bluuebunny/crossref_metadata_2025_split huggingface dataset:
Combining morphological and metabarcoding approaches reveals the freshwater eukaryotic phytoplankton community
Authors: Huo Shouliang , Li Xiaochuang , Xi Beidou , Zhang Hanxiao , Ma Chunzi , He Zhuoshi 
Published: March 2020

Abstract
Background
Phytoplankton diversity can be difficult to ascertain from morphological analyses, because of the existence of cryptic species and pico- and concealed phytoplankton. In-depth sequencing and metabarcoding can reveal microbial diversity, and identify novel diversity. However, there has been little comparison of metabarcoding and morphological datasets derived from the same samples, and metabarcoding studies covering total eukaryotic phytoplankton diversity are rare. In this study, the variable V7 region of the 18S rDNA gene was employed to explore eukaryotic phytoplankton diversity in 11 Chinese freshwater environments, and further compared with the dataset obtained through morphological identification.

Results
Annotation by the evolutionary placement algorithm (EPA) rather than alignment with the SILVA database improved the taxonomic resolution, with 346 of 524 phytoplankton operational taxonomic units (OTUs) being assigned to the genus or species level. The number of unassigned OTUs was greatly reduced from 259 to 178 OTUs by using the EPA in place of the SILVA database. Metabarcoding detected 3.5 times more OTUs than the number of morphospecies revealed by morphological identification; furthermore, the number of species and the Shannon–Wiener index inferred from the two methods were correlated. A total of 34 genera were identified via both methods, while 31 and 123 genera were detected solely in the morphological or metabarcoding dataset, respectively.

Conclusion
The dbRDA plot showed distinct separation of the phytoplankton communities between lakes and reservoirs according to the metabarcoding dataset. The same pattern was obtained on the basis of 10 environmental variables in the PCO ordination plot, while the separation of the populations based on morphological data was poor. However, 30 morphospecies contributed 70% of the community difference between lakes and reservoirs in the morphological dataset, while 11 morphospecies were not found by metabarcoding. Considering the limitations of each of the two methods, their combination could substantially improve phytoplankton community assessment.
Development of a test method for transformation of veterinary pharmaceuticals and biocides in anaerobic liquid manure
Authors: Junker Thomas , Atorf Cornelia , Berkner Silvia , Düring Rolf-Alexander , Hennecke Dieter , Herrchen Monika , Konradi Sabine , Merrettig-Bruns Ute , Römbke Jörg , Wagner Julia , Weinfurtner Karlheinz 
Published: March 2020

Abstract
Background
Spreading of manure on agricultural soils represents an important pathway by which veterinary medicinal and biocidal products enter the environment. To assess their environmental impact in the context of authorization processes, experimental testing of transformation of these compounds in manure is considered in regulatory guidance documents. However, there is no standardized experimental test method available so far. To fill this gap, an experimental test method was developed to examine transformation in liquid cattle and pig manure.

Results
To account for manure specifics and for a possible influence of manure parameters on transformation rates, a comprehensive data acquisition and statistical analysis were performed. To address the variability of liquid manure of different type and origin, 30 manures were sampled and characterized. Thereof, three cattle and three pig manures were selected to perform anaerobic transformation studies with two radiolabeled veterinary medicinal active substances (14C-salicylic acid and 14C-paracetamol) and a confidential radiolabeled “14C-biocide B” serving as test compounds. Spatial and seasonal variability of manure parameters was quantified, and a sampling technique to obtain homogenous manure samples was developed. Transformation studies with six replicates per sampling point were conducted to examine the influence of test setup, of manure storage conditions, and of parameter variations between manure of the same species and of different species on half-lives, formation of extractable and non-extractable residues and mineralization rates. Finally, a test design was established that yields reproducible results for transformation studies in liquid cattle and pig manure under anaerobic conditions.

Conclusions
Results give a reliable basis for an experimental test method to perform anaerobic transformation studies in liquid cattle and pig manure. The developed test method comprises detailed guidance on selection of sampling date and site, collection from manure tank, storage duration and temperature in the laboratory, duration of manure acclimation period, and the incubation system design. It proved to give reproducible results in a validation ring test performed in a follow-up project and is planned to be submitted as draft test guideline for approval by the OECD.
Identification of key differentially expressed genes and gene mutations in breast ductal carcinoma in situ using RNA-seq analysis
Authors: Zhu Congyuan , Hu Hao , Li Jianping , Wang Jingli , Wang Ke , Sun Jingqiu 
Published: March 2020

