bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microtubule self-organisation during seed germination in Arabidopsis
Authors: Yan Huifang , Chaumont Nicole , Gilles Jean François , Bolte Susanne , Hamant Olivier , Bailly Christophe 
Published: April 2020

AbstractBackgroundUpon water uptake and release of seed dormancy, embryonic plant cells expand, while being mechanically constrained by the seed coat. Cortical microtubules (CMTs) are key players of cell elongation in plants: their anisotropic orientation channels the axis of cell elongation through the guidance of oriented deposition of load-bearing cellulose microfibrils in the cell wall. Interestingly, CMTs align with tensile stress, and consistently, they reorient upon compressive stress in growing hypocotyls. How CMTs first organise in germinating embryos is unknown, and their relation with mechanical stress has not been investigated at such an early developing stage.ResultsHere, we analysed CMT dynamics in dormant and non-dormantArabidopsisseeds by microscopy of fluorescently tagged microtubule markers at different developmental time points and in response to abscisic acid and gibberellins. We found that CMTs first appear as very few thick bundles in dormant seeds. Consistently, analysis of available transcriptome and translatome datasets show that limiting amounts of tubulin and microtubule regulators initially hinder microtubule self-organisation. Seeds imbibed in the presence of gibberellic acid or abscisic acid displayed altered microtubule organisation and transcriptional regulation. Upon the release of dormancy, CMTs then self-organise into multiple parallel transverse arrays. Such behaviour matches the tensile stress patterns in such mechanically constrained embryos. This suggests that, as CMTs first self-organise, they also align with shape-derived tensile stress patterns.ConclusionsOur results provide a scenario in which dormancy release in the embryo triggers microtubule self-organisation and alignment with tensile stress prior to germination and anisotropic growth.
A scoping review of network meta-analyses assessing the efficacy and safety of complementary and alternative medicine interventions
Authors: Pratt Misty , Wieland Susan , Ahmadzai Nadera , Butler Claire , Wolfe Dianna , Pussagoda Kusala , Skidmore Becky , Veroniki Argie , Rios Patricia , Tricco Andrea C. , Hutton Brian 
Published: April 2020

Abstract
Background
Network meta-analysis (NMA) has rapidly grown in use during the past decade for the comparison of healthcare interventions. While its general use in the comparison of conventional medicines has been studied previously, to our awareness, its use to assess complementary and alternative medicines (CAM) has not been studied. A scoping review of the literature was performed to identify systematic reviews incorporating NMAs involving one or more CAM interventions.

Methods
An information specialist executed a multi-database search (e.g., MEDLINE, Embase, Cochrane), and two reviewers performed study selection and data collection. Information on publication characteristics, diseases studied, interventions compared, reporting transparency, outcomes assessed, and other parameters were extracted from each review.

Results
A total of 89 SR/NMAs were included. The largest number of NMAs was conducted in China (39.3%), followed by the United Kingdom (12.4%) and the United States (9.0%). Reviews were published between 2010 and 2018, with the majority published between 2015 and 2018. More than 90 different CAM therapies appeared at least once, and the median number per NMA was 2 (IQR 1–4); 20.2% of reviews consisted of only CAM therapies. Dietary supplements (51.1%) and vitamins and minerals (42.2%) were the most commonly studied therapies, followed by electrical stimulation (31.1%), herbal medicines (24.4%), and acupuncture and related treatments (22.2%). A diverse set of conditions was identified, the most common being various forms of cancer (11.1%), osteoarthritis of the hip/knee (7.8%), and depression (5.9%). Most reviews adequately addressed a majority of the PRISMA NMA extension items; however, there were limitations in indication of an existing review protocol, exploration of network geometry, and exploration of risk of bias across studies, such as publication bias.

Conclusion
The use of NMA to assess the effectiveness of CAM interventions is growing rapidly. Efforts to identify priority topics for future CAM-related NMAs and to enhance methods for CAM comparisons with conventional medicine are needed.

