bluuebunny/crossref_metadata_2025 huggingface dataset:
A thermostable and CBM2-linked GH10 xylanase from Thermobifida fusca for paper bleaching
Authors: Wu Xiuyun , Shi Zelu , Tian Wenya , Liu Mengyu , Huang Shuxia , Liu Xinli , Yin Hua , Wang Lushan
Published: August 2022

Xylanases have the potential to be used as bio-deinking and bio-bleaching materials and their application will decrease the consumption of the chlorine-based chemicals currently used for this purpose. However, xylanases with specific properties could act effectively, such as having significant thermostability and alkali resistance, etc. In this study, we found that TfXyl10A, a xylanase from Thermobifida fusca, was greatly induced to transcript by microcrystalline cellulose (MCC) substrate. Biochemical characterization showed that TfXyl10A is optimally effective at temperature of 80 °C and pH of 9.0. After removing the carbohydrate-binding module (CBM) and linker regions, the optimum temperature of TfXyl10A-CD was reduced by 10°C (to 70°C), at which the enzyme’s temperature tolerance was also weakened. While truncating only the CBM domain (TfXyl10AdC) had no significant effect on its thermostability. Importantly, polysaccharide-binding experiment showed that the auxiliary domain CBM2 could specifically bind to cellulose substrates, which endowed xylanase TfXyl10A with the ability to degrade xylan surrounding cellulose. These results indicated that TfXyl10A might be an excellent candidate in bio-bleaching processes of paper industry. In addition, the features of active-site architecture of TfXyl10A in GH10 family were further analyzed. By mutating each residue at the -2 and -1 subsites to alanine, the binding force and enzyme activity of mutants were observably decreased. Interestingly, the mutant E51A, locating at the distal -3 subsite, exhibited 90% increase in relative activity compared with wild-type (WT) enzyme TfXyl10A-CD (the catalytic domain of TfXyl110A). This study explored the function of a GH10 xylanase containing a CBM2 domain and the contribution of amino acids in active-site architecture to catalytic activity. The results obtained provide guidance for the rational design of xylanases for industrial applications under high heat and alkali-based operating conditions, such as paper bleaching.
Comprehensive landscape of the ST3GAL family reveals the significance of ST3GAL6-AS1/ST3GAL6 axis on EGFR signaling in lung adenocarcinoma cell invasion
Authors: Li Jiaxuan , Long Yiming , Sun Jingya , Wu Jiajun , He Xiao , Wang Simei , Wang Xiongbiao , Miao Xiayi , Huang Ruimin , Yan Jun
Published: August 2022

Sialylation aberration has been implicated in lung cancer development by altering signaling pathways. Hence, it is urgent to identify key sialyltransferases in the development of lung adenocarcinoma (LUAD), which is a common malignant subtype of non-small cell lung cancer. Herein, by systematically investigating the expression levels of ST3GAL family members in several public databases, we consistently found the frequent downregulation of ST3GAL6 in LUAD samples. Its downregulation is significantly negatively associated with stage, and significantly reduced in proximal-proliferative molecular subtype and predicts poor clinical outcomes. By protein–protein interaction network analysis and validation, we found that ST3GAL6 deficiency promotes LUAD cell invasiveness with the activated EGFR/MAPK signaling, accompanied by the elevated expression levels of matrix metalloproteinases 2 and 9, which can be partially reversed by EGFR inhibitor, gefitinib. Additionally, the ST3GAL6 level was positively regulated by ST3GAL6-AS1, an antisense long non-coding RNA to its host gene. The downregulation of ST3GAL6-AS1 also heralds a worse prognosis in LUAD patients and promotes LUAD cell invasiveness, recapitulating the function of its host gene, ST3GAL6. Altogether, ST3GAL6-AS1-regulated ST3GAL6 is a frequently downregulated sialyltransferase in LUAD patients and negatively regulates EGFR signaling, which can serve as a promising independent prognostic marker in LUAD patients.
Bioengineering the human spinal cord
Authors: Iyer Nisha R. , Ashton Randolph S.
Published: August 2022

Three dimensional, self-assembled organoids that recapitulate key developmental and organizational events during embryogenesis have proven transformative for the study of human central nervous system (CNS) development, evolution, and disease pathology. Brain organoids have predominated the field, but human pluripotent stem cell (hPSC)-derived models of the spinal cord are on the rise. This has required piecing together the complex interactions between rostrocaudal patterning, which specifies axial diversity, and dorsoventral patterning, which establishes locomotor and somatosensory phenotypes. Here, we review how recent insights into neurodevelopmental biology have driven advancements in spinal organoid research, generating experimental models that have the potential to deepen our understanding of neural circuit development, central pattern generation (CPG), and neurodegenerative disease along the body axis. In addition, we discuss the application of bioengineering strategies to drive spinal tissue morphogenesis in vitro, current limitations, and future perspectives on these emerging model systems.
EyeVolve, a modular PYTHON based model for simulating developmental eye type diversification
Authors: Lavin Ryan , Rathore Shubham , Bauer Brian , Disalvo Joe , Mosley Nick , Shearer Evan , Elia Zachary , Cook Tiffany A. , Buschbeck Elke K.
Published: August 2022

