bluuebunny/crossref_metadata_2025_split huggingface dataset:
A protocol for reconstructing the dynamics of real-world systems from observational data: Application for establishing a digital proxy of a bioreactor (DIYBOT)
Authors: Huffaker Ray , McLamore Eric S. 
Published: September 2020

Abstract
This protocol sets out a broadly-applicable framework for empirically reconstructing the dynamics of biosystems from observational data, modeling reconstructed dynamics phenomenologically with systems of ordinary differential equations extracted from the data, and detecting and quantifying causal interactions among system components. The protocol draws from well-established procedures in Nonlinear Time Series Analysis (NLTS) that can be run with existing R packages. The protocol was applied in McLamore et al. (2020)1 to develop a phenomenological digital proxy of a bioreactor (DIYBOT) from real-time sensor data. DIYBOT was used to investigate whether bioreactor dynamics self-corrected in response to contamination spikes of increasing degrees; and consequently, the extent to which corrective human-in-the-loop management might be required.
Differences in trochlear groove based on morphometric measurements of three-dimensional reconstruction models between native knees and five different femoral component designs in Chinese subjects
Authors: Chen Shi Chang , Xu Hua , Gong Shaohua 
Published: September 2020

Abstract
Background: The prosthetic trochlear design is important in postoperative patellofemoral kinematics and knee function. However, little research has been conducted on the differences in trochlear groove between native and prosthetic knees. We aimed to investigate the differences between Chinese native knees and prosthetic knees of five different femoral component designs using three-dimensional computerized quantification of the entire trochlear length.Methods: Virtual total knee arthroplasty was performed using three-dimensional models of 42 healthy Chinese knees matched to the femoral components of five different prosthetic systems by mechanical alignment. The deepest points of the trochlear groove were marked in multiple cross sections for both the native and prosthetic knees. Taking the lower extremity mechanical axis as reference line, the differences in the mediolateral location of the trochlear groove were analyzed between the native and prosthetic knees.Results: From the proximal to the distal end, the native trochlear groove started from 0° cross section and extended laterally and then medially, with its turning point located at 69° cross section. The prosthetic trochlear groove showed a similar medial orientation and extended more proximally, but varied in mediolateral location and the length extending to the intercondylar notch. Compared with the proximal portion of the native trochlear groove, the prosthetic knees extended along a paradoxical orientation and started from a more proximal and lateral position to 3.2 mm in the 0° cross section, with maximal discrepancy. Distally, the prosthetic trochlear grooves were located significantly medial to 2.4 mm in the 69° cross section, with maximal discrepancy.Conclusion: The prosthetic trochlear design varied among the different types and did not conform to the native knee in terms of shape, orientation, and location, which may cause soft tissue tension imbalance and abnormal patellofemoral biomechanics during knee flexion. This study may provide useful information for creating prosthetic trochlear designs that conform with the native knee anatomy to optimize patellofemoral biomechanics and reduce the risk of patellofemoral complications.
White Thrombosis on Optical Coherence Tomography after Rotational Atherectomy of Severely Coronary Calcified Lesions
Authors: CAO Cheng-fu , MA Yu-liang , LI Qi , LIU Jian , ZHAO Hong , LU Ming-yu , wang weimin 
Published: September 2020

