bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impacts of microplastics and heavy metals on the earthworm Eisenia foetida and on soil organic carbon, nitrogen and phosphorus
Authors: Mai Huong , Thien Nguyen Danh , Dung Nguyen Thuy , Valentin Christian 
Published: September 2022

Abstract
Microplastics (MPs) are increasingly being studied because they have become ubiquitous in aquatic and terrestrial environments. For example, little is known about the negative effects of co-contamination by polypropylene microplastic (PP MPs) and heavy metal mixtures on terrestrial environment and biota. This study assesses the adverse effects of co-exposure to PP MPs and heavy metal mixture (Cu2+, Cr6+ and Zn2+) on soil quality and the earthworm Eisenia foetida. Soil samples were collected in the Dong Cao catchment, near Hanoi, Vietnam, and analyzed for changes in extracellular enzyme activity and carbon, nitrogen and phosphorus availability in the soil. We determined the survival rate of earthworms Eisenia foetida that had ingested MPs and two doses of heavy metals (the environmental level – 1X – and its double – 2X). Earthworm ingestion rates were not significantly impacted by the exposure conditions but the mortality rate for the 2X exposure conditions was 100%. Metals-associated PP MPs stimulated the activities of β-glucosidase, β-N-acetyl glucosaminidase and phosphatase enzymes in soil. Principle component analysis showed that these enzymes were positively correlated with Cu2+ and Cr6+ concentrations, but negatively correlated with microbial activity. Zn2+ showed no correlation with soil extracellular enzyme activity or soil microbial activity. Our results showed that co-exposure of earthworms to MPs and heavy metals had no impact on soil nitrogen and phosphorus but caused a decrease in total soil carbon content, with a possible associated risk of increased CO2 emissions.
Real-time in vivo dose measurement using ruby-based fibre optic dosimetry during internal radiation therapy
Authors: Birajdar Shalee , Zhang Wen Qi , Santos Alexandre , Hickson Kevin , Afshar-Vahid Shahraam 
Published: September 2022

Abstract
In vivo dosimetry (IVD) in a commonly used liver cancer treatment of selective internal radiation therapy (SIRT) has been done based on the post-treatment image-based dosimetry approach. Real-time IVD is necessary to verify the dose delivery and detect errors during the treatment for better patient outcomes. This study aims to develop a fibre optic dosimeter (FOD) for in vivo real-time dose rate measurement during internal beta radiation therapy, e.g., SIRT. A ruby fibre optic probe was prepared and studied the radioluminescence (RL) characteristics, including its major challenge of stem effect arising from Cherenkov radiation and luminescence from the irradiated fibre. The stem signal was suppressed adequately using the stem removal technique of optical filtering, and only 2.3 ± 1. % stem signal was contributed to the measured RL signal. A linear dose rate response was observed during the exposure of the ruby probe to varying dose rates using a 6 MeV electron beam and a positron-emitting radionuclide fluorine-18. The ruby exhibited a temporally non-constant RL signal, which increased the RL signal by 0.84 ± 0.29 counts / sec2 during the irradiation of the maximum dose rate used in this study of 9 Gy / min for 2 minutes. The ability of ruby FOD to measure the absolute dose rate with sufficient stem effect suppression and the linear RL dose rate response indicates its suitability for real-time IVD during internal beta radiation therapy. Future work will investigate the time-dependent RL characteristic of ruby and validate post-treatment image-based dosimetry using ruby-based FOD.
Variant spectrum of PIEZO1 and KCNN4 in Japanese patients with dehydrated hereditary stomatocytosis
Authors: Yamamoto Keiko Shimojima , Nakahara Erina , Ogura Hiromi , Aoki Takako , Utsugisawa Taiju , Azuma Kenkou , Akagawa Hiroyuki , Watanabe Kenichiro , Muraoka Michiko , Nakamura Fumihiko , Kamei Michi , Tatebayashi Koji , Shinozuka Jun , Yamane Takahisa , Hibino Makoto , Katsura Yoshiya , Nakano-Akamatsu Sonoko , Kadowaki Norimitsu , Maru Yoshiro , Ito Etsuro , Ohga Shouichi , Yagasaki Hiroshi , Morioka Ichiro , Yamamoto Toshiyuki , Kanno Hitoshi 
Published: September 2022

