bluuebunny/crossref_metadata_2025_split huggingface dataset:
Diversity of isoprene-degrading bacteria in phyllosphere and soil communities from a high isoprene-emitting environment: a Malaysian oil palm plantation
Authors: Carrión Ornella , Gibson Lisa , Elias Dafydd M. O. , McNamara Niall P. , van Alen Theo A. , Op den Camp Huub J. M. , Supramaniam Christina Vimala , McGenity Terry J. , Murrell J. Colin 
Published: June 2020

Abstract
Background
Isoprene is the most abundantly produced biogenic volatile organic compound (BVOC) on Earth, with annual global emissions almost equal to those of methane. Despite its importance in atmospheric chemistry and climate, little is known about the biological degradation of isoprene in the environment. The largest source of isoprene is terrestrial plants, and oil palms, the cultivation of which is expanding rapidly, are among the highest isoprene-producing trees.

Results
DNA stable isotope probing (DNA-SIP) to study the microbial isoprene-degrading community associated with oil palm trees revealed novel genera of isoprene-utilising bacteria including Novosphingobium, Pelomonas, Rhodoblastus, Sphingomonas and Zoogloea in both oil palm soils and on leaves. Amplicon sequencing of isoA genes, which encode the α-subunit of the isoprene monooxygenase (IsoMO), a key enzyme in isoprene metabolism, confirmed that oil palm trees harbour a novel diversity of isoA sequences. In addition, metagenome-assembled genomes (MAGs) were reconstructed from oil palm soil and leaf metagenomes and putative isoprene degradation genes were identified. Analysis of unenriched metagenomes showed that isoA-containing bacteria are more abundant in soils than in the oil palm phyllosphere.

Conclusion
This study greatly expands the known diversity of bacteria that can metabolise isoprene and contributes to a better understanding of the biological degradation of this important but neglected climate-active gas.
Local adaptive evolution of two distinct clades of Beijing and T families of Mycobacterium tuberculosis in Chongqing: a Bayesian population structure and phylogenetic study
Authors: Liang Peng-Kuan , Zheng Chao , Xu Xiao-Fang , Zhao Zhe-Ze , Zhao Chang-Song , Li Chang-He , Couvin David , Reynaud Yann , Zozio Thierry , Rastogi Nalin , Sun Qun 
Published: June 2020

Abstract
Background
Beijing sub-pedigree 2 (BSP2) and T sub-lineage 6 (TSL6) are two clades belonging to Beijing and T family of Mycobacterium tuberculosis (MTB), respectively, defined by Bayesian population structure analysis based on 24-loci mycobacterial interspersed repetitive unit-variable number of tandem repeats (MIRU-VNTR). Globally, over 99% of BSP2 and 89% of TSL6 isolates were distributed in Chongqing, suggesting their possible local adaptive evolution. The objective of this paper is to explore whether BSP2 and TSL6 originated by their local adaptive evolution from the specific isolates of Beijing and T families in Chongqing.

Methods
The genotyping data of 16 090 MTB isolates were collected from laboratory collection, published literatures and SITVIT database before subjected to Bayesian population structure analysis based on 24-loci MIRU-VNTR. Spacer Oligonucleotide Forest (Spoligoforest) and 24-loci MIRU-VNTR-based minimum spanning tree (MST) were used to explore their phylogenetic pathways, with Bayesian demographic analysis for exploring the recent demographic change of TSL6.

Results
Phylogenetic analysis suggested that BSP2 and TSL6 in Chongqing may evolve from BSP4 and TSL5, respectively, which were locally predominant in Tibet and Jiangsu, respectively. Spoligoforest showed that Beijing and T families were genetically distant, while the convergence of the MIRU-VNTR pattern of BSP2 and TSL6 was revealed by WebLogo. The demographic analysis concluded that the recent demographic change of TSL6 might take 111.25 years.

