bluuebunny/crossref_metadata_2025_split huggingface dataset:
Design and Testing of an Underwater Microscope with Variable Objective Lens for the Study of Benthic Communities
Authors: Shahani Kamran , Song Hong , Mehdi Syed Raza , Sharma Awakash , Tunio Ghulam , Qureshi Junaidullah , Kalhoro Noor , Khaskheli Nooruddin 
Published: March 2021

AbstractMonitoring the ecology and physiology of corals, sediments, planktons, and microplastic at a suitable spatial resolution is of great importance in oceanic scientific research. To meet this requirement, an underwater microscope with an electrically controlled variable lens was designed and tested. The captured microscopic images of corals, sediments, planktons, and microplastic revealed their physical, biological, and morphological characteristics. Further studies of the images also revealed the growth, degradation, and bleaching patterns of corals; the presence of plankton communities; and the types of microplastics. The imaging performance is majorly influenced by the choice of lenses, camera selection, and lighting method. Image dehazing, global saturation masks, and image histograms were used to extract the image features. Fundamental experimental proof was obtained with micro-scale images of corals, sediments, planktons, and microplastic at different magnifications. The designed underwater microscope can provide relevant new insights into the observation and detection of the future conditions of aquatic ecosystems.
Context-Aware Business Process Management
Authors: vom Brocke Jan , Baier Marie-Sophie , Schmiedel Theresa , Stelzl Katharina , Röglinger Maximilian , Wehking Charlotte 
Published: March 2021

AbstractContext awareness is essential for successful business process management (BPM). So far, research has covered relevant BPM context factors and context-aware process design, but little is known about how to assess and select BPM methods in a context-aware manner. As BPM methods are involved in all stages of the BPM lifecycle, it is key to apply appropriate methods to efficiently use organizational resources. Following the design science paradigm, the study at hand addresses this gap by developing and evaluating the Context-Aware BPM Method Assessment and Selection (CAMAS) Method. This method assists method engineers in assessing in which contexts their BPM methods can be applied and method users in selecting appropriate BPM methods for given contexts. The findings of this study call for more context awareness in BPM method design and for a stronger focus on explorative BPM. They also provide insights into the status quo of existing BPM methods.
Vulnerability of groundwater to iron and manganese contamination in the coastal alluvial plain of a developing Indonesian city
Authors: Rusydi Anna Fadliah , Onodera Shin-Ichi , Saito Mitsuyo , Ioka Seiichiro , Maria Rizka , Ridwansyah Iwan , Delinom Robert M. 
Published: March 2021

AbstractThis paper evaluates environmental conditions responsible for the high concentrations of trace metals in Indonesian coastal groundwater. Indramayu, which has significant potential groundwater resources, but for which limited information is available regarding its vulnerability, is selected as our study area. Results show that Fe2+ and Mn2+ are natural contaminants in the groundwater of the study site. The correlations of trace metals with salinity and redox-sensitive parameters verify that saline water has a significant impact upon the dissolution of Fe and Mn. Furthermore, reductive condition is confirmed to be responsible for Fe and Mn dissolution with a less significant correlation compared to salinity. Moreover, the high concentrations of trace metals are coupled with high dissolved organic carbon (DOC), which indicates that reductive environment may arise because of organic-matter decomposition. Finally, the impact of human activity upon Fe and Mn dissolution is identified at the northern tip of Indramayu, where trace-metal contents are significantly elevated. Further, in the southern part, the groundwater condition is relatively more natural; thus, the impact of human activity upon the presence of Fe and Mn is lesser in this region.
DTFLOW: Inference and Visualization of Single-Cell Pseudotime Trajectory Using Diffusion Propagation
Authors: Wei Jiangyong , Zhou Tianshou , Zhang Xinan , Tian Tianhai 
Published: March 2021

