructose‐1,6‐bisphosphate and the bacterial transcription factors CggR and Cra
Authors: Bley Folly Brenda , Ortega Alvaro D. , Hubmann Georg , Bonsing‐Vedelaar Silke , Wijma Hein J. , van der Meulen Pieter , Milias‐Argeitis Andreas , Heinemann Matthias
Published: June 2018

Bacteria regulate cell physiology in response to extra‐ and intracellular cues. Recent work showed that metabolic fluxes are reported by specific metabolites, whose concentrations correlate with flux through the respective metabolic pathway. An example of a flux‐signaling metabolite is fructose‐1,6‐bisphosphate (FBP). In turn, FBP was proposed to allosterically regulate master regulators of carbon metabolism, Cra in Escherichia coli and CggR in Bacillus subtilis. However, a number of questions on the FBP‐mediated regulation of these transcription factors is still open. Here, using thermal shift assays and microscale thermophoresis we demonstrate that FBP does not bind Cra, even at millimolar physiological concentration, and with electrophoretic mobility shift assays we also did not find FBP‐mediated impairment of Cra’s affinity for its operator site, while fructose‐1‐phosphate does. Furthermore, we show for the first time that FBP binds CggR within the millimolar physiological concentration range of the metabolite, and decreases DNA‐binding activity of this transcription factor. Molecular docking experiments only identified a single FBP binding site CggR. Our results provide the long thought after clarity with regards to regulation of Cra activity in E. coli and reveals that E. coli and B. subtilis use distinct cellular mechanism to transduce glycolytic flux signals into transcriptional regulation.
Variation in hydroclimate sustains tropical forest biomass and promotes functional diversity
Authors: Powell Thomas L. , Koven Charles D. , Johnson Daniel J. , Faybishenko Boris , Fisher Rosie A. , Knox Ryan G. , McDowell Nate G. , Condit Richard , Hubbell Stephen P. , Wright S. Joseph , Chambers Jeffrey Q. , Kueppers Lara M.
Published: June 2018

The fate of tropical forests under climate change is unclear as a result, in part, of the uncertainty in projected changes in precipitation and in the ability of vegetation models to capture the effects of drought‐induced mortality on aboveground biomass (AGB).

We evaluated the ability of a terrestrial biosphere model with demography and hydrodynamics (Ecosystem Demography, ED2‐hydro) to simulate AGB and mortality of four tropical tree plant functional types (PFTs) that operate along light‐ and water‐use axes. Model predictions were compared with observations of canopy trees at Barro Colorado Island (BCI), Panama. We then assessed the implications of eight hypothetical precipitation scenarios, including increased annual precipitation, reduced inter‐annual variation, El Niño‐related droughts and drier wet or dry seasons, on AGB and functional diversity of the model forest.

When forced with observed meteorology, ED2‐hydro predictions capture multiple BCI benchmarks. ED2‐hydro predicts that AGB will be sustained under lower rainfall via shifts in the functional composition of the forest, except under the drier dry‐season scenario.

These results support the hypothesis that inter‐annual variation in mean and seasonal precipitation promotes the coexistence of functionally diverse PFTs because of the relative differences in mortality rates. If the hydroclimate becomes chronically drier or wetter, functional evenness related to drought tolerance may decline.
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

Objectives

The 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.

Methods

DNA 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.

Results

All 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.

Conclusion

Short 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

Purpose

A 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.

Methods

A 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.

Results

Stakeholders 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’.

Conclusions

This 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

GI 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

We 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).
GmRAV1 regulates regeneration of roots and adventitious buds by the cytokinin signaling pathway in Arabidopsis and soybean
Authors: Zhang Kexin , Zhao Lin , Yang Xue , Li Minmin , Sun Jingzhe , Wang Kuo , Li Yinghua , Zheng Yanhong , Yao Yuheng , Li Wenbin
Published: June 2018