Conclusions
BSP2 and TSL6 clades might originate from BSP4 and TSL5, respectively, by their local adaptive evolution in Chongqing. Our study suggests MIRU-VNTR be combined with other robust markers for a more comprehensive genotyping approach, especially for families of clades with the same MIRU-VNTR pattern.
No symphony without bassoon and piccolo: changes in synaptic active zone proteins in Huntington’s disease
Authors: Huang Ting-Ting , Smith Ruben , Bacos Karl , Song Dong-Yan , Faull Richard M. , Waldvogel Henry J. , Li Jia-Yi 
Published: June 2020

AbstractProminent features of HD neuropathology are the intranuclear and cytoplasmic inclusions of huntingtin and striatal and cortical neuronal cell death. Recently, synaptic defects have been reported on HD-related studies, including impairment of neurotransmitter release and alterations of synaptic components. However, the definite characteristics of synapse dysfunction and the underlying mechanisms remain largely unknown. We studied the gene expression levels and patterns of a number of proteins forming the cytoskeletal matrix of the presynaptic active zones in HD transgenic mice (R6/1), in hippocampal neuronal cultures overexpressing mutant huntingtin and in postmortem brain tissues of HD patients. To investigate the interactions between huntingtin and active proteins, we performed confocal microscopic imaging and immunoprecipitation in mouse and HEK 293 cell line models. The mRNA and protein levels of Bassoon were reduced in mouse and cell culture models of HD and in brain tissues of patients with HD. Moreover, a striking re-distribution of a complex of proteins including Bassoon, Piccolo and Munc 13–1 from the cytoplasm and synapses into intranuclear huntingtin aggregates with loss of active zone proteins and dendritic spines. This re-localization was age-dependent and coincided with the formation of huntingtin aggregates. Using co-immunoprecipitation, we demonstrated that huntingtin interacts with Bassoon, and that this interaction is likely mediated by a third linking protein. Three structural proteins involved in neurotransmitter release in the presynaptic active zones of neurons are altered in expression and that the proteins are redistributed from their normal functional site into mutant huntingtin aggregates.
Fusions involving BCOR and CREBBP are rare events in infiltrating glioma
Authors: Pisapia David J. , Ohara Kentaro , Bareja Rohan , Wilkes David C. , Hissong Erika , Croyle Jaclyn A. , Kim Joon-Hyung , Saab Jad , MacDonald Theresa Y. , Beg Shaham , O’Reilly Catherine , Kudman Sarah , Rubin Mark A. , Elemento Olivier , Sboner Andrea , Greenfield Jeffrey , Mosquera Juan Miguel 
Published: June 2020

AbstractBCOR has been recognized as a recurrently altered gene in a subset of pediatric tumors of the central nervous system (CNS). Here, we describe a novel BCOR-CREBBP fusion event in a case of pediatric infiltrating astrocytoma and further probe the frequency of related fusion events in CNS tumors. We analyzed biopsy samples taken from a 15-year-old male with an aggressive, unresectable and multifocal infiltrating astrocytoma. We performed RNA sequencing (RNA-seq) and targeted DNA sequencing. In the index case, the fused BCOR-CREBBP transcript comprises exons 1–4 of BCOR and exon 31 of CREBBP. The fused gene thus retains the Bcl6 interaction domain of BCOR while eliminating the domain that has been shown to interact with the polycomb group protein PCGF1. The fusion event was validated by FISH and reverse transcriptase PCR. An additional set of 177 pediatric and adult primary CNS tumors were assessed via FISH for BCOR break apart events, all of which were negative. An additional 509 adult lower grade infiltrating gliomas from the publicly available TCGA dataset were screened for BCOR or CREBBP fusions. In this set, one case was found to harbor a CREBBP-GOLGA6L2 fusion and one case a CREBBP-SRRM2 fusion. In a third patient, both BCOR-L3MBTL2 and EP300-BCOR fusions were seen. Of particular interest to this study, EP300 is a paralog of CREBBP and the breakpoint seen involves a similar region of the gene to that of the index case; however, the resultant transcript is predicted to be completely distinct. While this gene fusion may play an oncogenic role through the loss of tumor suppressor functions of BCOR and CREBBP, further screening over larger cohorts and functional validation is needed to determine the degree to which this or similar fusions are recurrent and to elucidate their oncogenic potential.
Stress loading and the occurrence of normal-type earthquakes under Boso Peninsula, Japan
Authors: Hashima Akinori , Sato Hiroshi , Sato Toshinori 
Published: June 2020