Abstract
Background: Rotational atherectomy (RA) has improved percutaneous treatment of severe coronary calcified lesions, but the "no-reflow" phenomenon remains a serious complication. Platelet activation by RA may contribute to the no-reflow, we use optical coherence tomography (OCT) to test the effect of RA on white thrombosis that could confirm platelet activation indirectly. Methods: We analyzed 53 consecutive patients with coronary angiographic severe calcified lesions. All the patients were examined by OCT. Twenty patients received RA and OCT imaging performed before and after RA and after stent implantation. The remaining patients were as a control group and OCT imaging performed before balloon dilatation and after stent implantation. Results: The patients were older and higher incidence of Diabetes mellitus in the RA group. In the RA group, the mean burr size was 1.48±0.14mm. The mean rotation speed was 152,300±4,200rpm. The mean number of rotations per patient was 5.3±2.1 times and the mean ablation time per RA was 11.3±3.2 seconds. In the control group, there was no thrombogenesis during the procedure, but in the RA group, all the target vessels had only white thrombosis on OCT after RA. The average number of white thrombus per lesion after RA was 7.23±4.4, and the average length of every white thrombus was 0.51±0.33mm. In Pearson Correlation Analysis, Thrombotic load was related with burr size (r=0.575, P=0.040) and rotation number (r=0.599, P=0.031).Conclusions: White thrombosis during RA is proved by OCT in vivo. Treating calcified lesions with RA may enhance thrombogenesis. These data suggest using a proper therapy to avoid no-reflow during RA.
Significant reduction in abundance of&nbsp;peridomestic mosquitoes (Culicidae) and&nbsp;Culicoides&nbsp;midges (Ceratopogonidae) after chemical intervention in western São Paulo,&nbsp;Brazil
Authors: González Mikel A. , Dilger Erin , Ronderos María M. , Spinelli Gustavo R. , Courtenay Orin , Hamilton James Gordon Campbell 
Published: September 2020

Abstract
Background: We assessed the impact of two sand fly insecticide interventions (insecticide spraying and insecticide-impregnated dog collars) on the peridomestic abundance and distribution of mosquitoes (Culicidae) and biting midges (Ceratopogonidae) in Western São Paulo (Brazil) in a long-term (42-month) evaluation. Both of these Dipteran groups are vectors of diseases of medical and veterinary relevance to humans and domestic animals in Brazil. Methods: The interventions in the 3-arm stratified randomised control trial were: pheromone + insecticide (PI) (chicken roosts were sprayed with microencapsulated lambda-cyhalothrin; pheromone lure has no effect on the Diptera pests studied here), dog-collars (DC) (dogs fitted with deltamethrin-impregnated collars), and control (C) (unexposed to pyrethroids) were extended by 12 months. During that time, adult mosquitoes and midges were sampled along 280 households at three household locations (inside human dwellings, dog sleeping sites, and chicken roosts).Results: We collected 3,145 culicids (9 genera, 87.6% Culex spp.) distributed relatively uniformly across all 3 arms; 41.9% at chicken roosts, 37.7% inside houses, and 20.3% at dog sleeping sites. We collected 11,464 Culicoides (15 species) found mostly at chicken roosting sites (84.7%) compared with dog sleeping sites (12.9%) or houses (2.4%). Mosquitoes and Culicoides were most abundant during the hot and rainy season. Increased daytime temperature was marginally associated with increased mosquito abundance (z = 1.97; P = 0.049) and Culicoides abundance (z = 1.71; P = 0.087). There was no significant association with daily average rainfall for either group. Household-level mosquito and midge numbers were both significantly reduced by the PI intervention 56% [Incidence Rate Ratio, IRR = 0.54 (95% C.I. 0.30, 0.97), P ≤ 0.05] and 53% [IRR = 0.47 (0.26, 0.85), P ≤ 0.05], respectively, compared to the control intervention. The abundance of both Dipteran groups at dog sleeping sites was largely unaffected by the PI and DC interventions. The PI intervention significantly reduced abundance of mosquitoes inside houses (41%) and at chicken roosting sites (48%) and reduced midge abundance by 51% in chicken roosting sites.Conclusions: Sprayed insecticide at chicken roosting sites reduced the abundance of mosquitoes and midges at the peridomestic level while dog collars had no effect on numbers for any group.
Relationship Between the Levels of Inflammatory Cytokines in the Aqueous Humor and Cataract in Fuchs Uveitis Syndrome-A Case Control Study
Authors: Wang Hui , Tao Yong 
Published: September 2020

