bluuebunny/crossref_metadata_2025_split huggingface dataset:
Principles and best practices of optimizing a micromirror-based multicolor TIRF microscopy system
Authors: McCluskey Kaley , Dekker Nynke H. 
Published: March 2023

AbstractTIRF (Total Internal Reflection Fluorescence) microscopy is a powerful tool for measuring the intra- and intermolecular dynamics of fluorescently-labeled single molecules. As TIRF measurements move to more complex biological systems with more fluorescent probes, the multi-band-pass dichroic that separates excitation from emission becomes limiting for the microscope’s detection efficiency. To avoid this, multicolor colocalization-based experiments can employ “micromirror” (mm)TIRF, which replaces the dichroic with two 45°-angled rod mirrors that control the TIR excitation beam(s). Whereas a dichroic spectrally separates excitation and emission wavelengths, the micromirrors act to spatially separate the excitation beams from the collected emission photons within the objective lens itself. Comprehensive control of the TIR beam in mmTIRF can yield excellent signal to noise, and hence data quality, but at the price of increased optical complexity. Here, we introduce the theory behind these additional optical components and provide practical advice from our experience on the best way to set up, align, optimize, and maintain a mmTIRF instrument. We also demonstrate the practical effects of small misalignments to illustrate both the optimized signal quality and the degree of accuracy required to achieve it. We hope that this guide increases the accessibility of this type of instrumentation and helps researchers use it to produce data of the highest quality possible.
Selective S1PR1 activation improves brain infarction, neurological outcome, and cerebrovascular endothelial health following experimental ischemic injury
Authors: Shi Samuel X. , Li Yu-Jing , Wendt Trevor S. , Shi Kaibin , Jin Weina , Liu Qiang , Gonzales Rayna J. 
Published: March 2023

AbstractSphingosine-1-phosphate receptor 1 (S1PR1) is highly expressed in endothelial cells and receptor activation plays an important role in mediating endothelial function and health, thus showing promise as a pharmacologic target for acute ischemic stroke (AIS) treatment. Here, we examined the effect of a selective S1PR1 ligand, RP101075, on infarct volume and neurological outcome in adult male mice subjected to transient middle cerebral artery occlusion (tMCAO). Concomitantly, we examined S1PR1 expression profile in the ischemic mouse brain, as well as S1PR1 expression and impact of receptor activation on human brain microvascular endothelial cell (HBMEC) proliferation and survival following hypoxia plus glucose deprivation (HGD). We observed that RP101075 administration at onset of reperfusion reduced infarct volume and lessened neurological deficits in tMCAO mice and these responses were S1PR1 dependent. Additionally, we observed that tMCAO increased brain S1PR1 protein levels and flow cytometry revealed increases in S1PR1 levels are greatest in brain endothelial cells compared to other brain cell types (astrocyte, neuron, microglia). In cultured HBMECs, RP101075 increased cell proliferation and ozanimod, parent compound of RP1010175, increased live cell count during HGD; this response was S1PR1 dependent. In conclusion, S1PR1 activation improves neuroprotection/outcome post-stroke and preserves brain endothelial cell survival following ischemia-like injury.
Transcriptional Activation of Regenerative Hematopoiesis via Vascular Niche Sensing
Authors: Itkin Tomer , Houghton Sean , Schreiner Ryan , Lin Yang , Badwe Chaitanya R. , Voisin Veronique , Murison Alex , Seyedhassantehrani Negar , Kaufmann Kerstin B. , Garcia-Prat Laura , Booth Gregory T. , Geng Fuqiang , Liu Ying , Gomez-Salinero Jesus M. , Shieh Jae-Hung , Redmond David , Xiang Jenny Z. , Josefowicz Steven Z. , Trapnell Cole , Spencer Joel A. , Zangi Lior , Hadland Brandon , Dick John E. , Xie Stephanie Z. , Rafii Shahin 
Published: March 2023

