bluuebunny/crossref_metadata_2025 huggingface dataset:
Effective DNA extraction methods for mitochondrial phylogenomics of the sea urchins
Authors: WAKAYAMA NORIO , KIYONO YUKI , MATSUMOTO NATSUKI , SAITOH MASAYA , KANAZAWA KEN’ICHI
Published: October 2019

In the present study, we evaluated the efficiency of a minimally destructive and a destructive mitochondrial DNA extraction method. The first method extracted total DNA from epidermis and muscles of the spines and yielded varying PCR efficiency values that are dependent on the template concentration, which could be attributed to contamination by pigment and/or genomic DNA in the tissue. The second method extracted mitochondrial DNA from fractionated mitochondria obtained from tissues and coelomic fluid inside the test. Using this method, PCR products and purified mitochondrial DNA were used for sequencing on a next generation sequencer (Ion PGM). Direct sequencing of the purified mitochondrial DNA led to complete recovery of the mitochondrial genomes; however, contaminants were present. PCR failure was commonly encountered using the first method but was absent using the second method. The two extraction methods were compared to the commonly used destructive method that extracted total DNA from gonad or coelomic fluid inside the test. PCR results indicated that the destructive method exhibited similar performance as the first method. The present study generated 11 complete and one partial mitochondrial genome sequences for 12 species. The complete mitochondrial sequences from the order Cidaroida were sequenced for the first time. Phylogenetic trees constructed based on individual genes showed various topologies. Phylogenetic relationships estimated from all protein-coding regions of the mitochondrial genome were consistent with the order-level relationships estimated from molecular and morphological data in previous studies.
First observation of the "double-faced X-framed cup ossicle" extracted from a deep sea holothurian in Japan

Authors: YAMANA YUSUKE , HAYASHIBARA TAKESHI , YAMAMOTO MASAKI , SETIAMARGA DAVIN H.E.
Published: October 2019

A New type ossicle form, “double-faced x-framed cup ossicle” is discovered from the undescribed deep sea holothuroid. To give a definite view on the substantial qualities of this ossicle, a SEM observation on the ossicles and a DNA barcoding analysis are conducted. Although the most internal and external morphologies of the present species agree well with the characteristics of the family Cucumariidae Ludwig, 1894, the ossicles morphologies mostly does not agree with the congeners of Cucumariidae. On the other hand, our molecular study indicates a possibility that the specimens are not cucumariids, but belong to a sister group of Cucumariidae. In our present observation, some of the peri-oral ossicles show a very similar property with the small x-framed cup-shaped structures (which sometimes occurs in cucumariids). Therefore, the double-faced x-framed cup ossicle probably could be considered as the results of derivation from the x-body: in which four extra-arms developed on the bottom face of a cup ossicle, and finally these arms equipped with an extra-rim.
Experimental hybridization of sympatric temnopleurid sea urchins living in Yamaguchi, Japan

Authors: YAMANAKA AKIRA , TAKUWA YUKI , KITAZAWA CHISATO
Published: October 2019

Three sympatric species of temnopleurid sea urchins, Temopleurus toreumaticus (Leske, 1778), T. hardwickii (Gray, 1855) and Mespilia globulus (Linnaeus, 1758), occupy a habitat located a short distance from the shore of the Seto Inland Sea, Yamaguchi Prefecture, Japan. Breeding seasons overlap considerably among these species. These species exhibit species-specific differences in embryonic and larval development such as a wrinkled zygote, wrinkled blastula, archenteron invagination, larval skeleton and juvenile morphology. In this study, we determined whether interbreeding among these species is possible. Investigations revealed that fertilization succeeded with all mating combination patterns and that all fertilized eggs developed to the gastrula stage. The blastula and gastrula of hybrids formed in a manner similar to the maternal whereas the developmental delay observed followed the pattern of the paternal species T. toreumaticus fertilized at a greater proportion than other pairs and metamorphosed. These results suggest that eggs of this species may have weaker fertilization block in general. At the early developmental stages, hybrid embryos from T. toreumaticus mothers express maternal, while some hybrids derived from sperm of T. toreumaticus and the eggs of other species ceased development at the 4-armed larval stage. The hybrids of T. hardwickii and M. globulus ceased development at the gastrula stage, suggesting that these species have a greater degree of genetically isolation distance. In hybrids of T. toreumaticus and strongylocentrotid Hemicentrotus pulcherrimus (A. Agassiz, 1864), larval skeletons expressed features from both species. These results suggest that traits of hybrids are derived not only from one or both original species, but that a mosaic effect can be obtained depending on the traits. These results indicate that temnopleurids have the weaker fertilization block mechanisms. Isozyme analyses showed that hybrid prisms of T. toreumaticus eggs and M. globulus sperm possess enzymatic patterns of malate dehydrogenase derived from each parent, whereas the enzymatic pattern of glucose-6-phosphate dehydrogenase is derived from eggs, suggesting that malate dehydrogenase activity may be useful in detecting naturally occurring adult hybrids among these species in the Yamaguchi coastal area.
New reports of echinoderms on the Caribbean continental slope of central America
Authors: CAMBRONERO-SOLANO SERGIO , BENAVIDES R. , SOLÍS-MARÍN F. A. , ALVARADO J. J.
Published: October 2019