Vision is among the oldest and arguably most important sensory modalities for animals to interact with their external environment. Although many different eye types exist within the animal kingdom, mounting evidence indicates that the genetic networks required for visual system formation and function are relatively well conserved between species. This raises the question as to how common developmental programs are modified in functionally different eye types. Here, we approached this issue through EyeVolve, an open-source PYTHON-based model that recapitulates eye development based on developmental principles originally identified in Drosophila melanogaster. Proof-of-principle experiments showed that this program’s animated timeline successfully simulates early eye tissue expansion, neurogenesis, and pigment cell formation, sequentially transitioning from a disorganized pool of progenitor cells to a highly organized lattice of photoreceptor clusters wrapped with support cells. Further, tweaking just five parameters (precursor pool size, founder cell distance and placement from edge, photoreceptor subtype number, and cell death decisions) predicted a multitude of visual system layouts, reminiscent of the varied eye types found in larval and adult arthropods. This suggests that there are universal underlying mechanisms that can explain much of the existing arthropod eye diversity. Thus, EyeVolve sheds light on common principles of eye development and provides a new computational system for generating specific testable predictions about how development gives rise to diverse visual systems from a commonly specified neuroepithelial ground plan.
Long non-coding RNAs: Modulators of phenotypic transformation in vascular smooth muscle cells
Authors: Lu Bing-Han , Liu Hui-Bing , Guo Shu-Xun , Zhang Jie , Li Dong-Xu , Chen Zhi-Gang , Lin Fei , Zhao Guo-An
Published: August 2022

Long non-coding RNA (lncRNAs) are longer than 200 nucleotides and cannot encode proteins but can regulate the expression of genes through epigenetic, transcriptional, and post-transcriptional modifications. The pathophysiology of smooth muscle cells can lead to many vascular diseases, and studies have shown that lncRNAs can regulate the phenotypic conversion of smooth muscle cells so that smooth muscle cells proliferate, migrate, and undergo apoptosis, thereby affecting the development and prognosis of vascular diseases. This review discusses the molecular mechanisms of lncRNA as a signal, bait, stent, guide, and other functions to regulate the phenotypic conversion of vascular smooth muscle cells, and summarizes the role of lncRNAs in regulating vascular smooth muscle cells in atherosclerosis, hypertension, aortic dissection, vascular restenosis, and aneurysms, providing new ideas for the diagnosis and treatment of vascular diseases.
Research on the sedimentary characteristics of organic matter in lacustrine mudrocks and their hydrocarbon generation potential based on palynofacies analysis: Eocene shahejie formation, dongying sag
Authors: Zeng Xiang , Cai Jingong , Wang Xuejun , Zhang Xuejun , Yan Jianping , Zhu Weilin , Dong Zhe , Bian Lizeng
Published: August 2022

Lacustrine mudrocks are important hydrocarbon source rocks due to their high contents of organic matter (OM). An accurate determination of the origins of OM in the rocks can contribute greatly to the identification of the sedimentary environment and the evaluation of the hydrocarbon generation capacity of the mudrocks. In this study, the lacustrine mudrocks of the Eocene Shahejie Formation in the Dongying Sag of China were sampled for further discussion of the types and origins of OM and the hydrocarbon generation capacity of the mudrocks. On that basis, the classical palynofacies classification scheme was improved, and five palynofacies types (PF1 to PF5) were classified to accurately reflect different lacustrine environments. Among them, PF1 to PF3 are rich in various amorphous organic matter (AOM), including benthic microbial mats, organic aggregates and algal aggregates, which are part of the lake environment in which aquatic organisms bloom. The hydrocarbon generation abilities of the three palynofacies are different but generally strong. PF5 and PF4 have abundant terrestrial plant fragments and macrophyte fragments, respectively, indicating a shallow, near-provenance lake environment and a shallow, macrophyte-flourishing lake environment. These two types of palynofacies have weaker hydrocarbon generation capacities than the former three. Due to the enrichment of different types of palynofacies, each formation of the Dongying Sag shows distinct hydrocarbon generation potentials. Therefore, it is important to pay special attention to the origin of OM and its influences on the hydrocarbon generation capacity of lacustrine mudrocks for a better understanding of the deposition and hydrocarbon generation potential of source rocks.
Business English instruction: Empowering learners with the 4Cs of the 21st century
Authors: Aben Ahmed Mahdi
Published: August 2022

This research aims to measure the perceptions of business English teachers regarding the effectiveness of the proposed communication, collaboration, critical thinking, and creativity (4Cs) teaching model. Furthermore, it also identifies some of the gaps that emerged while applying the 4Cs model, and finally recommends deliberate instructional steps for using the model. The participants in the study are 140 Business English teachers at an academic institution in the eastern part of Saudi Arabia. The study is driven by the belief that educators in this field need to create modern language instruction involving the 21st century 4Cs: communication, collaboration, critical thinking, and creativity by the intervention of carefully planned objectives, varied activities, varieties of teaching methodologies, technological tools and materials, interaction patterns, teachers’ professional development and students’ awareness and cultural background. Using two questionnaires, the study gauged EFL teachers’ perceptions of the application of a specially developed 4Cs framework for Business English, to ensure that the students enrolled in these courses are fit to take on the role of global citizens. Findings show that teachers are positive about the appropriateness of applying the framework in the context of 21st century skills, and a viable degree of effectiveness in a learning environment. Participant teachers who applied this approach using the conceptualized paradigm in teaching Business English recommend its efficacy due to relevant pedagogical implications and practical principles that were discovered. The study concludes with six principles that can be directly used to ensure that the 4Cs which are a necessity in the 21st education system is integrated by educators in English language teaching (ELT) instruction.
Agonist triggering in oocyte donation programs—Mini review
Authors: Najdecki Robert , Michos Georgios , Peitsidis Nikos , Timotheou Evangelia , Chartomatsidou Tatiana , Kakanis Stelios , Chouliara Foteini , Mamopoulos Apostolos , Papanikolaou Evangelos
Published: August 2022

