bluuebunny/crossref_metadata_2025_split huggingface dataset:
Multi-level dilated residual network for biomedical image segmentation
Authors: Gudhe Naga Raju , Behravan Hamid , Sudah Mazen , Okuma Hidemi , Vanninen Ritva , Kosma Veli-Matti , Mannermaa Arto 
Published: July 2021

AbstractWe propose a novel multi-level dilated residual neural network, an extension of the classical U-Net architecture, for biomedical image segmentation. U-Net is the most popular deep neural architecture for biomedical image segmentation, however, despite being state-of-the-art, the model has a few limitations. In this study, we suggest replacing convolutional blocks of the classical U-Net with multi-level dilated residual blocks, resulting in enhanced learning capability. We also propose to incorporate a non-linear multi-level residual blocks into skip connections to reduce the semantic gap and to restore the information lost when concatenating features from encoder to decoder units. We evaluate the proposed approach on five publicly available biomedical datasets with different imaging modalities, including electron microscopy, magnetic resonance imaging, histopathology, and dermoscopy, each with its own segmentation challenges. The proposed approach consistently outperforms the classical U-Net by 2%, 3%, 6%, 8%, and 14% relative improvements in dice coefficient, respectively for magnetic resonance imaging, dermoscopy, histopathology, cell nuclei microscopy, and electron microscopy modalities. The visual assessments of the segmentation results further show that the proposed approach is robust against outliers and preserves better continuity in boundaries compared to the classical U-Net and its variant, MultiResUNet.
Exosomal hsa_circRNA_104484 and hsa_circRNA_104670 may serve as potential novel biomarkers and therapeutic targets for sepsis
Authors: Tian Chang , Liu Jiaying , Di Xin , Cong Shan , Zhao Min , Wang Ke 
Published: July 2021

AbstractIn order to explore the role of exosomal circRNAs in the occurrence and development of sepsis, we looked for potential diagnostic markers to accurately identify sepsis and to lay a molecular basis for precise treatment. Ultracentrifugation was used to extract exosomes from the serum of patients with sepsis and healthy individuals. Then, changes in circRNA expression in exosomes were studied by circRNA microarray analysis. Gene ontology (GO) analysis and Kyoto City Encyclopaedia of Genes and Genomes (KEGG) pathway analysis were used to annotate the biological functions and pathways of genes, and a circRNA-miRNA-mRNA regulatory network was constructed. In the microarray analysis, 132 circRNAs were significantly differentially expressed, including 80 and 52 that were upregulated and downregulated, respectively. RT-qPCR verified the results of microarray analysis: hsa_circRNA_104484 and hsa_circRNA_104670 were upregulated in sepsis serum exosomes. ROC analysis showed that hsa_circRNA_104484 and hsa_circRNA_104670 in serum exosomes have the potential to be used as diagnostic markers for sepsis. The circRNA-miRNA-mRNA network predicted the potential regulatory pathways of differentially expressed circRNAs. There are differences in the expression of circRNA in serum exosomes between patients with sepsis and healthy individuals, which may be involved in the occurrence and development of the disease. Among them, elevations in hsa_circRNA_104484 and hsa_circRNA_104670 could be used as novel diagnostic biomarkers and molecular therapeutic targets.
The value of autopsy in preterm infants at a Swedish tertiary neonatal intensive care unit 2002–2018
Authors: Hoffsten Alice , Markasz Laszlo , Ericson Katharina , Nelin Leif D. , Sindelar Richard 
Published: July 2021

AbstractReliable data on causes of death (COD) in preterm infants are needed to assess perinatal care and current clinical guidelines. In this retrospective observational analysis of all deceased preterm infants born < 37 weeks’ gestational age (n = 278) at a Swedish tertiary neonatal intensive care unit, we compared preliminary COD from Medical Death Certificates with autopsy defined COD (2002–2018), and assessed changes in COD between two periods (period 1:2002–2009 vs. period 2:2011–2018; 2010 excluded due to centralized care and seasonal variation in COD). Autopsy was performed in 73% of all cases and was more than twice as high compared to national infant autopsy rates (33%). Autopsy revised or confirmed a suspected preliminary COD in 34.9% of the cases (23.6% and 11.3%, respectively). Necrotizing enterocolitis (NEC) as COD increased between Period 1 and 2 (5% vs. 26%). The autopsy rate did not change between the two study periods (75% vs. 71%). We conclude that autopsy determined the final COD in a third of cases, while the incidence of NEC as COD increased markedly during the study period. Since there is a high risk to determine COD incorrectly based on clinical findings in preterm infants, autopsy remains a valuable method to obtain reliable COD.
Impact of antifungal stewardship interventions on the susceptibility of colonized Candida species in pediatric patients with malignancy
Authors: Amanati Ali , Badiee Parisa , Jafarian Hadis , Ghasemi Fatemeh , Nematolahi Samane , Haghpanah Sezaneh , Hamzavi Seyedeh Sedigheh 
Published: July 2021