The Caribbean is considered a unique biogeographic region that represents an important hotspot of marine diversity in the Atlantic Ocean. The Caribbean Continental Slope of Central America (CCCA) is a largely unexplored area that exhibits a variety of habitats. Among this unstudied biodiversity, special importance has been given to the benthic communities associated with deep bottoms, a diverse group that plays a major role in the ocean carbon cycling and nutrient flux. Echinoderms are one of the main benthic deep sea taxa, in which Holothuroidea is the globally dominant class. We present the results from the first exploratory fishing survey campaign on the CCCA, done under the regional coordination of OSPESCA (Central America Fisheries and Aquaculture Organization) on board of the R/V Miguel Oliver in January 2011. Data was collected from a total of 96 trawls arranged in 25 transects that started in Panama and finished in Belize. A Lofoten bottom trawling net was dragged for 30 min between 0 to 1500m depth. The major component of the total invertebrate catch was Holothuroidea with a biomass of 593 kg (16.49% of the total) and represented by seven species. The following are new reports for the Caribbean: Bathyplotes natans in Honduras and Guatemala, Bentothuria funebris in Panama, Benthodytes sanguinolenta in Panama, Costa Rica, Nicaragua and Belize; Hansenothuria sp. in Panama, Costa Rica and Honduras. Paroriza pallens extends its distribution to Panama, Costa Rica, Nicaragua and Honduras, Zygothuria lactea its reported in Panama. We also present the first records of the crinoid Neocomatella pulchella in Honduras, theasteroid Cheiraster (Cheiraster) planusin Panama, and, for Costa Rica (Asteroidea: Doraster constellatus and Echinoidea: Clypeaster euclastus).Holothurians are the predominant invertebrate fauna in terms of biomass in the entire region of the CCCA. These findings suggest that CCCA presents a high echinoderm biodiversity  and also supports the ecoregional variation theory. We report higher echinoderm biomass (75%) in the Southwestern Caribbean compared to Western Caribbean ecoregion. The information presented in this paper establishes the baseline information of echinoderms depth fauna in the Caribbean of Central America, and opens new opportunities for future research.
Ophiuroid locomotion from fundamental structures to integrated systems
Authors: CLARK ELIZABETH G.
Published: October 2019

The phylum Echinodermata includes an estimated 7,000 extant and 13,000 extinct species. Each living class represents a separate body plan with a unique mode of movement and locomotion. Brittle stars (Class Ophiuroidea) utilize complex arm musculoskeletal physiology for rapid locomotion, in contrast to the other echinoderm classes, which are typically slow moving. Ophiuroid locomotion and its origins are poorly understood. This paper is a review of the current state of ophiuroid research, with a focus on topics relevant to ophiuroid movement and locomotion, including anatomy, physiology, functional morphology, disparity, ecology, and evolutionary history.
Estimating survival in echinoid populations
Authors: EBERT THOMAS A. , HERNÁNDEZ JOSÉ CARLOS , CLEMENTE SABRINA
Published: October 2019

Estimating survival rate is a basic part of population studies. Generally it is assumed that populations being studied are both stable and stationary. This probably is seldom the case although as a long-term average populations may persist at a mean density. Estimating survival in short-term studies may fail to capture average rates. A long-term study of the purple sea urchin Strongylocentrotus purpuratus at Sunset Bay, OR, USA from 1964–2009 is used to demonstrate methods for estimating survival based on the coefficient of variation of size distributions, the fraction of new recruits in a population, means of size data coupled with estimates of growth, and a method that uses rates of flow through size categories. A short-term study of just a few years may by chance sample when an unusual recruitment event drives a population far from stationary structure and so distorts the estimate of mean survival. The best solution, as shown for S. purpuratus, is a long time series but in advance it cannot be determined how long this should be. If a study of three years shows no substantial change in population size structure it may be reasonable to accept estimates of survival.
A field guide to coastal echinoderms of the Kerguelen Islands
Authors: FERAL J.-P. , POULIN E. , DE RIDDER C. , SAUCEDE T.
Published: October 2019

One of the current challenges in today’s ecology research is to understand and quantify the effects of climate changes on biodiversity. In order to detect possible trends in biodiversity patterns, it is necessary to conduct long-term observations in various and representative environments. This is always challenging, even more difficult in marine habitats and in the Southern Ocean in particular.      Since 2012, a submarine observatory of the coastal benthos has been in operation in the Kerguelen Islands. Eight contrasting sites are monitored using photo and video surveys, loggers, and settlement plots. To quantify potential changes, several photographic analysis techniques are also complemented by scuba diving and ROV (Remotely Operated Vehicle) observations. Investigator scientists have developed and improved new protocols that will be carried out in the long term by the staff of the National Natural Reserve of the French Southern Territories. In order to provide reliable support of species identification, the Proteker program supported by IPEV, French Polar Institute, is currently developing several field guides that should improve the identification of the main taxa being monitored. In light of their abundance in coastal environments of the Kerguelen Islands, and because they are among the most visible invertebrates and the easiest of organisms to consider for monitoring surveys, we first focused on echinoderms. Results of this first study are presented here.      For each echinoderm species, a spreadsheet provides the species name with synonymies, a description of diagnostic features, the recorded distribution, as well as three different types of illustrations: (i) living specimens in their environment, which is useful for scuba divers, (ii) fresh collected specimens out of water, and (iii) specimens fixed in ethanol. Therefore, species can be identified alive while diving, but also after sampling in the field, and after several years in the laboratory. An assessment of Kerguelen’s coastal echinoderms is also given.
Reinterpretation of the enigmatic Ordovician genus Bolboporites (Echinodermata)

