bluuebunny/crossref_metadata_2025_split huggingface dataset:
On using undirected graph techniques for directed graphs through Category Theory
Authors: Guerra Sebastian Prado , George Vivek Kurien , Morar Vikash , Joshua Roldan , Silva Gabriel 
Published: August 2022

Abstract
Many complex systems are modeled as graphs. Depending on the setting, graphs can be either directed or undirected. While many computational tools have been developed for both types of graphs, some tools only exist for undirected graphs. Thus, creating a ’bridge’ that connects directed graphs to undirected graphs would unlock the potential for using undirected graph techniques in appropriate directed graph contexts. We used Category Theory in a novel way to map a simple directed graph to a bipartite undirected graph that we call a prime graph. Formally, we show that there exists an isomorphism between the category of simple directed graphs and a category of prime graphs whose objects are labeled undirected bipartite graphs. The labeling is what gives the notion of direction to an undirected graph. By taking advantage of the isomorphism between these two categories, we extend undirected graph techniques to directed graph contexts by converting the directed graphs into prime graphs. We demonstrate this framework by applying it to the problems of network alignment and spectral graph clustering.
Effects of different short-term tillage managements on soil microbial biomass turnover in the double-cropping rice field of southern China
Authors: Tang Haiming , Li Chao , Shi Lihong , Wen Li , Li Weiyan , Cheng Kaikai , Xiao Xiaoping 
Published: August 2022

Abstract
Soil microbial biomass were usually regarded as a sensitive indicators in varied of soil fertility and soil quality, and its turnover in paddy field were mainly influenced on by applied with different tillage managements. However, the effects of different short-term (7-years) tillage managements on soil microbial biomass turnover in paddy field under the double-cropping rice system were still need to further investigate. Therefore, the varied of soil microbial biomass carbon (SMBC), soil microbial biomass nitrogen (SMBN) contents, flux turnover rate of SMBC and SMBN at 0–10 cm and 10–20 cm layers in the double-cropping rice field of southern China with different tillage practices were studied. The tillage experiment set up four treatments: conventional tillage and straw returning (CT), rotary tillage and straw returning (RT), no-tillage and straw returning (NT), and rotary tillage with all straw removed from paddy field as a control (RTO). The results showed that SMBC and SMBN contents at 0–10 cm and 10–20 cm layers in paddy field with CT, RT and NT treatments were significantly increased, compared with RTO treatment. Compared with RTO treatment, SMBC and SMBN contents at 0–10 cm and 10–20 cm layers in paddy field with CT treatment increased by 28.99%, 33.31% and 17.84%, 16.52%, respectively. Flux of SMBC and SMBN at 0–10 cm and 10–20 cm layers in paddy field with CT and RT treatments were significantly higher than that of RTO treatment. This results indicated that flux turnover rate of SMBC and SMBN at 0–10 cm and 10–20 cm layers in paddy field with CT, RT treatments were significantly higher than that of RTO treatment. Compared with RTO treatment, flux turnover rate of SMBC and SMBN at 0–10 cm and 10–20 cm layers in paddy field with CT treatment increased by 65.49%, 39.61% and 114.91%, 119.35%, respectively. SMBC and SMBN contents, flux turnover rate of SMBC and SMBN at 0–10 cm layer were higher than that of 10–20 cm layer in paddy field with the same tillage treatment. Therefore, applied with rotary tillage or conventional tillage and straw returning were beneficial managements for increasing soil nutrient and soil productivity under the double-cropping rice system in southern of China.
Differential diagnosis of uterine adenosarcoma: identification of JAZF1-BCORL1 rearrangement by comprehensive cancer genome profiling
Authors: Hasegawa Chie , Washimi Kota , Hiroshima Yukihiko , Kasajima Rika , Kikuchi Keiji , Notomi Tsuguto , Kato Hisamori , Hiruma Toru , Sato Shinya , Okubo Yoichiro , Yoshioka Emi , Ono Kyoko , Miyagi Yohei , Yokose Tomoyuki 
Published: August 2022