The division and differentiation of cells are the basis of growth and development. Cytokinin plays an active role in cell growth division and differentiation. The Related to ABI3/VP1 (RAV) family comprises transcription factors in plants and all contain both AP2‐ and B3‐like domains. In this study, GmRAV1 (Glycine max), which belongs to the AP2/ERF transcription factor family, was isolated and functionally characterized. Subcellular localization showed that GmRAV1 was localized to the nucleus and quantitative real‐time polymerase chain reaction (qRT‐PCR) analysis indicated that GmRAV1 was induced by cytokinin. Furthermore, compared with wild‐type plants, plants overexpressing GmRAV1 showed dwarfism and late maturity. In contrast, the mutant of TEMPRANILLO (tem1) and GmRAV‐i plants had an opposite phenotype. More interestingly, a root and shoot regeneration experiment indicated that GmRAV1 is one of the most important positive regulators of the cytokinin signaling pathway, which is involved in promoting root and shoot regeneration. In addition, RNA‐seq and qRT‐PCR results indicated that GmRAV1 is related to the key factors involved in the cytokinin signaling pathway, namely, cytokinin oxidase (GmCKX6 and GmCKX7), purine permease (GmPUP1), cell cyclin‐related genes (GmCycA2;4, GmCycD3 and GmCYC1), cyclin‐dependent kinase (GmCDKB2), cell division cycle (GmCDC20), E2F transcription factors (GmE2FE) and authentic response regulator (GmARR9). In conclusion, GmRAV1, one of the most important positive regulators involved in promoting root and shoot regeneration, was induced by cytokinin and is related to the key factors of the cytokinin signaling pathways.
Prediction of hydraulic conductivity loss from relative water loss: new insights into water storage of tree stems and branches
Authors: Rosner Sabine , Heinze Berthold , Savi Tadeja , Dalla‐Salda Guillermina
Published: June 2018

More frequently occurring, drought waves call for a deeper understanding of tree hydraulics and fast and easily applicable methods to measure drought stress. The aim of this study was to establish empirical relationships between the percent loss of hydraulic conductivity (PLC) and the relative water loss (RWL) in woody stem axes with different P50, i.e. the water potential (Ψ) that causes 50% conductivity loss. Branches and saplings of temperate conifer (Picea abies, Larix decidua) and angiosperm species (Acer campestre, Fagus sylvatica, Populus x canescens, Populus tremula, Sorbus torminalis) and trunk wood of mature P. abies trees were analyzed. P50 was calculated from hydraulic measurements following bench top dehydration or air injection. RWL and PLC were fitted by linear, quadratic or cubic equations. Species‐ or age‐specific RWLs at P50 varied between 10 and 25% and P88, the Ψ that causes 88% conductivity loss, between 18 and 44%. P50 was predicted from the relationship between Ψ and the RWL. The predictive quality for P50 across species was almost 1:1 (r2 = 0.99). The approach presented allows thus reliable and fast prediction of PLC from RWL. Branches and saplings with high hydraulic vulnerability tended to have lower RWLs at P50 and at P88. The results are discussed with regard to the different water storage capacities in sapwood and survival strategies under drought stress. Potential applications are screening trees for drought sensitivity and a fast interpretation of diurnal, seasonal or drought induced changes in xylem water content upon their impact on conductivity loss.
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

The 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

There 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

Background

Diagnostics 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.

Methods

Measurements 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.

Results

The 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.

Conclusions

Phases 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.
Biased sampling activity: an investigation to promote discussion
Authors: White Simon R. , Bonnett Laura J.
Published: June 2018

The statistical concept of sampling is often given little direct attention, typically reduced to the mantra “take a random sample”. This low resource and adaptable activity demonstrates sampling and explores issues that arise due to biased sampling.
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

Plant 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.
Stochastic matched-field localization of an acoustic source based on principles of Riemannian geometry
Authors: Finette Steven , Mignerey Peter C.
Published: June 2018

Passive localization of acoustic sources is treated within a geometric framework where non-Euclidean distance measures are computed between a cross-spectral density estimate of received data on a vertical array and a set of stochastic replica steering matrices, rather than traditional replica steering vectors. A processing scheme involving matrix-matrix comparisons where steering matrices, as functions of the replica source coordinates, naturally incorporate environmental variability or uncertainty provides a general framework for considering the acoustic inverse source problem in an ocean waveguide. Within this context a subset of matched-field processors is examined, based on recent advances in the application of non-Euclidean geometry to statistical classification of data feature clusters. The matrices are interpreted abstractly as points in a Riemannian manifold, and an appropriately defined distance measure between pairs of matrices on this manifold defines a matched-field processor for estimating source location. Acoustic simulations are performed for a waveguide comprising both a depth-dependent sound-speed profile perturbed by linear internal gravity waves and a depth-correlated surface noise field, providing an example of the viability of this approach to passive source localization in the presence of sound-speed variability.
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.
Ketogenic bugs as epilepsy drugs
Authors: Nance Elizabeth A.
Published: June 2018

The gut microbiome mediates the beneficial effects of a ketogenic diet on epileptic seizures through modulation of GABA/glutamate ratios in the hippocampus.
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

