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Deep learning based evaluation of the nightly behaviour of African ungulates in zoos
Max Hahn-Klimroth
Tobias Kapetanopoulos

Max Hahn-Klimroth

and 3 more

January 13, 2021
1. The description and analysis of animal behaviour over long periods of time is one of the most important challenges in ecology. However, most of these studies are limited due to the time and cost required by human observers. The collection of data via video recordings allows observation periods to be extended. However, their evaluation by human observers is very time-consuming. Progress in automated evaluation, using suitable deep learning methods, seems to be a forwardlooking approach to analyse even large amounts of video data in an adequate time frame. 2. In this study we present amulti-step convolutional neural network system for detecting animal behaviour states, which works with high accuracy. An important aspect of our approach is the introduction of model averaging and post-processing rules to make the system robust to outliers. 3. Our trained system achieves an in-domain classification accuracy of >0.92, which is improved to >0.96 by a postprocessing step. In addition, the whole system performs even well in an out-of-domain classification task with two unknown types, achieving an average accuracy of 0.93. We provide our system at https://github.com/Klimroth/Video-Action-Classifier-for-African-Ungulates-in-Zoos/tree/main/mrcnn_based so that interested users can train their own models to classify images and conduct behavioural studies of wildlife. 4. The use of a multi-step convolutional neural network for fast and accurate classification of wildlife behaviour facilitates the evaluation of large amounts of image data in ecological studies and reduces the effort of manual analysis of images to a high degree. Our system also shows that post-processing rules are a suitable way to make species-specific adjustments and substantially increase the accuracy of the description of single behavioural phases (number, duration). The results in the out-of-domain classification strongly suggest that our system is robust and achieves a high degree of accuracy even for new species, so that other settings (e.g. field studies) can be considered.
Targeted miRNA Profiling in Gastric Cancer with Clinical Assessment
Hikmet Pehlevan Özel
Tolga Dinç

Hikmet Pehlevan Özel

and 6 more

January 13, 2021
Background The purpose of this study was to determine the alterations of a specific set of miRNA levels in gastric adenocarcinoma tissues in order to identify gastric cancer specific miRNAs. Identification of the relationship between alteration of miRNA expressions and clinical features of these gastric cancer patients was set as a secondary outcome. Material and Methods Gastric adenocarcinoma and normal stomach tissue samples of 20 patients who underwent surgery for gastric cancer were studied. miRNA expression profiling was performed for 8 miRNAs (2 of which has not been studied in detail for gastric cancer) in a total of 40 tissue samples using Quantitative Reverse Transcription Polymerase Chain Reaction. Alterations in expressions were compared with the clinicopathological characteristics of the patients. Results Five out of eight miRNAs were underexpressed in malignant tissues. A decrease in the expression levels of miR-375-3p, miR-196a-5p, miR-376c-3p, miR-34c-5p, and miR-767-5p were observed. Furthermore, the expression of miR-662 was reversely related with age (r: -0,44, p: 0.04933); miR-129-3p and miR34c-5p levels were correlated with an increase in the number of metastatic lymph nodes (r: 0,47, p: 0.036495; r: 0,51, p: 0.020289); and miR-376c-3p levels were negatively associated with smoking (p: 0.04321). In addition, the variability of miRNA expression in cancerous tissues was lower than that in normal tissues. Conclusion Alterations in miRNA expressions in gastric adenocarcinoma tissues compared to healthy tissues of each individual may serve as a starting point for research and development of a diagnostic tool for gastric cancer.
Changes in sediment budget and morphology in the floodplains of the braided reach of...
Yan Li
Jinliang Zhang

