bluuebunny/crossref_metadata_2025_split huggingface dataset:
What plant is that? Tests of automated image recognition apps for plant identification on plants from the British flora
Authors: Jones Hamlyn G 
Published: September 2020

Abstract
There has been a recent explosion in development of image recognition technology and its application to automated plant identification, so it is timely to consider its potential for field botany. Nine free apps or websites for automated plant identification and suitable for use on mobile phones or tablet computers in the field were tested on a disparate set of 38 images of plants or parts of plants chosen from the higher plant flora of Britain and Ireland. There were large differences in performance with the best apps identifying &gt;50 % of samples tested to genus or better. Although the accuracy is good for some of the top-rated apps, for any quantitative biodiversity study or for ecological surveys, there remains a need for validation by experts or against conventional floras. Nevertheless, the better-performing apps should be of great value to beginners and amateurs and may usefully stimulate interest in plant identification and nature. Potential uses of automated image recognition plant identification apps are discussed and recommendations made for their future use.
IntAPT: integrated assembly of phenotype-specific transcripts from multiple RNA-seq profiles
Authors: Shi Xu , Neuwald Andrew F , Wang Xiao , Wang Tian-Li , Hilakivi-Clarke Leena , Clarke Robert , Xuan Jianhua 
Published: September 2020

Abstract

Motivation
High-throughput RNA sequencing has revolutionized the scope and depth of transcriptome analysis. Accurate reconstruction of a phenotype-specific transcriptome is challenging due to the noise and variability of RNA-seq data. This requires computational identification of transcripts from multiple samples of the same phenotype, given the underlying consensus transcript structure.

Results
We present a Bayesian method, integrated assembly of phenotype-specific transcripts (IntAPT), that identifies phenotype-specific isoforms from multiple RNA-seq profiles. IntAPT features a novel two-layer Bayesian model to capture the presence of isoforms at the group layer and to quantify the abundance of isoforms at the sample layer. A spike-and-slab prior is used to model the isoform expression and to enforce the sparsity of expressed isoforms. Dependencies between the existence of isoforms and their expression are modeled explicitly to facilitate parameter estimation. Model parameters are estimated iteratively using Gibbs sampling to infer the joint posterior distribution, from which the presence and abundance of isoforms can reliably be determined. Studies using both simulations and real datasets show that IntAPT consistently outperforms existing methods for the IntAPT. Experimental results demonstrate that, despite sequencing errors, IntAPT exhibits a robust performance among multiple samples, resulting in notably improved identification of expressed isoforms of low abundance.

Availability and implementation
The IntAPT package is available at http://github.com/henryxushi/IntAPT.

Supplementary information
Supplementary data are available at Bioinformatics online.
Sister species, different histories: comparative phylogeography of two bird species associated with Amazonian open vegetation
Authors: Ritter Camila D , Coelho Laís A , Capurucho João Mg , Borges Sergio H , Cornelius Cíntia , Ribas Camila C 
Published: September 2020

AbstractAlthough the expansion of open vegetation within Amazonia was the basis for the Forest Refugia hypothesis, studies of Amazonian biota diversification have focussed mostly on forest taxa. Here we compare the phylogeographic patterns and population history of two sister species associated with Amazonian open-vegetation patches, Elaenia cristata and Elaenia ruficeps (Aves: Tyrannidae). We sampled individuals across Amazonia for both species, and in the central Brazilian savannas (Cerrado) for E. cristata. We sequenced one mitochondrial (ND2) and two nuclear (BFib7 and ACO) markers. We tested for population structure, estimated migration rates and elucidated the historical demography of each species. The Amazon River is the strongest barrier for E. ruficeps and the Branco River is a secondary barrier. For the more broadly distributed E. cristata, there was no discernible population structure. Both species attained their current genetic diversity recently and E. cristata has undergone demographic expansion since the Last Glacial Maximum, The results suggest distinct effects of recent landscape change on population history for the two species. E. ruficeps, which only occurs in Amazonian white sand habitats, has been more isolated in open-vegetation patches than E. cristata, which occupies Amazonian savannas, and extends into the Central Brazilian Cerrado.
Actinomycin D causes oocyte maturation failure by inhibiting chromosome separation and spindle assembly†
Authors: Li Tianjie , Liu Changyu , Zhen Xiumei , Yu Yang , Qiao Jie 
Published: September 2020