Abstract
Hereditary stomatocytosis (HSt) is a type of congenital hemolytic anemia caused by abnormally increased cation permeability of erythrocyte membranes. Dehydrated HSt (DHSt) is the most common subtype of HSt and is diagnosed based on clinical and laboratory findings related to the erythrocytes. PIEZO1 and KCNN4 have been recognized as causative genes, and many related variants have been reported. We analyzed the genomic background of 23 Japanese patients suspected DHSt using a target capture sequence and identified pathogenic/likely pathogenic variants of PIEZO1 or KCNN4 in 12 families.
Effects of regorafenib on the mononuclear/phagocyte system and how these contribute to the inhibition of colorectal tumors in mice
Authors: Grünewald Sylvia , Stecklum Maria , Rizzo Manuel , Rathjens Jonathan , Fiebig Lukas , Zopf Dieter 
Published: September 2022

Abstract
Background
Regorafenib was previously shown to reduce tumor-associated macrophages and potently inhibit colony-stimulating factor 1 receptor (CSF1R), also known as CD115, in biochemical assays. The CSF1R signaling pathway is essential in the biology of the mononuclear/phagocyte system, which itself can promote the development of cancer.
Methods
A deeper investigation of regorafenib’s effects on CSF1R signaling was performed using preclinical in vitro and in vivo studies with syngeneic CT26 and MC38 mouse models of colorectal cancer. Peripheral blood and tumor tissue were analyzed mechanistically by flow cytometry using antibodies against CD115/CSF1R and F4/80 and by ELISA for chemokine (C-C motif) ligand 2 (CCL2) levels. These read-outs were correlated with drug levels for the detection of pharmacokinetic/pharmacodynamic relationships.
Results
Potent inhibition of CSF1R by regorafenib and its metabolites M-2 and M-5 was confirmed in vitro in RAW264.7 macrophages. The dose-dependent growth inhibition of subcutaneous CT26 tumors by regorafenib was associated with a significant reduction in both the number of CD115hi monocytes in peripheral blood and the number of selective subpopulations of intratumoral F4/80hi tumor-associated macrophages. CCL2 levels in blood were not affected by regorafenib but increased in tumor tissue, which may contribute to drug resistance and prevent complete tumor remission. An inverse relationship between regorafenib concentration and the number of CD115hi monocytes and CCL2 levels was observed in peripheral blood, supporting the mechanistic involvement of regorafenib.
Conclusions
These findings may be clinically useful in optimizing drug dosing by blood-based pharmacodynamic markers, and in identifying resistance mechanisms and ways to overcome them by appropriate drug combinations.
Evaluating changes in hepatic microcirculation in mild and severe acute pancreatitis through dynamic volume perfusion computed tomography
Authors: Lan Xilin , Zhang Shiyong , Sun Qing , Zou Qing , Liu Ting , Deng Hongyi , Guo Kaichan , Yu Xi , Ming Bing 
Published: September 2022

Abstract

Objectives:
Based on one-stop upper abdominal dynamic volume perfusion computed tomography (dVPCT) data stacks, we reconstructed images from multiple contrast enhancement phases to determine the severity of acute pancreatitis (AP) and further evaluated hepatic perfusion in mild and severe AP through multiple perfusion parameters.
Methods:
We prospectively enrolled 77 patients from the database of upper abdominal dVPCT between July 2018 and April 2019, including 62 with AP, as well as 15 without pancreatic and hepatic disorders as the control group. All patients underwent dVPCT, and we reconstructed the mean temporal arterial, mean temporal pancreatic, and mean temporal portal venous images to evaluate the severity of AP according to the CT severity index. We further divided AP into mild and severe AP groups. A deconvolution algorithm was applied to calculate multiple hepatic perfusion parameters, including blood flow (BF), blood volume (BV), arterial liver perfusion (ALP), portal venous liver perfusion (PVP), mean transit time (MTT), hepatic perfusion index (HPI), and time to peak (TTP).
Results
The hepatic perfusion parameters BF, BV, PVP, MTT, HPI, and TTP differed significantly between the severe AP patients and control group. Only PVP and MTT were significantly different between the mild AP patients and the control group. The mild AP group had significantly higher BF, BV and MTT values but a significantly lower TTP than the severe AP group.
Conclusions
Hepatic perfusion differed according to the severity of AP. Severe AP shows altered hepatic haemodynamics and disturbances of the hepatic microcirculation.
Peaksat: An R package for ChIP-seq peak saturation analysis
Authors: Boyd Joseph , Gao Cong , Quinn Kathleen , Fritz Andrew , Stein Janet , Stein Gary , Glass Karen , Frietze Seth 
Published: September 2022

