bluuebunny/crossref_metadata_2025 huggingface dataset:
Antibiotic resistance genes in different animal manures and their derived organic fertilizer
Authors: Xu Yan , Li Houyu , Shi Rongguang , Lv Jiapei , Li Bihan , Yang Fengxia , Zheng Xiangqun , Xu Jian
Published: July 2020

Background

The prevalence of antibiotic resistance genes (ARGs) in animal manure poses a threat to environmental safety. Organic fertilizers fermented by livestock and poultry manure are directly applied to farmland and have the potential to cause outbreaks of bacterial resistance in agricultural environments. This study investigated the composition of ARGs in different animal manures and their derived organic fertilizers.

Results

The results showed that the abundance of several ARGs, such as sul2, TetB-01, TetG-01 and TetM-01, in organic fertilizer samples was 12–96% lower than that in animal manure. However, the abundance of TetK and ermC was higher in animal manure than in organic fertilizers. No correlation between ARGs and environmental factors such as pH, TN, and antibiotics was observed by redundancy analysis (RDA). Procrustes analysis revealed a significant correlation between bacterial community structures and ARG abundance (r = 0.799, p < 0.01). Nonmetric multidimensional scaling (NMDS) analysis suggested that microorganisms in organic fertilizer may be derived from animal manure. Additionally, the abundance of pathogenic bacteria (especially Actinomadura) would increase rather than decrease in manure compared to organic fertilizer.

Conclusion

The diversity and abundance of most ARGs significantly decreased from animal manure to organic fertilizer. Microorganisms in the prepared organic fertilizer may mainly be inherited from the animal manure. The results also showed that the pathogens in the prepared organic fertilizer would significantly reduce, but would still cause partial pathogen proliferation.
Multi-omics sequencing provides insight into floral transition in Catalpa bungei. C.A. Mey
Authors: Wang Zhi , Ma Wenjun , Zhu Tianqing , Lu Nan , Ouyang Fangqun , Wang Nan , Yang Guijuan , Kong Lisheng , Qu Guanzheng , Zhang Shougong , Wang Junhui
Published: July 2020

Background

Floral transition plays an important role in development, and proper time is necessary to improve the value of valuable ornamental trees. The molecular mechanisms of floral transition remain unknown in perennial woody plants. “Bairihua” is a type of C. bungei that can undergo floral transition in the first planting year.

Results

Here, we combined short-read next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing to provide a more complete view of transcriptome regulation during floral transition in C. bungei. The circadian rhythm-plant pathway may be the critical pathway during floral transition in early flowering (EF) C. bungei, according to horizontal and vertical analysis in EF and normal flowering (NF) C. bungei. SBP and MIKC-MADS-box were seemingly involved in EF during floral transition. A total of 61 hub genes were associated with floral transition in the MEturquoise model with Weighted Gene Co-expression Network Analysis (WGCNA). The results reveal that ten hub genes had a close connection with the GASA homologue gene (Cbu.gene.18280), and the ten co-expressed genes belong to five flowering-related pathways. Furthermore, our study provides new insights into the complexity and regulation of alternative splicing (AS). The ratio or number of isoforms of some floral transition-related genes is different in different periods or in different sub-genomes.

Conclusions

Our results will be a useful reference for the study of floral transition in other perennial woody plants. Further molecular investigations are needed to verify our sequencing data.
A single nucleotide substitution at the 3′-end of SBPase gene involved in Calvin cycle severely affects plant growth and grain yield in rice
Authors: Li Chun , Li Na , Huang Rui , Chen Congping , Guo Jia , Yang Xiaorong , Zhang Xiangyu , Sun Changhui , Deng Xiaojian , Wang Pingrong
Published: July 2020

Background

Calvin cycle plays a crucial role in carbon fixation which provides the precursors of organic macromolecules for plant growth and development. Currently, no gene involved in Calvin cycle has been identified in monocotyledonous plants through mutant or/and map-based cloning approach.

Results

Here, we isolated a low-tillering mutant, c6635, in rice (Oryza sativa). The mutant displayed light green leaves and intensely declined pigment contents and photosynthetic capacity at early growth stage. Moreover, its individual plant showed a much smaller size, and most individuals produced only two tillers. At mature stage, its productive panicles, grain number and seed setting rate were significantly decreased, which lead to a sharp reduction of the grain yield. We confirmed that a single nucleotide mutation in LOC_Os04g16680 gene encoding sedoheptulose 1,7-bisphosphatase (SBPase) involved in Calvin cycle was responsible for the mutant phenotype of c6635 through map-based cloning, MutMap analysis and complementation experiments. Sequence analysis suggested that the point mutation caused an amino acid change from Gly-364 to Asp at the C-terminal of SBPase. In addition, OsSBPase gene was mainly expressed in leaf, and the encoded protein was located in chloroplast. The mutation of OsSBPase could significantly affect expression levels of some key genes involved in Calvin cycle.

