bluuebunny/crossref_metadata_2025_split huggingface dataset:
Brassicaceous roots as an unexpected diversity hot-spot of helotialean endophytes
Authors: Macia-Vicente Jose G , Piepenbring Meike , Koukol Ondřej 
Published: May 2020

Abstract
A high number of fungal strains were isolated from roots of Brassicaceae species collected across western and southern Europe, resulting in an unexpectedly rich collection of Cadophora species. These isolates enable us to present a new and comprehensive view of the ecological, morphological, and phylogenetic traits of root-inhabiting members of this helotialean genus. We provide phylogenetic placement of all of our isolates based on a four-gene dataset, analyze their phenotypic traits in relation to their phylogenetic relationships, and infer the potential distribution ranges of the species by sequence comparisons with available databases. We consider seven well supported phylogenetic lineages as species new to science. Six further lineages probably also represent new species but remain undescribed due to the lack of diagnostic morphological characters. Our results show that Cadophora , as currently circumscribed, is paraphyletic and encompasses a broad spectrum of morphologies and lifestyles. Among the new species, only two ( C. ferruginea and C. constrictospora ) form phialides and conidia typical of Cadophora , three species ( C. echinata , C. gamsii and C. variabilis ) produce chains of swollen hyphal segments that may function as holoblastic conidia, and one species ( C. fascicularis ) produces chains of holoblastic ramoconidia and conidia. Ancestral state reconstruction analysis suggests that phialidic conidiogenesis evolved several times in Cadophora sensu lato from a putatively holoblastic common ancestor. Most Cadophora lineages are rare as estimated from the availability of sequence data, in spite of having relatively wide distribution ranges, whereas five lineages may represent endemic relationships given their restricted distributions. Our dataset, probably the most comprehensive available for Cadophora , nevertheless shows knowledge gaps concerning the phylogenetic relationships within this genus and highlights a need for further investigation.
GhCIPK6 Increases Salt Tolerance in Transgenic Upland Cotton by Involving in ROS Scavenging and MAPK Signaling Pathways
Authors: Su Ying , Guo Anhui , Huang Yi , Wang Yumei , Hua Jinping 
Published: May 2020

Abstract
Background: Salt stress is one of the most damaging abiotic stresses in production of Upland cotton ( Gossypium hirsutum ). Upland cotton is defined as a medium salt-tolerant crop. Salinity hinders root development, shoots growth, and reduces the fiber quality. Results: Our previous study verified a GhCIPK6 gene response to salt stress in G. hirsutum . The homologs of GhCIPK6 were analyzed in A 2 ( G. arboreum ), D 5 ( G . raimondii ), and AD 1 ( G . hirsutum ) genomes. GhCIPK6 localized to the vacuole and cell membrane. The GhCBL1-GhCIPK6 and GhCBL8-GhCIPK6 complexes localized to the nucleus and cytomembrane. Overexpression of GhCIPK6 enhanced expression levels of co-expressed genes induced by salt stress, which scavenged ROS and involved in MAPK signaling pathways verified by RNA-seq analysis. Water absorption capacity and cell membrane stability of seeds from GhCIPK6 overexpressed lines was higher than that of wild-type seeds during imbibed germination stage. The seed germination rates and seedling field emergence percentages of GhCIPK6 overexpressed lines were higher than that of control line under salt stress. Moreover, overexpressing of GhCIPK6 in cotton increased lint percentage, and fiber length uniformity under salt stress. Conclusions: We verified the function of GhCIPK6 by transformation and RNA-seq analysis. GhCIPK6 overexpressed lines exhibited higher tolerance to abiotic stresses, which functioned by involving in ROS scavenging and MAPK pathways. Therefore, GhCIPK6 has the potential for cotton breeding to improve stress-tolerance.
The Molecular Pathogenesis of Trichilemmal Carcinoma
Authors: Ha Jeong Hyun , Lee Cheol , Lee Kyu Sang , Pak Chang-sik , Sun Choong-Hyun , Koh Youngil , Chang Hak 
Published: May 2020

