bluuebunny/crossref_metadata_2025 huggingface dataset:
Targeted capture enrichment followed by NGS: development and validation of a single comprehensive NIPT for chromosomal aneuploidies, microdeletion syndromes and monogenic diseases
Authors: Koumbaris George , Achilleos Achilleas , Nicolaou Michalis , Loizides Charalambos , Tsangaras Kyriakos , Kypri Elena , Mina Petros , Sismani Carolina , Velissariou Voula , Christopoulou Georgia , Constantoulakis Pantelis , Manolakos Emmanouil , Papoulidis Ioannis , Stambouli Danai , Ioannides Marios , Patsalis Philippos
Published: November 2019

Background

Non-invasive prenatal testing (NIPT) has been widely adopted for the detection of fetal aneuploidies and microdeletion syndromes, nevertheless, limited clinical utilization has been reported for the non-invasive prenatal screening of monogenic diseases. In this study, we present the development and validation of a single comprehensive NIPT for prenatal screening of chromosomal aneuploidies, microdeletions and 50 autosomal recessive disorders associated with severe or moderate clinical phenotype.

Results

We employed a targeted capture enrichment technology powered by custom TArget Capture Sequences (TACS) and multi-engine bioinformatics analysis pipeline to develop and validate a novel NIPT test. This test was validated using 2033 cell-fee DNA (cfDNA) samples from maternal plasma of pregnant women referred for NIPT and paternal genomic DNA. Additionally, 200 amniotic fluid and CVS samples were used for validation purposes. All NIPT samples were correctly classified exhibiting 100% sensitivity (CI 89.7–100%) and 100% specificity (CI 99.8–100%) for chromosomal aneuploidies and microdeletions. Furthermore, 613 targeted causative mutations, of which 87 were unique, corresponding to 21 monogenic diseases, were identified. For the validation of the assay for prenatal diagnosis purposes, all aneuploidies, microdeletions and point mutations were correctly detected in all 200 amniotic fluid and CVS samples.

Conclusions

We present a NIPT for aneuploidies, microdeletions, and monogenic disorders. To our knowledge this is the first time that such a comprehensive NIPT is available for clinical implementation.
Postsynaptic density protein 95 (PSD-95) is transported by KIF5 to dendritic regions
Authors: Yoo Ki-Seo , Lee Kina , Oh Jun-Young , Lee Hyoeun , Park Hyungju , Park Young Seok , Kim Hyong Kyu
Published: November 2019

Postsynaptic density protein 95 (PSD-95) is a pivotal postsynaptic scaffolding protein in excitatory neurons. Although the transport and regulation of PSD-95 in synaptic regions is well understood, dendritic transport of PSD-95 before synaptic localization still remains to be clarified. To evaluate the role of KIF5, conventional kinesin, in the dendritic transport of PSD-95 protein, we expressed a transport defective form of KIF5A (ΔMD) that does not contain the N-terminal motor domain. Expression of ΔMD significantly decreased PSD-95 level in the dendrites. Consistently, KIF5 was associated with PSD-95 in in vitro and in vivo assays. This interaction was mediated by the C-terminal tail regions of KIF5A and the third PDZ domain of PSD-95. Additionally, the ADPDZ3 (the association domain of NMDA receptor and PDZ3 domain) expression significantly reduced the levels of PSD-95, glutamate receptor 1 (GluA1) in dendrites. The association between PSD-95 and KIF5A was dose-dependent on Staufen protein, suggesting that the Staufen plays a role as a regulatory role in the association. Taken together, our data suggest a new mechanism for dendritic transport of the AMPA receptor-PSD-95.
Pre-sternal thyroid swellings: a case of rare aberrant site recurrence and review of literature
Authors: Bains Lovenish , Bhatia Sushant , Kaushik Rohit , Jain Sudhir Kumar , Singh Chandra Bhushan , Mandal Shramana , Kaur Daljit
Published: November 2019

Background

Thyroid swellings enlarge caudally into the mediastinum behind the sternum. Pre-sternal swelling of thyroid origin is very rare. We present our case of pre-sternal thyroid swelling which was albeit a surprisingly rare site of papillary thyroid carcinoma recurrence and review of pre-sternal thyroid swellings reported till date.

Case summary

A 60 year old female presented with a painless, progressive swelling on the anterior part of the chest for the past 2 years. A 15 cm × 8 cm vertically aligned, non tender, well defined swelling was present on the pre-sternal region, with consistency ranging from soft to firm. The swelling was fixed to the underlying tissues and a fixed level IV lymph node was palpable on the right side. Ultrasonography revealed a large mass of 15 × 7 cm with multiple cystic areas. Fine needle aspiration cytology was inconclusive twice. Patient had undergone a total thyroidectomy for papillary carcinoma 10 years back. Computed tomography findings revealed a large 15 × 6.6 × 7 cm lobulated, pre-sternal, soft tissue lesion with solid & cystic components. The mass was infiltrating the right sided strap muscles and sternocleidomastoid. FNAC was inconclusive and thyroid scan could not pick up any activity in the mass. Henceforth a PET scan was done that showed increased FDG uptake by the lesion and the level IV lymph node. The patient underwent wide excision of the mass with right functional neck dissection, along with removal with both sternal head of sternocleido-mastoid, the strap muscles and the surrounding fascia. Histopathology confirmed papillary thyroid carcinoma. Patient received post-operative radioactive iodine ablation and is healthy with no recurrence up to 30 months of follow up.

