bluuebunny/crossref_metadata_2025_split huggingface dataset:
Visualization of a Standing Lattice of Scattered Light on Spherical Water Droplets under an Acoustic Field Using Biogenic Microparticles
Authors: Iwasaka Masakazu 
Published: November 2021

AbstractMicromanipulation using acoustic sound is a promising technique for drug delivery, cell manipulation, biosensors, and microfluidic devices. Additionally, the visualization of acoustic fields by advanced optical measurement techniques can be combined with this micromanipulation technique. The present study reveals that a lattice pattern of reflected light appears on the surface of water droplets containing microparticles when the droplets are exposed to audible sound in the range of 1900–10000 Hz. A piezoelectric membrane providing an audible acoustic field induced a stream of microparticles on which the lattice pattern overlapped, with the appearance of a standing wave. The effects of microparticles, including BaSO4, TiO2, and guanine platelets derived from fish scales, on the formation of the lattice pattern were investigated. These three types of microparticles in water enabled a visualization of the vortex streams and generated a lattice pattern of reflected light. The guanine platelets exhibited the most precise lattice pattern over the droplet surface, with a lattice width of 100–200 μm. This phenomenon may provide a new tool for detecting and manipulating micro vortex flows in the aqueous chamber of a microfluidic device combined with an acoustic transducer.
Banp regulates DNA damage response and chromosome segregation during the cell cycle in zebrafish retina
Authors: Babu Swathy , Takeuchi Yuki , Masai Ichiro 
Published: November 2021

AbstractBtg3-associated nuclear protein (Banp) was originally identified as a nuclear matrix-associated region (MAR)-binding protein and it functions as a tumor suppressor. At the molecular level, Banp regulates transcription of metabolic genes via a CGCG-containing motif called the Banp motif. However, its physiological roles in embryonic development are unknown. Here we report that Banp is indispensable for the DNA damage response and chromosome segregation during mitosis. Zebrafishbanpmutants show mitotic cell accumulation and apoptosis in developing retina. We found that DNA replication stress and tp53-dependent DNA damage responses were activated to induce apoptosis inbanpmutants, suggesting that Banp is required for regulation of DNA replication and DNA damage repair. Furthermore, consistent with mitotic cell accumulation, chromosome segregation was not smoothly processed from prometaphase to anaphase inbanpmorphants, leading to a prolonged M-phase. Our RNA- and ATAC-sequencing identified 31 candidates for direct Banp target genes that carry the Banp motif. Interestingly, a DNA replication fork regulator,wrnip1,and two chromosome segregation regulators,cenptandncapg, are included in this list. Thus, Banp directly regulates transcription ofwrnip1for recovery from DNA replication stress, andcenptandncapgfor chromosome segregation during mitosis. Our findings provide the firstin vivoevidence that Banp is required for cell-cycle progression and cell survival by regulating DNA damage responses and chromosome segregation during mitosis.
Thymic macrophages consist of two populations with distinct localization and origin
Authors: Zhou Tyng-An , Hsu Hsuan-Po , Tu Yueh-Hua , Cheng Hui-Kuei , Lin Chih-Yu , Chen Nien-Jung , Tsai Jin-Wu , Robey Ellen A. , Huang Hsuan-Cheng , Hsu Chia-Lin , Dzhagalov Ivan L. 
Published: November 2021

