bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enabling reusability of plant phenomic datasets with MIAPPE 1.1
Authors: Papoutsoglou Evangelia A. , Faria Daniel , Arend Daniel , Arnaud Elizabeth , Athanasiadis Ioannis N. , Chaves Inês , Coppens Frederik , Cornut Guillaume , Costa Bruno V. , Ćwiek‐Kupczyńska Hanna , Droesbeke Bert , Finkers Richard , Gruden Kristina , Junker Astrid , King Graham J. , Krajewski Paweł , Lange Matthias , Laporte Marie‐Angélique , Michotey Célia , Oppermann Markus , Ostler Richard , Poorter Hendrik , Ramı́rez‐Gonzalez Ricardo , Ramšak Živa , Reif Jochen C. , Rocca‐Serra Philippe , Sansone Susanna‐Assunta , Scholz Uwe , Tardieu François , Uauy Cristobal , Usadel Björn , Visser Richard G. F. , Weise Stephan , Kersey Paul J. , Miguel Célia M. , Adam‐Blondon Anne‐Françoise , Pommier Cyril 
Published: March 2020

Summary

Enabling data reuse and knowledge discovery is increasingly critical in modern science, and requires an effort towards standardising data publication practices. This is particularly challenging in the plant phenotyping domain, due to its complexity and heterogeneity.

We have produced the MIAPPE 1.1 release, which enhances the existing MIAPPE standard in coverage, to support perennial plants, in structure, through an explicit data model, and in clarity, through definitions and examples.

We evaluated MIAPPE 1.1 by using it to express several heterogeneous phenotyping experiments in a range of different formats, to demonstrate its applicability and the interoperability between the various implementations. Furthermore, the extended coverage is demonstrated by the fact that one of the datasets could not have been described under MIAPPE 1.0.

MIAPPE 1.1 marks a major step towards enabling plant phenotyping data reusability, thanks to its extended coverage, and especially the formalisation of its data model, which facilitates its implementation in different formats. Community feedback has been critical to this development, and will be a key part of ensuring adoption of the standard.
In vitro evidence of root colonization suggests ecological versatility in the genus Mycena
Authors: Thoen Ella , Harder Christoffer Bugge , Kauserud Håvard , Botnen Synnøve S. , Vik Unni , Taylor Andy F. S. , Menkis Audrius , Skrede Inger 
Published: March 2020

Summary

The root‐associated habit has evolved on numerous occasions in different fungal lineages, suggesting a strong evolutionary pressure for saprotrophic fungi to switch to symbiotic associations with plants. Species within the ubiquitous, saprotrophic genus Mycena are frequently major components in molecular studies of root‐associated fungal communities, suggesting that an evaluation of their trophic status is warranted. Here, we report on interactions between a range of Mycena species and the plant Betula pendula.

In all, 17 Mycena species were inoculated onto B. pendula seedlings. Physical interactions between hyphae and fine roots were examined using differential staining and fluorescence microscopy. Physiological interactions were investigated using 14C and 32P to show potential transfer between symbionts.

All Mycena species associated closely with fine roots, showing hyphal penetration into the roots, which in some cases were intracellular. Seven species formed mantle‐like structures around root tips, but none formed a Hartig net. Mycena pura and Mycena galopus both enhanced seedling growth, with M. pura showing significant transfer of 32P to the seedlings.

Our results support the view that several Mycena species can associate closely with plant roots and some may potentially occupy a transitional state between saprotrophy and biotrophy.
Antibodies against human papillomavirus proteins in Barrett's dysplasia and intramucosal esophageal adenocarcinoma
Authors: Rajendra Shanmugarajah , Xuan Wei , Hufnagel Katrin , Sharma Prateek , Pavey Darren , Alhajjiri Noureddin , Rattan Arti , Wang Bin 
Published: March 2020