Abstract
Background: Uterine adenosarcoma is a rare malignant tumor that accounts for 8% of all uterine sarcomas, and less than 0.2% of all uterine malignancies. However, it is frequently misdiagnosed in clinical examinations, including pathological diagnosis, and imaging studies owing to its rare and non-specific nature, which is further compounded by the lack of specific diagnostic markers. Case Presentation: We report a case of uterine adenosarcoma for which a comprehensive genomic profiling (CGP) test provided a chance to reach the proper diagnosis. The patient, a woman in her 60s with a history of uterine leiomyoma was diagnosed with an intra-abdominal mass post presentation with abdominal distention and loss of appetite. She was suspected to have gastrointestinal stromal tumor (GIST), and the laparotomically excised mass was found to comprise uniform spindle-shaped cells that grew in bundles with a herringbone architecture, and occasional myxomatous stroma. Immunostaining revealed no specific findings, resulting in the tumor being diagnosed as a spindle cell tumor/suspicious adult fibrosarcoma. The tumor relapsed during postoperative follow-up, and showed size reduction with chemotherapy, prior to regrowing. CGP was performed to identify a possible treatment, which resulted in detection of a JAZF1-BCORL1 rearrangement. Since the rearrangement has been reported in uterine sarcomas, we reevaluated specimens of the preceding uterine leiomyoma, which revealed the presence of adenosarcoma components in the corpus uteri. Further, both the uterine adenosarcoma and intra-abdominal mass were partially positive for CD10 and BCOR staining. Conclusions: These results conclusively identified the abdominal tumor as a metastasis of the uterine adenosarcoma. The JAZF1-BCORL1 rearrangement is predominantly associated with uterine stromal sarcomas, and ours is the second report of the same in an adenosarcoma thus far. Adenosarcomas are rare and difficult to diagnose, especially in atypical cases with scarce glandular epithelial components. Identification of rearrangements involving BCOR or BCORL1, will encourage BCOR staining analysis, thereby potentially resulting in better diagnostic outcomes. Given that platinum-based chemotherapy was proposed as the treatment choice for this patient post diagnosis with adenosarcoma, CGP also indirectly contributed to designing the best suited treatment protocol.
Formation of Ir-MgO solid solutions analyzed with X-ray absorption spectroscopy
Authors: Okumura Kazu , Hoshi Hitomi , Iiyoshi Hikaru 
Published: August 2022

Abstract
Thermal treatment of MgO-loaded Ir nanoparticles or Ir(OAc)3 formed Ir-MgO solid solutions (Ir valence 3+). Characteristic Ir − O bond distance shrinkage was observed compared with that of the nearest neighboring Mg − O bond in MgO. Ir-MgO dispersion exhibited a two-spike pattern depending on the treatment temperature owing to the formation and successive segregation of the solid solutions.
A Randomized, Controlled Phase I clinical study to assess the Safety and Immunogenicity of a Yellow Fever Vaccine in adults
Authors: Kulkarni Prasad , Desai Sajjad , K Anil , Potey Anirudha , Y Sindhu , Grappi Silvia , Lapini Giulia , Montomoli Emanuele , Poonawalla Cyrus 
Published: August 2022

Abstract
Background
Yellow fever, a mosquito borne flavivirus infection, is an important public health problem in Africa and Latin America. A Yellow Fever vaccine (YFV) was developed and tested in a study in India.
Methods
This was a Phase I, open-label, randomized, controlled study where healthy adults received SII YFV intramuscularly (SII YFV IM), SII YFV subcutaneously (SII YFV SC) or STAMARIL® (Sanofi-Pasteur) in 1:1:1 ratio. They were followed for solicited reactions for 10 days and unsolicited events for 28 days and serious adverse events for 3 months. YF neutralizing antibodies were measured at baseline and on Days 10, 14, 28.
Results
A total of 60 adults were enrolled in the study. The proportion of participants with solicited reactions was 10%, 40% and 25% in SII YFV SC, SII YFV IM and STAMARIL® arms, respectively. No causally related unsolicited AEs or any SAE was reported. After vaccination, the seroconversion was 94.44%, 100% and 100%, in the three arms respectively. The post-vaccination GMTs were similar in the study arms.
Conclusion
The new YFV was found safe and immunogenic by IM as well as SC routes. The vaccine can be tested in further phases of clinical studies.
Effects of sodium dodecyl benzene sulfonate on the combined toxicity of multi-walled carbon nanotubes and cadmium to Escherichia coli
Authors: Li Mei , Fu Yong , Pei Jianchuan , Huang Yuehong 
Published: August 2022