Abstract
Background: Trichilemmal carcinoma (TC) is an extremely rare hair follicle tumor. We aimed to explore the genetic abnormalities involved in TC to gain insight into its molecular pathogenesis.Methods: Data from patients diagnosed with TC within a 12-year period were retrospectively reviewed. Genomic DNA isolated from a formalin-fixed paraffin-embedded (FFPE) tumor tissue block was sequenced and explored for a panel of cancer genes.Results: DNA was extracted from the FFPE tissue of four patients (50% female; mean age, 51.5 years) diagnosed with TC for analysis. The tumor was located in the head and neck of three patients and in the shoulder of one patient. TP53 mutations (p.Arg213*, p.Arg249Trp, and p.Arg248Gln) were found in three patients. Fusions previously identified in melanoma were detected in two patients (TACC3-FGFR3 and ROS1-GOPC fusions). Other mutations found included NF1-truncating mutation (Arg1362*), NRAS mutation (p.Gln61Lys), TOP1 amplification, and PTEN deletion. Overall, genetic changes found in TC resemble that of other skin cancers, suggesting similar pathogenesis. All patients with TP53 mutations had aggressive clinical course, two who died (OS 93 and 36 months), and one who experienced recurrent relapse.Conclusions: We reported the genomic variations found in TC, which may give insight into the molecular pathogenesis. Overall, genetic changes found in TC resembled that of other skin cancers, suggesting similar pathogenesis. TP53 mutations was were identified in patients who had an aggressive clinical course. Genetic alterations identified may further suggest the potential treatment options of TC.
Bioassay and molecular monitoring of insecticide resistance status in Aedes albopictus populations from Greece, to support evidence-based vector control
Authors: Balaska Sofia , Fotakis Emmanouil Alexandros , Kioulos Ilias , Grigoraki Linda , Mpellou Spyridoula , Chaskopoulou Alexandra , Vontas John 
Published: May 2020

Abstract
Background: Aedes albopictus has a well-established presence in southern European countries, associated with recent disease outbreaks (e.g. Chikungunya). Development of insecticide resistance in the vector is a major concern as its control mainly relies on the use of biocides. Data on the species’ resistance status is essential for efficient and sustainable control. To date the insecticide resistance status of Ae. albopictus populations from Greece against major insecticides used in vector control remains largely unknown. Methods: We investigated the insecticide resistance status of nineteen Ae. albopictus populations from 11 regions of Greece. Bioassays were performed against diflubenzuron (DFB), B. thuringiensis var. israelensis (Bti), deltamethrin and malathion. Known insecticide resistance loci were molecularly analysed, i.e. voltage-gated sodium channel (VGSC) mutations associated with pyrethroid resistance; presence and frequency of carboxylesterases 3 (CCEae3a) and 6 (CCEae6a) gene amplification associated with organophosphate (OP) resistance and; chitin synthase-1 (CHS-1) for the possible presence of DFB resistance mutations. Results: Bioassays showed full susceptibility to DFB, Bti and deltamethrin, but resistance against the OP malathion (range of mortality: 55.30-91.40%). VGSC analysis revealed a widespread distribution of mutations F1534C (in all populations, with allelic frequencies between 6.6% - 68.3%), and I1532T (in 6 populations; allelic frequencies below 22.70%), but absence of V1016G. CCE gene amplifications were recorded in 8 out of 11 populations (overall frequency: 33%). Co-presence of mutation F1534C and CCEae3a amplification was reported in 39 of the 156 samples commonly analysed. No mutations at the CHS-1 locus I1043 were detected. Conclusions: The results indicate: (i) the suitability of larvicides DFB and Bti for Ae. albopictus control in Greece, (ii) possible incipient pyrethroid resistance due to the presence of kdr mutations and (iii) possible reduced efficacy of OPs, in a scenario of re-introducing them for vector control. The study highlights the need for systematic resistance monitoring for developing and implementing appropriate evidence-based control programs.
Alteration of lung tissues proteins in birch pollen induced asthma mice before and after SCIT
Authors: Xie Zhijuan , Sun Haidan , Li Xiaogang , Sun Wei , Yin Jia 
Published: May 2020