Discussion

The mechanisms for pre-sternal thyroid swelling are not understood due to paucity of cases. The mechanisms proposed are invasion of strap muscles and cervical linea alba and tumor cells spread anterior to sternum, truly ectopic thyroid tissue, de novo carcinogenesis in the embryonal remnants like the thyro-thymic residues, sequestered thyroid tissue which grows later or migration of thyroid cells, incomplete clearance at the time of primary surgery or intraoperative seeding.

Conclusion

Pre-sternal region masses of thyroid origin are very rare. A proper work up, suspicion for thyroid mass and array of tests will be required to come to a provisional diagnosis. Since the masses reported in literature were primarily malignant, any such mass may be treated on lines of malignancy with radical surgery.
Chimeric antigen receptor T cell therapies for multiple myeloma
Authors: Wu Chao , Zhang Lina , Brockman Qierra R. , Zhan Fenghuang , Chen Lijuan
Published: November 2019

Multiple myeloma (MM) is the second most common hematologic malignancy and remains incurable despite the advent of numerous new drugs such as proteasome inhibitors (PIs), immunomodulatory agents (IMiDs), and monoclonal antibodies. There is an unmet need to develop novel therapies for refractory/relapsed MM. In the past few years, chimeric antigen receptor (CAR)-modified T cell therapy for MM has shown promising efficacy in preclinical and clinical studies. Furthermore, the toxicities of CAR-T cell therapy are manageable. This article summarizes recent developments of CAR-T therapy in MM, focusing on promising targets, new technologies, and new research areas. Additionally, a comprehensive overview of antigen selection is presented along with preliminary results and future directions of CAR-T therapy development.
Downregulation of class II phosphoinositide 3-kinase PI3K-C2β delays cell division and potentiates the effect of docetaxel on cancer cell growth
Authors: Cisse Ouma , Quraishi Muzthahid , Gulluni Federico , Guffanti Federica , Mavrommati Ioanna , Suthanthirakumaran Methushaa , Oh Lara C. R. , Schlatter Jessica N. , Sarvananthan Ambisha , Broggini Massimo , Hirsch Emilio , Falasca Marco , Maffucci Tania
Published: November 2019

Background

Alteration of signalling pathways regulating cell cycle progression is a common feature of cancer cells. Several drugs targeting distinct phases of the cell cycle have been developed but the inability of many of them to discriminate between normal and cancer cells has strongly limited their clinical potential because of their reduced efficacy at the concentrations used to limit adverse side effects. Mechanisms of resistance have also been described, further affecting their efficacy. Identification of novel targets that can potentiate the effect of these drugs or overcome drug resistance can provide a useful strategy to exploit the anti-cancer properties of these agents to their fullest.

Methods

The class II PI3K isoform PI3K-C2β was downregulated in prostate cancer PC3 cells and cervical cancer HeLa cells using selective siRNAs and the effect on cell growth was determined in the absence or presence of the microtubule-stabilizing agent/anti-cancer drug docetaxel. Mitosis progression was monitored by time-lapse microscopy. Clonogenic assays were performed to determine the ability of PC3 and HeLa cells to form colonies upon PI3K-C2β downregulation in the absence or presence of docetaxel. Cell multi-nucleation was assessed by immunofluorescence. Tumour growth in vivo was assessed using a xenograft model of PC3 cells upon PI3K-C2β downregulation and in combination with docetaxel.

Results

Downregulation of PI3K-C2β delays mitosis progression in PC3 and HeLa cells, resulting in reduced ability to form colonies in clonogenic assays in vitro. Compared to control cells, PC3 cells lacking PI3K-C2β form smaller and more compact colonies in vitro and they form tumours more slowly in vivo in the first weeks after cells implant. Stable and transient PI3K-C2β downregulation potentiates the effect of low concentrations of docetaxel on cancer cell growth. Combination of PI3K-C2β downregulation and docetaxel almost completely prevents colonies formation in clonogenic assays in vitro and strongly inhibits tumour growth in vivo.

Conclusions

These data reveal a novel role for the class II PI3K PI3K-C2β during mitosis progression. Furthermore, data indicate that blockade of PI3K-C2β might represent a novel strategy to potentiate the effect of docetaxel on cancer cell growth.
Derivation and validation of an easy-to-compute trauma score that improves prognostication of mortality or the Trauma Rating Index in Age, Glasgow Coma Scale, Respiratory rate and Systolic blood pressure (TRIAGES) score
Authors: Shiraishi Atsushi , Otomo Yasuhiro , Yoshikawa Shunsuke , Morishita Koji , Roberts Ian , Matsui Hiroki
Published: November 2019

Background

Multiple trauma scores have been developed and validated, including the Revised Trauma Score (RTS) and the Mechanism, Glasgow Coma Scale, Age, and Arterial Pressure (MGAP) score. However, these scores are complex to calculate or have low prognostic abilities for trauma mortality. Therefore, we aimed to develop and validate a trauma score that is easier to calculate and more accurate than the RTS and the MGAP score.

