bluuebunny/crossref_metadata_2025 huggingface dataset:
MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes
Authors: Rocha Ulisses Nunes da , Nata’ala Muhammad Kabiru , Santos Anderson Paulo Avila , Kasmanas Jonas Coelho , Bartholomäus Alexander , Saraiva João Pedro , Silva Sandra Godinho , Keller-Costa Tina , Costa Rodrigo , de Carvalho André Carlos Ponce de Leon Ferreira , Stadler Peter F. , Sanches Danilo Sipoli
Published: April 2022

BackgroundMetagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. However, data mining and interpretation can be challenging due to mis-annotated and misleading entries of metadata. In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. To this end, we have manually curated the associated metadata of several thousands of microbial metagenomes currently deposited at SRA and MG-RAST.ResultsIn total, 125 terms were curated according to 17 different classes (e.g., biome, material, oceanic zone, geographic feature, oceanographic phenomena). Other standardized features include sample attributes (e.g., salinity, depth), sample location (e.g., latitude, longitude), and sequencing features (e.g., sequencing platform, sequence count). MarineMetagenomeDB version 1.0 contains 11,449 marine metagenomes from SRA and MG-RAST distributed across all oceans and several seas. Most of the samples were sequenced using Illumina sequencing technology (84.33%). More than 55%of the samples were collected from the Pacific and the Atlantic Oceans. About 40% of the samples had their biomes assigned as ‘ocean’. The ‘Quick Search’ and ‘Advanced Search’ tabs allow users to use different filters to select samples of interest dynamically in the web app. The interactive map allows the visualization of samples based on their location on the world map. The web app is also equipped with a novel download tool (on both Windows and Linux operating systems), that allow easy download of raw sequence data of selected samples from their respective repositories. We demonstrated how users may use the MarineMetagenomeDB web app to select estuarine metagenomes for large-scale microbial biogeography studies quickly.ConclusionThe MarineMetagenomeDB is a powerful resource for non-bioinformaticians to find marine metagenome samples with curated metadata and stimulate meta-studies involving marine microbiomes. Our user-friendly web app is publicly available at https://webapp.ufz.de/marmdb/.
The possibility of angiogenesis inhibition in cutaneous melanoma by Bevacizumab-loaded lipid-chitosan nanoparticle
Authors: Abdi fershteh , Arkan Elham , Eidizadeh Mojtaba , Valipour Elahe , Naseriyeh Tahereh , Gamizgy Younes Hossainy , Mansouri Kamran
Published: April 2022

Cutaneous malignant melanoma is fastest-growing cancer in white populations with a large majority of dermal cancer death. The activity of vascular endothelial growth factors (VEGFs) results in the signaling of a variety of downstream intracellular pathways that ultimately leads to cell activation, proliferation, migration, and angiogenesis. VEGF inhibitors such as Bevacizumab are widely used in chemotherapy with systemic administration, which in many cases is associated with a variety of side effects. Here, we designed and synthesized a lipid-polymer nanoparticle for local administration of Bevacizumab. Drug release, dermal absorption, and the effects of synthesized nanoparticles containing Bevacizumab on cell proliferation and in vitro and in vivo angiogenesis were investigated. Encapsulating Bevacizumab in the synthesized nanoparticles resulted in a significant increase in its dermal absorption compared to free Bevacizumab. Also, the suppressor effects of Bevacizumab encapsulated in the synthesized nanoparticle on cell proliferation and angiogenesis were significantly more than those of free Bevacizumab. Our findings indicate the remarkable effects of lipid-polymer nanoparticles in dermal absorption and in maintaining Bevacizumab bioactivity, suggesting therapeutic benefits of local Bevacizumab administration for angiogenesis-related disorders such as cutaneous melanoma.
Effects of ICT hardware, software and FDI on CO2 emissions in China
Authors: Chi Fangyuan , Meng Zhuo
Published: April 2022

With the rapid development of information and communication technology (ICT) and counter-cyclical expanding of foreign direct investment (FDI), most foreign-invested companies in China are highly polluting. Meanwhile, new research shows that the impact of ICT on the environment is uncertain. This study is an effort in dividing ICT into hardware and software, aiming to explore its effects on CO2 emissions from 2003 to 2017 in 31 provinces, autonomous regions and municipalities in China, and further explore the impacts of its application to foreign-invested enterprises on environmental quality. The findings show that ICT software specifies negative and statistically significant effects on CO2 emissions, but ICT hardware and FDI indicate positive and statistically significant effects on CO2 emissions. However, when ICT software and hardware are applied to foreign-invested enterprises, they can significantly improve the environmental quality. It is noteworthy that previous period of ICT software will increase current CO2 emissions significantly, yet ICT hardware lagged three years will reduce current CO2 emissions significantly.
Third primary SARS-CoV-2 prophylactic mRNA vaccines enhances antibody responses in the majority of patients with haematological malignancies: Results from the MARCH study
Authors: Cook Lucy , O'Dell Gillian , Vourvou Eleni , Palanicawandar Renuka , Marks Sasha , Milojkovic Dragana , Apperley Jane , Loaiza Sandra , Claudiani Simone , Bua Marco , Hockings Catherine , MacDonald Donald , Chaidos Aristeidis , Pavlu Jiri , Cooper Nichola , Fidler Sarah , Randell Paul , Innes Andrew
Published: April 2022