Abstract
The combined biological toxicity of carbon nanotubes (CNTs) and the coexisting pollutants have attracted increasing attention. As a common used surfactant, sodium dodecyl benzenesulfonate (SDBS) could interact with both CNTs and heavy metals. Escherichia coli ( E.coli ) was chosen as a model microorganism, and the effects of SDBS on the combined toxicity of three types of multi-walled carbon nanotubes (MWCNTs) and Cd 2+ were studied. The three types of MWCNTs with the concentration below 200 mg∙L -1 didn’t show obvious growth inhibition to E.coli , and they reduced the toxicity of Cd 2+ to different degrees with the order of carboxylated MWCNTs > hydroxylated MWCNTs > MWCNTs without surface functional groups. The combined toxicity of all the three types of MWCNTs and 10 mg∙L -1 of Cd 2+ increased with the increasing SDBS concentration. The free Cd 2+ and Cd 2+ complexing with SDBS (SDBS-Cd + ) were the main toxicity sources for the mixture of MWCNTs, Cd 2+ , and SDBS. SDBS-Cd + increased the bacterial outer membrane permeability, and thus enhanced the combined toxicity of Cd 2+ and MWCNTs. The results could provide a scientific basis for the ecological risk assessment of water polluted by surfactants, carbon nanotubes and heavy metals.
Expression of PSTPIP1 in kidney renal clear cell carcinoma and its prognostic value
Authors: Sun Li , Liu Zhenghong , Qin Xiaowen , Wang Heng , Zhang Pu , Zheng Bin , Mou Yixuan , Zhang Dahong 
Published: August 2022

Abstract
Purpose: Kidney renal clear cell carcinoma is the most common histological form of kidney cancer, but targeted therapy is still lacking. PSTPIP1 is associated with multiple immune-related pathways and has higher expression in tumor tissue. Thus, the correlation of PSTPIP1 and KIRC was studied to evaluate the effect of PSTPIP1 on KIRC progression.Methods: The Oncomine and UALCAN databases were used to analyze PSTPIP1 mRNA expression in KIRC. Then, IHC was performed to detect PSTPIP1 protein in clinical samples. Next, the chi-square test, univariate analysis and multivariate analysis were performed to verify the relationship between PSTPIP1 and KIRC. Finally, coexpressed genes and enriched pathways were obtained from the TCGA and GSEA databases. A protein‒protein interaction network was constructed to assist in mechanism analysis.Results: Both the bioinformatics analysis based on several databases and IHC experiment results showed an obvious upregulation of PSTPIP1 expression in cancer tissue. The high expression of PSTPIP1 significantly reduced the median survival time and was related to tumor size, Edmondson grade and TNM stage. Further analysis indicated that PSTPIP1 may promote prognosis through various immune responses, suggesting that PSTPIP1 may be a potential biomarker for KIRC diagnosis and therapy.
BuscoPhylo: A webserver for Busco-Based Phylogenomic Analysis for Non-specialists
Authors: Sahbou Alae-Eddine , Iraqi Driss , Mentag Rachid , KHAYI Slimane 
Published: August 2022

Abstract
Here we present BuscoPhylo tool that enables to both students and established scientists to easily perform Busco-Based Phylogenomic Analysis starting from a set of genomes sequences. BuscoPhylo is an efficient and user-friendly web server freely accessible at https://buscophylo.inra.org.ma/. The source code, along with documentation, is freely available under an MIT license at https://github.com/alaesahbou/BuscoPhylo.
A Genetic Risk Score using human chromosomal-scale length variation can predict breast cancer
Authors: Ko Charmeine , Brody James P. 
Published: August 2022

Abstract
Introduction.The ability to accurately predict whether a woman will develop breast cancer later in her life, should reduce the number of breast cancer deaths. Different predictive models exist for breast cancer based on family history, BRCA status, and SNP analysis. The best of these models has an accuracy (area under the receiver operating characteristic curve, AUC) of about 0.65. We have developed computational methods to characterize a genome by a small set of numbers that represent the length of segments of the chromosomes, called chromosomal-scale length variation (CSLV).Methods.We built machine learning models to differentiate between women who had breast cancer and women who did not based on their CSLV characterization. We applied this procedure to two different datasets: the UK Biobank (1,534 women with breast cancer and 4,391 women who did not) and the Cancer Genome Atlas (TCGA) 874 with breast cancer and 3,381 without.Results.We found a machine learning model that could predict breast cancer with an AUC of 0.836 95% CI(0.830.0.843) in the UK Biobank data. Using a similar approach with the TCGA data, we obtained a model with an AUC of 0.704 95%CI(0.702,0.706). Variable importance analysis indicated that no single chromosomal region was responsible for significant fraction of the model results.Conclusion.Chromosomal-scale length variation can be used to effectively predict whether or not a woman will develop breast cancer.
Techno-economic performance comparison of wind turbines with different rated power at the Gwadar wind corridor using RET Screen 4
Authors: Muddasar Muhammad 
Published: August 2022

