bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dihydroartemisinin regulates immune cell heterogeneity by triggering a cascade reaction of CDK and MAPK phosphorylation
Authors: Li Qilong , Yuan Quan , Jiang Ning , Zhang Yiwei , Su Ziwei , Lv Lei , Sang Xiaoyu , Chen Ran , Feng Ying , Chen Qijun 
Published: July 2022

AbstractArtemisinin (ART) and dihydroartemisinin (DHA), apart from their profound anti-malaria effect, can also beneficially modulate the host immune system; however, the underlying molecular mechanisms remain unclear. Here, we report that DHA selectively induced T-cell activation, with an increased proportion of Ki67+CD4+ T cells, CD25+CD4+ T cells, interferon (IFN)-γ-producing CD8+ T cells, Brdu+ CD8+ T cells and neutrophils, which was found to enhance cellular immunity to experimental malaria and overcome immunosuppression in mice. We further revealed that DHA upregulated the expression of cell proliferation-associated proteins by promoting the phosphorylation of mitogen-activated protein kinase (MAPK), cyclin-dependent kinases (CDKs), and activator protein 1 in the spleen. This study is the first to provide robust evidence that DHA selectively induced the expansion of subsets of splenic T cells through phosphorylated CDKs and MAPK to enhance cellular immune responses under non-pathological or pathological conditions. The data significantly deepened our knowledge in the mechanism underlying DHA-mediated immunomodulation.
Regulation of AUXIN RESPONSE FACTOR condensation and nucleo-cytoplasmic partitioning
Authors: Jing Hongwei , Korasick David A. , Emenecker Ryan J. , Morffy Nicholas , Wilkinson Edward G. , Powers Samantha K. , Strader Lucia C. 
Published: July 2022

AbstractAuxin critically regulates plant growth and development. Auxin-driven transcriptional responses are mediated through the AUXIN RESPONSE FACTOR (ARF) family of transcription factors. ARF protein condensation attenuates ARF activity, resulting in dramatic shifts in the auxin transcriptional landscape. Here, we perform a forward genetics screen for ARF hypercondensation, identifying an F-box protein, which we named AUXIN RESPONSE FACTOR F-BOX1 (AFF1). Functional characterization of SCFAFF1 revealed that this E3 ubiquitin ligase directly interacts with ARF19 and ARF7 to regulate their accumulation, condensation, and nucleo-cytoplasmic partitioning. Mutants defective in AFF1 display attenuated auxin responsiveness, and developmental defects, suggesting that SCFAFF1 -mediated regulation of ARF protein drives aspects of auxin response and plant development.
Spatially resolved proteomic map shows that extracellular matrix regulates epidermal growth
Authors: Li Jun , Ma Jie , Zhang Qiyu , Gong Huizi , Gao Dunqin , Wang Yujie , Li Biyou , Li Xiao , Zheng Heyi , Wu Zhihong , Zhu Yunping , Leng Ling 
Published: July 2022

AbstractHuman skin comprises stratified squamous epithelium and dermis with various stromal cells and the extracellular matrix (ECM). The basement membrane (BM), a thin layer at the top of the dermis, serves as a unique niche for determining the fate of epidermal stem cells (EpSCs) by transmitting physical and biochemical signals to establish epidermal cell polarity and maintain the hierarchical structure and function of skin tissue. However, how stem cell niches maintain tissue homeostasis and control wound healing by regulating the behavior of EpSCs is still not completely understood. In this study, a hierarchical skin proteome map is constructed using spatial quantitative proteomics combined with decellularization, laser capture microdissection, and mass spectrometry. The specific functions of different structures of normal native skin tissues or tissues with a dermatologic disease are analyzed in situ. Transforming growth factor-beta (TGFβ)-induced protein ig-h3 (TGFBI), an ECM glycoprotein, in the BM is identified that could enhance the growth and function of EpSCs and promote wound healing. Our results provide insights into the way in which ECM proteins facilitate the growth and function of EpSCs as part of an important niche. The results may benefit the clinical treatment of skin ulcers or diseases with refractory lesions that involve epidermal cell dysfunction and re-epithelialization block in the future.
Chiral self-sorting and guest recognition of porous aromatic cages
Authors: Cui Dong-Xu , Geng Yun , Kou Jun-Ning , Shan Guo-Gang , Sun Chun-Yi , Zhang Kun-Hao , Wang Xin-Long , Su Zhong-Min 
Published: July 2022