Abstract
Subcutaneous immunotherapy (SCIT) is a classic form of allergen-specific immunotherapy that is used to treat birch pollen induced allergic asthma. To investigate the underlying molecular mechanisms of SCIT, we aimed to profile lung samples to explore changes in the differential proteome before and after SCIT in mice with allergic asthma. Fresh lungs were collected from three groups of mice: 1) control mice, 2) birch pollen-induced allergic mice and 3) birch pollen-induced allergic mice with SCIT. Tandem mass tag (TMT) labelling coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) was used to analyze the lung proteome in the mice. Ingenuity pathway analysis (IPA) and Gene Ontology (GO) classification analysis were applied to identify differentially expressed proteins (DEPs) and crucial pathways. The screened DEPs were validated by immunohistochemistry analysis. A total of 317 proteins were upregulated and 184 proteins were downregulated in the asthma group compared to those of the control group. In contrast, 639 DEPs (163 upregulated and 456 downregulated proteins) were identified after SCIT in comparison with those of the asthma group. Among the 639 DEPs, 277 proteins returned to similar levels as those of the relative non-asthma condition. Bioinformatic analysis revealed that the 277 proteins played a significant role in the leukocyte extravasation signaling pathway. Of note, this is the first report that Vav1 (proto-oncogene vav) may serve as a biomarker of birch pollen-specific SCIT in mice. The leukocyte extravasation signaling pathway and related DEPs were of crucial importance in birch pollen SCIT.
CT, US and MRI of Xanthine Urinary Stones: An In-Vitro Analysis
Authors: Shamir Stephanie , Peng Qi , Schoenfeld Alan , Drzewiecki Beth , Liszewski Mark 
Published: May 2020

Abstract
Background: Xanthine urinary stones are a rare entity that may occur in patients with Lesch-Nyhan Syndrome receiving allopurinol. There is little literature describing imaging characteristics of these stones, and the most appropriate approach to imaging these stones is therefore unclear. We performed an in-vitro analysis of xanthine stones using computed tomography (CT) at different energy levels, ultrasound (US), and magnetic resonance imaging (MRI). Methods: Five pure xanthine stones from a boy with Lesch-Nyhan were imaged. CT of the stones was performed at 80kVp, 100kVp, 120kVp and 140kVp and CT numbers of the stones were recorded in Hounsfield units (HU). US of the stones was performed and echogenicity, acoustic shadowing and twinkle artifact were assessed. MRI of the stones was performed and included T2-weighted, ultrashort echo-time (UTE)-weighted and T2/T1-weighted 3D bFFE sequences and signal was assessed.Results: On CT, xanthine stones were radiodense and the average attenuation coefficient did not differ with varying kVp, measuring 331.0+/-51.7HU at 80kVp, 321.4+/-63.4HU at 100kVp, 329.7+/-54.2HU at 120kVp and 328.4+/-61.1HU at 140kVp. On US, xanthine stones where echogenic with acoustic shadowing and twinkle artifact. On MRI, stones lacked signal on all tested sequences.Conclusion: Xanthine stones demonstrate imaging characteristics typical of most urinary stones: dense on CT, echogenic on US, and lack signal on MRI. Therefore, the approach to imaging xanthine urinary stones should identical to the approach with other urinary stones.
High Mortality Rate of Obstetric Critically ILL Patients in Rwanda and Its Predictability
Authors: RUDAKEMWA Alcade , Cassidy Amy Lucille , Twagirumugabe Theogene 
Published: May 2020

Abstract
BackgroundReasons for obstetric admission in intensive care unit (ICU) vary from a setting to another. Outcomes from ICU and its prediction models are not well explored in Rwanda because of lack of appropriate scores. This study intended to assess profile and accuracy of predictive models for obstetric patients admitted in ICU in the two public tertiary hospitals in Rwanda.MethodsWe prospectively collected data from all obstetric patients admitted in the ICU of public referral hospitals in Rwanda from March 2017 to February 2018 to identify reasons for admissions and factors for prognosis. We analysed the accuracy of mortality prediction by the quick Sequential Organ Failure Assessment (qSOFA) and Modified Early Obstetric Warning Score (MEOWS). ResultsObstetric patients represented 12.8% of all ICU admissions and 1.8% of all deliveries. Sepsis (31.9%) and haemorrhage (25.5%) were the two commonest reasons of admission. Mortality was 54.3% while the average length of stay was 6.6 days. MEOWS was an independent predictor to mortality (adjusted OR=1.25[1.07-1.46]; p=0.005). Similarly, one point of increase of the qSOFA increased odds of ICU mortality by 181% (adjusted OR=2.81[1.25-6.30]; p=0.012). The Area Under the Receiver Operating Characteristic Curve (AUROC) for MEOWS was 0.773[0.666-0.880], p=0.0001 and that of the qSOFA was 0.764[0.654-0.873]; p=0.0001.ConclusionSepsis is the most common reason for obstetric admissions to ICU in Rwanda. MEOWS and qSOFA could accurately predict the mortality for those patients but further explorations on a larger sample size are guaranteed.
Prevalence and predictors of HIV-associated Neurocognitive Disorder in Ethiopians
Authors: Salahuddin Mohammed , Manzar Md Dilshad , Hassen Hamid Yimam , Ashuro Mihretu , Unissa Aleem , Mohammed Mohammed Aziz , Hameed Unaise Abdul , Spence David Warren , Pandi-Perumal Seithikurippu R. 
Published: May 2020

