bluuebunny/crossref_metadata_2025 huggingface dataset:
When CKD-MBD is not just CKD-MBD, a case of humoral hypercalcemia of malignancy in a dialysis patient
Authors: Gandhi Pulkit , Gandhi Roopali Goyal , Shah Ankur D
Published: September 2020

Patients on maintenance hemodialysis have dysregulations of calcium and phosphorus homeostasis which results in a plethora of mineral and bone pathologies. Management is typically focused on maintenance eucalcemia and limiting hyperphosphatemia while avoiding extremes of intact parathyroid hormone. Hypercalcemia in this setting is often iatrogenic. We present a case of humoral hypercalcemia of malignancy initially thought to be iatrogenic due to mineral bone management and discuss the overlap of management of hypercalcemia and management of mineral bone disease in end stage kidney disease. We highlight the relationship between malignancy and end stage kidney disease and the increased risk of hypercalcemia associated with malignancy.
Treatment Patterns and Outcomes in Bleb-Related Endophthalmitis: A 9-Year Analysis at a Tertiary Eye Center
Authors: Robbins Cason B. , Feng Henry L. , Gupta Divakar , Fekrat Sharon
Published: September 2020

Purpose:

Clinical presentation, treatment choices, and outcomes in cases of bleb-related endophthalmitis (BRE) at a tertiary care center over a 9-year period are described.

Methods:

A retrospective review was conducted of patients diagnosed with BRE at Duke Eye Center (Durham, North Carolina) from January 1, 2009 to January 1, 2018, with at least 6 months of follow-up, assessing demographic data, initial management, and visual acuity (VA).

Results:

Twenty eyes of 20 patients with BRE were identified. Median time from surgery to presentation was 6.53 years. Presenting VA of light perception only was significantly associated with the decision to pursue pars plana vitrectomy (PPV) as initial treatment (odds ratio 59.4, 95% CI, 2.1-1670.8, P = .016). Twelve eyes (60%) had culture-proven infectious endophthalmitis. Eleven eyes (55%) underwent PPV during treatment; 5 eyes underwent PPV on presentation, and 6 eyes underwent PPV after initial presentation. Compared with pre-endophthalmitis VA, 6 eyes that underwent subsequent PPV had greater VA loss at 6 months than cases not undergoing subsequent PPV (Early Treatment Diabetic Retinopathy Study line loss of 14 vs 4 lines, respectively; P = .044).

Conclusions:

BRE eyes presenting with light-perception VA were more likely to undergo initial PPV; yet many eyes in this study required PPV during treatment. Visual outcomes are often poor in BRE despite intensive management. There was greater VA loss from pre-endophthalmitis VA levels at 6 months in eyes undergoing PPV after initial treatment. Prospective studies are needed to assess the optimal role of PPV in patients with BRE.
Implementing horizontal-to-vertical Fourier spectral ratios and spatial correlation in a ground-motion prediction equation to predict site effects
Authors: Chao Shu-Hsien , Lin Che-Min , Kuo Chun-Hsiang , Huang Jyun-Yan , Wen Kuo-Liang , Chen Yi-Hau
Published: September 2020

We propose a methodology to implement horizontal-to-vertical Fourier spectral ratios (HVRs) evaluated from strong ground motion induced by earthquake (EHVRs) or ambient ground motion observed from microtremor (MHVRs) individually and simultaneously with the spatial correlation (SC) in a ground-motion prediction equation (GMPE) to improve the prediction accuracy of site effects. We illustrated the methodology by developing an EHVRs-SC-based model which supplements Vs30 and Z1.0 with the SC and EHVRs collected at strong motion stations, and a MHVRs-SC-based model that supplements Vs30 and Z1.0 with the SC and MHVRs observed from microtremors at sites which were collocated with strong motion stations. The standard deviation of the station-specific residuals can be reduced by up to 90% when the proposed models are used to predict site effects. In the proposed models, the spatial distribution of the predicted station terms for peak ground acceleration (PGA) from MHVRs at 3699 sites is consistent with that of the predicted station terms for PGA from EHVRs at 721 strong motion stations. Prediction accuracy for stations with inferred Vs30 is similar to that of stations with measured Vs30 with the proposed models. This study provides a methodology to simultaneously implement SC and EHVRs, or SC and MHVRs in a GMPE to improve the prediction accuracy of site effects for a target site with available EHVRs or MHVRs information.
Asthma medication use in obese and healthy weight asthma: systematic review/meta-analysis
Authors: Thompson Cherry A. , Eslick Shaun R. , Berthon Bronwyn S. , Wood Lisa G.
Published: September 2020

Background

Obesity is a common comorbidity in asthma and associated with poorer asthma control, more frequent/severe exacerbations, and reduced response to asthma pharmacotherapy.

Objective

This review aims to compare use of all classes of asthma medications in obese (body mass index (BMI) ≤30 kg·m−2)versushealthy-weight (BMI <25 kg·m−2) subjects with asthma.

Design

Databases including CINAHL (Cumulative Index to Nursing and Allied Health Literature), Cochrane, Embase and MEDLINE were searched up to July 2019 for English-language studies that recorded medication use or dose in obese and healthy-weight adults with asthma. A critical appraisal checklist was utilised for scrutinising methodological quality of eligible studies. Meta-analysis was performed and heterogeneity was examined with the use of the Chi-squared test. This review was conducted based on a published protocol (www.crd.york.ac.uk/PROSPEROCRD42020148671).

