bluuebunny/crossref_metadata_2025_split huggingface dataset:
Study on the community structure and function of symbiotic bacteria from different growth and developmental stages of Hypsizygus marmoreus
Authors: Sun Shujing , Li Fan , Xu Xin , Liu Yunchao , Kong Xuqiang , Chen Jianqiu , Liu Ting , Chen Liding 
Published: October 2020

Abstract
Background
The symbiotic bacteria associated with edible fungi are valuable microbial resources worthy of in-depth exploration. It is important to analyze the community structure and succession of symbiotic bacteria in mushrooms. This can assist in the isolation of growth-promoting strains that have an essential relationship with the cultivation cycle as well as the agronomic traits and yields of fruiting bodies.

Results
In all of the samples from cultivation bags of Hypsizygus marmoreus, 34 bacterial phyla were detected. Firmicutes was the most abundant bacterial phylum (78.85%). The genus Serratia showed an exponential increase in abundance in samples collected from the cultivation bags in the mature period, reaching a peak abundance of 55.74% and the dominant symbiotic flora. The most predominant strain was Serratia odorifera HZSO-1, and its abundance increased with the amount of hyphae of H. marmoreus. Serratia odorifera HZSO-1 could reside in the hyphae of H. marmoreus, promote growth and development, shorten the fruiting cycle by 3–4 days, and further increase the fruiting body yield by 12%.

Conclusions
This study is a pioneering demonstration of the community structure of the symbiotic microbiota and bacteria-mushroom interaction in the growth and development of edible fungi. This work lays a theoretical foundation to improve the industrial production of mushrooms with symbiotic bacteria as assisting agents.
Identification, gene expression and genetic polymorphism of zinc finger A20/AN1 stress-associated genes, HvSAP, in salt stressed barley from Kazakhstan
Authors: Baidyussen Akmaral , Aldammas Maryam , Kurishbayev Akhylbek , Myrzabaeva Malika , Zhubatkanov Askar , Sereda Grigory , Porkhun Raisa , Sereda Sergey , Jatayev Satyvaldy , Langridge Peter , Schramm Carly , Jenkins Colin L. D. , Soole Kathleen L. , Shavrukov Yuri 
Published: October 2020

Abstract
Background
A family of genes designated as the Zinc finger A20/AN1 Transcription factors encoding stress-associated proteins (SAP) are well described in Arabidopsis and rice, and include 14 AtSAP and 18 OsSAP genes that are associated with variable tolerances to multiple abiotic stresses. The SAP gene family displays a great diversity in its structure and across different plant species. The aim of this study was to identify all HvSAP genes in barley (Hordeum vulgare L.), to analyse the expression of selected genes in response to salinity in barley leaves and develop SNP marker for HvSAP12 to evaluate the association between genotypes of barley plants and their grain yield in field trials.

Results
In our study, 17 HvSAP genes were identified in barley, which were strongly homologous to rice genes. Five genes, HvSAP5, HvSAP6, HvSAP11, HvSAP12 and HvSAP15, were found to be highly expressed in leaves of barley plants in response to salt stress in hydroponics compared to controls, using both semi-quantitative RT-PCR and qPCR analyses. The Amplifluor-like SNP marker KATU-B30 was developed and used for HvSAP12 genotyping. A strong association (R2 = 0.85) was found between KATU-B30 and grain yield production per plant of 50 F3 breeding lines originating from the cross Granal × Baisheshek in field trials with drought and low to moderate salinity in Northern and Central Kazakhstan.

Conclusions
A group of HvSAP genes, and HvSAP12 in particular, play an important role in the tolerance of barley plants to salinity and drought, and is associated with higher grain yield in field trials. Marker-assisted selection with SNP marker KATU-B30 can be applied in barley breeding to improve grain yield production under conditions of abiotic stress.
Identification of polycomb repressive complex 1 and 2 core components in hexaploid bread wheat
Authors: Strejčková Beáta , Čegan Radim , Pecinka Ales , Milec Zbyněk , Šafář Jan 
Published: October 2020

Abstract
Background
Polycomb repressive complexes 1 and 2 play important roles in epigenetic gene regulation by posttranslationally modifying specific histone residues. Polycomb repressive complex 2 is responsible for the trimethylation of lysine 27 on histone H3; Polycomb repressive complex 1 catalyzes the monoubiquitination of histone H2A at lysine 119. Both complexes have been thoroughly studied in Arabidopsis, but the evolution of polycomb group gene families in monocots, particularly those with complex allopolyploid origins, is unknown.