AbstractTissue-resident macrophages are essential to protect from pathogen invasion and maintain organ homeostasis. The ability of thymic macrophages to engulf apoptotic thymocytes is well appreciated, but little is known about their ontogeny, maintenance, and diversity. Here, we characterized the surface phenotype and transcriptional profile of these cells and defined their expression signature. Thymic macrophages were most closely related to spleen red pulp macrophages and Kupffer cells and shared the expression of the transcription factor SpiC with these cells. Single-cell RNA sequencing showed that the macrophages in the adult thymus are composed of two populations distinguished by the expression ofTimd4andCx3cr1. Remarkably,Timd4+cells were located in the cortex, whileCx3cr1+macrophages were restricted to the medulla and the cortico-medullary junction. Using shield chimeras, transplantation of embryonic thymuses, and genetic fate mapping, we found that the two populations have distinct origins.Timd4+thymic macrophages are of embryonic origin, whileCx3cr1+macrophages are derived from adult hematopoietic stem cells. Aging has a profound effect on the macrophages in the thymus.Timd4+cells underwent gradual attrition, whileCx3cr1+cells slowly accumulated with age and, in older mice, were the dominant macrophage population in the thymus. Altogether, our work defines the phenotype, origin, and diversity of thymic macrophages.
Integration of physiologically relevant photosynthetic energy flows into whole genome models of light-driven metabolism
Authors: Broddrick Jared T. , Ware Maxwell A. , Jallet Denis , Palsson Bernhard O. , Peers Graham 
Published: November 2021

AbstractCharacterizing photosynthetic productivity is necessary to understand the ecological contributions and biotechnology potential of plants, algae, and cyanobacteria. Light capture efficiency and photophysiology have long been characterized by measurements of chlorophyll fluorescence dynamics. However, these investigations typically do not consider the metabolic network downstream of light harvesting. In contrast, genome-scale metabolic models capture species-specific metabolic capabilities but have yet to incorporate the rapid regulation of the light harvesting apparatus. Here we combine chlorophyll fluorescence parameters defining photosynthetic and non-photosynthetic yield of absorbed light energy with a metabolic model of the pennate diatom Phaeodactylum tricornutum. This integration increases the model predictive accuracy regarding growth rate, intracellular oxygen production and consumption, and metabolic pathway usage. Additionally, our simulations recapitulate the link between mitochondrial dissipation of photosynthetically-derived electrons and the redox state of the photosynthetic electron transport chain. We use this framework to assess engineering strategies for rerouting cellular resources toward bioproducts. Overall, we present a methodology for incorporating a common, informative data type into computational models of light-driven metabolism for characterization, monitoring and engineering of photosynthetic organisms.
Intracellular development and impact of a eukaryotic parasite on its zombified microalgal host in the marine plankton
Authors: Decelle Johan , Kayal Ehsan , Bigeard Estelle , Gallet Benoit , Bougoure Jeremy , Clode Peta , Schieber Nicole , Templin Rachel , Hehenberger Elisabeth , Prensier Gerard , Chevalier Fabien , Schwab Yannick , Guillou Laure 
Published: November 2021

SummaryParasites are widespread and diverse in the oceanic plankton, and many of them infect single-celled algae for survival. How these parasites develop and scavenge energy within the host and whether the cellular organization and metabolism of the host is altered remain open questions. Combining quantitative structural and chemical imaging with time-resolved transcriptomics, we unveil dramatic morphological and metabolic changes of the parasite Amoebophrya (Syndiniales) during intracellular infection (e.g. 200-fold increase of mitochondrion volume), particularly following digestion of nutrient-rich host chromosomes. Some of these changes are also found in the apicomplexan parasites (e.g. sequential acristate and cristate mitochondrion, switch from glycolysis to TCA), thus underlining key evolutionary-conserved mechanisms. In the algal host, energy-producing organelles (chloroplast) remain intact during most of the infection, but sugar reserves diminish while lipid droplets increase. Thus, rapid infection of the host nucleus could be a zombifying strategy to digest nutrient-rich chromosomes and escape cytoplasmic defense while benefiting from the maintained C-energy production of the host cell.
System Environmental Metrics Collector for EM facilities
Authors: Alink Lambertus Michael , Eng Edward T. , Gheorghita Robert , Rice William , Cheng Anchi , Carragher Bridget , Potter Clinton S. 
Published: November 2021