Methods

The study was a retrospective prognostic study. Data from patients registered in the Japan Trauma Databank (JTDB) were dichotomized into derivation and validation cohorts. Patients’ data from the Clinical Randomisation of an Antifibrinolytic in Significant Haemorrhage-2 (CRASH-2) trial were assigned to another validation cohort. We obtained age and physiological variables at baseline, created ordinal variables from continuous variables, and defined integer weighting coefficients. Score performance to predict all-cause in-hospital death was assessed using the area under the curve in receiver operating characteristics (AUROC) analyses.

Results

Based on the JTDB derivation cohort (n = 99,867 with 12.5% mortality), the novel score ranged from 0 to 14 points, including 0–2 points for age, 0–6 points for the Glasgow Coma Scale, 0–4 points for systolic blood pressure, and 0–2 points for respiratory rate. The AUROC of the novel score was 0.932 for the JTDB validation cohort (n = 76,762 with 10.1% mortality) and 0.814 for the CRASH-2 cohort (n = 19,740 with 14.6% mortality), which was superior to RTS (0.907 and 0.808, respectively) and MGAP score (0.918 and 0.774, respectively) results.

Conclusions

We report an easy-to-use trauma score with better prognostication ability for in-hospital mortality compared to the RTS and MGAP score. Further studies to test clinical applicability of the novel score are warranted.
Why physiology will continue to guide the choice between balanced crystalloids and normal saline: a systematic review and meta-analysis
Authors: Zwager Charlotte L. , Tuinman Pieter Roel , de Grooth Harm-Jan , Kooter Jos , Ket Hans , Fleuren Lucas M. , Elbers Paul W. G.
Published: November 2019

Background

Crystalloids are the most frequently prescribed drugs in intensive care medicine and emergency medicine. Thus, even small differences in outcome may have major implications, and therefore, the choice between balanced crystalloids versus normal saline continues to be debated. We examined to what extent the currently accrued information size from completed and ongoing trials on the subject allow intensivists and emergency physicians to choose the right fluid for their patients.

Methods

Systematic review and meta-analysis with random effects inverse variance model. Published randomized controlled trials enrolling adult patients to compare balanced crystalloids versus normal saline in the setting of intensive care medicine or emergency medicine were included. The main outcome was mortality at the longest follow-up, and secondary outcomes were moderate to severe acute kidney injury (AKI) and initiation of renal replacement therapy (RRT). Trial sequential analyses (TSA) were performed, and risk of bias and overall quality of evidence were assessed. Additionally, previously published meta-analyses, trial sequential analyses and ongoing large trials were analysed for included studies, required information size calculations and the assumptions underlying those calculations.

Results

Nine studies (n = 32,777) were included. Of those, eight had data available on mortality, seven on AKI and six on RRT. Meta-analysis showed no significant differences between balanced crystalloids versus normal saline for mortality (P = 0.33), the incidence of moderate to severe AKI (P = 0.37) or initiation of RRT (P = 0.29). Quality of evidence was low to very low. Analysis of previous meta-analyses and ongoing trials showed large differences in calculated required versus accrued information sizes and assumptions underlying those. TSA revealed the need for extremely large trials based on our realistic and clinically relevant assumptions on relative risk reduction and baseline mortality.

Conclusions

Our meta-analysis could not find significant differences between balanced crystalloids and normal saline on mortality at the longest follow-up, moderate to severe AKI or new RRT. Currently accrued information size is smaller, and the required information size is larger than previously anticipated. Therefore, completed and ongoing trials on the topic may fail to provide adequate guidance for choosing the right crystalloid. Thus, physiology will continue to play an important role for individualizing this choice.
Evaluation of honey-baited FTA cards in combination with different mosquito traps in an area of low arbovirus prevalence
Authors: Wipf Nadja C. , Guidi Valeria , Tonolla Mauro , Ruinelli Michela , Müller Pie , Engler Olivier
Published: November 2019

Background

The threat of mosquito-borne diseases is increasing in continental Europe as demonstrated by several autochthonous chikungunya, dengue and West Nile virus outbreaks. In Switzerland, despite the presence of competent vectors, routine surveillance of arboviruses in mosquitoes is not being carried out, mainly due to the high costs associated with the need of a constant cold chain and laborious processing of thousands of mosquitoes. An alternative approach is using honey-baited nucleic acid preserving cards (FTA cards) to collect mosquito saliva that may be analysed for arboviruses. Here, we evaluate whether FTA cards could be used to detect potentially emerging viruses in an area of low virus prevalence in combination with an effective mosquito trap.

Methods

In a field trial in southern Switzerland we measured side-by-side the efficacy of the BG-Sentinel 2, the BG-GAT and the Box gravid trap to catchAedesandCulexmosquitoes in combination with honey-baited FTA cards during 80 trapping sessions of 48 hours. We then screened both the mosquitoes and the FTA cards for the presence of arboviruses using reverse-transcription PCR. The efficacy of the compared trap types was evaluated using generalized linear mixed models.

Results

The Box gravid trap collected over 11 times more mosquitoes than the BG-GAT and BG-Sentinel 2 trap. On average 75.9% of the specimens fed on the honey-bait with no significant difference in feeding rates between the three trap types. From the total of 1401 collected mosquitoes, we screened 507Aedesand 500Culexfemales for the presence of arboviruses. A pool of sixCx. pipiens/Cx. torrentiummosquitoes and also the FTA card from the same Box gravid trap were positive for Usutu virus. Remarkably, only two of the sixCulexmosquitoes fed on the honey-bait, emphasising the high sensitivity of the method. In addition, twoAe. albopictuscollections but no FTA cards were positive for mosquito-only flaviviruses.