AbstractActinomycin D (ActD) has been considered as one of the most effective and safe chemotherapeutic medications for treating a number of cancers. Although ActD has been used in the treatment of gynecological tumors and pediatric tumors for more than 50 years, the toxic effects of ActD on mammalian oocytes remain unknown. In this study, the influence of ActD on mouse and human oocyte maturation and the possible mechanisms were investigated. Notably, ActD inhibited oocyte maturation and arrested oocytes at the metaphase I (MI) stage in a dose-dependent manner. In addition, ActD arrested oocyte maturation when the oocytes were treated at different successive stages, including the germinal vesicle (GV), germinal vesicle breakdown, and MI stages. In ActD-treated oocytes, disordered chromosome condensation and irregular spindle assembly occurred, resulting in incomplete chromosome segregation and oocytes arresting at the MI phase; these results possibly occurred because ActD triggered the formation of reactive oxygen species, resulting in DNA damage and decreased ATP in mouse GV oocytes. Besides, in vivo treatment with ActD also inhibited mouse oocyte maturation. Similar effects were seen in human oocytes. Collectively, our results indicated that ActD exposure disrupted oocyte maturation by increasing DNA damage, which is a finding that might help with optimizing future methods for female fertility preservation before undergoing chemotherapy.
Cytoplasmic maturation in human oocytes: an ultrastructural study †
Authors: Trebichalská Z , Kyjovská D , Kloudová S , Otevřel P , Hampl A , Holubcová Z 
Published: September 2020

Abstract
Female fertility relies on successful egg development. Besides chromosome segregation, complex structural and biochemical changes in the cytoplasmic compartment are necessary to confer the female gamete the capacity to undergo normal fertilization and sustain embryonic development. Despite the profound impact on egg quality, morphological bases of cytoplasmic maturation remain largely unknown. Here, we report our findings from the ultrastructural analysis of 69 unfertilized human oocytes from 34 young and healthy egg donors. By comparison of samples fixed at three consecutive developmental stages, we explored how ooplasmic architecture changes during meiotic maturation in vitro. The morphometric image analysis supported observation that the major reorganization of cytoplasm occurs before polar body extrusion. The organelles initially concentrated around prophase nucleus were repositioned toward the periphery and evenly distributed throughout the ooplasm. As maturation progressed, distinct secretory apparatus appeared to transform into cortical granules that clustered underneath the oocyte's surface. The most prominent feature was the gradual formation of heterologous complexes composed of variable elements of endoplasmic reticulum and multiple mitochondria with primitive morphology. Based on the generated image dataset, we proposed a morphological map of cytoplasmic maturation, which may serve as a reference for future comparative studies. In conclusion, this work improves our understanding of human oocyte morphology, cytoplasmic maturation, and intracellular factors defining human egg quality. Although this analysis involved spare oocytes completing development in vitro, it provides essential insight into the enigmatic process by which human egg progenitors prepare for fertilization.
Variants in the SK2 channel gene (KCNN2) lead to dominant neurodevelopmental movement disorders
Authors: Mochel Fanny , Rastetter Agnès , Ceulemans Berten , Platzer Konrad , Yang Sandra , Shinde Deepali N , Helbig Katherine L , Lopergolo Diego , Mari Francesca , Renieri Alessandra , Benetti Elisa , Canitano Roberto , Waisfisz Quinten , Plomp Astrid S , Huisman Sylvia A , Wilson Golder N , Cathey Sara S , Louie Raymond J , Del Gaudio Daniela , Waggoner Darrel , Kacker Shawn , Nugent Kimberly M , Roeder Elizabeth R , Bruel Ange-Line , Thevenon Julien , Ehmke Nadja , Horn Denise , Holtgrewe Manuel , Kaiser Frank J , Kamphausen Susanne B , Abou Jamra Rami , Weckhuysen Sarah , Dalle Carine , Depienne Christel 
Published: September 2020