SARS-CoV-2 infection, and resulting disease, COVID-19, has a high mortality amongst patients with haematological malignancies. Global vaccine rollouts have successfully reduced hospitalisations and deaths, but the efficacy of vaccination in patients with haematological malignancies is known to be reduced. The UK-strategy offered a third, mRNA-based, vaccine as an extension to the primary course in these patients. Here we quantify serological responses following these vaccines in a cohort of 381 patients with haematological malignancies attending routine haematology outpatient clinics. By comparison with healthy controls, we report suboptimal responses following two primary vaccines, with significantly enhanced responses following the third primary dose. These responses however are heterogeneous and determined by haematological malignancy sub-type and therapy. We identify a group of patients with continued sub-optimal vaccine responses who may benefit from additional doses, as well as early intervention with monoclonal therapies in the event of developing SARS-CoV-2 infection.
Simultaneous determination of benzothiazoles, benzotriazoles and benzotriazole UV absorbers by solid-phase extraction-gas chromatography-mass spectrometry
Authors: Zhao Mingliang , Chen Yan , Yang Guipeng , Chen Rong
Published: April 2022

This paper proposes a new method for the simultaneous determination of emerging contaminants (ECS) in the marine environment by solid-phase extraction (SPE)-gas chromatography-mass spectrometry (GC-MS). Organic corrosion inhibitors (OCI) and UV absorbers are common products in plastic rubber and personal care products, and they have been acknowledged as emerging contaminants due to their toxicity and bio-accumulative effects in the environment. In addition to common persistent organic pollutants (POPs), it is also necessary to detect and analyze the concentration and composition of these emerging organic contaminants in the ocean. Solid-phase extraction (SPE) and solid-phase microextraction (SPME) were used as two common pretreatment methods. After comparing their recoveries, SPE was used for treatment, and the conditions such as SPE cartridge, extraction solvent, extraction time, pH and elution solvent were optimized. The method was applied to determine the concentrations of these contaminants in seawater and sediments from the Yangtze River Estuary and its adjacent areas with a precision of about 10% and recoveries in the range of 67.40%-102.3% and 77.35%-101.8%, respectively. The detection limits of this method for the determination of contaminants in seawater and sediment were 0.03-0.47 ng/g and 0.01-0.58 ng/g. The method is simple to operate and has high precision, and can be applied to the detection of emerging pollutant concentrations in marine environments.
Public Preferences Regarding the Priority Setting Criteria of Health Interventions for Budget Allocation: Results of a Survey of Iranian Adults
Authors: Darvishi Ali , Daroudi Rajabali , Yaseri Mehdi , sari Ali Akbari
Published: April 2022

Objectives: Priority setting in health has a direct impact on the general public as payer and final consumers, so the public preferences must be considered. The present study aimed to provide public preferences about health intervention allocation criteria for the optimal allocation of public resources in the health budget in Iran.Methods: A choice-based survey method was used to assess the general public’s preferences regarding 8 important criteria with a societal aspect. 1064 adult citizens of Tehran, Iran participated in the study. Participants were asked to allocate a hypothetical budget between the two groups with differences in terms of allocation criteria. Public preferences were inferred from absolute majority responses i.e. more than 50% of participants' allocation for a criterion. To investigate the factors affecting the preferences regarding the importance of allocation criteria, the Logistic Regression Model was used. Results: Based on expressed participants’ preferences, criteria of disease severity, age, daily care needs, number of alternative interventions, individual's economic status, and diseases with absence from work were important. Thus, 77, 69, 61, 57, 54, and 51% of participants preferred to allocate the hypothetical budget to the treatment of patients with poor economic status, treatment of patients with diseases leading to absence from work, treating patients with severe diseases, treatment of diseases in need of daily care and treatment of children's diseases, respectively. Findings from the factors affecting participants' preferences regarding allocation criteria also showed that people with different characteristics had different preferences.Conclusions: Iranian general public pays special attention to the criteria of equitable allocation including patients’ economic status, criteria with societal aspects such as absenteeism from work and the need for daily care, as well as criteria with medical aspects such as disease severity and access to alternative interventions which may sometimes be less considered in decision making.
A novel model possible cardiotoxicity associated with administration of Boldenone and Tramadol, alone or in combination in Wistar rats
Authors: El-Shamarka Marwa E. A. , Asaad Gihan F. , Mowaad Noha A. , Kozman Magy R.
Published: April 2022