Abstract
Background This study aims to compare the levels of intraocular cytokines between FUS eyes and the senile cataract eyes. The association between inflammatory cytokine levels and cataract severity in FUS is evaluated to find the possible mechanism of cataract in FUS eyes. Methods A retrospective study of 28 eyes with FUS was performed. Auxiliary examinations were performed, including ophthalmic examinations, laser flare-cell photometry, and levels of inflammatory cytokines in the aqueous humor were measured. The control group included 25 eyes with senile cataract. Data on the aqueous humor inflammatory cytokines were compared between the two groups. The association between the aqueous humor cytokine levels and severity of posterior subcapsular cataract was assessed. Results There were 28 eyes with FUS in 27 patients. Unilateral involvement was noted in 26 patients (96.30%). Stellate keratic precipitates (KPs) were noted in 16 eyes (57.14%). Heterochromia was observed in 21.43% of affected eyes. Posterior subcapsular cataract (PSC) was observed in 16 of the 28 eyes. Eyes with FUS had significantly higher aqueous humor (AH) cytokine levels (VEGF, bFGF, IL-6, IL-8 and IL-10) compared with the control eyes (P<0.05). There was a statistically significant positive correlation between the severity of cataract and IL-6 and IL-8 levels in the AH (τ = 0.675 and 0.793, respectively; P = 0.001, P<0.001, respectively). Conclusions Expression of VEGF, bFGF, IL-6, IL-8 and IL-10 in the AH of FUS patients was significantly higher than in senile cataract eyes, and the aqueous humor levels of IL-6 and IL-8 were significantly positively associated with the severity of posterior subcapsular cataract. Our results imply that an inflammation mechanism may be involved in the early development of cataract in FUS.
Prevalence and social determinants of psychological distress among people who use drugs in Cambodia
Authors: Saing Chan Hang , Prem Kiesha , Uk Ponha , Chann Navy , Chhoun Pheak , Mun Phalkun , Tuot Sovannary , Yi Siyan 
Published: September 2020

Abstract
Background: People who use drugs are at a disproportionately higher risk of mental disorders due to prolonged exposure to psychosocial challenges. However, studies on mental health among people who use drugs in resource-constrained countries are scarce. This study sheds light on the prevalence and correlates of psychological distress among people who use drugs in Cambodia.Methods: We conducted this cross-sectional study in 12 provinces in 2017. The Respondent Driven Sampling method was adapted to recruit 1677 people who used drugs for face-to-face interviews using a structured questionnaire. Psychological distress was measured using the General Health Questionnaire (GHQ-12). A total score of GHQ-12>2 indicated high psychological distress. We performed a multiple logistic regression analysis to examine factors associated with psychological distress. Results: The mean age of the participants was 28.6 years (SD= 7.8). Of the total, 41.9% had high psychological distress – 49.7% in women and 37.3% in men. We included 1598 participants in the multiple logistic regression analysis. The adjusted odds of having high psychological distress was significantly higher among participants who were 25-34 years old (AOR 1.30, 95% CI 1.01-1.70) and 35 years and above (AOR 1.68, 95% CI 1.19-2.35), had been to a drug rehabilitation center (AOR 2.06, 95% CI 1.48-2.86), had been insulted by family members (AOR 2.09, 95% CI 1.62-2.70), and had been sexually harassed/abused by someone when they were growing up (AOR 1.80, 95% CI 1.38-2.36). The odds of having high psychological distress was significantly lower among participants who were male (AOR 0.53, 95% CI 0.41-0.69), lived in own dwelling (AOR 0.56, 95% CI 0.41-0.77), reported injecting as the mode of the first drug use (AOR 0.56, 95% CI 0.34-0.91), and had someone taking care of when getting sick (AOR 0.68, 95% CI 0.47-0.99).Conclusions: This study documents a high prevalence of psychological distress among people who use drugs in Cambodia. Intervention programs that attempt to address mental health problems among people who use drugs in resource-limited settings should be gender- and age-sensitive and target more marginalized subpopulations. Mental health services can be integrated into HIV and harm-reduction programs for people who use drugs.
Spread of SARS-CoV-2 Genomes on Genomic Index Maps of Hierarchy
Authors: Zheng Jeffrey , Zhou Yang , Zhu Minghan , Qiao Mu , Zhang Zhigang 
Published: September 2020