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

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

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

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.
Genome Sequence of a Staphylococcus epidermidis Strain (GTH12) Associated with Candida albicans SC5314 Cultured under Hypoxia at 37°C in Glycerol for 12 Weeks
Authors: Bruno Danielle do Carmo Ferreira , Bartelli Thais Fernanda , Briones Marcelo R. S.
Published: June 2018

Polymicrobial infections with mixed-species biofilms are important health problems because of increased antimicrobial resistance and worse patient outcomes than with monomicrobial infections. Here, we present the whole-genome sequence of
Staphylococcus epidermidis
strain GTH12, which was cocultured with the yeast
Candida albicans
SC5314 (generating
C. albicans
strain SC5314 GTH12), thus providing genomic information on polymicrobial infections.
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

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

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

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

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

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 Whole-Genome Sequence of “Candidatus Liberibacter asiaticus” Strain TX1712 from Citrus in Texas
Authors: Cai W. , Yan Z. , Rascoe J. , Stulberg M. J.
Published: June 2018

The draft genome sequence of “
Candidatus
Liberibacter asiaticus” strain TX1712, obtained from a Texas citrus tree, is reported here. Strain TX1712 has a draft genome size of 1,203,333 bp, a G+C content of 36.4%, 1,230 predicted open reading frames, and 41 RNAs and comprises 97.4% of the psy62 reference genome.
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

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

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.
Draft Genome Sequences of Two Basal Members of the
Anaerolineae
Class of
Chloroflexi
from a Sulfidic Hot Spring
Authors: Ward L. M. , McGlynn S. E. , Fischer W. W.
Published: June 2018

Here, we describe the first genome sequences of the
Anaerolineae
from a sulfidic environment, expanding the environmental distribution of sequenced
Anaerolineae
. These genomes represent basal
Anaerolineae
lineages, branching soon after the divergence of the sister class “
Candidatus
Thermofonsia,” expanding our understanding of the metabolic evolution of this group.
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

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
.
Zika Virus Attenuation by Codon Pair Deoptimization Induces Sterilizing Immunity in Mouse Models
Authors: Li Penghui , Ke Xianliang , Wang Ting , Tan Zhongyuan , Luo Dan , Miao Yuanjiu , Sun Jianhong , Zhang Yuan , Liu Yan , Hu Qinxue , Xu Fuqiang , Wang Hanzhong , Zheng Zhenhua
Published: June 2018

Due to unprecedented epidemics of Zika virus (ZIKV) across the Americas and the unexpected clinical symptoms, including Guillain-Barré syndrome, microcephaly, and other birth defects in humans, there is an urgent need for ZIKV vaccine development. Here we provided the first attenuated versions of ZIKV with two important genes (E and/or NS1) that were subjected to codon pair deoptimization. Compared to parental ZIKV, the codon pair-deoptimized ZIKVs were mammal attenuated and preferred insect to mammalian cells. Min E+NS1, the most restrictive variant, induced sterilizing immunity with a robust neutralizing antibody titer and achieved complete protection against lethal challenge and vertical virus transmission during pregnancy. More importantly, the massive synonymous mutational approach made it impossible for the variant to revert to wild-type virulence. Our results have proven the feasibility of codon pair deoptimization as a strategy to develop live attenuated vaccine candidates against flaviviruses such as ZIKV, Japanese encephalitis virus, and West Nile virus.
Reduced Susceptibility to VIRIP-Based HIV-1 Entry Inhibitors Has a High Genetic Barrier and Severe Fitness Costs
Authors: Müller Janis A. , Glöckle Anna , Gawanbacht Ali , Geyer Matthias , Münch Jan , Kirchhoff Frank
Published: June 2018

Many viral pathogens are critically dependent on fusion peptides (FPs) that are inserted into the cellular membrane for infection. Initially, it was thought that FPs cannot be targeted for therapy because they are hardly accessible. However, an optimized derivative (VIR-576) of an endogenous fragment of α1-antitrypsin, named VIRIP, targeting the gp41 FP reduced viral loads in HIV-1-infected individuals. Characterization of HIV-1 variants selected during long-term cell-culture passage in the presence of a VIRIP derivative suggested that just three mutations in the HIV-1 Env protein might be sufficient for VIRIP resistance and that four subsequent changes restored viral fitness. Here, we show that all seven mutations contribute to reduced viral susceptibility to VIRIP-based inhibitors and demonstrate that the additional changes strongly impair rather than rescue HIV-1 infectivity, fusogenicity, and replication fitness. High genetic barrier to resistance and severe fitness cost support further clinical development of this class of antiviral agents.