Yan Li

and 4 more

January 13, 2021
Floodplains provide valuable social and ecological environment functions, and understanding the rates and patterns of floodplain sedimentation/erosion is critical for floodplain management and rehabilitation. The sediment entering the lower Yellow River has been dramatically reduced, and the geomorphology has changed greatly during the operation of the Xiaolangdi (XLD) reservoir since 2000. Utilizing sediment resources is the key to managing the downstream river, and the floodplains not only play the roles of flood mitigation, detention and de-sanding but also provide land to support local residents and economic development; however, the floodplain currently faces competition between land development and protection. This research presents a detailed investigation of changes in the sediment budget and morphology of the braided reach between Huayuankou (HYK) and Gaocun (GC) during 2000-2017 using digital elevation models (DEMs) and the historical bathymetry of the braided reach. During the implementation of the water-sediment regulation scheme (WSRS), the long-term low-concentration flow released from the XLD reservoir leads to a fully scoured long channel, further improving the bank-full discharge and reducing the risk of floods on floodplains. However, the floodplains have gradually changed from sedimentation to erosion due to the continual construction of farm dykes and control works, land use changes and other forms of land disturbance, including water and soil conservation measures and climate change. The cumulative eroded volume was approximately 11.47×108 m3 along the HYK - GC reach between 2000 and 2017, of which 3.08×108 m3 originated from the floodplains, with an average annual erosion rate of 1.3 cm/yr. To develop the economy and guide floodplain construction, we propose a new method of environmental management to reconstruct the floodplain domain into different zones for immigration resettlement areas, agricultural areas and resource development and utilization areas, with the methods of river dredging and floodplain filling.
Low frequency operation and micro-controller implementation for multilevel quasi Z so...
Salman Ahmad
Rahim Uddin

Salman Ahmad

and 2 more

January 13, 2021
A microcontroller based pulse width modulation implementation for multilevel quasi Z source inverter is proposed in this paper. The component design of quasi z source inverter (qZSI) is first considered with continuous and discontinuous mode of operations. The low switching frequency operation of multilevel quasi Z source inverter is proposed in this paper. The detailed modelling for qZSI is then established for effective implementation of PIC microcontroller (PIC 16F877A) for generating the switching signals. A prototype of five level quasi z-source inverter have been developed and the control signal to the gate drivers have been applied by properly adjusting the shoot through and non shoot through switching states. The hardware result shows the effective implementation of the proposed scheme.
A comparison of tamsulosin and silodosin versus tadalafil in medical expulsive therap...
Metin Gur
Suleyman Tumer Caliskan

Metin Gur

and 4 more

January 13, 2021
Objectives: To evaluate the efficacy of tamsulosin, silodosin, and tadalafil as medical expulsive therapy for distal ureteral stones in men. Methods: Adult males meeting the inclusion criteria were randomized into one of four treatment arms - dexketoprofen (control group), tamsulosin (Group 1), silodosin (Group 2), and tadalafil (Group 3). The stone expulsion rate after four weeks represented the primary endpoint, while the stone expulsion rate at the end of the study and the incidence of adverse events constituted secondary endpoints. Clinical findings were compared between all four drug groups. Results: No statistically significant difference was observed among the groups in terms of age, body mass index, stone futures, expulsion time, pain episodes, or total analgesic use. Expulsion rates in the fourth week were 42.5%, 80%, 82.5%, and 75%, respectively. The stone expulsion rates in groups 1, 2, and 3 were significantly higher than in the control group (p < 0.001). However, the differences between groups 1, 2, and 3 were not statistically significant. No serious adverse effects were observed during the study period. Conclusion: The study results showed a higher expulsion rate in male patients using tamsulosin, silodosin and tadalafil for distal ureteral stones, but no significant superiority between these. All three are safe, effective, and well-tolerated, causing minimal side-effects.
COMPARISON OF PATIENTS WITH MALIGNANT OR BENIGN LARYNGEAL LESIONS AND HEALTHY INDIVDU...
BİLAL SİZER
Ümit Yılmaz