AbstractBoso Peninsula, Japan, was formed by the interaction of the Philippine Sea, Eurasian and Pacific plates around the trench–trench–trench Boso triple junction. Normal-type earthquakes are persistently observed in the subducting Philippine Sea slab under the peninsula at a depth of ~ 30 km, including a recent (2019) Mw 4.9 earthquake which caused shaking throughout the Kanto region (greater Tokyo). Such shallow intraplate earthquakes are potentially hazardous to this heavily populated region, yet their mechanism is poorly understood, especially in the context of a three-plate system. Here, we calculate stress rates in the Philippine Sea slab and the surrounding area, using a subduction model constructed in a previous study, to explain the generation of the regional stress field and its effect on earthquake occurrence. In general, the calculated stress rates under Boso Peninsula are horizontally extensional both above and below the Eurasian–Philippine Sea plate interface. We apply our calculated stress rates to the nodal planes of the observed earthquakes to calculate the Coulomb failure function (ΔCFF). These calculated ΔCFFs are generally positive on normal-type earthquakes under Boso. The ΔCFFs are also consistent with earthquakes in adjacent areas that are seismically active, for example, in the Philippine Sea plate to the south, in the collision zone around Izu Peninsula, and in the cluster in the Eurasian plate northeast of Boso Peninsula, which further supports our stress loading model. Calculation of the individual contributions of Philippine Sea plate and Pacific plate subduction shows that the development of the stress field around Boso is dependent upon contributions from both subducting plates. In contrast, the arc–arc collision at Izu Peninsula has little influence.
Toward comparable relative locations between the mainshock slip and aftershocks via empirical approaches
Authors: Chang Ta-Wei , Ide Satoshi 
Published: June 2020

AbstractThe relative locations between mainshocks and their aftershocks have long been studied to characterize the mainshock–aftershock relationships, yet these comparisons may be subjected to biases inherited from various sources, such as the analysis method, data, and model parameters. Here, we perform both a relocation analysis of interplate events to obtain accurate relative centroid locations and a slip inversion analysis of the mainshock slip relative to the relocated events, with some of the relocated events used as empirical Green’s functions, to retrieve the spatiotemporal slip features of the mainshock relative to all of the relocated events. We perform these analyses on the large ($$6.0 \le M_{W} \le 7.3$$6.0≤MW≤7.3) interplate earthquakes that occurred near four giant ($$M_{W} \ge 8.5$$MW≥8.5) megathrust earthquakes: the 2007$$M_{W} \;8.5$$MW8.5Bengkulu (Indonesia), 2005$$M_{W} \;8.6$$MW8.6Nias (Indonesia), 2010$$M_{W} \;8.8$$MW8.8Maule (Chile), and 2011$$M_{W} \;9.1$$MW9.1Tohoku-Oki (Japan) earthquakes. Most of the spatiotemporal slip features of the mainshocks are consistently recovered using different empirical Green’s functions. We qualitatively and quantitatively demonstrate that the large interplate aftershocks within 5 years of the four analyzed mainshocks are largely located on the periphery or outside of the large-slip regions of these four giant megathrust earthquakes.
Colonic varices treated with embolization after pancreatoduodenectomy with portal vein resection: a case report
Authors: Kuwabara Shota , Matsumoto Joe , Tojima Hiroyasu , Wada Hideyuki , Kato Kohei , Tabata Yukiko , Ichinokawa Masaomi , Yoshioka Tatsuya , Murakawa Katsuhiko , Ikeda Atsushi , Ohtake Setsuyuki , Ono Koichi 
Published: June 2020

Abstract
Background
Pancreatoduodenectomy with resection of the portal vein or superior mesenteric vein confluence has been safely performed in patients with pancreatic head cancer associated with infiltration of the portal vein or superior mesenteric vein. In recent years, left-sided portal hypertension, a late postoperative complication, has received focus owing to increased long-term survival with advances in chemotherapy. Left-sided hypertension may sometimes cause fatal gastrointestinal bleeding because of the rupture of gastrointestinal varices. Here, we present a case of colonic varices caused by left-sided portal hypertension after pancreatoduodenectomy with portal vein resection.