AbstractBackgroundThe aim of this study was to identify the key differentially expressed genes (DEGs) and high-risk gene mutations in breast ductal carcinoma in situ (DCIS).MethodsRaw data (GSE36863) were downloaded from the database of Gene Expression Omnibus (GEO), including three DCIS samples (DCIS cell lines MCF10.DCIS, Sum102, and Sum225) and one normal control sample (normal mammary epithelial cell line MCF10A). The DEGs were analyzed using NOIseq and annotated via DAVID. Motif scanning in the promoter region of DEGs was performed via SeqPos. Additionally, single nucleotide variations (SNVs) were identified via GenomeAnalysisTK and SNV risk was assessed via VarioWatch. Mutant genes with a high frequency and risk were validated by RT-PCR analyses.ResultsFinally, 5391, 7073, and 7944 DEGs were identified in DCIS, Sum102, and Sum22 cell lines, respectively, when compared with MCF10A. VENN analysis of the three cell lines revealed 603 upregulated and 1043 downregulated DEGs, including 16 upregulated and 36 downregulated transcription factor (TF) genes. In addition, six TFs each (e.g.,E2F1andCREB1) were found to regulate the core up- and downregulated DEGs, respectively. Furthermore, SNV detection results revealed 1104 (MCF10.DCIS), 2833 (Sum102), and 1132 (Sum22) mutation sites. Four mutant genes (RWDD4,SDHC,SEPT7, andSFN) with high frequency and risk were identified. The results of RT-PCR analysis as well as bioinformatics analysis consistently demonstrated that the expression ofRWDD4,SDHC,SEPT7, andSFNwas downregulated in the tumor tissues as compared with that in adjacent non-tumor tissues.ConclusionsThe differentially expressed TFs, TFs regulating DEGs (e.g.,E2F1andCREB1), and high-frequency mutant genes (RWDD4,SDHC,SEPT7, andSFN) might play key roles in the pathogenesis of DCIS.
Implementation of opioid maintenance treatment in prisons in North Rhine-Westphalia, Germany – a top down approach
Authors: Böhmer Kathrin , Schecke Henrike , Render Irmgard , Scherbaum Norbert 
Published: March 2020

Abstract
Background
Opioid Maintenance Treatment (OMT) is a well-evaluated treatment of opioid use disorder (OUD). Especially, under the condition of imprisonment, OMT is a preventive measure regarding infectious diseases such as hepatitis C. However, only a minority of prisoners with OUD are currently in OMT in numerous countries. In 2009, the Ministry of Justice of the federal state of North Rhine-Westphalia (NRW), Germany, launched the process of implementing OMT in prisons with various elements (e.g. development of recommendations regarding the treatment of prisoners with OUD, monitoring the number of prisoners in OMT, education of prison doctors). In the recommendations OMT was defined as the gold standard of treatment of OUD.

Methods
To assess the effectiveness of the implementation strategy a survey on the prevalence of OMT in prisons in NRW was carried out twice a year by the Ministry of Justice between 2008 and 2016. Participants were prisoners in NRW, Germany. The diagnosis of OUD at admission to prison and the treatment state on survey dates was measured.

Results
The number of prisoners in NRW dropped from 17,301 in 2008 to 16,432 in 2016. In the same period, the number of prisoners with OUD (mainly males) dropped from 4201 persons to 3650 persons and the number of prisoners in OMT increased from 139 persons (3.3%) to 1415 (38.7%) persons.

Discussion
Currently, the percentage of prisoners with OUD in OMT in NRW is almost reaching the treatment rate outside prisons in Germany (45–50%). However, after release from prison there is still a high risk for a discontinuation of OMT.

Conclusions
Overall, the top-down approach of implementing OMT in prisons in the federal state of NRW was effective.
Effects of fasting on the expression pattern of FGFs in different skeletal muscle fibre types and sexes in mice
Authors: Jia Wei-hua , Wang Nuo-qi , Yin Lin , Chen Xi , Hou Bi-yu , Wang Jin-hua , Qiang Gui-fen , Chan Chi Bun , Yang Xiu-ying , Du Guan-hua 
Published: March 2020