Abstract
One of the major challenges in single-cell data analysis is the determination of cellular developmental trajectories using single-cell data. Although substantial studies have been conducted in recent years, more effective methods are still strongly needed to infer the developmental processes accurately. This work devises a new method, named DTFLOW, for determining the pseudo-temporal trajectories with multiple branches. DTFLOW consists of two major steps: a new method called Bhattacharyya kernel feature decomposition (BKFD) to reduce the data dimensions, and a novel approach named Reverse Searching on k-nearest neighbor graph (RSKG) to identify the multi-branching processes of cellular differentiation. In BKFD, we first establish a stationary distribution for each cell to represent the transition of cellular developmental states based on the random walk with restart algorithm, and then propose a new distance metric for calculating pseudotime of single cells by introducing the Bhattacharyya kernel matrix. The effectiveness of DTFLOW is rigorously examined by using four single-cell datasets. We compare the efficiency of DTFLOW with the published state-of-the-art methods. Simulation results suggest that DTFLOW has superior accuracy and strong robustness properties for constructing pseudotime trajectories. The Python source code of DTFLOW can be freely accessed at https://github.com/statway/DTFLOW.
Integrative Proteomic Analysis of Multiple Posttranslational Modifications in Inflammatory Response
Authors: Ji Feiyang , Zhou Menghao , Zhu Huihui , Jiang Zhengyi , Li Qirui , Ouyang Xiaoxi , Lv Yiming , Zhang Sainan , Wu Tian , Li Lanjuan 
Published: March 2021

Abstract
Posttranslational modifications (PTMs) of proteins, particularly acetylation, phosphorylation, and ubiquitination, play critical roles in the host innate immune response. PTMs’ dynamic changes and the crosstalk among them are complicated. To build a comprehensive dynamic network of inflammation-related proteins, we integrated data from the whole-cell proteome (WCP), acetylome, phosphoproteome, and ubiquitinome of human and mouse macrophages. Our datasets of acetylation, phosphorylation, and ubiquitination sites helped identify PTM crosstalk within and across proteins involved in the inflammatory response. Stimulation of macrophages by lipopolysaccharide (LPS) resulted in both degradative and non-degradative ubiquitination. Moreover, this study contributes to the interpretation of the roles of known inflammatory molecules and the discovery of novel inflammatory proteins.
Determinants of dietary diversity and its relationship with the nutritional status of pregnant women
Authors: Saaka Mahama , Mutaru Sofo , Osman Shaibu Mohammed 
Published: March 2021

AbstractThere is little information regarding factors that determine dietary diversity among pregnant women in Ghana. The present study, therefore, sought to assess the independent predictors of dietary diversity and its relationship with nutritional status of pregnant women in the Northern Region of Ghana. The present study was an analytical cross-sectional survey involving 423 pregnant women in different stages of gestation. The 24-h dietary recall method was used to assess minimum dietary diversity for women (MDD-W), and nutritional status was assessed using mid-upper arm circumference (MUAC) measurements. Binary logistic regression was performed to assess the association between maternal dietary diversity and maternal thinness and aPvalue of <0⋅05 was considered statistically significant. Of the 423 women, 79⋅9 % (95 % CI 76⋅1, 83⋅7) met the MDD-W and the prevalence of undernutrition among the pregnant women was 26⋅0 %. The analysis showed that women of low household wealth index were 48 % less likely (AOR 0⋅52, CI 0⋅31, 0⋅88) of meeting the MDD-W, whereas women from households of poor food insecurity were 88 % less likely (AOR 0⋅12, CI 0⋅05, 0⋅27) of achieving the MDD-W. Women of low household size were three times more likely of meeting the MDD-W (AOR 3⋅07, CI 1⋅13, 8⋅39). MDD-W was not associated with maternal underweight during pregnancy. In conclusion, the results of the present study showed that food insecurity and not low MDD-W, associated with mothers’ thinness (underweight) during pregnancy in peri-urban setting of Northern Ghana.
Humanoid NAO: A Kinematic Encounter
Authors: Sahu Chinmaya , Parhi Dayal R. , Kumar Priyadarshi Biplab , Muni Manoj Kumar , Chhotray Animesh , Pandey Krishna Kant 
Published: March 2021

SUMMARYIn the current research, kinematic analysis of a humanoid NAO is attempted. Here, both Denavit–Hartenberg (DH) parameter approach and multibody formulation approach have been analyzed. In the DH parameter approach, the NAO robot is solved by separating it into five individual kinematic chains. In the multibody formulation approach, NAO is divided into 15 segments, and each segment is analyzed. Kinematic analysis holds a significant importance; as from the data obtained in the kinematic analysis, the robots can be designed for real-time path planning and navigation. The current analysis is a novel approach to analyze the NAO based on its kinematic constraints.
Neuroprotective effects of Sonic hedgehog agonist SAG in a rat model of neonatal stroke
Authors: Nguyen Vien , Chavali Manideep , Larpthaveesarp Amara , Kodali Srikirti , Gonzalez Ginez , Franklin Robin J. M. , Rowitch David H. , Gonzalez Fernando 
Published: March 2021