AbstractRecent developments in cryo-electron microscopy (cryoEM) have led to the routine determination of structures at near atomic resolution and greatly increased the number of biomedical researchers wanting access to high-end cryoEM instrumentation. The high costs and long wait times for gaining access encourages facilities to maximize instrument uptime for data collection. To support these goals, we developed a System Environmental Metrics Collector for facilities (SEMCf) that serves as a laboratory performance and management tool. SEMCf consists of an architecture of automated and robust sensors that track, organize and report key facility metrics. The individual sensors are connected to Raspberry Pi (RPi) single board computers installed in close proximity to the input metrics being measured. The system is controlled by a central server that may be installed on a RPi or existing microscope support PC. Tracking the system and the environment provides feedback of imminent issues, suggestions for interventions that are needed to optimize data production, and indications as to when preventative maintenance should be scheduled. The sensor components are relatively inexpensive and widely commercially available, and the open-source design and software enables straightforward implementation, customization, and optimization by any facility that would benefit from real time environmental monitoring and reporting.
Effect of vitamin C and E supplementation on human gastrointestinal tract tissues and cells: Raman spectroscopy and imaging studies
Authors: Miazek Krystian , Beton Karolina , Brozek-Pluska Beata 
Published: November 2021

AbstractCancer of gastrointestinal tract, such as colorectal cancer (CRC) and gastric cancer (GC), are common types of cancer globally and their origin can be linked to oxidative stress conditions. Commonly available antioxidants, such as vitamins C and E, are widely considered as potential anti-cancer agents. Raman spectra have great potential in the biochemical characterization of matter based on the fact that each molecule has its own unique vibrational properties. Raman spectroscopy allows to precisely characterized cell substructures (nucleus, mitochondria, cytoplasm, cell membrane) and components (proteins, lipids, nucleic acids).The paper presents the application of the Raman spectroscopy technique for the analysis of tissue samples and cells of the human colon and stomach. The main goal of this study is to show the differences between healthy and cancerous tissues from the human digestive tract and human normal and cancer colon and gastric cell lines. The paper presents the spectroscopic characterization of normal colon cells - CCD-18 Co in physiological and oxidative conditions and effect of oxidative injury of normal colon cells upon supplementation with vitamin C at various concentrations based on Raman spectra. The obtained results were related to the Raman spectra recorded for human colon cancer cells - Caco-2. In addition, the effect of the antioxidant in the form of vitamin E on gastric cancer cells - HTB-135 is presented and compared with normal gastric cells - CRL-7869. All measured gastric samples were biochemically and structurally characterized by means of Raman spectroscopy and imaging. Statistically assisted analysis has shown that normal, ROS injured and cancerous human gastrointestinal cells can be distinguished based on their unique vibrational properties.The conducted research based on Raman spectra proved that antioxidants in the form of vitamin C and E exhibit anti-cancer properties. In consequence, conducted studies proved that label-free Raman spectroscopy may play an important role in clinical diagnostics differentiation of human normal and cancerous gastrointestinal tissues and may be a source of intraoperative information supporting histopathological analysis.
Lateral entorhinal cortex suppresses drift in cortical memory representations
Authors: Pilkiw Maryna , Jarovi Justin , Takehara-Nishiuchi Kaori 
Published: November 2021

ABSTRACTMemory retrieval is thought to depend on the reinstatement of cortical memory representations guided by pattern completion processes in the hippocampus. The lateral entorhinal cortex (LEC) is one of the intermediary regions supporting hippocampal-cortical interactions and houses neurons that prospectively signal past events in a familiar environment. To investigate the functional relevance of the LEC’s activity for cortical reinstatement, we pharmacologically inhibited the LEC and examined its impact on the stability of ensemble firing patterns in one of the LEC’s efferent targets, the medial prefrontal cortex (mPFC). When male rats underwent multiple epochs of identical stimulus sequences in the same environment, the mPFC maintained a stable ensemble firing pattern across repetitions, particularly when the sequence included pairings of neutral and aversive stimuli. With LEC inhibition, the mPFC still formed an ensemble pattern that accurately captured stimuli and their associations within each epoch. However, LEC inhibition markedly disrupted its consistency across the epochs by decreasing the proportion of mPFC neurons that stably maintained firing selectivity for stimulus associations. Thus, the LEC stabilizes cortical representations of learned stimulus associations, thereby facilitating the recovery of the original memory trace without generating a new, redundant trace for familiar experiences. Failure of this process might underlie retrieval deficits in conditions associated with degeneration of the LEC, such as normal aging and Alzheimer’s disease.SIGNIFICANCE STATEMENTTo recall past events, the brain needs to reactivate the activity patterns that occurred during those events. However, such reinstatement of memory traces is not trivial because it goes against the brain’s natural tendency to restructure the activity patterns continuously. We found that dysfunction of a brain region called the lateral entorhinal cortex (LEC) worsened the drift of the brain activity when rats repeatedly underwent the same events in the same room and made them behave as if they had never experienced these events before. Thus, the LEC stabilizes the brain activity to facilitate the recovery of the original memory trace. Failure of this process might underlie memory problems in elderly and Alzheimer’s disease patients with the degenerated LEC.
Instructional leadership in sub-Saharan Africa: policy and practice
Authors: Bush Tony , Fadare Mofoluwake , Chirimambowa Tamuka , Enukorah Emmanuel , Musa Daniel , Nur Hala , Nyawo Tatenda , Shipota Maureen 
Published: November 2021