Abstract
Background: Epigenomic profiling assays such as ChIP-seq have been widely used to map the genome-wide enrichment profiles of chromatin-associated proteins and posttranslational histone modifications. Sequencing depth is a key parameter in experimental design and quality control. However, due to variable sequencing depth requirements across experimental conditions, it can be challenging to determine optimal sequencing depth, particularly for projects involving multiple targets or cell types.
Results: We developed the Peaksat R package to provide target read depth estimates for epigenomic experiments based on the analysis of peak saturation curves. We applied Peaksat to establish the distinctive read depth requirements for ChIP-seq studies of histone modifications in different cell lines. Using Peaksat, we were able to estimate the target read depth required per library to obtain high-quality peak calls for downstream analysis. In addition, Peaksat was applied to other sequence-enrichment methods including Cut&Run and ATAC-seq.
Conclusion: Peaksat addresses a need for researchers to make informed decisions about whether their sequencing data has been generated to an adequate depth and subsequently sufficient meaningful peaks, and failing that, how many more reads would be required per library. Peaksat is applicable to other sequence-based methods that include calling peaks in their analysis.
Data Science Technology Course: The Design, Assessment and Computing Environment Perspectives
Authors: Ismail Azlan , Mutalib Sofianita , Haron Haryani 
Published: September 2022

Abstract
This article discusses the key elements of the Data Science Technology course offered to postgraduate students enrolled in the Master of Data Science program. This course complements the existing curriculum by providing the skills to handle the Big Data platform and tools, in addition to data science activities. We tackle the discussion about this course based on three main requirements, which are related to the need to exploit the key skills from two dimensions, namely, Data Science and Big Data, and the need for a cluster-based computing platform and its accessibility. We address these requirements by presenting the course design and its assessments, the configuration of the computing platform, and the strategy to enable flexible accessibility. In terms of course design, the offered course contributes to several innovative elements and has covered multiple key areas of the data science body of knowledge and multiple quadrants of the job and skills matrix. In the case of the computing platform, a stable deployment of a Hadoop cluster with flexible accessibility, triggered by the pandemic situation, has been established. Furthermore, through our experience with the implementation of the cluster, it has shown the ability of the cluster to handle computing problems with a larger dataset than the one used for the semesters within the scope of the study. We also provide some reflections and highlight future improvements.
Effect of interpregnancy interval on outcomes of transposal pregnancy: a retrospective study
Authors: Li Dong , Hong Jie , Hou Yi 
Published: September 2022

Abstract
Background: This study was aimed to explore the effect of interpregnancy interval (IPI) on outcomes of transposal pregnancy.
Methods: A retrospective study was conducted in Maternal and Child Health Hospital of Jiaxing, Zhejiang Province in China. The participants were divided into five groups according to IPI: 0-1 year, 2-3 years, 4-5 years, 6-10 years and ³11 years. Logistic analysis was further carried out to explore the differences in the effects of IPI on pregnancy outcomes.
Results: A total of 4862 women were included in this study. (1) The age, gestational diabetes mellitus (GDM), gestational hypertension, preeclampsia, anemia, oligohydramnios, postpartum hemorrhage, placenta previa and cesarean section delivery rate were gradually increased with the prolong of IPI (P<0.05). (2) After adjusting for potential confounding factors, compared with women in the IPI of 2-3years group, the risk of gestational hypertension (OR=3.6, 95%CI: 1.27-10.26, P=0.016), preeclampsia (OR=2.44, 95%CI:1.25-4.73, P=0.009), oligohydramnios (OR=1.81, 95%CI:1.14-2.89, P=0.012) and premature rupture of membranes (PROM) (OR=1.39, 95%CI: 1.04-1.84, P=0.025) were increased significantly for women in the IPI ≥11 years group. After adjusting for potential confounding factors, the risk of anemia, placenta previa, precipitate labor and cesarean section delivery rate in the 6-10 years group and ³11 years group were increased with the prolong of IPI compared with women in the IPI of 2-3 years group.
Conclusions: IPI ≥6 years would increase the risk of adverse pregnancy outcomes in the subsequent pregnancy. Healthcare education and consultation should be conducted for women to maintain an appropriate IPI.
Simultaneous Establishing Single-cell Transcriptome Atlas and Chromatin Accessibility Landscapes in Allotetraploid Leguminous Plant
Authors: Liu Hao , Deng Quanqing , Du Puxuan , Lu Qing , Gangurde Sunil , Xiao Yuan , Hu Dongxiu , Wang Wenyi , Li Haifen , Li Shaoxiong , Liu Haiyan , Huang Lu , Wang Runfeng , Liang Xuanqiang , Varshney Rajeev , Hong Yanbin , Chen Xiaoping 
Published: September 2022