AbstractTransition between activation and quiescence programs in hematopoietic stem and progenitor cells (HSC/HSPCs) is perceived to be governed intrinsically and by microenvironmental co-adaptation. However, HSC programs dictating both transition and adaptability, remain poorly defined. Single cell multiome analysis divulging differential transcriptional activity between distinct HSPC states, indicated for the exclusive absence of Fli-1 motif from quiescent HSCs. We reveal that Fli-1 activity is essential for HSCs during regenerative hematopoiesis. Fli-1 directs activation programs while manipulating cellular sensory and output machineries, enabling HSPCs co-adoptability with a stimulated vascular niche. During regenerative conditions, Fli-1 presets and enables propagation of niche-derived Notch1 signaling. Constitutively induced Notch1 signaling is sufficient to recuperate functional HSC impairments in the absence of Fli-1. Applying FLI-1 modified-mRNA transduction into lethargic adult human mobilized HSPCs, enables their vigorous niche-mediated expansion along with superior engraftment capacities. Thus, decryption of stem cell activation programs offers valuable insights for immune regenerative medicine.
Maximal coral thermal tolerance is found at intermediate diel temperature variability
Authors: Brown Kristen T. , Martynek Marcelina , Barott Katie L. 
Published: March 2023

AbstractIt has become critically important to identify environmental drivers of enhanced thermal tolerance in coral populations as ocean warming threatens the persistence of coral reef ecosystems globally. Variable temperature regimes that expose corals to sub-lethal heat stress have been recognized as a mechanism to increase coral thermotolerance and lessen coral bleaching; however, there is a need to better understand which thermal regimes are best for promoting coral stress hardening, and if thermal priming results in consistent benefits across species with distinct life-history strategies.Standardized thermal stress assays were used to determine the relative thermal tolerance of three divergent genera of corals (Acropora, PocilloporaandPorites) originating from six reef sites fluctuating in temperature by up to 7.7°C day-1, with an annual mean diel variability of 1–3°C day-1. Bleaching severity and dark-acclimated photochemical yield (Fv/Fm) were quantified following exposure to five temperature treatments ranging from 23.0 to 36.3°C — up to 9°C above the regional maximum monthly mean.The greatest thermal tolerance across all species was found at the site with intermediate mean diel temperature variability (2.2°C day-1), suggesting there is an optimal priming exposure that leads to maximal thermotolerance. Interestingly,AcroporaandPocilloporaoriginating from the least thermally variable regimes (i.e., <1.3°C day-1) had lower thermal tolerance than corals from the most variable sites (i.e., > 2.8°C day-1), whereas the opposite was true forPorites, suggesting divergent responses to priming across taxa.We highlight that fine-scale heterogeneity in temperature dynamics across habitats can increase coral thermal tolerance in diverse coral lineages, although in a non-linear manner. Remarkably, comparisons across global studies revealed that the range in coral thermotolerance uncovered in this study across a single reef system (<5 km) were as large as differences observed across vast latitudinal gradients (>300 km). This important finding indicates that local gene flow could improve thermal tolerance between habitats. However, as climate change continues, exposure to intensifying marine heatwaves is already compromising thermal priming as a mechanism to enhance coral thermal tolerance and bleaching resistance.
PIEZO1-mediated mechanosensing governs NK cell killing efficiency and infiltration in three-dimensional matrices
Authors: Yanamandra Archana K. , Zhang Jingnan , Montalvo Galia , Zhou Xiangda , Biedenweg Doreen , Zhao Renping , Sharma Shulagna , Hoth Markus , Lautenschläger Franziska , Otto Oliver , del Campo Aránzazu , Qu Bin 
Published: March 2023