Results
Here, we present the in silico identification of the Polycomb repressive complex 1 and 2 (PRC2, PRC1) subunits in allohexaploid bread wheat, the reconstruction of their evolutionary history and a transcriptional analysis over a series of 33 developmental stages. We identified four main subunits of PRC2 [E(z), Su(z), FIE and MSI] and three main subunits of PRC1 (Pc, Psc and Sce) and determined their chromosomal locations. We found that most of the genes coding for subunit proteins are present as paralogs in bread wheat. Using bread wheat RNA-seq data from different tissues and developmental stages throughout plant ontogenesis revealed variable transcriptional activity for individual paralogs. Phylogenetic analysis showed a high level of protein conservation among temperate cereals.

Conclusions
The identification and chromosomal location of the Polycomb repressive complex 1 and 2 core components in bread wheat may enable a deeper understanding of developmental processes, including vernalization, in commonly grown winter wheat.
Key metabolites associated with the onset of flowering of guar genotypes (Cyamopsis tetragonoloba (L.) Taub)
Authors: Arkhimandritova Serafima , Shavarda Alexey , Potokina Elena 
Published: October 2020

Abstract
Background
Guar (Cyamopsis tetragonoloba (L.) Taub.), a short-day plant, is an economically valuable legume crop. Seeds of guar serve as a source of galactomannan polysaccharide, known as guar gum, which is in demand in the gas and oil industries. The rapid and complete maturation of guar seeds depends on the flowering time of a particular genotype. It is known that flowering in guar is controlled by several gene systems. However, no information about the process and mechanisms that trigger flowering in guar on the molecular and biochemical levels was previously reported. The aim of the study was to investigate the metabolic landscape underlying transition to the flowering in guar using GC-MS-metabolomic analysis.

Results
82 diverse guar genotypes (each in 8 replicates) from the VIR collection were grown under experimental conditions of high humidity and long photoperiod. In the stress environment some guar genotypes turned to flowering early (41 ± 1,8 days from the first true leaf appearance) while for others the serious delay of flowering (up to 95 ± 1,7 days) was observed. A total of 244 metabolites were detected by GC-MS analysis on the third true leaves stage of 82 guar genotypes. Among them some molecules were associated with the transition of the guar plants to flowering. Clear discrimination was observed in metabolomic profiles of two groups of «early flowering» and «delayed flowering» plants, with 65 metabolites having a significantly higher abundance in early flowering genotypes. Among them 7 key molecules were identified by S-plot, as potential biomarkers discriminating of «early flowering» and «delayed flowering» guar genotypes.

Conclusions
The metabolomic landscape accompanying transition to flowering in guar was firstly described. The results obtained can be used in subsequent genomic research for identifying metabolite-gene associations and revealing genes responsible for the onset of flowering and photoperiod sensitivity of guar. In addition, the detected key metabolites associated with flowering of guar can be employed as biomarkers allowing rapid screening of breeding material for the potentially early flowering genotypes.
A competence of embryo-derived tissues of tetraploid cultivated wheat species Triticum dicoccum and Triticum timopheevii for efficient and stable transgenesis mediated by particle inflow gun
Authors: Miroshnichenko Dmitry , Klementyeva Anna , Pushin Alexander , Dolgov Sergey 
Published: October 2020

Abstract
Background
The ability to engineer cereal crops by gene transfer technology is a powerful and informative tool for discovering and studying functions of genes controlling environmental adaptability and nutritional value. Tetraploid wheat species such as emmer wheat and Timopheevi wheat are the oldest cereal crops cultivated in various world areas long before the Christian era. Nowadays, these hulled wheat species are gaining new interest as donors for gene pools responsible for the improved grain yield and quality, tolerance for abiotic and biotic stress, resistance to pests and disease. The establishing of efficient gene transfer techniques for emmer and Timopheevi wheat may help in creation of modern polyploid wheat varieties.

Results
In the present study, we describe a robust protocol for the production of fertile transgenic plants of cultivated emmer wheat (Russian cv. ‘Runo’) using a biolistic delivery of a plasmid encoding the gene of green fluorescent protein (GFP) and an herbicide resistance gene (BAR). Both the origin of target tissues (mature or immature embryos) and the type of morphogenic calli (white or translucent) influenced the efficiency of stable transgenic plant production in emmer wheat. The bombardment of nodular white compact calluses is a major factor allowed to achieve the highest transformation efficiency of emmer wheat (on average, 12.9%) confirmed by fluorescence, PCR, and Southern blot. In the absence of donor plants for isolation of immature embryos, mature embryo-derived calluses could be used as alternative tissues for recovering transgenic emmer plants with a frequency of 2.1%. The biolistic procedure based on the bombardment of immature embryo-derived calluses was also successful for the generation of transgenic Triticum timopheevii wheat plants (transformation efficiency of 0.5%). Most of the primary events transmitted the transgene expression to the sexual progeny.