Conclusions

Based on our results we conclude that honey-baited FTA cards, in combination with the Box gravid trap, are an effective method for arbovirus surveillance in areas of low prevalence, particularly where resources are limited for preservation and screening of individual mosquitoes.
Asthma and elevation of anti-citrullinated protein antibodies prior to the onset of rheumatoid arthritis
Authors: Zaccardelli Alessandra , Liu Xinyi , Ford Julia A. , Cui Jing , Lu Bing , Chu Su H. , Schur Peter H. , Speyer Cameron B. , Costenbader Karen H. , Robinson William H. , Sokolove Jeremy , Karlson Elizabeth W. , Camargo Carlos A. , Sparks Jeffrey A.
Published: November 2019

Background

Anti-citrullinated protein antibodies (ACPA) are central to rheumatoid arthritis (RA) pathogenesis and may develop at inflamed mucosa. We investigated whether asthma, a disease of airway mucosal inflammation, was associated with elevated ACPA before RA diagnosis.

Methods

We performed a nested case-control study among women in two prospective cohorts, the Nurses’ Health Study (NHS; 1976–2014) and NHSII (1989–2015). Blood was obtained on a subset (NHS: 1989–1990; NHSII: 1996–1999). Cases met 1987 ACR or 2010 ACR/EULAR RA criteria by medical record review and were classified as seropositive (ACPA+ or rheumatoid factor positivity) or seronegative by clinical laboratory testing at diagnosis. We identified RA cases with blood drawn before the date of RA diagnosis (index date), matching each to three controls by age, cohort, year, time from blood draw to index date, and menopause. Pre-RA ACPA elevation for cases was defined as >99th percentile of the control distribution on a research assay composed of autoantibodies targeting citrullinated protein epitopes or positivity on the second-generation commercial assay for cyclic citrullinated peptide. Asthma status and covariates were obtained through biennial questionnaires before blood draw. Conditional logistic regression estimated ORs and 95%CIs for RA by pre-RA ACPA and clinical serostatus, adjusted for matching factors, smoking pack-years, passive smoking, and body mass index (BMI).

Results

We identified 284 incident RA cases and 849 matched controls; mean age at the index date was 61.2 years (SD 10.1). Blood was drawn 9.7 years (mean; SD 5.8) before the index date. We identified 96 (33.8%) RA cases with elevated pre-RA ACPA. At blood draw, 17.7% of pre-RA ACPA+ cases and 6.3% of matched controls (p = 0.0008) reported clinician-diagnosed asthma. After adjusting for matching factors, smoking pack-years, passive smoking, and BMI, asthma was significantly associated with pre-RA ACPA+ RA (OR 3.57, 95%CI 1.58,8.04). Asthma was not associated with overall RA (OR 1.45, 95%CI 0.91,2.31), but was significantly associated with seropositive RA (OR 1.79, 95%CI 1.01,3.18).

Conclusions

Asthma was strongly associated with ACPA elevation in blood drawn prior to RA diagnosis, independent of smoking. Chronic mucosal airway inflammation may contribute to ACPA development and RA pathogenesis.
Searching for simple rules in Pseudomonas aeruginosa biofilm formation
Authors: Deveaux William , Selvarajoo Kumar
Published: November 2019

Objective

Living cells display complex and non-linear behaviors, especially when posed to environmental threats. Here, to understand the self-organizing cooperative behavior of a microorganism Pseudomonas aeruginosa, we developed a discrete spatiotemporal cellular automata model based on simple physical rules, similar to Conway’s game of life.

Results

The time evolution model simulations were experimentally verified for P. aeruginosa biofilm for both control and antibiotic azithromycin (AZM) treated condition. Our model suggests that AZM regulates the single cell motility, thereby resulting in delayed, but not abolished, biofilm formation. In addition, the model highlights the importance of reproduction by cell to cell interaction is key for biofilm formation. Overall, this work highlights another example where biological evolutionary complexity may be interpreted using rules taken from theoretical disciplines.
The factors present in regenerating muscles impact bone marrow-derived mesenchymal stromal/stem cell fusion with myoblasts
Authors: Kasprzycka Paulina , Archacka Karolina , Kowalski Kamil , Mierzejewski Bartosz , Zimowska Małgorzata , Grabowska Iwona , Piotrowski Mariusz , Rafałko Milena , Ryżko Agata , Irhashava Aliksandra , Senderowski Kamil , Gołąbek Magdalena , Stremińska Władysława , Jańczyk-Ilach Katarzyna , Koblowska Marta , Iwanicka-Nowicka Roksana , Fogtman Anna , Janowski Mirosław , Walczak Piotr , Ciemerych Maria A. , Brzoska Edyta
Published: November 2019

Background

Satellite cells, a population of unipotent stem cells attached to muscle fibers, determine the excellent regenerative capability of injured skeletal muscles. Myogenic potential is also exhibited by other cell populations, which exist in the skeletal muscles or come from other niches. Mesenchymal stromal/stem cells inhabiting the bone marrow do not spontaneously differentiate into muscle cells, but there is some evidence that they are capable to follow the myogenic program and/or fuse with myoblasts.

