Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultra-precise all-optical manipulation of neural circuits with multifunctional Cre-dependent transgenic mice

Determining which features of the neural code drive perception and behavior requires the ability to simultaneous read out and write in neural activity patterns with high precision across many neurons. All-optical systems that combine two photon (2p) calcium imaging and targeted 2p photostimulation enable the activation of specific, functionally defined groups of neurons in behaving animals. However, these techniques do not yet have the ability to reveal how the specific distribution of firing rates across a relevant neural population mediates neural computation and behavior. The key technical obstacle is the inability to transform single-cell calcium signals into accurate estimates of firing rate changes and then write in these cell-specific firing rate changes to each individual neuron in a targeted population. To overcome this challenge, we made two advances: first we introduce a new genetic line of mice for robust Cre-dependent co-expression of a high-performance calcium indicator and a potent soma-targeted microbial opsin. Second, using this line, we developed a pipeline that enables the read-out and write-in of precise population vectors of neural activity across a targeted group of neurons. The combination of the new multifunctional transgenic line and the photostimulation paradigm offer a powerful and convenient platform for investigating the neural codes of computation and behavior. It may prove particularly useful for probing causal features of the geometry of neural representations where the ability to directly control the topology of population activity is essential.
Green fluorescent protein-like pigments optimise the internal light environment in symbiotic reef-building corals

Pigments homologous to the Green Fluorescent Protein (GFP) have been proposed to fine-tune the internal light microclimate of corals, facilitating photoacclimation of photosynthetic coral symbionts (Symbiodiniaceae) to life in different reef habitats and environmental conditions. However, direct measurements of the in vivo light conditions inside the coral tissue supporting this conclusion are lacking. Here, we quantified the intra-tissue spectral light environment of corals expressing GFP-like proteins from widely different light regimes. We focus on (1) photoconvertible red fluorescent proteins (pcRFPs), thought to enhance photosynthesis in mesophotic habitats via wavelength conversion, and (2) chromoproteins (CPs), which provide photoprotection to the symbionts in shallow water via light absorption. Optical microsensor measurements indicated that both pigment groups strongly alter the coral tissue light environment. Estimates derived from light spectra measured in pcRFP-containing corals showed that fluorescence emission can contribute to >50% of orange-red light available to the photosynthetic symbionts at mesophotic depths. We further show that upregulation of pink CPs in shallow-water corals during bleaching leads to a reduction of orange light by 10-20% compared to low-CP tissue. Thus, screening by CPs has an important role in mitigating the light-enhancing effect of coral tissue scattering during bleaching. Our results provide the first experimental quantification of the importance of GFP-like proteins in fine-tuning the light microclimate of corals during photoacclimation.
A thermothickening polymer as a novel flocculant for oily wastewater treatment

ABSTRACT In this work, the effectiveness of poly(acrylamide-co-N,N-diethylacrylamide-co-n-butylstyrene), designated as TTF which exhibits a thermothickening behavior, was examined as a novel flocculant for oily wastewater treatment. The effects of flocculant concentration, temperature, and electrolyte on TTF flocculation performance were examined in comparison with cationic polyacrylamide (CPAM). TTF exhibited a lower critical solution temperature (LCST) of 53°C when the monomer feed molar ratio of acrylamide/N,N′-diethyl acrylamide/n-butylstyrene: 73/26/1 was used. Moreover, increasing the concentration of NaCl and CaCl2 adversely reduced the LCST of TTF. Furthermore, treatment with TTF proved excellent performance in removing oil and suspended solid than CPAM in all conditions investigated.
Toward a Global Public Repository of Community Protocols to Encourage Best Practices in Biomolecular Ocean Observing and Research