Results

Meta-analysis showed that obese subjects are more likely to use asthma medications, including short-acting β2-agonists (OR 1.75, 95% CI 1.17–2.60; p=0.006, I2=41%) and maintenance oral corticosteroids (OR 1.86, 95% CI 1.49–2.31; p<0.001, I2=0%) compared to healthy-weight subjects. Inhaled corticosteroid (ICS) dose (µg·day−1) was significantly higher in obese subjects (mean difference 208.14, 95% CI 107.01–309.27; p<0.001, I2=74%). Forced expiratory volume in 1 s (FEV1) % predicted was significantly lower in obese subjects (mean difference −5.32%, 95% CI −6.75–−3.89; p<0.001, I2=42%); however, no significant differences were observed in FEV1/forced vital capacity (FVC) ratio between groups.

Conclusions

We found that obese subjects with asthma have higher use of all included asthma medication classes and higher ICS doses than healthy-weight asthma subjects, despite lower FEV1and a similar FEV1/FVC %. A better understanding of the factors driving increased medication use is required to improve outcomes in this subgroup of asthmatics.
Phagosome-regulated mTOR signalling during sarcoidosis granuloma biogenesis
Authors: Crouser Elliott D. , Locke Landon W. , Julian Mark W. , Bicer Sabahattin , Sadee Wolfgang , White Peter , Schlesinger Larry S.
Published: September 2020

Introduction

Sarcoidosis and tuberculosis are granulomatous pulmonary diseases characterised by heightened immune reactivity toMycobacterium tuberculosisantigens. We hypothesised that an unsupervised analysis comparing the molecular characteristics of granulomas formed in response toM. tuberculosisantigens in patients with sarcoidosis or latent tuberculosis infection (LTBI) would provide novel insights into the pathogenesis of sarcoidosis.

Methods

A genomic analysis identified differentially expressed genes in granuloma-like cell aggregates formed by sarcoidosis (n=12) or LTBI patients (n=5) in an establishedin vitrohuman granuloma model wherein peripheral blood mononuclear cells were exposed toM. tuberculosisantigens (beads coated with purified protein derivative) and cultured for 7 days. Pathway analysis of differentially expressed genes identified canonical pathways, most notably antigen processing and presentationviaphagolysosomes, as a prominent pathway in sarcoidosis granuloma formation. The phagolysosomal pathway promoted mechanistic target of rapamycin complex 1 (mTORc1)/STAT3 signal transduction. Thus, granuloma formation and related immune mediators were evaluated in the absence or presence of various pre-treatments known to prevent phagolysosome formation (chloroquine) or phagosome acidification (bafilomycin A1) or directly inhibit mTORc1 activation (rapamycin).

Results

In keeping with genomic analyses indicating enhanced phagolysosomal activation and predicted mTORc1 signalling, it was determined that sarcoidosis granuloma formation and related inflammatory mediator release was dependent upon phagolysosome assembly and acidification and mTORc1/S6/STAT3 signal transduction.

Conclusions

Sarcoidosis granulomas exhibit enhanced and sustained intracellular antigen processing and presentation capacities, and related phagolysosome assembly and acidification are required to support mTORc1 signalling to promote sarcoidosis granuloma formation.
Aspirin reduces cardiovascular events in patients with pneumonia: a prior event rate ratio analysis in a large primary care database
Authors: Hamilton Fergus , Arnold David , Henley William , Payne Rupert A.
Published: September 2020

Background

Ischaemic stroke and myocardial infarction (MI) are common after pneumonia and are associated with long-term mortality. Aspirin may attenuate this risk and should be explored as a therapeutic option.

Methods

We extracted all patients with pneumonia (aged over 50 years) from the Clinical Practice Research Datalink (CPRD), a large UK primary care database, from inception until January 2019. We then performed a prior event rate ratio (PERR) analysis with propensity score matching (PSM), an approach that allows for control of measured and unmeasured confounding, with aspirin usage as the exposure and ischaemic events as the outcome. The primary outcome was the combined outcome of ischaemic stroke and MI. Secondary outcomes were ischaemic stroke and MI individually. Relevant confounders (smoking, comorbidities, age and gender) were included in the analysis.

Findings

48 743 patients were eligible for matching. Of these, 9864 were aspirin users who were matched to 9864 non-users. Aspirin users had a reduced risk of the primary outcome (adjusted hazard ratio 0.64, 95% CI 0.52–0.79) in the PERR analysis. For both secondary outcomes, aspirin use was also associated with a reduced risk for MI (hazard ratio 0.46, 95% CI 0.30–0.72) and stroke (hazard ratio 0.70, 95% CI 0.55–0.91), respectively.