A risk of cardiotoxicity has been associated with the use of anabolic-androgenic steroids (AAS) and analgesics, several deaths have been attributed to such medications. This study investigates the effects on the heart of AAS; namely, boldenone (BOLD) and opioid analgesics; namely, tramadol (TRAM) given alone or in combination, for the first time. Forty adult male rats were randomly divided into four groups; (n = 10). Normal control group, BOLD (5 mg/kg, i.m.) per week, tramadol Hcl (TRAM) (20 mg/kg, i.p.) daily, and a combination of BOLD (5 mg/kg) and TRAM (20 mg/kg), respectively for two months. Those that received BOLD and TRAM alone and in combination showed deteriorated cardiac functions, elevated serum biochemical parameters (AST, CK) and deviations in lipid profiles, elevation in oxidative and inflammatory parameters (MDA, TNF-α & IL-1β) and decrease in GSH, up-regulated cardiac troponin I as well as distorted cardiac histopathological pictures. The current study elucidated the risk of administration of these drugs for sustained periods as well as the marked detrimental effects of using these drugs in combination.
Compartment-dependent influence of sugarcane and soil on niche differentiation in metabolites, while silicon fertilizer mediates edaphic factors and sugarcane agronomic traits
Authors: Fallah Nyumah , Pang Ziqin , Dong Fei , Zhou Yongmei , Lin Wenxiong , Fabrice Kabore Manegdebwaoga Arthur , Hu Chaohua , Yuan Zhaonian
Published: April 2022

As one of the vital crops globally, sugarcane (Saccharum officinarum L.) has been one of model crops for conducting metabolome research. Although many studies have focused on understanding bioactive components in specific sugarcane tissues, crucial questions have been left unanswered about the response of niche differentiation of metabolites in different compartments of sugarcane (leaf, stem and root), and soil (rhizosphere and bulk) under silicon (Si) amended soils. In this study, nontargeted metabolite profiling method was leveraged to assess the similarities and differences in the abundance and community composition of metabolites in the different sugarcane and soil compartments. Identify the compartment-specific expression patterns of metabolites, and their association with cane agronomic traits and edaphic factors. We also investigated the response of sugarcane agronomic traits and edaphic factors to Si amended soil. We found that Si fertilizer exhibited the advantages of overwhelmingly promoting the height and theoretical production of cane, and profoundly increased soil Si content by 24.8% and 27.0%, while soil available potassium (AK) was enhanced by 3.07 and 2.67 folds in the bulk and rhizosphere soils, respectively. It was also noticed that available prosperous (AP) in the rhizosphere soil tremendously increased by 105.5%. We detected 339 metabolites in 30 samples using LC-MS/MS analyses, 161 of which were classified and annotated, including organooxygen compounds (19.9%), carboxylic acids and derivatives (15.5%), fatty acyls (15.5%), flavonoids (4.4%), phenols (4.4%), and benzene and substituted derivatives (3.7%). Multivariate ANOVA analysis revealed that the variations in metabolites abundance and community were compartment-dependent. We also observed that L-fucose and naringin and raffinose enrichment in the leaf and stem were unique to the Si treatment, respectively. Taken together, the results suggested that Si utilization can have a positive impact on edaphic factors and cane agronomic traits, and variations in metabolites community are tissue-dependent.
The antagonistic effect of Rhizospheric bacteria against white rot (Sclerotium cepivorum) of Garlic (Allium sativum L.) under in vitro and in vivo conditions
Authors: Mohammed Mussa Adal , Demeke Asmare Dejen
Published: April 2022

Purpose: Garlic (Allium sativum L.) is the second most widely used Allium, and it is used for food, medicine, condiments, and as a commercial crop. White rot (Sclerotium cepivorum) reduces its yield and productivity. Potential antagonists and the phytopathogen, white rot were isolated and characterized from the rhizosphere and infected garlic plant.Methods: Biocontrol properties including dual culture inhibition test, hydrolytic enzyme production and production of bioactive compounds such as ammonia and cyanide were determined. Moreover, the in vivo inhibition potential of selected antagonists was evaluated under greenhouse conditions.Results: Among these isolates, 47.8% prevented white rot radial growth, with 4 (36.4%) and 2 (18.2%) showing disease incidences of 1- 4 % and 33.3 %, respectively. Among the isolates, 6(54. 6%), 10(90.9%) and 5 (45.5 %) were positive for Chitinase, cellulase and protease production. Furthermore, all and 5 (45.5 %) of the isolates were positive for ammonia and hydrogen cyanide production, respectively.Garlic plants inoculated with isolates WUGR-14 and WUGRB- 92 grew and resisted disease better. WUGRB-14, WUGRB-92, and WUGRB-8 treated garlic plants grew to a height of 142.2 %, 141.8 %, and 135.0 %, respectively, higher than the control. Plants inoculated with these isolates also acquired the largest shoot dry weights, which were 370.8 %, 333.3 %, and 291.7 % higher than the control, respectively. WUGRB- 38 exhibited 99 % sequence identity to Pantoa species, Pantoa agglomerans, and Enterobacter species based on 16S rRNA gene sequencing, whereas WUGRB- 53, 91, and 92 showed the most homology to Enterococcus species, E. casseliflavus, and E. gallinarum. Conclusion: Under appropriate circumstances, the isolates WUGRB-8, WUGRB-14, and WUGRB-92 can be recommended as candidate microbial inoculant for applying under field conditions.
A systematic review and meta-analysis of unmet needs for healthcare and long-term care among older people
Authors: Rahman Md Mizanur , Rosenberg Megumi , Flores Gabriela , Parsell Nadia , Akter Shamima , Alam Md Ashraful , Rahman Md. Mahfuzur , Edejer Tessa
Published: April 2022