Case presentation
A 69-year-old man diagnosed with pancreatic head cancer was referred to our department for surgery after undergoing chemotherapy with nine courses of gemcitabine and nab-paclitaxel. Computed tomography showed a mass 25 mm in diameter and in contact with the portal vein. He had undergone subtotal stomach-preserving pancreatoduodenectomy with portal vein resection. Four centimeters of the portal vein had been resected, and end-to-end anastomosis was performed without splenic vein reconstruction. We had to completely resect the right colic vein, accessary right colic vein, and middle colic vein due to tumor invasion. The pathological diagnosis was ypT3, ypN1a, ypM0, and ypStageIIB, and he was administered TS-1 as postoperative adjuvant chemotherapy. Seven months after therapeutic radical surgery, he presented with melena with progressive anemia. Computed tomography revealed transverse colonic varices. He was offered interventional radiology. Trans-splenic arterial splenic venography showed that transverse colonic varices had developed as collateral circulation of the splenic vein and inferior mesenteric vein system. An embolic substance was injected into the transverse colonic varices, which halted the progression of the anemia caused by melena. Fifteen months after therapeutic radical surgery, local recurrence of the tumor occurred; he died 28 months after the surgery.

Conclusions
When subtotal stomach-preserving pancreatoduodenectomy with portal vein resection is performed without splenic vein reconstruction, colonic varices may result from left-sided portal hypertension. Interventional radiology is an effective treatment for gastrointestinal bleeding due to colonic varices, but it is important to be observant for colonic necrosis and new varices.
Efficacy of nanosecond laser treatment in central serous chorioretinopathy with and without atrophy of retinal pigment epithelium
Authors: Kaymak Hakan , Funk Saskia , Fricke Andreas , Fulga Roxana , Klabe Karsten , Seitz Berthold , Langenbucher Achim , Schwahn Hartmut 
Published: June 2020

Abstract
Background
To evaluate the outcomes of subthreshold nanosecond laser treatment of chronic central serous chorioretinopathy (CSC) as a function of the severity of concomitant of retinal pigment epithelium (RPE) defects.

Methods
This retrospective study compares data from 23 CSC diagnosed eyes with only mild RPE defects (group 1), 16 CSC eyes with moderate RPE defects (group 2), and 17 CSC eyes having severe RPE defects (group 3). After subthreshold treatment with the standard Ellex 2RT™ nanosecond laser (Ellex Medical Lasers Ltd, Australia), changes in macular structure and levels of subretinal fluid (SRF) were assessed by OCT-SD, OCT-A, functional integrity of the retina was assessed by corrected distance visual acuity (CDVA) and microperimetry, each at baseline and 1, 3, 6, and 12 months after initial treatment; re-treatment took place in cases of persistent SRF pro re nata.

Results
During the 12 months observation period, group 1 and 2 mostly required on initial and one re-treatment (1.9 ± 1.0 treatments; 1.9 ± 1.3 treatments). In contrast, group 3 was subject to three to four treatments (3.7 ± 1.5 treatments). 6 to 12 months after treatment, subretinal fluid (SRF) disappeared in 100% of the eyes of group 1 and in 76.9%, and 42.9% of the eyes of group 2 and group 3, respectively. Retinal sensitivity and CDVA improved in group 1 and 2, but did not change significantly in group 3 during the 12 months period.

Conclusions
Subthreshold nanosecond laser treatment is an effective and safe method for the restoration of macular anatomy and sensitivity in acute and chronic CSC cases with only mild or moderate RPE defects. However, this laser treatment has very limited outcome in CSC eyes with more severe RPE defects.
Toxoplasmosis chorioretinitis mimicking acute retinal necrosis associated with local corticosteroid
Authors: Crosson Jason N. , Kuthyar Sanjana , Shantha Jessica G. , Debiec Matthew R. , Laird Philip W. , Hwang Cindy S. , Grossniklaus Hans E. , Yeh Steven 
Published: June 2020

Abstract
Background
The cases discussed highlight the atypical presentation and diagnostic dilemmas of toxoplasmosis with fulminant retinal necrosis and the potentially devastating visual outcomes of toxoplasma chorioretinitis following local corticosteroid exposure.

Case presentation
We report a series of three patients who presented with toxoplasmosis mimicking severe acute retinal necrosis. Patients were between 59 and 77 years old and had been exposed to local corticosteroids preceding our evaluation. All patients demonstrated diffuse retinal whitening with severe vision loss on presentation. Polymerase chain reaction testing (PCR) was diagnostic in two patients, and histopathologic examination of a vitrectomy specimen was diagnostic in one patient. All cases of retinitis resolved with anti-parasitic medication; however, visual acuity failed to improve in all patients due to disease severity and presentation.