Biomolecular ocean observing and research is a rapidly evolving field that uses omics approaches to describe biodiversity at its foundational level, giving insight into the structure and function of marine ecosystems over time and space. It is an especially effective approach for investigating the marine microbiome. To mature marine microbiome research and operations within a global ocean biomolecular observing network (OBON) for the UN Decade of Ocean Science for Sustainable Development and beyond, research groups will need a system to effectively share, discover, and compare “omic” practices and protocols. While numerous informatic tools and standards exist, there is currently no global, publicly-supported platform specifically designed for sharing marine omics [or any omics] protocols across the entire value-chain from initiating a study to the publication and use of its results. Toward that goal, we propose the development of the Minimum Information for an Omic Protocol (MIOP), a community-developed guide of curated, standardized metadata tags and categories that will orient protocols in the value-chain for the facilitated, structured, and user-driven discovery of suitable protocol suites on the Ocean Best Practices System. Users can annotate their protocols with these tags, or use them as search criteria to find appropriate protocols. Implementing such a curated repository is an essential step toward establishing best practices. Sharing protocols and encouraging comparisons through this repository will be the first steps toward designing a decision tree to guide users to community endorsed best practices.
Identification and Characterization of Circulating MicroRNAs as Novel Biomarkers in Dogs With Heart Diseases

Background: Previous studies in humans have confirmed dysregulations of circulating microRNAs (miRNAs) in patients with various cardiovascular diseases. However, studies on circulating miRNAs in dogs with various heart diseases are limited in number. This study aimed to identify significantly dysregulated circulating miRNAs and characterize them as novel biomarkers in dogs with heart diseases. Materials and Methods: Circulating levels of 11 miRNAs were investigated in serum samples of 82 dogs (72 with heart diseases and 10 healthy dogs) using quantitative reverse transcription-polymerase chain reaction. The results were correlated to clinical data including echocardiographic results and N-terminal pro B-type natriuretic peptide (NT-proBNP) levels. Results: Upregulation of cfa-miR-130b was observed in dogs with myxomatous mitral valve degeneration (MMVD) stage B, patent ductus arteriosus, and pulmonic stenosis. In dogs with MMVD stage B, cfa-miR-130b was upregulated and correlated with clinical indices. In receiver operating characteristic (ROC) analysis, cfa-miR-130b accurately distinguished dogs with diseases from healthy dogs. We also observed that cfa-miR-375 and cfa-let-7b were upregulated in dogs with concentric cardiac hypertrophy. The cfa-miR-375 was correlated with concentric hypertrophy indices and was an accurate indicator of concentric hypertrophy in ROC analysis. Conclusions: The miRNAs identified in this study may be used as novel biomarkers and possible candidates for therapeutic targets in various canine heart diseases.
Dynamics of Nutrients and Colored Dissolved Organic Matter Absorption in a Wetland-Influenced Subarctic Coastal Region of Northeastern Japan: Contributions From Mariculture and Eelgrass Meadows

Coastal oceans interacting with terrestrial ecosystems play an important role in biogeochemical cycles. It is therefore essential to research land–ocean interactions for further understanding of the processes influencing nutrients dynamics in coastal areas. We investigated the seasonal and spatial distribution of nutrient concentrations and light absorption coefficients of colored dissolved organic matter (CDOM), non-algal particles (NAP), and phytoplankton in a wetland-influenced river–eelgrass meadows–coastal waters continuum in the protected and semi-enclosed coastal sea of Akkeshi-ko estuary (AKE) and Akkeshi Bay (AB), Japan from April 2014 to February 2015. The mixing dilution lines of the CDOM absorption coefficient at 355 nm [aCDOM(355)] relative to salinity predicted by two end-members between freshwater and coastal water showed conservative mixing in AB. Silicate concentrations were significantly correlated with salinity and aCDOM(355) in AB in each month except for December 2014. These results suggest that silicate and CDOM in AB primarily originates from wetland-influenced river discharge. However, samples collected from the eelgrass meadows of AKE, where mariculture is developed, showed non-conservative mixing of silicate concentrations and aCDOM(355) with salinity except for June 2014. Elevated phosphate concentrations, probably released from sediments, were also found in the eelgrass meadows of AKE, especially during summer. These results suggest that the metabolic activities of mariculture and seagrass ecosystem significantly contribute to the nutrient cycles and CDOM absorption in AKE and to the distinct water-mass systems inside and outside AKE. The relative absorption properties of NAP [aNAP(443)], phytoplankton [aph(443)], and aCDOM(443) showed that CDOM is the main factor affecting the light distribution in AKE. However, the relative absorption properties varied seasonally in AB because of spring and autumn phytoplankton blooms and ice cover during winter. Significant relationships were observed between the Secchi disk depth (ZSD), aNAP(443), and aCDOM(443). Chl a concentration and aph(443) were not good indicators for predicting ZSD in our study region. These results suggest that incorporating inherent optical properties and CDOM from mariculture and seagrass ecosystem into ecosystem models could improve predictions of light distribution along the freshwater–eelgrass–coastal waters continuum in optically complex coastal waters.
Efficacy, Immunogenicity and Safety of COVID-19 Vaccines: A Systematic Review and Meta-Analysis