Systematic review registration
https://ruor.uottawa.ca/handle/10393/35658
Infection with the sheep gastrointestinal nematode Teladorsagia circumcincta increases luminal pathobionts
Authors: Cortés Alba , Wills John , Su Xiaopei , Hewitt Rachel E. , Robertson Jack , Scotti Riccardo , Price Daniel R. G. , Bartley Yvonne , McNeilly Tom N. , Krause Lutz , Powell Jonathan J. , Nisbet Alasdair J. , Cantacessi Cinzia 
Published: April 2020

AbstractBackgroundThe multifaceted interactions between gastrointestinal (GI) helminth parasites, host gut microbiota and immune system are emerging as a key area of research within the field of host-parasite relationships. In spite of the plethora of data available on the impact that GI helminths exert on the composition of the gut microflora, whether alterations of microbial profiles are caused by direct parasite-bacteria interactions or, indirectly, by alterations of the GI environment (e.g. mucosal immunity) remains to be determined. Furthermore, no data is thus far available on the downstream roles that qualitative and quantitative changes in gut microbial composition play in the overall pathophysiology of parasite infection and disease.ResultsIn this study, we investigated the fluctuations in microbiota composition and local immune microenvironment of sheep vaccinated against, and experimentally infected with, the ‘brown stomach worm’Teladorsagia circumcincta, a parasite of worldwide socio-economic significance. We compared the faecal microbial profiles of vaccinated and subsequently infected sheep with those obtained from groups of unvaccinated/infected and unvaccinated/uninfected animals. We show that alterations of gut microbial composition are associated mainly with parasite infection, and that this involves the expansion of populations of bacteria with known pro-inflammatory properties that may contribute to the immunopathology of helminth disease. Using novel quantitative approaches for the analysis of confocal microscopy-derived images, we also show that gastric tissue infiltration of T cells is driven by parasitic infection rather than anti-helminth vaccination.ConclusionsTeladorsagia circumcinctainfection leads to an expansion of potentially pro-inflammatory gut microbial species and abomasal T cells. This data paves the way for future experiments aimed to determine the contribution of the gut flora to the pathophysiology of parasitic disease, with the ultimate aim to design and develop novel treatment/control strategies focused on preventing and/or restricting bacterial-mediated inflammation upon infection by GI helminths.
Gut bacterial ClpB-like gene function is associated with decreased body weight and a characteristic microbiota profile
Authors: Arnoriaga-Rodríguez María , Mayneris-Perxachs Jordi , Burokas Aurelijus , Pérez-Brocal Vicente , Moya Andrés , Portero-Otin Manuel , Ricart Wifredo , Maldonado Rafael , Fernández-Real José-Manuel 
Published: April 2020

AbstractBackgroundThe chaperone ClpB, a bacterial protein, is a conformational antigen-mimetic of α-melanocyte-stimulating hormone (α-MSH) implicated in body weight regulation in mice. We here investigated the potential associations of gut bacterial ClpB-like gene function with obesity status and gut microbiota in humans.ResultsGut microbiota ClpB KEGG function was negatively associated with body mass index, waist circumference, and total fat mass (DEXA). The relative abundance (RA) of several phyla and families directly associated with ClpB was decreased in subjects with obesity. Specifically, the RA ofRikenellaceae,Clostridiaceaeand not assignedFirmicutes were lower in subjects with obesity and positively associated with gut bacterial ClpB-like gene function (not assignedFirmicutes(r =0.405, FDR = 2.93 × 10−2),Rikenellaceae(r =0.217, FDR = 0.031), andClostridiaceae(r =0.239, FDR = 0.017)). The gut bacterial ClpB-like gene function was also linked to specific plasma metabolites (hippuric acid and 3-indolepropionic acid) and fecal lupeol. The α-MSH-like epitope similar to that ofEscherichia coliClpB was also identified in some sequences of those bacterial families.After fecal transplantation from humans to mice, the families that more contributed to ClpB-like gene function in humans were also associated with ClpB-like gene function in mice after adjusting for the donor’s body mass index (not assignedFirmicutes(r =0.621,p =0.003),Prevotellaceae(r =0.725,p =4.1 × 10−7),Rikenellaceae(r =0.702,p =3.9 × 10−4), andRuminococcaceae(r =0.526,p =0.014)).Clostridiaceae(r =− 0.445,p =0.038) andPrevotellaceaeRA (r = −0.479,p =0.024) and were also negatively associated with weight gain in mice. The absolute abundance (AA) ofPrevotellaceaein mice was also positively associated with the gut bacterial ClpB-like gene function in mice. DESeq2 identified species ofPrevotellaceae, both negatively associated with mice’ weight gain and positively with gut bacterial ClpB-like gene function.ConclusionsIn summary, gut bacterial ClpB-like gene function is associated with obesity status, a specific gut microbiota composition and a plasma metabolomics profile in humans that could be partially transplanted to mice.
Clinical evidence based review and systematic scientific review in the identification of malignant transformation of inverted papilloma
Authors: Long Cai , Jabarin Basel , Harvey Alexandra , Ham Jennifer , Javer Amin , Janjua Arif , Thamboo Andrew 
Published: April 2020