Authors: GILLET EMERIC , LEFEBVRE BERTRAND , GARDIEN VERONIQUE , STEIMETZ EMILIE , DURLET CHRISTOPHE , MARIN FREDERIC
Published: October 2019

Bolboporites is an enigmatic Ordovician cone-shaped fossil, the precise nature and systematic affinities of which have been controversial over almost two centuries. For the first time, a wide range of techniques (CT-scan, SEM, cathodoluminescence, XPL, UV epifluorescence, EBSD, FT-IR and XRF spectrometry) were applied to well-preserved specimens of Bolboporites from Norway and Russia. Our main finding confirms its echinoderm affinities, as shown by its stereomic microstructure and by the first definitive evidence of its monocrystalline nature. Each cone consists in a single, microporous calcitic crystal with a narrow longitudinal internal canal. These results are combined with all previous data on Bolboporites to critically discuss five alternative interpretations of this fossil, namely theca, basal cone, spine, columnal, and holdfast, respectively. The most parsimonious scenario considers Bolboporites as an isolated spine, which was articulated in life by a short biserial appendage to the body wall of an unknown echinoderm, possibly of echinozoan affinities.
Arrangement and size variation of intra-gonadal offspring in a viviparous asterinid sea star

Authors: KHAN M. S.R. , WHITTINGTON C. M. , THOMPSON M. B. , BYRNE M.
Published: October 2019

Sibling competition and developmental asynchrony may greatly influence the arrangement and size of offspring of marine invertebrates that care for their young. In Parvulastra parvivipara, an asterinid sea star that incubates its young in the gonads, sibling cannibalism supports post-metamorphic development. Offspring size varies within (coefficient of variation, CV = 22.6 %) and among (CV = 17.7%) the gonads. Confocal microscopy was used to visualize early embryos and oocytes, and revealed the presence of several developmental stages within individual gonads. The eggs were a mean diameter of 84 μm. The observation of a gastrula at 86 µm smaller than the largest egg observed (134 µm) suggests that terminal egg size varies. The appearance of early embryos surrounded by somatic cells suggests that they may receive nutrients through histotrophy. Sibling competition intensifies once the digestive tract is functional in the tiny juveniles which then start to consume siblings. The arrangement of the offspring in the gonads was observed using micro-computed tomography. The juveniles were oriented with their oral surface facing each other, presumably as a defensive strategy to protect themselves from being eaten. Periodic release of offspring in single or several cohorts indicates continual reproduction. Released and retained juveniles varied in size. It is not known what initiates birth but it may be mediated by sibling competition. Larger adults had a greater allocation to female reproductive output than smaller adults.
A project for analyzing the ecology and phylogeny of western Pacific echinoids
Authors: KANAZAWA K. , SAITOH M. , WAKAYAMA N. , OBUCHI M. , NAKACHI S. , KROH A.
Published: October 2019

In 2017 we started a project to analyze the ecology and phylogeny of western Pacific echinoids. As the first step, we are establishing methods to infer their phylogenetic relationships using molecular data; we developed effective methods to obtain complete mitochondrial DNA sequences, and determined their effectiveness in phylogenetic analysis. We have also been gathering data concerning the ecology and systematics of Japanese extant echinoids, which arguably has among the highest genus-level diversities in the West Pacific or perhaps even in the world. We have collected 58 species from middle and southern Japan representing 48 genera. In the next year, we will collect sea urchins from northern Japan, and within 2 years we will finish collecting data on ecology and systematics of Japanese echinoids, and provide a set of standardized data that will be useful for many researchers studying western Pacific echinoids. At that time, we will start comparative analyses of echinoid faunas distributed in the western Pacific.
Diversification in the mountains: a generic reappraisal of the Western Ghats endemic gecko genus Dravidogecko Smith, 1933 (Squamata: Gekkonidae) with descriptions of six new species
Authors: CHAITANYA R. , GIRI VARAD B. , DEEPAK V. , DATTA-ROY ANIRUDDHA , MURTHY B.H.C.K , KARANTH PRAVEEN
Published: October 2019

The monotypic genus Dravidogecko, represented by its type-species D. anamallensis, is singular amongst peninsular Indian gekkonid lineages in its endemism to the Western Ghats. Molecular species delimitation approaches reveal at least seven species-level lineages within the genus from its distribution range across the mid–high elevations of the southern Western Ghats of India. These lineages, albeit superficially cryptic, are patently diagnosable from each other by employing a limited but precise set of morphological characters. Six of these lineages that were obscured under the nomen D. anamallensis are herein recognized as distinct species. A reappraisal of the genus Dravidogecko is provided based on external morphology and osteological characters, along with a detailed redescription of the holotype of D. anamallensis. A key to the species based on diagnostic characters is presented. Gene-trees based on mitochondrial and nuclear DNA data recovered marginally disparate topologies and were consequently coalesced into a species-tree for phylogenetic inference. Timetree analysis reveals late Miocene cladogenesis in this group and establishes late Palaeocene divergence from its sister genus, Hemidactylus, making Dravidogecko one of the earliest, extant lizard lineages to have colonized peninsular India.
Neotype designation and re-description of Prolachlanius resinatus (Hagen) (Neuroptera, Hemerobiidae) from Baltic amber, with the first record of the species from Rovno amber
Authors: MAKARKIN VLADIMIR N. , PERKOVSKY EVGENY E. , GRÖHN CARSTEN
Published: October 2019