AbstractThe synthesis of ultra-stable chiral porous organic cages (POCs) and their controllable chiral self-sorting at the molecular and supramolecular level remains challening. Herein, we report the design and synthesis of a serial of axially chiral porous aromatic cages (PAC 1-S and 1-R) with high chemical stability. The theoretical and experimental studies on the chiral self-sorting reveal that the exclusive self-recognition on cage formation is an enthalpy-driven process while the chiral narcissistic and self-sorting on supramolecular assembly of racemic cages can be precisely regulated by π–π and C–H…π interactions from different solvents. Regarding the chemical stability, the crystallinity of PAC 1 is maintained in aqueous solvents, such as boiling water, high-concentrated acid and alkali; mixtures of solvents, such as 1 M H2SO4/MeOH/H2O solution, are also tolerated. Investigations on the chiral sensing performance show that PAC 1 enables enantioselective recognition of axially chiral biaryl molecules.
A comprehensive review on the chemical regeneration of biochar adsorbent for sustainable wastewater treatment
Authors: Alsawy Tariq , Rashad Emanne , El-Qelish Mohamed , Mohammed Ramy H. 
Published: July 2022

AbstractThe chemical regeneration process has been extensively applied to reactivate biochar, supporting its reusability and leading to significant operating cost reduction. However, no recent review discusses the effectiveness of biochar chemical regeneration. Thus, this article comprehensively reviews the chemical regeneration of biochar contaminated with organic and inorganic pollutants. Performance of the chemical regeneration depends on adsorption mechanism, functional groups, adsorbent pore structure, and changes in active adsorbent sites. Secondary contamination is one of the challenges facing the sustainable adaptation of the chemical regeneration process in the industry. The paper discusses these challenges and draws a roadmap for future research to support sustainable wastewater treatment by biochar.
A sequence-based global map of regulatory activity for deciphering human genetics
Authors: Chen Kathleen M. , Wong Aaron K. , Troyanskaya Olga G. , Zhou Jian 
Published: July 2022

AbstractEpigenomic profiling has enabled large-scale identification of regulatory elements, yet we still lack a systematic mapping from any sequence or variant to regulatory activities. We address this challenge with Sei, a framework for integrating human genetics data with sequence information to discover the regulatory basis of traits and diseases. Sei learns a vocabulary of regulatory activities, called sequence classes, using a deep learning model that predicts 21,907 chromatin profiles across >1,300 cell lines and tissues. Sequence classes provide a global classification and quantification of sequence and variant effects based on diverse regulatory activities, such as cell type-specific enhancer functions. These predictions are supported by tissue-specific expression, expression quantitative trait loci and evolutionary constraint data. Furthermore, sequence classes enable characterization of the tissue-specific, regulatory architecture of complex traits and generate mechanistic hypotheses for individual regulatory pathogenic mutations. We provide Sei as a resource to elucidate the regulatory basis of human health and disease.
Simple gene signature to assess murine fibroblast polarization
Authors: Ledoult Emmanuel , Jendoubi Manel , Collet Aurore , Guerrier Thomas , Largy Alexis , Speca Silvia , Vivier Solange , Bray Fabrice , Figeac Martin , Hachulla Eric , Labalette Myriam , Leprêtre Frédéric , Sebda Shéhérazade , Sanges Sébastien , Rolando Christian , Sobanski Vincent , Dubucquoi Sylvain , Launay David 
Published: July 2022

AbstractWe provide an original multi-stage approach identifying a gene signature to assess murine fibroblast polarization. Prototypic polarizations (inflammatory/fibrotic) were induced by seeded mouse embryonic fibroblasts (MEFs) with TNFα or TGFß1, respectively. The transcriptomic and proteomic profiles were obtained by RNA microarray and LC-MS/MS. Gene Ontology and pathways analysis were performed among the differentially expressed genes (DEGs) and proteins (DEPs). Balb/c mice underwent daily intradermal injections of HOCl (or PBS) as an experimental murine model of inflammation-mediated fibrosis in a time-dependent manner. As results, 1456 and 2215 DEGs, and 289 and 233 DEPs were respectively found in MEFs in response to TNFα or TGFß1, respectively. Among the most significant pathways, we combined 26 representative genes to encompass the proinflammatory and profibrotic polarizations of fibroblasts. Based on principal component analysis, this signature deciphered baseline state, proinflammatory polarization, and profibrotic polarization as accurately as RNA microarray and LC-MS/MS did. Then, we assessed the gene signature on dermal fibroblasts isolated from the experimental murine model. We observed a proinflammatory polarization at day 7, and a mixture of a proinflammatory and profibrotic polarizations at day 42 in line with histological findings. Our approach provides a small-size and convenient gene signature to assess murine fibroblast polarization.
A correlational analysis of COVID-19 incidence and mortality and urban determinants of vitamin D status across the London boroughs
Authors: Borna Mehrdad , Woloshynowych Maria , Schiano-Phan Rosa , Volpi Emanuela V. , Usman Moonisah 
Published: July 2022

