bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatio-temporal mRNA tracking in the early zebrafish embryo
Authors: Holler Karoline , Neuschulz Anika , Drewe-Boß Philipp , Mintcheva Janita , Spanjaard Bastiaan , Arsiè Roberto , Ohler Uwe , Landthaler Markus , Junker Jan Philipp 
Published: June 2021

AbstractEarly stages of embryogenesis depend on subcellular localization and transport of maternal mRNA. However, systematic analysis of these processes is hindered by a lack of spatio-temporal information in single-cell RNA sequencing. Here, we combine spatially-resolved transcriptomics and single-cell RNA labeling to perform a spatio-temporal analysis of the transcriptome during early zebrafish development. We measure spatial localization of mRNA molecules within the one-cell stage embryo, which allows us to identify a class of mRNAs that are specifically localized at an extraembryonic position, the vegetal pole. Furthermore, we establish a method for high-throughput single-cell RNA labeling in early zebrafish embryos, which enables us to follow the fate of individual maternal transcripts until gastrulation. This approach reveals that many localized transcripts are specifically transported to the primordial germ cells. Finally, we acquire spatial transcriptomes of two xenopus species and compare evolutionary conservation of localized genes as well as enriched sequence motifs.
The temporal mutational and immune tumour microenvironment remodelling of HER2-negative primary breast cancers
Authors: De Mattos-Arruda Leticia , Cortes Javier , Blanco-Heredia Juan , Tiezzi Daniel G. , Villacampa Guillermo , Gonçalves-Ribeiro Samuel , Paré Laia , Souza Carla Anjos , Ortega Vanesa , Sammut Stephen-John , Cusco Pol , Fasani Roberta , Chin Suet-Feung , Perez-Garcia Jose , Dienstmann Rodrigo , Nuciforo Paolo , Villagrasa Patricia , Rubio Isabel T. , Prat Aleix , Caldas Carlos 
Published: June 2021

AbstractThe biology of breast cancer response to neoadjuvant therapy is underrepresented in the literature and provides a window-of-opportunity to explore the genomic and microenvironment modulation of tumours exposed to therapy. Here, we characterised the mutational, gene expression, pathway enrichment and tumour-infiltrating lymphocytes (TILs) dynamics across different timepoints of 35 HER2-negative primary breast cancer patients receiving neoadjuvant eribulin therapy (SOLTI-1007 NEOERIBULIN-NCT01669252). Whole-exome data (N = 88 samples) generated mutational profiles and candidate neoantigens and were analysed along with RNA-Nanostring 545-gene expression (N = 96 samples) and stromal TILs (N = 105 samples). Tumour mutation burden varied across patients at baseline but not across the sampling timepoints for each patient. Mutational signatures were not always conserved across tumours. There was a trend towards higher odds of response and less hazard to relapse when the percentage of subclonal mutations was low, suggesting that more homogenous tumours might have better responses to neoadjuvant therapy. Few driver mutations (5.1%) generated putative neoantigens. Mutation and neoantigen load were positively correlated (R2 = 0.94, p = <0.001); neoantigen load was weakly correlated with stromal TILs (R2 = 0.16, p = 0.02). An enrichment in pathways linked to immune infiltration and reduced programmed cell death expression were seen after 12 weeks of eribulin in good responders. VEGF was downregulated over time in the good responder group and FABP5, an inductor of epithelial mesenchymal transition (EMT), was upregulated in cases that recurred (p < 0.05). Mutational heterogeneity, subclonal architecture and the improvement of immune microenvironment along with remodelling of hypoxia and EMT may influence the response to neoadjuvant treatment.
Climate change drives widespread shifts in lake thermal habitat
Authors: Kraemer Benjamin M. , Pilla Rachel M. , Woolway R. Iestyn , Anneville Orlane , Ban Syuhei , Colom-Montero William , Devlin Shawn P. , Dokulil Martin T. , Gaiser Evelyn E. , Hambright K. David , Hessen Dag O. , Higgins Scott N. , Jöhnk Klaus D. , Keller Wendel , Knoll Lesley B. , Leavitt Peter R. , Lepori Fabio , Luger Martin S. , Maberly Stephen C. , Müller-Navarra Dörthe C. , Paterson Andrew M. , Pierson Donald C. , Richardson David C. , Rogora Michela , Rusak James A. , Sadro Steven , Salmaso Nico , Schmid Martin , Silow Eugene A. , Sommaruga Ruben , Stelzer Julio A. A. , Straile Dietmar , Thiery Wim , Timofeyev Maxim A. , Verburg Piet , Weyhenmeyer Gesa A. , Adrian Rita 
Published: June 2021