Prolachlanius resinatus (Hagen) is re-described, based on five specimens from late Eocene Baltic amber (including the neotype designated herein) and the first recorded specimen from contemporaneous Rovno amber (Klesov locality). This is the most common species of Hemerobiidae in Baltic amber. The forewing venation of Prolachlanius is most similar to that of Sympherobius, and, therefore, its assignment to Sympherobiinae is confirmed. The genus differs from other Sympherobiinae by the distal branch of RP being not deeply forked, and the presence of crossvein 4r-m in the forewing. The male genitalia of Prolachlanius are sufficiently dissimilar from those of other Sympherobiinae to distinguish it as a separate genus, particularly by the structure of the ectoprocts, and the 8th and 9th sternites. The extremely short eighth sternite of Prolachlanius is especially noteworthy.
Taxonomic review of the leafhopper genus Grammacephalus Haupt (Hemiptera: Cicadellidae: Deltocephalinae: Scaphoideini) with description of a new species from Pakistan
Authors: SHAH BISMILLAH , NAVEED HASSAN , DUAN YANI
Published: October 2019

The leafhopper genus Grammacephalus Haupt is revised with the description and illustrations of a new species Grammacephalus punjabensis Shah & Duan sp. n. from Pakistan. A checklist of the species of Grammacephalus and key to distinguish known species in the genus are also given in the present study.
Three new species of the free-living marine nematode Metoncholaimus Filipjev, 1918 (Enoplida, Oncholaimidae) from Argentinean coasts
Authors: RUSSO VIRGINIA LO , DE WARD CATALINA T. PASTOR
Published: October 2019

Three new species of free-living marine nematodes of the genus Metoncholaimus are described from San Matías gulf (Río Negro, Argentina). Metoncholaimus sanmatiensis sp. n. is characterized by large body size, long spicules, small gubernaculum, presence of long setose pre- and postcloacal genital sensilla and presence of precloacal pores. Metoncholaimus perdisus sp. n. is characterized by small-sized body, short spicules, small gubernaculum, presence of long setose pre- and postcloacal genital sensilla and presence of pre- and postcloacal pores. Metoncholaimus paracavatus sp. n. is closely related to Oncholaimus cavatus but can be considered as a new Metoncholaimus species based on the presence of gubernaculum and the morphology of the demanian system. A compendium of all valid species, including new species, is given.
First record of two rare spider crabs (Crustacea: Decapoda: Brachyura: Majoidea) from Brazil
Authors: ALVES-JÚNIOR FLAVIO DE ALMEIDA , LUCATELLI DÉBORA , SANTANA WILLIAM , DE SOUZA-FILHO JESSER FIDELIS
Published: October 2019

In this paper we report the first occurrence of two rare spider crabs (Majoidea) from Brazil, with additional morphological information based on material collected in the upper continental slope of the Potiguar Basin, northeast of Brazil. Lepteces ornatus Rathbun, 1893 (Epialtidae), originally described from the Gulf of Mexico and also reported from Uruguay, is now recorded from Brazilian waters (off Rio Grande do Norte), whereas Collodes leptocheles Rathbun, 1894 (Inachoididae) was considered for a long time as an endemic species of Gulf of Mexico and herein is being recorded for the first time in the Southern Atlantic.
A new genus Microsarimodes with one species from Hainan Province in China (Hemiptera: Fulgoromorpha: Issidae)
Authors: CHANG ZHI-MIN , YANG LIN , CHEN XIANG-SHENG
Published: October 2019

A new genus Microsarimodes Chang & Chen, gen. nov. with type species Microsarimodes tumida Chang & Chen, sp. nov. are described and illustrated. All type specimens are deposited in Guizhou University. A short discussion on the tribe Sarimini to which these taxa belongs is provided.
Interannual Variability of North American Winter Temperature Extremes and Its Associated Circulation Anomalies in Observations and CMIP5 Simulations
Authors: Yu B. , Lin H. , Kharin V. V. , Wang X. L.
Published: October 2019

The interannual variability of wintertime North American surface temperature extremes and its generation and maintenance are analyzed in this study. The leading mode of the temperature extreme anomalies, revealed by empirical orthogonal function (EOF) analyses of December–February mean temperature extreme indices over North America, is characterized by an anomalous center of action over western-central Canada. In association with the leading mode of temperature extreme variability, the large-scale atmospheric circulation features an anomalous Pacific–North American (PNA)-like pattern from the preceding fall to winter, which has important implications for seasonal prediction of North American temperature extremes. A positive PNA pattern leads to more warm and fewer cold extremes over western-central Canada. The anomalous circulation over the PNA sector drives thermal advection that contributes to temperature anomalies over North America, as well as a Pacific decadal oscillation (PDO)-like sea surface temperature (SST) anomaly pattern in the midlatitude North Pacific. The PNA-like circulation anomaly tends to be supported by SST warming in the tropical central-eastern Pacific and a positive synoptic-scale eddy vorticity forcing feedback on the large-scale circulation over the PNA sector. The leading extreme mode–associated atmospheric circulation patterns obtained from the observational and reanalysis data, together with the anomalous SST and synoptic eddy activities, are reasonably well simulated in most CMIP5 models and in the multimodel mean. For most models considered, the simulated patterns of atmospheric circulation, SST, and synoptic eddy activities have lower spatial variances than the corresponding observational and reanalysis patterns over the PNA sector, especially over the North Pacific.
Femtosecond Laser Fabricated Elastomeric Superhydrophobic Surface with Stretching-Enhanced Water Repellency
Authors: Yang Huan , Xu Kaichen , Xu Changwen , Fan Dianyuan , Cao Yu , Xue Wei , Pang Jihong
Published: October 2019