AbstractNatural killer (NK) cells play a vital role in eliminating tumorigenic cells. Efficient locating and killing of target cells in complex three-dimensional (3D) environments are critical for their functions under physiological conditions. However, the role of mechanosensing in regulating NK cell killing efficiency in physiologically relevant scenarios is poorly understood. Here, we report that the responsiveness of NK cells is regulated by tumor cell stiffness. NK cell killing efficiency in 3D is impaired against softened tumor cells, while it is enhanced against stiffened tumor cells. Notably, the durations required for NK cell killing and detachment are significantly shortened for stiffened tumor cells. Furthermore, we have identified PIEZO1 as the predominantly expressed mechanosensitive ion channel among the examined candidates in NK cells. Perturbation of PIEZO1 abolishes stiffness-dependent NK cell responsiveness, significantly impairs the killing efficiency of NK cells in 3D, and substantially reduces NK cell infiltration into 3D collagen matrices. Conversely, PIEZO1 activation enhances NK killing efficiency as well as infiltration. In conclusion, our findings demonstrate that PIEZO1-mediated mechanosensing is crucial for NK killing functions, highlighting the role of mechanosensing in NK cell killing efficiency under 3D physiological conditions and the influence of environmental physical cues on NK cell functions.
Alopecosa nagpagacts on cardiac ventricular myocytes to kill prey
Authors: Gu Zhixin , Long Chenbo , Lu Yuehua , Huang Biao 
Published: March 2023

AbstractSpiders are excellent predator to kill their prey by peptide toxins from its venoms.Alopecosa nagpag(A. nagpag) is a new identified wolf spider distributing in Yunnan province and nothing has known about the venom. In this study, venom ofA. nagpagshowed mild toxicity to Kunming mouse with LD50of 3.32 mg/kg. Action potential duration (APD) was prolonged in a frequency-dependent manner and whole currents of neonatal rat ventricular myocytes (NRVMs) were inhibited by venom. Meanwhile, venom ofA. nagpagcould largely increase L calcium currents (ICaL). Whereas sodium current (INa) and rapidly activating delayed rectifier potassium current (IKr) were significantly decreased by 100 μg/mL venoms. No obvious inhibition was found on other ion channels such as rapidly activating and inactivating transient inward (IK1), rapid (IKr) and slow (IKs). As those ion channels play critical role in rhythm of cardiac ventricular myocytes,A. nagpagmay lead prey to death by changing cardiac rhythm.
Analytical Comparability to Evaluate Impact of Manufacturing Changes of ARX788, an Anti-HER2 ADC in Late-Stage Clinical Development
Authors: Yu Wayne , Ramprasad Mysore , Pal Manoj , Chen Chris , Paruchuri Shashi , Skidmore Lillian , Knudsen Nick , Allen Molly , Buechler Ying 
Published: March 2023

AbstractARX788 is an anti-HER2 antibody drug conjugate (ADC) developed using Ambrx proprietary Engineered Precision Biologics technology. The manufacturing process of ARX788 has been optimized during the course of early to late-phase clinical development. A comprehensive evaluation of side-by-side comparability between pre- and post-change process for ARX788 drug substance and drug product from a quality perspective was conducted based on ICH Q5E guidelines consisting of batch release assays, physicochemical and biophysical characterization, biological characterization, and forced degradation studies. All results have demonstrated a high degree of similarity between the pre- and post-change ARX788 drug substance batches and drug product lots, demonstrating that the process manufacturing changes did not impact product quality.
Neuromolecular interactions guiding homeostatic mechanisms underlying healthy ageing: A view from computational microscope
Authors: Saha Suman , Chakraborty Priyanka , Naskar Amit , Roy Dipanjan , Banerjee Arpan 
Published: March 2023