Methods

In the present study we analyzed whether IGF-1, IL-4, IL-6, and SDF-1 could impact human and porcine bone marrow-derived mesenchymal stromal/stem cells (hBM-MSCs and pBM-MSCs) and induce expression of myogenic regulatory factors, skeletal muscle-specific structural, and adhesion proteins. Moreover, we investigated whether these factors could induce both types of BM-MSCs to fuse with myoblasts. IGF-1, IL-4, IL-6, and SDF-1 were selected on the basis of their role in embryonic myogenesis as well as skeletal muscle regeneration.

Results

We found that hBM-MSCs and pBM-MSCs cultured in vitro in the presence of IGF-1, IL-4, IL-6, or SDF-1 did not upregulate myogenic regulatory factors. Consequently, we confirmed the lack of their naïve myogenic potential. However, we noticed that IL-4 and IL-6 impacted proliferation and IL-4, IL-6, and SDF-1 improved migration of hBM-MSCs. IL-4 treatment resulted in the significant increase in the level of mRNA encoding CD9, NCAM, VCAM, and m-cadherin, i.e., proteins engaged in cell fusion during myotube formation. Additionally, the CD9 expression level was also driven by IGF-1 treatment. Furthermore, the pre-treatment of hBM-MSCs either with IGF-1, IL-4, or SDF-1 and treatment of pBM-MSCs either with IGF-1 or IL-4 increased the efficacy of hybrid myotube formation between these cells and C2C12 myoblasts.

Conclusions

To conclude, our study revealed that treatment with IGF-1, IL-4, IL-6, or SDF-1 affects BM-MSC interaction with myoblasts; however, it does not directly promote myogenic differentiation of these cells.
Randomized SMILES strings improve the quality of molecular generative models
Authors: Arús-Pous Josep , Johansson Simon Viet , Prykhodko Oleksii , Bjerrum Esben Jannik , Tyrchan Christian , Reymond Jean-Louis , Chen Hongming , Engkvist Ola
Published: November 2019

Recurrent Neural Networks (RNNs) trained with a set of molecules represented as unique (canonical) SMILES strings, have shown the capacity to create large chemical spaces of valid and meaningful structures. Herein we perform an extensive benchmark on models trained with subsets of GDB-13 of different sizes (1 million, 10,000 and 1000), with different SMILES variants (canonical, randomized and DeepSMILES), with two different recurrent cell types (LSTM and GRU) and with different hyperparameter combinations. To guide the benchmarks new metrics were developed that define how well a model has generalized the training set. The generated chemical space is evaluated with respect to its uniformity, closedness and completeness. Results show that models that use LSTM cells trained with 1 million randomized SMILES, a non-unique molecular string representation, are able to generalize to larger chemical spaces than the other approaches and they represent more accurately the target chemical space. Specifically, a model was trained with randomized SMILES that was able to generate almost all molecules from GDB-13 with a quasi-uniform probability. Models trained with smaller samples show an even bigger improvement when trained with randomized SMILES models. Additionally, models were trained on molecules obtained from ChEMBL and illustrate again that training with randomized SMILES lead to models having a better representation of the drug-like chemical space. Namely, the model trained with randomized SMILES was able to generate at least double the amount of unique molecules with the same distribution of properties comparing to one trained with canonical SMILES.
Antibacterial activity of Bacillus species-derived surfactin on Brachyspira hyodysenteriae and Clostridium perfringens
Authors: Horng Yi-Bing , Yu Yu-Hsiang , Dybus Andrzej , Hsiao Felix Shih-Hsiang , Cheng Yeong-Hsiang
Published: November 2019

Swine dysentery and necrotic enteritis are a bane to animal husbandry worldwide. Some countries have already banned the use of antibiotics as growth promoters in animal production. Surfactin is a potential alternative to antibiotics and antibacterial agents. However, the antibacterial activity of Bacillus species-derived surfactin on Brachyspira hyodysenteriae and Clostridium perfringens are still poorly understood. In the current study, the antibacterial effects of surfactin produced from Bacillus subtilis and Bacillus licheniformis on B. hyodysenteriae and C. perfringens were evaluated. Results showed that multiple surfactin isoforms were detected in B. subtilis, while only one surfactin isoform was detected in B. licheniformis fermented products. The surfactin produced from B. subtilis exhibited significant antibacterial activity against B. hyodysenteriae compared with surfactin produced from B. licheniformis. B. subtilis-derived surfactin could inhibit bacterial growth and disrupt the morphology of B. hyodysenteriae. Furthermore, the surfactin produced from B. subtilis have the highest activity against C. perfringens growth. In contrast, B. licheniformis fermented product-derived surfactin had a strong bacterial killing activity against C. perfringens compared with surfactin produced from B. subtilis. These results together suggest that Bacillus species-derived surfactin have potential for development as feed additives and use as a possible substitute for antibiotics to prevent B. hyodysenteriae and C. perfringens-associated disease in the animal industry.
Soil microbial communities of Japanese apricot (Prunus mume) orchard under organic and conventional management
Authors: Cho Hyeon Ji , Lee Young Han , Choi Si-Lim , Seo Dong Cheol , Min Sung Ran , Heo Jae-Young
Published: November 2019

