bluuebunny/crossref_metadata_2025_split huggingface dataset:
Clinical analysis of 17 cases of neonatal osteomyelitis
Authors: Zhan Canyang , Zhou Bo , Du Jing , Chen Lihua 
Published: January 2019

Abstract
Although acute osteomyelitis is rare in neonates, it might result in severe sequelae such as joint destruction and growth failure if it is not diagnosed and treated early. However, few studies have focused on the clinical features and treatment of this disease.
A retrospective review of 17 cases of neonatal osteomyelitis, for which the patients underwent medical treatment alone or combined with surgery at the Children's Hospital of Zhejiang University School of Medicine between January 2009 and September 2016, was conducted. Medical treatment included the use of antibiotics and supportive care. Surgery was performed in cases with subperiosteal abscess (>1 cm) or clinical deterioration despite antibiotic therapy.
All of the patients (11 men and 6 women) were term neonates. The main complaints were redness or swelling around the affected bone and fever. The most common sites were the femur (29.4%) and humerus (23.5%). There were 14 (82.35%) cases with positive cultures: Staphylococcus accounted for 71.43% (n = 10), followed by Salmonella (n = 1), Streptococcus pneumoniae (n = 1), Klebsiella pneumoniae (n = 1), and Escherichia coli (n = 1). X-rays (n = 14), ultrasound (n = 6), computed tomography (CT) (n = 5), or magnetic resonance imaging (MRI) (n = 7) were performed. Three of 14 x-rays were not pathological at the onset of the disease, while the positive rate of MRI in detecting osteomyelitis was 100%. Eleven of 17 cases underwent surgical drainage, and higher white blood cell (WBC) counts were found in patients requiring surgery (P < .05). The prognosis for all patients was good without severe sequelae with a mean follow-up period of 49.47 ± 23.43 months.
In conclusion, the prognosis of neonatal osteomyelitis with early active treatment is good. MRI is advocated for detecting early osteomyelitis. Additionally, neonates with higher WBC count together with osteomyelitis have an increased risk for surgery.
Novel Three-Dimensional Morphometry to Reassess Orbit Deformities Associated With Orbital-Periorbital Plexiform Neurofibroma
Authors: Guo Chengrui , Chen Liangbo , Qu Yang , Hu Xiaojie 
Published: January 2019

Background:
Orbit deformities are usually found in neurofibromatosis type 1 patients, especially those with orbital-periorbital plexiform neurofibroma (OPPN). Unfortunately, current morphometry is complicated and, in some cases, cannot be performed on the deformed orbit due to the destruction of landmarks. Herein, we present a novel 3-dimensional (3D) morphometry for these orbital measurements.

Methods:
We retrospectively reviewed 29 patients with OPPN, and another 29 disseminated cutaneous neurofibroma patients served as controls. All patients had undergone craniofacial computed tomography and 3D reconstruction. New morphometry was used to measure the area of the orbital rim (OR) and superior orbital fissure (SOF).

Results:
For the 29 patients with OPPN, the area of the OR at the affected side was 14.18 ± 3.50 cm2, while the OR at the nonaffected side was 12.32 ± 1.38 cm2. In addition, the area of the SOF at the affected side was 5.37 ± 5.75 cm2, while that at the nonaffected side was 1.27 ± 1.03 cm2. The OR and SOF at the affected side are more likely to become enlarged compared with those at the nonaffected side. Among the 29 patients with OPPN, the novel morphometry could be performed in 19 cases (65.5%) that cannot be measured by previous morphometry.