Abstract
Using visual technologies, COVID-19 patients worldwide are conveniently described by position information to collect samples, and modern GIS maps are useful to show influenced flows and numbers of patients on various regions of a pendamic. From an analysis viewpoint, it is more interesting to organize genomic information into a phylogenic tree with multiple branches and leaves in representations. Clusters of genomes are organized as phylogenic trees to represent intrinsic information of genomes. However, there are structural difficulties in projecting phylogenetic information into 2D distributions as GIS maps naturally. In this paper, a novel projection is proposed to arrange SARS-CoV-2 genomes by genomic indexes to make a structural organization as 2D GIS maps. For any genome, there is a unique invariant under certain conditions to provide an absolute position on a specific region. In this hierarchical framework, it is possible to use a visual tool to represent any selected region for clustering genomes on refined effects. Complementary visual effects are provided with phylogenetic tree technology. Sample regions and various projections show spread effects of five thousand SARS-CoV-2 genomes in 72 countries, and four special countries are selected on genomic index maps.
Host phylogeny matters: Examining sources of variation in infection risk by blood parasites across a tropical montane bird community in India
Authors: Gupta Pooja , Vishnudas C.K. , Robin V.V. , Dharmarajan Guha 
Published: September 2020

Abstract
Background: Identifying patterns and drivers of infection risk among host communities is crucial to elucidate disease dynamics and predict infectious disease risk in wildlife populations. Blood parasites of genera Plasmodium and Haemoproteus are a diverse group of vector-borne protozoan parasites that affect bird populations globally. Despite their widespread distribution and exceptional diversity, factors underlying haemosporidian infection risk in wild bird communities remain poorly understood. While some studies have examined variation in avian haemosporidian risk, researchers have primarily focused on host ecological traits without considering host phylogenetic relationships. In this study, we employ a phylogenetically informed approach to examine the association between host ecological traits and haemosporidian infection risk in endemic bird communities in the Western Ghats Sky Islands.Methods: We used parasite sequence data based on partial mitochondrial cytochrome b gene, that was amplified from genomic DNA extracted from 1177 birds (28 species) across the Western Ghats to assess infection of birds with haemosporidian parasites. We employed a Bayesian phylogenetic mixed effect modelling approach to test whether haemosporidian infection risk was affected by seven species-specific and four individual level ecological predictors. We also examined the effect of host phylogenetic relationships on the observed patterns of variation in haemosporidian infection risk by estimating phylogenetic signal.Results: Our study shows that host ecological traits and host phylogeny differentially influence infection risk by Plasmodium (generalist parasite) and Haemoproteus (specialist parasite). For Plasmodium, we found that sociality, sexual dimorphism and feeding strata were important ecological predictors. For Haemoproteus, patterns of infection risk among host species were associated with sociality, elevation and individual body condition. Interestingly, variance in infection risk explained by host phylogeny was higher for Haemoproteus parasites compared to Plasmodium. Conclusion: Our study highlights that while host ecological traits promoting parasite exposure and host susceptibility are important determinants of infection risk, host phylogeny also contributes substantially to predicting patterns of haemosporidian infection risk in multi- host communities. Importantly, infection risk is driven by joint contributions of host ecology and host phylogeny and studying these effects together could increase our ability to better understand the drivers of infection risk and predict future disease threats.
Lung ultrasound and neonatal COVID-19 pneumonia: A case report.
Authors: Ríos Daniel Ibarra , García Dina Villanueva , Solano Edna Patricia Vázquez , García Alfonso de Jesús Martínez , Valdespino-Vázquez María Yolotzin , Repetto Addy Cecilia Helguera , González Horacio Márquez 
Published: September 2020