AbstractHigh‐risk human papillomavirus (HPV) types 16/18 have been associated with Barrett's dysplasia (BD)/esophageal adenocarcinoma (EAC). Nevertheless, no data exist in relation to serological analysis for HPV antibodies in BD/EAC with site‐specific viral DNA status. We prospectively examined antibodies to multiple HPV types in 438 patients representing hospital/reflux controls and Barrett's metaplasia (BM)/BD/intramucosal EAC. Antibody responses to HPV6/11/16/18/31/33/45/52/58 were analyzed using multiplex serology, including antibodies to E6/E7/E1/E2 and L1 antigens. Seropositivity for individual HPV proteins was infrequent in both cases and controls and was ≤10.2%. There was no difference in the seroprevalence of antibodies to any HPV antigen/antibody combination between reclassified cases (BD/EAC) and controls (hospital/reflux/BM) or between HPV16 or HPV18 DNA cases and controls, respectively. Among HPV16 DNA–positive BD/EAC cases, antibodies to HPV16 E7 were significantly more prevalent (3/26, 11.5%) than in hospital and reflux controls plus BM (5/328, 1.5%) (adjusted OR = 10.12, 95% CI: 1.61–63.73, P = 0.014). Among HPV18 DNA–positive cases, antibodies to HPV18 E1 were present in 3/6 (50%) cases versus 5/328 (1.5%) controls (adjusted OR = 44.28, 95% CI: 6.10–321.47, P = 0.0002). Although antibodies against HPV were generally uncommon in cases and controls, immune responses against two early proteins of HPV16/18 were significantly more frequent in viral DNA–positive BD/intramucosal EAC.
InvasiveChromolaena odorataspecies specifically affects growth of its co‐occurring weeds
Authors: Xu Qiu‐Yuan , Wang Dan , Quan Guo‐Ming , Xiang Hui‐Min , Zhang Jia‐En 
Published: March 2020

AbstractPlant–plant interaction is essential to weed invasion success and is related to impacts on the environment. To understand interactions of the well‐known invasive plant siamweed (Chromolaena odorata) and its neighbors (exoticPraxelis clematideaand native cadillo) in South China, and their competitive mechanisms above‐ and belowground, a multicultivation experiment was conducted. Competitive indices, plant morphological traits, soil nutrient contents, enzyme activities, and microbial biomass were measured. Competitive balance index and morphological traits revealed balanced competition betweenP. clematideaand siamweed, and suppressive effect of siamweed on cadillo. In coculture of siamweed andP. clematidea, the branch length of siamweed slightly lengthened, while the branch number ofP. clematideaincreased compared with their respective monocultures accordingly. Overall impacts of the two invaders on soil properties were near averages of their single impacts. In coculture of siamweed and cadillo, siamweed was more competitive in both light and nutrient capture; soil urease activity and acid phosphatase activity were magnified and mitigated compared with the averages of those in their respective monocultures, respectively. The species‐specific results of siamweed competing with its co‐occurring weeds would contribute to a better understanding of mechanism in synergistic effect of siamweed with the other invasive plants.
First‐generation genome editing in potato using hairy root transformation
Authors: Butler Nathaniel M. , Jansky Shelley H. , Jiang Jiming 
Published: March 2020

SummaryGenome editing and cis‐gene breeding have rapidly accelerated crop improvement efforts, but their impacts are limited by the number of species capable of being genetically transformed. Many dicot species, including some vital potato relatives being used to accelerate breeding and genetics efforts, remain recalcitrant to standard Agrobacterium tumefaciens‐based transformation. Hairy root transformation using Agrobacterium rhizogenes (A. rhizogenes) provides an accelerated approach to generating transgenic material but has been limited to analysis of hairy root clones. In this study, strains of A. rhizogenes were tested in the wild diploid potato relative Solanum chacoense, which is recalcitrant to infection by Agrobacterium tumefaciens. One strain of A. rhizogenes MSU440 emerged as being capable of delivering a T‐DNA carrying the GUS marker and generating transgenic hairy root clones capable of GUS expression and regeneration to whole plants. CRISPR/Cas9 reagents targeting the potato PHYTOENE DESATURASE (StPDS) gene were expressed in hairy root clones and regenerated. We found that 64%–98% of transgenic hairy root clones expressing CRISPR/Cas9 reagents carried targeted mutations, while only 14%–30% of mutations were chimeric. The mutations were maintained in regenerated lines as stable mutations at rates averaging at 38% and were capable of germ‐line transmission to progeny. This novel approach broadens the numbers of genotypes amenable to Agrobacterium‐mediated transformation while reducing chimerism in primary events and accelerating the generation of edited materials.
Heart‐rate evaluation using fetal ultrasonic Doppler during neonatal resuscitation
Authors: Kayama Kazunori , Hosono Shigeharu , Yoshikawa Kayo , Kato Ryota , Seimiya Ayako , Fuwa Kazumasa , Hijikata Midori , Aoki Ryoji , Okahashi Aya , Nagano Nobuhiko , Morioka Ichiro 
Published: March 2020