AbstractLake surfaces are warming worldwide, raising concerns about lake organism responses to thermal habitat changes. Species may cope with temperature increases by shifting their seasonality or their depth to track suitable thermal habitats, but these responses may be constrained by ecological interactions, life histories or limiting resources. Here we use 32 million temperature measurements from 139 lakes to quantify thermal habitat change (percentage of non-overlap) and assess how this change is exacerbated by potential habitat constraints. Long-term temperature change resulted in an average 6.2% non-overlap between thermal habitats in baseline (1978–1995) and recent (1996–2013) time periods, with non-overlap increasing to 19.4% on average when habitats were restricted by season and depth. Tropical lakes exhibited substantially higher thermal non-overlap compared with lakes at other latitudes. Lakes with high thermal habitat change coincided with those having numerous endemic species, suggesting that conservation actions should consider thermal habitat change to preserve lake biodiversity.
Dose–response effects of light therapy on sleepiness and circadian phase shift in shift workers: a meta-analysis and moderator analysis
Authors: Lam Calvin , Chung Min-Huey 
Published: June 2021

AbstractLight therapy has been considered to be effective in mitigating sleepiness and regulating circadian phase shift in shift workers. However, the effective treatment dose of light therapy remains undetermined. We performed a meta-analysis of randomized experimental studies to determine the effect of light therapy doses on sleepiness and circadian phase shift in shift workers. An article search was performed in 10 electronic databases from inception to June 2020. Two raters independently screened and extracted data and reached consensus. Twenty-one eligible studies were included. Analyses were performed using random-effects models. Light therapy exerted significantly small to medium effects on sleepiness and large treatment effects on circadian phase shift. Moderator analyses performed with subgroup and metaregression analyses revealed that medium-intensity light therapy for a shorter duration more effectively reduced sleepiness at night, whereas higher-intensity light therapy more effectively induced phase shifting, but the required treatment duration remained inconclusive. This study provides evidence regarding the effect of light therapy in reducing sleepiness and shifting circadian phase in shift workers. Exposure to medium-intensity light for a short duration at night reduced sleepiness, whereas exposure to high-intensity light improved sleep by shifting their circadian phase.
Age-sex population adjusted analysis of disease severity in epidemics as a tool to devise public health policies for COVID-19
Authors: Cannistraci Carlo Vittorio , Valsecchi Maria Grazia , Capua Ilaria 
Published: June 2021

AbstractGovernments continue to update social intervention strategies to contain COVID-19 infections. However, investigation of COVID-19 severity indicators across the population might help to design more precise strategies, balancing the need to keep people safe and to reduce the socio-economic burden of generalized restriction precedures. Here, we propose a method for age-sex population-adjusted analysis of disease severity in epidemics that has the advantage to use simple and repeatable variables, which are daily or weekly available. This allows to monitor the effect of public health policies in short term, and to repeat these calculations over time to surveille epidemic dynamics and impact. Our method can help to define a risk-categorization of likeliness to develop a severe COVID-19 disease which requires intensive care or is indicative of a higher risk of dying. Indeed, analysis of suitable open-access COVID-19 data in three European countries indicates that individuals in the 0–40 age interval and females under 60 are significantly less likely to develop a severe condition and die, whereas males equal or above 60 are more likely at risk of severe disease and death. Hence, a combination of age-adaptive and sex-balanced guidelines for social interventions could represent key public health management tools for policymakers.
Human immune system adaptations to simulated microgravity revealed by single-cell mass cytometry
Authors: Spatz J. M. , Fulford M. Hughes , Tsai A. , Gaudilliere D. , Hedou J. , Ganio E. , Angst M. , Aghaeepour N. , Gaudilliere Brice 
Published: June 2021