AbstractOne of the biggest challenges of the COVID-19 pandemic is the heterogeneity in disease severity exhibited amongst patients. Among multiple factors, latest studies suggest vitamin D deficiency and pre-existing health conditions to be major contributors to death from COVID-19. It is known that certain urban form attributes can impact sun exposure and vitamin D synthesis. Also, long-term exposure to air pollution can play an independent role in vitamin D deficiency. We conducted a correlational analysis of urban form and air quality in relation to the demographics and COVID-19 incidence and mortality across 32 London boroughs between March 2020 and January 2021. We found total population, number of residents of Asian ethnicity, 4-year average PM10 levels and road length to be positively correlated with COVID-19 cases and deaths. We also found percentage of households with access to total open space to be negatively correlated with COVID-19 deaths. Our findings link COVID-19 incidence and mortality across London with environmental variables linked to vitamin D status. Our study is entirely based on publicly available data and provides a reference framework for further research as more data are gathered and the syndemic dimension of COVID-19 becomes increasingly relevant in connection to health inequalities within large urban areas.
First tagging data on large Atlantic bluefin tuna returning to Nordic waters suggest repeated behaviour and skipped spawning
Authors: Aarestrup Kim , Baktoft Henrik , Birnie-Gauvin Kim , Sundelöf Andreas , Cardinale Massimiliano , Quilez-Badia Gemma , Onandia Iñigo , Casini Michele , Nielsen Einar Eg , Koed Anders , Alemany Francisco , MacKenzie Brian R. 
Published: July 2022

AbstractAtlantic bluefin tuna (Thunnus thynnus;ABFT) is one of the most iconic fish species in the world. Recently, after being very rare for more than half a century, large bluefin tunas have returned to Nordic waters in late summer and autumn, marking the return of the largest predatory fish in Nordic waters. By tagging 18 bluefin tunas with electronic tags (pop-up satellite archival tags), we show that bluefin tuna observed in Nordic waters undertake different migration routes, with individuals migrating into the western Atlantic Ocean, while others stay exclusively in the eastern Atlantic and enter the Mediterranean Sea to spawn. We additionally present evidence of possible skipped spawning inferred from behavioural analyses. In Nordic waters, ABFT are primarily using the upper water column, likely reflecting feeding activity. The results support the hypothesis that ABFT migrating to Nordic waters return to the same general feeding area within the region on an annual basis. These observations may have important implications for management because (1) tunas that come into Nordic waters might represent only a few year classes (as evidenced by a narrow size range), and thus may be particularly vulnerable to area-specific exploitation, and (2) challenge the assumption of consecutive spawning in adult Atlantic bluefin tuna, as used in current stock assessment models. Without careful management and limited exploitation of this part of the ABFT population, the species’ return to Nordic waters could be short-lived.
Whole-genome sequencing reveals de-novo mutations associated with nonsyndromic cleft lip/palate
Authors: Awotoye Waheed , Mossey Peter A. , Hetmanski Jacqueline B. , Gowans Lord J. J. , Eshete Mekonen A. , Adeyemo Wasiu L. , Alade Azeez , Zeng Erliang , Adamson Olawale , Naicker Thirona , Anand Deepti , Adeleke Chinyere , Busch Tamara , Li Mary , Petrin Aline , Aregbesola Babatunde S. , Braimah Ramat O. , Oginni Fadekemi O. , Oladele Ayodeji O. , Oladayo Abimbola , Kayali Sami , Olotu Joy , Hassan Mohaned , Pape John , Donkor Peter , Arthur Fareed K. N. , Obiri-Yeboah Solomon , Sabbah Daniel K. , Agbenorku Pius , Plange-Rhule Gyikua , Oti Alexander Acheampong , Gogal Rose A. , Beaty Terri H. , Taub Margaret , Marazita Mary L. , Schnieders Michael J. , Lachke Salil A. , Adeyemo Adebowale A. , Murray Jeffrey C. , Butali Azeez 
Published: July 2022