Conclusion:
The novel morphometry is convenient and reproducible, which optimizes its application in pathologic cases, especially those involving deformed orbits.
Selective enrichment of A-to-I edited transcripts from cellular RNA using Endonuclease V
Authors: Knutson Steve D. , Heemstra Jennifer M. 
Published: January 2019

AbstractImmunoprecipitation enrichment has significantly improved the sensitivity and accuracy of detecting RNA modifications in the transcriptome. However, there are no existing methods for selectively isolating adenosine-to-inosine (A-to-I) edited RNAs. Here we show thatEscherichia coliEndonuclease V (eEndoV), an inosine-cleaving enzyme, can be repurposed to bind and isolate A-to-I edited transcripts from cellular RNA through adjustment of cationic conditions. While Mg2+is required for eEndoV catalysis, it has also been shown that similar levels of Ca2+instead promote binding of inosine without cleavage. Leveraging these properties, we observe that Ca2+-supplemented eEndoV is highly specific for inosine in RNA and exhibits low nanomolar binding affinity. We then demonstrate EndoVIPER (EndonucleaseVinosine precipitationenrichment) as a facile and robust method to isolate A-to-I edited transcripts from cellular RNA. We envision the use of this approach as a straightforward and cost-effective strategy to enrich edited RNAs and detect A-to-I sites with improved sensitivity and fidelity.
Interspecies metabolite transfer and aggregate formation in a co-culture of Dehalococcoides and Sulfurospirillum dehalogenating tetrachloroethene to ethene
Authors: Kruse Stefan , Türkowsky Dominique , Birkigt Jan , Matturro Bruna , Franke Steffi , Jehmlich Nico , von Bergen Martin , Westermann Martin , Rossetti Simona , Nijenhuis Ivonne , Adrian Lorenz , Diekert Gabriele , Goris Tobias 
Published: January 2019

AbstractMicrobial communities involving dehalogenating bacteria assist in bioremediation of areas contaminated with halocarbons. To understand molecular interactions between dehalogenating bacteria, we co-cultured Sulfurospirillum multivorans, dechlorinating tetrachloroethene (PCE) to cis-1,2-dichloroethene (cDCE), and Dehalococcoides mccartyi strains BTF08 or 195, dehalogenating PCE to ethene. The co-cultures were cultivated with lactate as electron donor. In this co-culture, the bacterial cells formed aggregates and D. mccartyi established an unusual, barrel-like morphology. An extracellular matrix surrounding bacterial cells in the aggregates enhanced cell-to-cell contact. PCE was dehalogenated to ethene at least three times faster in the co-culture. The dehalogenation was carried out via PceA of S. multivorans, and PteA (a recently described PCE dehalogenase) and VcrA of D. mccartyi BTF08, as supported by protein abundance. The co-culture was not dependent on exogenous hydrogen and acetate, suggesting a syntrophic relationship in which the obligate hydrogen consumer D. mccartyi consumes hydrogen and acetate produced by S. multivorans. The cobamide cofactor of the reductive dehalogenase – mandatory for D. mccartyi – was also produced by S. multivorans. D. mccartyi strain 195 dechlorinated cDCE in the presence of norpseudo-B12 produced by S. multivorans, but D. mccartyi strain BTF08 depended on an exogenous lower cobamide ligand. This observation is important for bioremediation, since cofactor supply in the environment might be a limiting factor for PCE dehalogenation to ethene, described for D. mccartyi exclusively. The findings from this co-culture give new insights into aggregate formation and the physiology of D. mccartyi within a bacterial community.
Cortico-hippocampal network connections support the multidimensional quality of episodic memory
Authors: Cooper Rose A. , Ritchey Maureen 
Published: January 2019

SUMMARYEpisodic memories reflect a bound representation of multimodal features that can be reinstated with varying levels of precision. Yet little is known about how brain networks involved in memory, including the hippocampus and posterior-medial (PM) and anterior-temporal (AT) cortical systems, functionally interact to support the quality and the content of recollection. Participants learned color, spatial, and emotion associations of objects, later reconstructing the visual features using a continuous color spectrum and 360-degree panorama scenes. Behaviorally, dependencies in memory were observed for the gist but not precision of these event associations. Supporting this integration, hippocampus, AT, and PM regions showed increased inter-network connectivity and reduced modularity during retrieval compared to encoding. These network connections, particularly to hippocampus, tracked a multidimensional, continuous measure of objective memory quality. Moreover, distinct patterns of connectivity tracked item color precision and spatial memory precision. These findings demonstrate not only how hippocampal-cortical connections reconfigure during episodic retrieval, but how such dynamic interactions might flexibly support the multidimensional quality of remembered events.
Cell type composition and circuit organization of neocortical radial clones
Authors: Cadwell Cathryn R. , Scala Federico , Fahey Paul G. , Kobak Dmitry , Sinz Fabian H. , Johnsson Per , Li Shuang , Cotton R. James , Sandberg Rickard , Berens Philipp , Jiang Xiaolong , Tolias Andreas S. 
Published: January 2019