Oocyte donation programs involve young and healthy women undergoing heavy ovarian stimulation protocols in order to yield good-quality oocytes for their respective recipient couples. These stimulation cycles were for many years beset by a serious and potentially lethal complication known as ovarian hyperstimulation syndrome (OHSS). The use of the short antagonist protocol not only is patient-friendly but also has halved the need for hospitalization due to OHSS sequelae. Moreover, the replacement of beta-human chorionic gonadotropin (b-hCG) with gonadotropin-releasing hormone agonist (GnRH-a) triggering has reduced OHSS occurrence significantly, almost eliminating its moderate to severe presentations. Despite differences in the dosage and type of GnRH-a used across different studies, a comparable number of mature oocytes retrieved, fertilization, blastulation, and pregnancy rates in egg recipients are seen when compared to hCG-triggered cycles. Nowadays, GnRH-a tend to be the triggering agents of choice in oocyte donation cycles, as they are effective and safe and reduce OHSS incidence. However, as GnRH-a triggering does not eliminate OHSS altogether, caution should be practiced in order to avoid unnecessary lengthy and heavy ovarian stimulation that could potentially compromise both the donor’s wellbeing and the treatment’s efficacy.
Multi-instrumental investigation of the solar flares impact on the ionosphere on 05–06 December 2006
Authors: Barta Veronika , Natras Randa , Srećković Vladimir , Koronczay David , Schmidt Michael , Šulic Desanka
Published: August 2022

The sudden increase of X-radiation and EUV emission following solar flares causes additional ionization and increased absorption of electromagnetic (EM) waves in the Earth’s atmosphere. The solar flare impact on the ionosphere above Europe on 05 and 06 December 2006 was investigated using ground-based (ionosonde and VLF) and satellite-based data (Vertical Total Electron Content (VTEC) derived from GNSS observations and VLF measurements from DEMETER satellite). Based on the Kp and Dst indices, 05 December 2006 was a quiet day, while there was a geomagnetic storm on 06 December 2006. The total fade-out of the EM waves emitted by the ionosondes was experienced at all investigated stations during an X9 class flare on 05 December 2006. The variation of the fmin parameter (first echo trace observed on ionograms, it is a rough measure of the “non-deviative” absorption) and its difference between the quiet period and during the flares have been analyzed. A latitude dependent enhancement of fmin (2–9 MHz) and Δfmin (relative change of about 150%–300%) was observed at every station at the time of the X9 (on 05 December) and M6 (on 06 December) flares. Furthermore, we analyzed VTEC changes during and after the flare events with respect to the mean VTEC values of reference quiet days. During the X9 solar flare, VTEC increased depending on the latitude (2–3 TECU and 5%–20%). On 06 December 2006, the geomagnetic storm increased ionization (5–10 TECU) representing a “positive” ionospheric storm. However, an additional peak in VTEC related to the M6 flare could not be detected. We have also observed a quantifiable change in transionospheric VLF absorption of signals from ground transmitters detected in low Earth orbit associated with the X9 and M6 flare events on 05 and 06 December in the DEMETER data. Moreover, amplitude and phase of ground-based, subionospherically propagating VLF signals were measured simultaneously during the investigated flares to analyze ionosphere reaction and to evaluate the electron density profile versus altitude. For the X9 and M6 flare events we have also calculated the ionospheric parameters (sharpness, reflection height) important for the description and modelling of this medium under forced additional ionization.
Establishing log reduction values for wastewater treatment processes from ambient influent and effluent pathogen monitoring data
Authors: Tchobanoglous George , Kenny John , Leverenz Harold , Oliveri Adam
Published: August 2022

In developing wastewater treatment regulations and guidelines for potable reuse, the reduction of pathogens is of critical importance. In draft regulations, the state of California has proposed overall treatment process log reduction values (LRVs) of 20, 14, and 15 respectively for viruses, Giardia cysts, and Cryptosporidium oocysts, for direct potable reuse. In meeting the log reduction requirements, agencies have sought to obtain credit for LRVs achieved consistently through secondary biological and tertiary wastewater treatment, in addition to the LRVs achieved through advanced water treatment. The purpose of this paper is to illustrate how to determine pathogen LRVs, using ambient wastewater treatment pathogen monitoring data and the rank-paired covariant method of analysis.
Influence of energy structure, environmental regulations and human capital on ecological sustainability in EKC framework; evidence from MINT countries
Authors: Saqib Najia , Duran Ivan A. , Sharif Ilma
Published: August 2022