PurposeThe purpose of the paper is to report the findings of a synthesis of literature reviews and stakeholder interviews conducted in Nigeria, Sierra Leone, Sudan, Tanzania, Zambia and Zimbabwe. The synthesis provides an overview of instructional leadership policy and practice in these six countries.Design/methodology/approachThis paper reports the findings of a systematic literature review, and participant interviews, in six sub-Sahara African countries. The research links to the British Council's initiative to develop instructional leadership in developing contexts, including the six countries featured in this submission.FindingsThe findings show diverse policy and practice of instructional leadership in these African contexts. Three have no explicit policies on this important leadership construct, while the others have relevant policy statements but limited evidence of instructional leadership practice.Research limitations/implicationsThe research provides an overview of instructional leadership policy and practice in these six countries, but more school-based research is required to develop grounded evidence on whether and how this is practiced. The pandemic inhibited such school-based research in 2020. The study provides emerging evidence of the impact of instructional leadership on school and student outcomes, confirming what is known from international research.Practical implicationsDeveloping awareness of how instructional leadership can improve student learning, linked to appropriate training, could lead to more effective schools.Social implicationsThe Sustainable Development Goals stress the importance of high quality education for economic and social development. Leadership is an important aspect of quality, and the research reported in this paper shows the potential for instructional leadership to enhance student learning.Originality/valueThis is the first cross-national study of instructional leadership in sub-Saharan Africa.
Service outsourcing contract design under asymmetric information
Authors: Xia Yu , Xie Jiqing , Zhang Guangsi , Zhu Weijun 
Published: November 2021

PurposeUpstream suppliers attempt to outsource product after-sales services to midstream third-party service providers while selling the product directly to downstream sellers, forming a networked supply chain. However, a problem of information asymmetry in the market demand among supply chain members exists. The authors investigate the impact of demand information asymmetry among third-party service providers, upstream suppliers and downstream sellers in the supply chain on the supplier's contract selection under the networked framework.Design/methodology/approachThe authors establish a model in which the supplier can use a wholesale price contract and facilitate a signaling game between the third-party service provider and the seller. Conversely, the supplier could use a menu contract to establish an incentive mechanism to solve information asymmetry. The authors propose heuristic algorithms to quickly estimate a supplier's optimal profit.FindingsThe results show that when the demand forecasting bias is relatively small, the use of a menu contract by the supplier could eliminate information asymmetry; when the demand forecasting bias is large enough, the signaling mechanism between the third-party service provider and the seller could alleviate the double marginalization effect in the supply chain. Although it is common to solve the asymmetric information problem by establishing incentive mechanisms, the authors found that in the latter case, the supplier is better off when no incentive mechanisms are implemented in the networked supply chain.Originality/valueThis study compares screening and signaling effects and compares firms' profits in both cases.
COVID‐19 and vertical transmission: assessing the expression of ACE2/TMPRSS2 in the human fetus and placenta to assess the risk of SARS‐CoV‐2 infection
Authors: Beesley MA , Davidson JR , Panariello F , Shibuya S , Scaglioni D , Jones BC , Maksym K , Ogunbiyi O , Sebire NJ , Cacchiarelli D , David AL , De Coppi P , Gerli MFM 
Published: November 2021

