bluuebunny/crossref_metadata_2025 huggingface dataset:
Assessment of techniques used for superimposition of maxillary and mandibular 3D surface models to evaluate tooth movement: a systematic review
Authors: Stucki Sven , Gkantidis Nikolaos
Published: August 2019

Background

Superimposition of three-dimensional (3D) digital models offers great opportunities to assess tooth movement during time. In the literature, several superimposition techniques are described.

Objectives

To summarize and critically assess the available evidence from studies on serial digital 3D dental model superimposition.

Search methods

MEDLINE via Ovid and PubMed, EMBASE via Ovid, Cochrane Register of Diagnostic Test Accuracy Studies, and Google Scholar were searched with no time limit (last update: December 2018). Hand and unpublished literature searches were also performed.

Selection criteria

Studies of any design that had a sample size ≥5 and tested superimposition of serial 3D digital dental models to assess tooth movement were included.

Data collection and analysis

Study selection, data extraction, and risk of bias assessment were performed independently by the authors.

Results

Twelve studies met the eligibility criteria. The total risk of bias (QUADAS-2 tool) of 10 studies was high, whereas only 2 studies had unclear bias. Ten studies had high and two studies low overall applicability concerns. From these, one study tested the mandibular alveolar bone area, three studies the rugae area, nine studies a larger palatal area, and two studies the incisive papilla area. The high heterogeneity in samples, outcomes, and methods did not allow for synthesis of a considerable amount of studies in any case.

Limitations

The high heterogeneity among studies and the limited evidence did not allow for solid conclusions.

Conclusions and implications

The following areas of the maxilla could provide reliable outcomes: (1) the medial two-thirds of the third rugae and the area 5 mm dorsal to them and (2) an area including all rugae, with the lateral margins located at least 5 mm from the gingival margins and a distal margin that does not extend beyond the first molars. No recommendation is possible for other regions of the mouth. There is an urgent need for further research in the field.

Registration

PROSPERO (CRD42019124365).
Yeast prion-based metabolic reprogramming induced by bacteria in fermented foods
Authors: Watanabe Daisuke , Takagi Hiroshi
Published: August 2019

Microbial communities of yeast and bacterial cells are often observed in the manufacturing processes of fermented foods and drinks, such as sourdough bread, cheese, kefir, wine and sake. Community interactions and dynamics among microorganisms, as well as their significance during the manufacturing processes, are central issues in modern food microbiology. Recent studies demonstrated that the emergence of a yeast prion termed [GAR+] in Saccharomyces cerevisiae is induced by coculturing with bacterial cells, resulting in the switching of the carbon metabolism. In order to facilitate mutualistic symbiosis among microorganisms, this mode of microbial interaction is induced between yeasts and lactic acid bacteria species used in traditional sake making. Thus, yeast prions have attracted much attention as novel platforms that govern the metabolic adaptation of cross-kingdom ecosystems. Our minireview focuses on the plausible linkage between fermented-food microbial communication and yeast prion-mediated metabolic reprogramming.
Protection Deficit: The Failure of Australia’s Offshore Processing Arrangements to Guarantee ‘Protection Elsewhere’ in the Pacific
Authors: Gleeson Madeline
Published: August 2019

In 2012, Australia reintroduced arrangements for ‘offshore processing’ in the Pacific, which forcibly transferred asylum seekers arriving by boat to the Republic of Nauru and Papua New Guinea (PNG), purportedly for refugee status determination (RSD). Previous studies have focused on the detention of asylum seekers transferred to these States in ‘regional processing centres’ (RPCs). This article instead provides a factual foundation for more current inquiries into the content and scope of each State’s protection obligations under international law, which have increased in importance since the end of closed detention in the RPCs in 2015 and 2017. The formal legal and diplomatic arrangements established in and between the three States for the transfer of asylum seekers; processing of their claims; and provision of durable solutions will be examined, with reference to the minimum standards required. The article identifies a protection deficit in the legal architecture and bilateral arrangements underpinning offshore processing. Since their inception, the arrangements have lacked clarity regarding the respective obligations of the three States; involved transfers even in the absence of fair and efficient procedures for RSD in Nauru and PNG; and failed to ensure timely access to appropriate outcomes for all transferees (whether determined to be in need of international protection or not). The article therefore concludes that Australia should facilitate readmission to its territory for all people in Nauru and PNG who do not have access to an appropriate alternative outcome. It also suggests that any future attempts to establish third country transfer procedures will require radically different legal and diplomatic arrangements to enhance responsibility sharing and cooperation on refugee protection, and to comply with international law.
The Dark Side of Cooperation: International Organizations and Member Corruption
Authors: Hafner-Burton Emilie M , Schneider Christina J
Published: August 2019