Conclusion
The procedures described here can be further used to study the functional biology and contribute to the agronomic improvement of wheat. We also recommend involving in such research the Russian emmer wheat cv. ‘Runo’, which demonstrates a high capacity for biolistic-mediated transformation, exceeding the previously reported values for different genotypes of polyploid wheat.
Does sequential balloon expulsion test improve the screening of defecation disorders?
Authors: Caetano A. C. , Costa D. , Gonçalves R. , Correia-Pinto J. , Rolanda C. 
Published: October 2020

AbstractBackgroundA defecation disorder (DD) is a difficulty in evacuation documented by physiological exams. However, this physiological evaluation can be cumbersome, inaccessible and costly. Three “low-cost” tools to evaluate DD—a clinical DD score, the balloon expulsion test (BET) and a digital rectal examination (DRE) score were evaluated as separate or combined tests for DD screening.MethodsThis prospective study occurred between January 2015 and March 2019 in the Gastroenterology Department of a tertiary hospital. Besides the gold standard physiological tests, constipated patients answered the clinical DD score and were evaluated by DRE and BET [standard and variable volume (VV)].ResultsFrom 98 constipated patients, 35 (38.9%) were diagnosed with DD according to Rome IV criteria, mainly female (n = 30, 86%) with a median age of 60 years old. The clinical DD score revealed an AUC of 0.417 (SE = 0.07,p = 0.191). The DRE score displayed an AUC of 0.56 (SE = 0.063,p = 0.301). The standard BET displayed a sensitivity of 86%, specificity of 58%, positive predictive value (PPV) of 57% and negative predictive value (NPV) of 86%. The sequential VVBET followed by standard BET improved the BET performance regarding the evaluation of DD, with a sensitivity of 86%, specificity of 67%, PPV of 63% and NPV of 87%. The sequential BET had an OR 8.942,p > 0.001, CI 3.18–25.14, revealing to be the most significant predictor for DD screening.ConclusionThe sequential BET is a low cost, well-performing DD screening tool, appropriate to the Primary Care Setting.
Guillain-Barre syndrome: a typical paraneoplastic syndrome in a kidney transplant recipient with allograft renal cell carcinoma: a case report and review of the literature
Authors: Zakrocka Izabela , Baranowicz-Gąszczyk Iwona , Korolczuk Agnieszka , Załuska Wojciech 
Published: October 2020

Abstract
Background
Guillain-Barré syndrome (GBS) is an autoimmune polyneuropathy affecting the peripheral nervous system. This neurological disorder has been previously reported in bone marrow transplant recipients but is uncommon after kidney transplantation. Viral infections and calcineurin inhibitors are the main triggers of GBS in renal transplant recipients.

Case presentation
In this report, we present a case of a 47-year-old male patient 12 years after his second kidney transplantation who developed GBS due to papillary renal cell carcinoma. Infectious and drug-related origins of GBS were excluded. Despite intensive treatment, graftectomy was performed, after which neurological symptoms resolved.

Conclusions
In kidney transplant recipients, paraneoplastic aetiology should be considered in the differential diagnosis of GBS.
The relationship between consciousness and the ascending reticular activating system in patients with traumatic brain injury
Authors: Jang Sung Ho , Kwon Young Hyeon 
Published: October 2020

Abstract
Background
We investigated the relationship between consciousness and the ascending reticular activating system (ARAS) by using diffusion tensor tractography (DTT) in patients with traumatic brain injury (TBI).

Methods
Twenty-six patients with TBI and 13 healthy control subjects were recruited for this study. Glasgow Coma Scale (GCS) scores were used for evaluation of subject consciousness state at the chronic stage of TBI (at DTT scanning), According to the GCS score, the patient group was divided into two subgroups: A (14 patients;impaired consciousness: GCS score < 15, and B (12 patients;intact consciousness;GCS score = 15). Fractional anisotropy (FA) and tract volume (TV) values were assessed in the lower dorsal and upper ARAS.