AbstractThe majority (85%) of nonsyndromic cleft lip with or without cleft palate (nsCL/P) cases occur sporadically, suggesting a role for de novo mutations (DNMs) in the etiology of nsCL/P. To identify high impact protein-altering DNMs that contribute to the risk of nsCL/P, we conducted whole-genome sequencing (WGS) analyses in 130 African case-parent trios (affected probands and unaffected parents). We identified 162 high confidence protein-altering DNMs some of which are based on available evidence, contribute to the risk of nsCL/P. These include novel protein-truncating DNMs in theACTL6A, ARHGAP10, MINK1, TMEM5andTTNgenes; as well as missense variants inACAN, DHRS3, DLX6, EPHB2, FKBP10, KMT2D, RECQL4, SEMA3C, SEMA4D, SHH, TP63,andTULP4. Many of these protein-altering DNMs were predicted to be pathogenic. Analysis using mouse transcriptomics data showed that some of these genes are expressed during the development of primary and secondary palate. Gene-set enrichment analysis of the protein-altering DNMs identified palatal development and neural crest migration among the few processes that were significantly enriched. These processes are directly involved in the etiopathogenesis of clefting. The analysis of the coding sequence in the WGS data provides more evidence of the opportunity for novel findings in the African genome.
Sulindac acetohydrazide derivative attenuates against cisplatin induced organ damage by modulation of antioxidant and inflammatory signaling pathways
Authors: Razak Suhail , Afsar Tayyaba , Bibi Nousheen , Abulmeaty Mahmoud , Bhat Mashooq Ahmad , Inam Anam , Trembley Janeen H. , Almajwal Ali , Shabbir Maria , Alruwaili Nawaf W. , Algarni Abdulrahman 
Published: July 2022

AbstractThis study aimed to explore the mechanisms of action of a sulindac acetohydrazide derivative, N'-(4-dimethylaminobenzylidene)-2-1-(4-(methylsulfinyl) benzylidene)-5-fluoro-2-methyl-1H-inden-3-yl) acetohydrazide, against anticancer drug cisplatin induced organ damage. Using a rodent model, various markers of organ function and signaling pathways were examined and validated by molecular docking studies. The study involves five groups of animals: control, DMSO, CDDP, CDDP + DMFM, and DMFM. Biochemical enzyme activity, histopathology, tissue antioxidant, and oxidative stress markers were examined. RT-PCR and western blot analyses were conducted for the expression of inducible cyclooxygenase enzyme (COX-2), nuclear factor kappa beta (NF-κB), p65, IL-1, TNF-α, and inducible nitric oxide synthase (iNOS). Flow cytometry analysis of CD4 + TNF-α, CD4 + COX-2, and CD4 + STAT-3 cells in whole blood was performed. Structural and dynamic behavior of DMFM upon binding with receptor molecule molecular docking and dynamic simulations were performed using bioinformatics tools and software. Treatment with DMFM reversed cisplatin-induced malondialdehyde (MDA) and nitric oxide (NO) induction, whereas the activity of glutathione peroxidase (GPx), and superoxide dismutase (SOD) in the kidney, heart, liver, and brain tissues were increased. DMFM administration normalized plasma levels of biochemical enzymes. We observed a marked decline in CD4 + STAT3, TNF-α, and COX2 cell populations in whole blood after treatment with DMFM. DMFM downregulated the expression factors related to inflammation at the mRNA and protein levels, i.e., IL-1, TNF-α, iNOS, NF-κB, STAT-3, and COX-2. Dynamic simulations and in silico docking data supports the experimental findings. Our experimental and in silico results illustrated that DMFM may affect protective action against cisplatin-induced brain, heart, liver, and kidney damage via reduction of inflammation and ROS.
The emerging role of LRRK2 in tauopathies
Authors: Herbst Susanne , Lewis Patrick A. , Morris Huw R. 
Published: July 2022

Abstract
Parkinson’s disease (PD) is conventionally described as an α-synuclein aggregation disorder, defined by Lewy bodies and neurites, and mutations in leucine-rich repeat kinase 2 (LRRK2) are the most common autosomal dominant cause of PD. However, LRRK2 mutations may be associated with diverse pathologies in patients with Parkinson’s syndrome including tau pathology resembling progressive supranuclear palsy (PSP). The recent discovery that variation at the LRRK2 locus is associated with the progression of PSP highlights the potential importance of LRRK2 in tauopathies. Here, we review the emerging evidence and discuss the potential impact of LRRK2 dysfunction on tau aggregation, lysosomal function, and endocytosis and exocytosis.
Cross‐modality person re‐identification using hybrid mutual learning
Authors: Zhang Zhong , Dong Qing , Wang Sen , Liu Shuang , Xiao Baihua , Durrani Tariq S. 
Published: July 2022