Political corruption is rampant in—and destructive to—many parts of the world. A growing number of international organizations (IOs) claim to address the problem by encouraging good governance norms and rules, such as anti-corruption standards and practices. Whether membership in IOs dampens corruption, however, is unclear. Our central argument is that the characteristics of IO membership determine both whether corruption is tolerated and the extent to which formal anti-corruption rules effectively combat the problem. First, groups of corrupt states are reticent to enforce good governance norms or rules against other IO members, rendering punishment for corruption incredible. Second, leaders may witness the value of corruption to their IO peers and learn to act the same way. Using a variety of data sources and estimation strategies, including new data on IO anti-corruption mandates, we demonstrate that: (1) countries that participate in member-corrupted IOs are significantly more likely to engage in corruption themselves—and experience an increase in corruption over time—than are countries that participate in less corrupt IOs; and (2) this tolerance for corruption occurs even within IOs that have adopted formal anti-corruption mandates, rendering good governance rules largely cheap talk among organizations governed by corrupt principles.
Extended-spectrum resistance to β-lactams/β-lactamase inhibitors (ESRI) evolved from low-level resistant Escherichia coli
Authors: Rodríguez-Villodres Ángel , Gil-Marqués María Luisa , Álvarez-Marín Rocío , Bonnin Rémy A , Pachón-Ibáñez María Eugenia , Aguilar-Guisado Manuela , Naas Thierry , Aznar Javier , Pachón Jerónimo , Lepe José Antonio , Smani Younes
Published: August 2019

Objectives

Escherichia coli is characterized by three resistance patterns to β-lactams/β-lactamase inhibitors (BLs/BLIs): (i) resistance to ampicillin/sulbactam and susceptibility to amoxicillin/clavulanic acid and piperacillin/tazobactam (RSS); (ii) resistance to ampicillin/sulbactam and amoxicillin/clavulanic acid, and susceptibility to piperacillin/tazobactam (RRS); and (iii) resistance to ampicillin/sulbactam, amoxicillin/clavulanic acid and piperacillin/tazobactam (RRR). These resistance patterns are acquired consecutively, indicating a potential risk of developing resistance to piperacillin/tazobactam, but the precise mechanism of this process is not completely understood.

Methods

Clinical isolates incrementally pressured by piperacillin/tazobactam selection in vitro and in vivo were used. We determined the MIC of piperacillin/tazobactam in the presence and absence of piperacillin/tazobactam pressure. We deciphered the role of the blaTEM genes in the new concept of extended-spectrum resistance to BLs/BLIs (ESRI) using genomic analysis. The activity of β-lactamase was quantified in these isolates.

Results

We show that piperacillin/tazobactam resistance is induced in E. coli carrying blaTEM genes. This resistance is due to the increase in copy numbers and transcription levels of the blaTEM gene, thus increasing β-lactamase activity and consequently increasing piperacillin/tazobactam MICs. Genome sequencing of two blaTEM-carrying representative isolates showed that piperacillin/tazobactam treatment produced two types of duplications of blaTEM (8 and 60 copies, respectively). In the clinical setting, piperacillin/tazobactam treatment of patients infected by E. coli carrying blaTEM is associated with a risk of therapeutic failure.

Conclusions

This study describes for the first time the ESRI in E. coli. This new concept is very important in the understanding of the mechanism involved in the acquisition of resistance to BLs/BLIs.
Molecular and Functional Characterization of One Odorant-Binding Protein Gene OBP3 in Bemisia tabaci (Hemiptera: Aleyrodidae)
Authors: Wang Ran , Hu Yuan , Wei Peiling , Qu Cheng , Luo Chen
Published: August 2019

Odorant binding proteins (OBPs) of insects play a critical role in chemical perceptions and choice of insect host plant. Bemisia tabaci is a notorious insect pest which can damage more than 600 plant species. In order to explore functions of OBPs in B. tabaci, here we investigated binding characteristics and function of odorant-binding protein 3 in B. tabaci (BtabOBP3). The results indicated that BtabOBP3 shows highly similar sequence with OBPs of other insects, including the typical signature motif of six cysteines. The recombinant BtabOBP3 protein was obtained, and the evaluation of binding affinities to tested volatiles of host plant was conducted, then the results indicated that β-ionone had significantly higher binding to BtabOBP3 among other tested plant volatiles. Furthermore, silencing of BtabOBP3 significantly altered choice behavior of B. tabaci to β-ionone. In conclusion, it has been demonstrated that BtabOBP3 exerts function as one carrier of β-ionone and the results could be contributed to reveal the mechanisms of choosing host plant in B. tabaci.
Climate Change and the Risk of Malaria Transmission in Iran
Authors: Hanafi-Bojd Ahmad Ali , Vatandoost Hassan , Yaghoobi-Ershadi Mohammad Reza
Published: August 2019

Climate change is an important factor affecting the dynamics of the vectors population and, hence, the risk of vector-borne diseases. This study aimed to predict the environmental suitability for malaria vectors in Iran under climate change scenarios in 2030s and 2050s. Literature search was performed to find documents on the spatial distribution of Anopheles stephensi Liston, 1901, Anopheles culicifacies s.l. Giles, 1901, Anopheles fluviatilis s.l. James, 1902, Anopheles superpictus s.l. Grassi, 1899, Anopheles dthali Patton, 1905, Anopheles maculipennis s.l. Meigen, 1818, and Anopheles sacharovi Favre, 1903 (Diptera: Culicidae) published between 1970 and 2017. The bioclimatic data under three climate change scenarios (representative concentration pathway 2.6 [RCP2.6], RCP4.5, and RCP8.5) and MaxEnt model were used to predict the ecological niches for each species. Comparison between the two study periods under the three scenarios for each species revealed that RCP8.5 would reduce the area at risk for An. culicifacies s.l., An. dthali and An. superpictus s.l. in the 2050s compared to the 2030s, but the reverse will be induced by RCP2.6 and RCP4.5 scenarios. For An. fluviatilis s.l., RCP2.6 will reduce the risk areas in the 2050s, whereas an increase is expected under the two other scenarios. Moreover, all scenarios would decrease the high-risk areas of An. maculipennis s.l. in the 2050s. For An. sacharovi, RCP2.6 would increase its high-risk areas, whereas RCP4.5 and RCP8.5 would decrease its exposure. The high-risk area of An. stephensi is expected to increase under RCP8.5 in the 2030s and RCP4.5 in 2050s, but it will be almost unchanged or reduced under other scenarios.
Evaluating Clonal Hematopoiesis in Tumor-Infiltrating Leukocytes in Breast Cancer and Secondary Hematologic Malignancies
Authors: Comen Elizabeth A , Bowman Robert L , Selenica Pier , Kleppe Maria , Farnoud Noushin R , Pareja Fresia , Weigelt Britta , Hill Corinne E , Alon Abigail , Geyer Felipe C , Akturk Guray , Reis-Filho Jorge S , Norton Larry , Levine Ross L
Published: August 2019