Abstract
KCNN2 encodes the small conductance calcium-activated potassium channel 2 (SK2). Rodent models with spontaneous Kcnn2 mutations show abnormal gait and locomotor activity, tremor and memory deficits, but human disorders related to KCNN2 variants are largely unknown. Using exome sequencing, we identified a de novo KCNN2 frameshift deletion in a patient with learning disabilities, cerebellar ataxia and white matter abnormalities on brain MRI. This discovery prompted us to collect data from nine additional patients with de novo KCNN2 variants (one nonsense, one splice site, six missense variants and one in-frame deletion) and one family with a missense variant inherited from the affected mother. We investigated the functional impact of six selected variants on SK2 channel function using the patch-clamp technique. All variants tested but one, which was reclassified to uncertain significance, led to a loss-of-function of SK2 channels. Patients with KCNN2 variants had motor and language developmental delay, intellectual disability often associated with early-onset movement disorders comprising cerebellar ataxia and/or extrapyramidal symptoms. Altogether, our findings provide evidence that heterozygous variants, likely causing a haploinsufficiency of the KCNN2 gene, lead to novel autosomal dominant neurodevelopmental movement disorders mirroring phenotypes previously described in rodents.
Decreased Mortality in Coronavirus Disease 2019 Patients Treated With Tocilizumab: A Rapid Systematic Review and Meta-analysis of Observational Studies
Authors: Malgie Jishnu , Schoones Jan W , Pijls Bart G 
Published: September 2020

Abstract

Background
We systematically reviewed the literature to answer the following research questions: (1) Does interleukin 6 (IL-6) (receptor) antagonist therapy reduce mortality in coronavirus disease 2019 (COVID-19) patients compared to patients not treated with IL-6 (receptor) antagonists; and (2) is there an increased risk of side effects in COVID-19 patients treated with IL-6 (receptor) antagonists compared to patients not treated with IL-6 (receptor) antagonists?

Methods
We systematically searched PubMed, PMC PubMed Central, Medline, World Health Organization COVID-19 Database, Embase, Web of Science, Cochrane Library, Emcare, and Academic Search Premier (through 30 June 2020). Random effects meta-analysis was used to pool the risk ratios and risk differences of individual studies. Risk of bias was appraised using the Methodological Index for Non-randomized Studies (MINORS) checklist.

Results
The search strategy retrieved 743 unique titles, of which 10 studies (all on tocilizumab [TCZ]) comprising 1358 patients were included. Nine of 10 studies were considered to be of high quality. Meta-analysis showed that the TCZ group had lower mortality than the control group. The risk ratio was 0.27 (95% confidence interval [CI], .12–.59) and the risk difference was 12% (95% CI, 4.6%–20%) in favor of the TCZ group. With only a few studies available, there were no differences observed regarding side effects.

Conclusions
Our results showed that mortality was 12% lower for COVID-19 patients treated with TCZ compared with those not treated with TCZ. The number needed to treat was 11, suggesting that for every 11 (severe) COVID-19 patients treated with TCZ, 1 death is prevented. These results require confirmation by randomized controlled trials.
Chronic kidney disease progression among patients with type 2 diabetes identified in US administrative claims: a population cohort study
Authors: Kovesdy Csaba P , Isaman Danielle , Petruski-Ivleva Natalia , Fried Linda , Blankenburg Michael , Gay Alain , Velentgas Priscilla , Folkerts Kerstin 
Published: September 2020

ABSTRACT

Background
Chronic kidney disease (CKD), one of the most common complications of type 2 diabetes (T2D), is associated with poor health outcomes and high healthcare expenditures. As the CKD population increases, a better understanding of the prevalence and progression of CKD is critical. However, few contemporary studies have explored the progression of CKD relative to its onset in T2D patients using established markers derived from real-world care settings.

Methods
This retrospective, population-based cohort study assessed CKD progression among adults with T2D and with newly recognized CKD identified from US administrative claims data between 1 January 2008 and 30 September 2018. Included were patients with T2D and laboratory evidence of CKD as indicated by the established estimated glomerular filtration rate (eGFR) and urine albumin:creatinine ratio (UACR) criteria. Disease progression was described as transitions across the eGFR- and UACR-based stages.