BİLAL SİZER

and 2 more

January 13, 2021
Purpose: Recent studies have shown a relationship between cancer and inflammatory response. The aim of this study is to compare NLR and PLR values, which are inflammatory parameters, in precancerous and cancerous lesions and to determine whether there is a parameter that can be used in the early diagnosis of laryngeal squamous cell carcinoma. Methods:174 patients who were benign as a result of pathology, 122 patients who were malignant, 39 patients who were premalignant (335 patients in total) and 117 normal individuals were included in the study. Data groups were divided into 4 groups as Benign Laryngeal Lesion(BLL), Precancerous Laryngeal Lesion(PLL), Malignant Laryngeal Lesion(MLL) and Control Group(CG). In addition, the PLL group was subdivided into Mild Dysplasia(MiD), Moderate Dysplasia(MoD) and Severe dysplasia-carcinoma in situ (SeD/CIS). NLR, PLR and other parameters were calculated. Results: NLR and PLR values were significantly different between the groups. (p = 0.000, p = 0.002) The mean NLR was higher in the MLL and PLL groups, and was lower in the BLL and control groups. The mean PLR was also higher in the MLL and PLL groups. When the groups were compared in pairs, there was a significant difference between BLL and MLL (p = 0.001) and MLL and CG.(p = 0.006) The PLL group was subdivided into MiD, MoD and SeD / CIS. There was a significant difference in NLR when CG and other subgroups were compared.(p = 0.027) Significant differences were found between CG and SeD when the groups were compared in pairs.(p = 0.007) There was no significant difference between the groups in terms of PLR and dysplasia.(P = 0.516) Conclusion: As revealed in this study, these rates were low in the CG and BLL groups and high in the MLL group, so they could be used as markers to differentiate malignant lesions.
Walker and Syers enter the critical zone: Integrating decadal scale root development...
Emma Hauser
Jon Chorover

Emma Hauser

and 6 more

January 13, 2021
Most terrestrial nutrient sources are hypothesized to shift in dominance from mineral- to organic matter (OM)-derived over millennia. We investigated how overlaying this hypothesis with plant rooting dynamics that can feedback to soil development offers insight into ecosystem functioning. To test the hypothesis that the nutritional importance of OM as mineral weathering proceeds is mediated by rooting system nutrient economies that vary with vegetation development, we paired litterfall decay experiments with soil mineralogical data from diverse forests across the Critical Zone (CZ) Observatory Network. We demonstrate that sources of phosphorus shift from OM-bound stocks to minerals as the rooting zone expands during the transition from mid to late stages of forest growth. Root-driven, plant-soil feedbacks thus can prompt inconsistencies with soil development models that posit a unidirectional transition from mineral to organic nutrient dominance, and illuminate how forest growth and land use influence nutrient bioavailability in Earth’s CZ.
Effect of plateau pika disturbance on the ecosystem services of alpine grasslands
Ying Ying Chen
Huan Yang

Ying Ying Chen

and 4 more

January 13, 2021
Herbivore disturbance can affect the grassland ecosystem services though creating extensive disturbances vegetation and soil. This study focused on plateau pika (Ochotona curzoniae) disturbance to investigate the effect of disturbance by small burrowing herbivores on ecosystem services of alpine grasslands though five sites. In this study, the palatable plant biomass, plant species richness, soil water storage, soil organic carbon, total nitrogen, phosphorus and potassium stocks were used to estimate the forage availability, biodiversity conservation, water conservation, carbon sequestration and soil nutrient maintenance. This study showed that plateau pika disturbance was related to higher plant species richness and soil organic carbon stock, associated with lower palatable plant biomass and soil water storage, and had no effect on total potassium stock, whereas the responses of soil total nitrogen and phosphorus stocks to plateau pika disturbance were different among sites. The palatable plant biomass, plant species richness, soil organic carbon, total nitrogen and phosphorus stocks showed downward parabolas, whereas the soil water storage showed a decreasing trend with increasing plateau pika disturbance intensity. These results indicated that the role of plateau pikas is dependent not only on the management target of alpine grasslands but also on the plateau pika disturbance intensity.
School allergy training promotes internal policy review and enhances staff's prepared...
George Raptis
Rebecca Totterdell

George Raptis

and 4 more

January 13, 2021
Recently non-statutory allergy management guidance for schools has been produced in the United Kingdom however there has been limited progress in implementing this. The aim of this study was to evaluate the effect of face-to-face training on self-reported school staff preparedness in managing the severely allergic child and whether it would stimulate schools’ allergy policy review. A preparedness survey was conducted prior and 2 months post-intervention to assess the effect of training on self-reported preparedness and perceived confidence to manage children with food allergies. A sample of 18 (10%) primary schools that consented to participate were selected. Of the trained schools, 89% felt confident in dealing with an allergy emergency compared to 39% prior training (p=0.016). Post intervention all but one had arranged/were considering introducing allergy awareness sessions to help pupils manage their allergies (45% pre-training vs post-training 93%, p=003). Preventative measures for accidental exposure to food allergens (i.e. no food sharing policy) were adopted by all (pre-training 61% vs post- training 100%, p=0.03). A face-to-face school allergy training programme enhances self-reported staff preparedness and promotes internal allergy policy review in managing the needs of these children, hence addressing the current gap between recommendations and practice in schools.
Harnessing Pivotal Advances for Production and Structural Derivation of the Promising...
Hao-ran Liu
Nadeem Ahmad