Chemotherapy and radiation therapy are the foundations of adjuvant therapy for early-stage breast cancer. As a complication of cytotoxic regimens, breast cancer patients are at risk for therapy-related myeloid neoplasms (t-MNs). These t-MNs are commonly refractory to antileukemic therapies and result in poor patient outcomes. We previously demonstrated that somatic mutations in leukemia-related genes are present in the tumor-infiltrating leukocytes (TILeuks) of a subset of early breast cancers. Here, we performed genomic analysis of microdissected breast cancer tumor cells and TILeuks from seven breast cancer patients who subsequently developed leukemia. In four patients, mutations present in the leukemia were detected in breast cancer TILeuks. This finding suggests that TILeuks in the primary breast cancer may harbor the ancestor of the future leukemogenic clone. Additional research is warranted to ascertain whether infiltrating mutant TILeuks could constitute a biomarker for the development of t-MN and to determine the functional consequences of mutant TILeuks.
Case Study of a Breacher: Investigation of Neurotrauma Biomarker Levels, Self-reported Symptoms, and Functional MRI Analysis Before and After Exposure to Measured Low-Level Blast
Authors: Eonta Stephanie E , Kamimori Gary H , Wang Kevin K W , Carr Walter , LaValle Christina R , Egnoto Michael J , Tate Charmaine M
Published: August 2019

We report a case study on a single military member who received moderate blast overpressure (OP) exposure during routine breacher training. We extend previous research on blast exposure during training, which lacked sufficient data to assess symptom profiles and OP exposure. The present work was conducted because a subjective symptom profile similar to that seen in sports concussion has been reported by military personnel exposed to blast. Data collection for this study was carried out under a research protocol approved by the relevant Human Subjects Review Committees on one subject, who received the highest OP exposure during training. The volunteer was a 20-year-old male with no prior history of traumatic brain injury (TBI) or blast exposure. The volunteer was part of a breacher training team that completed a 2-week explosive entry course. The course included 3 classroom days and 9 days of practical training, held in the morning, afternoon, and evening sessions. Blast exposure occurred on five of the nine practical training days, with multiple exposures over the course of each day. Assessments of serum, self-reported symptoms, magnetic resonance imaging, and blast characterization were conducted. Results indicated changes in glial fibrillary acidic protein and ubiquitin C-terminal hydrolase-L1 postblast exposure but did not manifest changes in spectrin-derived breakdown product 150 or magnetic resonance imaging. No additional symptoms were reported by the subject. Objective markers of mild TBI remain elusive, but support for serum biomarkers as an early detection mechanism is promising. Additionally, this case study demonstrated an association between OP and high level of neurotrauma biomarker in an individual.
Unusual Patterns of Mitochondrial Inheritance in the Brown Alga Ectocarpus
Authors: Mignerot Laure , Nagasato Chikako , Peters Akira F , Perrineau Marie-Mathilde , Scornet Delphine , Pontheaux Florian , Djema Walid , Badis Yacine , Motomura Taizo , Coelho Susana M , Cock J Mark
Published: August 2019

Most eukaryotes inherit their mitochondria from only one of their parents. When there are different sexes, it is almost always the maternal mitochondria that are transmitted. Indeed, maternal uniparental inheritance has been reported for the brown alga Ectocarpus but we show in this study that different strains of Ectocarpus can exhibit different patterns of inheritance: Ectocarpus siliculosus strains showed maternal uniparental inheritance, as expected, but crosses using different Ectocarpus species 7 strains exhibited either paternal uniparental inheritance or an unusual pattern of transmission where progeny inherited either maternal or paternal mitochondria, but not both. A possible correlation between the pattern of mitochondrial inheritance and male gamete parthenogenesis was investigated. Moreover, in contrast to observations in the green lineage, we did not detect any change in the pattern of mitochondrial inheritance in mutant strains affected in life cycle progression. Finally, an analysis of field-isolated strains provided evidence of mitochondrial genome recombination in both Ectocarpus species.
Spacer acquisition from RNA mediated by a natural reverse transcriptase-Cas1 fusion protein associated with a type III-D CRISPR–Cas system in Vibrio vulnificus
Authors: González-Delgado Alejandro , Mestre Mario Rodríguez , Martínez-Abarca Francisco , Toro Nicolás
Published: August 2019