Interpretation

This study provides supporting evidence that aspirin use is associated with reduced ischaemic events after pneumonia in a primary care setting. This drug may have a future clinical role in preventing this important complication.
Birt–Hogg–Dubé syndrome
Authors: Daccord Cécile , Good Jean-Marc , Morren Marie-Anne , Bonny Olivier , Hohl Daniel , Lazor Romain
Published: September 2020

Birt–Hogg–Dubé syndrome (BHD) is a rare inherited autosomal dominant disorder caused by germline mutations in the tumour suppressor geneFLCN, encoding the protein folliculin. Its clinical expression typically includes multiple pulmonary cysts, recurrent spontaneous pneumothoraces, cutaneous fibrofolliculomas and renal tumours of various histological types. BHD has no sex predilection and tends to manifest in the third or fourth decade of life. Multiple bilateral pulmonary cysts are found on chest computed tomography in >80% of patients and more than half experience one or more episodes of pneumothorax. A family history of pneumothorax is an important clue, which suggests the diagnosis of BHD. Unlike other cystic lung diseases such as lymphangioleiomyomatosis and pulmonary Langerhans cell histiocytosis, BHD does not lead to progressive loss of lung function and chronic respiratory insufficiency. Renal tumours affect about 30% of patients during their lifetime, and can be multiple and recurrent. The diagnosis of BHD is based on a combination of genetic, clinical and/or skin histopathological criteria. Management mainly consists of early pleurodesis in the case of pneumothorax, periodic renal imaging for tumour detection, and diagnostic work-up in search of BHD in relatives of the index patient.
Depressive symptoms among patients with COPD according to smoking status: a Danish nationwide case�control study of 21 184 patients
Authors: Vestergaard Jakob Hedemark , Sivapalan Pradeesh , S�rensen Rikke , Ekl�f Josefin , Achir Alispahic Imane , von B�low Anna , Seersholm Niels , Jensen Jens-Ulrik St�hr
Published: September 2020

Introduction

Depressive symptoms appear more often among patients with COPD and are associated with reduced disease control and increased mortality. Both smoking and COPD increase the risk of depressive symptoms. Whether smoking cessation among COPD patients affects the occurrence of depressive symptoms is unknown. We hypothesised that smoking cessation in patients with COPD leads to reduced use of antidepressants and fewer admissions to psychiatric hospitals with depression, anxiety or bipolar disorder.

Methods

We conducted a nationwide retrospective case�control study, in patients from The Danish Register for COPD with spirometry-verified COPD, age =40 years, a history of smoking and absence of cancer. Consistent smokers were matched 1:1 with ex-smokers using a propensity score model. Prescription fillings of antidepressants and risk of admissions to psychiatric hospitals with either depression, anxiety or bipolar disorder both descriptively was assessed by Cox proportional hazard models.

Results

We included 21 184 patients. A total of 2011 consistent smokers collected antidepressant prescriptions compared with 1821 ex-smokers. Consistent smoking was associated with increased risk of filling prescription on antidepressants (HR 1.4, 95% CI 1.3�1.5, p<0.0001) and with increased risk of psychiatric hospital admission with either depression, anxiety or bipolar disorder (HR 2.0, 95% CI 1.6�2.5). The associations persisted after adjustment for former use of antidepressants.

Conclusion

Consistent smoking among COPD patients was associated with increased use of antidepressants and admissions to psychiatric hospitals with either depression, anxiety or bipolar disorder, compared to smoking cessation.
Identification and treatment of T2-low asthma in the era of biologics
Authors: Kyriakopoulos Chris , Gogali Athena , Bartziokas Konstantinos , Kostikas Konstantinos
Published: September 2020

Currently, and based on the development of relevant biologic therapies, T2-high is the most well-defined endotype of asthma. Although much progress has been made in elucidating T2-high inflammation pathways, no specific clinically applicable biomarkers for T2-low asthma have been identified. The therapeutic approach of T2-low asthma is a problem urgently needing resolution, firstly because these patients have poor response to steroids, and secondly because they are not candidates for the newer targeted biologic agents. Thus, there is an unmet need for the identification of biomarkers that can help the diagnosis and endotyping of T2-low asthma.

Ongoing investigation is focusing on neutrophilic airway inflammation mediators as therapeutic targets, including interleukin (IL)-8, IL-17, IL-1, IL-6, IL-23 and tumour necrosis factor-α; molecules that target restoration of corticosteroid sensitivity, mainly mitogen-activated protein kinase inhibitors, tyrosine kinase inhibitors and phosphatidylinositol 3-kinase inhibitors; phosphodiesterase (PDE)3 inhibitors that act as bronchodilators and PDE4 inhibitors that have an anti-inflammatory effect; and airway smooth muscle mass attenuation therapies, mainly for patients with paucigranulocytic inflammation.

This article aims to review the evidence for noneosinophilic inflammation being a target for therapy in asthma; discuss current and potential future therapeutic approaches, such as novel molecules and biologic agents; and assess clinical trials of licensed drugs in the treatment of T2-low asthma.
Thoracic ultrasound for malignant pleural effusion: a systematic review and meta-analysis
Authors: Shiroshita Akihiro , Nozaki Sayumi , Tanaka Yu , Luo Yan , Kataoka Yuki
Published: September 2020

This systematic review aimed to evaluate the diagnostic accuracy of thoracic ultrasound in malignant pleural effusion.

Articles published until December 2019 in MEDLINE, Embase, the Cochrane Central Register of Controlled Trials and the International Clinical Trials Registry Platform were screened by two authors independently to extract data and evaluate the risks of bias and applicability using the modified Quality Assessment of Diagnostic Accuracy Studies-2 tool. We described the forest plots of each thoracic ultrasound finding. We estimated the pooled sensitivity and specificity of pleural nodularity using the bivariate random-effects model.

We included seven articles and found that each thoracic ultrasound finding had low sensitivity. The pooled specificity of pleural nodularity was 96.9% (95% CI 93.2%–98.6%).