AbstractThere is a worldwide concern regarding the antimicrobial resistance and the inappropriate use of antifungal agents, which had led to an ever-increasing antifungal resistance. This study aimed to identify the antifungal susceptibility of colonized Candida species isolated from pediatric patients with cancer and evaluate the clinical impact of antifungal stewardship (AFS) interventions on the antifungal susceptibility of colonized Candida species. Candida species colonization was evaluated among hospitalized children with cancer in a tertiary teaching hospital, Shiraz 2017–2018. Samples were collected from the mouth, nose, urine, and stool of the patients admitted to our center and cultured on sabouraud dextrose agar. The isolated yeasts identified by polymerase chain reaction–restriction fragment length polymorphisms (PCR–RFLP). DNA Extracted and PCR amplification was performed using the ITS1 and ITS4 primer pairs and Msp I enzyme. The broth microdilution method was used to determine the minimum inhibitory concentrations (MICs) for amphotericin B, caspofungin, and azoles. The prevalence of Candida albicans in the present study was significantly higher than other Candida species. Candida albicans species were completely susceptible to the azoles. The susceptibility rate of C. albicans to amphotericin B and caspofungin was 93.1% and 97.1%, respectively. The fluconazole MIC values of Candida albicans decreased significantly during the post-AFS period (P < 0.001; mean difference: 72.3; 95% CI of the difference: 47.36–98.62). We found that ‏52.5% (53/117) of the isolated C. albicans were azole-resistant before AFS implementation, while only 1.5% (2/102) of the isolates were resistant after implementation of the AFS program (P < 0.001). C. albicans fluconazole and caspofungin resistant rate also decreased significantly (P < 0.001) after implementation of the AFS program [26 (32.9%) versus 0 (0.0%) and 11 (10.9%) versus 1 (0.9%), respectively]. Besides, fluconazole use (p < 0.05) and fluconazole expenditure reduced significantly (about one thousand US$ per year) after the AFS program. Our results confirm the positive effect of optimized antifungal usage and bedside intervention on the susceptibility of Candida species after the implementation of the AFS program. C. albicans and C. glabrata exhibited a significant increase in susceptibility after the execution of the AFS program.
Dysregulation of anti-Mullerian hormone expression levels in mural granulosa cells of FMR1 premutation carriers
Authors: Friedman-Gohas Moran , Orvieto Raoul , Michaeli Abigael , Aizer Adva , Kirshenbaum Michal , Cohen Yoram 
Published: July 2021

AbstractFMR1 premutation (55–200 CGG repeats) results in fragile X-associated primary ovarian insufficiency (FXPOI). We evaluated expression levels of folliculogenesis-related mediators, follicle-stimulating hormone (FSH) receptor and anti-Mullerian hormone (AMH), to gain insights into the mechanisms underlying the reduced ovarian function. Mural granulosa cells (MGCs) were collected from FMR1 premutation carriers and noncarriers undergoing IVF treatments. At baseline, MGCs of carriers demonstrated significantly higher mRNA expression levels of AMH (3.5 ± 2.2, n = 12 and 0.97 ± 0.5, n = 17, respectively; p = 0.0003) and FSH receptor (5.6 ± 2.8 and 2.7 ± 2.8, respectively; p = 0.02) and higher AMH protein expression on immunostaining. Accordingly, FMR1 premutation-transfected COV434 cells exhibited higher AMH protein expression than COV434 cells transfected with 20 CGG repeats. We conclude that FMR1 premutation may lead to dysregulation of AMH expression levels, probably due to a compensatory mechanism. Elucidating the pathophysiology of FXPOI may help in early detection of ovarian dysfunction and tailoring IVF treatments to FMR1 premutation carriers.
Heterodissemination: precision insecticide delivery to mosquito larval habitats by cohabiting vertebrates
Authors: Unlu Isik , Faraji Ary , Wang Yi , Rochlin Ilia , Gaugler Randy 
Published: July 2021