The association of reverse transcriptases (RTs) with CRISPR–Cas system has recently attracted interest because the RT activity appears to facilitate the RT-dependent acquisition of spacers from RNA molecules. However, our understanding of this spacer acquisition process remains limited. We characterized the in vivo acquisition of spacers mediated by an RT-Cas1 fusion protein linked to a type III-D system from Vibrio vulnificus strain YJ016, and showed that the adaptation module, consisting of the RT-Cas1 fusion, two different Cas2 proteins (A and B) and one of the two CRISPR arrays, was completely functional in a heterologous host. We found that mutations of the active site of the RT domain significantly decreased the acquisition of new spacers and showed that this RT-Cas1-associated adaptation module was able to incorporate spacers from RNA molecules into the CRISPR array. We demonstrated that the two Cas2 proteins of the adaptation module were required for spacer acquisition. Furthermore, we found that several sequence-specific features were required for the acquisition and integration of spacers derived from any region of the genome, with no bias along the 5′and 3′ends of coding sequences. This study provides new insight into the RT-Cas1 fusion protein-mediated acquisition of spacers from RNA molecules.
Training-free measures based on algorithmic probability identify high nucleosome occupancy in DNA sequences
Authors: Zenil Hector , Minary Peter
Published: August 2019

We introduce and study a set of training-free methods of an information-theoretic and algorithmic complexity nature that we apply to DNA sequences to identify their potential to identify nucleosomal binding sites. We test the measures on well-studied genomic sequences of different sizes drawn from different sources. The measures reveal the known in vivo versus in vitro predictive discrepancies and uncover their potential to pinpoint high and low nucleosome occupancy. We explore different possible signals within and beyond the nucleosome length and find that the complexity indices are informative of nucleosome occupancy. We found that, while it is clear that the gold standard Kaplan model is driven by GC content (by design) and by k-mer training; for high occupancy, entropy and complexity-based scores are also informative and can complement the Kaplan model.
Imaging challenges of immunotherapy and targeted therapy in patients with brain metastases: response, progression, and pseudoprogression
Authors: Galldiks Norbert , Kocher Martin , Ceccon Garry , Werner Jan-Michael , Brunn Anna , Deckert Martina , Pope Whitney B , Soffietti Riccardo , Le Rhun Emilie , Weller Michael , Tonn Jörg C , Fink Gereon R , Langen Karl-Josef
Published: August 2019

The advent of immunotherapy using immune checkpoint inhibitors (ICIs) and targeted therapy (TT) has dramatically improved the prognosis of various cancer types. However, following ICI therapy or TT—either alone (especially ICI) or in combination with radiotherapy—imaging findings on anatomical contrast-enhanced MRI can be unpredictable and highly variable, and are often difficult to interpret regarding treatment response and outcome. This review aims at summarizing the imaging challenges related to TT and ICI monotherapy as well as combined with radiotherapy in patients with brain metastases, and to give an overview on advanced imaging techniques which potentially overcome some of these imaging challenges. Currently, major evidence suggests that imaging parameters especially derived from amino acid PET, perfusion-/diffusion-weighted MRI, or MR spectroscopy may provide valuable additional information for the differentiation of treatment-induced changes from brain metastases recurrence and the evaluation of treatment response.
Solutions for whole grain food development
Authors: Tan Bin , Wu Na-Na , Zhai Xiao-Tong
Published: August 2019

Owing to the health benefits associated with whole grains, there has been a sustained global effort to increase their consumption, with many countries developing guidelines for recommended amounts of whole grain intake. In China, the consumption of whole grains is low. This is due, in part, to technical obstacles in the development of whole grain foods. This review focuses on possible solutions in the whole value chain and the application of new food technologies to develop whole grain foods that taste better, have more appealing texture, are safe to consume, and better retain bioactive compounds.
Clinical Characteristics and Outcome of Staphylococcus aureus Prostate Abscess From Ten Years of Experience at a Tertiary Care Center
Authors: Walker Bryan , Heidel Eric , Shorman Mahmoud
Published: August 2019

Objective

Prostatic abscess (PA) is an uncommon infection that is generally secondary to Escherichia coli and other members of the Enterobacteriaceae family. In recent years, although rare, more reports of Staphylococcus aureus (S. aureus) PA have been reported, especially with increasing reports of bacteremia associated with injection drug use (IDU).

Method

This was a retrospective review of adult patients admitted to a tertiary care hospital between 2008 and 2018 and who had a diagnosis of S. aureus PA.

Results

Twenty-one patients were included. The average age was 46 years. Fourteen (67%) patients presented with genitourinary concerns. Main risk factors included concurrent skin or soft tissue infections (52%), history of genitourinary disease or instrumentation (48%), IDU (38%), and diabetes mellitus (38%). Methicillin-resistant Staphylococcus aureus (MRSA) was identified in 57% and concomitant bacteremia in 81% of patients. Surgical or a radiologically guided drainage was performed in 81% of patients. Antibiotic treatment duration ranged from 3 to 8 weeks. Six patients were lost to follow-up. Clinical resolution was observed in the remaining 15 (81%) patients who had follow-up.