In conclusion, thoracic ultrasound is not useful in ruling out malignant pleural effusion. Physicians can proceed rigorously to repeat thoracentesis or other invasive procedures when pleural nodularity is detected.
Circulating fibrocytes as prognostic biomarkers of autoimmune interstitial lung disease
Authors: Odackal John , Yu Victor , Gomez-Manjerres Diana , Field Joshua J. , Burdick Marie D. , Mehrad Borna
Published: September 2020

Background

Autoimmunity is a common cause of pulmonary fibrosis and can present either as a manifestation of an established connective tissue disease or as the recently described entity of interstitial pneumonia with autoimmune features. The rate of progression and responsiveness to immunosuppression in these illnesses are difficult to predict. Circulating fibrocytes are bone marrow-derived progenitor cells that home to injured tissues and contribute to lung fibrogenesis. We sought to test the hypothesis that the blood fibrocyte concentration predicts outcome and treatment responsiveness in autoimmune interstitial lung diseases.

Methods

We compared the concentration of circulating fibrocytes in 50 subjects with autoimmune interstitial lung disease and 26 matched healthy controls and assessed the relationship between serial peripheral blood fibrocyte concentrations and clinical outcomes over a median of 6.25 years.

Results

As compared to controls, subjects with autoimmune interstitial lung disease had higher circulating concentrations of total fibrocytes, the subset of activated fibrocytes, and fibrocytes with activation of PI3K/AKT/mTOR, transforming growth factor-β (TGF-β) receptor and interleukin (IL)-4/IL-13 receptor signalling pathways. Over the follow-up period, there were episodes of marked elevation in the concentration of circulating fibrocytes in subjects with autoimmune interstitial lung disease but not controls. Initiation of immunosuppressive therapy was associated with a decline in the concentration of circulating fibrocytes. For each 100 000 cells·mL−1increase in peak concentration of circulating fibrocytes, we found a 5% increase in odds of death or lung function decline.

Conclusion

In patients with autoimmune interstitial lung disease, circulating fibrocytes may represent a biomarker of outcome and treatment response.
Functional characterization of rare NRXN1 variants identified in autism spectrum disorders and schizophrenia
Authors: Ishizuka Kanako , Yoshida Tomoyuki , Kawabata Takeshi , Imai Ayako , Mori Hisashi , Kimura Hiroki , Inada Toshiya , Okahisa Yuko , Egawa Jun , Usami Masahide , Kushima Itaru , Morikawa Mako , Okada Takashi , Ikeda Masashi , Branko Aleksic , Mori Daisuke , Someya Toshiyuki , Iwata Nakao , Ozaki Norio
Published: September 2020

Background

Rare genetic variants contribute to the etiology of both autism spectrum disorder (ASD) and schizophrenia (SCZ). Most genetic studies limit their focus to likely gene-disrupting mutations because they are relatively easier to interpret their effects on the gene product. Interpretation of missense variants is also informative to some pathophysiological mechanisms of these neurodevelopmental disorders; however, their contribution has not been elucidated because of relatively small effects. Therefore, we characterized missense variants detected in NRXN1, a well-known neurodevelopmental disease-causing gene, from individuals with ASD and SCZ.

Methods

To discover rare variants with large effect size and to evaluate their role in the shared etiopathophysiology of ASD and SCZ, we sequenced NRXN1 coding exons with a sample comprising 562 Japanese ASD and SCZ patients, followed by a genetic association analysis in 4273 unrelated individuals. Impact of each missense variant detected here on cell surface expression, interaction with NLGN1, and synaptogenic activity was analyzed using an in vitro functional assay and in silico three-dimensional (3D) structural modeling.

Results

Through mutation screening, we regarded three ultra-rare missense variants (T737M, D772G, and R856W), all of which affected the LNS4 domain of NRXN1α isoform, as disease-associated variants. Diagnosis of individuals with T737M, D772G, and R856W was 1ASD and 1SCZ, 1ASD, and 1SCZ, respectively. We observed the following phenotypic and functional burden caused by each variant. (i) D772G and R856W carriers had more serious social disabilities than T737M carriers. (ii) In vitro assay showed reduced cell surface expression of NRXN1α by D772G and R856W mutations. In vitro functional analysis showed decreased NRXN1α-NLGN1 interaction of T737M and D772G mutants. (iii) In silico 3D structural modeling indicated that T737M and D772G mutations could destabilize the rod-shaped structure of LNS2-LNS5 domains, and D772G and R856W could disturb N-glycan conformations for the transport signal.

Conclusions

The combined data suggest that missense variants in NRXN1 could be associated with phenotypes of neurodevelopmental disorders beyond the diagnosis of ASD and/or SCZ.
Twadn: an efficient alignment algorithm based on time warping for pairwise dynamic networks
Authors: Zhong Yuanke , Li Jing , He Junhao , Gao Yiqun , Liu Jie , Wang Jingru , Shang Xuequn , Hu Jialu
Published: September 2020

Background

Network alignment is an efficient computational framework in the prediction of protein function and phylogenetic relationships in systems biology. However, most of existing alignment methods focus on aligning PPIs based on static network model, which are actually dynamic in real-world systems. The dynamic characteristic of PPI networks is essential for understanding the evolution and regulation mechanism at the molecular level and there is still much room to improve the alignment quality in dynamic networks.

Results

In this paper, we proposed a novel alignment algorithm, Twadn, to align dynamic PPI networks based on a strategy of time warping. We compare Twadn with the existing dynamic network alignment algorithm DynaMAGNA++ and DynaWAVE and use area under the receiver operating characteristic curve and area under the precision-recall curve as evaluation indicators. The experimental results show that Twadn is superior to DynaMAGNA++ and DynaWAVE. In addition, we use protein interaction network of Drosophila to compare Twadn and the static network alignment algorithm NetCoffee2 and experimental results show that Twadn is able to capture timing information compared to NetCoffee2.