AbstractExposure to microgravity (µG) during space flights produces a state of immunosuppression, leading to increased viral shedding, which could interfere with long term missions. However, the cellular mechanisms that underlie the immunosuppressive effects of µG are ill-defined. A deep understanding of human immune adaptations to µG is a necessary first step to design data-driven interventions aimed at preserving astronauts’ immune defense during short- and long-term spaceflights. We employed a high-dimensional mass cytometry approach to characterize over 250 cell-specific functional responses in 18 innate and adaptive immune cell subsets exposed to 1G or simulated (s)µG using the Rotating Wall Vessel. A statistically stringent elastic net method produced a multivariate model that accurately stratified immune responses observed in 1G and sµG (p value 2E−4, cross-validation). Aspects of our analysis resonated with prior knowledge of human immune adaptations to µG, including the dampening of Natural Killer, CD4+ and CD8+ T cell responses. Remarkably, we found that sµG enhanced STAT5 signaling responses of immunosuppressive Tregs. Our results suggest µG exerts a dual effect on the human immune system, simultaneously dampening cytotoxic responses while enhancing Treg function. Our study provides a single-cell readout of sµG-induced immune dysfunctions and an analytical framework for future studies of human immune adaptations to human long-term spaceflights.
An easy-to-use function to assess deep space radiation in human brains
Authors: Khaksarighiri Salman , Guo Jingnan , Wimmer-Schweingruber Robert , Narici Livio 
Published: June 2021

AbstractHealth risks from radiation exposure in space are an important factor for astronauts’ safety as they venture on long-duration missions to the Moon or Mars. It is important to assess the radiation level inside the human brain to evaluate the possible hazardous effects on the central nervous system especially during solar energetic particle (SEP) events. We use a realistic model of the head/brain structure and calculate the radiation deposit therein by realistic SEP events, also under various shielding scenarios. We then determine the relation between the radiation dose deposited in different parts of the brain and the properties of the SEP events and obtain some simple and ready-to-use functions which can be used to quickly and reliably forecast the event dose in the brain. Such a novel tool can be used from fast nowcasting of the consequences of SEP events to optimization of shielding systems and other mitigation strategies of astronauts in space.
Evolution of social relationships between first-year students at middle school: from cliques to circles
Authors: Escribano Diego , Doldán-Martelli Victoria , Lapuente Francisco J. , Cuesta José A. , Sánchez Angel 
Published: June 2021

AbstractPeople organize their social relationships under a restriction on the number that a single individual can maintain simultaneously (the so-called Dunbar’s number, ~150). Additionally, personal networks show a characteristic layered structure where each layer corresponds to relationships of different emotional closeness. This structure, referred to as Dunbar’s circles, has mostly been considered from a static viewpoint, and their structure and evolution is largely unexplored. Here we study the issue of the evolution of the structure of positive and negative relationships in early adolescence by using data from students in their first year at middle school obtained from surveys conducted in class in two different waves separated by several months. Our results show that, initially, students have a lower number of total relationships but the majority are more intense and over time they report a higher number of total relationships, but the more intense relationships appear in a lower proportion. We have also found differences in the structure of communities at both temporal moments. While in the first instance the communities that appeared are mixed, made up of both boys and girls, in the second they changed so that they were separated primarily by gender. In addition, the size of each community was stabilized around 15 people, which coincides with the size of the second Dunbar’s circle, known as the sympathy group in social psychology. As a consequence, in groups with around 20 students of the same gender, they tend to split in two separate communities of about 10 each, below the second Dunbar’s circle threshold. On the other hand, groups with more stable community structure appear to go through the inverse process of friendship evolution, becoming more focused on their best relationships. All these results suggest how the layered structure of the personal network, as well as the community structure of the social network, emerge directly from the union of both positive and negative relationships. Thus, we provide a new perspective about its temporal evolution that may have relevant applications to improve school life and student performance.
Lost opportunities for mismatch repair (MMR) screening among minority women with endometrial cancer
Authors: Huang Marilyn , Hunter Tegan , Fein Lydia A. , Galli Johnny , George Sophia , Schlumbrecht Matthew , McCarter Kelly , Sinno Abdulrahman K. , Guido Luiz P. , Pinto Andre 
Published: June 2021