Conclusions

S. aureus PA continues to be a rare complication of S.aureus infections. In most published reports, MRSA is the culprit. In high risk patients with persistent bacteremia, physicians need to consider the prostate as a site of infection.
Associations of clinical and inflammatory biomarker clusters with juvenile idiopathic arthritis categories
Authors: Rezaei Elham , Hogan Daniel , Trost Brett , Kusalik Anthony J , Boire Gilles , Cabral David A , Campillo Sarah , Chédeville Gaëlle , Chetaille Anne-Laure , Dancey Paul , Duffy Ciaran , Duffy Karen Watanabe , Eng Simon W M , Gordon John , Guzman Jaime , Houghton Kristin , Huber Adam M , Jurencak Roman , Lang Bianca , Laxer Ronald M , Morishita Kimberly , Oen Kiem G , Petty Ross E , Ramsey Suzanne E , Scherer Stephen W , Scuccimarri Rosie , Spiegel Lynn , Stringer Elizabeth , Taylor-Gjevre Regina M , Tse Shirley M L , Tucker Lori B , Turvey Stuart E , Tupper Susan , Wintle Richard F , Yeung Rae S M , Rosenberg Alan M ,   for the BBOP Study Group
Published: August 2019

Objective

To identify discrete clusters comprising clinical features and inflammatory biomarkers in children with JIA and to determine cluster alignment with JIA categories.

Methods

A Canadian prospective inception cohort comprising 150 children with JIA was evaluated at baseline (visit 1) and after six months (visit 2). Data included clinical manifestations and inflammation-related biomarkers. Probabilistic principal component analysis identified sets of composite variables, or principal components, from 191 original variables. To discern new clinical-biomarker clusters (clusters), Gaussian mixture models were fit to the data. Newly-defined clusters and JIA categories were compared. Agreement between the two was assessed using Kruskal–Wallis analyses and contingency plots.

Results

Three principal components recovered 35% (three clusters) and 40% (five clusters) of the variance in patient profiles in visits 1 and 2, respectively. None of the clusters aligned precisely with any of the seven JIA categories but rather spanned multiple categories. Results demonstrated that the newly defined clinical-biomarker lustres are more homogeneous than JIA categories.

Conclusion

Applying unsupervised data mining to clinical and inflammatory biomarker data discerns discrete clusters that intersect multiple JIA categories. Results suggest that certain groups of patients within different JIA categories are more aligned pathobiologically than their separate clinical categorizations suggest. Applying data mining analyses to complex datasets can generate insights into JIA pathogenesis and could contribute to biologically based refinements in JIA classification.
A biopsychosocial network model of fatigue in rheumatoid arthritis: a systematic review
Authors: Geenen Rinie , Dures Emma
Published: August 2019

Fatigue in RA is prevalent, intrusive and disabling. We propose a network model of fatigue encompassing multiple and mutually interacting biological, psychological and social factors. Guided by this model, we reviewed the literature to offer a comprehensive overview of factors that have been associated with fatigue in RA. Six categories of variables were found: physical functioning, psychological functioning, medical status, comorbidities and symptoms, biographical variables and miscellaneous variables. We then systematically reviewed associations between fatigue and factors commonly addressed by rheumatology health professionals. Correlations of fatigue with physical disability, poor mental well-being, pain, sleep disturbance and depression and anxiety were ∼0.50. Mostly these correlations remained significant in multivariate analyses, suggesting partly independent influences on fatigue and differences between individuals. These findings indicate the importance of research into individual-specific networks of biopsychosocial factors that maintain fatigue and tailored interventions that target the influencing factors most relevant to that person.
Modification of Rhizosphere Bacterial Community Structure and Functional Potentials to Control Pseudostellaria heterophylla Replant Disease
Authors: Wu Linkun , Yang Bo , Li Manlin , Chen Jun , Xiao Zhigang , Wu Hongmiao , Tong Qingyu , Luo Xiaomian , Lin Wenxiong
Published: August 2019

Replant disease caused by negative plant-soil feedback commonly occurs in a Pseudostellaria heterophylla monoculture regime. Here, barcoded pyrosequencing of 16S ribosomal DNA amplicons combined with phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis was applied to study the shifts in soil bacterial community structure and functional potentials in the rhizosphere of P. heterophylla under consecutive monoculture and different soil amendments (i.e., bio-organic fertilizer application [MF] and paddy-upland rotation [PR]). The results showed that the yield of tuberous roots decreased under P. heterophylla consecutive monoculture and then increased after MF and PR treatments, which was consistent with the changes in soil bacterial diversity. Both principal coordinate analysis and the unweighted pair-group method with arithmetic means cluster analysis showed the distinct difference in bacterial community structure between the consecutively monocultured soil (relatively unhealthy soil) and other relatively healthy soils (i.e., newly planted soil, MF, and PR). Furthermore, taxonomic analysis showed that consecutive monoculture of P. heterophylla significantly decreased the relative abundances of the families Burkholderiaceae and Acidobacteriaceae (subgroup 1), whereas it increased the population density of families Xanthomonadaceae, Phyllobacteriaceae, Sphingobacteriaceae, and Alcaligenaceae, and Fusarium oxysporum. In contrast, the MF and PR treatments recovered the soil microbiome and decreased F. oxysporum abundance through the different ways; for example, the introduction of beneficial microorganisms (in MF) or the switching between anaerobic and aerobic conditions (in PR). In addition, PICRUSt analysis revealed the higher abundances of membrane transport, cell motility, and DNA repair in the consecutively monocultured soil, which might contribute to the root colonization and survival for certain bacterial pathogens under monoculture. These findings highlight the close association between replant disease of P. heterophylla and the variations in structure and potential functions of rhizosphere bacterial community.
Virulence Dynamics and Breeding for Resistance to Stripe, Stem, and Leaf Rust in Canada Since 2000
Authors: Brar Gurcharn S. , Fetch Thomas , McCallum Brent D. , Hucl Pierre J. , Kutcher Hadley R.
Published: August 2019