Results
A total of 65 731 and 23 035 patients with T2D contributed to the analysis of eGFR- and UACR-based CKD stage progression, respectively. CKD worsening was observed in approximately 10–17% of patients over a median follow-up of 2 years. Approximately one-third of patients experienced an increase in eGFR values or a decrease in UACR values during follow-up.

Conclusions
A relatively high proportion of patients were observed with disease progression over a short period of time, highlighting the need for better identification of patients at risk of rapidly progressive CKD. Future studies are needed to determine the clinical characteristics of these patients to inform earlier diagnostic and therapeutic interventions aimed at slowing disease progression.
Simulator-based hemodialysis cannulation skills training: a new horizon?
Authors: Singapogu Ravikiran , Chowdhury Aniqa , Roy-Chaudhury Prabir , Brouwer-Maier Deborah 
Published: September 2020

Abstract
In accordance with the recently released Kidney Disease Outcomes Quality Initiative (KDOQI) guidelines, there is a significant need for focused efforts on improving hemodialysis cannulation outcomes. Toward this, structured and meaningful training of our clinical personnel who cannulate in dialysis clinics is a priority. With the availability of advanced sensors and computing methods, simulators could be indispensable tools for standardized skills assessment and training. In this article we present ways in which sensor data could be used to quantify cannulation skill. As with many other medical specialties, implementation of simulator-based training holds the promise of much-needed improvement in end-stage kidney disease patient outcomes.
Targeted RNA-Sequencing Enables Detection of Relevant Translocations and Single Nucleotide Variants and Provides a Method for Classification of Hematological Malignancies–RANKING
Authors: de Lange Kim , de Boer Eddy N , Bosga Anneke , Alimohamed Mohamed Z , Johansson Lennart F , Mulder André B , Vellenga Edo , van Diemen Cleo C , Deelen Patrick , van den Berg Eva , Sikkema-Raddatz Birgit 
Published: September 2020

Abstract

Background
Patients with hematological malignancies (HMs) carry a wide range of chromosomal and molecular abnormalities that impact their prognosis and treatment. Since no current technique can detect all relevant abnormalities, technique(s) are chosen depending on the reason for referral, and abnormalities can be missed. We tested targeted transcriptome sequencing as a single platform to detect all relevant abnormalities and compared it to current techniques.

Material and Methods
We performed RNA-sequencing of 1385 genes (TruSight RNA Pan-Cancer, Illumina) in bone marrow from 136 patients with a primary diagnosis of HM. We then applied machine learning to expression profile data to perform leukemia classification, a method we named RANKING. Gene fusions for all the genes in the panel were detected, and overexpression of the genes EVI1, CCND1, and BCL2 was quantified. Single nucleotide variants/indels were analyzed in acute myeloid leukemia (AML), myelodysplastic syndrome and patients with acute lymphoblastic leukemia (ALL) using a virtual myeloid (54 genes) or lymphoid panel (72 genes).

Results
RANKING correctly predicted the leukemia classification of all AML and ALL samples and improved classification in 3 patients. Compared to current methods, only one variant was missed, c.2447A&gt;T in KIT (RT-PCR at 10−4), and BCL2 overexpression was not seen due to a t(14; 18)(q32; q21) in 2% of the cells. Our RNA-sequencing method also identified 6 additional fusion genes and overexpression of CCND1 due to a t(11; 14)(q13; q32) in 2 samples.

Conclusions
Our combination of targeted RNA-sequencing and data analysis workflow can improve the detection of relevant variants, and expression patterns can assist in establishing HM classification.
Electrical characteristics of pacing different portions of the His bundle in bradycardia patients
Authors: Hu Yiran , Gu Min , Hua Wei , Niu Hongxia , Li Hui , Chen Xuhua , Zhang Nixiao , Liu Xi , Zhang Shu 
Published: September 2020

Abstract

Aims
His-bundle pacing (HBP) can be achieved in either atrial-side HBP (aHBP) or ventricular-side HBP (vHBP). The study compared the pacing parameters and electrophysiological characteristics between aHBP and vHBP in bradycardia patients.