Conclusions

Twadn is a versatile and efficient alignment tool that can be applied to dynamic network. Hopefully, its application can benefit the research community in the fields of molecular function and evolution.
A learning-based method for drug-target interaction prediction based on feature representation learning and deep neural network
Authors: Peng Jiajie , Li Jingyi , Shang Xuequn
Published: September 2020

Background

Drug-target interaction prediction is of great significance for narrowing down the scope of candidate medications, and thus is a vital step in drug discovery. Because of the particularity of biochemical experiments, the development of new drugs is not only costly, but also time-consuming. Therefore, the computational prediction of drug target interactions has become an essential way in the process of drug discovery, aiming to greatly reducing the experimental cost and time.

Results

We propose a learning-based method based on feature representation learning and deep neural network named DTI-CNN to predict the drug-target interactions. We first extract the relevant features of drugs and proteins from heterogeneous networks by using the Jaccard similarity coefficient and restart random walk model. Then, we adopt a denoising autoencoder model to reduce the dimension and identify the essential features. Third, based on the features obtained from last step, we constructed a convolutional neural network model to predict the interaction between drugs and proteins. The evaluation results show that the average AUROC score and AUPR score of DTI-CNN were 0.9416 and 0.9499, which obtains better performance than the other three existing state-of-the-art methods.

Conclusions

All the experimental results show that the performance of DTI-CNN is better than that of the three existing methods and the proposed method is appropriately designed.
Spark-based parallel calculation of 3D fourier shell correlation for macromolecule structure local resolution estimation
Authors: Lü Yongchun , Zeng Xiangrui , Tian Xinhui , Shi Xiao , Wang Hui , Zheng Xiaohui , Liu Xiaodong , Zhao Xiaofang , Gao Xin , Xu Min
Published: September 2020

Background

Resolution estimation is the main evaluation criteria for the reconstruction of macromolecular 3D structure in the field of cryoelectron microscopy (cryo-EM). At present, there are many methods to evaluate the 3D resolution for reconstructed macromolecular structures from Single Particle Analysis (SPA) in cryo-EM and subtomogram averaging (SA) in electron cryotomography (cryo-ET). As global methods, they measure the resolution of the structure as a whole, but they are inaccurate in detecting subtle local changes of reconstruction. In order to detect the subtle changes of reconstruction of SPA and SA, a few local resolution methods are proposed. The mainstream local resolution evaluation methods are based on local Fourier shell correlation (FSC), which is computationally intensive. However, the existing resolution evaluation methods are based on multi-threading implementation on a single computer with very poor scalability.

Results

This paper proposes a new fine-grained 3D array partition method by key-value format in Spark. Our method first converts 3D images to key-value data (K-V). Then the K-V data is used for 3D array partitioning and data exchange in parallel. So Spark-based distributed parallel computing framework can solve the above scalability problem. In this distributed computing framework, all 3D local FSC tasks are simultaneously calculated across multiple nodes in a computer cluster. Through the calculation of experimental data, 3D local resolution evaluation algorithm based on Spark fine-grained 3D array partition has a magnitude change in computing speed compared with the mainstream FSC algorithm under the condition that the accuracy remains unchanged, and has better fault tolerance and scalability.

Conclusions

In this paper, we proposed a K-V format based fine-grained 3D array partition method in Spark to parallel calculating 3D FSC for getting a 3D local resolution density map. 3D local resolution density map evaluates the three-dimensional density maps reconstructed from single particle analysis and subtomogram averaging. Our proposed method can significantly increase the speed of the 3D local resolution evaluation, which is important for the efficient detection of subtle variations among reconstructed macromolecular structures.
Control of Panama disease of banana by intercropping with Chinese chive (Allium tuberosum Rottler): cultivar differences
Authors: Li Zhenfang , Wang Tong , He Chenling , Cheng Kelin , Zeng Rensen , Song Yuanyuan
Published: September 2020

Panama disease (Fusarium wilt disease) caused by Fusarium oxysporum f. sp. cubense race 4 (FOC) severely threatens banana (Musa spp.) production worldwide. Intercropping of banana with Allium plants has shown a potential to reduce Panama disease. In this study, six cultivars of Chinese chive (Allium tuberosum Rottler) were selected to compare their differences in antifungal activity and active compounds. Three cultivars Duokang Fujiu 11, Fujiuhuang 2, and Duokang Sijiqing with higher levels of antifungal compounds were further used for intercropping with banana in the pots and field to compare their effects on growth and disease incidence of banana.

The six cultivars showed significant differences in antifungal activity against FOC mycelia growth in both leaf volatiles and aqueous leachates. The aqueous leachates displayed stronger antifungal activity than the volatiles. FJH cultivar showed the best inhibitory effect among all six cultivars. Contents of three main antifungal compounds dipropyl trisulfide (DPT), dimethyl trisulfide (DMT), and 2-methyl-2-pentenal (MP) in volatiles and aqueous leachates varied considerably among cultivars. Pot and field experiments showed that intercropping with three selected Chinese chive cultivars significantly improved banana vegetative growth, increased photosynthetic characteristics and yield but decreased disease incidence of Panama disease.