AbstractCross‐modality person re‐identification (Re‐ID) aims to retrieve a query identity from red, green, blue (RGB) images or infrared (IR) images. Many approaches have been proposed to reduce the distribution gap between RGB modality and IR modality. However, they ignore the valuable collaborative relationship between RGB modality and IR modality. Hybrid Mutual Learning (HML) for cross‐modality person Re‐ID is proposed, which builds the collaborative relationship by using mutual learning from the aspects of local features and triplet relation. Specifically, HML contains local‐mean mutual learning and triplet mutual learning where they focus on transferring local representational knowledge and structural geometry knowledge so as to reduce the gap between RGB modality and IR modality. Furthermore, Hierarchical Attention Aggregation is proposed to fuse local feature maps and local feature vectors to enrich the information of the classifier input. Extensive experiments on two commonly used data sets, that is, SYSU‐MM01 and RegDB verify the effectiveness of the proposed method.
BMFN3D: Bidirectional multilayer fusion network for indoor 3D object detection
Authors: Cheng Jun , Zhang Sheng 
Published: July 2022

AbstractAmong various indoor 3D object detection methods, one of which is based on 3D convolution. However, in current 3D convolutional method for indoor 3D object detection, feature fusion is only implemented in a single direction and adjacent layer, which leads to the feature loss during feature propagation and weakens the detection performance. To solve the above problem, a bidirectional multilayer fusion network (BMFN) is proposed to enrich features for prediction. Furthermore, we propose a new network based on BMFN for 3D object detection, BMFN3D. In BMFN3D, the channel and spatial attention mechanisms are introduced into the backbone and head of detection network, so as to enhance the selection of effective feature information. Finally, a new calculation method for regression loss is proposed with the consideration of the 3D spatial information. We validate our method with two indoor datasets of SUN RGB‐D and ScanNet, and achieve state‐of‐the‐art results.
Iron-Catalyzed Synthesis of Pyrrolo[2,1-a]isoquinolines via 1,3-Dipolar Cycloaddition/Elimination/Aromatization Cascade and Modifications
Authors: Cui Hai-Lei , Chen Xiao-Hui , Pan Yu-Yi , Wang Wei-Xun 
Published: July 2022

AbstractWe have developed an iron-catalyzed synthesis of pyrrolo[2,1-a]isoquinoline derivatives with tetrahydroisoquinolines, arylacyl bromides, and nitroolefins. Highly functionalized pyrrolo[2,1-a]isoquinolines can be obtained in moderate to good yields through a three-component N-alkylation/oxidative 1,3-dipolar cycloaddition/elimination/aromatization cascade. The obtained products in this study can be easily modified by easy chemical transformations to structurally complex molecules bearing privileged framework.
Elective Delivery versus Expectant Management for Gastroschisis: A Systematic Review and Meta-Analysis
Authors: Chen Yong , Zhao Jiashen , Alganabi Mashriq , Mesas-Burgos Carmen , Eaton Simon , Wester Tomas , Pierro Agostino 
Published: July 2022

Abstract
Introduction The optimal timing of delivery for pregnancies complicated by prenatally diagnosed gastroschisis remains controversial. Therefore, the aim of this study was to find whether elective or expectant delivery is associated with improved neonatal outcome.
Materials and Methods MEDLINE and Embase databases were searched for studies up to 2021 that reported timing of delivery for prenatally diagnosed gastroschisis. A systematic review and meta-analysis were then performed in group 1: moderately preterm (gestational age [GA]: 34–35 weeks) elective delivery versus expectant management after GA 34–35 weeks; and group 2: near-term (GA: 36–37 weeks) elective delivery versus expectant management after GA 36–37 weeks. The following clinical outcomes were evaluated: length of stay (LOS), total parenteral nutrition (TPN) days, bowel morbidity (atresia, perforation, and volvulus), sepsis, time of first feeding, short gut syndrome and respirator days, and mortality.
Results Two randomized controlled trials (RCT)s and eight retrospective cohort studies were included, comprising 629 participants. Moderately preterm elective delivery failed to improve clinical outcomes. However, near-term elective delivery significantly reduced bowel morbidity (7.4 vs. 15.4%, relative risk = 0.37; 95% confidence interval [CI]: 0.18, 0.74; p = 0.005; I2 = 0%) and TPN days (mean difference =−13.44 days; 95% CI: −26.68, −0.20; p = 0.05; I2 = 45%) compared to expectant delivery. The mean LOS was 39.2 days after near-term delivery and 48.7 days in the expectant group (p = 0.06).
Conclusion Based on the data analyzed, near-term elective delivery (GA 36–37 weeks) appears to be the optimal timing for delivery of pregnancies complicated by gastroschisis as it is associated with less bowel morbidity and shorter TPN days. However, more RCTs are necessary to better validate these findings.