Abstract
Plant cell proliferation associated with multiple layers of gene regulation, including modulation of transcriptome by changes in chromatin accessibility. However, cell proliferation is an asynchronous process precluding a temporal understanding of regulatory events leading to single-cell fate commitment. Here, a robust single nucleus RNA sequencing approach, where single nucleus employed for simultaneous investigation of transcriptome (snRNA-seq) and chromatin accessibility (snATAC-seq) landscapes in the same single-cell of Arachis hypogaea leaves. A total of 5,930 leaf cells with 10,793 expressed genes were used to construct development trajectory and characterized large-scale critical differentially expressed genes (DEGs). Additionally, uncovered extending insights of chromatin opening guided 5,315 DEGs expression involved biological pathway determines differentiation direction in distinct cell-types. But obtained members in each cell-clusters not exhibits obvious difference in distinct cell-cycling regulated genome duplication phases. Furthermore, snRNA-seq identified AT-hook transcription factor AhAHL11 promotes leaf area growth by modulating auxin content, but snATAC-seq identified AhBHLH143 displays contrasting results to repress the leaf development by jasmonic acid pathway in ectopically expressed Arabidopsis. We concluded that, snRNA-seq combined with snATAC-seq is an extensible platform to explore association between the chromatin regulatory events and gene expression across diversity cell-types in peanut leaf, broadly application of this approach will enable significant advances in the functional research of tissues ontology in plant species.
Polypharmacy associated with renal impairment in elderly people attending primary health care centers
Authors: Naghnaghia Shayma , Nazzal Zaher , Abualia Laian , AL-Ramahi Rowa ’ , Hamdan Zakaria , Samara Esra'a 
Published: September 2022

Abstract
Purpose: This study aimed to estimate the prevalence of renal impairment among primary health care (PHC) elderly, its association with polypharmacy, and the most frequent potentially inappropriate prescription (PIP) in renal impairment patients.
Methods: A cross-sectional study was conducted among PHC clinic attendees aged 65 and older. We used medical records and an interviewer-administered questionnaire for data collection. Participants with eGFR less than 60mls/min/1.73m2 were categorized as renal impaired; we then calculated the prevalence of renal impairment and used multivariable analysis to identify its predictors. Beer's criteria and literature reviews were used to evaluate renal impairment patients' medication and to determine the frequency of PIPs.
Results: The study included 421 participants (224 female, 197 male), and 66.3% were between the ages of 65 and 75. The prevalence of renal impairment was 30.2% (95%CI: 25.8-34.6%). Polypharmacy [aOR= 5.9, 95%CI: 2.4-14.6], stroke [aOR= 2.5, 95%CI: 1.2-5.4], Females [aOR= 2.6, 95%CI: 1.5-4.7], and elderly over the age of 80 [aOR= 4.4, 95%CI: 2.2-8.8] were the main predictors of renal impairment. RAAS (54.3%), metformin (39.3%) and sulfonylurea (20.4%) were the most frequent reported PIP in renal impairment patients.
Conclusion: Renal impairment affects nearly one-third of elderly Palestinians who attend PHC clinics and has been strongly linked to polypharmacy in this population. Stroke, age, and gender are other identified risk factors in our study. It is recommended to raise healthcare providers' awareness to control elderly patients’ chronic conditions by cautiously prescribing only necessary medication, choosing non-nephrotoxic alternatives, and monitoring their renal function frequently.
Effects of brewer’s spent yeast inclusion level and ensiling duration on fermentative, fungal load dynamics, and nutritional characteristics of fresh brewer’s spent yeast-based silage
Authors: Yadessa Endale , Tamir Berhan , Kitaw Getu , Dejene Mesfin , Terefe Gebremaryam 
Published: September 2022