AbstractFibroblast growth factors (FGFs) belong to a large family comprising 22 FGF polypeptides that are widely expressed in tissues. Most of the FGFs can be secreted and involved in the regulation of skeletal muscle function and structure. However, the role of fasting on FGF expression pattern in skeletal muscles remains unknown. In this study, we combined bioinformatics analysis and in vivo studies to explore the effect of 24-h fasting on the expression of Fgfs in slow-twitch soleus and fast-twitch tibialis anterior (TA) muscle from male and female C57BL/6 mice. We found that fasting significantly affected the expression of many Fgfs in mouse skeletal muscle. Furthermore, skeletal muscle fibre type and sex also influenced Fgf expression and response to fasting. We observed that in both male and female mice fasting reduced Fgf6 and Fgf11 in the TA muscle rather than the soleus. Moreover, fasting reduced Fgf8 expression in the soleus and TA muscles in female mice rather than in male mice. Fasting also increased Fgf21 expression in female soleus muscle and female and male plasma. Fasting reduced Fgf2 and Fgf18 expression levels without fibre-type and sex-dependent effects in mice. We further found that fasting decreased the expression of an FGF activation marker gene—Flrt2 in the TA muscle but not in the soleus muscle in both male and female mice. This study revealed the expression profile of Fgfs in different skeletal muscle fibre types and different sexes and provides clues to the interaction between the skeletal muscle and other organs, which deserves future investigations.
Recombinant expression and characterization of two glycoside hydrolases from extreme alklinphilic bacterium Cellulomonas bogoriensis 69B4T
Authors: Li Fan , Dong Jiaying , Lv Xue , Wen Yanqiu , Chen Shan 
Published: March 2020

AbstractTwo novel glycoside hydrolases were cloned from the genomic DNA of alklinphilic bacterium Cellulomonas bogoriensis 69B4T and functionally expressed in Escherichia coli. The two enzymes shared less than 73% of identities with other known glycosidases and belonged to glycoside hydrolase families 5 and 9. Recombinant Cel5A exhibited optimum activity at pH 5.0 and at a temperature of 70 °C, and Cel9A showed optimum activity at pH 7.0 and at a temperature of 60 °C. The two enzymes exhibited activity at alkaline pH 11 and were stable over a wide range of pH. The maximum activities of Cel5A and Cel9A were observed in 0.5 M NaCl and 1 M KCl, respectively. In addition, these two enzymes exhibited excellent halostability with residual activities of more than 70% after pre-incubation for 6 days in 5 M NaCl or 4 M KCl. Substrate specificity analysis revealed that Cel5A and Cel9A specifically cleaved the β-1,4-glycosidic linkage in cellulose with the highest activity on carboxymethyl cellulose sodium (78.3 and 145.3 U/mg, respectively). Cel5A is an endoglucanase, whereas Cel9A exhibits endo and exo activities. As alkali-activated, thermo-tolerant, and salt-tolerant cellulases, Cel5A and Cel9A are promising candidates for further research and industrial applications.
Alternative lengthening of telomeres: from molecular mechanisms to therapeutic outlooks
Authors: Zhang Jia-Min , Zou Lee 
Published: March 2020

AbstractTo escape replicative senescence, cancer cells have to overcome telomere attrition during DNA replication. Most of cancers rely on telomerase to extend and maintain telomeres, but 4–11% of cancers use a homologous recombination-based pathway called alternative lengthening of telomeres (ALT). ALT is prevalent in cancers from the mesenchymal origin and usually associates with poor clinical outcome. Given its critical role in protecting telomeres and genomic integrity in tumor cells, ALT is an Achilles heel of tumors and an attractive target for cancer therapy. Here, we review the recent progress in the mechanistic studies of ALT, and discuss the emerging therapeutic strategies to target ALT-positive cancers.
mTOR signaling pathway and mTOR inhibitors in cancer: progress and challenges
Authors: Zou Zhilin , Tao Tao , Li Hongmei , Zhu Xiao 
Published: March 2020

AbstractMammalian target of rapamycin (mTOR) regulates cell proliferation, autophagy, and apoptosis by participating in multiple signaling pathways in the body. Studies have shown that the mTOR signaling pathway is also associated with cancer, arthritis, insulin resistance, osteoporosis, and other diseases. The mTOR signaling pathway, which is often activated in tumors, not only regulates gene transcription and protein synthesis to regulate cell proliferation and immune cell differentiation but also plays an important role in tumor metabolism. Therefore, the mTOR signaling pathway is a hot target in anti-tumor therapy research. In recent years, a variety of newly discovered mTOR inhibitors have entered clinical studies, and a variety of drugs have been proven to have high activity in combination with mTOR inhibitors. The purpose of this review is to introduce the role of mTOR signaling pathway on apoptosis, autophagy, growth, and metabolism of tumor cells, and to introduce the research progress of mTOR inhibitors in the tumor field.
Alternative splicing signatures in preimplantation embryo development
Authors: Tian Geng G. , Li Jing , Wu Ji 
Published: March 2020