AbstractLynch Syndrome (LS) prevalence in underrepresented minorities are lacking. The objective of this study was to assess the prevalence of LS in a minority patient population. Secondary objectives included identifying factors associated with successful LS screening and to characterize clinicopathologic features. Women with endometrial cancer treated within a university system from 2014 and 2016 were included. Immunohistochemistry (IHC) results of MLH1, PMS2, MSH2 and MSH6 were obtained from medical records and clinicopathologic factors abstracted. Patients not previously screened for LS were screened. 276 patients were evaluable. More minority women were screened as part of their routine cancer care (p = 0.005). Additionally, women 50 years or younger were more likely to be screened for LS compared to women older than 51(p = 0.009) and uninsured or reliant on Medicaid patients (p = 0.011) were more likely to be screened during routine care. Six patients received confirmatory germline testing for LS (4.3%), and another 8 patients had a staining pattern suggestive of LS. In an underrepresented population, the rate of LS in endometrial cancer is similar to previous reports. LS may be under diagnosed and opportunities missed when universal screening is not applied in minority women.
Hydroxychloroquine plus standard of care compared with standard of care alone in COVID-19: a meta-analysis of randomized controlled trials
Authors: Amani Bahman , Khanijahani Ahmad , Amani Behnam 
Published: June 2021

AbstractThe efficacy and safety of Hydroxychloroquine (HCQ) in treating coronavirus disease (COVID-19) is disputed. This systematic review and meta-analysis aimed to examine the efficacy and safety of HCQ in addition to standard of care (SOC) in COVID-19. PubMed, the Cochrane Library, Embase, Web of sciences, and medRxiv were searched up to March 15, 2021. Clinical studies registry databases were also searched for identifying potential clinical trials. The references list of the key studies was reviewed to identify additional relevant resources. The quality of the included studies was evaluated using the Cochrane Collaboration tool and Jadad checklist. Meta-analysis was performed using RevMan software (version 5.3). Eleven randomized controlled trials with a total number of 8161 patients were identified as eligible for meta-analysis. No significant differences were observed between the two treatment groups in terms of negative rate of polymerase chain reaction (PCR) (Risk ratio [RR]: 0.99, 95% confidence interval (CI) 0.90, 1.08; P = 0.76), PCR negative conversion time (Mean difference [MD]: − 1.06, 95% CI − 3.10, 0.97; P = 0.30), all-cause mortality (RR: 1.09, 95% CI 1.00, 1.20; P = 0.06), body temperature recovery time (MD: − 0.64, 95% CI − 1.37, 0.10; P = 0.09), length of hospital stay (MD: − 0.17, 95% CI − 0.80, 0.46; P = 0.59), use of mechanical ventilation (RR: 1.12, 95% CI 0.95, 1.32; P = 0.19), and disease progression (RR = 0.82, 95% CI 0.37, 1.85; P = 0.64). However, there was a significant difference between two groups regarding adverse events (RR: 1.81, 95% CI 1.36, 2.42; P < 0.05). The findings suggest that the addition of HCQ to SOC has no benefit in the treatment of hospitalized patients with COVID-19. Additionally, it is associated with more adverse events.
Facile synthesis of PEDOT-rGO/HKUST-1 for high performance symmetrical supercapacitor device
Authors: Mohanadas Dharshini , Mohd Abdah Muhammad Amirul Aizat , Azman Nur Hawa Nabilah , Ravoof Thahira B. S. A. , Sulaiman Yusran 
Published: June 2021

AbstractA novel poly(3,4-ethylenedioxythiophene)-reduced graphene oxide/copper-based metal–organic framework (PrGO/HKUST-1) has been successfully fabricated by incorporating electrochemically synthesized poly(3,4-ethylenedioxythiophene)-reduced graphene oxide (PrGO) and hydrothermally synthesized copper-based metal–organic framework (HKUST-1). The field emission scanning microscopy (FESEM) and elemental mapping analysis revealed an even distribution of poly(3,4-ethylenedioxythiophene) (PEDOT), reduced graphene oxide (rGO) and HKUST-1. The crystalline structure and vibration modes of PrGO/HKUST-1 were validated utilizing X-ray diffraction (XRD) as well as Raman spectroscopy, respectively. A remarkable specific capacitance (360.5 F/g) was obtained for PrGO/HKUST-1 compared to HKUST-1 (103.1 F/g), PrGO (98.5 F/g) and PEDOT (50.8 F/g) using KCl/PVA as a gel electrolyte. Moreover, PrGO/HKUST-1 composite with the longest charge/discharge time displayed excellent specific energy (21.0 Wh/kg), specific power (479.7 W/kg) and an outstanding cycle life (95.5%) over 4000 cycles. Thus, the PrGO/HKUST-1 can be recognized as a promising energy storage material.
Measurements of the swimming speeds of motile microorganisms using object tracking and their correlation with water pollution and rheology levels
Authors: Shunmugam Ashaa Preyadharishini , Subramanian Gowtham , Fernandez Javier G. 
Published: June 2021

