Miracle-dz/UniFAR-FTUs huggingface dataset:
Predator or provider? How wild animals respond to mixed messages from humans

Wild animals encounter humans on a regular basis, but humans vary widely in their behaviour: whereas many people ignore wild animals, some people present a threat, while others encourage animals' presence through feeding. Humans thus send mixed messages to which animals must respond appropriately to be successful. Some species appear to circumvent this problem by discriminating among and/or socially learning about humans, but it is not clear whether such learning strategies are actually beneficial in most cases. Using an individual-based model, we consider how learning rate, individual recognition (IR) of humans, and social learning (SL) affect wild animals' ability to reach an optimal avoidance strategy when foraging in areas frequented by humans. We show that ‘true’ IR of humans could be costly. We also find that a fast learning rate, while useful when human populations are homogeneous or highly dangerous, can cause unwarranted avoidance in other scenarios if animals generalize. SL reduces this problem by allowing conspecifics to observe benign interactions with humans. SL and a fast learning rate also improve the viability of IR. These results provide an insight into how wild animals may be affected by, and how they may cope with, contrasting human behaviour.
On the origin of TSAR: morphology, diversity and phylogeny of Telonemia

Telonemia is a poorly known major phylum of flagellated eukaryotes with a unique combination of morphological traits. Phylogenomics recently revealed the phylogenetic position of telonemids as sister to SAR, one of the largest groups of eukaryotes, comprising Stramenopiles, Alveolata and Rhizaria. Due to this key evolutionary position, investigations of telonemids are of critical importance for elucidating the origin and diversification of an astounding diversity of eukaryotic forms and life strategies. To date, however, only two species have been morphologically characterized from Telonemia, which do not represent this genetically very diverse group. In this study, we established cultures for six new telonemid strains, including the description of five new species and a new genus. We used these cultures to update the phylogeny of Telonemia and provide a detailed morphological and ultrastructural investigation. Our data elucidate the origin of TSAR from flagellates with complex morphology and reconstruction of the ancestral structure of stramenopiles, alveolates and rhizarians, and their main synapomorphic characters. Since telonemids are a common component of aquatic environments, the features of their feeding, behaviour and ecological preferences observed in clonal cultures and the results of global metabarcoding analysis contribute to a deeper understanding of organization of microbial food webs.
Improvement of the antibody-dependent respiratory burst assay for assessing protective immune responses to malaria

The antibody-dependent respiratory burst (ADRB) assay is a sensitive isoluminol-based chemiluminescence (CL) functional assay designed to assess the capacity of opsonizing antibodies against merozoites to induce neutrophil respiratory burst. ADRB was shown to measure protective immunity against malaria in endemic areas, but the assay needed further improvement to ensure better sensitivity and reproducibility. Here, we adjusted parameters such as the freezing–thawing procedure of merozoites, merozoites's concentration and the buffer solution's pH, and we used the improved assay to measure ADRB activity of 207 sera from 97 and 110 individuals living, respectively, in Dielmo and Ndiop villages with differing malaria endemicity. The improvement led to increased CL intensity and assay sensitivity, and a higher reproducibility. In both areas, ADRB activity correlated with malaria endemicity and individual's age discriminated groups with and without clinical malaria episodes, and significantly correlated with in vivo clinical protection from Plasmodium falciparum malaria. Our results demonstrate that the improved ADRB assay can be valuably used to assess acquired immunity during monitoring by control programmes and/or clinical trials.
COVID-19 and health inequities: the case for embracing complexity and investing in equity- and community-driven approaches to communication

COVID-19 and health inequities: the case for embracing complexity and investing in equityand community-driven approaches to communication Renata Schiavo, Gretchen Van Wye and Erma Manoncourt Editor-in-Chief; Department of Sociomedical Sciences, Columbia University Mailman School of Public Health, New York, NY, USA; Health Equity Initiative, New York, NY, USA; Strategies for Equity and Communication Impact (SECI), New York, NY, USA; New York City Department of Health and Mental Hygiene, New York, NY, USA; International Union for Health Promotion and Education (IUPHE), Paris, France; Paris School of International Affairs, Sciences Po, Paris, France; New York University School of Global Public Health, New York, NY, USA
WSCC: Social and Emotional Climate and Physical Environment

Abstract The social and emotional climate and the physical environment components of the Whole School, Whole Community, Whole Child (WSCC) model contribute to promoting a safe and nurturing learning environment in PK–12 schools. In this article, the authors review research on the social and emotional climate and the physical environment over the past decade. Recommendations for health and physical education (HPE) teachers to lead, promote, implement, and sustain these components in schools, as well as practical examples are provided. Strategies for HPE Teacher Education programs that prepare preservice teachers to lead and promote these components in schools are also presented.
Flexibility Versus Routineness in Multimodal Health Indicators: A Sensor-based Longitudinal in Situ Study of Information Workers