Abstract
Introduction: Severe Novel Coronavirus Disease 2019 (COVID-19) infection in neonates is possible but reports are scarce. Lung ultrasound (LUS) has been reported useful for triaging, diagnosing, and monitoring of patients with COVID-19.Material and methods: We describe SARS-CoV-2 confirmed infection on a term newborn that developed pneumonia and pulmonary hypertension requiring mechanical ventilation. Ultrasonographic follow up of COVID-19 pneumonia and pulmonary hypertension was carried out. Histopathological and genetic study of the placenta was performed. Results: A 3,140-g male infant born at 40.3 weeks’ gestation developed progressive respiratory distress (pulmonary hypertension) requiring mechanical ventilation. Real time PCR respiratory tract swabs for SARS COV 2 sampled on day 3 were positive for the baby and both parents. Lung ultrasound showed an irregular pleural line (shred sign), multiple confluent B-lines and bilateral ≥ 0.5 cm subpleural consolidations. Improvement of the lung and cardiac conditions were documented by ultrasound. The newborn was supported 6 days with mechanical ventilation, 3 days on CPAP and 3 days on oxygen. No antibiotics were used. The placenta showed histological findings linked to SARS-CoV-2 infection. RT-PCR from placental tissue showed amplification of viral E gene.Conclusion: Our case represents a severe presentation of COVID-19 pneumonia with pulmonary hypertension requiring mechanical ventilation. LUS showed to be useful for diagnosis and follow up. Transversal infection was possible.
What Factors Contribute to High Mechanical Strength of Tabia? Case Study of the Tabia from Coastal Forts Sites at Zhejiang, China
Authors: Zhang Cuisong , Zhang Bingjian , Cui Biao , Lin Guocong 
Published: September 2020

Abstract
Tabia is one of the most widely used construction materials in ancient China. In this work, the tabia samples from three coastal defense fort sites at Zhejiang Province, China, we analyzed to determine their component composition and physiochemical properties. The results show that these tabia samples exhibited high compressive strength, which could be as high as 4-9 MPa. Furthermore, the systematic analysis demonstrated that the high compressive strength was related to the following factors: 1) a suitable mass ratio of sand, lime, and clay; 2) an appropriate sand particle size ratio; and 3) the formation of hydrated calcium silicate (C-S-H). Moreover, sticky rice was also detected in the tabia samples. These findings are fundamentally important, which could be beneficial to further study of the craftsmanship of the coastal defense forts and could further provide essential guidance for the protection and restoration of the tabia relics.
Transcriptome analysis and differential gene expression profiling of two contrasting quinoa genotypes in response to salt stress
Authors: Shi Pibiao , Gu Minfeng 
Published: September 2020

Abstract
Background: Soil salinity is one of the major abiotic stress factors that affect crop growth and yield, which seriously restricts the sustainable development of agriculture. Quinoa is considered as one of the most promising crops in the future for its high nutrition value and strong adaptability to extreme weather and soil conditions. However, the molecular mechanisms underlying the adaptive response to salinity stress of quinoa remain poorly understood. To identify candidate genes related to salt tolerance, we performed reference-guided assembly and compared the gene expression in roots treated with 300 mM NaCl for 0, 0.5, 2, and 24 h of two contrasting quinoa genotypes differing in salt tolerance.Results: The salt-tolerant (ST) genotype displayed higher seed germination rate and plant survival rate, and stronger seedling growth potential as well than the salt-sensitive (SS) genotype under salt stress. An average of 38,510,203 high-quality clean reads were generated. Significant Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified to deeper understand the differential response. Transcriptome analysis indicated that salt-responsive genes in quinoa were mainly related to biosynthesis of secondary metabolites, alpha-Linolenic acid metabolism, plant hormone signal transduction, and metabolic pathways. Moreover, several pathways were significantly enriched amongst the differentially expressed genes (DEGs) in ST genotypes, such as phenylpropanoid biosynthesis, plant-pathogen interaction, isoquinoline alkaloid biosynthesis, and tyrosine metabolism. 117 DEGs were common to various stages of both genotypes, identified as core salt-responsive genes, including some transcription factor members, like MYB, WRKY and NAC, and some plant hormone signal transduction related genes, like PYL, PP2C and TIFY10A, which play an important role in the adaptation to salt conditions of this species. The expression patterns of 21 DEGs were detected by quantitative real-time PCR (qRT-PCR) and confirmed the reliability of the RNA-Seq results. Conclusions: We identified candidate genes involved in salt tolerance in quinoa, as well as some DEGs exclusively expressed in ST genotype. The DEGs common to both genotypes under salt stress may be the key genes for quinoa to adapt to salinity environment. These candidate genes regulate salt tolerance primarily by participating in reactive oxygen species (ROS) scavenging system, protein kinases biosynthesis, plant hormone signal transduction and other important biological processes. These findings provide theoretical basis for further understanding the regulation mechanism underlying salt tolerance network of quinoa, as well establish foundation for improving its tolerance to salinity in future breeding programs.