AbstractAgeing brain is associated with a slow drift in structural network properties over the lifespan accompanied by reorganization in neuromolecular interactions giving rise to changes in global functional markers. What are the guiding principles of the homeostatic mechanisms that maintain the desired performance of functional neural circuits and preserve brain health during healthy ageing? We hypothesize that an ageing brain alters two primary neurotransmitters, glutamate andγ-aminobutyric acid (GABA), responsible for excitation-inhibition regulation, concomitant with anatomical demyelination to preserve critical neural dynamics that are necessary to uphold optimal network performance. Thus, often observed re-organized functional connectivity with age by several investigations is a byproduct of this adaptive process. We demonstrate that the adaptive mechanism is driven by the tuning of glutamate and GABA concentration over a very slow time scale (lifespan) that can be estimated by tracking criticality from co-ordinated neural dynamics at a resting state via a biophysically driven computational framework, introduced as a computational microscope. We validate several empirical observations and model predictions across three independent aging cohorts using this computational microscope. One of the key mechanisms we discover is the reduction in local glutamate levels employed by brain regions to maintain a homeostatic balance with aging. This is further supported by the invariance of measures of global functional integration during the healthy ageing process.
Ability of Bifidobacterium breve 702258 to transfer from mother to infant: the MicrobeMom randomised controlled trial
Authors: Moore Rebecca L. , Feehily Conor , Killeen Sarah Louise , Yelverton Cara A. , Geraghty Aisling A. , Walsh Calum J , O’Neill Ian J. , Nielsan Ida Bush , Lawton Elaine M. , Gallardo Rocio Sanchez , Chandra Nori Sai Ravi , Shanahan Fergus , Murphy Eileen F. , Van Sinderen Douwe , Cotter Paul D. , McAuliffe Fionnuala M. 
Published: March 2023

AbstractBackgroundThe composition of the infant microbiome can have a variety of short- and long-term implications for health. It is unclear if maternal probiotic supplementation in pregnancy can impact infant gut microbiome.ObjectiveThe aim of our study was to investigate if maternal supplementation of a formulation of Bifidobacterium breve 702258 from early pregnancy until three months postpartum could transfer to the infant gut.Study designThis was a double-blinded placebo controlled randomised-controlled trial of B. breve 702258 (minimum 1×109colony forming units) or placebo taken orally from 16-weeks’ gestation until three-months postpartum in healthy pregnant women. The primary outcome was presence of the supplemented strain in infant stool up to 3 months of life, detected by at a least two of three methods, i.e., strain specific PCR, shotgun metagenomic sequencing, or genome sequencing of cultured B. breve. 120 individual infants’ stool samples were required for 80% power to detect a difference in strain transfer between groups. Rates of detection were compared using Fishers exact test.Results160 pregnant women with average age 33.6 (3.9) years, mean BMI of 24.3 (22.5, 26.5) kg/m2and 43% with nulliparity (n=58) were recruited from September 2016 to July 2019. Neonatal stool samples were obtained from 135 infants (65 in intervention and 70 in control). The presence of the supplemented strain was detected through at least two methods (PCR and culture) in two infants in the intervention group (n=2/65, 3.1%) and none in the control group (n=0, 0%),p= 0.230.ConclusionDirect strain transfer from mothers to infants of B. breve 772058 occurred, albeit infrequently. This study highlights potential for maternal supplementation to introduce microbial strains into the infant microbiome.Trial registration numberISRCTN53023014
The effects of weather and mobility on respiratory viruses dynamics before and after the COVID-19 pandemic
Authors: Varela-Lasheras Irma , Perfeito Lília , Mesquita Sara , Gonçalves-Sá Joana 
Published: March 2023