BackgroundThe absolute number of older individuals needing medical care and long-term care (LTC) is increasing globally due to the growing ageing population. However, it is uncertain who and what proportion of the population has access to care. Therefore, a systematic review and meta-analysis of the prevalence and reasons for unmet needs for healthcare and long-term care among older people, 65 years old and above, across countries was conducted. MethodsAn information specialist performed a comprehensive search of four major databases (PubMed, EMBASE, Web of Science, and CINAHL) from inception to June 2020 without restrictions on language and date. We did random-effects meta-analysis to obtain pooled prevalence. We stratified the meta-analysis by reasons for unmet need categorized by barrier dimension (availability, accessibility, affordability, and acceptability), survey year, geographic location, and socio-demographic characteristics of the older individual. ResultsAfter screening 3912 articles, we included 101 studies published between 1996 and 2020. Of the 101 studies, 87 studies reported unmet healthcare needs and 14 studies reported unmet LTC needs. Overall, 10.4% of the older population had unmet needs for healthcare. The common reasons for unmet healthcare needs were cost of treatment, lack of health facilities, lack of/conflicting time, health problem not viewed as serious, and mistrust/fear of provider. A significant variation in pooled prevalence of unmet healthcare needs due to cost was found by gender (male [10.9%] vs female [14.4%]), educational level (primary or less [13.3%] vs higher [7.5%]), self-reported health (poor [23.2%] vs good [4.4%]), insurance status (insured [9.0%] vs uninsured [27.7%]), and economic status of population (poorest [28.2%] vs richest [7.1%]). One in four (25.1%) older people had unmet needs in LTC. Rural residents had a higher prevalence of unmet needs in LTC compared to their urban counterparts. ConclusionWith the population ageing globally, it is necessary to improve access to health care and LTC for older people. Ensuring affordability of health services, reducing geographical barriers, and improving acceptability, will be critical in reducing unmet need.
Development and validation of a Cox model nomogram to predict the recurrence of pulmonary aspergillosis after antifungal therapy
Authors: Guo Lu , Qian Weiwei , Yang Yan , Pan Lingai
Published: April 2022

Background: Recurrence after antifungal therapy is a challenging complication of pulmonary aspergillosis (PA). However, the exact factors associated with the recurrence of PA are still unclear. The aim of this study was to develop and validate a Cox model nomogram for the prediction of the recurrence of PA after antifungal therapy.Methods: A total of 105 patients with PA were enrolled in this retrospective cohort study from January 2018 to December 2020 and followed up at least 12 month. The risk factors for the recurrence of PA were identified and the prediction model was developed using R software. Results: All 105 patients received effective antifungal therapy during their first admission; PA recurred in 18 patients during the follow-up period (mean, 5.5±5.2 months). Cox univariate analysis showed that immune deficiency, C-reactive protein level, galactomannan test (GM test), wheezing, pleural thickening, lung nodules, and prednisone therapy were prognostic factors for overall recurrence of PA after antifungal therapy (P<0.1). Multivariate Cox analysis indicated that pleural thickening and prednisone therapy were independent risk factors for the recurrence of PA (P<0.05). The nomogram plot was constructed based on the results of the univariate and multivariate analyses. The C-index of the predictive model was 0.90, 0.83, 0.81, and 0.81 for the 2- , 4-, 6-, and 8- month follow-up timepoints, respectively. The area under the receiver operating characteristic curve was 0.78, 0.63, and 0.61 for the 3-, 6-, and 12-month follow-up timepoints, respectively. The calibration curve showed a consistent tendency with the actual curve for the 3-month and 6-month follow-up timepoints.Conclusion: Pleural thickening on computed tomography images and prednisone therapy are independent predictive factors for the recurrence of PA after antifungal therapy. The nomogram developed in this study provided accurate individualized estimates for predicting the recurrence of PA.
Ethnobotanical study of medicinal plants and its Economic importance in Dalomana district, Southeastern Oromia, Ethiopia
Authors: Shure Hasen Abdela , Talila Habte , Mohammed Umer , Jilo Sufian Abdo
Published: April 2022

Ethnobotanical study of medicinal plants was carried out March 25 to September 5, 2021, in Dalomana district of Oromia region, Ethiopia. The study focused on documentation of medicinal plants used to treat various human diseases in the study area. Ethnobotanical data were collected using semistructured interviews, group discussion, guided field walks, and observations with participants. Preference ranking, paired comparison, direct matrix ranking, and informant consensus factors (ICF) were used to analyze the importance of some plant species. A total of 93 medicinal plants, distributed in 31 families, 59 genera and 5 of them are unknown were collected and identified. Plant family with the highest medicinal plants in the study area used for various diseases treatment was Fabaceae 10 (10.8 %) followed by Euphorbaieae 6 (6.5%). The result of growth form analysis showed that shrubs constituted the highest proportion of medicinal plants (48.6%). Roots (48.9%) were the most frequently utilized plant parts for preparation of traditional herbal medicines. Crushing was a widely used mode of preparation of traditional remedies where oral administration (37.5%) was the dominant route. The highest informants consensus factor (ICF) values were linked to eye disease (0.66); the lowest was linked with external parasites and wound (0.21). Local people in the study area possess traditional knowledge of medicinal plants to treat various human ailments; however, agricultural expansion and disinterest of young generation became the major threat to medicinal plants. In this study area the total benefits (profits) from the traditional healer practices is estimated to be 237542 birr annually generated as income. It is, therefore, necessary to preserve this indigenous knowledge on traditional medicines by proper documentation, identification of plant species used, and herbal preparation. To save medicinal plants from further loss, involving local communities in cultivation of the most utilized medicinal plants is recommended.
keywords: Ethnobotany, Medicinal Plants, Threat, Conservation
Analysis and modeling of dolomite sealing potential
Authors: zhang sihai , Xu Yin , Lu Peng
Published: April 2022