Conclusions

We successfully identified a SBPase gene in monocotyledonous plants. Meanwhile, we demonstrated that a single nucleotide substitution at the 3′-end of this gene severely affects plant growth and grain yield, implying that the Gly-364 at the C-terminal of SBPase could play an important role in SBPase function in rice.
Genome-wide association mapping reveals novel genes associated with coleoptile length in a worldwide collection of barley
Authors: Luo Hao , Hill Camilla Beate , Zhou Gaofeng , Zhang Xiao-Qi , Li Chengdao
Published: July 2020

Background

Drought is projected to become more frequent and severe in a changing climate, which requires deep sowing of crop seeds to reach soil moisture. Coleoptile length is a key agronomic trait in cereal crops such as barley, as long coleoptiles are linked to drought tolerance and improved seedling establishment under early water-limited growing conditions.

Results

In this study, we detected large genetic variation in a panel of 328 diverse barley (Hordeum vulgareL.) accessions. To understand the overall genetic basis of barley coleoptile length, all accessions were germinated in the dark and phenotyped for coleoptile length after 2 weeks. The investigated barleys had significant variation for coleoptile length. We then conducted genome-wide association studies (GWASs) with more than 30,000 molecular markers and identified 8 genes and 12 intergenic loci significantly associated with coleoptile length in our barley panel. TheSquamosa promoter-binding-like protein 3gene (SPL3) on chromosome 6H was identified as a major candidate gene. The missense variant on the second exon changed serine to alanine in the conserved SBP domain, which likely impacted its DNA-binding activity.

Conclusion

This study provides genetic loci for seedling coleoptile length along with candidate genes for future potential incorporation in breeding programmes to enhance early vigour and yield potential in water-limited environments.
Anti-diabetic activity of field cricket glycosaminoglycan by ameliorating oxidative stress
Authors: Ahn Mi Young , Kim Ban Ji , Kim Ha Jeong , Jin Jang Mi , Yoon Hyung Joo , Hwang Jae Sam , Lee Byung Mu
Published: July 2020

Background

Field cricket (Gryllus bimaculatus) is newly emerged as an edible insect in several countries. Anti-inflammatory effect of glycosaminoglycan derived from this cricket on chronic disease animal model such as diabetic mouse has not been fully investigated yet. Thus, the objective of this study was to determine the anti-oxidative effect of such glycosaminoglycan on diabetic mouse.

Methods

To discover potential therapeutic agents, field cricket glycosaminoglycan (GbG) was tested in the present study. Its anti-oxidative activities in diabetic mice were determined based on its abilities to reduce glucose, ALT, AST, ALP, LDL-cholesterol and BUN levels. Dung beetle (C. molossus) glycosaminoglycan (CaG) was used as a positive control. Db mice were intraperitoneally administered for 1 month according to their group assignments: 1) normal (DB-Hetero); 2) control (DB-Homo); 3) 5 mg/kg treatment of CaG (CaG5); 4) 5 mg/kg treatment of GbG (GbG5); and 5) 10 mg/kg treatment of metformin (Metformin 10).

Results

Blood glucose level decreased after 1st week of treatment with GbG. LDL-cholesterol and alkaline phosphatase levels were also inhibited by GbG. Markers of oxidative damage, such as protein carbonyl content and levels of hepatocellular biomarkers, were reduced in db mice treated with GbG. Especially anti-oxidative activities of catalase, superoxide dismutase and glutathione peroxidase were significantly increased in GbG treated group compared to those in the control (Db Homo). GbG was composed of heparin disaccharides. Its main N-glycan was identified as Hex9GlcNAc2 (m/z 1905.7) with neutral mono-sugar mainly comprising of hexose and L (+) rhamnose by mass spectroscopy.

Conclusions

Sero-biochemical and hepatocellular anti-oxidant assay results in db mice suggest that cricket (G. bimaculatus) glycosaminoglycan might possess anti-oxidative effect in diabetic state.
Validation and psychometric properties of the drug users’ quality of life scale in Iranian population
Authors: Heydarpour Sousan , Jalali Amir , Baghaei Fatemeh , Salari Nader
Published: July 2020

Introduction

Drug dependence and the resultant problems notably decrease the quality of life (QOL). Measuring the QOL in persons who use drugs (PWUDs) and planning to improve it can be helpful for rehabilitation programs. Given the absence of a standard tool to measure the quality of life of PWUD, the present study is an attempt to validate psychometric and cultural characteristics of non-injection drug users’ QOL scale.

Method

The study was carried out as a validation and methodological work. The study population consisted of 273 PWUDs in Kermanshah-based drug clinics including outgoing and hospitalized patients. The participants were selected through convenient-quota sampling. After securing the required permission from the copyright owner of the tool, it was forward/backward translated. Face validity and content validity were determined quantitatively and qualitatively. To examine construct validity of the tool, explorative factor analysis and confirmatory factor analysis were used. Internal consistency was measured using Cronbach’s alpha and statistical analyses were performed using SPSS (v.25) and LISREL (v.8).

Results

Explorative factor analysis (EFA) and confirmatory factor analysis (CFA) results supported the tool with one factor and 22 items. The R2 index in the model was equal to 0.99, which means that 99% of the variation of dependent variable (total score of QOL) is attributed to independent variable (22 statements). In other words, 99% of the variation of dependent variable is due to the independent variables in the model. The main indices of the model based on CFA all were higher than 0.9, which indicates goodness of fit of the model (χ2/DF = 2.18, CFI, NFI, TLI = 0.93 GF = 0.84, REMSEA = 0.066, R2 = 0.99). The correlative coefficient was significant (p < 0.05). The reliability of the tool based on internal consistency (Cronbach’s alpha) for the subscales ranged from 0.84 to 0.85 and equal to 0.84 for the whole tool.