AbstractSelf-propelled microscopic organisms are ubiquitous in water. Such organisms’ motility depends on hydrodynamic and physical factors related to the rheology of the surrounding media and biological factors depending on the organisms’ state and well-being. Here we demonstrate that the swimming speed of Paramecium aurelia, a unicellular protozoan, globally found in fresh, brackish, and salt waters, can be used as a measurable frugal indicator of the presence of pollutants in water. This study establishes a significant and consistent relationship between Paramecia’s swimming speed and the presence of five different organic and inorganic contaminants at varying concentrations centered around drinking water thresholds. The large size and ubiquity of the targeted microorganism, the avoidance of reagents or specialized tools for the measurement, and the simple data collection based on an object tracking algorithm enable the automatization of the assessment and real-time results using globally available technology.
Genes encoding putative bicarbonate transporters as a missing molecular link between molt and mineralization in crustaceans
Authors: Abehsera Shai , Bentov Shmuel , Li Xuguang , Weil Simy , Manor Rivka , Sagi Shahar , Li Shihao , Li Fuhua , Khalaila Isam , Aflalo Eliahu D. , Sagi Amir 
Published: June 2021

AbstractDuring their life, crustaceans undergo several molts, which if theoretically compared to the human body would be equivalent to replacing all bones at a single event. Such a dramatic repetitive event is coupled to unique molecular mechanisms of mineralization so far mostly unknown. Unlike human bone mineralized with calcium phosphate, the crustacean exoskeleton is mineralized mainly by calcium carbonate. Crustacean growth thus necessitates well-timed mobilization of bicarbonate to specific extracellular sites of biomineralization at distinct molt cycle stages. Here, by looking at the crayfish Cherax quadricarinatus at different molting stages, we suggest that the mechanisms of bicarbonate ion transport for mineralization in crustaceans involve the SLC4 family of transporters and that these proteins play a key role in the tight coupling between molt cycle events and mineral deposition. This discovery of putative bicarbonate transporters in a pancrustacean with functional genomic evidence from genes encoding the SLC4 family—mostly known for their role in pH control—is discussed in the context of the evolution of calcium carbonate biomineralization.
Study of deactivation in mesocellular foam carbon (MCF-C) catalyst used in gas-phase dehydrogenation of ethanol
Authors: Klinthongchai Yoottapong , Prichanont Seeroong , Praserthdam Piyasan , Jongsomjit Bunjerd 
Published: June 2021

AbstractMesocellular foam carbon (MCF-C) is one the captivating materials for using in gas phase dehydrogenation of ethanol. Extraordinary, enlarge pore size, high surface area, high acidity, and spherical shape with interconnected pore for high diffusion. In contrary, the occurrence of the coke is a majority causes for inhibiting the active sites on catalyst surface. Thus, this study aims to investigate the occurrence of the coke to optimize the higher catalytic activity, and also to avoid the coke formation. The MCF-C was synthesized and investigated using various techniques. MCF-C was spent in gas-phase dehydrogenation of ethanol under mild conditions. The deactivation of catalyst was investigated toward different conditions. Effects of reaction condition including different reaction temperatures of 300, 350, and 400 °C on the deactivation behaviors were determined. The results indicated that the operating temperature at 400 °C significantly retained the lowest change of ethanol conversion, which favored in the higher temperature. After running reaction, the physical properties as pore size, surface area, and pore volume of spent catalysts were decreased owing to the coke formation, which possibly blocked the pore that directly affected to the difficult diffusion of reactant and caused to be lower in catalytic activity. Furthermore, a slight decrease in either acidity or basicity was observed owing to consumption of reactant at surface of catalyst or chemical change on surface caused by coke formation. Therefore, it can remarkably choose the suitable operating temperature to avoid deactivation of catalyst, and then optimize the ethanol conversion or yield of acetaldehyde.