Hao-ran Liu

and 3 more

January 13, 2021
Ursolic acid (UA) is a ursane-type pentacyclic triterpenoid compound, naturally produced in plants via specialized metabolism and exhibits vast range of remarkable physiological activities and pharmacological manifestations. Owing to significant safety and efficacy in different medical conditions, UA may serve as a backbone to produce its derivatives with novel therapeutic functions. This review systematically provides an overview of the pharmacological activities, acquisition methods and structural modification methods of UA. In addition, we focused on the synthetic modifications of UA to yield its valuable derivatives with enhanced therapeutic potential. Furthermore, harnessing the essential advances for green synthesis of UA and its derivatives by advent of metabolic engineering and synthetic biology are highlighted. In combination with the advantages of UA biosynthesis and transformation strategy, large-scale production and applications of UA is a promising platform for further exploration.
Omega-3 polyunsaturated fatty acids supplementation improve clinical symptoms in pati...
Mohsen Sedighiyan
Hamed  Abdollahi

Mohsen Sedighiyan

and 9 more

January 13, 2021
Objective: We hypothesized that omega-3 fatty acids would be an appropriate adjunct therapy for alleviating the inflammatory response and clinical manifestation in hospitalized patients with covid-19 disease. Methods: This was a single-blind randomized controlled trial in Amir-Alam hospital in Tehran. Thirty adult men and women diagnosed with covid-19 were allocated to either control group (receiving Hydroxychloroquine) or intervention group (receiving Hydroxychloroquine plus 2 grams of DHA+EPA) for 2 weeks. Primary outcome of the intervention including CRP, ESR as well as clinical symptoms including body pain, fatigue, appetite and olfactory and secondary outcomes including liver enzymes were determined at the baseline and after omega-3 supplementation. Clinical signs were measured using self-reported questionnaires. There were commercial kits for determination of CRP and liver enzymes concentrations in the serum of patients. For determination of ESR automated hematology analyzer was applied. Results: In comparison to control group, patients receiving omega-3 indicated favorable changes in all clinical symptoms except for olfactory ((p<0.001 for body pain and fatigue, p= 0.03 for appetite and p=0.21 for olfactory). Reducing effects of omega-3 supplementation compared to control group were also observed in the levels of ESR and CRP after treatment (p<0.001 for CRP and p=0.02 for ESR). However, no between group differences in the liver enzymes serum concentrations were observed after supplementation (p>0.05). Conclusion: Current observations are very promising and indicate that supplementation with moderate dosages of omega-3 fatty acids may be beneficial in the management of inflammation-mediated clinical symptoms in covid-19 patients. Key words: Covid-19, omega-3, inflammation, clinical symptoms
Evaluation of Ultrasound-Guided Adductor Canal Block With Two Different Concentration...
selin guven kose
Halil Cihan Kose

selin guven kose

and 4 more

January 13, 2021
Study Objective: The application of regional anesthesia techniques as a component of multimodal analgesia in knee arthroscopic surgeries increases the quality of postoperative analgesia. Adductor canal block (ACB) is an effective “motor sparing” analgesia technique used in knee surgeries. In this study, we aimed to evaluate the efficacy of two different concentrations of local anesthetic mixtures in terms of postoperative analgesia in patients undergoing knee arthroscopic intervention compared to each other and the control group. Design: Prospective, randomized, controlled, blinded Setting: Tertiary hospital Patients: A total of 60 patients (ASA I-II) were evaluated in three groups, with 20 in each group. Interventions: Standardized postoperative analgesia was planned for all groups. In addition, ultrasound guided ACB (same volume / two different concentrations of bupivacaine-0.25% vs 0.16%) was applied to the experimental groups. Measurements: Tramadol consumption, rescue analgesic requirement and Numeric Rating Scores (NRS). Main Results: Tramadol requirement in the first 24 hours was significantly higher in the control group (209.5±23.27 mg),(p<0.001), and there was no difference between the experimental groups (63±42.06 mg vs 80.5±36.63 mg). Although the mean NRS score in the first three hours was higher in the control group than in both block groups, it was similar in all groups in the following measurements. Conclusion: In arthroscopic knee surgery, ACB interventions with 0.25% and 0.16% concentrations of bupivacaine were similar in terms of postoperative analgesic efficacy, and they increased the quality of multimodal analgesics more than the control group.
Epidemiological Factors in Patients with Dermatologic Conditions Referring to Clinic...
Mohammad Mahdi Parvizi
Nazanin  Fatehi