AbstractBackgroundPreimplantation embryo development is a highly ordered sequence of processes and it requires a precise temporal and spatial control of gene expression. Alternative splicing (AS) is a crucial process that changes the genomic instructions into functional proteins, playing a critical role in the regulation of gene expression. Therefore, studies of AS can significantly improve our understanding of transcription and splicing events in preimplantation embryo development.ResultsTo study signatures of AS in embryo development, we firstly identified the critical stage for gene transcription during the preimplantation embryo development. By analyzing single cells RNA-seq (scRNA-seq) data, we found that the two-cell stage is a critical stage for gene transcription in preimplantation embryo development. Further study showed that AS was widespread in preimplantation embryo development, especially at the two-cell stage. In combination with high-throughput chromosome conformation (Hi-C) data, we demonstrated that AS genes were highly enriched in TAD boundaries, while they had no relationship with the A/B compartment and TAD.ConclusionOur results provide new insight into the relationship among AS, gene transcription and chromatin structure in preimplantation embryo development.
Matrix transformations of Norlund–Orlicz difference sequence spaces of nonabsolute type and their Toeplitz duals
Authors: Kılıçman Adem , Raj Kuldip 
Published: March 2020

AbstractIn this paper, the Nörlund–Orlicz difference sequence space$\mathcal{N}^{t}(\mathcal{F},\Delta^{m}_{n},u,q)$Nt(F,Δnm,u,q)of nonabsolute type is introduced as a domain of Nörlund means which is isomorphic to the space$\ell(p)$ℓ(p)and the basis of the space is constructed. Additionally, theα−,β−, andγ-duals of the spaces are computed and their matrix transformations are given. Finally, the properties like rotundity, modularity of the newly formed spaces are established.
Flexural Capacity and Behaviour of Geopolymer Concrete Beams Reinforced with Glass Fibre-Reinforced Polymer Bars
Authors: Ahmed Hemn Qader , Jaf Dilshad Kakasor , Yaseen Sinan Abdulkhaleq 
Published: March 2020

AbstractGeopolymer concrete (GPC) with Glass fibre-reinforced polymer (GFRP) bars can provide a better construction system with high sustainability, high durability, and adequate strength. Few studies deal with the combination of these materials. The present investigation obtains the flexural capacity and behaviour of GPC and ordinary Portland concrete beams reinforced with GFRP bars (GFRP-RGPC and GFRP-ROPC, respectively). Twelve beams consisting of nine GFRP-RGPC and three GFRP-ROPC beams were cast and tested by using the four-point bending test over an active span of 2000 mm. Rebar ratio, compressive strength, and concrete types were taken as the variables. Initial cracking load, ultimate load capacity, load–deflection behaviour, Load–strain curves, crack width, the number of cracks and failure modes, were studied. Experimental results of beams were compared with the proposed equations provided by ACI 440.1R-15, CSA S806-12, and parabolic stress block method. The Results showed the decrease of deflection and increase of first cracking load by increasing the compressive strength. A slight increase in the deflection of GFRP-RGPC beams and approximately the same value of ultimate load were observed. GFRP-RGPC beams also recorded a higher value of crack width compared with GFRP-ROPC beams. The parabolic stress block method predicted the flexural capacity of the beams close to the experimental results rather than ACI 440.1R-15 and CSA S806-12.
Biometric and genetic differences in kelabau (Osteochilus spp.) as revealed using cytochrome c oxidase subunit 1
Authors: Asiah Nur , Junianto Junianto , Yustiati Ayi , Sukendi Sukendi , Fahmi Melta Rini , Muchlisin Zainal A. , Kadapi Muhamad , Windarti Windarti 
Published: March 2020