Background Inverted papilloma (IP) is an unusual type of benign tumor that has high recurrence rates and the potential to transform into squamous cell carcinomas (SCC). The mechanism of the transformation process from IP to IP-SCC is uncertain and there is no consensus regarding the best practice for IP-SCC detection. The goal of this study is to identify the best clinical methods to detect for IP-SCC. Methods An evidence-based review was performed using Medline and Ovid to obtain all articles up to October 10th, 2019 pertaining to identification of IP malignant transformation. All manuscripts discussing clinical methods or biomarkers were included. Results Based on clinical research studies, convoluted cerebriform pattern and apparent diffusion coefficient values on Magnetic Resonance Imaging (MRI) can help differentiate benign IP from SCC and increased SUVmax on PET/CT is associated with higher probability of malignancy although not as specific. No consensus about the best biomarker for IP-SCC has been reached among researchers and continues to be exploratory. Conclusion Endoscopy with biopsy is the gold standard practice to identify IP-SCC; however, MRI is the preferred imaging modality to recognize malignant transformation in cases where biopsy is difficult. Multiple biomarkers have shown positive results, but no single indicator with clinical significance for monitoring malignant transformation process has been found.
Comparing the intestinal bacterial communies of sympatric wintering Hooded Crane (Grus monacha) and Domestic Goose (Anser anser domesticus)
Authors: Fu Rong , Xiang Xingjia , Dong Yuanqiu , Cheng Lei , Zhou Lizhi 
Published: April 2020

Abstract
Background
Gut microbiota play crucial roles in host health. Wild birds and domestic poultry often occupy sympatric habitats, which facilitate the mutual transmission of intestinal microbes. However, the distinct intestinal microbial communities between sympatric wild birds and poultry remain unknown. At present, the risk of interspecies transmission of pathogenic bacteria between wild and domestic host birds is also a research hotspot.

Methods
This study compared the intestinal bacterial communities of the overwintering Hooded Crane (Grus monacha) and the Domestic Goose (Anser anser domesticus) at Shengjin Lake, China, using Illumina high-throughput sequencing technology (Mi-Seq platform).

Results
Our results revealed that Firmicutes, Actinobacteria, Proteobacteria, Bacteroidetes and Chloroflexi were the dominant bacterial phyla in both hosts. The gut bacterial community composition differed significantly between sympatric Hooded Cranes and Domestic Geese. However, the hosts exhibited little variation in gut bacterial alpha-diversity. The relative abundance of Firmicutes was significantly higher in the guts of the Hooded Cranes, while the relative abundances of Actinobacteria, Proteobacteria, Bacteroidete and Chloroflexi were significantly higher in guts of Domestic Geese. Moreover, a total of 132 potential pathogenic operational taxonomic units (OTUs) were detected in guts of Hooded Cranes and Domestic Geese, and 13 pathogenic OTUs (9.8%) were found in both host guts. Pathogenic bacterial community composition and diversity differed significantly between hosts.

Conclusions
The results showed that the gut bacterial community composition differs significantly between sympatric Hooded Cranes and Domestic Geese. In addition, potential pathogens were detected in the guts of both Hooded Cranes and Domestic Geese, with 13 pathogenic OTUs overlapping between the two hosts, suggesting that more attention should be paid to wild birds and poultry that might increase the risk of disease transmission in conspecifics and other mixed species.
Objective measurement in Parkinson’s disease: a descriptive analysis of Parkinson’s symptom scores from a large population of patients across the world using the Personal KinetiGraph®
Authors: Pahwa Rajesh , Bergquist Filip , Horne Malcolm , Minshall Michael E. 
Published: April 2020

Abstract
Background
The Personal KinetiGraph® (PKG®) Movement Recording System provides continuous, objective, ambulatory movement data during routine daily activities and provides information on medication compliance, motor fluctuations, immobility, and tremor for patients with Parkinson’s disease (PD). Recent evidence has proposed targets for treatable symptoms. Indications for PKG vary by country and patient selection varies by physician.