BackgroundPregnant women have been identified as a potentially at‐risk group concerning COVID‐19 infection, but little is known regarding the susceptibility of the fetus to infection. Co‐expression of ACE2 and TMPRSS2 has been identified as a prerequisite for infection, and expression across different tissues is known to vary between children and adults. However, the expression of these proteins in the fetus is unknown.MethodsWe performed a retrospective analysis of a single cell data repository. The data were then validated at both gene and protein level by performing RT‐qPCR and two‐colour immunohistochemistry on a library of second‐trimester human fetal tissues.FindingsTMPRSS2 is present at both gene and protein level in the predominantly epithelial fetal tissues analysed. ACE2 is present at significant levels only in the fetal intestine and kidney, and is not expressed in the fetal lung. The placenta also does not co‐express the two proteins across the second trimester or at term.InterpretationThis dataset indicates that the lungs are unlikely to be a viable route of SARS‐CoV2 fetal infection. The fetal kidney, despite presenting both the proteins required for the infection, is anatomically protected from the exposure to the virus. However, the gastrointestinal tract is likely to be susceptible to infection due to its high co‐expression of both proteins, as well as its exposure to potentially infected amniotic fluid.Tweetable abstractThis work provides detailed mechanistic insight into the relative protection & vulnerabilities of the fetus & placenta to SARS‐CoV‐2 infection by scRNAseq & protein expression analysis for ACE2 & TMPRSS2. The findings help to explain the low rate of vertical transmission.
Predicting the recurrence of chronic rhinosinusitis with nasal polyps using nasal microbiota
Authors: Zhao Yan , Chen Junru , Hao Yun , Wang Boqian , Wang Yue , Liu Qinghua , Zhao Jinming , Li Ying , Wang Ping , Wang Xiangdong , Zhang Peng , Zhang Luo 
Published: November 2021

AbstractBackgroundRecent studies have revealed that the nasal microbiota in patients with chronic rhinosinusitis with nasal polyps (CRSwNP) is profoundly altered and is correlated with systemic inflammation. However, little is known regarding whether the microbiota can be utilized to predict nasal polyp recurrence. This study is aimed to determine whether altered nasal microbiota constituents could be used as biomarkers to predict CRSwNP recurrence.MethodsNasal microbiota constituents were quantified and characterized using bacterial 16S ribosomal RNA gene sequencing. Selected features for least absolute shrinkage and selection operator regression‐based predictors were the nasal microbiota community composition and CRSwNP patient clinical characteristics. The primary outcome was recurrence, which was determined post‐admission.ResultsBy distinguishing recurrence‐associated nasal microbiota taxa and exploiting the distinct nasal microbiota abundance between patients with recurrent and non‐recurrent CRSwNP, we developed a predictive classifier for the diagnosis of nasal polyps' recurrence with 91.4% accuracy.ConclusionsKey taxonomical features of the nasal microbiome could predict recurrence in CRSwNP patients. The nasal microbiome is an understudied source of clinical variation in CRSwNP and represents a novel therapeutic target for future prevention and treatment.
Accelerating adaptation in the adaptive Metropolis–Hastings random walk algorithm
Authors: Spencer Simon E.F. 
Published: November 2021

SummaryThe Metropolis–Hastings random walk algorithm remains popular with practitioners due to the wide variety of situations in which it can be successfully applied and the extreme ease with which it can be implemented. Adaptive versions of the algorithm use information from the early iterations of the Markov chain to improve the efficiency of the proposal. The aim of this paper is to reduce the number of iterations needed to adapt the proposal to the target, which is particularly important when the likelihood is time‐consuming to evaluate. First, the accelerated shaping algorithm is a generalisation of both the adaptive proposal and adaptive Metropolis algorithms. It is designed to remove, from the estimate of the covariance matrix of the target, misleading information from the start of the chain. Second, the accelerated scaling algorithm rapidly changes the scale of the proposal to achieve a target acceptance rate. The usefulness of these approaches is illustrated with a range of examples.