Background: Kelabau (Osteochilus spp.) is a freshwater fish commonly found in the rivers of Riau, Indonesia. Researchers believe that these are Osteochilus kelabau; however, accurate taxonomic determination of these fish in Riau waters has not been made. The purpose of this study was to facilitate the identification of the kelabau based on its morphology and genetics using biometric and cytochrome c oxidase subunit 1 (CO1) analyses, respectively. Methods: Fish samples were collected from the Siak, Kampar and Rokan rivers in Riau Province, Indonesia. The DNA of 90 fish was extracted from the caudal fins using a DNA extraction kit, after which it was amplified using primers Fish-F1 and Fish-R1. Sequencing was conducted by Applied Biosystems Macrogen Korea, and the DNA sequences were then edited and aligned using MEGA v. 7. All samples were BLAST-searched for identification using the National Center for Biotechnology Information and BOLD System. Phylogenetic trees were constructed, and the similarity index was calculated using accession numbers AP011385.1 and KC631202.1 in GenBank. Results: Analysis of the consensus barcode sequence for 86 species revealed a high percentage of barcode matches (96%–97% in GenBank and 96.6%–96.76% in the BOLD System). The nucleotide distance between groups of kelabau from the different rivers based on the Kimura 2-parameter model gave the following results: 0.05% between groups from the Siak and Kampar rivers, 0.09% between those from the Siak and Rokan rivers and 0.05% between those from the Kampar and Rokan rivers. The nucleotide distance between the groups in the Siak (0.09%), Kampar (0.00%) and Rokan (0.10%) Rivers indicated that the kelabau in those rivers were related to each other. Conclusions: Based on the results of the research data using CO1 and biometric analyses, the kelabau were confirmed to be O. melanopleurus.
Tunable mode-locked erbium-doped fiber laser based on a digital micro-mirror device
Authors: Wang Whenhao , Tian Meng , Yang Yan , Huang Yanhua , Li Cong , Chen Guoliang , Lv Min 
Published: March 2020

A tunable mode-locked erbium-doped fiber laser with a digital micro-mirror device (DMD) as the wavelength tuner and nonlinear amplifying loop mirror as the mode-locked device is proposed and experimentally demonstrated. The mode-locked pulse with the center wavelength of 1538–1565 nm continuously tunable is achieved. The average power of the output pulse is 1.028 mW, the pulse repetition frequency is 1.7 MHz, the pulse duration is 616 fs, and the single pulse energy is 0.6 nJ. By controlling the DMD, the center wavelength can be fine-tuned with the tuning accuracy of 0.07 nm. With the increase of the pump power, the traditional soliton pulse is transformed into a noise-like pulse (NLP), and the power of the NLP can reach 34 mW. This mode-locked process can work for a long time and is almost unaffected by the external environment. These results are very useful for applications where pulsed lasers with different wavelengths are needed.
Density functional theory study of mixed halide influence on structures and optoelectronic attributes of CsPb(I/Br)3
Authors: Jbara Ahmed S. , Munir Junaid , Ul Haq Bakhtiar , Saeed M. A. 
Published: March 2020

This paper reports on the influence of the bromine (Br) atoms substitution on the structures and optoelectronic traits of

CsPbI
3

, wherein the density functional theory (DFT) simulation was performed, using all electrons full potential linearized augmented plane-wave method. Furthermore, the generalized gradient approximation, local density approximation, and modified Becke–Johnson exchange-correlation potential were used to improve the optimization and band structure calculations. The calculated lattice constants of

CsPbI
3

and

CsPbBr
3

were consistent with the experimental values. All the studied compounds revealed wide and direct bandgap energies at the R-symmetry point, which varied from 1.74–2.23 eV. The obtained refractive indices of the

CsPbI
3

,

CsPbBrI
2

,

CsPbIBr
2

, and

CsPbBr
3

compounds were correspondingly 2.265, 2.245, 2.090, and 2.086. Present findings may contribute towards the development of experimental studies on the proposed compounds with controlled properties useful for the solar cells.
Micromirror array allocation algorithm based on deconvolution
Authors: Liu Zhifan , Yang Chaoxing , Bu Yang , Li Sikun , Zhang Jianhua , Wang Xiangzhao , Sun Gang 
Published: March 2020

Freeform illumination is one of the necessary techniques in 28 nm technology nodes and beyond. The micromirror array (MMA) has been widely used in lithography freeform illumination systems due to its programmability and high free degree. The MMA allocation algorithm is the key to generate the target freeform illumination source. Its computational speed and precision affect the generation speed and precision of the target illumination source as well as the process window size of the generated illumination pupil directly. In this paper, an MMA allocation method based on deconvolution is proposed. The target freeform illumination source can be obtained directly with the deconvolution and quantization processes. Without the iterative optimization process, the computational speed of the proposed method is much faster than that of the traditional method. The numerical simulation results show that the difference between the target source and the MMA source generated using the proposed method is less than 0.2%. Compared with the process window loss of the target source, the process window loss of the MMA source generated by the proposed deconvolution method is less than 0.5%. Compared with the traditional allocation method, the runtime of the proposed method is less than 0.05 s and has improved by 1463 times.