Heterogeneous anthropogenic and insufficient development strategies have caused an international compromise between sustainable growth and environmental deterioration. Environmental concerns have necessitated rules and human capital to protect the global ecosystem. Literature is ambiguous on the usefulness of environmental rules in reducing environmental deterioration. This study examines the impact of environmental regulations and education as a proxy for human capital in Mexico, Indonesia, Nigeria, and Turkey (MINT) countries’ ecological footprints between 1990 and 2020. The econometric research shows that present environmental restrictions in MINT countries are unsuccessful at reducing their ecological footprints. Energy consumption and trade-openness also increase ecological footprints. The MINT countries panel also confirms the Environmental Kuznets Curve idea. The country-specific findings show that energy use silently harmed the environment in MINT nations, whereas environmental legislation, economic growth, and trade-openness had diverse effects. These findings suggest that in order for MINT nations to achieve environmental sustainability, they should strengthen and enforce environmental regulations; adopt policies that promote sustainable economic growth; reduce their reliance on fossil-fuels; improve quality education and awareness; and actively engage in sustainable trading activities.
Yield, nitrogen-use efficiency, and distribution of nitrate-nitrogen in the soil profile as influenced by irrigation and fertilizer nitrogen levels under zero-till wheat in the eastern Indo-Gangetic plains of India
Authors: Sahoo Samaresh , Mukhopadhyay P. , Sinha A. K. , Bhattacharya P. M. , Rakesh S. , Kumar Rajkishore , Padbhushan Rajeev , Bijay-Singh  , Parmar Brajendra , Vishwakarma Anand , Kumar Amarendra , Yadav Brahamdeo Kumar , Bhushan Shanti , Kumar Atul , Kaviraj Megha , Kumar Upendra
Published: August 2022

Due to the introduction of zero-till wheat in the Indo-Gangetic plains (IGP) in India, irrigation and fertilizer nitrogen (N) management needs to be modified from that followed under conventionally tilled fields. A field experiment was conducted to study the effect of irrigation and N levels on yield and N uptake by zero-till wheat, fertilizer N-use efficiency, and distribution of nitrate-N (NO3-N) in a soil profile under zero-till conditions in an acidic alluvial soil of the eastern IGP. The experiment was laid out in a split-plot design with four levels of irrigation as main plots (I0-no irrigation, rain-fed, I1-122 mm in one irrigation at 21 days after sowing (DAS), I2-263 mm in two irrigations at 21 and 42 DAS, and I3-386 mm in three irrigations at 21, 42, and 84 DAS) and 4 N levels [0 (N0), 60 (N1), 120 (N2), and 150 (N3) kg N ha−1] as subplots. Grain and straw yields were significantly higher at the irrigation level-I2 and 120 kg N ha−1-N2 over the control (I0 and N0) and were at par with the highest applied levels of irrigation and N (I3 and N3). The nitrogen uptake by wheat followed a trend similar to yield for irrigation levels; however, it increased significantly up to 150 kg N ha−1. After the harvest of wheat crop, more NO3-N was observed in the 60–90 cm subsurface soil layer than in the surface 0–15 cm and/or 15–30 cm and 30–60 cm subsurface soil layers. The highest NO3-N concentration was recorded in the treatment I2N2. Accumulation of NO3-N in the soil increased up to irrigation levels I2 and with increasing doses of fertilizer N application. Combined applications of irrigation and N had a positive and significant influence on agronomic efficiency (AE) and apparent N recovery (ANR) but had no significant effect on physiological efficiency (PE). This study suggests that an appropriate combination of irrigation and N levels in zero-till wheat can lead to not only high-yield levels and N-use efficiency but also adequately control NO3-N leaching under acidic alluvial soils in the eastern IGP.
Interaction and spatial effects of green technology innovation and financial agglomeration: Empirical evidence from China under the goal of “double carbon”
Authors: Han Zhixuan , Li Xingyi , Yan Zhen , Zhong Kaiyang
Published: August 2022

Green technology innovation is an important means to help reduce carbon emissions. Most of the current researches focus on the evaluation of green technology innovation and its relationship with economic factors, while ignoring its relationship with financial factors. In fact, financial development is an important driving force for further improving the efficiency of technological innovation, especially in developing countries. China, which has put forward the “double carbon” strategy (achieve peak carbon dioxide emission and carbon neutrality) in recent years, has a lot of interaction between green technology innovation and financial development, which is a good research sample. Based on the provincial panel data of 30 provinces in China from 2003 to 2020, this paper follows the research steps: 1) From the perspective of carbon emissions, we use the non-radial super-efficiency SBM-ML model to measure the total factor productivity of green technology innovation. 2) We analyze the temporal and spatial changes of green technology innovation and financial agglomeration in each province. 3) We establish a spatial simultaneous model of generalized three-stage least squares to study the intrinsic relationship between green technology innovation and financial agglomeration. The results show that: 1) The financial agglomeration level of each province is basically stable due to the fixedness of the financial core area, but the development speed of green technology innovation in the southeast coastal area is significantly higher than that in the inland area. 2) The interaction between green technology innovation and financial agglomeration has a nonlinear mechanism of “low-level inhibition and high-level promotion,” that is, low-level financial agglomeration has an inhibitory effect on green technology innovation, and as the level of financial agglomeration increases, its impact on green technology innovation gradually develops positively, and vice versa. 3) The green technology innovation and financial agglomeration in the surrounding provinces have positive and significant promoting effects on the green technology innovation and financial agglomeration in the province, but the impact of green technology innovation is significantly stronger than that of financial agglomeration. Finally, suggestions are put forward for further reducing carbon emissions, realizing the sustainable economic growth and approaching goals of “carbon peaking and carbon neutrality.”
Impact of transition risks of climate change on Chinese financial market stability
Authors: An Qiguang , Zheng Lin , Li Qingzhao , Lin Chengwei
Published: August 2022