Mohammad Mahdi Parvizi

and 5 more

January 13, 2021
Introduction: Many patients with chronic diseases often use the traditional medicine approach in addition to conventional medicine. The aim of this study was to evaluate the epidemiological factors of patients with dermatologcal conditions referring to traditional Persian Medicine (TPM) clinic. Materials and Methods: In this cross-sectional study, we reviewed all the patients’ medical documents with dermatological conditions referred to the TPM clinic at Shiraz, Southern Iran in 2018. Then, the epidemiological factors of the patients were recorded to a researcher-made data collection form. SPSS software version 22 was conducted to data analysis. Results: Overall, 631 patients consist of 151 (23.9%) male individuals and 580 (76.1%) female individuals were enrolled to the study. Most of the patients were aged between 31 and 40 years, and 347 (55%) patients were married, and most of them were housewives. The frequency of patients in spring was higher than other seasons. Furthermore, the most of the patients were university educated. Acne, eczema and hair loss were the three most complaints of the patients referring to the traditional medicine clinic. 301(47.7%) patients reported gastrointestinal problems as another complaint concomitant with their skin problems. Conclusion: It seems that women with skin problems, including acne, eczema, and hair loss, were more likely to refer to the TPM clinic. Therefore, development of TPM clinics in dermatology field as a scientific and academic approach can be effective in the treatment of patients with dermatological condition accompanied by traditional medicine.
Asynchronous diversification and distinct demographic trajectories in Ethiopian monta...
Joseph Manthey
Yann Bourgeois

Joseph Manthey

and 3 more

January 13, 2021
Taxon-specific characteristics and extrinsic climatic and geological forces may both shape population differentiation and speciation. In geographically and taxonomically focused investigations, differentiation may occur synchronously as species respond to the same external conditions. Conversely, when evolution is investigated in taxa with largely varying traits, population differentiation and speciation is complex and shaped by interactions of Earth’s template and species-specific traits. As such, it is important to characterize evolutionary histories broadly across the tree of life, especially in geographic regions that are exceptionally diverse and under pressures from human activities such as in biodiversity hotspots. Here, using whole-genome sequencing data, we characterize genomic variation in populations of six Ethiopian Highlands forest bird species separated by a lowland biogeographic barrier, the Great Rift Valley (GRV). In all six species, populations on either side of the GRV exhibited significant but varying levels of genetic differentiation. Species with lower dispersal ability generally had higher levels of population differentiation. Divergence dating indicated asynchronous population differentiation histories, with at least three distinct diversification periods. We found that demographic histories—estimated for each individual—varied by both species and population but were consistent between individuals of the same species and sampling region. We found that genomic diversity varied by half an order of magnitude across species, and that this variation could largely be explained by the harmonic mean of effective population size over the past 200,000 years. Overall, we found that even in highly dispersive species like birds, the GRV acts as a substantial biogeographic barrier.
CATHETER ABLATION FOR ATRIAL FIBRILLATION USING THE ABLATION INDEX-HIGH POWER STRATEG...
oluwaseun adeola
asad Al Aboud

oluwaseun adeola

and 3 more

January 12, 2021
Pulmonary vein isolation (PVI) is the cornerstone of catheter ablation for atrial fibrillation (AF) However AF recurrence after a single ablation procedure is common and often attributed to ineffective lesion delivery during PVI. In this issue of the Journal of Cardiovascular Electrophysiology, Chen et al reported their experience with 122 patients who underwent an ablation index-high power (AI-HP) strategy RF ablation for AF using 50W power, targeting AI values of 550 on the anterior left atrium (LA), 400 on the posterior wall and inter-lesion distance (ILD) 6mm. They achieved 1st pass PVI in 96.7% of cases, mean RF time was 11.5min and total procedure time was only 55.8min. All patients had 72h-Holter monitor and trans-telephonic follow up. They reported 89.4% arrhythmia free survival among patients with paroxysmal AF and 80.4% among patients with persistent AF at 15-month follow up. Sixty (49%) patients had luminal esophageal temperature (LET) >390C out of which 3 (2.5%) had asymptomatic endoscopic esophageal erosions/erythema. Four (3%) patients had clinically apparent steam pops during ablation with no adverse clinical sequela. While AI-HP guided RF ablation may be an attractive strategy for PVI that likely reduces procedure times and probably has comparable efficacy to conventional ablation settings, its safety requires further evaluation. Feedback from the ablated tissue may need to be incorporated into optimized ablation energy parameters to further improve outcomes.
The transformation of Caribbean coral communities since humans
Katie Cramer
Mary Donovan