Organic farming has positive effects on soil microbial population, process, and activity. To examine effects of two different management methods (organic farming vs. conventional farming) on the cultivation of Japanese apricot, contents of fatty acid methyl ester (FAME), total glomalin, and soil chemical properties were analyzed and compared. The organic farming practice resulted in significantly higher contents of organic matter, total FAME, total bacteria, Gram-negative bacteria, arbuscular mycorrhizal fungi, and total glomalin than the conventional farming practice. Soil organic matter showed positive correlation with contents of soil microbial biomass, total bacteria, total glomalin, Gram-positive bacteria, Gram-negative bacteria, actinomycetes, and arbuscular mycorrhizal fungi. In 2018, the organic farming practice resulted in lower ratios of cy17:0 and 16:1ω7c than the conventional farming practice, indicating that microbial stress was reduced by the input of organic fertilizer into soil. Based on principal component analyses (PCA) of soil microbial communities, ratios of cy17:0 to 16:1ω7c in orchid soil can be used as microbial indicators to distinguish organically farmed orchard soil from conventionally farmed orchard soil.
Comparison of the adhesive joints’ strength of the similar and dissimilar systems of metal alloy/polymer composite
Authors: Rudawska Anna
Published: November 2019

The aim of the present article is to compare the strength of the adhesive lap joints of the selected materials used in aviation. The joints were made in the similar and dissimilar systems with the use of three epoxy adhesives. Three different adherends were used: the EN AW-7075 aluminium alloy, the aramid-epoxy composite and the carbon-epoxy composite. Three adhesive compounds based on the Epidian 53 epoxy resin and three types of curing agents: two amine curing agents—Z1 (triethylenetetramine curing agent) and IDA, and one polyamide curing agent—PAC (polyaminoamide C) were used to make the adhesive joints. Three variants of similar joints and two variants of dissimilar joints were prepared for the tests. The shear strength was defined according to the ISO 4587 standard, with the use of Zwick/Roell 150 testing machine. In addition, the joined materials’ surface roughness was measured. Based on the strength test’s results, it was observed that the highest strength was obtained by the adhesive joints made with the Epidian 53/PAC/100:80 adhesive compound and that, in the majority of cases; similar joints show higher strength.
An investigation of solar flare effects on equatorial ionosphere and thermosphere using co-ordinated measurements
Authors: Sumod S. G. , Pant Tarun Kumar
Published: November 2019

The response of equatorial ionosphere–thermosphere system to the X3.8 solar flare of January 17, 2005 has been studied using the coordinated measurements of GPS-derived Total Electron Content (TEC), OI 630.0 nm dayglow and magnetic field measurements over a dip equatorial station Trivandrum (8.5° N, 77° E, dip 0.5° N), in India. It has been observed that Equatorial Electrojet (EEJ) as inferred using the ground-based magnetometers and GPS-derived TEC measurements show prompt enhancements during the peak flare, as expected. Interestingly, the temporal evolution of TEC at different latitudes revealed that the X3.8 class flare produced significant weakening of the plasma fountain and hence in the Equatorial Ionization Anomaly (EIA). Furthermore, the response of OI 630.0 nm dayglow during the flare is found to be strongly affected by the prevailing electrodynamics. The plausible physical mechanism for these effects is discussed in context of the current understanding of the neutral and electrodynamical coupling processes.
Measuring energy, macro and micronutrient intake in UK children and adolescents: a comparison of validated dietary assessment tools
Authors: Bush Linda A. , Hutchinson Jayne , Hooson Jozef , Warthon-Medina Marisol , Hancock Neil , Greathead Katharine , Knowles Bethany , Vargas-Garcia Elisa J. , Gibson Lauren E. , Margetts Barrie , Robinson Sian , Ness Andy , Alwan Nisreen A. , Wark Petra A. , Roe Mark , Finglas Paul , Steer Toni , Page Polly , Johnson Laura , Roberts Katharine , Amoutzopoulos Birdem , Greenwood Darren C. , Cade Janet E.
Published: November 2019

Background

Measuring dietary intake in children and adolescents can be challenging due to misreporting, difficulties in establishing portion size and reliance on recording dietary data via proxy reporters. The aim of this review was to present results from a recent systematic review of reviews reporting and comparing validated dietary assessment tools used in younger populations in the UK.

Methods

Validation data for dietary assessment tools used in younger populations (≤18 years) were extracted and summarised using results from a systematic review of reviews of validated dietary assessment tools. Mean differences and Bland-Altman limits of agreement (LOA) between the test and reference tool were extracted or calculated and compared for energy, macronutrients and micronutrients.

Results

Seventeen studies which reported validation of 14 dietary assessment tools (DATs) were identified with relevant nutrition information. The most commonly validated nutrients were energy, carbohydrate, protein, fat, calcium, iron, folate and vitamin C. There were no validated DATs reporting assessment of zinc, iodine or selenium intake. The most frequently used reference method was the weighed food diary, followed by doubly labelled water and 24 h recall. Summary plots were created to facilitate comparison between tools. On average, the test tools reported higher mean intakes than the reference methods with some studies consistently reporting wide LOA. Out of the 14 DATs, absolute values for LOA and mean difference were obtained for 11 DATs for EI. From the 24 validation results assessing EI, 16 (67%) reported higher mean intakes than the reference. Of the seven (29%) validation studies using doubly labelled water (DLW) as the reference, results for the test DATs were not substantially better or worse than those using other reference measures. Further information on the studies from this review is available on the www.nutritools.org website.