Transition risks caused by climate change are becoming an important issue in finance research. In this study, we first construct the transmission mechanism of “climate change–change in investor attention–financial stability” and analyze the impact of transition risks on Chinese financial market stability. Second, we construct a Climate Change Index (CCI). The CCI depicts changes in investors’ attention to the transition risks of climate change based on the Baidu Index. We also use the dynamic factor model (DFM) to construct a Financial Stress Index (FSI) that describes the Chinese financial market stability. The FSI can also effectively identify financial events within the sample interval. We then use the TVP-VAR model to empirically analyze the impact of the transition risks of climate change on Chinese financial market stability. We present the following results: in the short and medium terms, more financial market pressure will be caused by an increase in the CCI. In the long run, the impact of an increase in CCI on Chinese financial market pressure is uncertain. Finally, we present valuable countermeasures and suggestions from the different perspectives of investors, financial institutions, and regulators.
Recent advances in hidradenitis suppurativa: Role of race, genetics, and immunology
Authors: Vellaichamy Gautham , Amin Anya T. , Dimitrion Peter , Hamzavi Zaakir , Zhou Li , Adrianto Indra , Mi Qing-Sheng
Published: August 2022

Hidradenitis suppurativa (HS) is a multifactorial chronic skin disease characterized by inflammation around the hair follicles commonly affecting intertriginous areas. The underlying pathogenesis of HS and its molecular mechanisms are largely understudied. Genetic studies in families have identified variants within the γ-secretase complex associated with HS; however, no definitive genotype-phenotype correlations have been made. The lack of knowledge regarding the intersection of genetics, immunology and environmental risk factors is a major obstacle to improving treatment for patients with HS. This article provides an overview of the role of race, genetics, and immunology in HS to provide insight into the multiple factors influencing the pathophysiology of HS.
TaNAC020 homoeologous genes are associated with higher thousand kernel weight and kernel length in Chinese wheat
Authors: Majeed Uzma , Hou Jian , Hao Chenyang , Zhang Xueyong
Published: August 2022

NAC proteins constitute one of the largest plant-specific transcription factor (TF) families and play significant roles in plant growth and development. In the present study, three TaNAC020 homoeologous genes located on chromosomes 7A, 7B, and 7D were isolated from wheat (Triticum aestivum L.). TaNAC020s were predominantly expressed in developing grains. The developed transgenic rice lines for TaNAC020-B showed higher starch density and lower amylose contents than those of the wild type (WT). Sequence polymorphism studies showed seven and eight SNPs in TaNAC020-A/B, making three and two haplotypes, respectively. No sequence polymorphism was identified in TaNAC020-D. Association analysis revealed that HAP-2 of TaNAC020-A and TaNAC020-B was the favored haplotype for higher thousand kernel weight and length. Geographic distribution and allelic frequency showed that our favored haplotype experienced strong selection in China, and likewise, diversity increased in TaNAC020s during wheat polyploidization. The results obtained in this study demonstrate that TaNAC020s positively influence starch synthesis and accumulation and are one of the key regulators of the kernel (seed) size and kernel number and have the potential for utilization in wheat breeding to improve grain yield. Molecular markers developed in this study stand instrumental in marker-assisted selection for genetic improvement and germplasm enhancement in wheat.
Exploring the optimal strategy of imputation from SNP array to whole-genome sequencing data in farm animals
Authors: Jiang Yifan , Song Hailiang , Gao Hongding , Zhang Qin , Ding Xiangdong
Published: August 2022

Genotype imputation from BeadChip to whole-genome sequencing (WGS) data is a cost-effective method of obtaining genotypes of WGS variants. Beagle, one of the most popular imputation software programs, has been widely used for genotype inference in humans and non-human species. A few studies have systematically and comprehensively compared the performance of beagle versions and parameter settings of farm animals. Here, we investigated the imputation performance of three representative versions of Beagle (Beagle 4.1, Beagle 5.0, and Beagle 5.4), and the effective population size (Ne) parameter setting for three species (cattle, pig, and chicken). Six scenarios were investigated to explore the impact of certain key factors on imputation performance. The results showed that the default Ne (1,000,000) is not suitable for livestock and poultry in small reference or low-density arrays of target panels, with 2.47%–10.45% drops in accuracy. Beagle 5 significantly reduced the computation time (4.66-fold–13.24-fold) without an accuracy loss. In addition, using a large combined-reference panel or high-density chip provides greater imputation accuracy, especially for low minor allele frequency (MAF) variants. Finally, a highly significant correlation in the measures of imputation accuracy can be obtained with an MAF equal to or greater than 0.05.
Construction of a novel Wheat 55 K SNP array-derived genetic map and its utilization in QTL mapping for grain yield and quality related traits
Authors: Fan Xiaoli , Liu Xiaofeng , Feng Bo , Zhou Qiang , Deng Guangbing , Long Hai , Cao Jun , Guo Shaodan , Ji Guangsi , Xu Zhibin , Wang Tao
Published: August 2022