There is a significant research gap in meta-analysis on the efficacy and safety of coronavirus disease 2019 (COVID-19) vaccines. This study analyzed the efficacy of COVID-19 vaccines. Published phase I, phase II, and phase III trials analyzing safety and immunogenicity and phase III randomized clinical trials evaluating the efficacy of COVID-19 vaccines were included. We searched MEDLINE, Scopus, and The Lancet for published articles evaluating the relative reduction in COVID-19 risk after vaccination. Selected literatures were published between December 15, 2019 and May 15, 2021 on the safety, efficacy, and immunogenicity of COVID-19 vaccines. This meta-analysis included studies that confirmed cases of COVID-19 using reverse transcriptase polymerase chain reaction. This study detected 8,926 eligible research articles published on COVID-19 vaccines. Of these, 25 studies fulfilled the inclusion criteria. Among the selected articles, 19 randomized clinical trials, 2 non-randomized clinical trials, and 3 observational studies were analyzed. Seven (28%) studies were included in the meta-analysis. The efficacy of the adenovirus vector vaccine was 73% (95% CI = 69–77) and that of the messenger RNA (mRNA) vaccine was 85% (95% CI = 82–88) in participants aged ≥18 years. There are no reports of clinical trials in participants aged under 16 years. The production of neutralizing antibodies against receptor-binding domains (RBDs) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in >90% of the vaccinated samples was reported within 0–30 days of the first or the second dose of the vaccine. Pain at the injection site was the most common local symptom in people receiving mRNA vaccines (29%–85% of participants). Fever (0.2%–95%) was the most prevalent in people receiving adenovirus vector vaccines, and fatigue (8.4%–55%) was the most common side effect in people receiving the mRNA vaccines. Studies suggest that mRNA vaccines and adenovirus vector vaccines can provide moderate to high protection against COVID-19 infection in people over 18 years. Evidence of the long-term protection of the vaccines in people aged under 16 years against the multiple variants of COVID-19 are limited. This study will provide an integrated evaluation on the efficacy, safety, and immunogenicity of the COVID-19 vaccines.
Effects of Neutrophil Extracellular Traps in Patients With Septic Coagulopathy and Their Interaction With Autophagy