Abstract
Background

Modern antiretroviral therapy has extended the life expectancies of people living with HIV; the prevention and treatment of their associated neurocognitive decline has remained a challenge. Consequently, it is desirable to investigate the prevalence and predictors of HIV-associated Neurocognitive Disorder (HAND) to help in targeted screening and disease prevention.
Methods:

Two hundred and forty-four people living with HIV were interviewed in a study using a cross-sectional design and International HIV Dementia scale (IHDS). Additionally, the sociodemographic, clinical and psychosocial characteristics of the patients were recorded. Chi-square and binary logistic regression analysis were used to determine the level of significance among the independent risk factors and probable HAND.
Results

The point prevalence of HAND was found to be 39.3%. Participants’ characteristics of being older than 40 years (AOR = 2.81 (95% CI; 1.11–7.15)), having a history of recreational drug use (AOR = 13.67 (95% CI; 6.42–29.13)), and being non-compliant with prescribed medications (AOR = 2.99 (95% CI; 1.01–8.87)) were independent risk factors for HAND.
Conclusion

The identification of predictors, some of which may be more closely related to the Ethiopian people living with HIV, may help in targeted screening of vulnerable groups during cART follow-up visits. This may greatly help in strategizing and implementation of the prevention program, more so, because: (i) HAND is an asymptomatic condition for considerable durations, and (ii) clinical trials of HAND therapies have been unsuccessful.
Relationship between ACL reconstruction and meniscal repair. Quality of life, sports return and meniscal failure rate. 2 to 12 years follow-up
Authors: Rodriguez-Roiz Juan Miguel , Sastre-Solsona Sergi , Popescu Dragos , Montañana-Burillo Jordi , Combalia-Aleu Andres 
Published: May 2020

Abstract
Background few studies approach with long follow up, meniscal repair at amateur level, specially studying variables as quality of life and failure rate. The purpose of this review is study medium to long-term clinical results in patients at amateur spors level, that have required meniscal sutures at our centre, with or without ACL reconstruction. We evaluate the objective function of the knee, as well as the patients’ return to sports activities, quality of life and the rate of failed repair and study the possible reasons.Methods We retrospectively assessed 92 patients who regularly perform amateur sports activities (Tegner 4 to 7), minimum follow-up period of 2 years, divided into 2 groups: group 1 isolated meniscal suture (43 cases), group 2 associated to ACL reconstruction (49 cases).Results high return to amateur sports rate (92%), which was even higher in the isolated reconstruction group in comparison to the group with associated ACL. We have not found statistically significant differences between sports return and: age, gender, injured meniscus, chondral injuries, preoperative Tegner score, or motivation. No significant differences in physical or mental health fields between both groups. Meniscal repair failed in 12 patients (13%). Higher rate of failure in isolated bucket-handle tear injuries (p < 0.0062). We have not found a statistically significant association between the other variables studied.Conclusions good results with 92% of sports return, low rate of complications, and low retear rate, even lower when is associated to ACL reconstruction and in external meniscus repair. High values at SF-12 between 2 groups.
Characteristics and predictors of muscle strength deficit in mechanical ankle instability
Authors: Hou Zong-chen , Miao Xin , Ao Ying-fang , Hu Yue-lin , Jiao Chen , Guo Qin-wei , Xie Xing , Zhao Feng , Pi Yan-bin , Li Nan , Zhang Zhi-yu , Jiang Dong 
Published: May 2020

Abstract
Purpose

Muscle strength training is a common strategy for treating chronic ankle instability (CAI), but the effectiveness decreases for mechanical ankle instability (MAI) patients with initial severe ligament injuries. The purpose of this study was to investigate the characteristics and the potential predictors of muscle strength deficit in MAI patients, with a view to proposing a more targeted muscle strength training strategy.