Methods and results
Fifty patients undergoing HBP implantation assisted by visualization of the tricuspid valvular annulus (TVA) were enrolled. The HBP lead position was identified by TVA angiography. Twenty-five patients were assigned to undergo aHBP and compared with 25 patients who underwent vHBP primarily in a prospective and randomized fashion. Pacing parameters and echocardiography were routinely assessed at implant and 3-month follow-up. His-bundle pacing was successfully performed in 45 patients (90% success rate with 44.4% aHBP and 55.6% vHBP). The capture threshold was lower in vHBP than aHBP at implant (vHBP: 1.1 ± 0.5 vs. aHBP: 1.4 ± 0.4 V/1.0 ms, P = 0.014) and 3-month follow-up (vHBP: 0.8 ± 0.4 vs. aHBP: 1.7 ± 0.8 V/0.4 ms, P &lt; 0.001). The R-wave amplitude was higher in vHBP than in aHBP at implant (vHBP: 4.5 ± 1.4 vs. aHBP: 2.0 ± 0.8 mV, P &lt; 0.001) and at 3-month follow-up (vHBP: 4.4 ± 1.5 vs. aHBP: 1.8 ± 0.7 mV, P &lt; 0.001). No procedure-related complications and aggravation of tricuspid valve regurgitation were observed in most patients and echocardiographic assessment of cardiac function remained in the normal range in all patients during the follow-up.

Conclusion
This study demonstrates that vHBP features a low and stable pacing capture threshold and high R-wave amplitude, suggesting better pacing mode management and battery longevity can be achieved by HBP in the ventricular side.
The greater wax mothGalleria mellonella: biology and use in immune studies
Authors: Wojda Iwona , Staniec Bernard , Sułek Michał , Kordaczuk Jakub 
Published: September 2020

ABSTRACTThe greater wax moth Galleria mellonella is an invertebrate that is increasingly being used in scientific research. Its ease of reproduction, numerous offspring, short development cycle, and finally, its known genome and immune-related transcriptome provide a convenient research model for investigation of insect immunity at biochemical and molecular levels. Galleria immunity, consisting of only innate mechanisms, shows adaptive plasticity, which has recently become the subject of intensive scientific research. This insect serves as a mini host in studies of the pathogenicity of microorganisms and in vivo tests of the effectiveness of single virulence factors as well as new antimicrobial compounds. Certainly, the Galleria mellonella species deserves our attention and appreciation for its contribution to the development of research on innate immune mechanisms. In this review article, we describe the biology of the greater wax moth, summarise the main advantages of using it as a model organism and present some of the main techniques facilitating work with this insect
Fault interactions in a complex fault system: insight from the 1936–1997 NE Lut earthquake sequence
Authors: Marchandon M , Vergnolle M , Cavalié O 
Published: September 2020

SUMMARYCalculations of Coulomb stress changes have shown that moderate to large earthquakes may increase stress at the location of future earthquakes. Coulomb stress transfers have thus been widely accepted to explain earthquake sequences, especially for sequences occurring within parallel or collinear fault systems. Relating, under this framework, successive earthquakes occurring within more complex fault systems (i.e. conjugate fault system) is more challenging. In this study, we assess which ingredients of the Coulomb stress change theory are decisive for explaining the succession of three large (Mw 7+) earthquakes that occurred on a conjugate fault system in the NE Lut, East Iran, during a 30-yr period. These earthquakes belong to a larger seismic sequence made up of 11 earthquakes (Mw 5.9+) from 1936 to 1997. To reach our goal, we calculate, at each earthquake date, the stress changes generated by the static deformation of the preceding earthquakes, the following post-seismic deformation due to the viscoelastic relaxation of the lithosphere, and the interseismic deformation since 1936. We first show that accurately modelling the source and receiver fault geometry is crucial to precisely estimating Coulomb stress changes. Then we show that 7 out of 10 earthquakes of the NE Lut sequence, considering the uncertainties, are favoured by the previous earthquakes. Furthermore, the last two M7+ earthquakes of the sequence (1979 and 1997) have mainly been favoured by the moderate Mw ∼ 6 earthquakes. Finally, we investigate the link between the Coulomb stress changes due to previous earthquakes and the rupture extension of the next earthquake and show that a correlation does exist for some earthquakes but is not systematic.