Introduction Neutrophil extracellular traps (NETs) act as a critical trigger of inflammation and coagulation. We hypothesized that NETs are associated with septic hypercoagulability. Materials and Methods In total, 82 patients admitted with sepsis in the Department of Critical Care Medicine of Peking Union Medical College Hospital were enrolled between February 2017 and April 2018. Clinical and hematological parameters and thrombotic or hemorrhagic events were recorded. Blood samples were obtained to assess biomarkers of NET formation, including neutrophil elastase 2 (ELA2) and citrullinated histone H3, and endothelial-derived biomarker syndecan-1. Autophagy levels and their regulation pathway were also examined to explore their interaction with NETs. Result Sepsis patients with disseminated intravascular coagulation (DIC) showed significantly higher levels of NET formation [ELA2, 1,247 (86–625) vs. 2,039 (1,544–2,534), p < 0.0001; H3, 140 (47–233) vs. 307 (199–415), p < 0.0001]. NET formation was independently associated with DIC risk [ELA2, OR 1.0028, 95% CI, 1.0010–1.0045; H3, OR 1.0104, 95% CI, 1.0032–1.0176] and mortality [ELA2, HR 1.0014, 95% CI, 1.0004–1.0024; H3, HR 1.0056, 95% CI, 1.0008–1.0115]. The area under the curve value for ELA2 in predicting DIC occurrence was 0.902 (95% CI, 0.816–0.957), and that of H3 was 0.870 (95% CI, 0.778–0.934). Furthermore, biomarkers of NET formation, endothelial cells, and autophagy exhibited a significant correlation [ELA2 and Syn (r = 0.5985, p < 0.0001), LC3B (r = −0.4224, p < 0.0001); H3 and Syn (r = 0.6383, p < 0.0001), LC3B (r = −0.3005, p = 0.0061)]. Conclusion Increased NET formation is significantly associated with sepsis-induced DIC incidence and mortality in sepsis patients, revealing a significant relationship with the autophagy pathway. Clinical Trial Registration chictr.org. cn, identifier ChiCTR-ROC-17010750.
U-Hack Med Gap Year—A Virtual Undergraduate Internship Program in Computer-Assisted Healthcare and Biomedical Research

The COVID-19 healthcare crisis dramatically changed educational opportunities for undergraduate students. To overcome the lack of exposure to lab research and provide an alternative to cancelled classes and online lectures, the Lyda Hill Department of Bioinformatics at UT Southwestern Medical Center established an innovative, fully remote and paid “U-Hack Med Gap Year” internship program. At the core of the internship program were dedicated biomedical research projects spanning nine months in fields as diverse as computational microscopy, bioimage analysis, genome sequence analysis and establishment of a surgical skill analysis platform. To complement the project work, a biweekly Gap Year lab meeting was devised with opportunities to develop important skills in presenting, data sharing and analysis of new research. Despite a challenging year, all selected students completed the full internship period and over 30% will continue their project remotely after the end of the program.
Exome-Wide Association Study Identifies East Asian-Specific Missense Variant MTHFR C136T Influencing Homocysteine Levels in Chinese Populations RH: ExWAS of tHCY in a Chinese Population

Plasma total homocysteine (tHCY) is a known risk factor of a wide range of complex diseases. No genome scans for tHCY have been conducted in East Asian populations. Here, we conducted an exome-wide association study (ExWAS) for tHCY in 5,175 individuals of Chinese Han origin, followed by a replication study in 668 Chinese individuals. The ExWAS identified two loci, 1p36.22 (lead single-nucleotide polymorphism (SNP) rs1801133, MTHFR C677T) and 16q24.3 (rs1126464, DPEP1), showing exome-wide significant association with tHCY (p < 5E−7); and both loci have been previously associated with tHCY in non-East Asian populations. Both SNPs were replicated in the replication study (p < 0.05). Conditioning on the genotype of C677T and rs1126464, we identified a novel East Asian-specific missense variant rs138189536 (C136T) of MTHFR (p = 6.53E−10), which was also significant in the replication study (p = 9.8E−3). The C136T and C677T variants affect tHCY in a compound heterozygote manner, where compound heterozygote and homozygote genotype carriers had on average 43.4% increased tHCY than had other genotypes. The frequency of the homozygote C677T genotype showed an inverse-U-shaped geospatial pattern globally with a pronounced frequency in northern China, which coincided with the high prevalence of hyperhomocysteinemia (HHCY) in northern China. A logistic regression model of HHCY status considering sex, age, and the genotypes of the three identified variants reached an area under the receiver operating characteristic curve (AUC) value of 0.74 in an independent validation cohort. These genetic observations provide new insights into the presence of multiple causal mutations at the MTHFR locus, highlight the role of genetics in HHCY epidemiology among different populations, and provide candidate loci for future functional studies.
insideOut: A Bio-Inspired Machine Learning Approach to Estimating Posture in Robots Driven by Compliant Tendons