Conclusion

The Farsi version of non-injection drug users’ QOL scale had acceptable indices and it was applicable to assess QOL in the target population. The tool can be used in different fields of drug addiction.
Impact of hydrogel peri-rectal spacer insertion on prostate gland intra-fraction motion during 1.5 T MR-guided stereotactic body radiotherapy
Authors: Cuccia Francesco , Mazzola Rosario , Nicosia Luca , Figlia Vanessa , Giaj-Levra Niccolò , Ricchetti Francesco , Rigo Michele , Vitale Claudio , Mantoan Beatrice , De Simone Antonio , Sicignano Gianluisa , Ruggieri Ruggero , Cavalleri Stefano , Alongi Filippo
Published: July 2020

Background

The assessment of organ motion is a crucial feature for prostate stereotactic body radiotherapy (SBRT). Rectal spacer may represent a helpful device in order to outdistance rectal wall from clinical target, but its impact on organ motion is still a matter of debate. MRI-Linac is a new frontier in radiation oncology as it allows a superior visualization of the real-time anatomy of the patient and the current highest level of adaptive radiotherapy.

Methods

We present data regarding a total of 100 fractions in 20 patients who underwent MRI-guided prostate SBRT for low-to-intermediate risk prostate cancer with or without spacer. Translational and rotational shifts were computed on the pre- and post-treatment MRI acquisitions referring to the delivery position for antero-posterior, latero-lateral and cranio-caudal direction, and assessed using the Mann-Whitney U-Test.

Results

All patients were treated with a five sessions schedule (35 Gy/5fx) using MRI-Linac for a median fraction treatment time of 50 min (range, 46–65). In the entire study sample, median rotational displacement was 0.1° in cranio-caudal, − 0.002° in latero-lateral and 0.01° in antero-posterior direction; median translational shift was 0.11 mm in cranio-caudal, − 0.24 mm in latero-lateral and − 0.22 mm in antero-posterior. A significant difference between spacer and no-spacer patients in terms of rotational shifts in the antero-posterior direction (p = 0.033) was observed; also for translational shifts a positive trend was detected in antero-posterior direction (p = 0.07), although with no statistical significance. We observed statistically significant differences in the pre-treatment planning phase in favor of the spacer cohort for several rectum dose constraints: rectum V32Gy < 5% (p = 0.001), V28 Gy < 10% (p = 0.001) and V18Gy < 35% (p = 0.039). Also for bladder V35 Gy < 1 cc, the use of spacer provided a dosimetric advantage compared to the no-spacer subpopulation (p = 0.04). Furthermore, PTV V33.2Gy > 95% was higher in the spacer cohort compared to the no-spacer one (p = 0.036).

Conclusion

In our experience, the application of rectal hydrogel spacer for prostate SBRT resulted in a significant impact on rotational antero-posterior shifts contributing to limit prostate intra-fraction motion. Further studies with larger sample size and longer follow-up are required to confirm this ideally favorable effect and to assess any potential impact on clinical outcomes.
Two cases of nodular smooth muscle proliferation suspected of primary lung cancer from preoperative images: a case report
Authors: Ikeda Toshihiro , Go Tetsuhiko , Kadota Kyuichi , Ibuki Emi , Yokomise Hiroyasu
Published: July 2020

Background

It is difficult to obtain a definitive diagnosis for nodular smooth muscle proliferation (NSMP) before surgery, and a pathological diagnosis is necessary to differentiate it from primary lung cancer. We report two cases of NSMP that were suspected to be primary lung cancer on preoperative images.

Case presentation

Case 1: An 81-year-old man who had undergone right upper lobectomy for lung cancer 2 years earlier was point out a nodular shadow with ground glass opacity (GGO) in the lower right lobe, suggesting a second primary lung cancer by chest computed tomography (CT). A thoracoscopic partial resection of the right lower lobe was performed, and pathological diagnosis was NSMP. The patient was discharged without any problems at 3 days postoperatively.

Case 2: A 72-year-old woman was pointed out a nodular shadow suspected primary lung cancer in the left lower lobe by chest CT. Therefore, thoracoscopic partial resection of the left lower lobe was performed, and pathological diagnosis was NSMP. The patient was discharged without any problems at 5 days postoperatively.

Conclusion

This report demonstrates that NSMP can be distinguished from leiomyoma and hamartoma by imaging features and pathological findings.
Non-specific diagnoses are frequent in patients hospitalized after calling 112 and their mortality is high – a register-based Danish cohort study
Authors: Nielsen Frederikke Vestergaard , Nielsen Mette Rønn , Amstrup Jesper , Lorenzen Ida Lund , Kløjgaard Torben A. , Færk Emil , Bøggild Henrik , Christensen Erika Frischknecht
Published: July 2020

Background

The number of patients calling for an ambulance increases. A considerable number of patients receive a non-specific diagnosis at discharge from the hospital, and this could imply less serious acute conditions, but the mortality has only scarcely been studied. The aim of this study was to examine the most frequent sub-diagnoses among patients with hospital non-specific diagnoses after calling 112 and their subsequent mortality.