Katie Cramer

and 6 more

January 12, 2021
The mass die-off of Caribbean corals has transformed many of this region’s reefs to macroalgal-dominated habitats since systematic monitoring began in the 1970s. Although attributed to a combination of local and global human stressors, the lack of long-term data on Caribbean reef coral communities has prevented a clear understanding of the causes and consequences of coral declines. We integrated paleoecological, historical, and modern survey data to track the prevalence of major coral species and life history groups throughout the Caribbean from the pre-human period to present. The regional loss of Acropora corals beginning by the 1960s from local human disturbances resulted in increases in the prevalence of formerly subdominant stress-tolerant and weedy scleractinian corals and the competitive hydrozoan Millepora beginning in the 1970s and 1980s. These transformations have resulted in the homogenization of coral communities within individual countries. However, increases in stress-tolerant and weedy corals have slowed or reversed since the 1980s and 1990s in tandem with intensified coral bleaching. These patterns reveal the long history of increasingly stressful environmental conditions on Caribbean reefs that began with widespread local human disturbances and have recently culminated in the combined effects of local and global change.
Biodegradable and Biocompatible Graphene-based Scaffolds for Functional Neural Tissue...
Negar Mansouri
Said Al-Sarawi

Negar Mansouri

and 6 more

January 12, 2021
Neural tissue engineering aims to restore function of nervous system tissues using biocompatible cell-seeded scaffolds. Graphene-based scaffolds combined with stem cells deserve special attention to enhance tissue regeneration in a controlled manner. However, it is believed that minor changes in scaffold biomaterial composition, internal porous structure, and physicochemical properties can impact cellular growth and adhesion. The current work aims to investigate in vitro biological effects of 3D graphene oxide (GO)/sodium alginate (GOSA) and reduced GOSA (RGOSA) scaffolds on dental pulp stem cells (DPSCs) in terms of cell viability and cytotoxicity. Herein, the effects of the 3D scaffolds, coating conditions, and serum supplementation on DPSCs functions are explored extensively. Biodegradation analysis revealed that addition of GO enhanced the degradation rate of composite scaffolds. Compared to the 2D surface, the cell viability of 3D scaffolds was higher (p <0.0001), highlighting the optimal initial cell adhesion to the scaffold surface and cell migration through pores. Moreover, the cytotoxicity study indicated that the incorporation of graphene supported higher DPSCs viability. It is also shown that when the mean pore size of scaffold increases, DPSCs activity decreases. In terms of coating conditions, poly-l-lysine (PLL) was the most robust coating reagent that improved cell-scaffold adherence and DPSCs metabolism activity. The cytotoxicity of GO-based scaffolds showed that DPSCs can be seeded in serum-free media without cytotoxic effects. This is critical for human translation as cellular transplants are typically serum-free. These findings suggest that proposed 3D GO-based scaffolds have favourable effects on the biological responses of DPSCs.
An exploration of assembly strategies and quality metrics on the accuracy of the Knig...
Ann McCartney
Elena Hilario