Wheat (Triticum spp.) is a major field crop in Canada in terms of acreage, annual production, and export market value. There are nine classes of Canadian wheat based on growth habit (winter or spring), kernel hardness (hard or soft), seed coat color (red or white), and quality factors (grain protein content and gluten strength). Wheat was described by Newman in 1928 as “the economic fairy to the industrial and commercial life of Canada, having built practically the whole economic structure of the Prairie Provinces.” Wheat production in Canada is affected by several biotic and abiotic stresses. The major abiotic stresses are frost damage, drought, and heat stress. Among biotic stresses, diseases caused by fungal pathogens are the most important although wheat streak mosaic virus (WSMV) has caused some localized outbreaks in some years. In context of cultivar registration in Canada, there are certain diseases that breeders have to take into account while developing resistant cultivars. The Prairie Recommending Committee for Wheat, Rye, and Triticale (PRCWRT) classify wheat diseases into priority one, priority two, and priority three depending on prevalence and potential damage they can cause. However, priority one diseases are more of a concern and a minimum level of resistance in commercial cultivars is recommended for those.
Interdisciplinary Pain Neuroscience Continuing Education in the Veterans Affairs
Authors: Louw Adriaan , Vogsland Rebecca , Marth Lindsay , Marshall Peter , Cox Terry , Landers Merrill
Published: August 2019

Objective:

Because of the pain and opioid epidemic in the United States, there is a need to update clinician’s knowledge, attitudes, and beliefs regarding persistent pain across health care disciplines. The aim of this study was to determine if health care professionals can positively change their knowledge, attitudes, and beliefs regarding chronic pain, following a pain neuroscience education (PNE) lecture and 1 year follow-up.

Materials and Methods:

A total of 270 health care providers at the Minneapolis Veterans Affairs Health Care System received a 3.5-hour PNE lecture in person or via live-stream. Primary outcomes were the Neurophysiology of Pain Questionnaire (NPQ) and Health Care Providers’ Pain and Impairment Relationship Scale (HC-PAIRS) measured before, immediately after, and 1 year after the PNE lecture. At 1 year participants were also asked how the PNE lecture affected their practice.

Results:

Pain knowledge (NPQ) (P<0.01) and attitudes and beliefs regarding persistent pain (HC-PAIRS) (P<0.01) improved for all providers, with specific improvements across several disciplines. Positive gains in outcomes were equal for in-person attendance, and live-streaming of the lecture. One year later, NPQ and HC-PAIRS gains diminished, yet clinicians reported a large positive impact on daily clinical practice.

Discussion:

PNE resulted in a positive clinical impact for health care providers treating patients with persistent pain. The mechanism of this effect may be about healthier attitudes and beliefs regarding persistent pain rather than increased knowledge about pain.
Improved periodontal disease and prevention of tooth loss in osteoporosis patients receiving once-yearly zoledronic acid: a randomized clinical trial
Authors: Taguchi Akira , Shiraki Masataka , Tanaka Satoshi , Ohshige Hideyo , Nakamura Toshitaka
Published: August 2019

Objective:

This randomized, clinical trial investigated whether zoledronic acid combined with oral health maintenance can improve periodontal disease associated with osteoporosis, thus reducing the risk of tooth loss.

Methods:

Participants were those of the ZONE (ZOledroNate treatment in efficacy to osteoporosis) study. None of the participants had symptomatic periodontal disease at baseline. Participants received either zoledronic acid (5 mg; n = 333 [male 21, female 312]) or placebo (n = 332 [male 19, female 313]) once yearly for 2 years, and their age was 74.0 ± 5.3 (65-88) and 74.3 ± 5.4 (65-87) years, respectively. Participants were instructed to maintain good oral hygiene at baseline and every 3 months. Participants with signs or symptoms involving their oral cavity at the monthly visit with their physician were referred to dentists for examination of oral disease. All cases were included to analyze adverse events in this study. Testing for significance was conducted using Fisher exact test (P < 0.05).

Results:

The incidence of oral adverse events was significantly higher in the control group (67 cases, 20.2%) than in the zoledronic acid group (47 cases, 14.1%; P = 0.04). The frequency of symptomatic periodontal disease observed during the study was significantly higher in the control group (40 cases, 12.0%) than in the zoledronic acid group (18 cases, 5.4%; P = 0.002). Loss of teeth was more frequent in the control group (36 cases, 10.8%) than in the zoledronic acid group (24 cases, 7.2%), although the difference was not significant.

Conclusions:

Zoledronic acid effectively prevented symptomatic periodontal disease in patients with osteoporosis who maintained good oral hygiene.