Highly stretchable and robust superhydrophobic surfaces have attracted tremendous interest due to their broad application prospects. In this work, silicone elastomers were chosen to fabricate superhydrophobic surfaces with femtosecond laser texturing method, and high stretchability and tunable adhesion of the superhydrophobic surfaces were demonstrated successfully. To our best knowledge, it is the first time flexible superhydrophobic surfaces with a bearable strain up to 400% are fabricated by simple laser ablation. The test also shows that the strain brings no decline of water repellency but an enhancement to the superhydrophobic surfaces. In addition, a stretching-induced transition from “petal” state to “lotus” state of the laser-textured surface was also demonstrated by non-loss transportation of liquid droplets. Our results manifest that femtosecond laser ablating silicone elastomer could be a promising way for fabricating superhydrophobic surface with distinct merits of high stretchability, tunable adhesion, robustness, and non-fluorination, which is potentially useful for microfluidics, biomedicine, and liquid repellent skin.
Prediction of sgRNA on-target activity in bacteria by deep learning
Authors: Wang Lei , Zhang Juhua
Published: October 2019

Background

One of the main challenges for the CRISPR-Cas9 system is selecting optimal single-guide RNAs (sgRNAs). Recently, deep learning has enhanced sgRNA prediction in eukaryotes. However, the prokaryotic chromatin structure is different from eukaryotes, so models trained on eukaryotes may not apply to prokaryotes.

Results

We designed and implemented a convolutional neural network to predict sgRNA activity in Escherichia coli. The network was trained and tested on the recently-released sgRNA activity dataset. Our convolutional neural network achieved excellent performance, yielding average Spearman correlation coefficients of 0.5817, 0.7105, and 0.3602, respectively for Cas9, eSpCas9 and Cas9 with a recA coding region deletion. We confirmed that the sgRNA prediction models trained on prokaryotes do not apply to eukaryotes and vice versa. We adopted perturbation-based approaches to analyze distinct biological patterns between prokaryotic and eukaryotic editing. Then, we improved the predictive performance of the prokaryotic Cas9 system by transfer learning. Finally, we determined that potential off-target scores accumulated on a genome-wide scale affect on-target activity, which could slightly improve on-target predictive performance.

Conclusions

We developed convolutional neural networks to predict sgRNA activity for wild type and mutant Cas9 in prokaryotes. Our results show that the prediction accuracy of our method is improved over state-of-the-art models.
Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L.
Authors: Alam Intikhab , Liu Cui-Cui , Ge Hong-Liu , Batool Khadija , Yang Yan-Qing , Lu Yun-Hai
Published: October 2019

Background

Plant homeodomain (PHD) finger proteins are widely present in all eukaryotes and play important roles in chromatin remodeling and transcriptional regulation. The PHD finger can specifically bind a number of histone modifications as an “epigenome reader”, and mediate the activation or repression of underlying genes. Many PHD finger genes have been characterized in animals, but only few studies were conducted on plant PHD finger genes to this day.Brassica rapa(AA, 2n = 20) is an economically important vegetal, oilseed and fodder crop, and also a good model crop for functional and evolutionary studies of important gene families amongBrassicaspecies due to its close relationship toArabidopsis thaliana.

Results

We identified a total of 145 putative PHD finger proteins containing 233 PHD domains from the current version ofB. rapagenome database. Gene ontology analysis showed that 67.7% of them were predicted to be located in nucleus, and 91.3% were predicted to be involved in protein binding activity. Phylogenetic, gene structure, and additional domain analyses clustered them into different groups and subgroups, reflecting their diverse functional roles during plant growth and development. Chromosomal location analysis showed that they were unevenly distributed on the 10B. rapachromosomes. Expression analysis from RNA-Seq data showed that 55.7% of them were constitutively expressed in all the tested tissues or organs with relatively higher expression levels reflecting their important housekeeping roles in plant growth and development, while several other members were identified as preferentially expressed in specific tissues or organs. Expression analysis of a subset of 18B. rapaPHD finger genes under drought and salt stresses showed that all these tested members were responsive to the two abiotic stress treatments.

Conclusions

Our results reveal that the PHD finger genes play diverse roles in plant growth and development, and can serve as a source of candidate genes for genetic engineering and improvement ofBrassicacrops against abiotic stresses. This study provides valuable information and lays the foundation for further functional determination of PHD finger genes across theBrassicaspecies.
Pruritus in patients with chronic liver disease and serum autotaxin levels in patients with primary biliary cholangitis
Authors: Fujino Hatsue , Tanaka Mio , Imamura Michio , Morio Kei , Ono Atsushi , Nakahara Takashi , Murakami Eisuke , Kawaoka Tomokazu , Takahashi Shoichi , Miki Daiki , Tsuge Masataka , Hiramatsu Akira , Aikata Hiroshi , Hayes C. Nelson , Chayama Kazuaki
Published: October 2019

Background

Pruritus is a common symptom seen in patients with chronic liver disease. However, frequency and severity of pruritus in patients with chronic liver disease is unclear. We investigated frequency, severity and predictive factors of pruritus in these patients from a large cohort.