Results
The FA values of the lower dorsal ARAS and the upper ARAS in patient subgroup A were significantly lower than those in patient subgroup B and the control group(p <  0.05). However, the FA and TV values for the lower dorsal ARAS and the upper ARAS were not significantly different between patient subgroup B and the control group(p > 0.05). The FA value of the lower dorsal ARAS(r = 0.473,p <  0.05) and the TV of upper ARAS(r = 0.484,p <  0.05) had moderate positive correlations with the GCS score. The FA value of the upper ARAS had a strong positive correlation with the GCS score of the patient group(r = 0.780,p <  0.05).

Conclusions
We detected a close relationship between consciousness at the chronic stage of TBI and injuries of the lower dorsal and upper ARAS (especially, the upper ARAS) in patients who showed impaired consciousness at the onset of TBI. We believe that our results can be useful during the development of therapeutic strategies for patients with impaired consciousness following TBI.

Trial registration
YUMC 2019–06–032-003. Retrospectively registered 06 Jun 2020.
USP6NL mediated by LINC00689/miR-142-3p promotes the development of triple-negative breast cancer
Authors: Ma Teng , Liu Huaidong , Liu Yan , Liu Tingting , Wang Hui , Qiao Fulu , Song Lu , Zhang Lin 
Published: October 2020

AbstractBackgroundTriple-negative breast cancer (TNBC), in part because of the high metastasis rate, is one of the most prevalent causes of malignancy-related mortality globally. Ubiquitin specific peptidase 6 N-terminal like (USP6NL) has been unmasked to be implicated in some human cancers. However, the precise biological function of USP6NL in TNBC has not been defined.MethodsRNA expression was examined by real-time quantitative PCR (RT-qPCR), while USP6NL protein level was tested through western blot. Besides, cell proliferation was assessed by using colony formation assay, whereas cell apoptosis estimated by flow cytometry analysis, JC-1 assay and TUNEL assay. Transwell assays were adopted to detect the migration and invasion of indicated TNBC cells. Immunofluorescence (IF) assay evaluated epithelial-mesenchymal transitions (EMT) progress in TNBC. Further, RNA immunoprecipitation (RIP), RNA pull down and luciferase reporter assays were implemented for measuring the mutual interplay among USP6NL, miR-142-3p and long intergenic non-protein coding RNA 689 (LINC00689).ResultsElevated USP6NL level was uncovered in TNBC cells. RNA interference-mediated knockdown of USP6NL inhibited TNBC cell growth, motility and EMT. Further, USP6NL was proved as the target of a tumor-inhibitor miR-142-3p, and LINC00689 augmented USP6NL expression by absorbing miR-142-3p. Importantly, miR-142-3p deficiency or USP6NL overexpression fully abolished the inhibitory effect of LINC00689 silence on TNBC cellular behaviors.ConclusionAll data revealed the important role of USP6NL/LINC00689/miR-142-3p signaling in TNBC. The findings might provide a new and promising therapeutic biomarker for treating patients with TNBC.
Limb salvage versus amputation in patients with osteosarcoma of the extremities: an update in the modern era using the National Cancer Database
Authors: Evans Daniel R. , Lazarides Alexander L. , Visgauss Julia D. , Somarelli Jason A. , Blazer Dan G. , Brigman Brian E. , Eward William C. 
Published: October 2020

Abstract
Background
Historically, amputation was the primary surgical treatment for osteosarcoma of the extremities; however, with advancements in surgical techniques and chemotherapies limb salvage has replaced amputation as the dominant treatment paradigm. This study assessed the type of surgical resection chosen for osteosarcoma patients in the twenty-first century.

Methods
Utilizing the largest registry of primary osteosarcoma, the National Cancer Database (NCDB), we retrospectively analyzed patients with high grade osteosarcoma of the extremities from 2004 through 2015. Differences between patients undergoing amputation and patients undergoing limb salvage are described. Unadjusted five-year overall survival between patients who received limb salvage and amputation was assessed utilizing Kaplan Meier curves. A multivariate Cox proportional hazard model and propensity matched analysis was used to determine the variables independently correlated with survival.

Results
From a total of 2442 patients, 1855 underwent limb salvage and 587 underwent amputation. Patients undergoing amputation were more likely to be older, male, uninsured, and live in zip codes associated with lower income. Patients undergoing amputation were also more likely to have larger tumors, more comorbid conditions, and metastatic disease at presentation. After controlling for confounders, limb salvage was associated with a significant survival benefit over amputation (HR: 0.70; p < 0.001). Although this may well reflect underlying biases impacting choice of treatment, this survival benefit remained significant after propensity matched analysis of all significantly different independent variables (HR: 0.71; p < 0.01).