One of the challenges toward understanding and predicting carbonate reservoir quality is the complex syn- to post-depositional diagenetic processes. Dolomitization is a critical modifier for carbonate reservoir quality in transforming the original grain-pore framework. Dolomitization especially leads to the redistribution of pore structure and connectivity, permeability, pathways, and reservoir producibility. Dolomite may behave as either a conduit or a barrier to flow depending on the original depositional texture, the chemistry of dolomitizing fluid, previous diagenetic stages, the timing and type of dolomitization, and the presence of anhydrite. A quantitative conceptual model of dolomite sealing potential was established based on theoretical calculations of dolomitization for reservoir quality, supported by core and thin section data. The dolomite volume fraction-porosity relationships suggest that (1) generally, dolomitization can be divided into replacement and pore-filling (over-dolomitization) phases; (2) porosity preservation characterizes the former phase, and reduction of porosity for the latter phase; (3) grain-dominated limestone facies usually have less dolomitization potential (e.g., the dolomite fraction is usually < 0.8), whereas muddy facies have a higher dolomitization potential. Away from the dolomitizing fluid source, low flux and normal concentrations cause porosity preservation. Near the fluid source, high flux and high concentrations cause over-dolomitization. Tight dolomite can be an effective seal featuring high dolomite content, small pore throats, low porosity and low permeability. 3D geological models based on well logs and seismic data were built to help understanding the dolomitization mechanism, predict replacive dolomite and dolomite seal distribution. Modeling results very well proved the two phase’s dolomitization and the sealing potential of tight dolomite.
Healthcare use and costs among individuals receiving mental health services for depression within primary care in Nepal
Authors: Aldridge Luke R , Garman Emily C , Patenaude Bryan , Bass Judith K , Jord Mark JD , Luitel Nagendra P
Published: April 2022

BackgroundMental health services integrated into primary care is a key strategy for reducing the mental healthcare treatment gap in low- and middle-income countries. We examined trends in healthcare use and costs among individuals with depression and subclinical depressive symptoms in Chitwan, Nepal to understand the impact of integrated care on individual and health system resources. MethodsIndividuals diagnosed with depression at ten primary care facilities were randomized to receive a package of integrated care based on the Mental Health Gap Action Programme (treatment group; TG) or this package plus individual psychotherapy (TG+P); individuals with subclinical depressive symptoms received primary care as usual (UC). Primary outcomes were changes in use and health system costs of outpatient healthcare at 3- and 12-month follow up. Secondary outcomes examined use and costs by type. We used Poisson and log-linear models for use and costs, respectively, with an interaction term between time point and study group, and with TG as reference. ResultsThe study included 188 primary care service users (TG=59, TG+P=60, UC=69; 86% female, 24% formally employed, mean age 41.1). At baseline, outpatient visits were similar (-11%, p=0.51) among TG+P and lower (-35%, p=0.01) among UC compared to TG. Visits increased 2.30 times (p<0.001) at 3 months among TG, with a 50% greater increase (p=0.03) among TG+P, before returning to baseline levels among all groups at 12 months. Comparing TG+P to TG, costs were similar at baseline (-1%, p=0.97) and cost changes did not significantly differ at three (-16%, p=0.67) or 12 months (-45%, p=0.13). Costs among UC were 54% lower than TG at baseline (p=0.005), with no significant differences in cost changes over follow up. ConclusionDelivering psychotherapy within integrated services for depression resulted in greater healthcare use without significantly greater costs to the health system or individual. Post hoc analysis indicated individuals not receiving psychotherapy used less frequent, more costly healthcare. Previous research in Chitwan demonstrated psychotherapy determined treatment effectiveness for people with depression. While additional research is needed into health system implementation costs, our findings provide further evidence for including psychotherapy within mental healthcare integration in Nepal and similar contexts.
Canopies, the Final Frog-tier: Exploring responses of a specialist treefrog to prescribed fire in a pyrogenic ecosystem
Authors: Biazzo Ian , Quintana-Ascencio Pedro F.
Published: April 2022