Wheat is one of the most important staple crops for supplying nutrition and energy to people world. A new genetic map based on the Wheat 55 K SNP array was constructed using recombinant inbred lines derived from a cross between Zhongkemai138 and Kechengmai2 to explore the genetic foundation for wheat grain features. This new map covered 2,155.72 cM across the 21 wheat chromosomes with 11,455 markers. And 2,846 specific markers for this genetic map and 148 coincident markers among different maps were documented, which was helpful for improving and updating wheat genetic and genomic information. Using this map, a total of 68 additive QTLs and 82 pairs of epistatic QTLs were detected for grain features including yield, nutrient composition, and quality-related traits by QTLNetwork 2.1 and IciMapping 4.1 software. Fourteen additive QTLs and one pair of epistatic QTLs could be detected by both software programs and thus regarded as stable QTLs here, all of which explained higher phenotypic variance and thus could be utilized for wheat grain improvement. Additionally, thirteen additive QTLs were clustered into three genomic intervals (C4D.2, C5D, and C6D2), each of which had at least two stable QTLs. Among them, C4D.2 and C5D have been attributed to the famous dwarfing geneRht2and the hardness locusPina, respectively, while endowed with main effects on eight grain yield/quality related traits and epistatically interacted with each other to control moisture content, indicating that the correlation of involved traits was supported by the pleotropic of individual genes but also regulated by the gene interaction networks. Additionally, the stable additive effect of C6D2 (QMc.cib-6D2andQTw.cib-6D2) on moisture content was also highlighted, potentially affected by a novel locus, and validated by its flanking Kompetitive Allele-Specific PCR marker, andTraesCS6D02G109500, encoding aleurone layer morphogenesis protein, was deduced to be one of the candidate genes for this locus. This result observed at the QTL level the possible contribution of grain water content to the balances among yield, nutrients, and quality properties and reported a possible new locus controlling grain moisture content as well as its linked molecular marker for further grain feature improvement.
Genome-wide association study for grain yield and component traits in bread wheat (Triticum aestivum L.)
Authors: Khan Hanif , Krishnappa Gopalareddy , Kumar Satish , Mishra Chandra Nath , Krishna Hari , Devate Narayana Bhat , Rathan Nagenahalli Dharmegowda , Parkash Om , Yadav Sonu Singh , Srivastava Puja , Biradar Suma , Kumar Monu , Singh Gyanendra Pratap
Published: August 2022

Genomic regions governing days to heading (DH), grain filling duration (GFD), grain number per spike (GNPS), grain weight per spike (GWPS), plant height (PH), and grain yield (GY) were investigated in a set of 280 diverse bread wheat genotypes. The genome-wide association studies (GWAS) panel was genotyped using a 35K Axiom Array and phenotyped in five environments. The GWAS analysis showed a total of 27 Bonferroni-corrected marker-trait associations (MTAs) on 15 chromosomes representing all three wheat subgenomes. The GFD showed the highest MTAs (8), followed by GWPS (7), GY (4), GNPS (3), PH (3), and DH (2). Furthermore, 20 MTAs were identified with more than 10% phenotypic variation. A total of five stable MTAs (AX-95024590, AX-94425015, AX-95210025 AX-94539354, and AX-94978133) were identified in more than one environment and associated with the expression of DH, GFD, GNPS, and GY. Similarly, two novel pleiotropic genomic regions with associated MTAs i.e. AX-94978133 (4D) and AX-94539354 (6A) harboring co-localized QTLs governing two or more traits were also identified. In silico analysis revealed that the SNPs were located on important putative candidate genes such as F-box-like domain superfamily, Lateral organ boundaries, LOB, Thioredoxin-like superfamily Glutathione S-transferase, RNA-binding domain superfamily, UDP-glycosyltransferase family, Serine/threonine-protein kinase, Expansin, Patatin, Exocyst complex component Exo70, DUF1618 domain, Protein kinase domain involved in the regulation of grain size, grain number, growth and development, grain filling duration, and abiotic stress tolerance. The identified novel MTAs will be validated to estimate their effects in different genetic backgrounds for subsequent use in marker-assisted selection (MAS).
Exploration of barriers to postnatal care service utilization in Debre Libanos District, Ethiopia: A descriptive qualitative study
Authors: Girma Tareke Kasahun , Feyissa Garumma Tolu , Kebede Yohannes
Published: August 2022

Background

In Ethiopia, postnatal care (PNC) service utilization was low although many interventions had been implemented. Previous studies showed community-/caregiver-related barriers to PNC service utilization, but limited evidence was available on the health facilities and health care provider-related barriers. Therefore, the study was aimed at exploring both community and health care provider-related barriers to PNC service utilization.

Methods

A descriptive qualitative study was conducted at Debre Libanos District, Ethiopia, from 11 March to 7 April 2019. A purposive sampling technique was used to recruit study participants among recently delivered women (<2 months), health care providers, and community members. A total of five in-depth interviews, 12 key informant interviews, and four FGDs were conducted. Data were audio-recorded, transcribed verbatim, and translated, and inductive thematic analysis was used to analyze the data using the atlas ti.7.1 software.