Although some research highlights the benefits of behavioral routines for individual functioning, other research indicates that routines can reflect an individual's inflexibility and lower well-being. Given conflicting accounts on the benefits of routine, research is needed to examine how routineness versus flexibility in health-related behaviors correspond to personality traits, health, and occupational outcomes. We adopt a nonlinear dynamical systems approach to understanding routine using automatically sensed health-related behaviors collected from 483 information workers over a roughly two-month period. We utilized multidimensional recurrence quantification analysis to derive a measure of health regularity (routineness) from measures of daily step count, sleep duration, and heart rate variability (which relates to stress). Participants also completed measures of personality, health, and job performance at the start of the study and for two months via Ecological Momentary Assessments. Greater regularity was associated with higher neuroticism, lower agreeableness, and greater interpersonal and organizational deviance. Importantly, these results were independent of overall levels of each health indicator in addition to demographics. It is often believed that routine is desirable, but the results suggest that associations with routineness are more nuanced, and wearable sensors can provide insights into beneficial health behaviors.
Clean Vibes: Hand Washing Monitoring Using Structural Vibration Sensing

We present a passive and non-intrusive sensing system for monitoring hand washing activity using structural vibration sensing. Proper hand washing is one of the most effective ways to limit the spread and transmission of disease, and has been especially critical during the COVID-19 pandemic. Prior approaches include direct observation and sensing-based approaches, but are limited in non-clinical settings due to operational restrictions and privacy concerns in sensitive areas such as restrooms. Our work introduces a new sensing modality for hand washing monitoring, which measures hand washing activity-induced vibration responses of sink structures, and uses those responses to monitor the presence and duration of hand washing. Primary research challenges are that vibration responses are similar for different activities, occur on different surfaces/structures, and tend to overlap/coincide. We overcome these challenges by extracting information about signal periodicity for similar activities through cepstrum-based features, leveraging hierarchical learning to differentiate activities on different surfaces, and denoting “primary/secondary” activities based on their relative frequency and importance. We evaluate our approach using real-world hand washing data across four different sink structures/locations, and achieve an average F1-score for hand washing activities of 0.95, which represents an 8.8X and 10.2X reduction in error over two different baseline approaches.
Hyperuricemia triggers Renal Tubular Epithelial Pyroptosis by using ROS to activate the NLRP3 inflammasome

Renal injury resulting from hyperuricemia has gained a lot of interest. Pyroptosis refers to inflammatory cell death. The activated caspase-1 cleavage, and the pivotal protein - GSDMD could have an association with the hyperuricemic kidney lesion pathogenesis. ROS is a vital NLRP3 inflammasome antagonist in various cells. We investigated the mechanism through which ROS stimulates NLRP3 to modulate pyroptosis in renal tubular epithelial cells as well as hyperuricemic rat kidneys. Methods In vitro cultured renal tubular epithelial cells (NRK-52E cells) were incubated with a gradient concentration of uric acid for 24 hr to investigate the pyroptosis through flow cytometry. Next, we used the inhibitors of ROS, mitochondrial ROS, NLRP3 and Caspase-1 respectively to intervene in uric acid treated cells to analyse pyproptosis and activation of ROS- NLRP3 inflammasome signal pathway. Finally, we evaluated the mechanism of hyperuricemia triggering renal tubular epithelial pyroptosis in rat kidney tissues. Results The levels of ROS and mitochondrial ROS, the mRNA and protein expression of pyroptosis-associated factors Caspase-1 (p45, p20/10), NLRP3, and GSDMD were upregulated in uric acid, the induced NRK-52E cells as well as hyperuricemic model kidneys. The inhibition of ROS, mitochondrial ROS, NLRP3, or caspase-1 in the uric acid-induced NRK-52E cells may help in controlling pyroptosis. The expression of mRNA and protein by the cytokines IL-18 and IL-1β also increased. Conclusions Generally, hyperuricemia triggered renal tubular epithelial pyroptosis via excessive ROS to modulate NLRP3 inflammasome activation in uric acid stimulated renal tubular epithelial cells as well as the oxonic acid potassium induced hyperuricemia.
Piezo2 expressing nociceptors mediate mechanical sensitization in experimental osteoarthritis