Conclusions

Validated dietary assessment tools for use with children and adolescents in the UK have been identified and compared. Whilst tools are generally validated for macronutrient intakes, micronutrients are poorly evaluated. Validation studies that include estimates of zinc, selenium, dietary fibre, sugars and sodium are needed.
Developing a competency taxonomy for teacher design knowledge in technology-enhanced learning environments: a literature review
Authors: Kim Mi Song
Published: November 2019

Recent research in technology-enhanced learning environments has indicated the need to redefine the role of teachers as designers. This supports successful learners better able to adapt to twenty-first century education, in particular STEM education. However, such a repositioning of teaching as a design science challenges teachers to reconceptualize educational practice as an act of design, not in the artistic meaning of the word. Our recent research finding also indicated that teacher design knowledge (TDK) processes are often invisible to both the teacher educators and the teachers. To respond to these challenges, this paper will define TDK for STEM teachers by making TDK visible in the form of a TDK competency taxonomy. A systematic literature review was conducted to identify the characteristics of teaching practices in technology-enhanced learning environments. This TDK competency taxonomy consists of four main categories drawing on existing literature on teacher design work and teacher instructional design: data practice, design practice, knowledge creation practice, and professional teaching practice. The implications of these findings were discussed.
Individualised prediction of psychosis in individuals meeting at-risk mental state (ARMS) criteria: protocol for a systematic review of clinical prediction models
Authors: Bonnett Laura J. , Varese Filippo , Smith Catrin Tudur , Flores Allan , Yung Alison R.
Published: November 2019

Background

Psychotic disorders affect about 3% of the population worldwide and are associated with high personal, social and economic costs. They tend to have their first onset in adolescence. Increasing emphasis has been placed on early intervention to detect illness and minimise disability. In the late 1990s, criteria were developed to identify individuals at high risk for psychotic disorder. These are known as the at-risk mental state (ARMS) criteria. While ARMS individuals have a risk of psychosis much greater than the general population, most individuals meeting the ARMS criteria will not develop psychosis. Despite this, the National Institute for Health and Care Excellence recommends cognitive behavioural therapy (CBT) for all ARMS people.

Clinical prediction models that combine multiple patient characteristics to predict individual outcome risk may facilitate identification of patients who would benefit from CBT and conversely those that would benefit from less costly and less intensive regular mental state monitoring. The study will systematically review the evidence on clinical prediction models aimed at making individualised predictions for the transition to psychosis.

Methods

Database searches will be conducted on PsycINFO, Medline, EMBASE and CINAHL. Reference lists and subject experts will be utilised. No language restrictions will be placed on publications, but searches will be restricted to 1994 onwards, the initial year of the first prospective study using ARMS criteria. Studies of any design will be included if they examined, in ARMS patients, whether more than one factor in combination is associated with the risk of transition to psychosis. Study quality will be assessed using the prediction model risk of bias assessment tool (PROBAST). Clinical prediction models will be summarised qualitatively, and if tested in multiple validation studies, their predictive performance will be summarised using a random-effects meta-analysis model.

Discussion

The results of the review will identify prediction models for the risk of transition to psychosis. These will be informative for clinicians currently treating ARMS patients and considering potential preventive interventions. The conclusions of the review will also inform the possible update and external validation of prediction models and clinical prediction rules to identify those at high or low risk of transition to psychosis.

Trial registration

The review has been registered with PROSPERO (CRD42018108488).
Business ecosystem modeling- the hybrid of system modeling and ecological modeling: an application of the smart grid
Authors: Ma Zheng
Published: November 2019

Business ecosystem is popularly used to investigate a complex social system with the business perspective, and particularly contributes to the understanding of actors and their relations in the innovation research. However, the aspect of business ecosystem modeling is limited discussed in the literature, although the importance has emerged significantly in recent years due to the emphasis on cross-disciplinary research and digitalization with artificial intelligence. Therefore, this paper proposes a framework for business ecosystem modeling with the discussion of system engineering and ecological modeling. The domain of smart grid is selected to demonstrate how system engineering, especially standards and ontologies contribute to the business ecosystem modeling. The proposed framework of the business ecosystem modeling includes three parts and nine stages that combines theories from system engineering, ecology, and business ecosystem. Part I-Business ecosystem architecture development includes four stages which aims to identify a target business ecosystem and its elements (actors, roles, and interactions). Part II-Factor analysis includes two stages to identify potential changes (and the dimensions of the changes) in the ecosystem. Part III- Ecosystem simulation and reconfiguration aims to use simulations to investigate the transition of an ecosystem and the re-configurated ecosystem. The framework not only provides a systematic approach for modeling a business ecosystem but also provides a methodological foundation for research on the aspect of complex systems in the business ecosystem field.
Recent advances in ion sensing with conducting polymers
Authors: Sethumadhavan Vithyasaahar , Rudd Sam , Switalska Eliza , Zuber Kamil , Teasdale Peter , Evans Drew
Published: November 2019