Results

A total of 51 participants were involved in the study. The findings were organized into two major themes: (1) Community/caregiver-related barriers to PNC service utilization: lack of awareness about PNC, its importance, and schedules; lack of awareness about postnatal danger signs, sociocultural and religious beliefs, topographical and transportation problems, non-functionality of the health developmental armies (HDA); (2) health facility and health care provider-related barriers to PNC service utilization: poor supportive supervision and monitoring, lack of health extension workers' (HEW) commitment, lack of an organized system to notify delivery to HEW, shortage of HEWs, the residence of the HEWs, closure of health posts (HP) on working hours, and non-functionality of HPs.

Conclusions

The study findings underscore the need to develop different strategies and take actions. Therefore, the health centers and district health offices should have to assign the required number of HEWs at HPs, regularly supervise and monitor HEWs, and develop an organized system to facilitate early notification of delivery to HEWs. The HEWs should have to live near the HP, re-organize HDAs, create awareness of maternal and newborn danger signs, and conduct social and behavioral change communications to increase the health-seeking behavior of community members for utilizing PNC services.
Comprehensive analyses identify RIPOR2 as a genomic instability-associated immune prognostic biomarker in cervical cancer
Authors: Xu Fangfang , Zou Chang , Gao Yueqing , Shen Jiacheng , Liu Tingwei , He Qizhi , Li Shuangdi , Xu Shaohua
Published: August 2022

Cervical cancer (CC) is a malignancy that tends to have a poor prognosis when detected at an advanced stage; however, there are few studies on the early detection of CC at the genetic level. The tumor microenvironment (TME) and genomic instability (GI) greatly affect the survival of tumor patients via effects on carcinogenesis, tumor growth, and resistance. It is necessary to identify biomarkers simultaneously correlated with components of the TME and with GI, as these could predict the survival of patients and the efficacy of immunotherapy. In this study, we extracted somatic mutational data and transcriptome information of CC cases from The Cancer Genome Atlas, and the GSE44001 dataset from the Gene Expression Omnibus database was downloaded for external verification. Stromal components differed most between genomic unstable and genomic stable groups. Differentially expressed genes were screened out on the basis of GI and StromalScore, using somatic mutation information and ESTIMATE methods. We obtained the intersection of GI- and StromalScore-related genes and used them to establish a four-gene signature comprising RIPOR2, CCL22, PAMR1, and FBN1 for prognostic prediction. We described immunogenomic characteristics using this risk model, with methods including CIBERSORT, gene set enrichment analysis (GSEA), and single-sample GSEA. We further explored the protective factor RIPOR2, which has a close relationship with ImmuneScore. A series of in vitro experiments, including immunohistochemistry, immunofluorescence, quantitative reverse transcription PCR, transwell assay, CCK8 assay, EdU assay, cell cycle detection, colony formation assay, and Western blotting were performed to validate RIPOR2 as an anti-tumor signature. Combined with integrative bioinformatic analyses, these experiments showed a strong relationship between RIPOR2 with tumor mutation burden, expression of genes related to DNA damage response (especially PARP1), TME-related scores, activation of immune checkpoint activation, and efficacy of immunotherapy. To summarize, RIPOR2 was successfully identified through comprehensive analyses of the TME and GI as a potential biomarker for forecasting the prognosis and immunotherapy response, which could guide clinical strategies for the treatment of CC patients.
Pharmacological activation of the C5a receptor leads to stimulation of the β-adrenergic receptor and alleviates cognitive impairment in a murine model of familial Alzheimer’s disease
Authors: Fella Eleni , Papacharalambous Revekka , Kynigopoulos Demos , Ioannou Maria , Derua Rita , Christodoulou Christiana , Stylianou Myrto , Karaiskos Christos , Kagiava Alexia , Petroula Gerasimou , Pierides Chryso , Kyriakou Maria , Koumas Laura , Costeas Paul , Panayiotou Elena
Published: August 2022

Alzheimer’s disease (AD) is a progressive neurodegenerative disease of the brain causing either familial or sporadic dementia. We have previously administered the modified C5a receptor agonist (EP67) for a short period to a transgenic mouse model of AD (5XFAD) and have observed not only reduction in β-amyloid deposition and gliosis but also improvement in cognitive impairment. Inquiring, however, on the effects of EP67 in an already heavily burdened animal, thus representing a more realistic scenario, we treated 6-month-old 5XFAD mice for a period of 14 weeks. We recorded a significant decrease in both fibrillar and pre-fibrillar β-amyloid as well as remarkable amelioration of cognitive impairment. Following proteomic analysis and pathway association, we postulate that these events are triggered through the upregulation of β-adrenergic and GABAergic signaling. In summary, our results reveal how inflammatory responses can be employed in inducing tangible phenotype improvements even in advanced stages of AD.
Current knowledge of the implication of lipid mediators in psoriasis
Authors: Simard Mélissa , Morin Sophie , Ridha Zainab , Pouliot Roxane
Published: August 2022