Abstract
This rigorous study is based on techno-economic performance analysis of wind turbines with different rated power (2MW & 3MW) for Gwadar using RETScreen 4 software. The software collects climatic data form its database and requires input parameters including wind shear exponent, wind turbine selection, hub height, and some costs to generate outcomes required for financial and technical analysis. Hellman power law is used to extrapolate wind speed at the required height. It is verified that the speed of wind significantly gets stronger with an increase in height. The techno-economic analysis is subdivided into three analyses named energy production, financial and emission analysis and then comparative analysis of both wind turbines is performed for each analysis to select the best turbine for the Gwadar site. Comparative analysis of 2MW & 3MW wind turbines is performed based on a capacity factor, the electricity that can be exported to the grid, Net Present Value, Internal Rate of Return, payback period, annual savings and GHG emissions reduction. The study indicates that the 3MW wind turbine is a suitable and profitable option to be installed at Gwadar.Statement of Industrial relevance:Wind energy is a viable option used for the clean generation of energy in Pakistan to meet the electricity demands of the nation and to reduce dependency on fossil fuel power plants. This study provides helpful insights to wind energy sector of Pakistan. The major objective of this research is to help the renewable energy companies to invest in the wind corridors of Pakistan.Novelty statement:The author believes to the best of his knowledge that none other work has previously been reported for the selection of most suitable wind turbine at Gwadar wind corridor on the basis of technoeconomic analysis. RET Screen 4 utilization for this purpose is also a novelty of this work. This study indicates that the 3MW wind turbine is a suitable and profitable option to be installed at Gwadar.
Monitoring and Dietary Exposure Assessment of Elements in Mediterranean Mussels in İstanbul, Türkiye
Authors: TÜRKOĞLU Semra 
Published: August 2022

Abstract
In this study, concentrations of elements were determined by an ICP-MS device in the edible tissues of Mytilus galloprovincialis. According to the results obtained in the study, As, Pb, Cd, Ni, and Zn in the digestive gland of M. galloprovincialis were above the maximum limits (mgkg-1), which were 0.67 for Cd, 6.9 for As, 0.79 for Pb, 2 for Ni and 42.6 for Zn. The results show that Cd and As mean concentrations in muscle of M. galloprovincialis and Cd and Ni mean concentrations in gills of M. galloprovincialis were above the maximum limits. Furthermore, it was observed that the highest value belonged to As in the digestive gland of mussels with 65.4% of Provisional Tolerable Weekly Intake. In addition to, the lowest percentage belonged to Zn with 0.2% of PTWI in muscles and 0.3% of PTWI in gills of the mussels.
Determinants of diarrhoeal infections among users of shared sanitation in informal settlements in Durban, South Africa
Authors: Ramlal Preshod Sewnand , Lin J. , Buckley C. A. , Stenström T. A. , Amoah I. D. 
Published: August 2022

Abstract
Diarrhoeal disease continues to be a major health problem in many parts of the world, especially in developing countries, mainly due to the lack of access to sanitation, water, and hygienic living conditions. Identifying the determinants of diarrhoeal infections continues to be a challenge in developing countries. In this study, we ascertained the factors behind diarrhoea among inhabitants of informal settlements in the city of Durban, South Africa. Prevalence of diarrhoea in the study area varied between 7-year historical clinical records and data collected during the current study (primary data), with the primary data giving the highest monthly prevalence odds ratio (POR) up to 18.1 (±1.6)%. The main factors associated with diarrhoeal infections were open defaecation (POR = 1.8; 95% confidence interval (CI): 0.9–3.12), use of shared sanitation (POR = 1.7; 95%; CI: 1.05–2.26), and exposure to faecal matter around the homes (POR = 1.69; 95% CI: 1.25–3.10). Several other factors were also determined to be associated with diarrhoeal infections, such as hygiene practices in the communities, the non-treatment of water before use, and the presence of solid waste and faecal materials around the households. This study shows that diarrhoeal disease infections in informal settlements could be multifactorial; therefore, a multifactorial approach is needed to reduce these infections. These could include improving education on hygiene practices within the home setting as well as in public places, such as the community ablution blocks.
Divergences Between Resting State Networks and Meta-Analytic Maps Of Task-Evoked Brain Activity
Authors: Palmucci Matías , Tagliazucchi Enzo 
Published: August 2022