Ions are present throughout our environment—from biological systems to agriculture and beyond. Many important processes and mechanisms are driven by their presence and their relative concentration. In order to study, understand and/or control these, it is important to know what ions are present and in what concentration—highlighting the importance of ion sensing. Materials that show specific ion interaction with a commensurate change in measurable properties are the key components of ion sensing. One such type are conducting polymers. Conducting polymers are referred to as ‘active’ because they show observable changes in their electrical and optical (and other) properties in response to changing levels of doping with ions. For example, p-type conducting polymers such as poly(3,4-ethylenedioxythiophene) and polypyrrole, can transition from semi-conducting to metallic in response to increasing levels of anions inserted into their structure. Under certain circumstances, conducting polymers also interact with cations—showing their utility in sensing. Herein, recent advances in conducting polymers will be reviewed in the context of sensing ions. The main scope of this review is to critically evaluate our current understanding of ion interactions with conducting polymers and explore how these novel materials can contribute to improving our ion-sensing capabilities.
Connecting theory and practice in teacher education: English-as-a-foreign-language pre-service teachers’ perceptions of practicum experience
Authors: Yin Judy
Published: November 2019

The present study explores the perceptions of pre-service teachers regarding their experiences in the university teacher-training course during the practicum. In particular, the study focuses on how the pre-service teachers perceived the effects of the university course, as they tried to connect theory and practice during the practicum. A total of 15 participants enrolled in the methodology course for teaching speaking attended a 4-week practicum in secondary schools. They recorded their reflections on their teaching experiences in their reflective journals and they were interviewed after the practicum. The results of the study showed that the university course prepared them the fundamental skills to prepare for lessons and reflect on their teaching practice. However, the course failed to prepare them adequately to cope with the realities of the classroom context, as the university course only provided them with an idealistic view of the classroom. The implication of the study suggests ways to better connect university courses with the actual classroom practices to provide pre-service teachers the maximum support to practicalize their knowledge during the practicum.
Right ventricular 2D speckle-tracking echocardiography in children with osteosarcoma under chemotherapy
Authors: Khairat Ibtsam , Khalfallah Mohamed , Shaban Aliaa , Farag Ibrahim Abu , Elkady Asmaa
Published: November 2019

Background

Cardiotoxicity from anthracyclin chemotherapy is a leading cause of death in patients with cancer. Therefore, left ventricular (LV) function is routinely assessed during protocol to detect cardiotoxicity; however, animal studies suggest that right ventricular (RV) function may be also impaired. So, our objective was to investigate the incidence of RV dysfunction in children with osteosarcoma receiving anthracyclines and to highlight the role of 2D STE in early detection of RV dysfunction.

Results

RV function was affected by anthacyclines through direct cardiotoxic effect on RV myocardium without simultaneous derangement of LV function. Furthermore, there is a direct proportion between the incidence of RV dysfunction and the cumulative dose of anthracyclines. At the first echo follow-up at 10th week, 7 patients had impaired RV GLS in comparison to baseline study. At 20th week, the number of patients with impaired RV strain increased to 10. At 29th week, it reaches 12 patients. This effect was early detected by RV 2DSTE before adversely affecting TAPSE and FAC. The incidence of RV dysfunction from anthracyclines was around 12%, and the recovery rate was around 8% in 3 months after completion of chemotherapy.

Conclusion

RV 2DSTE is the best modality to detect early affection of RV function in comparison with other modalities. RV function decreases early even before derangement of LV function. Accordingly, it should be assessed separately in all patients who received anthracyclines even without evident LV affection.
Detection of positively remodeled coronary artery lesions by multislice CT and its impact on cardiovascular future events
Authors: Galal Haitham , Rashid Tarek , Alghonaimy Wesam , Kamal Diaa
Published: November 2019

Background

Positive arterial remodeling may be a characteristic of early proliferative lesions. The study was done to identify the different morphological characteristics of the positively remodeled coronary lesions, and causing non-significant arterial stenosis, as detected by multislice computed tomography coronary angiography (MSCT CA) and its predictors of cardiovascular clinical events at 90-day follow-up. The study included 55 patients who were candidate for MSCT CA and found to have a single-vessel disease with less than 70% stenosis positively remodeled lesions. The most expansive or solitary lesion was selected for each patient. Positive remodeling defined as remodeling index (RI) > 1.05. We followed the patients clinically for 90 days.

Results

Twenty-four patients had a history of acute coronary syndrome at initial presentation with normal LV systolic function for all studied patients. Dyslipidemia was found in 37 patients (67.3%) while diabetes was found in 29 patients (52.7%). The majority of the lesions were found in the proximal LAD (43.6%). The mean calculated remodeling index was 1.41 ± 0.25. At the end of 90 days, 25 patients had clinical events in the form of unstable coronary syndromes, coronary interventions, or coronary angiography related to the index lesion. The predictors of clinical events were duration of DM, higher degree of luminal narrowing, calculated wall/lumen area percentage, plaque burden, plaque-specific calcification, and total calcium score at remodeling site as well as a lower percentage of low-attenuation plaque area. The mean calculated wall/lumen area percentage was 263.72 ± 122.71%. A cut-off value of > 226% was found a predictor for clinical events. The mean plaque burden percentage was 69.72 ± 9.71%, a value of > 69% was found a predictor for clinical events. Both values had a sensitivity of 68% and specificity of 86.6% and PPV of 81%. Positively remodeled lesions with a high RI > 1.4 were correlated with patients who had acute coronary syndrome on their initial presentation.

Conclusion

Different morphological characteristics of positively remodeled non-occlusive atherosclerotic plaques as detected by multislice CT coronary angiography may be good potential predictors of future cardiovascular events.