The skin is an organ involved in several biological processes essential to the proper functioning of the organism. One of these essential biological functions of the skin is its barrier function, mediated notably by the lipids of the stratum corneum, and which prevents both penetration from external aggression, and transepidermal water loss. Bioactive lipid mediators derived from polyunsaturated fatty acids (PUFAs) constitute a complex bioactive lipid network greatly involved in skin homeostasis. Bioactive lipid mediators derived from n-3 and n-6 PUFAs have well-documented anti- and pro-inflammatory properties and are recognized as playing numerous and complex roles in the behavior of diverse skin diseases, including psoriasis. Psoriasis is an inflammatory autoimmune disease with many comorbidities and is associated with enhanced levels of pro-inflammatory lipid mediators. Studies have shown that a high intake of n-3 PUFAs can influence the development and progression of psoriasis, mainly by reducing the severity and frequency of psoriatic plaques. Herein, we provide an overview of the differential effects of n-3 and n-6 PUFA lipid mediators, including prostanoids, hydroxy-fatty acids, leukotrienes, specialized pro-resolving mediators, N-acylethanolamines, monoacylglycerols and endocannabinoids. This review summarizes current findings on lipid mediators playing a role in the skin and their potential as therapeutic targets for psoriatic patients.
Construction of an easily detectable transgenic Synechococcus elongatus PCC 7942 against White Spot Syndrome Virus using vp28 and mOrange Gene and its metabolism in shrimp
Authors: Peng Wen , Bao Qunjing , Jia Rui , He Peimin
Published: August 2022

White spot syndrome is an epidemic disease caused by the highly contagious and lethal white spot syndrome virus (WSSV), resulting in huge economic losses to the global aquaculture industry. VP28 is the main structural protein in the capsule of WSSV and is important in the early stage of infection. Under an excitation wavelength of 548 nm, the mOrange fluorescent protein releases a 562 nm emission wavelength, which is different from the autofluorescence of cyanobacteria. Therefore, using this characteristic combined with the receptor system of Synechococcus elongatus PCC 7942, we constructed transgenic S. elongatus to express the recombinant protein VP28-mOrange. In addition, PCR and western blotting were used to confirm the stable expression of the target gene in cyanobacteria. Using mOrange tracer features, we explored the recombinant protein VP28-mOrange in the metabolic cycle of young Litopenaeus Vannamei after feeding. After the young shrimp had stopped consuming transgenic cyanobacteria, the 24 to 33 h fluorescence signal in the intestine was very weak, and almost disappeared after 36 h. We explored the protective effect of transgenic vp28-mOrange S. elongatus within 48 h of being ingested by L. vannamei and set WSSV challenges at 2, 12, 24, and 48 h post-immunization. However, the survival rate of L. vannamei decreased as the time of the WSSV challenge increased. The survival rate on the seventh day was 81%, 52%, 45.5%, and 33.3% for shrimps challenged for 2, 12, 24, and 48 h, respectively. Enzyme activity can also support this conjecture, the enzyme activity indexes of the experimental groups were significantly reduced compared to positive and wild-type controls. Therefore, this immune agent functioned as a preventive agent. Compared with the traditional method, this method was easy to detect and can visualize the digestion of transgenic cyanobacteria in the Litopenaeus vannamei intestine.
NT5E upregulation in head and neck squamous cell carcinoma: A novel biomarker on cancer-associated fibroblasts for predicting immunosuppressive tumor microenvironment
Authors: Chen Xue-min , Liu Yu-yang , Tao Bing-yan , Xue Xin-miao , Zhang Xin-xin , Wang Lin-lin , Zhong Hui , Zhang Jun , Yang Shi-ming , Jiang Qing-qing
Published: August 2022

Despite tremendous progress made in the diagnosis and managements, head and neck squamous cell carcinoma (HNSC) remains a global medical dilemma with dismal clinical prognosis and high mortality. Gene NT5E encodes the ecto-5’-nucleotidase (CD73), which facilitates the formation of immunosuppressive tumor microenvironment (TME) permissive for tumor progression in various malignancies. Nevertheless, the cell subsets NT5E expressed on and the potential function of NT5E in the TME of HNSC remain virgin lands in HNSC. In this study, we comprehensively performed integrated prognostic analysis and elucidated that NT5E was an independent prognostic indicator for HNSC, for which a high NT5E level predicted poor overall survival (OS), disease-specific survival (DSS) and progression-free interval (PFI) in HNSC patients (p<0.05). Enrichment analyses revealed the close correlation between NT5E and ECM remodeling, and the latent function of NT5E may involve in epithelial-to-mesenchymal transition (EMT) and metastasis during HNSC progression. HNSC-related immune infiltration analysis and single-cell type analysis demonstrated that NT5E expression was significantly positively associated with cancer-associated fibroblasts (CAFs) in HNSC (p<0.01). NT5E-related TME analysis revealed that NT5E-high group are characterized by low neoantigen loads (NAL, p<0.001) and tumor mutation burden (TMB, p<0.01), indicating high-NT5E-expression HNSC patients may be recalcitrant to immunotherapy. In-situ multicolor immunofluorescence staining was later conducted and the results further verified our findings. Taken together, NT5E could be a novel biomarker in HNSC. Predominantly expressed on CAFs, the upregulation of NT5E might predict an immunosuppressive TME for HNSC patients who may benefit little from immunotherapy. Targeting CAFs with high NT5E expression might be a novel therapeutic strategy for HNSC patients.