Video Summary:
Supplemental Digital Content 1, http://links.lww.com/MENO/A438.
Early onset of action with a 17β-estradiol, softgel, vaginal insert for treating vulvar and vaginal atrophy and moderate to severe dyspareunia
Authors: Constantine Ginger , Millheiser Leah S. , Kaunitz Andrew M. , Parish Sharon J. , Graham Shelli , Bernick Brian , Mirkin Sebastian
Published: August 2019

Objective:

The softgel 17β-estradiol (E2) vaginal inserts (4 and 10 μg; Imvexxy; TherapeuticsMD, Boca Raton, FL) are FDA approved for treating moderate to severe dyspareunia associated with postmenopausal vulvar and vaginal atrophy (VVA). The objective here was to determine responder rates at week 2 and whether week-2 findings predicted week-12 responders in the REJOICE trial.

Methods:

Postmenopausal women received E2 vaginal inserts 4, 10, or 25 μg, or placebo for 12 weeks. Proportion of responders (having ≥2 of the following: vaginal superficial cells >5%, vaginal pH <5.0, or dyspareunia improvement of ≥1 category) were calculated. Odds ratios (ORs) for positive response at week 12 given a positive response at week 2 were determined in the efficacy evaluable (EE) population.

Results:

The responder rate (in EE population [n = 695]) was 74% to 82% with E2 inserts versus 24% with placebo at week 2, and 72% to 80% versus 33% at week 12. Positive treatment responses were 9- to 14-fold higher with vaginal E2 than with placebo at week 2, and 5- to 8-fold higher at week 12. Response at week 2 predicted response at week 12 in the total population (OR 13.1; 95% CI, 8.8-19.7) and with active treatment only (OR 7.9; 95% CI, 4.7-13.2).

Conclusions:

A high percentage of postmenopausal women with moderate to severe dyspareunia responded with the E2 softgel vaginal insert at week 2, and a positive response at week 2 predicted a positive response at week 12.
Association of bone mineral density with a first-degree family history of diabetes in normoglycemic postmenopausal women
Authors: Yang Lijuan , Hu Xiang , Zhang Hailing , Pan Wei , Yu Weihui , Gu Xuejiang
Published: August 2019

Objective:

A first-degree family history of diabetes (FHD) contributes to increased risks of metabolic and cardiovascular diseases. Bone is an insulin-resistant site and an organ susceptible to microvascular complications. The goal of the present study was to investigate the association of FHD with bone mineral density (BMD) in postmenopausal women.

Methods:

In all, 892 normoglycemic postmenopausal women were divided into subgroups of participants with or without a first-degree FHD. BMD was measured using dual-energy x-ray absorptiometry. Fasting plasma insulin and glucose levels were measured, and insulin resistance was evaluated using the Homeostasis Model Assessment—Insulin Resistance (HOMA-IR) index.

Results:

The BMD of the lumbar spine and femoral neck were much higher in the participants with a first-degree FHD than in those without an FHD (all P < 0.05). Lumbar spine BMD and femoral neck BMD were both positively associated with HOMA-IR (P = 0.041 and P = 0.005, respectively). Multiple stepwise regression analysis showed that a first-degree FHD was an independent factor that was positively associated with lumbar spine BMD (standardized β = 0.111, P = 0.001) and femoral neck BMD (standardized β = 0.078, P = 0.021). A first-degree FHD was associated with increased BMD, insulin resistance, and hyperinsulinemia.

Conclusions:

Our study indicated that normoglycemic postmenopausal women with a first-degree FHD exhibit increased BMD with insulin resistance and hyperinsulinemia. A first-degree FHD was an independent factor associated with elevated BMD in Chinese women after menopause.
The HIV-Associated Neurocognitive Disorders in Zambia (HANDZ) Study: Protocol of a research program in pediatric HIV in sub-Saharan Africa
Authors: Adams Heather R. , Mwanza-Kabaghe Sylvia , Mbewe Esau G. , Kabundula Pelekelo P. , Potchen Michael J. , Maggirwar Sanjay , Johnson Brent A. , Schifitto Giovanni , Gelbard Harris A. , Birbeck Gretchen L. , Bearden David R.
Published: August 2019

Approximately 10% of youth in sub-Saharan Africa are infected with the Human Immunodeficiency Virus. In Zambia, it is estimated that over 72,000 children have HIV infection, and despite access to combination antiretroviral therapy, many will experience HIV-associated neurocognitive deficits (HAND) encompassing cognitive and psychiatric sequelae such as global intellectual delay, executive dysfunction, and depressed mood. However, little is known about the neurocognitive profile of such children, the long-term outcomes and impacts of HAND, or the predictors and risk factors for HAND-related impairment. We have initiated the first-ever prospective, longitudinal study of neurocognition in children with HIV-infection in Zambia. Our overarching study goals are to validate cognitive and psychiatric testing tools in children with HIV infection in Zambia, and to determine if inflammatory biomarkers and brain imaging can prospectively identify children at high risk of developing HAND. This article outlines the study methods, highlights several challenges encountered in the initiation of the study, and offers solutions to these challenges.
Multivariate analysis of EEG activity indexes contingent and non-contingent attentional capture
Authors: Munneke Jaap , Fahrenfort Johannes , Sutterer David , Theeuwes Jan , Awh Edward
Published: August 2019