Methods

A historical cohort study of patients brought to the hospital by ambulance after calling 112 in 2007–2014 and diagnosed with a non-specific diagnosis, chapter R or Z, in the International Classification of Diseases, 10th edition (ICD-10). 1-day and 30-day mortality was analyzed by survival analyses and compared by the log-rank test.

Results

We included 74,847 ambulance runs in 53,937 unique individuals. The most frequent diagnoses were ‘unspecified disease’ (Z039), constituting 47.0% (n 35,279). In children 0–9 years old, ‘febrile convulsions’ was the most frequent non-specific diagnosis used in 54.3% (n 1602). Overall, 1- and 30-day mortality was 2.2% (n 1205) and 6.0% (n 3258). The highest mortality was in the diagnostic group ‘suspected cardiovascular disease’ (Z035) and ‘unspecified disease’ (Z039) with 1-day mortality 2.6% (n 43) and 2.4% (n 589), and 30 day mortality of 6.32% (n 104) and 8.1% (n 1975).

Conclusion

Among patients calling an ambulance and discharged with non-specific diagnoses the 1- and 30-day mortality, despite modest mortality percentages lead to a high number of deaths.
Single-cell RNA-seq analysis reveals ploidy-dependent and cell-specific transcriptome changes in Arabidopsis female gametophytes
Authors: Song Qingxin , Ando Atsumi , Jiang Ning , Ikeda Yoko , Chen Z. Jeffrey
Published: July 2020

Background

Polyploidy provides new genetic material that facilitates evolutionary novelty, species adaptation, and crop domestication. Polyploidy often leads to an increase in cell or organism size, which may affect transcript abundance or transcriptome size, but the relationship between polyploidy and transcriptome changes remains poorly understood. Plant cells often undergo endoreduplication, confounding the polyploid effect.

Results

To mitigate these effects, we select female gametic cells that are developmentally stable and void of endoreduplication. Using single-cell RNA sequencing (scRNA-seq) in Arabidopsis thaliana tetraploid lines and isogenic diploids, we show that transcriptome abundance doubles in the egg cell and increases approximately 1.6-fold in the central cell, consistent with cell size changes. In the central cell of tetraploid plants, DEMETER (DME) is upregulated, which can activate PRC2 family members FIS2 and MEA, and may suppress the expression of other genes. Upregulation of cell size regulators in tetraploids, including TOR and OSR2, may increase the size of reproductive cells. In diploids, the order of transcriptome abundance is central cell, synergid cell, and egg cell, consistent with their cell size variation. Remarkably, we uncover new sets of female gametophytic cell-specific transcripts with predicted biological roles; the most abundant transcripts encode families of cysteine-rich peptides, implying roles in cell-cell recognition during double fertilization.

Conclusions

Transcriptome in single cells doubles in tetraploid plants compared to diploid, while the degree of change and relationship to the cell size depends on cell types. These scRNA-seq resources are free of cross-contamination and are uniquely valuable for advancing plant hybridization, reproductive biology, and polyploid genomics.
Vestibular prognosis in idiopathic sudden sensorineural hearing loss with vestibular dysfunction treated with oral or intratympanic glucocorticoids: a protocol for randomized controlled trial
Authors: Hao Weiming , Zhao Liping , Yu Huiqian , Li Huawei
Published: July 2020

Background

Idiopathic sudden sensorineural hearing loss (ISSNHL) is a rapid-onset sensorineural hearing impairment with unclear etiology and unsatisfying treatment effects. Vestibular dysfunction has been considered as a poor indicator in the clinical manifestations and prognosis of ISSNHL, which occurred in approximately 28–57% cases. Glucocorticoids, administered through oral or intratympanic way, are currently regularly and standardly applied for ISSNHL to improve the hearing outcome. However, the vestibular prognosis of ISSNHL after routine treatments remains seldom explored. This study aims to compare the effectiveness of oral and intratympanic glucocorticoids in ISSNHL with vestibular dysfunction in terms of the pattern and trajectory of possible process of vestibular function recovery.

Methods/design

A randomized, outcome-assessor- and analyst-blinded, controlled, clinical trial (RCT) will be carried out. Seventy-two patients with ISSNHL complaining of vestibular dysfunction appearing as vertigo or imbalance will be recruited and randomized into either oral or intratympanic glucocorticoid therapy group with a 1:1 allocation ratio. The primary outcomes will be vestibular function outcomes assessed by sensory organization test, caloric test, video head impulse test, cervical vestibular evoked myogenic potential, and ocular vestibular evoked myogenic potential; the secondary outcomes include self-reported vestibular dysfunction symptoms; dizziness-related handicap, visual analogue scale for vertigo and tinnitus; and pure tone audiometry. Assessments of primary outcomes will be performed at baseline and at 4 and 8 weeks post-randomization, while assessments of secondary outcomes will be performed at baseline and 1, 2, 4, and 8 weeks post-randomization.

Discussion

Previous intervention studies of ISSNHL included only hearing outcomes, with little attention paid on the prognosis of vestibular dysfunction. This trial will be the first RCT study focusing on the progress and prognosis of vestibular dysfunction in ISSNHL. The efficacy of two commonly used therapies of glucocorticoids will be compared in both auditory and vestibular function fields, rather than in the hearing outcome alone.