Methods
The analyses were based upon 27,834 complete and de-identified PKGs from January 2012 to August 2018 used globally for routine clinical care. Median scores for bradykinesia (BKS) and dyskinesia (DKS) as well as percent time with tremor (PTT) and percent time immobile (PTI) were included as well as proportions of PKGs above published PKG summary score target values (BKS > 25, DKS > 9, PTT > 1%, PTI > 10%). Two sub-analyses included subjects who had 2+ PKG records and scores above proposed BKS and DKS targets, respectively, on their first PKG. Median BKS and DKS scores for subsequent PKGs (1st, 2nd, etc.) were summarized and limited to those with 100+ subsequent PKGs for each data point.

Results
Significant differences between countries were found for all 4 PKG parameter median scores (all p < 0.0001). Overall, 54% of BKS scores were > 25 and ranged from 46 to 61% by country. 10% of all DKS scores were > 9 and ranged from 5 to 15% by country. Sub-analysis for BKS showed global median BKS and DKS scores across subsequent PKGs for subjects who had 2+ PKGs and had BKS > 25 on their first PKG. There were significant changes in BKS from 1st to 2nd-6th PKGs (all p < 0.0001). Sub-analysis for DKS showed global median BKS & DKS scores across subsequent PKGs for subjects who had 2+ PKGs and had DKS > 9 on their first PKG. There were significant changes in DKS from 1st to 2nd and 3rd PKGs (both p < 0.0001).

Conclusions
This analysis shows that in every country evaluated a meaningful proportion of patients have sub-optimal PD motor symptoms and substantial variations exist across countries. Continuous objective measurement (COM) in routine care of PD enables identification and quantification of PD motor symptoms, which can be used to enhance clinical decision making, track symptoms over time and improve PD symptom scores. Thus, clinicians can use these PKG scores during routine clinical management to identify PD symptoms and work to move patients into a target range or a more controlled symptom state.
Intraoperative optical coherence tomographic findings in patients undergoing subretinal gene therapy surgery
Authors: Vasconcelos Huber M. , Lujan Brandon J. , Pennesi Mark E. , Yang Paul , Lauer Andreas K. 
Published: April 2020

Abstract
Background
To analyze intraoperative OCT (iOCT) findings during subretinal gene therapy.

Methods
A single-center, retrospective, observational, case series study of twenty one eyes submitted to subretinal gene therapy. Intrasurgical high definition videos were included for analyzes. Cases with absence of iOCT video or unsuccessful bleb creation were excluded. Sharp needle tip (SNT) or blunted needle tip (BNT) and their interaction with neurosensory retina were evaluated. Presence of subretinal air bubbles, visible opened retinotomy, and medication reflux were also correlated and analyzed.

Results
Nineteen of twenty-one eyes were included. Of the two excluded eyes, subretinal bleb creation was unsuccessful in one and technical issues prevented OCT image acquisition in the other. Immediately before subretinal injection, needle indention/penetration of the neurosensory retina with temporary indentation of the RPE/choroid was evident in 16 (84%) of the 19 eyes. Complete RPE/choroid indentation was needed with BNT use compared to SNT (p = 0.0114). An open retinotomy was identified in 14 (74%) of 19 eyes at the conclusion of bleb injection and was more commonly associated with SNT (p = 0.0108).

Conclusions
iOCT provides valuable real-time feedback of cross-sectional retinal anatomy during subretinal gene therapy surgeries. The type of needle tip and its use during the gene therapy procedure seems to influence in the bleb creation and presence of visible open retinotomy. Further studies of iOCT findings during gene therapy delivery procedures are likely to help refine the surgical technique.
Skin disorders among children living in orphanage centres in Dar es Salaam, Tanzania
Authors: Amiri Mwanaidi , Furia Francis F. , Bakari Muhammad 
Published: April 2020

Abstract
Background
Skin conditions contribute significantly to the global burden of diseases and are among the leading causes of non-fatal disease burden. Children living in orphanage centres are vulnerable to several conditions including dermatological disorders, and there is limited data on the burden of these conditions among orphans in Tanzania. This study was carried out to determine the pattern of dermatological conditions and contributing factors among orphans in Dar es Salaam, Tanzania.