SummaryExcitatory neurons arising from a common progenitor establish radially-oriented clonal units in the neocortex which have been proposed to serve as elementary information processing modules. To characterize the cell types and circuit diagram within these clonal units, we performed single-cell RNA-sequencing and multi-cell patch clamp recordings of neurons derived fromNestin-positive progenitors. We found that radial clones do not appear to be fate-restricted, but instead individual clones are composed of a random sampling of the transcriptomic cell types present in a particular cortical area. The effect of lineage on synaptic connectivity depends on the type of connection tested: pairs of clonally related neurons were more likely to be connected vertically, across cortical layers, but not laterally within the same layer, compared to unrelated pairs. We propose that integration of vertical input from related neurons with lateral input from unrelated neurons may represent a developmentally programmed motif for assembling neocortical circuits.
Intra-familial phenotypic heterogeneity and telomere abnormality in von Hippel-Lindau disease
Authors: Wang Jiangyi , Peng Xiang , Chen Cen , Ning Xianghui , Peng Shuanghe , Li Teng , Liu Shengjie , Hong Baoan , Zhou Jingcheng , Ma Kaifang , Cai Lin , Gong Kan 
Published: January 2019

AbstractVon Hippel-Lindau (VHL) disease is a hereditary cancer syndrome with poor survival. The current recommendations have proposed uniform surveillance strategies for all patients, neglecting the obvious phenotypic varieties. In this study, we aim to confirm the phenotypic heterogeneity in VHL disease and the underlying mechanism. A total of 151 parent-child pairs were enrolled for genetic anticipation analysis, and 77 sibling pairs for birth order effect analysis. Four statistical methods were used to compare the onset age of patients among different generations and different birth orders. The results showed that the average onset age was 18.9 years earlier in children than in their parents, which was statistically significant in all of the four statistical methods. Furthermore, the first-born siblings were affected 8.3 years later than the other ones among the maternal patients. Telomere shortening was confirmed to be associated with genetic anticipation in VHL families, while it failed to explain the birth order effect. Moreover, no significant difference was observed for overall survival between parents and children (p=0.834) and between first-born patients and the other siblings (p=0.390). This study provides definitive evidence and possible mechanisms of intra-familial phenotypic heterogeneity in VHL families, which is helpful to the update of surveillance guidelines.
AirSurf-Lettuce: an aerial image analysis platform for ultra-scale field phenotyping and precision agriculture using computer vision and deep learning
Authors: Bauer Alan , Bostrom Aaron George , Ball Joshua , Applegate Christopher , Cheng Tao , Laycock Stephen , Rojas Sergio Moreno , Kirwan Jacob , Zhou Ji 
Published: January 2019

AbstractAerial imagery is regularly used by farmers and growers to monitor crops during the growing season. To extract meaningful phenotypic information from large-scale aerial images collected regularly from the field, high-throughput analytic solutions are required, which not only produce high-quality measures of key crop traits, but also support agricultural practitioners to make reliable management decisions of their crops. Here, we report AirSurf-Lettuce, an automated and open-source aerial image analysis platform that combines modern computer vision, up-to-date machine learning, and modular software engineering to measure yield-related phenotypes of millions of lettuces across the field. Utilising ultra-large normalized difference vegetation index (NDVI) images acquired by fixed-wing light aircrafts together with a deep-learning classifier trained with over 100,000 labelled lettuce signals, the platform is capable of scoring and categorising iceberg lettuces with high accuracy (>98%). Furthermore, novel analysis functions have been developed to map lettuce size distribution in the field, based on which global positioning system (GPS) tagged harvest regions can be derived to enable growers and farmers’ precise harvest strategies and marketability estimates before the harvest.
Removal of Spo11 from meiotic DNA breaksin vitrobut notin vivoby Tyrosyl DNA Phosphodiesterase 2
Authors: Johnson Dominic , Allison Rachal M , Cannavo Elda , Cejka Petr , Neale Matthew J 
Published: January 2019