Trial registration

ClinicalTrials.govNCT03974867. Registered on 23 July 2019
Nanosecond pulsed electric fields enhance mesenchymal stem cells differentiation via DNMT1-regulated OCT4/NANOG gene expression
Authors: Li Kejia , Ning Tong , Wang Hao , Jiang Yangzi , Zhang Jue , Ge Zigang
Published: July 2020

Background

Multiple strategies have been proposed to promote the differentiation potential of mesenchymal stem cells (MSCs), which is the fundamental property in tissue formation and regeneration. However, these strategies are relatively inefficient that limit the application. In this study, we reported a novel and efficient strategy, nanosecond pulsed electric fields (nsPEFs) stimulation, which can enhance the trilineage differentiation potential of MSCs, and further explained the mechanism behind.

Methods

We used histological staining to screen out the nsPEFs parameters that promoted the trilineage differentiation potential of MSCs, and further proved the effect of nsPEFs by detecting the functional genes. In order to explore the corresponding mechanism, we examined the expression of pluripotency genes and the methylation status of their promoters. Finally, we targeted the DNA methyltransferase which was affected by nsPEFs.

Results

The trilineage differentiation of bone marrow-derived MSCs was significantly enhanced in vitro by simply pre-treating with 5 pulses of nsPEFs stimulation (energy levels as 10 ns, 20 kV/cm; 100 ns, 10 kV/cm), due to that the nsPEFs demethylated the promoters of stem cell pluripotency genes OCT4 and NANOG through instantaneous downregulation of DNA methylation transferase 1 (DNMT1), thereby increasing the expression of OCT4 and NANOG for up to 3 days, and created a treatment window period of stem cells.

Conclusions

In summary, nsPEFs can enhance MSCs differentiation via the epigenetic regulation and could be a safe and effective strategy for future stem cell application.
Small extracellular vesicles secreted by human iPSC-derived MSC enhance angiogenesis through inhibiting STAT3-dependent autophagy in ischemic stroke
Authors: Xia Yuguo , Ling Xiaozheng , Hu Guowen , Zhu Qingwei , Zhang Juntao , Li Qing , Zhao Bizeng , Wang Yang , Deng Zhifeng
Published: July 2020

Background

Small extracellular vesicles (sEV) secreted by mesenchymal stem cells (MSC) derived from human induced pluripotent stem cells (iPSC, iMSC-sEV) are considered to have great potential in treating ischemic diseases. Angiogenesis play an important role in post-stroke recovery. However, no studies have yet been conducted to systemically examine the effect and the underlying mechanism of iMSC-sEV on angiogenesis under brain ischemia conditions.

Methods

Ischemic stroke model was performed in rats induced by middle cerebral artery occlusion (MCAO), and the pro-angiogenic capacity of iMSC-sEV was measured. The in vitro effects of iMSC-sEV on the migration and tube formation of endothelial cells were investigated, respectively. Autophagy and autophagy-related signaling pathway were detected in vivo and in vitro.

Results

We found that iMSC-sEV significantly reduced infarct volume, enhanced angiogenesis, and alleviated long-term neurological deficits in rats after stroke. We also demonstrated that iMSC-sEV increased migration and tube formation of endothelial cells in vitro. A further mechanism study revealed that the pro-angiogenic effect of iMSC-sEV was correlated with a reduction in autophagy. Furthermore, iMSC-sEV significantly activated signal transducer and activator of transcription 3 (STAT3), and suppression of STAT3 abolished iMSC-sEV-induced inhibition of autophagy and promotion of angiogenesis in vivo and in vitro.

Conclusions

Taken together, our data indicate that iMSC-sEV promote angiogenesis after ischemic stroke, potentially, by inhibiting autophagy, a process that is partially dependent on STAT3 activation.
A review of computational drug repositioning: strategies, approaches, opportunities, challenges, and directions
Authors: Jarada Tamer N. , Rokne Jon G. , Alhajj Reda
Published: July 2020

Drug repositioning is the process of identifying novel therapeutic potentials for existing drugs and discovering therapies for untreated diseases. Drug repositioning, therefore, plays an important role in optimizing the pre-clinical process of developing novel drugs by saving time and cost compared to the traditional de novo drug discovery processes. Since drug repositioning relies on data for existing drugs and diseases the enormous growth of publicly available large-scale biological, biomedical, and electronic health-related data along with the high-performance computing capabilities have accelerated the development of computational drug repositioning approaches. Multidisciplinary researchers and scientists have carried out numerous attempts, with different degrees of efficiency and success, to computationally study the potential of repositioning drugs to identify alternative drug indications. This study reviews recent advancements in the field of computational drug repositioning. First, we highlight different drug repositioning strategies and provide an overview of frequently used resources. Second, we summarize computational approaches that are extensively used in drug repositioning studies. Third, we present different computing and experimental models to validate computational methods. Fourth, we address prospective opportunities, including a few target areas. Finally, we discuss challenges and limitations encountered in computational drug repositioning and conclude with an outline of further research directions.
Using the complement of the cosine to compute trigonometric functions
Authors: Guerrero Martos David , Millán Calderón Alejandro , Juan Chico Jorge , Viejo Cortés Julian , Bellido Díaz Manuel J. , Ruiz-de-Clavijo Vazquez Paulino , Ostúa Arangüena Enrique
Published: July 2020