Background: Pine flatwoods of the Southeast United States evolved with frequent wildfires. Land managers today mostly use prescribed burns to control fuels but also to restore historical lightning-caused wildfires dynamics. Though coarse outcomes of this practice are well-understood, fine scale impacts on many animal assemblages are still being explored. Frogs, for example, have upland and wetland requirements, limited mobility, and skin susceptible to desiccation and chemicals. Treefrogs, which are typically nontargeted for management, spend most of their lives in uplands away from water. When fire approaches, these animals will escape to an unburned area, hide in place, or die. Results: We assessed impacts of prescribed fire on the dynamics of an upland flatwoods specialist, the pinewoods treefrog Dryophytes femoralis using a replicated before-after-control-impact field experiment. Using single rope technique and climbing equipment, we set PVC pipes as treefrog refugia at 3m, 6m, 9m, and 9+m in Longleaf Pines, Pinus palustris (n=12 tress). Three trees were selected in each patch per treatment: two unburned and two burned patches during the 2021 burning season (n=4 patches). Every two weeks between March and September we checked pipes for frogs and assigned them unique Visible Implant Elastomer (VIE) marks. We obtained data from 76 individuals with an additional 198 recaptures. Using mark-recapture methods and mixed linear models with Bayesian framework, we modeled abundance, survival, and vertical movement. Survival and recapture were comparable among treatments, but abundance, new frogs and probability of moving up or down a tree varied. Frogs in trees in burned units were more likely to stay in place and less likely to descend to lower heights. We observed an increased probability of finding new frogs and more abundance in trees after a fire compared to unburned controls. Conclusions: We found the prevailing mechanism for resiliency to fire for pinewoods treefrogs was migration up large pines, then recolonization of the shrub layer when it regreens post-fire. This finding substantiates conclusions from other works that integrity of mature pines is key to sustaining native biodiversity. Future work and management should consider the three-dimensional structure of habitat when developing burn prescriptions and study designs.
Clinicopathological Patterns and Surgical Outcomes of Primary Brain Tumors Managed at a Tertiary Hospital in Arusha, Tanzania:a Cross-sectional Analysis.
Authors: Magwesela Faraja M. , Msemakweli Doreen , Rabiel Happiness
Published: April 2022

Purpose: The epidemiology of brain tumors varies globally between different countries and there is observed poor outcomes in lower- and middle-income countries. Our aim is to analyze the clinicopathological pattern of intracranial tumors in our setting and their post-surgical outcomes.Methods: This is a retrospective study. Data was obtained from clinical records of patients with intracranial tumors treated at our neurosurgery unit between 2019 and 2020. Only patients with primary brain tumors who underwent surgical intervention were included. Analysis was done to identify factors associated with patient outcomes (mortality/survival and performance status).Results: 39 patients with primary brain tumors underwent surgery (adults 72.8%, males 53.8%, mean age 35.8years). Gliomas (46.2%) comprised the most common tumor diagnosis overall and craniopharyngiomas were the most common tumors in pediatric patients (27.3%). Most patients (83.3%) had a poor performance status before surgery. Gross tumor resection (25.6%) was low and few patients (31.4%) underwent adjuvant therapy. 30-day mortality rate (10.3%) and one year mortality rate (46.2%) were high. Pediatric patients had a much worse outcome (46.2% mortality rate compared to 25% in adults, and 80% with poor performance status) as did males (38.1% mortality rate compared to 27.8% in females). Gliomas accounted for majority (69.2%) of the deaths.Conclusion: Delayed presentation and poor access to adjuvant therapies are important contributors of the high mortality and abandonment of treatment. Inadequate long-term follow-up is a hinderance to optimal neurooncological care in our setting.
Small and large scale engineering design optimization using an innovative hybrid algorithm
Authors: Parouha Raghav Prasad
Published: April 2022

An innovative hybrid algorithm (ihPSODE) present in this paper, for finding the solution of small and large scale engineering design optimization problems. A new particle swarm optimization (nPSO) and differential evolution (nDE) introduced in ihPSODE, to promote the search accuracy. Besides, a novel inertia weight, acceleration factor and position update structure is adopted in nPSO to increase the population diversity as well as a novel mutation approach and crossover rate is implemented in nDE to escape from local optima. After fitness function calculations recognize the top half member with discard rest half and apply nPSO which help to sustain exploration and exploitation competency of the algorithm. Furthermore, to achieve rapid convergence and stability, apply nDE on offspring created by nPSO. The population resultant by nPSO and nDE are combined for repetition. The efficiency of ihPSODE with its integrating nPSO and nDE algorithm validated on 23 unconstrained benchmark functions and utilized to solve 5 small (structural optimization) and 1large (economic dispatch with 3-, 6-, 15-, 40-, 140-unit test system considering with or without valve point effect) scale engineering design optimization problems plus comparing the results with various modern algorithms. Experimental and equated results confirm the superiority of the proposed algorithms.
Automatic classification of experimental models in biomedical literature to support searching for alternative methods to animal experiments
Authors: Neves Mariana , Klippert Antonina , Knöspel Fanny , Rudeck Juliane , Stolz Ailine , Ban Zsofia , Becker Markus , Diederich Kai , Grune Barbara , Kahnau Pia , Ohnesorge Nils , Pucher Johannes , Schönfelder Gilbert , Bert Bettina , Butzke Daniel
Published: April 2022