Our results indicate that intercropping with Chinese chive shows potential to reduce banana Panama disease and selection of appropriate cultivars is vital for effective disease control.
Impact of temperature variability on childhood allergic rhinitis in a subtropical city of China
Authors: Wang Xu , Cheng Jian , Ling Li , Su Hong , Zhao Desheng , Ni Hong
Published: September 2020

Background

Many studies have shown an association of childhood respiratory diseases with short-term temperature variability such as diurnal temperature range (DTR) and temperature change between two neighboring days (TCN). However, the impact of temperature variability on allergic rhinitis (AR) has not been investigated so far. This study sought to evaluate the short-term effect of temperature variability (i.e., TCN and DTR) on AR, as well as to identify vulnerable subpopulations.

Method

We collected daily data on emergency room visits and outpatients for AR and weather variables in Hefei, China during 2014–2016. A distributed lag non-linear model that controlled for long-term trend and seasonality, mean temperature, relative humidity, day of week was used to fit the associations of AR with DTR and TCN. Stratified analyses by age, sex and occupation were also performed.

Results

During the study period, there were a total of 53,538 cases and the average values of DTR and TCN were 8.4 °C (range: 1.0 °C to 21.2 °C) and 0 °C (range: − 12.2 °C to 5.9 °C), respectively. While we did not observe an adverse effect of DTR on AR, TCN was significantly associated with increased risk of AR. Specifically, a large temperature drop between two adjacent days (3.8 °C, 5th percentile of TCN) has a delayed and short-lasting effect on AR, with the estimated relative risk of 1.02 (95% confidence interval: 1.01 to 1.04) at lag 12. Moreover, boys and children older than 15 years seemed to be more vulnerable to the effect of TCN.

Conclusions

This study provided evidence of an adverse effect of large temperature drops between two adjacent days on childhood AR. Attention paid to boys and older children may help prevent AR attacks.
An improved strategy to analyse strigolactones in complex sample matrices using UHPLC–MS/MS
Authors: Floková Kristýna , Shimels Mahdere , Andreo Jimenez Beatriz , Bardaro Nicoletta , Strnad Miroslav , Novák Ondřej , Bouwmeester Harro J.
Published: September 2020

Background

Strigolactones represent the most recently described group of plant hormones involved in many aspects of plant growth regulation. Simultaneously, root exuded strigolactones mediate rhizosphere signaling towards beneficial arbuscular mycorrhizal fungi, but also attract parasitic plants. The seed germination of parasitic plants induced by host strigolactones leads to serious agricultural problems worldwide. More insight in these signaling molecules is hampered by their extremely low concentrations in complex soil and plant tissue matrices, as well as their instability. So far, the combination of tailored isolation—that would replace current unspecific, time-consuming and labour-intensive processing of large samples—and a highly sensitive method for the simultaneous profiling of a broad spectrum of strigolactones has not been reported.

Results

Depending on the sample matrix, two different strategies for the rapid extraction of the seven structurally similar strigolactones and highly efficient single-step pre-concentration on polymeric RP SPE sorbent were developed and validated. Compared to conventional methods, controlled temperature during the extraction and the addition of an organic modifier (acetonitrile, acetone) to the extraction solvent helped to tailor strigolactone isolation from low initial amounts of root tissue (150 mg fresh weight, FW) and root exudate (20 ml), which improved both strigolactone stability and sample purity. We have designed an efficient UHPLC separation with sensitive MS/MS detection for simultaneous analysis of seven natural strigolactones including their biosynthetic precursors—carlactone and carlactonoic acid. In combination with the optimized UHPLC–MS/MS method, attomolar detection limits were achieved. The new method allowed successful profiling of seven strigolactones in small exudate and root tissue samples of four different agriculturally important plant species—sorghum, rice, pea and tomato.

Conclusion

The established method provides efficient strigolactone extraction with aqueous mixtures of less nucleophilic organic solvents from small root tissue and root exudate samples, in combination with rapid single-step pre-concentration. This method improves strigolactone stability and eliminates the co-extraction and signal of matrix-associated contaminants during the final UHPLC–MS/MS analysis with an electrospray interface, which dramatically increases the overall sensitivity of the analysis. We show that the method can be applied to a variety of plant species.
Antimicrobial prophylaxis is considered sufficient to preserve an acceptable surgical site infection rate in clean orthopaedic and neurosurgeries in dogs
Authors: Välkki Kirsi Johanna , Thomson Katariina Hanne , Grönthal Thomas Sven Christer , Junnila Jouni Juho Tapio , Rantala Merja Hilma Johanna , Laitinen-Vapaavuori Outi Maria , Mölsä Sari Helena
Published: September 2020

Background

Surgical site infections (SSI) are associated with increased morbidity and mortality. To lower the incidence of SSI, antimicrobial prophylaxis is given 30–60 min before certain types of surgeries in both human and veterinary patients. However, due to the increasing concern of antimicrobial resistance, the benefit of antimicrobial prophylaxis in clean orthopaedic and neurosurgeries warrants investigation. The aims of this retrospective cross-sectional study were to review the rate of SSI and evaluate the compliance with antimicrobial guidelines in dogs at a veterinary teaching hospital in 2012–2016. In addition, possible risk factors for SSI were assessed.