Methodology
A cross-sectional study was conducted among 420 children aged less than 18 years from 12 orphanage centres in Dar es Salaam. Guided interviews using structured questionnaires were carried out to obtain socio-demographic and clinical data from participants. Clinical examination was performed for each participant and whenever indicated skin scrapings and biopsy were obtained.

Results
Four hundred and twenty participants were recruited out of which 281 (66.9%) were male, mean and median ages of participants were 11 ± 3.7 and 12 years, respectively. Two hundred and twenty-five (53.6%) participants were aged between 6 and12 years. Proportion of children with dermatological manifestations among participants was 57.4%. Two hundred and ninety-six diagnoses were made comprising of 192 (64.9%) infections and 104 (35.1%) non-infectious conditions. Tinea capitis was the commonest infection while acne vulgaris was the most common non-infectious condition. Proportionately more male children were affected as compared to female ones, p = 0.006.

Conclusion
Skin conditions are common among children living in orphanage centres in Dar es Salaam. Infectious conditions were predominant conditions and male children were more affected than female children. Reducing crowding and improving hygienic practices in these centres will be important in reducing the burden of these conditions.
Defining and conceptualizing outcomes for de-implementation: key distinctions from implementation outcomes
Authors: Prusaczyk Beth , Swindle Taren , Curran Geoffrey 
Published: April 2020

Abstract
Background
Increasingly, scholars argue that de-implementation is a distinct concept from implementation; factors contributing to stopping a current practice might be distinct from those that encourage adoption of a new one. One such distinction is related to de-implementation outcomes. We offer preliminary analysis and guidance on de-implementation outcomes, including how they may differ from or overlap with implementation outcomes, how they may be conceptualized and measured, and how they could be measured in different settings such as clinical care vs. community programs.

Conceptualization of outcomes
We conceptualize each of the outcomes from Proctor and colleagues’ taxonomy of implementation outcomes for de-implementation research. First, we suggest key considerations for researchers assessing de-implementation outcomes, such as considering how the cultural or historical significance to the practice may impact de-implementation success and, as others have stated, the importance of the patient in driving healthcare overuse. Second, we conceptualize de-implementation outcomes, paying attention to a number of factors such as the importance of measuring outcomes not only of the targeted practice but of the de-implementation process as well. Also, the degree to which a practice should be de-implemented must be distinguished, as well as if there are thresholds that certain outcomes must reach before action is taken. We include a number of examples across all outcomes, both from clinical and community settings, to demonstrate the importance of these considerations. We also discuss how the concepts of health disparities, cultural or community relevance, and altruism impact the assessment of de-implementation outcomes.

Conclusion
We conceptualized existing implementation outcomes within the context of de-implementation, noted where there are similarities and differences to implementation research, and recommended a clear distinction between the target for de-implementation and the strategies used to promote de-implementation. This critical analysis can serve as a building block for others working to understand de-implementation processes and de-implement practices in real-world settings.
Conical diffraction from type-II Dirac point at metasurfaces
Authors: Li Haitao , Hu Chuandeng , Zhou Xiaoxi , Lu Weixin , Hou Bo , Wen Weijia 
Published: April 2020

Abstract
Type-II Dirac point degeneracy can be realized at two-dimensional metasurfaces, where a pair of tilted cones is formed in the dispersion relation

whose equal-frequency contour at the degeneracy frequency presents an X-shaped cross in k-space. Consequently, two group velocities are obtained at the Dirac point, due to the peculiar shape of the spatial dispersion, and point to the different directions with the intersection angle dependent on the cone's geometry. Therefore, a conical-diffraction phenomenon takes place. We observe the conical diffraction through launching into the metasurface a Gaussian-like beam at the Dirac frequency and mapping the propagation of the wave field. Both experimental and simulating results demonstrate the conical diffraction at the type-II Dirac point.