Ann McCartney

and 7 more

January 12, 2021
We used long read sequencing data generated from Knightia excelsaI R.Br, a nectar producing Proteaceae tree endemic to Aotearoa New Zealand, to explore how sequencing data type, volume and workflows can impact final assembly accuracy and chromosome construction. Establishing a high-quality genome for this species has specific cultural importance to Māori, the indigenous people, as well as commercial importance to honey producers in Aotearoa New Zealand. Assemblies were produced by five long read assemblers using data subsampled based on read lengths, two polishing strategies, and two Hi-C mapping methods. Our results from subsampling the data by read length showed that each assembler tested performed differently depending on the coverage and the read length of the data. Assemblies that used longer read lengths (>30 kb) and lower coverage were the most contiguous, kmer and gene complete. The final genome assembly was constructed into pseudo-chromosomes using all available data assembled with FLYE, polished using Racon/Medaka/Pilon combined, scaffolded using SALSA2 and AllHiC, curated using Juicebox, and validated by synteny with Macadamia. We highlighted the importance of developing assembly workflows based on the volume and type of sequencing data and establishing a set of robust quality metrics for generating high quality assemblies. Scaffolding analyses highlighted that problems found in the initial assemblies could not be resolved accurately by utilizing Hi-C data and that scaffolded assemblies were more accurate when the underlying contig assembly was of higher accuracy. These findings provide insight into what is required for future high-quality de-novo assemblies of non-model organisms.
Traumatic aortic root rupture leading to acute aortic insufficiency and acute Type A...
Subash Nepal
Vijay Raj

Subash Nepal

and 3 more

January 12, 2021
A 17-year-old male was admitted for the management of multiple fractures after sustaining blunt thoracic trauma. He was hemodynamically stable and without any cardiac symptoms. He was admitted with fracture of T4 end plate, manubrium and left first rib, right pulmonary contusion, left apical pneumothorax and pneumomediastinum. The patient underwent echocardiography and cardiac CT angiogram for the work up of aortic injury as the patient had new aortic regurgitation murmur, troponin rise and RBBB. He was found to have aortic root rupture, type A aortic dissection and acute severe aortic insufficiency. The patient underwent surgical aortic valve and root replacement with Bentall procedure with good outcome.
Roles of host mitochondria in the development of COVID-19 pathology
Kavya Srinivasan
Ashutosh Pandey

Kavya Srinivasan

and 2 more

January 12, 2021
The recent emergence of Severe Acute Respiratory Syndrome-Corona Virus 2 (SARS-CoV-2) in late 2019 and its spread worldwide caused an acute pandemic of Coronavirus disease 19 (COVID-19). COVID-19 pathologies are currently under intense scrutiny as its outbreak led to immense and urgent changes worldwide. Although many theories have been introduced on how SARS-CoV-2 enters the host, the ACE-2 receptor is shown to be the primary mechanism of SARS-CoV-2 entry. However, the mechanism behind the establishment and pathology of infection is poorly understood. As recent studies show that host mitochondria play an essential role in virus-mediated innate immune response, in this review, we will discuss, in detail, the entry and progression of SARS-CoV-2 and how mitochondria play a role in the establishment of viral infection and the development of an immune response, whether it is beneficial or not. We will also review the possible treatments that could be used to prevent the surgency of COVID-19 infection with respect to the role of mitochondria. Understanding the mitochondria-mediated SARS-CoV-2 establishment may provide a unique mechanism and conceptual advancement in finding a novel treatment for COVID-19.
Large Impact of obesity on the disposition of ivermectin, moxidectin and eprinomectin...
Alain Bousquet-Melou
Anne Lespine

Alain Bousquet-Melou

and 4 more

January 12, 2021
Background and Purpose: Based on in vitro data, ivermectin (IVM) has been proposed for the prevention and treatment of COVID-19, a condition for which obesity is a major risk factor. IVM dosage is based on total body weight and there are no recommendations to adjust dosage in obese patients. The objective of this study was to establish, in a canine model, the influence of obesity on the clearance and steady-state volume of distribution of IVM and two analog compounds, moxidectin (MOX) and eprinomectin (EPR). Experimental Approach: An experimental model of obesity in dogs was based on a high calorie diet. IVM, MOX and EPR were administered intravenously, simultaneously in combination, to a single group of dogs in two circumstances, during a control period and when body weight had been increased by 50%. Key Results: In obese dogs, clearance, expressed in absolute values (L/day), was not modified for MOX and reduced for IVM and EPR, compared to the initial control state. When scaled by body weight (L/day/kg), plasma clearance was reduced by 42, 55 and 63%, for MOX, IVM and EPR, respectively. In contrast, the steady-state volume of distribution was markedly increased in absolute values (L) by obesity. Conclusion and Implications: For IVM and MOX, the obese dog model suggests that the maintenance dose should not be adjusted by total body weight in the obese subject but should be based on lean body weight. On the other hand, the loading dose should be computed based on the total body weight of the obese subject.
Potential of Selective Serotonin Reuptake Inhibitors in preventing clinical deteriora...
TATHAGATA BISWAS
BISWA MISHRA