Methods

A total of 2477 patients with chronic liver disease without allergies or skin diseases were investigated for itch frequency and severity. Itch severity was self-assessed using pruritus scores using the numerical rating scale (NRS). Multivariate regression analysis was performed to identify factors associated with pruritus. Serum autotaxin levels were measured in patients with primary biliary cholangitis (PBC), and the relationship to liver fibrosis and pruritus was analyzed.

Results

The frequency of pruritus in patients with chronic liver disease was significantly higher than in subjects without liver disease (29.8 and 16.2%, respectively,P < 0.001). NRS was high in patients with chronic liver disease, especially in those with PBC, as is generally expected. Multivariate analysis identified lower albumin, higher eosinophil count, and etiology of PBC as independent factors associated with severe pruritus (≥5 points of NRS). In patients with PBC, serum autotaxin levels were significantly correlated with liver fibrosis markers such as platelet count and liver stiffness, and hepatobiliary enzymes such as total bilirubin, aspartate aminotransferase and alkaline phosphatase. However, no significant correlations between serum autotaxin levels and frequency and severity of pruritus were observed in patients with PBC.

Conclusion

The frequency of pruritus was high in patients with chronic liver disease. Reduction of liver function is associated with severe pruritus based on the large number of patients with chronic liver disease. Serum autotaxin is useful for assessing liver fibrosis and severity of cholangitis; however, it is not a predictive marker for severe pruritus in patients with PBC.
Correction to: HCV-infected individuals have higher prevalence of comorbidity and multimorbidity: a retrospective cohort study
Authors: Cooper Curtis L. , Galanakis Chrissi , Donelle Jessy , Kwong Jeffery C. , Boyd Rob , Boucher Lisa , Kendall Claire E.
Published: October 2019

After publication of the original article [1], we were notified that an author’s name has been incorrectly spelled. Jeff Kwong’s full name is Jeffery C. Kwong.
The impact of D-cycloserine and sarcosine on in vivo frontal neural activity in a schizophrenia-like model
Authors: Yao Lulu , Wang Zongliang , Deng Di , Yan Rongzhen , Ju Jun , Zhou Qiang
Published: October 2019

Background

N-methyl-D-aspartate receptor (NMDAR) hypofunction has been proposed to underlie the pathogenesis of schizophrenia. Specifically, reduced function of NMDARs leads to altered balance between excitation and inhibition which further drives neural network malfunctions. Clinical studies suggested that NMDAR modulators (glycine, D-serine, D-cycloserine and glycine transporter inhibitors) may be beneficial in treating schizophrenia patients. Preclinical evidence also suggested that these NMDAR modulators may enhance synaptic NMDAR function and synaptic plasticity in brain slices. However, an important issue that has not been addressed is whether these NMDAR modulators modulate neural activity/spiking in vivo.

Methods

By using in vivo calcium imaging and single unit recording, we tested the effect of D-cycloserine, sarcosine (glycine transporter 1 inhibitor) and glycine, on schizophrenia-like model mice.

Results

In vivo neural activity is significantly higher in the schizophrenia-like model mice, compared to control mice. D-cycloserine and sarcosine showed no significant effect on neural activity in the schizophrenia-like model mice. Glycine induced a large reduction in movement in home cage and reduced in vivo brain activity in control mice which prevented further analysis of its effect in schizophrenia-like model mice.

Conclusions

We conclude that there is no significant impact of the tested NMDAR modulators on neural spiking in the schizophrenia-like model mice.
Association between back muscle degeneration and spinal-pelvic parameters in patients with degenerative spinal kyphosis
Authors: Xia Weiwei , Fu Han , Zhu Zhenqi , Liu Chenjun , Wang Kaifeng , Xu Shuai , Liu Haiying
Published: October 2019

Background

The paraspinal and psoas muscles have been considered to be essentially important for stabilizing the spinal column, and the muscle degeneration was found to exist in degenerative spinal kyphosis (DSK) patients. However, it is still not clear the relationship between muscle degeneration and spinal-pelvic alignment. The purpose of this study was to determine the correlations between the individual muscle degeneration at each lumbar spinal level and spinal-pelvic parameters in DSK patients.

Methods

The imaging data of 32 patients with DSK were retrospectively analyzed. The fat infiltration (FI) and relative cross-sectional area of muscle (RCSA) were quantitatively measured for multifidus (MF), erector spinae (ES) and psoas (PS) at each spinal level from L1/2 to L5/S1. The correlations were analyzed between RCSA and the sagittal vertical axis (SVA), thoracic kyphosis (TK), thoracolumbar kyphosis (TLK), lumbar lordosis (LL), sacral slope (SS), pelvic tilt (PT) and pelvic incidence (PI).