Osteoarthritis is characterized by mechanically driven pain but lacks adequate treatments. Here, the authors show that inhibiting a mechanically-sensitive ion channel expressed by nociceptors reduces pain behaviors in mouse models of joint pain. Non-opioid targets are needed for addressing osteoarthritis pain, which is mechanical in nature and associated with daily activities such as walking and climbing stairs. Piezo2 has been implicated in the development of mechanical pain, but the mechanisms by which this occurs remain poorly understood, including the role of nociceptors. Here we show that nociceptor-specific Piezo2 conditional knock-out mice were protected from mechanical sensitization associated with inflammatory joint pain in female mice, joint pain associated with osteoarthritis in male mice, as well as both knee swelling and joint pain associated with repeated intra-articular injection of nerve growth factor in male mice. Single cell RNA sequencing of mouse lumbar dorsal root ganglia and in situ hybridization of mouse and human lumbar dorsal root ganglia revealed that a subset of nociceptors co-express Piezo2 and Ntrk1 (the gene that encodes the nerve growth factor receptor TrkA). These results suggest that nerve growth factor-mediated sensitization of joint nociceptors, which is critical for osteoarthritic pain, is also dependent on Piezo2, and targeting Piezo2 may represent a therapeutic option for osteoarthritis pain control.
ILnc: Prioritizing Long Non-coding RNAs for Pan-cancer Analysis of Immune Cell Infiltration

The distribution and extent of immune cell infiltration into solid tumors play pivotal roles in cancer immunology and therapy. Here we introduced an immune long non-coding RNA (lncRNA) signature-based method (ILnc), for estimating the abundance of 14 immune cell types from lncRNA transcriptome data. Performance evaluation through pure immune cell data shows that our lncRNA signature sets can be more accurate than protein-coding gene signatures. We found that lncRNA signatures are significantly enriched to immune functions and pathways, such as immune response and T cell activation. In addition, the expression of these lncRNAs is significantly correlated with expression of marker genes in corresponding immune cells. Application of ILnc in 33 cancer types provides a global view of immune infiltration across cancers and we found that the abundance of most immune cells is significantly associated with patient clinical signatures. Finally, we identified six immune subtypes spanning cancer tissue types which were characterized by differences in immune cell infiltration, homologous recombination deficiency (HRD), expression of immune checkpoint genes, and prognosis. Altogether, these results demonstrate that ILnc is a powerful and exhibits broad utility for cancer researchers to estimate tumor immune infiltration, which will be a valuable tool for precise classification and clinical prediction.
Comparison of CRISPR-Cas9-mediated megabase-scale genome deletion methods in mouse embryonic stem cells

The genome contains large functional units ranging in size from hundreds of kilobases to megabases, such as gene clusters, promoter-enhancer loops, and topologically associating domains. To analyze these large functional units, the technique of deleting the entire functional unit is effective. However, deletion of such large regions is less efficient than conventional genome editing, especially in cultured cells, and a method that can ensure success is anticipated. Here, we compared methods to delete the 2.5-Mb Krüppel-associated box zinc finger protein (KRAB-ZFP) gene cluster on chromosome 4 in mouse embryonic stem cells using CRISPR/Cas9. Three methods were used: first, deletion by non-homologous end joining (NHEJ); second, homology-directed repair (HDR) using a single-stranded oligodeoxynucleotide (ssODN) with 70-bp homology arms; and third, HDR employing targeting vectors with a selectable marker and 1-kb homology arms. NHEJ-mediated deletion was achieved in 9% of the transfected cells. The deletion frequency of NHEJ and HDR was found to be comparable when the ssODN was transfected. Deletion frequency was highest when targeting vectors were introduced, with deletions occurring in 31–63% of the drug-resistant clones. Biallelic deletion was observed when targeting vectors were used. This study will serve as a benchmark for the introduction of large deletions into the genome.
Experimental study of the flow field around cube artificial reef

Effects of hollow cube artificial reefs(90° and 45°) and their compounds(parallel and vertical) on flow field have been studied by use of particle image velocimetry techniques for two-dimensional flow field testing under conditions of 6.7 cm/s,11.0 cm/s and 18.0 cm/s.The results show that the scale and intensity of upwelling field of artificial reef at the angle of 90° are larger than those at the angle of 45°;however the scale and intensity of back flow field are smaller.The effects of flow field caused by a single artificial reef are weaker than the one in parallel combination.The flow velocity distributions within the first artificial reef of the vertical combination with different spacing are similar to a single reef.The values of horizontal flow velocities within the second artificial reef are obviously smaller than a single artificial reef and increase with the vertical spacing.
Life history diversity and signals of trade-offs in a large group of chloroviruses