AbstractConventional larvicide delivery strategies originally developed for permanent and floodwater mosquitoes have proved suboptimal in the small, scattered, and cryptic larval habitats preferred by container-inhabiting Aedes mosquitoes. New methods such as autodissemination, wherein adult mosquitoes spread insecticides to their own larval habitats, have been under study. Another novel delivery method termed heterodissemination, i.e. larvicide delivery by other species sharing the same habitats, has also been proposed. We conducted a proof-of-concept study with four independent experiments using American bullfrogs (Lithobates catesbeianus) and green frogs Lithobates clamitans as carriers of pyriproxyfen, an insect growth regulator, under semi-field conditions in three different locations, two in New Jersey, and one in Utah. Frogs with attached slow-release pyriproxyfen tablets were introduced into outdoor enclosures with water containers. Water samples from the containers were periodically tested using larval Aedes albopictus and Culex pipiens mosquitoes to assess mortality and percent eclosure inhibition. Overall pupal mortality [95% credible intervals] estimated by Bayesian analysis for the treatment group was 73.4% [71.3–75.2] compared to 4.1% [2.9–5.5] for the control group. Mortality within treatment groups in four different experiments ranged from 41 to 100%, whereas control mortalities ranged from 0.5% to 11%. We conclude that heterodissemination is a promising and effective approach deserving of further study.
Metamaterial array based meander line planar antenna for cube satellite communication
Authors: Alam Touhidul , Almutairi Ali F. , Samsuzzaman Md , Cho Mengu , Islam Mohammad Tariqul 
Published: July 2021

AbstractThis research article presents a design and performance analysis of a metamaterial inspired ultra-high frequency (UHF) compact planar patch antenna for the CubeSat communication system that could be smoothly integrated with commercially available 2U Cube Satellite structure and onboard subsystem. The proposed antenna consists of two layers, one is two different width meander line antenna patch with partial ground plane and another layer is 3 × 2 near-zero-indexed metamaterial (NZIM) metamaterial array structure with ground plane. The NZIM array layer has been utilized to minimize the coupling effect with Cube Satellite structure and improve the frequency stability with enhanced antenna gain and efficiency. The fabricated antenna can operate within the lower UHF frequency band of 443.5–455 MHz. with an average peak gain of 2.5 dB. The designed antenna impedance stability characteristic has been explored after integration with the 2U Cube Satellite body layout. Besides, the antenna communication performance has been verified using 2U Cube Satellite free space path loss investigation. Small antenna volume with trade-off between the antenna size and performance are the key advantages of the proposed design, as the antenna occupies only 80 × 40 × 3.35 mm3 space of the 2U Cube Satellite body structure and the geometrical parameters can be designed to provide the best performance between 449 and 468.5 MHz.
Mapping habitat suitability for Asiatic black bear and red panda in Makalu Barun National Park of Nepal from Maxent and GARP models
Authors: Su Huiyi , Bista Manjit , Li Mingshi 
Published: July 2021