Conclusions
Local corticosteroid injection may trigger or exacerbate toxoplasmosis chorioretinitis, leading to fulminant retinal necrosis and severe vision loss. Toxoplasma chorioretinitis should be considered in the differential diagnosis of patients presenting with clinical features of acute retinal necrosis, particularly following local corticosteroid injection regardless of their baseline systemic immune status. Diagnostic vitrectomy may be helpful in patients in whom PCR testing is negative and ocular toxoplasmosis is suspected.
Evaluating diurnal variations in retinal perfusion using optical coherence tomography angiography
Authors: Rommel Felix , Rothe Matthias , Kurz Maximilian , Prasuhn Michelle , Grisanti Salvatore , Ranjbar Mahdy 
Published: June 2020

Abstract
Background
Optical coherence tomography angiography (OCTA) is a non-invasive tool for imaging and quantifying the retinal and choroidal vasculature as well as perfusion state in healthy eyes. Choroidal perfusion is subject to diurnal variation, showing lowest perfusion in the morning and highest in the afternoon. In this index study, OCTA was used to investigate diurnal changes of the retinal perfusion in healthy adult eyes and to identify impacting factors since retinal perfusion is known to be mainly determined by autoregulatory mechanisms.

Methods
A prospective study was conducted on healthy volunteers, each of whom underwent repeated measurements of mean arterial pressure (MAP), intraocular pressure (IOP), macular volume (MV), subfoveal choroidal thickness (SFCT), foveal avascular zone (FAZ) and retinal perfusion of the superficial capillary plexus (SCP), deep capillary plexus (DCP) and full retina (FR) slab at 7 a.m. and 4 p.m. Possible influence of MAP or IOP on the retinal perfusion was evaluated.

Results
A total of 22 eyes of 22 participants (mean age 55.91 ± 14.84) were analysed. Significant diurnal changes from 7 a.m. to 4 p.m. were observed for MAP (p < 0.001) and SFCT (p = 0.017). The perfusion of SCP, DCP and FR as well as the size of the FAZ and the MV did not show significant fluctuation during the day. No significant correlation between MAP or IOP and retinal perfusion values were detectable.

Conclusion
OCTA-based analysis of the retina in healthy adults demonstrated a steady perfusion of both plexus during the day, independently of changes in MAP. These findings support the theory of autoregulatory mechanisms of the retinal blood flow.
Logistic regression has similar performance to optimised machine learning algorithms in a clinical setting: application to the discrimination between type 1 and type 2 diabetes in young adults
Authors: Lynam Anita L. , Dennis John M. , Owen Katharine R. , Oram Richard A. , Jones Angus G. , Shields Beverley M. , Ferrat Lauric A. 
Published: June 2020

AbstractBackgroundThere is much interest in the use of prognostic and diagnostic prediction models in all areas of clinical medicine. The use of machine learning to improve prognostic and diagnostic accuracy in this area has been increasing at the expense of classic statistical models. Previous studies have compared performance between these two approaches but their findings are inconsistent and many have limitations. We aimed to compare the discrimination and calibration of seven models built using logistic regression and optimised machine learning algorithms in a clinical setting, where the number of potential predictors is often limited, and externally validate the models.MethodsWe trained models using logistic regression and six commonly used machine learning algorithms to predict if a patient diagnosed with diabetes has type 1 diabetes (versus type 2 diabetes). We used seven predictor variables (age, BMI, GADA islet-autoantibodies, sex, total cholesterol, HDL cholesterol and triglyceride) using a UK cohort of adult participants (aged 18–50 years) with clinically diagnosed diabetes recruited from primary and secondary care (n= 960, 14% with type 1 diabetes). Discrimination performance (ROC AUC), calibration and decision curve analysis of each approach was compared in a separate external validation dataset (n= 504, 21% with type 1 diabetes).ResultsAverage performance obtained in internal validation was similar in all models (ROC AUC ≥ 0.94). In external validation, there were very modest reductions in discrimination with AUC ROC remaining ≥ 0.93 for all methods. Logistic regression had the numerically highest value in external validation (ROC AUC 0.95). Logistic regression had good performance in terms of calibration and decision curve analysis. Neural network and gradient boosting machine had the best calibration performance. Both logistic regression and support vector machine had good decision curve analysis for clinical useful threshold probabilities.ConclusionLogistic regression performed as well as optimised machine algorithms to classify patients with type 1 and type 2 diabetes. This study highlights the utility of comparing traditional regression modelling to machine learning, particularly when using a small number of well understood, strong predictor variables.