Results

Nearly all dogs (377/406; 92.9%) received antimicrobial prophylaxis. Twenty-nine dogs (7.1%) did not receive any antimicrobials and only four (1.1%) received postoperative antimicrobials. The compliance with in-house and national protocols was excellent regarding the choice of prophylactic antimicrobial (cefazolin), but there was room for improvement in the timing of prophylaxis administration. Follow-up data was available for 89.4% (363/406) of the dogs. Mean follow-up time was 464 days (range: 3–2600 days). The overall SSI rate was 6.3%: in orthopaedic surgeries it was 6.7%, and in neurosurgeries it was 4.2%. The lowest SSI rates (0%) were seen in extracapsular repair of cranial cruciate ligament rupture, ulnar ostectomy, femoral head and neck excision, arthrotomy and coxofemoral luxation repair. The highest SSI rate (25.0%) was seen in arthrodesis. Omission of antimicrobials did not increase the risk for SSI (P = 0.56; OR 1.7; CI95%0.4–5.0). Several risk factors for SSI were identified, including methicillin-resistantStaphylococcus pseudintermediuscarriage (P = 0.02; OR 9.0; CI95%1.4–57.9) and higher body temperature (P = 0.03; OR 1.69; CI95%1.0–2.7; mean difference + 0.4 °C compared to dogs without SSI).

Conclusions

Antimicrobial prophylaxis without postoperative antimicrobials is sufficient to maintain the overall rate of SSI at a level similar to published data in canine clean orthopedic and neurosurgeries.
Whether the risk of gestational diabetes mellitus is affected by TNF-α, IL-6, IL-10 or ADIPOQ polymorphisms: a meta-analysis
Authors: Huang Qiqi , Wang Yi , Gu Binbin , Xu Yanwen
Published: September 2020

Background

Whether polymorphisms in tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), interleukin-10 (IL-10) or adiponectin (ADIPOQ) influence the risk of gestational diabetes mellitus (GDM) or not remain inconclusive. Therefore, the authors conducted a meta-analysis to robustly assess relationships between polymorphisms in TNF-α, IL-6, IL-10 or ADIPOQ and the risk of GDM by merging the results of eligible publications.

Methods

A through literature searching in Medline, Embase, Wanfang, VIP and CNKI was conducted by the authors to identify eligible publications, and twenty-two publications were finally found to be eligible for merged quantitative analyses.

Results

The merged quantitative analyses revealed that ADIPOQ + 45T/G (rs2241766) polymorphism was significantly associated with the risk of GDM in overall population (dominant comparison: OR = 0.70, p < 0.001; recessive comparison: OR = 1.95, p < 0.001; over-dominant comparison: OR = 1.18, p = 0.03; allele comparison: OR = 0.71, p < 0.001) and Asians (dominant comparison: OR = 0.70, p < 0.001; recessive comparison: OR = 1.94, p < 0.001; allele comparison: OR = 0.72, p < 0.001). Nevertheless, we did not observe any positive results for TNF-α − 238G/A (rs361525), TNF-α − 308G/A (rs1800629), IL6 − 174G/C (rs1800795), IL-10 − 819C/T (rs1800871), IL-10 − 592C/A (rs1800872), IL-10 − 1082A/G (rs1800896) and ADIPOQ + 276G/T (rs1501299) polymorphisms.

Conclusions

The present meta-analysis shows that among investigated TNF-α, IL-6, IL-10 or ADIPOQ polymorphisms, only ADIPOQ + 45T/G (rs2241766) polymorphism may affect the risk of GDM.
Dynamic changes of the fecal bacterial community in dairy cows during early lactation
Authors: Huang Shuai , Ji Shoukun , Wang Feiran , Huang Jie , Alugongo Gibson Maswayi , Li Shengli
Published: September 2020

The dynamics of the community structure and composition of the dairy cow fecal bacterial communities during early lactation is unclear, therefore this study was conducted to characterize the fecal bacterial communities in dairy cows during early lactation using 16S rRNA gene sequencing. Feces were sampled from 20 healthy fresh Holstein dairy cows on day 1 (Fresh1d group) and day 14 (Fresh14d group) after calving. After calving, cows were fed the same fresh diet. The dominant phyla Firmicutes and Proteobacteria were decreased (P ≤ 0.01) with lactating progress and phyla Bacteroidetes were increased (P = 0.008) with lactating progress and dietary transition. At family level, the predominant families were Ruminococcaceae (35.23%), Lachnospiraceae (11.46%), Rikenellaceae (10.44%) and Prevotellaceae (6.89%). A total of 14 genera were different between fecal samples from Fresh1d and Fresh14d, included the predominant genera, such as Ruminococcaceae_UCG-005 (P = 0.008), Rikenellaceae_RC9_gut_group (P = 0.043) and Christensenellaceae_R-7_group (P = 0.008). All fecal bacterial communities shared members of the genera Ruminococcaceae_UCG-005, Bacteroides and Rikenellaceae_RC9_gut_group. These findings help to improve our understanding of the composition and structure of the fecal microbial community in fresh cows and may provide insight into bacterial adaptation time and dietary in lactating cows.
What is the prevalence of current alcohol dependence and how is it measured for Indigenous people in Australia, New Zealand, Canada and the United States of America? A systematic review
Authors: Weatherall Teagan J. , Conigrave Katherine M. , Conigrave James H. , Lee K. S. Kylie
Published: September 2020

Background

Alcohol affects Indigenous communities globally that have been colonised. These effects are physical, psychological, financial and cultural. This systematic review aims to describe the prevalence of current (12-month) alcohol dependence in Indigenous Peoples in Australia, New Zealand, Canada and the United States of America, to identify how it is measured, and if tools have been validated in Indigenous communities. Such information can help inform estimates of likely treatment need.