AbstractHabitat evaluation is essential for managing wildlife populations and formulating conservation policies. With the rise of innovative powerful statistical techniques in partnership with Remote Sensing, GIS and GPS techniques, spatially explicit species distribution modeling (SDM) has rapidly grown in conservation biology. These models can help us to study habitat suitability at the scale of the species range, and are particularly useful for examining the overlapping habitat between sympatric species. Species presence points collected through field GPS observations, in conjunction with 13 different topographic, vegetation related, anthropogenic, and bioclimatic variables, as well as a land cover map with seven classification categories created by support vector machine (SVM) were used to implement Maxent and GARP ecological niche models. With the resulting ecological niche models, the suitable habitat for asiatic black bear (Ursus thibetanus) and red panda (Ailurus fulgens) in Nepal Makalu Barun National Park (MBNP) was predicted. All of the predictor variables were extracted from freely available remote sensing and publicly shared government data resources. The modeled results were validated by using an independent dataset. Analysis of the regularized training gain showed that the three most important environmental variables for habitat suitability were distance to settlement, elevation, and mean annual temperature. The habitat suitability modeling accuracy, characterized by the mean area under curve, was moderate for both species when GARP was used (0.791 for black bear and 0.786 for red panda), but was moderate for black bear (0.857), and high for red panda (0.920) when Maxent was used. The suitable habitat estimated by Maxent for black bear and red panda was 716 km2 and 343 km2 respectively, while the suitable area determined by GARP was 1074 km2 and 714 km2 respectively. Maxent predicted that the overlapping area was 83% of the red panda habitat and 40% of the black bear habitat, while GARP estimated 88% of the red panda habitat and 58% of the black bear habitat overlapped. The results of land cover exhibited that barren land covered the highest percentage of area in MBNP (36.0%) followed by forest (32.6%). Of the suitable habitat, both models indicated forest as the most preferred land cover for both species (63.7% for black bear and 61.6% for red panda from Maxent; 59.9% black bear and 58.8% for red panda from GARP). Maxent outperformed GARP in terms of habitat suitability modeling. The black bear showed higher habitat selectivity than red panda. We suggest that proper management should be given to the overlapping habitats in the buffer zone. For remote and inaccessible regions, the proposed methods are promising tools for wildlife management and conservation, deserving further popularization.
Cortical correlates in upright dynamic and static balance in the elderly
Authors: Rubega Maria , Formaggio Emanuela , Di Marco Roberto , Bertuccelli Margherita , Tortora Stefano , Menegatti Emanuele , Cattelan Manuela , Bonato Paolo , Masiero Stefano , Del Felice Alessandra 
Published: July 2021

AbstractFalls are the second most frequent cause of injury in the elderly. Physiological processes associated with aging affect the elderly’s ability to respond to unexpected balance perturbations, leading to increased fall risk. Every year, approximately 30% of adults, 65 years and older, experiences at least one fall. Investigating the neurophysiological mechanisms underlying the control of static and dynamic balance in the elderly is an emerging research area. The study aimed to identify cortical and muscular correlates during static and dynamic balance tests in a cohort of young and old healthy adults. We recorded cortical and muscular activity in nine elderly and eight younger healthy participants during an upright stance task in static and dynamic (core board) conditions. To simulate real-life dual-task postural control conditions, the second set of experiments incorporated an oddball visual task. We observed higher electroencephalographic (EEG) delta rhythm over the anterior cortex in the elderly and more diffused fast rhythms (i.e., alpha, beta, gamma) in younger participants during the static balance tests. When adding a visual oddball, the elderly displayed an increase in theta activation over the sensorimotor and occipital cortices. During the dynamic balance tests, the elderly showed the recruitment of sensorimotor areas and increased muscle activity level, suggesting a preferential motor strategy for postural control. This strategy was even more prominent during the oddball task. Younger participants showed reduced cortical and muscular activity compared to the elderly, with the noteworthy difference of a preferential activation of occipital areas that increased during the oddball task. These results support the hypothesis that different strategies are used by the elderly compared to younger adults during postural tasks, particularly when postural and cognitive tasks are combined. The knowledge gained in this study could inform the development of age-specific rehabilitative and assistive interventions.
Bacillus firmus I-1582 promotes plant growth and impairs infection and development of the cyst nematode Heterodera schachtii over two generations
Authors: Huang Mengmeng , Bulut Aylin , Shrestha Bidhya , Matera Christiane , Grundler Florian M. W. , Schleker A. Sylvia S. 
Published: July 2021

AbstractPlant-parasitic nematodes wreak havoc on crops by root parasitism worldwide. An approach to combat nematode root parasitism is the application of antagonistic microbes like the rhizobacterium Bacillus firmus I-1582 which is promoted as biological control agent. Although B. firmus is a known nematode antagonist in general, the underlying mechanisms about its interaction with nematodes and plants have not yet been elucidated. Therefore, we explored the influence of B. firmus I-1582 as well as its extracellular and secreted molecules on plant–nematode interaction utilizing the plant–pathogen system Arabidopsis thaliana–Heterodera schachtii. We demonstrated that B. firmus I-1582 is attracted by A. thaliana root exudates, particularly by those of young plants. The bacterium colonized the root and showed a strictly pH-dependent development and plant growth promotion effect. Our results revealed that root colonization by B. firmus I-1582 significantly protected A. thaliana from infestation by the beet cyst nematode whereas dead bacterial cells or the culture supernatant were not effective. The bacterium also negatively affected nematode reproduction as well as pathogenicity and development of next generation nematodes. The obtained results highlight B. firmus I-1582 as a promising biocontrol agent that is well suited as an element of integrated control management strategies in sustainable agriculture.
CPT to RVU conversion improves model performance in the prediction of surgical case length
Authors: Garside Nicholas , Zaribafzadeh Hamed , Henao Ricardo , Chung Royce , Buckland Daniel 
Published: July 2021