AbstractBackgroundThe objective of the present study was to verify the speed and accuracy of fetal ultrasonic Doppler (fetal Doppler) in measuring heart rate of newborns at rest, including preterm, low‐birthweight infants, and its efficacy during neonatal resuscitation, including cases of neonatal asphyxia.MethodsA three‐lead electrocardiogram and fetal Doppler were used to measure resting heart rates in 100 newborns, including 48 preterm, low‐birthweight infants, at 0 to 72 h after birth. Times to display heart rate were compared between electrocardiogram and fetal Doppler by the Bland–Altman analysis and Wilcoxon signed‐rank test. The time required for the fetal Doppler to measure heart rate during neonatal resuscitation was also assessed.ResultsIn 100 newborns, the mean error of the resting heart rate in 1,293 measurement points was 0.07 beats/min. To display the heart rate, the fetal Doppler required a median time of 5 s, and electrocardiogram required a median time of 10 s (P < 0.001). During neonatal resuscitation, the heart rate was measured within 10 s in 18 of 21 cases (86%) and displayed with a median time of 5 s; this was measured in all neonatal asphyxia cases (9/9, 100%).ConclusionsFetal Doppler can measure heart rate in newborns accurately and rapidly and is useful for evaluating heart rate not only at rest but also during neonatal resuscitation, especially in asphyxia.
Echinococcus multilocularis vesicular fluid induces the expression of immune checkpoint proteins in vitro
Authors: Bellanger Anne‐Pauline , Courquet Sandra , Pallandre Jean‐René , Godet Yann , Millon Laurence 
Published: March 2020

AbstractAimsAlveolar echinococcosis is a severe chronic helminthic infection that mimics a tumour‐like disease. This study aimed at investigating in vitro interactions between Echinococcus multilocularis vesicular fluid (VF) and different immune checkpoints (PD‐1/PD‐L1, CTLA‐4, LAG‐3 and TIM‐3).Methods and ResultsPeripheral blood mononuclear cells (PBMC) from healthy blood donors were isolated by Ficoll. Natural killer (NK) cells were selected. Each type of cell was stimulated individually with E. multilocularis‐VF. Expression of the different immune checkpoints was measured by flow cytometry on day 3 and day 6; all supernatants were used for immunoassays. Cells and supernatants from 22 healthy donors were analysed. A significant increase of PD‐1, PD‐L1, LAG‐3 and TIM‐3 was observed upon E. multilocularis‐VF exposure for NK cells on day 3 (P < .05, Wilcoxon signed‐rank test). A significant increase of PD‐L1 and CTLA‐4 was observed upon E. multilocularis‐VF exposure for T cells on day 6 (P < .05, Wilcoxon signed‐rank test), which was associated with increased levels of Th1 and Th2 cytokines P < .05, Wilcoxon signed‐rank test).ConclusionThese preliminary data suggest that immune checkpoints could be a way for E. multilocularis to modulate the host immune response during alveolar echinococcosis.
Application of a Risk Analysis Tool to Middle East Respiratory Syndrome Coronavirus (MERS‐CoV) Outbreak in Saudi Arabia
Authors: Chen Xin , Chughtai Abrar A. , MacIntyre Chandini R. 
Published: March 2020

AbstractThe Grunow–Finke assessment tool (GFT) is an accepted scoring system for determining likelihood of an outbreak being unnatural in origin. Considering its high specificity but low sensitivity, a modified Grunow–Finke tool (mGFT) has been developed with improved sensitivity. The mGFT has been validated against some past disease outbreaks, but it has not been applied to ongoing outbreaks. This study is aimed to score the outbreak of Middle East respiratory syndrome coronavirus (MERS‐CoV) in Saudi Arabia using both the original GFT and mGFT. The publicly available data on human cases of MERS‐CoV infections reported in Saudi Arabia (2012–2018) were sourced from the FluTrackers, World Health Organization, Saudi Ministry of Health, and published literature associated with MERS outbreaks investigations. The risk assessment of MERS‐CoV in Saudi Arabia was analyzed using the original GFT and mGFT criteria, algorithms, and thresholds. The scoring points for each criterion were determined by three researchers to minimize the subjectivity. The results showed 40 points of total possible 54 points using the original GFT (likelihood: 74%), and 40 points of a total possible 60 points (likelihood: 67%) using the mGFT, both tools indicating a high likelihood that human MERS‐CoV in Saudi Arabia is unnatural in origin. The findings simply flag unusual patterns in this outbreak, but do not prove unnatural etiology. Proof of bioattacks can only be obtained by law enforcement and intelligence agencies. This study demonstrated the value and flexibility of the mGFT in assessing and predicting the risk for an ongoing outbreak with simple criteria.
The effects of exergames on anxiety levels: A systematic review and meta‐analysis
Authors: Viana Ricardo Borges , Dankel Scott J. , Loenneke Jeremy P. , Gentil Paulo , Vieira Carlos Alexandre , Andrade Marília dos Santos , Vancini Rodrigo Luiz , de Lira Claudio Andre Barbosa 
Published: March 2020