Results

The FI of MF and ES at L3/4, L4/5 and L5/S1 were higher than that at L1/2 and L2/3. The FI of PS at L4/5 and L5/S1 were lower than that of L1/2, L2/3 and L3/4. The RCSA of ES and PS from L1/2 to L5/S1 gradually increased, whereas the RCSA of ES from L1/2 to S5/S1 gradually decreased. The RCSA of MF at the L1/2 level was negatively correlated SVA (r = − 0.397,p = 0.024); the RCSA at L3/4, L4/5 and L5/S1 levels were negatively correlated with TK (r = − 0.364, p = 0.04; r = − 0.38, p = 0.032; r = − 0.432, p = 0.014); the RCSA at L4/5 level was positively correlated with LL (r = 0.528, p = 0.002). The RCSA of ES at L3/4 and L4/5 levels were positively correlated with PI (r = 0.377, p = 0.037) and SS (r = 0.420, p = 0.019).

Conclusions

FI of MF and ES at lower lumbar level is higher than that at upper level, but FI of PS at upper lumbar level is higher than that at lower level. MF and ES have different roles for maintaining the sagittal spinal-pelvic balance.
Aneurysmal bone cyst: results of an off label treatment with Denosumab
Authors: Dürr Hans Roland , Grahneis Ferdinand , Baur-Melnyk Andrea , Knösel Thomas , Birkenmaier Christof , Jansson Volkmar , Klein Alexander
Published: October 2019

Background

The treatment of aneurysmal bone cysts (ABCs) has evolved and less invasive methods have been tried. Denosumab is a monoclonal antibody which inhibits osteoclasts. It has been shown to be effective in giant cell tumour of bone (GCT) of bone and hence promises some effect also in ABC. We report on 6 patients treated with Denosumab and compare our results to the cases already published.

Methods

Data of 6 patients with ABCs and patients whose treatment included Denosumab were retrospectively analyzed. Denosumab was used at a dose of 120 mg on days 1, 8, 15 and 29, and every 4 weeks thereafter. In some of these patients the dose was reduced at the end of the treatment. Clinical and radiological responses were evaluated.

Results

In 4 female and 2 male patients with a mean age of 17 years (range: 6–30 years) the lesions were located in the sacrum (2), in distal radius, distal femur, talus and pelvis. One of the sacral lesions healed after 12 months and has stayed stable for 3 years since. The second patient received 2 years of therapy with recalcification, but recurred 1 year later and is under renewed therapy. The pelvic lesion improved but recurred. This patient has a 13-years history of intermittent therapy including surgery, two pregnancies and remains in a stable situation. The lesion of the talus did not improve with Denosumab after surgery and was complicated by destruction of the ankle joint with osteoarthritis. Recurrent lesions of the distal femur and the distal radius, previously treated by curettage and bone grafting healed under Denosumab and have remained stable for 2 and 3 years, respectively. One case of severe hypercalcemia was observed in a 7-year old child 6 months after discontinuation of Denosumab.

Conclusion

Denosumab provides a treatment option for ABCs in anatomically critical locations. Adjuvant application might reduce the rate of local recurrence. In young patients, severe rebound hypercalcemia months after discontinuation of Denosumab may occur.
Changes in circulating cell-free nuclear DNA and mitochondrial DNA of patients with adolescent idiopathic scoliosis
Authors: Li Jiong , Wang Longjie , Yang Guanteng , Wang Yunjia , Guo Chaofeng , Liu Shaohua , Gao Qile , Zhang Hongqi
Published: October 2019

Background

Adolescent idiopathic scoliosis (AIS) which characterized by complex three-dimensional deformity of spine has been difficult to cure because of the unknown etiopathology and uncertainty of progression. Nowadays, circulating cell-free (ccf) DNA was found to be a potential biomarker for several benign and malignant diseases. However, whether ccf DNA can be a biomarker for AIS has not been reported yet. In this study, we investigate the circulating cell-free nuclear DNA (ccf n-DNA) and mitochondrial DNA (ccf mt-DNA) concentrations in the plasma of patients with AIS and controls (CT), and the changed plasma ccf n-DNA and ccf mt-DNA levels and their association with clinical parameters were assessed.

Methods

The plasma of peripheral blood from 69 AIS patients and 21 age-matched CT was collected for ccf DNA analysis. Quantitative PCR was used to detect ccf n-DNA and ccf mt-DNA levels, and correlation analyses between the ccf n-DNA and ccf mt-DNA levels and clinical characteristics were conducted. Receiver operator curves (ROC) were used to analyze the sensitivity and specificity of ccf n-DNA and ccf mt-DNA levels to different characteristics.

Results

The plasma ccf n-DNA levels of both GAPDH and ACTB were significantly decreased in AIS patients compared with those in controls, while the plasma ccf mt-DNA levels did not changed. According to sex-related analyses, the ccf n-DNA levels in male CT-M was higher than that in female CT and male AIS, but the ccf n-DNA levels in female AIS was not significantly changed when compared with male AIS or female CT. However, the concentration of ccf mt-DNA in female AIS increased significantly when compared with male AIS. Surprisingly, Lenke type-related analyses suggested that Lenke type 1 patients had lower ccf n-DNA levels, whereas Lenke type 5 patients had higher ccf mt-DNA levels compared with those of controls. However, a lower sensitivity and specificity of AIS predicted by ccf n-DNA or ccf mt-DNA levels was observed, whether in total, by sex, or by Lenke type.