Conclusion
Among patients in the NCDB, amputation for osteosarcoma is associated with advanced age, advanced stage, larger tumors, greater comorbidities, and lower income. Limb salvage is associated with a significant survival benefit, even when controlling for significant confounding variables and differences between cohorts.
YB-1 transferred by gastric cancer exosomes promotes angiogenesis via enhancing the expression of angiogenic factors in vascular endothelial cells
Authors: Xue Xiaoxia , Huang Jin , Yu Kai , Chen Xinyue , He Yini , Qi Dianjun , Wu Ying 
Published: October 2020

Abstract
Background
Angiogenesis is important for the progression of gastric cancer (GC). Y-box binding protein 1 (YB-1) predicts advanced disease and indicates neovasculature formation in GC tissues, while the related mechanisms remain elusive. Exosomes mediate intercellular communications via transferring various molecules including proteins, lipids, mRNAs, and microRNAs, while the cargos of GC exosomes and the related mechanisms in GC angiogenesis were rarely reported except for several microRNAs.

Methods
In this study, human umbilical vein endothelial cells (HUVECs) were, respectively, treated by the exosomes isolated from the YB-1 transfected and the control SGC-7901 cells (SGC-7901-OE-Exo and SGC-7901-NC-Exo), and their apoptosis, proliferation, migration, invasion, and angiogenesis were, sequentially, compared. The levels of angiogenic factors including VEGF, Ang-1, MMP-9 and IL-8 in the exosome-treated HUVECs and the GC-derived exosomes were, separately, detected using PCR and Western blotting as well as RNA sequencing assays.

Results
We observed the consistent level of YB-1 in the exosomes and their originated GC cells, and the internalization of exosomes into HUVECs. Comparing with SGC-7901-NC-Exo, SGC-7901-OE-Exo significantly inhibited the apoptosis but promoted the proliferation, migration, invasion, and angiogenesis of HUVECs, within which the increased mRNA and protein levels of VEGF, Ang-1, MMP-9 and IL-8 were demonstrated. Meanwhile, mRNA levels of VEGF, Ang-1, MMP-9 and IL-8 showed no significant difference between SGC-7901-NC-Exo and SGC-7901-OE-Exo, although statistically higher mRNA of YB-1 was detected in the SGC-7901-OE-Exo.

Conclusions
Our findings illustrate YB-1 as the key component of exosome to promote GC angiogenesis by upregulating specific angiogenic factors in the exosome-treated endothelial cells but not in the exosomes themselves.
Case report – Acute Corneal Subepithelial Hydrops (ACSH) during Micropulse Transscleral Cyclophotocoagulation (MPTSC)
Authors: Chan Poemen P. , Lam Matthew C.W. , Baig Nafees 
Published: October 2020

Abstract
Background
To present an unusual intra-operative complication of micropulse transscleral cyclophotocoagulation (MPTSC).

Case presentation
A 72-year old Chinese gentleman, who had primary angle closure glaucoma and had received bilateral laser iridotomy, presented with progressive left eye blurred vision (visual acuity of 20/40 OD and 20/200 OS). Examination reviewed left eye central retinal venous occlusion. The intraocular pressure (IOP) was 19 mmHg OS and was on maximally tolerated topical medications. Four weeks later, the left eye was complication by neovascular glaucoma; the IOP was raised to 26 mmHg despite additional oral acetazolamide and remained elevated after pan-retinal photocoagulation as well as cataract extraction by phacoemulsification. MPTSC was performed 8 days after the phacoemulsification. During the procedure, a sudden protrusion was formed on the corneal surface. On-table examination with operating microscope and portable slit-lamp reviewed an intact corneal epithelium with a globular-shaped collection of fluid at the subepithelial layer – acute corneal subepithelial hydrops (ACSH). The anterior chamber was formed and the globe was intact. After approximately 10–15 minutes, the swelling spontaneously ruptured and became a corneal epithelial defect. The defect healed on the tenth day after the event with conservative management. There was no irreversible corneal damage and the patient subsequently underwent a successful second MPTSC of the left eye because of poorly controlled IOP.

Conclusion
ACSH is a possible intra-operative complication of MPTSC. We have proposed the possible mechanisms of ACSH. It is best to exercise caution when using MPTSC shortly after any incisional intraocular surgery.