There are currently many different approaches to performing exergames and there is still no consensus as to whether exergames are able to reduce anxiety levels, as well as whether exergames provide greater reductions on anxiety levels when added to traditional forms of clinical interventions. Therefore, the aim of the present systematic review and meta‐analysis was to access data from studies that evaluated the effects of exergames on anxiety levels in humans. PubMed, Scopus and Cochrane databases were searched up to 22 February 2019. Inclusion criteria were acute and chronic (short‐term and long‐term interventions) studies which evaluated the effects of exergames in anxiety levels as primary or secondary aim. Of the 1342 studies found, 17 and 10 were included in qualitative analyses and meta‐analyses, respectively. The within‐group analysis found that exergames (standardized mean difference [SMD]: −0.57 [95% Confidence interval (CI): −0.86 to −0.28], P < .001) and usual care (SMD: −0.21 [95% CI: −0.34 to −0.08], P = .002) resulted in significant improvements on anxiety levels. However, the between‐group meta‐analysis on the effects of control interventions vs exergames (SMD: 0.02 [95% CI: −0.55 to 0.60], P = .939) found no significant difference between groups in anxiety levels reductions. There was also no significant difference (SMD: −0.04 [95% CI: −0.32 to 0.25], P = .805) between usual care vs exergames plus usual care interventions in anxiety levels reductions. Although exergames demonstrated within‐group improvements in anxiety levels across different clinical populations, it was not greater than the effects from non‐exercise interventions. Also, given the paucity of studies, small sample sizes, different research designs, and different population investigated, the existing evidence is insufficient to support the advantages of usual care supplemented by exergame intervention over usual care standalone in anxiety levels reduction.
Quantifying farmland shelterbelt impacts on catchment soil erosion and sediment yield for the black soil region, northeastern China
Authors: Fang Haiyan 
Published: March 2020

AbstractAs one part of the ‘Three Norths’ forest protection system, dense farmland shelterbelt networks in northeastern China could greatly modify water and sediment flows. In this paper, catchment soil erosion rate and sediment yield (SY) that are impacted by farmland shelterbelts were estimated using WaTEM/SEDEM model. The shelterbelts reduced catchment soil erosion and SY to some extent. The mean soil erosion rate and specific sediment yield (SSY; defined as the ratio of SY to catchment area; t km−2 yr−1) of the 25 reservoir catchments decreased from 351.6 and 93.9 t km−2 yr−1 under the supposed scenario without shelterbelts to 331.1 t km−2 yr−1 and 86.3% t km−2 yr−1 under the current situation with shelterbelts. The sediment trap efficiencies (STEs) varied from 0.01% to 23.6% with an average value of 7.6%. The STEs were significantly correlated with shelterbelt density, catchment perimeter, topographic factors, RUSLEP‐factor and land use patterns including patch density (PD), patch cohesion index (COHESION), Shannon's diversity index (SHDI) and aggregation index (AI). The multiple regression equation involving factors of catchment's topography and morphology and land use pattern has a satisfactory performance, and mean slope gradient (MSG) and AI explained most of the variability of shelterbelts’ STE. This information can help land managers to better design shelterbelts and to reduce water‐derived soil loss at catchment scale.
Extending cytomegalovirus prophylaxis in high‐risk (D+/R−) lung transplant recipients from 6 to 9 months reduces cytomegalovirus disease: A retrospective study
Authors: Herrera Sabina , Khan Basha , Singer Lianne G. , Binnie Matthew , Chaparro Cecilia , Chow Chung‐Wai , Martinu Tereza , Tomlinson George , Keshavjee Shaf , Husain Shahid , Tikkanen Jussi M. 
Published: March 2020