Conclusion

Although with no/little predictive accuracy of AIS/progressed AIS by ccf DNA levels, significantly changed plasma ccf DNA levels were observed in AIS patients compared with those in controls.
Intravenous and subsequent long-term oral tranexamic acid in enhanced-recovery primary total knee arthroplasty without the application of a tourniquet: a randomized placebo-controlled trial
Authors: Wang Hao-Yang , Wang Liu , Luo Ze-Yu , Wang Duan , Tang Xin , Zhou Zong-Ke , Pei Fu-Xing
Published: October 2019

Background

To assess the efficacy and safety of intravenous and subsequent long-term oral tranexamic acid (TXA) following total knee arthroplasty (TKA) without a tourniquet.

Methods

In this double-blinded trial, 118 patients undergoing primary TKA were randomized into two groups: the patients in group A received intravenous TXA at 20-mg/kg 10 min before the surgery and 3 h postoperatively, and then oral 1 g TXA from postoperative day (POD) 1 to POD 14, and the patients in group B received intravenous TXA at 20-mg/kg 10 min before surgery and 3 h postoperatively, and then oral 1 g placebo from postoperative day (POD) 1 to POD 14. The primary outcome was total blood loss. Secondary outcomes included ecchymosis area and morbidity, postoperative transfusion, postoperative laboratory values, postoperative knee function and length of hospital stay. Complications, and patient satisfaction were also recorded.

Results

The mean total blood loss was lower in Group A than in Group B (671.7 ml vs 915.8 ml, P = 0.001). There was no significant difference in the transfusion rate between the two groups. Group A had a higher hemoglobin than Group B on POD 3 (106.0 g/L vs 99.7 g/L, P = 0.001). However, no significant difference was found for Hb or hematocrit on POD 1 or POD 14 between the two groups. Patients in Group A had less ecchymosis morbidity (7 vs 38, P = 0.001), smaller ecchymosis area (1.6 vs 3.0, P = 0.001) than Group B. The blood coagulation level as measured by fibrinolysis (D-Dimer) was lower in Group A than in Group B on POD 1 and POD 3 (4.6 mg/L vs. 8.4 mg/L, respectively, P = 0.001; 1.5 mg/L vs. 3.3 mg/L, respectively, P = 0.001). However, there was no significant difference on POD 14, and the fibrin degradation products showed the same trend. Patients in Group A had less swelling than those in Group B on POD 3 and POD 14. The circumference of the knee was 43.1 cm vs. 46.1 cm (POD 3, P = 0.001) and 41.4 cm vs. 44.9 cm (POD 14, P = 0.001) in Group A vs Group B, respectively. Nevertheless, the circumference of the knee in the two groups was similar on POD 1 and POD 3 M. No significant differences were identified in knee function, pain score, or hospital stay. No significant differences were identified in thromboembolic complications, infection, hematoma, wound healing and patients satisfaction between the two groups.

Conclusion

Intravenous and subsequent long-term oral TXA produced less blood loss and less swelling and ecchymosis compared with short-term TXA without increasing the risk of complications.

Trial registration

The trial was registered in the Chinese Clinical Trial Registry (ChiCTR-IPR-17012264).
One-leg rise performance and associated knee kinematics in ACL-deficient and ACL-reconstructed persons 23 years post-injury
Authors: Strong Andrew , Tengman Eva , Srinivasan Divya , Häger Charlotte K.
Published: October 2019

Background

Research indicates reduced knee function and stability decades after anterior cruciate ligament (ACL) injury. Assessment requires reliable functional tests that discriminate such outcomes from asymptomatic knees, while providing suitable loading for different populations. The One-leg rise (OLR) test is common in clinics and research but lacks scientific evidence for its implementation. Our cross-sectional study compared performance including knee kinematics of the OLR between ACL-injured persons in the very long term to controls and between legs within these groups, and assessed the within-session reliability of the kinematics.

Methods

Seventy ACL-injured individuals (mean age 46.9 ± 5.4 years) treated with either reconstructive surgery and physiotherapy (ACLR; n = 33) or physiotherapy alone (ACLPT; n = 37), on average 23 years post-injury, and 33 age- and sex-matched controls (CTRL) attempted the OLR. Participants completed as many repetitions as possible to a maximum of 50 while recorded by motion capture. We compared between all groups and between legs within groups for total repetitions and decomposed the OLR into movement phases to compare phase completion times, maximum and range of knee abduction and adduction angles, and mediolateral knee control in up to 10 repetitions per participant.

Results

ACLPT performed significantly fewer OLR repetitions with their injured leg compared to the CTRL non-dominant leg (medians 15 and 32, respectively) and showed significantly greater knee abduction than ACLR and CTRL (average 2.56°-3.69° depending on phase and leg). Distribution of repetitions differed between groups, revealing 59% of ACLPT unable to complete more than 20 repetitions on their injured leg compared to 33% ACLR and 36% CTRL for their injured and non-dominant leg, respectively. Within-session reliability of all kinematic variables for all groups and legs was high (ICC 3,10 0.97–1.00, 95% CI 0.95–1.00, SEM 0.93–1.95°).

Conclusions

Negative outcomes of OLR performance, particularly among ACLPT, confirm the need to address aberrant knee function and stability even decades post-ACL injury. Knee kinematics derived from the OLR were reliable for asymptomatic and ACL-injured knees. Development of the OLR protocol and analysis methods may improve its discriminative ability in identifying reduced knee function and stability among a range of clinical populations.