Methods

A systematic search of the literature was completed in six electronic databases for reports on current alcohol dependence (moderate to severe alcohol use disorder) published between 1 January 1989–9 July 2020. The following data were extracted: (1) the Indigenous population studied; country, (2) prevalence of dependence, (3) tools used to screen, assess or diagnose current dependence, (4) tools that have been validated in Indigenous populations to screen, assess or diagnose dependence, and (5) quality of the study, assessed using the Appraisal Tool for Cross-Sectional Studies.

Results

A total of 11 studies met eligibility criteria. Eight were cross-sectional surveys, one cohort study, and two were validation studies. Nine studies reported on the prevalence of current (12-month) alcohol dependence, and the range varied widely (3.8–33.3% [all participants], 3–32.8% [males only], 1.3–7.6% [females only]). Eight different tools were used and none were Indigenous-specific. Two tools have been validated in Indigenous (Native American) populations.

Conclusion

Few studies report on prevalence of current alcohol dependence in community or household samples of Indigenous populations in these four countries. Prevalence varies according to sampling method and site (for example, specific community versus national). Prior work has generally not used tools validated in Indigenous contexts. Collaborations with local Indigenous people may help in the development of culturally appropriate ways of measuring alcohol dependence, incorporating local customs and values. Tools used need to be validated in Indigenous communities, or Indigenous-specific tools developed, validated and used. Prevalence findings can inform health promotion and treatment needs, including funding for primary health care and specialist treatment services.
Screening and evaluation of key genes in contributing to pathogenesis of hepatic fibrosis based on microarray data
Authors: Wu Furong , Ning Lijuan , Zhou Ran , Shen Aizong
Published: September 2020

Background

Hepatic fibrosis (HF), which is characterized by the excessive accumulation of extracellular matrix (ECM) in the liver, usually progresses to liver cirrhosis and then death. To screen differentially expressed (DE) long non-coding RNAs (lncRNAs) and mRNAs, explore their potential functions to elucidate the underlying mechanisms of HF.

Methods

The microarray of GSE80601 was downloaded from the Gene Expression Omnibus database, which is based on the GPL1355 platform. Screening for the differentially expressed LncRNAs and mRNAs was conducted between the control and model groups. Then, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses were performed to analyze the biological functions and pathways of the DE mRNAs. Additionally, the protein–protein interaction (PPI) network was delineated. In addition, utilizing the Weighted Gene Co-expression Network Analysis (WGCNA) package and Cytoscape software, we constructed lncRNA-mRNA weighted co-expression networks.

Results

A total of 254 significantly differentially expressed lncRNAs and 472 mRNAs were identified. GO and KEGG analyses revealed that DE mRNAs regulated HF by participating in the GO terms of metabolic process, inflammatory response, response to wounding and oxidation–reduction. DE mRNAs were also significantly enriched in the pathways of ECM-receptor interaction, PI3K-Akt signaling pathway, focal adhesion (FA), retinol metabolism and metabolic pathways. Moreover, 24 lncRNAs associated with 40 differentially expressed genes were observed in the modules of lncRNA-mRNA weighted co-expression network.

Conclusions

This study revealed crucial information on the molecular mechanisms of HF and laid a foundation for subsequent genes validation and functional studies, which could contribute to the development of novel diagnostic markers and provide new therapeutic targets for the clinical treatment of HF.
Associations of mitochondrial genomic variation with corticobasal degeneration, progressive supranuclear palsy, and neuropathological tau measures
Authors: Valentino Rebecca R. , Tamvaka Nikoleta , Heckman Michael G. , Johnson Patrick W. , Soto-Beasley Alexandra I. , Walton Ronald L. , Koga Shunsuke , Uitti Ryan J. , Wszolek Zbigniew K. , Dickson Dennis W. , Ross Owen A.
Published: September 2020

Mitochondrial health is important in ageing and dysfunctional oxidative phosphorylation (OXPHOS) accelerates ageing and influences neurodegeneration. Mitochondrial DNA (mtDNA) codes for vital OXPHOS subunits and mtDNA background has been associated with neurodegeneration; however, no study has characterised mtDNA variation in Progressive supranuclear palsy (PSP) or Corticobasal degeneration (CBD) risk or pathogenesis. In this case–control study, 910 (42.6% male) neurologically-healthy controls, 1042 (54.1% male) pathologically-confirmed PSP cases, and 171 (52.0% male) pathologically-confirmed CBD cases were assessed to determine how stable mtDNA polymorphisms, in the form of mtDNA haplogroups, were associated with risk of PSP, risk of CBD, age of PSP onset, PSP disease duration, and neuropathological tau pathology measures for neurofibrillary tangles (NFT), neuropil threads (NT), tufted astrocytes (TA), astrocytic plaques (AP), and oligodendroglial coiled bodies (CB). 764 PSP cases and 150 CBD cases had quantitative tau pathology scores. mtDNA was genotyped for 39 unique SNPs using Agena Bioscience iPlex technologies and mitochondrial haplogroups were defined to mitochondrial phylogeny. After adjustment for multiple testing, we observed an association with risk of CBD for mtDNA sub-haplogroup H4 (OR = 4.51, P = 0.001) and the HV/HV0a haplogroup was associated with a decreased severity of NT tau pathology in PSP cases (P = 0.0023). Our study reports that mitochondrial genomic background may be associated with risk of CBD and may be influencing tau pathology measures in PSP. Replication of these findings will be important.