Background: European Union legislature requires replacement of animal experiments with alternative methods, whenever such methods are suitable to reach the intended scientific objective. However, searching for alternative methods in the scientific literature is a time-consuming task that requires careful screening of an enormously large number of experimental biomedical publications. The identification of potentially relevant methods, e.g. organ or cell culture models, or computer simulations, can be supported with text mining tools specifically built for this purpose. Such tools are trained (or fine tuned) on relevant data sets labeled by human experts. Methods: We developed the GoldHamster corpus, composed of 1,600 PubMed (Medline) abstracts, in which we manually identified the used experimental model according to a set of eight labels, namely: “in vivo”, “organs”, “primary cells”, “immortal cell lines”, “invertebrates”, “humans”, “in silico” and “other” (models). We recruited 13 annotators with expertise in the biomedical domain and assigned each article to two individuals. Three additional rounds of annotation aimed at improving the quality of the annotations with disagreements in the first round. Furthermore, we conducted various machine learning experiments based on supervised learning to evaluate the suitability of the corpus for our classification task. Results: We obtained more than 7,000 abstract-level annotations for the above labels. The inter-annotator agreement (kappa coefficient) varied among labels, and ranged from 0.63 (for “others”) to 0.82 (for “invertebrates”), with an overall score of 0.74. The best-performing machine learning experiment used the BioBERT pre-trained model with fine-tuning to our corpus, which gained an overall f-score of 0.82. Conclusions: We obtained a high agreement for most of the labels, and our evaluation demonstrated, that our corpus is suitable for training reliable predictive models for automatic classification of biomedical literature according to the used experimental models. Our “Smart feature-based interactive” search tool (SMAFIRA) will employ this classifier for supporting the retrieval of alternative methods to animal experiments. The corpus and the source code will be made available.
Integrating Network Pharmacology and Pharmacological Validation for Deciphering the Mechanism of Qishen Yixin Granules in Suppressing myocardial fibrosis
Authors: Jiang Hugang , Wang Xinqiang , Lin Wenyan , Liu Kai , Li Yingdong , Zhao Xinke
Published: April 2022

The present study aimed to reveal the bioactive compounds and molecular mechanisms of Qishen Yixin Granules (QSYXG) in the treatment of MF using an integrated network pharmacology and pharmacological validation approach. All active ingredients, drug targets, MF genes were screened from the TCMSP database, drug-target databases, GeneCard database, respectively. Functional and pathway enrichment analyses were operated through the clusterProfiler package in R programming language. Experimental validation was performed using haematoxylin-eosin staining, Masson’s trichrome staining and immunohistochemistry in isoproterenol-induced MF rats, and western blot analysis, phalloidin staining and immunofluorescence staining were used to elucidate the predicted mechanism on H9C2 cells. In this study, 55 bioactive components and 59 putative targets were collected. Functional enrichment analysis revealed that responses to lipopolysaccharides, oxidative stress and hypoxia were the key biological processes and were regulated simultaneously by six direct targets, including PTGS2, MAPK14, AKT1, MAPK8, IL-6 and IL-1β. Five pathways were determined by KEGG pathway enrichment analysis. The experiment results indicate QSYXG could down-regulated expression of PTGS2, MAPK14 and MAPK8 and up-regulated expression of AKT1 in the treatment of MF. This study revealed QSYXG could alleviate MF based on multiple components, targets and pathways.
Insect netting: effect of mesh size and shape on exclusion of some fruit pests and natural enemies under laboratory and orchard conditions
Authors: Chouinard Gérald , Pelletier Francine , Larose Mikael , Knoch Simon , Pouchet Catherine , Dumont Marie-Josée , Tavares Jason R.
Published: April 2022

To improve exclusion systems for fruit trees, insect nets of various types were evaluated for their permeability to different beneficial and pest species, under laboratory and field conditions. Pests studied were the apple maggot, Rhagoletis pomonella (Diptera: Tephritidae) and the spotted wing drosophila, Drosophila suzukii (Diptera: Drosophilidae). Beneficials were Aphidoletes aphidimyza (Diptera: Cecidomyiidae), Aphidius matricariae (Hymenoptera: Braconidae) and Aphelinus abdominalis (Hymenoptera: Aphelinidae). Mesh nets with five different apertures (square, rectangle, triangle, rhombus and hexagon) and six different sizes (from 0.4 to 2.8 mm) were 3D-printed from strands of polylactic acid and tested in the laboratory along with two commercially available nets made of polyethylene. The physical and behavioral characteristics of the six studied species affected their ability to cross the nets. For an equal size (open area), the intrusion rate was generally greater through the square- and / or hexagonal-shaped meshes. Rectangular-shaped apertures totally excluded the apple maggot in both laboratory and field trials, provided their shortest side did not exceed 1.9 mm. For the spotted-wing drosophila, a maximum of 1.0 mm was similarly required for exclusion in the laboratory. The shape factor (length / width ratio) of the apertures appeared to affect net selectivity. Field trials confirmed that more aphid predators and leafroller parasitoids colonized trees covered with larger mesh nets (2.3 x 3.4 mm), while still excluding the apple maggot. Thus, for a similar aperture size (area), an elongated rectangular shaped mesh appears to facilitate access for beneficials, while continuing to provide effective protection against apple pests.
Quantitative evaluation of neuron developmental morphology in vitro using the change-point test
Authors: Liao Ashlee , Cui Wenxin , Zhang Yongjie Jessica , Webster-Wood Victoria
Published: April 2022