AbstractMethods used to predict surgical case time often rely upon the current procedural terminology (CPT) code as a nominal variable to train machine-learned models, however this limits the ability of the model to incorporate new procedures and adds complexity as the number of unique procedures increases. The relative value unit (RVU, a consensus-derived billing indicator) can serve as a proxy for procedure workload and could replace the CPT code as a primary feature for models that predict surgical case length. Using 11,696 surgical cases from Duke University Health System electronic health records data, we compared boosted decision tree models that predict individual case length, changing the method by which the model coded procedure type; CPT, RVU, and CPT–RVU combined. Performance of each model was assessed by inference time, MAE, and RMSE compared to the actual case length on a test set. Models were compared to each other and to the manual scheduler method that currently exists. RMSE for the RVU model (60.8 min) was similar to the CPT model (61.9 min), both of which were lower than scheduler (90.2 min). 65.2% of our RVU model’s predictions (compared to 43.2% from the current human scheduler method) fell within 20% of actual case time. Using RVUs reduced model prediction time by ninefold and reduced the number of training features from 485 to 44. Replacing pre-operative CPT codes with RVUs maintains model performance while decreasing overall model complexity in the prediction of surgical case length.
mTOR inhibitors potentially reduce TGF-β2-induced fibrogenic changes in trabecular meshwork cells
Authors: Igarashi Nozomi , Honjo Megumi , Aihara Makoto 
Published: July 2021

AbstractWe examined the effects of mTOR inhibitors on the fibrotic response induced by transforming growth factor-beta2 (TGF-β2) in cultured human trabecular meshwork (hTM) cells. TGF-β2-induced expression of fibronectin, collagen type I, alpha 1 chain (COL1A1), and alpha-smooth muscle actin (αSMA) in hTM cells was examined in the presence or absence of mTOR inhibitors using quantitative real-time polymerase chain reaction, Western blotting, and immunohistochemistry. The migration rates of hTM cells were examined in the presence of TGF-β2 with or without mTOR inhibitors. An in vitro study showed that the expression of fibronectin, COL1A1, and αSMA was upregulated by TGF-β2 treatment of hTM cells; such upregulation was significantly suppressed by mTOR inhibitors. The inhibitors significantly reduced the migration rate of TGF-β2-stimulated hTM cells. mTOR inhibitors may usefully reduce the fibrotic response of hTM cells and we may have to explore if it is also effective in in vivo model.
TIFA protein expression is associated with pulmonary arterial hypertension
Authors: Chang Hao-Chih , Wei Tong-You Wade , Wu Pei-Yu , Tsai Ming-Daw , Yu Wen-Chung , Chen Chen-Huan , Sung Shih-Hsien 
Published: July 2021

AbstractTumor necrosis factor receptor-associated factor-interacting protein with a forkhead-associated domain (TIFA), a key regulator of inflammation, may be involved in the pathogenesis of pulmonary arterial hypertension (PAH). A total of 48 PAH patients (age 50.1 ± 13.1 years, 22.9% men), 25 hypertensive subjects, and 26 healthy controls were enrolled. TIFA protein expression in peripheral blood mononuclear cells (PBMCs) and plasma interleukin (IL)-1β and tumor necrosis factor (TNF)-α were measured. Pulmonary arterial hemodynamics were derived from right heart catheterization. PAH patients had the highest expression of TIFA, TNF-α, and IL-1β. TIFA protein expression was significantly associated with IL-1β (r = 0.94; P < 0.001), TNF-α (r = 0.93; P < 0.001), mean pulmonary artery pressure (r = 0.41; P = 0.006), and pulmonary vascular resistance (r = 0.41; P = 0.007). TIFA protein expression could independently predict the presence of PAH (odds ratio [95% confidence interval per-0.1 standard deviation]: 1.72 [1.37–2.16]; P < 0.001) and outperformed echocardiographic estimation. Ex vivo silencing of TIFA protein expression in PBMCs led to the suppression of the cellular expression of IL-1β and TNF-α. IL-1β and TNF-α mediated 80.4% and 56.6% of the causal relationship between TIFA and PAH, respectively, supporting the idea that TIFA protein is involved in the pathogenesis of PAH.