TATHAGATA BISWAS

and 5 more

January 12, 2021
COVID-19 has an unpredictable course with substantial percentage of infected patients developing clinical deterioration and increasing health care burden. With no specific treatment or vaccination, the current search is for drugs that can limit the disease progression. Recently Fluvoxamine has been reported to have disease modifying effects in COVID-19. We suggest the hypothesis that short term routine use of Selective Serotonin Reuptake Inhibitors (SSRIs) can prevent clinical deterioration of asymptomatic or mild COVID-19 cases by the following ways: a) anti-inflammatory actions through sigma-1 agonism and reducing release of pro-inflammatory cytokines, b) anti-coagulant action by reducing platelet aggregation, c) specific antiviral and antibacterial effects, d) Immunomodulation through Serotonin pathway and anti-oxidation. The routine short term use of SSRIs can also alleviate the psychological impact of the disease. We hope our hypothesis will encourage future clinical trials to validate the routine use of SSRIs against COVID-19.
Improving Vitamin D testing and supplementation in children with newly-diagnosed canc...
Ksenya Shliakhtsitsava
Erin  Stucky Fisher

Ksenya Shliakhtsitsava

and 8 more

January 12, 2021
Background: Vitamin D deficiency and insufficiency have been associated with poorer health outcomes. Children with cancer are at high risk for Vitamin D deficiency and insufficiency. At our institution, we identified high variability in Vitamin D testing and supplementation in this population. Of those tested, 65% were Vitamin D deficient/insufficient. We conducted a quality improvement (QI) initiative with aim to improve Vitamin D testing and supplementation among children aged 2-18 years old with newly-diagnosed cancer to ≥ 80% over 6 months. Methods: An inter-professional team reviewed baseline data, then developed and implemented interventions using Plan-Do-Study-Act (PDSA) cycles. Barriers were identified using QI tools, including lack of automated triggers for testing and inconsistent supplementation criteria and follow-up testing post-supplementation. Interventions included an institutional Vitamin D guideline, clinical decision-making tree for Vitamin D deficiency, insufficiency and sufficiency, electronic medical record triggers, and automated testing options. Results: Pre-intervention: N=26 patients, four (15%) had baseline Vitamin D testing; two (8%) received appropriate supplementation. Post-intervention: N=33 patients; 32 (97%) had baseline Vitamin D testing; 33 (100%) received appropriate supplementation and completed follow-up testing timely (6-8 weeks post-supplementation). Change was sustained over 24 months. Conclusions: We achieved and sustained our aim for Vitamin D testing and supplementation in children with newly-diagnosed cancer through inter-professional collaboration of hematology/oncology, endocrinology, hospital medicine, pharmacy, nursing, and information technology. Future PDSA cycles will address patient compliance with Vitamin D supplementation and impact on patients’ Vitamin D levels.
High-resolution imaging of depth filter structures using X-ray computed tomography
Thomas Johnson
Francesco Iacoviello

Thomas Johnson

and 4 more

January 12, 2021
A multiple length scale approach to the imaging and measurement of depth filters using X-ray computed tomography is described. Three different filter grades of varying nominal retention ratings were visualized in 3D and compared quantitatively based on porosity, pore size and tortuosity. Positional based analysis within the filters revealed greater voidage and larger average pore sizes in the upstream quartile before reducing progressively through the filter from the center to the downstream quartile, with these results visually supported by voidage distance maps in each case. Flow simulation to display tortuous paths that flow may take through internal voidage were examined. Digital reconstructions were capable of identifying individual constituents of voidage, cellulose and perlite inside each depth filter grade, with elemental analysis on upstream and downstream surfaces confirming perlite presence. Achieving an appropriate pixel size was of particular importance when optimizing imaging conditions for all grades examined. A 3 µm pixel size was capable of representing internal macropores of each filter structure, however for the finest grade an improvement to a 1 µm pixel size was required in order to resolve micropores and small perlite shards. Enhancing pixel size resulted in average porosity measurements of 70% to 80% for all grades.
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