ABSTRACTMeiotic recombination events are initiated by DNA double-strand breaks (DSBs) created by the topoisomerase-like protein, Spo11. Similar to type-II topoisomerases, Spo11 becomes covalently linked to the 5′ ends generated on each side of the DSB. Whilst Spo11-oligos—the product of nucleolytic removal by Mre11—have been detected in a number of biological systems, the lifetime of the covalent Spo11-DSB precursor has not been systematically determined and may be subject to alternative processing reactions. Here we explore the activity of human Tyrosyl DNA Phosphodiesterase, TDP2, on Spo11-DSBs isolated fromS. cerevisiaecells. We demonstrate that TDP2 can remove Spo11 from natural ssDNA-oligos, and dsDNA ends even when in the presence of excess competitor genomic DNA. Interestingly, TDP2-processed Spo11-DSBs are refractory to resection by Exo1, suggesting that ssDNA generated by Mre11 may be essentialin vivoto facilitate resection-dependent HR at Spo11-DSBs even if TDP2 were active. Moreover, although TDP2 can remove Spo11 peptidesin vitro, TDP2 was unable to remove Spo11in vivo—unlike during the repair of topoisomerase-induced DNA lesions. These results suggest that Spo11-DNA, but not topoisomerase-DNA cleavage complexes, are inaccessible to the TDP2 enzyme, perhaps due to occlusion by higher order protein complexes resident at sites of meiotic recombination.
Inferring phenotypic plasticity and local adaptation to climate across tree species ranges using forest inventory data
Authors: Fréjaville Thibaut , Fady Bruno , Kremer Antoine , Ducousso Alexis , Garzón Marta Benito 
Published: January 2019

ABSTRACTAimTo test whether adaptive and plastic trait responses to climate across species distribution ranges can be untangled using field observations, under the rationale that, in natural forest tree populations, long-term climate shapes local adaptation while recent climate change drives phenotypic plasticity.LocationEurope.Time period1901-2014.TaxaSilver fir (Abies alba Mill.) and sessile oak (Quercus petraea (Matt.) Liebl.).MethodsWe estimated the variation of individual tree height as a function of long-term and short-term climates to tease apart local adaptation, plasticity and their interaction, using mixed-effect models calibrated with National Forest Inventory data (in-situ models). To validate our approach, we tested the ability of in-situ models to predict independently tree height observations in common gardens where local adaptation to climate of populations and their plasticity can be measured and separated. In-situ model predictions of tree height variation among provenances (populations of different geographical origin) and among planting sites were compared to observations in common gardens and to predictions from a similar model calibrated using common garden data (ex-situ model).ResultsIn Q. petraea, we found high correlations between in-situ and ex-situ model predictions of provenance and plasticity effects and their interaction on tree height (r > 0.80). We showed that the in-situ models significantly predicted tree height variation among provenances and sites for Abies alba and Quercus petraea. Spatial predictions of phenotypic plasticity across species distribution ranges indicate decreasing tree height in populations of warmer climates in response to recent anthropogenic climate warming.Main conclusionsOur modelling approach using National Forest Inventory observations provides a new perspective for understanding patterns of intraspecific trait variation across species ranges. Its application is particularly interesting for species for which common garden experiments do not exist or do not cover the entire climatic range of the species.
Conduit integrity is compromised during acute lymph node expansion
Authors: Martinez Victor G. , Pankova Valeriya , Krasny Lukas , Singh Tanya , White Ian J. , Benjamin Agnesska C. , Dertschnig Simone , Horsnell Harry L. , Kriston-Vizi Janos , Burden Jemima J. , Huang Paul H. , Tape Christopher J. , Acton Sophie E. 
Published: January 2019