The computation of the sine and cosine functions is required in devices ranging from application-specific signal processors to general purpose floating-point units. Even in the latter case, the required functionality can be reduced to computing the sine and/or cosine of multiples of a constant angle. The latency of a sine/cosine generator can be reduced by using look-up tables. However, a direct implementation with look-up tables may be unfeasible if the input space is huge. In such a case, look-up tables with a number of entries lower than the size of the input space can be used indirectly. In previously published methods, the reduction in the number of table entries is obtained at the expense of increasing the table width and the computational cost. This paper introduces an alternative technique that makes it possible to reduce the size of the look-up tables as well as the required multiplications. The proposed technique can be used to implement sine/cosine generators of huge input space. It has been used to implement several twiddle factor generators in reconfigurable hardware and has enabled the number of look-up tables to be reduced by between 6 and 26% with respect to previous table-based techniques. Also, these implementations are about 50% faster than those based on Volder’s algorithm.
Gut microbiome composition differences among breeds impact feed efficiency in swine
Authors: Bergamaschi Matteo , Tiezzi Francesco , Howard Jeremy , Huang Yi Jian , Gray Kent A. , Schillebeeckx Constantino , McNulty Nathan P. , Maltecca Christian
Published: July 2020

Background

Feed efficiency is a crucial parameter in swine production, given both its economic and environmental impact. The gut microbiota plays an essential role in nutrient digestibility and is, therefore, likely to affect feed efficiency. This study aimed to characterize feed efficiency, fatness traits, and gut microbiome composition in three major breeds of domesticated swine and investigate a possible link between feed efficiency and gut microbiota composition.

Results

Average daily feed intake (ADFI), average daily gain (ADG), feed conversion ratio (FCR), residual feed intake (RFI), backfat, loin depth, and intramuscular fat of 615 pigs belonging to the Duroc (DR), Landrace (LR), and Large White (LW) breeds were measured. Gut microbiota composition was characterized by 16S rRNA gene sequencing. Orthogonal contrasts between paternal line (DR) and maternal lines (LR+LW) and between the two maternal lines (LR versus LW) were performed. Average daily feed intake and ADG were statistically different with DR having lower ADFI and ADG compared to LR and LW. Landrace and LW had a similar ADG and RFI, with higher ADFI and FCR for LW. Alpha diversity was higher in the fecal microbial communities of LR pigs than in those of DR and LW pigs for all time points considered. Duroc communities had significantly higher proportional representation of theCatenibacteriumandClostridiumgenera compared to LR and LW, while LR pigs had significantly higher proportions ofBacteroidesthan LW for all time points considered. Amplicon sequence variants from multiple genera (includingAnaerovibrio,Bacteroides,Blautia,Clostridium,Dorea,Eubacterium,Faecalibacterium,Lactobacillus,Oscillibacter, andRuminococcus) were found to be significantly associated with feed efficiency, regardless of the time point considered.

Conclusions

In this study, we characterized differences in the composition of the fecal microbiota of three commercially relevant breeds of swine, both over time and between breeds. Correlations between different microbiome compositions and feed efficiency were established. This suggests that the microbial community may contribute to shaping host productive parameters. Moreover, our study provides important insights into how the intestinal microbial community might influence host energy harvesting capacity. A deeper understanding of this process may allow us to modulate the gut microbiome in order to raise more efficient animals.
Saliva as a diagnostic specimen for detection of SARS-CoV-2 in suspected patients: a scoping review
Authors: Fakheran Omid , Dehghannejad Mandana , Khademi Abbasali
Published: July 2020

Background

From the begging months of 2020 a severe acute respiratory syndrome coronavirus (SARS-CoV-2, also called 2019-nCoV) caused a devastating global outbreak. At present, the diagnosis of coronavirus disease 2019 (COVID-19) is made through a nasopharyngeal swab based on reverse transcription polymerase chain reaction (RT-PCR) technique. However, some recent studies suggested the possible role of oral fluids and saliva in the detection of SARS-CoV-2. The purpose of this scoping review is evaluating the available evidence regarding the efficacy of saliva as a diagnostic specimen in COVID-19 patients.

Methods

A systematic literature review of six databases (PubMed, Scopus, The Cochrane Central Register of Controlled Trials [CENTRAL], Science Direct, Web of Science and Google scholar) was carried out without any restrictions on date of publication to identify the reliability of saliva as a diagnostic specimen for detection of SARS-CoV-2 in suspected patients.

Results

Nine eligible articles were included in this review based on our described method. All the included studies are based on clinical surveys among patients with confirmed SARS-CoV-2 infection. Most of studies included in this review, reported that there is no statistically significant difference between nasopharyngeal or sputum specimens and saliva samples regarding viral load.