Background:
Spontaneous human neural activity is organized into resting state networks, complex patterns of synchronized activity that account for the major part of brain metabolism. The correspondence between these patterns and those elicited by the performance of cognitive tasks would suggest that spontaneous brain activity originates from the stream of ongoing cognitive processing.

Objective:
To investigate a large number of meta-analytic activation maps obtained from Neurosynth (www.neurosynth.org), establishing the extent of task-rest similarity in large-scale human brain activity.

Methods:
We applied a hierarchical module detection algorithm to the Neurosynth activation map similarity network, and then compared the average activation maps for each module with a set of resting state networks by means of spatial correlations.

Results:
We found that the correspondence between resting state networks and task-evoked activity tended to hold only for the largest spatial scales. We also established that this correspondence could be biased by the inclusion of maps related to neuroanatomical terms in the database (e.g. “parietal”, “occipital”, “cingulate”, etc.).

Conclusion:
Our results establish divergences between brain activity patterns related to spontaneous cognition and the spatial configuration of RSN, suggesting that anatomically-constrained homeostatic processes could play an important role in the inception and shaping of human resting state activity fluctuations.
Multiple-Inputs Convolutional Neural Network for COVID-19 Classification and Critical Region Screening From Chest X-ray Radiographs: Model Development and Performance Evaluation
Authors: Li Zhongqiang , Li Zheng , Yao Luke , Chen Qing , Zhang Jian , Li Xin , Feng Ji-Ming , Li Yanping , Xu Jian 
Published: August 2022

Background
The COVID-19 pandemic is becoming one of the largest, unprecedented health crises, and chest X-ray radiography (CXR) plays a vital role in diagnosing COVID-19. However, extracting and finding useful image features from CXRs demand a heavy workload for radiologists.

Objective
The aim of this study was to design a novel multiple-inputs (MI) convolutional neural network (CNN) for the classification of COVID-19 and extraction of critical regions from CXRs. We also investigated the effect of the number of inputs on the performance of our new MI-CNN model.

Methods
A total of 6205 CXR images (including 3021 COVID-19 CXRs and 3184 normal CXRs) were used to test our MI-CNN models. CXRs could be evenly segmented into different numbers (2, 4, and 16) of individual regions. Each region could individually serve as one of the MI-CNN inputs. The CNN features of these MI-CNN inputs would then be fused for COVID-19 classification. More importantly, the contributions of each CXR region could be evaluated through assessing the number of images that were accurately classified by their corresponding regions in the testing data sets.

Results
In both the whole-image and left- and right-lung region of interest (LR-ROI) data sets, MI-CNNs demonstrated good efficiency for COVID-19 classification. In particular, MI-CNNs with more inputs (2-, 4-, and 16-input MI-CNNs) had better efficiency in recognizing COVID-19 CXRs than the 1-input CNN. Compared to the whole-image data sets, the efficiency of LR-ROI data sets showed approximately 4% lower accuracy, sensitivity, specificity, and precision (over 91%). In considering the contributions of each region, one of the possible reasons for this reduced performance was that nonlung regions (eg, region 16) provided false-positive contributions to COVID-19 classification. The MI-CNN with the LR-ROI data set could provide a more accurate evaluation of the contribution of each region and COVID-19 classification. Additionally, the right-lung regions had higher contributions to the classification of COVID-19 CXRs, whereas the left-lung regions had higher contributions to identifying normal CXRs.

Conclusions
Overall, MI-CNNs could achieve higher accuracy with an increasing number of inputs (eg, 16-input MI-CNN). This approach could assist radiologists in identifying COVID-19 CXRs and in screening the critical regions related to COVID-19 classifications.