Lymph nodes (LNs) work as filtering organs, constantly sampling peripheral cues. This is facilitated by the conduit network, a parenchymal tubular-like structure formed of bundles of aligned extracellular matrix (ECM) fibrils ensheathed by fibroblastic reticular cells (FRCs). LNs undergo 5-fold expansion with every adaptive immune response and yet these ECM-rich structures are not permanently damaged. Whether conduit integrity and filtering functions are affected during cycles of LN expansion and resolution is not known. Here we show that the conduit structure is disrupted during acute LN expansion but FRC-FRC contacts remain intact. In homeostasis, polarised FRCs adhere to the underlying substrate to deposit ECM ba-solaterally. ECM production by FRCs is regulated by the C-type lectin CLEC-2, expressed by dendritic cells (DCs), at transcriptional and secretory levels. Inflamed LNs maintain conduit size-exclusion, but flow becomes leaky, which allows soluble antigens to reach more antigen-presenting cells. We show how dynamic communication between peripheral tissues and LNs changes during immune responses, and describe a mechanism that enables LNs to prevent inflammation-induced fibrosis.HighlightsFRCs use polarized microtubule networks to guide matrix depositionCLEC-2/PDPN controls matrix production at transcriptional and post-transcriptional levelsFRCs halt matrix production and decouple from conduits during acute LN expansionConduits leak soluble antigen during acute LN expansion
Empirical and Computational Comparison of Alternative Therapeutic Exon Skip Repairs for Duchenne Muscular Dystrophy
Authors: Ma Krystal Manyuan , Thomas Evelyn S , Wereszczynski Jeff , Menhart Nick 
Published: January 2019

AbstractDuchenne muscular dystrophy is a common and devastating genetic disease that is primarily caused by exon deletions that create a genetic frameshift in dystrophin. Exon skipping therapy seeks to correct this by masking an exon during the mRNA maturation process, which restores dystrophin expression, but creates an edited protein missing both the original defect and the therapeutically skipped region. Crucially, it is possible to correct many defects in alternative ways, by skipping an exon either before, or after the patient’s defect. This results in alternatively edited, hybrid proteins, of possibly different properties and therapeutic consequences. Here, we examined three such dystrophin exon skipped edits, comprising two pairs of alternative repairs of the same underlying DMD defect. We found that in both cases, one member of each alternative repair was more stable than the other by a variety of thermodynamic and biochemical measures. We also examined the origin of these differences by molecular dynamics simulations, which showed that these stability differences were the result of different types of structural perturbations. For example, in one edit there was partial unfolding at the edit site which caused domain-localized perturbations, while in another there was unfolding at the protein domain junctions distal to the edit site which increased molecular flexibility. These results demonstrate that alternative exon skip repairs of the same underlying defect can have very different consequences at the level of protein structure and stability, and furthermore that these can arise by different mechanisms, either locally, or by more subtle long-range perturbations.
Worldwide impacts of humans on animal genetic diversity
Authors: Millette K.L , Fugère V. , Debyser C. , Greiner A. , Chain F.J.J. , Gonzalez A 
Published: January 2019

SummaryHuman impacts on genetic diversity are poorly understood yet critical to understanding the evolutionary capacity of the world’s biodiversity. We used global maps of land use and human density to assess human impacts on the intraspecific genetic diversity of 15,946 species of birds, fishes, insects, and mammals over time and across four spatial scales worldwide. We analyzed 164,518 mitochondrial cytochromecoxidase subunit I (COI) sequences to quantify changes in genetic diversity between 1980-2016. We found temporal change in genetic diversity, with both increasing and decreasing trends observed. The magnitude and sign of human impacts on genetic diversity depended on scale and taxon. In contrast, latitude was a strong predictor of diversity in fish, insects, and mammals. Our analyses provide a first worldwide picture of human impacts on animal genetic diversity. A global effort to systematically monitor genetic diversity is needed to fill the gaps in taxonomic and geographic coverage in this dataset.