Abstract
Background
Neonatal stroke affects 1 in 2800 live births and is a major cause of neurological injury. The Sonic hedgehog (Shh) signaling pathway is critical for central nervous system (CNS) development and has neuroprotective and reparative effects in different CNS injury models. Previous studies have demonstrated beneficial effects of small molecule Shh-Smoothened agonist (SAG) against neonatal cerebellar injury and it improves Down syndrome-related brain structural deficits in mice. Here we investigated SAG neuroprotection in rat models of neonatal ischemia–reperfusion (stroke) and adult focal white matter injury.

Methods
We used transient middle cerebral artery occlusion at P10 and ethidium bromide (EB) injection in adult rats to induce damage. Following surgery and SAG or vehicle treatment, we analyzed tissue loss, cell proliferation and fate, and behavioral outcome.

Results
We report that a single dose of SAG administered following neonatal stroke preserved brain volume, reduced gliosis, enhanced oligodendrocyte progenitor cell (OPC) and EC proliferation, and resulted in long-term cognitive improvement. Single-dose SAG also promoted proliferation of OPCs following focal demyelination in the adult rat.

Conclusions
These findings indicate benefit of one-time SAG treatment post insult in reducing brain injury and improving behavioral outcome after experimental neonatal stroke.

Impact

A one-time dose of small molecule Sonic hedgehog agonist protected against neonatal stroke and improved long-term behavioral outcomes in a rat model.

This study extends the use of Sonic hedgehog in treating developing brain injury, previously shown in animal models of Down syndrome and cerebellar injury.

Sonic hedgehog agonist is one of the most promising therapies in treating neonatal stroke thanks to its safety profile and low dosage.
Delivery mode and altered infant growth at 1 year of life in India
Authors: Babu Giridhara R. , Mueller Noel T. , Lewis Melissa Glenda , Krishnan Anjaly , Lobo Eunice , Deepa R. , Khetrapal Sonalini , Benjamin-Neelon Sara E. 
Published: March 2021

Abstract
Background
Cesarean section (C-section) delivered infants are more likely to be colonized by opportunistic pathogens, resulting in altered growth. We examined whether C-section (elective/emergency) vs vaginal delivery was associated with altered weight and linear growth at 1 year of life.

Methods
A total of 638 mother–infant pairs were included from MAASTHI cohort 2016–2019. Information on delivery mode was obtained from medical records. Based on WHO child growth standards, body mass index-forage z-score (BMI z) and length-for-age z-score (length z) were derived. We ran multivariable linear and Poisson regression models before and after multiple imputation.

Results
The rate of C-section was 43.4% (26.5%: emergency, 16.9%: elective). Percentage of infant overweight was 14.9%. Compared to vaginal delivery, elective C-section was associated with β = 0.57 (95% CI 0.20, 0.95) higher BMI z. Also infants born by elective C-section had RR = 2.44 (95% CI 1.35, 4.41) higher risk of being overweight; no such association was found for emergency C-section. Also, elective C-section delivery was associated with reduced linear growth at 1 year after multiple imputation (β = −0.38, 95% CI −0.76, −0.01).

Conclusions
Elective C-section delivery might contribute to excess weight and also possibly reduced linear growth at 1 year of age in children from low- and middle-income countries.

Impact

Our study, in a low-income setting, suggests that elective, but not emergency, C-section is associated with excess infant BMI z at 1 year of age and elective C (C-section) was also associated with altered linear growth but only in multiple imputation analyses.

Elective C-section was associated with a higher risk of being overweight at 1 year of age.

Our results indicate that decreasing medically unnecessary elective C-section deliveries may help limit excess weight gain and stunted linear growth among infants.
Depression, anxiety and associated factors among Chinese adolescents during the COVID-19 outbreak: a comparison of two cross-sectional studies
Authors: Chen Xu , Qi Han , Liu Rui , Feng Yuan , Li Wen , Xiang Mi , Cheung Teris , Jackson Todd , Wang Gang , Xiang Yu-Tao 
Published: March 2021