AbstractRationaleCytomegalovirus (CMV)‐seronegative recipients receiving a seropositive allograft (D+/R−) are at a high risk of developing CMV disease. Our program increased the duration of CMV prophylaxis from 6 to 9 months in May 2013. Here, we present the impact on the incidence of CMV infection, disease, side effects, rejection, and other factors.MethodsRetrospective cohort of 241 CMV (D+/R−) patients transplanted between January 1, 2008, and December 31, 2017. Blood CMV testing was done according to protocol. All patients received ganciclovir/valganciclovir as prophylaxis. We compared the incidence and timing of CMV infection and disease up to 6 months after cessation of prophylaxis between patients who received 9 months (May 2013 onwards) and a historical control group who received 6 months of prophylaxis (prior to May 2013). CMV infection was defined as detectable CMV viremia in the absence of symptoms. CMV disease was defined as CMV syndrome or tissue‐invasive disease. Side effects of prophylaxis and CMV resistance were recorded.ResultsA total of 116 patients were included in the 6‐month group and 125 in the 9‐month group. The extended 9‐month CMV prophylaxis delayed the onset of CMV infection (median time to CMV infection after lung transplantation 295 vs 353 days, P < .01) but did not significantly reduce the incidence of CMV infection (65% vs 64%, P = .06, log‐rank). The 9‐month prophylaxis delayed the onset and decreased the incidence of CMV disease from 50% in the 6‐month group to 42% (P = .02 log‐rank). There was no difference in the rate of adverse effects (leukopenia in 32% in both groups, P = .53) or development of CMV resistance between the two groups (4 cases in both groups, P = .92). There were no significant differences in overall survival or the rate of chronic lung allograft dysfunction between the groups.ConclusionsExtending duration of CMV prophylaxis from 6 to 9 months resulted in a delayed and decreased incidence of CMV disease in our lung transplant population. The absolute risk reduction achieved by extended CMV prophylaxis was 8%. The incidence of CMV infection, and ganciclovir resistance and side effects were similar between the two groups. Our results suggest that extending CMV prophylaxis in the highest risk CMV D+/R− group is effective in reducing CMV disease.
Disseminated Mycobacterium massiliense infection in a patient with myelodysplastic syndrome undergoing allogeneic bone marrow transplantation
Authors: Toyama Takaaki , Mori Takehiko , Kato Jun , Sugita Kayoko , Hasegawa Naoki , Nakata Noboru , Hoshino Yoshihiko , Okamoto Shinichiro 
Published: March 2020

AbstractNontuberculous mycobacteria are ubiquitous in water and soil, and the subset of rapidly growing mycobacteria species can cause severe infections in immunocompromised patients. Solid organ or hematopoietic stem cell transplantation (HSCT) recipients are known to be susceptible to infection by nontuberculous mycobacteria. The nontuberculous mycobacteria species Mycobacterium massiliense (M massiliense) has been classified as a rapidly growing mycobacteria and recognized as a pathogen causing lung and soft tissue infections in humans. However, there have been only a few reported cases of M massiliense infection after solid organ transplantation and HSCT. We herein report another case of M massiliense infection after allogeneic HSCT, which manifested as soft tissue infection, lung infection, and bacteremia.
Tuberculosis disease and infection among household contacts of bacteriologically confirmed and non‐confirmed tuberculosis patients
Authors: Warria Ken , Nyamthimba Peter , Chweya Alex , Agaya Janet , Achola Millicent , Reichler Mary , Cowden Jessica , Heilig Charles M. , Borgdorff Martien W. , Cain Kevin P. , Yuen Courtney M. 
Published: March 2020

AbstractObjectiveTo compare the prevalence of tuberculosis infection and disease in household contacts of patients with bacteriologically confirmed tuberculosis disease and contacts of non‐bacteriologically confirmed disease in western Kenya.MethodsWe enrolled newly diagnosed index patients and their household contacts from March 2014 to June 2016. All contacts were evaluated with a symptom questionnaire, tuberculin skin test (TST) and HIV test. Clinical evaluation and sputum testing were performed for those with symptoms, positive TST result or HIV infection.ResultsWe enrolled 1155 contacts of 330 index patients with bacteriologically confirmed tuberculosis and 192 contacts of 55 index patients with non‐bacteriologically confirmed tuberculosis. 3.5% of contacts of patients with bacteriologically confirmed tuberculosis were diagnosed with tuberculosis, whereas no contacts of index patients with non‐bacteriologically confirmed tuberculosis were. Of those diagnosed with tuberculosis disease, 58.5% reported symptoms, 34.1% reported no symptoms but had positive TST results, and 7.3% had neither symptoms nor positive TST but were HIV‐positive. Among 872 contacts with a TST result, 50.9% of contacts of index patients with bacteriologically confirmed tuberculosis and 41.0% of contacts of index patients with non‐bacteriologically confirmed tuberculosis had a positive result (prevalence ratio = 1.16, 95% confidence interval 0.92–1.48).ConclusionIn a high‐burden setting, tuberculosis disease was more prevalent among contacts of patients with bacteriologically confirmed tuberculosis than contacts of patients with non‐bacteriologically confirmed disease. TST was feasible to perform and helped to detect cases that would have been missed had only symptomatic contacts been evaluated.