It is well known that salient yet irrelevant singleton can capture attention, even when this is inconsistent with the current goals of the observer (Theeuwes, 1992; 2010). Others however have claimed that capture is critically contingent on the goals of the observer: Capture is strongly modulated (or even eliminated) when the irrelevant singleton does not match the target-defining properties (Folk, Remington, & Johnston, 1992). There has been a long-standing debate on whether attentional capture can be explained by goal-driven and/or stimulus-driven accounts. Here, we shed further light on this phenomenon by using EEG activity (raw EEG and alpha power) to provide a time-resolved index of attentional orienting. Participants searched for a target defined by a pre-specified color. The search display was preceded by a singleton cue that either matched the color of the upcoming target (contingent cues), or that appeared in an irrelevant color (non-contingent cues). Multivariate analysis of raw EEG and alpha power revealed preferential tuning to the location of both contingent and non-contingent cues, with a stronger bias towards contingent than non-contingent cues. The time course of these effects, however, depended on the neural signal. Raw EEG data revealed attentional orienting towards the cue early on in the trial (>156 ms), while alpha power revealed sustained spatial selection in the cued locations at a later moment in the trial (>250 ms). Moreover, while raw EEG showed stronger capture by contingent cues during this early time window, the advantage for contingent cues arose during a later time window in alpha band activity. Thus, our findings suggest that raw EEG activity and alpha-band power tap into distinct neural processes that index movements of covert spatial attention. Both signals provide clear neural evidence that both contingent and non-contingent cues can capture attention, and that this process is robustly shaped by the target-defining properties in the current block of trials.
A Fast and Memory-Efficient Implementation of the Transfer Bootstrap
Authors: Lutteropp Sarah , Kozlov Alexey M. , Stamatakis Alexandros
Published: August 2019

Recently, Lemoine et al. suggested the Transfer Bootstrap Expectation (TBE) branch support metric as an alternative to classical phylogenetic bootstrap support metric on taxon-rich datasets. However, the original TBE implementation in the booster tool is compute- and memory-intensive. Therefore, we developed a fast and memory-efficient TBE implementation. We improved upon the original algorithm described by Lemoine et al. by introducing multiple algorithmic and technical optimizations. On empirical as well as on random tree sets with varying taxon counts, our implementation is up to 480 times faster than booster. Furthermore, it only requires memory that is linear in the number of taxa, which leads to 10× - 40× memory savings compared to booster. Our implementation has been partially integrated into pll-modules and RAxML-NG and is available under the GNU Affero General Public License v3.0 at https://github.com/ddarriba/pll-modules and https://github.com/amkozlov/raxml-ng. The parallelized version that also computes additional TBE-related statistics is available in pll-modules and RAxML-NG forks at: https://github.com/lutteropp/pll-modules/tree/tbe and https://github.com/lutteropp/raxml-ng/tree/tbe.
Ovule development in Cycads: observation on anatomy and nucellus morphology in Zamia and Cycas
Authors: Zhang Xin
Published: August 2019

In the ovule evolution, the integument is the most attention point in discussion as a morphologic character of the seed plants. There are several theories and hypotheses about the origin of the integument were presented in the history. However, the development and function of the ovule envelopes are not so clear until now. The development of thehe basal gymnosperms Cycas and Zamia were to investigated, especially of the integument to complement the existing knowledge in seed plants. The development of ovules of seed plant is documented with morphological and anatomical using LM and SEM.

The nucellar beak found in Zamia is a structure that has not been recorded previously. It protrudes from the micropyle at pollination and may be the primary acceptor for pollen. There are striking similarities to the lagenostom or salpinx in Lyginopteridatae. There may be an evolutionary way to interpret the pollination drop existing in the Lyginopteridatae. Probably the nucellar beak of Cycads, even Ginkgoales have the same function with the lagenostom or salpinx of the Lyginopteridatea. Unfortunately, pollen and transport inside the pollination chambers have not been observed. Further analysis of this unusual structure seems to be very important.
Genome-wide identification and transcriptomic analysis of microRNAs across various amphioxus organs using deep sequencing
Authors: Zhang Qi-Lin , Wang Hong , Zhu Qian-Hua , Wang Xiao-Xue , Li Yi-Min , Chen Jun-Yuan , Morikawa Hideaki , Yang Lin-Feng , Wang Yu-Jun
Published: August 2019

Amphioxus is the closest living invertebrate proxy of the vertebrate ancestor. Systematic gene identification and expression profile analysis of amphioxus organs is thus important for clarifying the molecular mechanisms of organ function formation and further understanding the evolutionary origin of organs and genes in vertebrates. The precise regulation of microRNAs (miRNAs) is crucial for the functional specification and differentiation of organs. In particular, those miRNAs that are expressed specifically in organs (OSMs) play key roles in organ identity, differentiation, and function. In this study, the genome-wide miRNA transcriptome was analyzed in eight organs of adult amphioxus Branchiostoma belcheri using deep sequencing. A total of 167 known miRNAs and 23 novel miRNAs (named novel_mir), including 139 conserved miRNAs, were discovered, and 79 of these were identified as OSMs. Additionally, analyses of the expression patterns of eight randomly selected known miRNAs demonstrated the accuracy of the miRNA deep sequencing that was used in this study. Furthermore, potentially OSM-regulated genes were predicted for each organ type. Functional enrichment of these predicted targets, as well as further functional analyses of known OSMs, was conducted. We found that the OSMs were potentially to be involved in organ specific functions, such as epidermis development, gonad development, muscle cell development, proteolysis, lipid metabolism and generation of neurons. Moreover, OSMs with non-organ specific functions were detected, and primarily include those related to innate immunity and response to stimuli. These findings provide insights into the regulatory roles of OSMs in various amphioxus organs.