Abstract
A Small proportion of brewer’s spent yeast (BSY) is used as a protein source to replace costly but conventionally used agro-industrial by-product feeds in Ethiopia with large volumes seen accumulated at production sites causing disposal and public health problems. Consequently, there is a need to develop appropriate ways of using this by-product as livestock feed. This study was conducted to evaluate the effect BSY inclusion level and ensiling duration (ED) on fermentative, fungal load dynamics, and nutritional characteristics of fresh brewer’s spent-yeast based silage. Fresh brewery by-product samples were obtained from Heineken beer factory whereas wheat bran (WB) used as an input for formulating the silage material was purchased from a nearby animal feed processing plant. The ratio of brewery spent grain (BSG) to WB used majorly as protein and energy sources, respectively were 30:69 with 1% salt addition. To prepare the silages materials, 4 BSY inclusion levels (0, 10, 20 and, 30%) to replace BSG and 3 ED (2,4 and 6 weeks) were arranged in 4x3 factorial combination using completely randomized design (CRD) in 5 replications. Parameters measured include: observation for surface spoilage, yeast and mold colony count, silage temperature, pH, total dry matter loss (TDML), major proximate, detergent fractions and permanganate lignin, in-vitro organic matter digestibility (IVOMD) and estimated metabolizable energy (EME) values. The study revealed that at any BSY inclusion level and ED, extensive mold growths and discolorations were not observed. However, slightly higher values of 6.5, 5.7, and 12.2 colony forming unit (CFU)/g DM yeast, mold and total fungal counts (TFC), respectively were recorded only at the 6 weeks of the fermentation period with 30% BSY inclusion level. Brewer’s spent yeast inclusion level and ED had significant (P < 0.05) effect on silage temperature (mean = 18.05 0C) and pH (mean = 4.16). Among proximate and detergent values, crude protein (mean CP g/kg DM = 204.5), neutral detergent fiber (mean NDF g/kg DM = 552.9), and acid detergent fiber (mean ADF g/kg DM = 115.9) responded significantly (P < 0.05) to both BSY inclusion levels and ED. Among nutritional quality, CP, IVOMD, and EME of silage samples were subjected to substantial improvements when silage masses were prepared from 20% BSY inclusion levels and when the same silage materials were allowed to ferment for four weeks. Therefore, before making any further recommendation it is, thus, important to verify the current finding with additional animal response trials that take both biological and economic feasibilities into account.
On-top plasty for atypical Wassel type VI thumb duplication: Timing and key points of surgery
Authors: Xu Jianglong , Zhao Zhanbo , Du Yi , Huang Qi , Liu Yushu 
Published: September 2022

Abstract
Background: Thumb duplication is one of the most common congenital hand deformities, while atypical Wassel type VI thumb duplication is rare and challenging. This study aims to evaluate the clinical efficacy of on-top plasty for atypical Wassel type VI thumb duplication.
Methods: The clinical data of 5 children with atypical Wassel type VI thumb duplication treated by on-top plasty from May 2018 to April 2021 were studied retrospectively. There were 4 males and 1 female with an average age of 28.6(11~47) months. During the surgery, the distal portion of the ulnar thumb was transposed onto the top of the radial thumb, accompanied by tendon transfer from the radial thumb to the ulnar thumb. The patients were followed up postoperatively for the assessment of thumb’s appearance and function by the modified Tada scoring.
Results: All patients were followed up for an average of 29(16~51) months, and acquired good healing. No digit ischemic necrosis or bone nonunion occurred in all patients. The appearance of reconstructed thumbs was excellent, and the function was good and sufficient for patients to carry out activities of daily living. According to the modified Tada scoring, 4 thumbs were good, and 1 thumb was fair.
Conclusions: The on-top plasty is a reliable method for atypical Wassel type VI thumb duplication. The good surgical timing is 1~3 years. The appropriate osteotomy, transposing of digit and transferring of tendons are key points of on-top plasty.