Methods

A total of 220 MAI patients with confirmed initial lateral ankle ligament rupture and a postinjury duration of more than 6 months were included. All patients underwent a Biodex isokinetic examination of the ankle joints of both the affected and unaffected sides. Then, the associations between the limb symmetry index (LSI) (mean peak torque of the injury side divided by that of the healthy side) and the patients’ sex, body mass index, postinjury duration, presence of intra-articular osteochondral lesions, presence of osteophytes and ligament injury pattern (i.e., isolated anterior talofibular ligament (ATFL) injury or combined with calcaneofibular ligament injury) were analysed.

Results

There was significantly weaker muscle strength on the affected side than on the unaffected side in all directions ( p <0.05). The LSI in plantar flexion was significantly lower than that in dorsiflexion at 60°/s (0.87 vs 0.98, p <0.001). A lower LSI in eversion was significantly correlated with female sex (0.82 vs 0.94, p =0.016) and isolated ATFL injury (0.86 vs 0.95, p =0.012). No other factors were found to be associated with muscle strength deficits.

Conclusion

MAI patients showed significant muscle strength deficits on the affected side, especially in plantar flexion. There were greater strength deficits in eversion in females and individuals with an isolated ATFL injury. Thus, a muscle strength training programme for MAI patients was proposed that focused more on plantar flexion training and eversion training for females and those with an isolated ATFL injury.
Maternal High Fat Diet and Diabetes Disrupts Transcriptomic Pathways that Regulate Cardiac Metabolism and Cell Fate in Newborn Rat Hearts
Authors: Preston Claudia C. , Larsen Tricia D. , Eclov Julie A. , Louwagie Eli J. , Gandy Tyler C. T. , Faustino Randolph S. , Baack Michelle L. 
Published: May 2020

Abstract
Background

Children born to diabetic or obese mothers have a higher risk of heart disease at birth and later in life. Our previous work using chromatin immunoprecipitation sequencing revealed that late-gestation diabetes in combination with maternal high fat (HF) diet cause a distinct fuel-mediated epigenetic reprogramming of rat cardiac tissue during fetal cardiogenesis. The objective of the present study was to investigate the overall transcriptional signature of newborn offspring exposed to the combination of maternal diabetes and maternal HF diet.
Methods

Gene expression profiling from hearts of diabetes exposed, HF diet exposed, combination exposed and control newborn rats was compared for differential transcriptome expression. Functional annotation, pathway and network analysis was performed on statistically significant differentially expressed genes from the combination exposed group compared with controls. Downstream metabolic assessments included measurement of total and phosphorylated AKT2 and GSK3β assays, as well as quantification of glycolytic capacity by extracellular flux analysis and glycogen staining.
Results

Transcriptome analysis of newborn rat hearts showed significant changes in cardiac gene expression following exposure to maternal diabetes or HF diet individually, as well as the combination of diabetes + HF compared with controls. Reactome analyses identified expression changes in two key signaling cascades functionally prioritized in male control and combination exposed offspring hearts. These pathways included downregulation of the fibroblast growth factor (FGF) pathway and concomitant downstream PI3K/AKT activation canonically recognized as a regulator of cell metabolism, growth, and development. In contrast, the second pathway exhibited significant upregulation of mitoribosomal signaling that regulates mitochondrial biogenesis, mitophagy and cell fate. Focused bioinformatic analysis on mitochondrial genes enriched in the combination exposed dataset revealed genes associated with diverse aspects of mitochondrial structure, function, and dynamism. Functional biochemical, metabolic, and histochemical assays supported these transcriptome changes, confirming the essential role of mitochondrial energetics in facilitating diabetes- and diet-induced cardiac transcriptome remodeling and phenotype in offspring.
Conclusions

This study provides the first data accounting for the compounding effects of maternal hyperglycemia and hyperlipidemia on the developmental cardiac transcriptome, and elucidates nuanced and novel features of maternal diabetes and diet on intergenerational regulation of heart health.