Neuron morphology gives rise to distinct axons and dendrites and plays an essential role in neuronal functionality and circuit dynamics. In rat hippocampal neurons, morphological development occurs over roughly one week in vitro. This development has been qualitatively described as occurring in 5 stages. Still, there is a need to quantify cell growth to monitor cell culture health, understand cell responses to sensory cues, and compare experimental results and computational growth model predictions. To address this need, embryonic rat hippocampal neurons were observed in vitro over six days, and their processes were quantified using both standard morphometrics (degree, number of neurites, total length, and tortuosity) and new metrics (distance between change points, relative turning angle, and the number of change points) based on the Change-Point Test to track changes in path trajectories. Of the standard morphometrics, the total length of neurites per cell and the number of endpoints were significantly different between 0.5, 1.5, and 5 days in vitro, which are typically associated with Stages 2-4. Using the Change-Point Test, the number of change points and the average distance between change points per cell were also significantly different between those key time points. This work highlights key quantitative characteristics, both among common and novel morphometrics, that can describe neuron development in vitro and provides a foundation for analyzing directional changes in neurite growth for future studies.
Genetic background and clinical characteristics of infantile hyperammonaemia
Authors: Li Mengyao , Chen Xiang , Chen Huiyao , Hu Liyuan , Cao Yun , Cheng Guoqiang , Wang Laishuan , Wu Bingbing , Lu Wei , Yang Lin , Zhou Wenhao
Published: April 2022

Purpose: This study was conducted to analyse the genetic spectrum and clinical characteristics of infantile hyperammonaemia (HA).Methods: Between January 2016 and June 2020, we enrolled patients with definitive genetic diagnosis of infantile HA at the Children’s Hospital of Fudan University. Based on the age of HA onset, patients were grouped into neonatal and post-neonatal subgroups to compare their genetic and clinical features. Results: Collectively, 136 pathogenic or likely pathogenic variants of the 33 genes were identified. Fourteen genes were reported with HA (42%, 14/33), with SLC25A13 and MUT being the top two detected genes. In contrast, 19 genes were not reported with HA (58%, 19/33), in which JAG1 and ABCC8 were the most frequently mutated genes. Compared with post-neonatal HA, neonatal HA patients presented with higher rates of organic acidemia (p = 0.001) and fatty acid oxidation disorder (p = 0.006), but a lower rate of cholestasis (p < 0.001). Neonatal HA patients had a higher ratio of peak plasma ammonia level ≥ 500 μmol/L (p = 0.003) and were more likely to receive precision medicine (p = 0.027); however, they had a refractory clinical course (p = 0.001) and poorer prognosis than the infantile group.Conclusions: There were significant differences in the genetic spectrum, clinical features, clinical course, and outcomes between infants with different HA onset ages.
Risk factors of preterm birth among newborns delivered in public hospitals of Southern Ethiopia: A case-control study
Authors: Zewde Ashenafi , Gebremichael Bereket , Tesfaye Tewodros , Sibhat Migbar Mekonnen , Bimer Kirubel
Published: April 2022

Introduction:
The rate of premature birth appears to have increased over time. Over 3.1 million babies died due to prematurity and its complications. The definite cause of preterm birth remains concealed with a wide setting variation that puts difficulty in drawing the national figure. Hence, this study scrutinized the determinants of premature delivery.
Methods
Unmatched case-control study was employed on 266 newborns. Data were collected using an interviewer-administered questionnaire, entered into Epi data 4.4.2, and analyzed using SPSS 25. Data were analyzed using binary logistic regression. Variables with p < 0.25 in the bi-variable analysis were included in the final model. Finally, a p-value of ≤ 0.05 and an AOR with 95% CI was used to declare the statistical significance and strength of associations.
Findings:
An overall 266 mothers of neonates (89 cases and 177 controls) participated in the study with a 98.5% response rate. Having short inter-pregnancy interval [AOR = 4.00;95%CI:1.12,14.21], antepartum hemorrhage [AOR = 7.27;95%CI:2.16,35.50], premature rupture of membrane [AOR = 5.21;95%CI:1.10,24.72], intimate partner violence [AOR = 8.00;95%CI:1.93,33.21], and residing in rural areas [AOR = 3.72;95%CI:1.14,12.18] showed statistically significant association with preterm birth. Thereby, it is essential to strengthen screening and preventive services focusing on mothers who are at risk for obstetric complications such as antepartum hemorrhage and premature rupture of the membrane.
Going off the rails with Sally Jones: Promoting literary understanding in character-focused read-aloud discussions
Authors: Walldén Robert
Published: April 2022

Although discussion-based approaches to literature have been researched extensively, there has been little qualitative research on read-aloud discussions focusing on specific aspects of literature. Moreover, considering the current bias towards comprehension and analytical skills in language arts curricula, an on-going discussion about different dimensions of literary understanding in classroom practice is necessary. Therefore, the present study seeks to contribute knowledge about possibilities for literary understanding in character-focused classroom discussions. Data, comprised of field notes and transcribed audio recordings, were collected throughout 12 lessons in a Swedish Grade 4 during the reading aloud of the picture book Legenden om Sally Jones (The Legend of Sally Jones). The analysis was guided by thematic content analysis and reader-response theories, enabling a broad view of literary understanding. The result shows that character-focused discussions promoted evaluating the characters, making inferences, and considering important events. Occasionally, the students made analytical remarks about how the story worked. In addition, the students were encouraged to empathise with the characters while making connections between the text and their lives. Furthermore, the students drew on intertextual knowledge to use the text in creative expressions involving pleasurable narrative deaths. Implications for teaching and language arts curricula are discussed.