AbstractThe flu season is caused by a combination of different pathogens, including influenza viruses (IVS), that cause the flu, and non-influenza respiratory viruses (NIRVs), that cause common colds or influenza-like illness. These viruses have similar circulation patterns, and weather has been considered a main driver of their dynamics, with peaks in the winter and almost no circulation during the summer in temperate regions. However, after the emergence of SARS-CoV2, in 2019, the dynamics of these respiratory viruses were strongly perturbed worldwide: some infections almost disappeared, others were delayed or occurred “off-season”. This disruption raised questions regarding the dominant role of weather while also providing an unique opportunity to investigate the relevance of different driving factors on the epidemiological dynamics of IVs and NIRVs, including viral interactions, non-pharmacological individual measures (such as masking), or mobility. Here, we use epidemiological surveillance data on several respiratory viruses from Canada and the USA from 2016 to 2023, and tested the effects of weather and mobility in their dynamics before and after the COVID-19 pandemic. Using statistical modelling, we found evidence that whereas in the pre-COVID-19 pandemic period, weather had a strong effect and mobility a limited effect on dynamics; in the post-COVID-19 pandemic period the effect of weather was strongly reduced and mobility played a more relevant role. These results, together with previous studies, indicate that at least some of the behavioral changes resulting from the non-pharmacological interventions implemented during COVID-19 pandemic had a strong effect on the dynamics of respiratory viruses. Furthermore, our results support the idea that these seasonal dynamics are driven by a complex system of interactions between the different factors involved, which probably led to an equilibrium that was disturbed, and perhaps permanently altered, by the COVID-19 pandemic.
A combination of annual and nonannual forces drive respiratory disease in the tropics
Authors: Yang Fuhan , Servadio Joseph L , Le Thanh Nguyen Thi , Lam Ha Minh , Choisy Marc , Thai Pham Quang , Nhu Thao Tran Thi , Thao Vy Nguyen Ha , Phuong Huynh Thi , Nguyen Tran Dang , Hoai Tam Dong Thi , Hanks Ephraim M , Vinh Ha , Bjornstad Ottar N , Van Vinh Chau Nguyen , Boni Maciej F 
Published: March 2023

AbstractBackgroundIt is well known that influenza and other respiratory viruses are wintertime-seasonal in temperate regions. However, respiratory disease seasonality in the tropics remains elusive. In this study, we aimed to characterize the seasonality of influenza-like illness (ILI) and influenza virus in Ho Chi Minh City (HCMC), Vietnam.MethodsWe monitored the daily number of ILI patients in 89 outpatient clinics from January 2010 to December 2019. We collected nasal swabs and tested for influenza from a subset of clinics from May 2012 to December 2019. We used spectral analysis to describe the periodicities in the system. We evaluated the contribution of these periodicities to predicting ILI and influenza patterns through lognormal and gamma hurdle models.FindingsDuring ten years of community surveillance, 66,799 ILI reports were collected covering 2.9 million patient visits; 2604 nasal swabs were collected 559 of which were PCR-positive for influenza virus. Both annual and nonannual cycles were detected in the ILI time series, with the annual cycle showing 8.9% lower ILI activity (95% CI: 8.8%-9.0%) from February 24 to May 15. Nonannual cycles had substantial explanatory power for ILI trends (ΔAIC = 183) compared to all annual covariates (ΔAIC = 263). Near-annual signals were observed for PCR-confirmed influenza but were not consistent along in time or across influenza (sub)types.InterpretationOur study reveals a unique pattern of respiratory disease dynamics in a tropical setting influenced by both annual and nonannual drivers. Timing of vaccination campaigns and hospital capacity planning may require a complex forecasting approach.FundingNational Institutes of Health, Wellcome Trust.
Patient engagement in research; benefits, challenges, importance, and implications
Authors: Ivany Caitlyn , Hudson Tess , Schneider Patricia , Farrukh Hadia , Swinton Marilyn , Ghert Michelle 
Published: March 2023

AbstractObjectivePatient engagement (PE) and patient-oriented research have begun to reshape the thought process behind conducting research with the aim of maximizing the relevance of findings for patients. This study aimed to examine the perceived benefits, challenges, importance, and implications of patient engagement from the perspectives of sarcoma patient advisors and researchers.MethodsThis study utilized a mixed model design. Qualitative data was collected through two focus group discussions with sarcoma patients. Quantitative data was collected via a survey containing Likert scale questions completed by the Centre for Evidence-Based Orthopaedics Musculoskeletal Oncology research team at McMaster University.ResultsResults showed that patients value the opportunity to contribute to research and support future patients. Being a patient advisor also creates a sense of community and fosters support through building connections and communicating with other patients. Members of the research team noted that patient engagement is important for the study of patient relevant topics and provides insight into the improvement of patient care. However, an added challenge is the lack of current guidance surrounding the implementation of patient engagement.ConclusionThese findings emphasize the potential value of patient engagement while also highlighting the need for further research into best practices for the implementation of patient engagement efforts. Overall, patient engagement is an essential area in need of further exploration to enhance future research and clinical trials.