AbstractThe 2019 coronavirus disease (COVID-19) is a public health emergency of international concern. In China, all schools were shut down and students were home quarantined to prevent disease spread; these steps could have potential negative effects on mental health of adolescents. This study aimed to examine changes in depression and anxiety among Chinese adolescents during the COVID-19 epidemic, and explore factors associated with depression and anxiety. Two survey administrations were conducted among Chinese adolescents between February 20 and February 27 and between April 11 and April 19, 2020, respectively. The Center for Epidemiological Studies-Depression Scale (CES-D) and the 7-item Generalized Anxiety Disorder (GAD-7) scale were used to assess depressive symptoms and anxiety symptoms, respectively. A total of 9554 and 3886 adolescents participated in the first and second surveys. During the initial survey, the prevalence of depression was 36.6% (95% CI: 35.6–37.6%) while the prevalence of anxiety was 19% (95% CI: 18.2–19.8%). Rates of depression and anxiety increased to 57.0% (95% CI: 55.4–58.6%) and 36.7% (95% CI: 35.2–38.2%), respectively, in the second survey. Multivariable logistic regression analyses revealed that group membership in the second survey, female gender, senior secondary school enrollment, and concerns about entering a higher grade were positively associated with both depression and anxiety. Conversely, a sleep duration of ≥6 h/day, an exercise duration ≥30 min/day, having the same as typical or higher study efficiency during the COVID-19 outbreak, and living in provinces with 1000–9999 confirmed COVID-19 cases were negatively associated with depression and anxiety. In conclusion, compared to figures reported during the COVID-19 outbreak, the prevalence of depression and anxiety in Chinese adolescents significantly increased after the initial outbreak. Regular screening and appropriate interventions are urgently needed to reduce the risk for emotional disturbances among adolescents during and after the initial COVID-19 outbreaks.
A molecular switch in sulfur metabolism to reduce arsenic and enrich selenium in rice grain
Authors: Sun Sheng-Kai , Xu Xuejie , Tang Zhong , Tang Zhu , Huang Xin-Yuan , Wirtz Markus , Hell Rüdiger , Zhao Fang-Jie 
Published: March 2021

AbstractRice grains typically contain high levels of toxic arsenic but low levels of the essential micronutrient selenium. Anthropogenic arsenic contamination of paddy soils exacerbates arsenic toxicity in rice crops resulting in substantial yield losses. Here, we report the identification of the gain-of-function arsenite tolerant 1 (astol1) mutant of rice that benefits from enhanced sulfur and selenium assimilation, arsenic tolerance, and decreased arsenic accumulation in grains. The astol1 mutation promotes the physical interaction of the chloroplast-localized O-acetylserine (thiol) lyase protein with its interaction partner serine-acetyltransferase in the cysteine synthase complex. Activation of the serine-acetyltransferase in this complex promotes the uptake of sulfate and selenium and enhances the production of cysteine, glutathione, and phytochelatins, resulting in increased tolerance and decreased translocation of arsenic to grains. Our findings uncover the pivotal sensing-function of the cysteine synthase complex in plastids for optimizing stress resilience and grain quality by regulating a fundamental macronutrient assimilation pathway.
RNA m6A methylation orchestrates cancer growth and metastasis via macrophage reprogramming
Authors: Yin Huilong , Zhang Xiang , Yang Pengyuan , Zhang Xiaofang , Peng Yingran , Li Da , Yu Yanping , Wu Ye , Wang Yidi , Zhang Jinbao , Ding Xiaochen , Wang Xiangpeng , Yang Angang , Zhang Rui 
Published: March 2021

AbstractN6-methyladenosine (m6A) is a reversible mRNA modification that has been shown to play important roles in various biological processes. However, the roles of m6A modification in macrophages are still unknown. Here, we discover that ablation of Mettl3 in myeloid cells promotes tumour growth and metastasis in vivo. In contrast to wild-type mice, Mettl3-deficient mice show increased M1/M2-like tumour-associated macrophage and regulatory T cell infiltration into tumours. m6A sequencing reveals that loss of METTL3 impairs the YTHDF1-mediated translation of SPRED2, which enhances the activation of NF-kB and STAT3 through the ERK pathway, leading to increased tumour growth and metastasis. Furthermore, the therapeutic efficacy of PD-1 checkpoint blockade is attenuated in Mettl3-deficient mice, identifying METTL3 as a potential therapeutic target for tumour immunotherapy.
Caldera resurgence during the 2018 eruption of Sierra Negra volcano, Galápagos Islands
Authors: Bell Andrew F. , La Femina Peter C. , Ruiz Mario , Amelung Falk , Bagnardi Marco , Bean Christopher J. , Bernard Benjamin , Ebinger Cynthia , Gleeson Matthew , Grannell James , Hernandez Stephen , Higgins Machel , Liorzou Céline , Lundgren Paul , Meier Nathan J. , Möllhoff Martin , Oliva Sarah-Jaye , Ruiz Andres Gorki , Stock Michael J. 
Published: March 2021