Estimates of limb posture are critical for controlling robotic systems. This is generally accomplished with angle sensors at individual joints that simplify control but can complicate mechanical design and robustness. Limb posture should be derivable from each joint's actuator shaft angle but this is problematic for compliant tendon-driven systems where (i) motors are not placed at the joints and (ii) nonlinear tendon stiffness decouples the relationship between motor and joint angles. Here we propose a novel machine learning algorithm to accurately estimate joint posture during dynamic tasks by limited training of an artificial neural network (ANN) receiving motor angles and tendon tensions, analogous to biological muscle and tendon mechanoreceptors. Simulating an inverted pendulum—antagonistically-driven by motors and nonlinearly-elastic tendons—we compare how accurately ANNs estimate joint angles when trained with different sets of non-collocated sensory information generated via random motor-babbling. Cross-validating with new movements, we find that ANNs trained with motor angles and tendon tension data predict joint angles more accurately than ANNs trained without tendon tension. Furthermore, these results are robust to changes in network/mechanical hyper-parameters. We conclude that regardless of the tendon properties, actuator behavior, or movement demands, tendon tension information invariably improves joint angle estimates from non-collocated sensory signals.
How Singing can Help People With Dementia and Their Family Care-Partners: A Mixed Studies Systematic Review With Narrative Synthesis, Thematic Synthesis, and Meta-Integration

Background: Recent research on the efficacy of music-based interventions for people with dementia have focused on specific outcomes and methods, and singing has been noted as a particularly beneficial activity. However, due to heterogeneity of research methods, there is a need to synthesise the findings of both quantitative and qualitative research in order to better understand both the impact and potential mechanisms of singing for people in this population. Method: This systematic review included quantitative, qualitative and mixed-methods studies, and analysed these using a systematic mixed-studies synthesis (with a results-based convergent approach). Quantitative and qualitative data were initially synthesised using a narrative synthesis and thematic synthesis method, respectively, before a final meta-integration method was used to synthesise common themes across the two data forms. Results: Electronic and hand search strategies revealed 1,815 relevant studies, 40 of which met the full eligibility criteria. Narrative synthesis of quantitative data revealed six key outcome areas (quality of life; psychological well-being; cognition; engagement; activities of daily living; care-partner well-being), and thematic synthesis of qualitative data generated seven themes relating to the impact and mechanisms of singing (pragmatic elements; social benefits; mood; identity; memory; flow-on effects; and relationships). Meta-integration identified four key areas relating to the impact and mechanisms of singing for people with dementia and care-partners: psychological well-being, quality of life, cognition, and care-partner well-being. Conclusion: Results from the syntheses suggest that singing can positively impact the lives of people with dementia and their care-partners, although due to heterogeneity of study design and outcome measures, it is difficult to draw conclusions based on quantitative data alone. Qualitative data provides further context and insights from participant perspectives, and when integrated with quantitative data, contextual factors that may influence the benefits that participants experience from singing are revealed.
Podoplanin Drives Motility of Active Macrophage via Regulating Filamin C During Helicobacter pylori Infection

Podoplanin (Pdpn) is a mucin-type transmembrane protein that has been implicated in multiple physiological settings including lymphangiogenesis, platelet aggregation, and cancer metastasis. Here, we reported an absence of Pdpn transcript expression in the resting mouse monocytic macrophages, RAW264.7 cells; intriguingly, a substantial upregulation of Pdpn was observed in activated macrophages following Helicobacter pylori or lipopolysaccharide stimulation. Pdpn-knockout macrophages demonstrated intact phagocytic and intracellular bactericidal activities comparable to wild type but exhibited impaired migration due to attenuated filopodia formation. In contrast, an ectopic expression of Pdpn augmented filopodia protrusion in activated macrophages. NanoString analysis uncovered a close dependency of Filamin C gene on the presence of Pdpn, highlighting an involvement of Filamin C in modulation of actin polymerization activity, which controls cell filopodia formation and migration. In addition, interleukin-1β production was significantly declined in the absence of Pdpn, suggesting a role of Pdpn in orchestrating inflammation during H. pylori infection besides cellular migration. Together, our findings unravel the Pdpn network that modulates movement of active macrophages.