Conclusions

Despite limitations of this study, the findings of this review suggest that the use of self-collected saliva as a non-invasive specimen has proper accuracy and reliability regarding detection of SARS-CoV-2 based on RT-PCR technique.
On the diet of Tycho Brahe and his wife: did they consume fish from stagnant pools?
Authors: van der Plicht Johannes , Kaupová Sylva Drtikolová , Velemínský Petr , Smolík Jiří , Kučera Jan , Kameník Jan , Havránek Vladimír , Brůžek Jaroslav , Vellev Jens , Rasmussen Kaare Lund
Published: July 2020

Radiocarbon dating has been performed on cortical femoral tissue samples from Tycho Brahe (1546–1601) and his wife Kirsten Barbara Jørgensdatter (1549–1604). No discernible reservoir effect has been observed in either skeleton. This combined with unusually high δ15N values and seemingly terrestrial δ13C values, makes us suggest that a large fraction of their protein intake came from freshwater fish raised in stagnant pools.
Precipitation is the dominant driver for bird species richness, phylogenetic and functional structure in university campuses in northern China
Authors: Liang Chenxia , Liu Jun , Pan Bin , Wang Na , Yang Jie , Yang Guisheng , Feng Gang
Published: July 2020

Background

Although urbanization is threatening biodiversity worldwide, the increasing green urban spaces could harbor relatively high biodiversity. Therefore, how to maintain the biodiversity in urban ecosystem is crucial for sustainable urban planning and management, especially in arid and semiarid regions with relatively fragile environment and low biodiversity. Here, for the first time we linked species richness, phylogenetic and functional structure of bird assemblages in university campuses in northern China with plant species richness, glacial-interglacial climate change, contemporary climate, and anthropogenic factors to compare their relative roles in shaping urban bird diversity.

Methods

Bird surveys were conducted in 20 university campuses across Inner Mongolia, China. Ordinary least squares models and simultaneous autoregressive models were used to assess the relationships between bird species richness, phylogenetic and functional structure with environmental factors. Structural equation models were used to capture the direct and indirect effects of these factors on the three components of bird diversity.

Results

Single-variable simultaneous autoregressive models showed that mean annual precipitation was consistently a significant driver for bird species richness, phylogenetic and functional structure. Meanwhile, mean annual temperature and plant species richness were also significant predictors for bird species richness.

Conclusions

This study suggests that campuses with warmer and wetter climate as well as more woody plant species could harbor more bird species. In addition, wetter campuses tended to sustain over-dispersed phylogenetic and functional structure. Our findings emphasize the dominant effect of precipitation on bird diversity distribution in this arid and semiarid region, even in the urban ecosystem.
Successful treatment of enterocutaneous fistula after esophagectomy with scopolamine ointment and negative pressure wound therapy: a case report
Authors: Suzuki Shigemasa , Aihara Ryusuke , Ooki Takashi , Matsumura Naoki , Wada Wataru , Mogi Akira , Hosouchi Yasuo , Nishida Yasuji , Sakai Makoto , Sohda Makoto , Saeki Hiroshi , Shirabe Ken
Published: July 2020

Background

Despite improved surgical techniques and perioperative management, anastomotic leakage (AL) after esophageal cancer surgery remains a potential complication. In most cases, spontaneous healing upon proper drainage is observed, but sometimes, AL results in intractable enterocutaneous fistulas. We here report a case of intractable enterocutaneous fistula caused by post-esophagectomy AL and successfully treated by scopolamine ointment and negative pressure wound therapy (NPWT).

Case presentation

A 77-year-old man underwent thoracoscopic subtotal esophagectomy with 3-field lymph node dissection, followed by gastric tube reconstruction through the posterior mediastinal route. On the 6th postoperative day, AL was identified, forming an enterocutaneous fistula. Initially, conservative treatment was performed, but the fistula failed to close. We hypothesized that the substantial amount of exudate might be hampering fistula closure. Scopolamine ointment was used to reduce the amount of fluid. NPWT was also initiated to promote wound healing. Approximately 3 weeks after the beginning of the treatment, the fistula closed; oral intake became possible, and the patient was discharged from the hospital without any symptoms.

Conclusions

The combination of scopolamine ointment and NPWT may be regarded as one effective treatment option for intractable enterocutaneous fistula due to AL after esophagectomy.
Total thoracic herniation of the liver: a case of delayed right-sided diaphragmatic hernia after blunt trauma
Authors: Kesavaramanujam Satish , Morell Michael C. , Harigovind Dhanush , Bhimmanapalli Chandana , Cassaro Sebastiano
Published: July 2020

Background

Traumatic diaphragmatic injuries (TDIs) are relatively uncommon and require surgical repair to prevent or address herniation. Three quarters of TDIs are due to blunt thoraco-abdominal trauma. In blunt TDIs, variable clinical presentations and frequent concurrent life-threatening injuries may hinder early recognition and treatment, leading to diagnostic delays, which may result in technically more challenging repairs. Right-sided blunt TDIs are much less common than left-sided ones, are difficult to visualize on imaging studies, are more frequently associated with other potentially lethal injuries, and tend to present more subtly, so that diagnostic delays are more likely.

Case presentation

We report the diagnosis and elective repair of a large right-sided traumatic diaphragmatic hernia resulting from a distant blunt abdominal injury, describing the techniques used to address the challenges presented by the chronic intrathoracic displacement of the entire liver with the gallbladder, as well as the right side of the colon and part of the duodenum.

Conclusions

Early diagnosis of right-sided TDIs can be especially elusive. The management of delayed diaphragmatic hernias can be challenging, but with meticulous planning and a flexible surgical approach, a repair can be achieved resulting in good recovery and low risk of recurrence.
Current imaging techniques for evaluation of fistula in ano: a review
Authors: Sharma Ashish , Yadav Priyanka , Sahu Manoranjan , Verma Ashish
Published: July 2020

Background

Fistula in ano is one of the common anorectal disorders which have a tendency to recur specially in complex cases usually due to missed or undetected sepsis at the time of examination or surgery. A correct identification of the primary source of crypt infection along with a complete understanding of the anatomical course of primary and secondary tracks and abscesses is a prerequisite for the successful management of fistula. Preoperative evaluation of fistula in ano using radio-imaging techniques provides a handy insight of fistula anatomy and helps in planning the appropriate treatment strategy. The objective of this article is to review the role of different radio-imaging techniques in the diagnosis and evaluation of fistula in ano along with their advantages and disadvantages over one another.