AbstractRecent large basaltic eruptions began after only minor surface uplift and seismicity, and resulted in caldera subsidence. In contrast, some eruptions at Galápagos Island volcanoes are preceded by prolonged, large amplitude uplift and elevated seismicity. These systems also display long-term intra-caldera uplift, or resurgence. However, a scarcity of observations has obscured the mechanisms underpinning such behaviour. Here we combine a unique multiparametric dataset to show how the 2018 eruption of Sierra Negra contributed to caldera resurgence. Magma supply to a shallow reservoir drove 6.5 m of pre-eruptive uplift and seismicity over thirteen years, including an Mw5.4 earthquake that triggered the eruption. Although co-eruptive magma withdrawal resulted in 8.5 m of subsidence, net uplift of the inner-caldera on a trapdoor fault resulted in 1.5 m of permanent resurgence. These observations reveal the importance of intra-caldera faulting in affecting resurgence, and the mechanisms of eruption in the absence of well-developed rift systems.
Structure–function analysis of oncogenic EGFR Kinase Domain Duplication reveals insights into activation and a potential approach for therapeutic targeting
Authors: Du Zhenfang , Brown Benjamin P. , Kim Soyeon , Ferguson Donna , Pavlick Dean C. , Jayakumaran Gowtham , Benayed Ryma , Gallant Jean-Nicolas , Zhang Yun-Kai , Yan Yingjun , Red-Brewer Monica , Ali Siraj M. , Schrock Alexa B. , Zehir Ahmet , Ladanyi Marc , Smith Adam W. , Meiler Jens , Lovly Christine M. 
Published: March 2021

AbstractMechanistic understanding of oncogenic variants facilitates the development and optimization of treatment strategies. We recently identified in-frame, tandem duplication of EGFR exons 18 - 25, which causes EGFR Kinase Domain Duplication (EGFR-KDD). Here, we characterize the prevalence of ERBB family KDDs across multiple human cancers and evaluate the functional biochemistry of EGFR-KDD as it relates to pathogenesis and potential therapeutic intervention. We provide computational and experimental evidence that EGFR-KDD functions by forming asymmetric EGF-independent intra-molecular and EGF-dependent inter-molecular dimers. Time-resolved fluorescence microscopy and co-immunoprecipitation reveals EGFR-KDD can form ligand-dependent inter-molecular homo- and hetero-dimers/multimers. Furthermore, we show that inhibition of EGFR-KDD activity is maximally achieved by blocking both intra- and inter-molecular dimerization. Collectively, our findings define a previously unrecognized model of EGFR dimerization, providing important insights for the understanding of EGFR activation mechanisms and informing personalized treatment of patients with tumors harboring EGFR-KDD. Finally, we establish ERBB KDDs as recurrent oncogenic events in multiple cancers.
Trace element catalyses mineral replacement reactions and facilitates ore formation
Authors: Xing Yanlu , Brugger Joël , Etschmann Barbara , Tomkins Andrew G. , Frierdich Andrew J. , Fang Xiya 
Published: March 2021

AbstractReaction-induced porosity is a key factor enabling protracted fluid-rock interactions in the Earth’s crust, promoting large-scale mineralogical changes during diagenesis, metamorphism, and ore formation. Here, we show experimentally that the presence of trace amounts of dissolved cerium increases the porosity of hematite (Fe2O3) formed via fluid-induced, redox-independent replacement of magnetite (Fe3O4), thereby increasing the efficiency of coupled magnetite replacement, fluid flow, and element mass transfer. Cerium acts as a catalyst affecting the nucleation and growth of hematite by modifying the Fe2+(aq)/Fe3+(aq) ratio at the reaction interface. Our results demonstrate that trace elements can enhance fluid-mediated mineral replacement reactions, ultimately controlling the kinetics, texture, and composition of fluid-mineral systems. Applied to some of the world’s most valuable orebodies, these results provide new insights into how early formation of extensive magnetite alteration may have preconditioned these ore systems for later enhanced metal accumulation, contributing to their sizes and metal endowment.