Main text

A comprehensive literature review was performed searching through the electronic databases as well as the standard textbooks of colorectal surgery. X-rays (plain radiographs and contrast fistulography), computed tomography (CT) scanning, anal endosonography, and magnetic resonance (MR) imaging are the modalities used for preoperative imaging of fistula in ano. Due to low accuracy, X-ray fistulography is not used now for fistula imaging. CT fistulography can be more accurate in cases associated with acute inflammations and abscesses and the fistulas related with inflammatory bowel disease. Anal endosonography and MRI are two of the mostly used and reliable imaging techniques for fistula in ano. Though the use of a 3D technology has improved the accuracy of anal endosonography, MRI is the preferred choice by many. However, various reports have depicted comparable accuracies for both MRI and anal endosonography showing both to be equally sensitive but MRI to be more specific. 3D endoanal ultrasound, on the other hand, is more rapid and can also be used intraoperatively to provide live imaging during surgical exploration.

Conclusion

Complex and recurrent fistula cases should undergo a preoperative imaging to reduce the chances of recurrence. MRI is recommended as the imaging modality of choice for such cases. 3D anal endosonography may however be a good option over MRI owing to its rapidity, availability, and potential of intraoperative assistance during surgery.
Gallstones in Egyptian infants and children: risk factors, complications and outcome: a single center experience
Authors: Enayet A. , Afifi R. A. , Mogahed E. A. , El-Raziky M. S. , Abdellatif M. A. K.
Published: July 2020

Background

The widespread use of abdominal ultrasonography in children documented increased detection rate of gallstones. The aim of this study was to assess the possible risk factors of gallstones and to detect the complication rate and outcome of the disease in Egyptian infants and children from a hepatologist perspective. This prospective study included 35 cases, with ultrasound-detected gallstones, who presented to the Pediatric Hepatology Unit from July 2015 to October 2017. All patients were initially evaluated by full history, general and abdominal examination, laboratory assessment, and ultrasound findings to detect possible risk factors of gallstones. Management approach was individualized for each patient according to his/her condition, and the patients were followed up at 3 months interval.

Results

The patients’ ages ranged from 3.5 months up to 17 years. The median age of gallstone detection was 2 years. Gallstones were symptomatic in 62.9% with abdominal pain in 51.4%. Complications in the form of choledocholithiasis were detected in 7 patients (20%). Laparoscopic cholecystectomy was done for 7 patients while conservative management was applied for 24 patients. Complete resolution occurred in 8.3% and partial resolution in 33.3%. Chronic hemolytic anemia was the most commonly identified risk factor for gallstones. Patients needed surgical intervention had significant higher serum cholesterol and LDL levels (P = 0.006 and P = 0.002 respectively).

Conclusion

Risk factors for gallstones could be identified in most of pediatric cases. Symptomatic presentation is common among the pediatric population. Conservative management is recommended for asymptomatic cases of gallstones in children. Laparoscopic cholecystectomy is a safe and recommended procedure for complicated and symptomatic cases of gallstones.
Study of serum and synovial fluid Dickkopf-1 levels in patients with primary osteoarthritis of the knee joint in correlation with disease activity and severity
Authors: Ibrahim Noha Hosni , Abdel-Monem Samia Mohammed , Elbarashy Abdel-Wahab S. E. , Elhussieny Heba A. W. , Elsayed Rasha A. H.
Published: July 2020

Background

Osteoarthritis (OA) is a typical complex degenerative articular ailment that shows focal cartilage loss, new bone formation with involvement of entire joint tissues. Dkk-1 assumes a job in controlling the pattern of bone repair and regeneration in both OA and RA. This study aimed to determine serum and synovial fluid levels of Dickkopf-1 (Dkk-1) in patients with primary OA of the knee joint and study their correlations with disease activity and severity. This study included 45 patients, 30 of them were diagnosed as primary knee OA. Fifteen rheumatoid arthritis patients as well as 15 healthy subjects were enrolled in the study as control groups, serum and synovial levels of Dkk-1 were estimated utilizing the ELISA technique.

Results

Serum levels of Dkk-1 were significantly higher in OA patients than healthy subjects (p < 0.001), although it was even significantly higher in RA patients than OA patients (p < 0.001). There was a highly significant decrease in the median synovial level of Dkk-1 in OA patients compared to the RA control group (p < 0.001). There was a highly statistically significant inverse correlation between circulating as well as synovial fluid Dkk-1 levels and radiological disease grading in knee OA (p < 0.001). There was a statistically significant decrease in serum levels of Dkk-1 in patients with severe OA (grade 3, 4) compared to those with mild OA (Grade 2) (p < 0.001).

Conclusion

Dkk-1 is an interesting marker that is related to articular disease .It could play an important role in decelerating the degenerative process of OA and can reflects radiographic severity of the disease as well.