5 Life cycle traits shape viral evolution through their effects on epidemiology, their diversity, and their 6 trade-offs. Despite their importance, characterizations of viral life history diversity are hampered by 7 the difficulty of measuring viral phenotypes. In this study, we overcame these challenges to describe 8 the life history diversity of the genus Chlorovirus , which contains lytic dsDNA viruses that infect 9 unicellular green algae. We developed efficient methods to measure adsorption rate, depolarization 10 probability, lysis completion probability, lysis time, burst size, specific infectivity, and mortality rate. 11 We used these methods to quantify the life history traits of 35 chloroviruses from three host range 12 groups (NC64A, Osy, and SAG viruses). The trait estimates varied between 5- and 75-fold across all 13 the virus strains, with most traits varying substantially both within and across groups. We then used 14 the largest virus group in our study, the NC64A viruses ( n = 20), to look for correlations that could 15 signal trade-offs between traits. This revealed that viruses with high depolarization probabilities also 16 had higher burst sizes, but lower probabilities of completing lysis. We also found a strong negative 17 correlation between growth rate and survival. Finally, we discovered biphasic or ‘tailing’ decay in all 18 the chlorovirus groups. The nature and diversity of these traits have major implications for the 19 ecology and evolutionary potential of the chloroviruses, and reinforce the importance of studying 20 viral life histories.
Chondroitin sulfate proteoglycan 4,6 sulfation regulates sympathetic nerve regeneration after myocardial infarction

Sympathetic denervation of the heart following myocardial infarction (MI) is sustained by chondroitin sulfate proteoglycans (CSPGs) in the cardiac scar, and denervation predicts risk of sudden cardiac death. Blocking CSPG signaling restores sympathetic axon outgrowth into the cardiac scar, decreasing arrhythmia susceptibility. Axon growth inhibition by CSPGs is thought to depend on the sulfation status of the glycosaminoglycans (CS-GAGs) attached to the core protein. Tandem sulfation of CS-GAGs at the 4th (4S) and 6th (6S) positions of n-acetyl-galactosamine inhibits outgrowth in several types of neurons within the central nervous system, but it is not known if sulfation is similarly critical during peripheral nerve regeneration. We asked if CSPG sulfation prevented sympathetic axon outgrowth. Sympathetic neurite outgrowth across purified CSPGs is restored in vitro by reducing 4S with the 4-sulfatase enzyme Arylsulfatase-B (ARSB). Additionally, we co-cultured cardiac scar tissue with sympathetic ganglia ex vivo and found that reducing 4S with ARSB restored axon outgrowth to control levels. We examined levels of the enzymes responsible for adding and removing sulfation to CS-GAGs by western blot to determine if they were altered in the left ventricle after MI. We found that CHST15 (4S dependent 6-sulfotransferase) was upregulated, and ARSB was downregulated after MI. Increased CHST15 combined with decreased ARSB suggests a mechanism for production and maintenance of sulfated CSPGs in the cardiac scar. We altered tandem sulfated 4S,6S CS-GAGs in vivo by transient siRNA knockdown of Chst15 and found that reducing 4S,6S restored Tyrosine Hydroxylase (TH) positive sympathetic nerve fibers in the cardiac scar after MI and reduced arrhythmias. Overall, our results suggest that modulating CSPG-sulfation after MI may be a therapeutic target to promote sympathetic nerve regeneration in the cardiac scar and reduce post-MI cardiac arrhythmias.
Effects of an IgE receptor polymorphism acting on immunity, susceptibility to infection, and reproduction in a wild rodent

The genotype of an individual is an important predictor of their immune function, and subsequently, their ability to control or avoid infection and ultimately contribute offspring to the next generation. However, the same genotype, subjected to different intrinsic and/or extrinsic environments can also result in different phenotypic outcomes, which can be missed in controlled laboratory studies. Natural wildlife populations, which capture both genotypic and environmental variability, provide an opportunity to more fully understand the phenotypic expression of genetic variation. We identified a synonymous polymorphism in the high-affinity Immunoglobulin E (IgE) receptor (GC and non-GC haplotypes) that has sex-dependent effects on immune gene expression, susceptibility to infection and reproductive success of individuals in a natural population of field voles (Microtus agrestis). We found that the effect of the GC haplotype on the expression of immune genes differed between sexes. While males with the GC haplotype had upregulated more pro-inflammatory genes, including the cytokine Il33, females had upregulated more anti-inflammatory genes, including the cytokine inhibitor Socs3. Furthermore we found an effect of the GC haplotype on the probability of infection with a common microparasite, Babesia microti, in females - with females carrying the GC haplotype being more likely to be infected. Finally, we found an effect of the GC haplotype on reproductive success in males - with males carrying the GC haplotype having a lower reproductive success. This is a rare example of a polymorphism whose consequences we are able to follow across immunity, infection and reproduction for both males and females in a natural population.
Experimental study of bond-slip performance of corroded reinforced concrete under cyclic loading

Reinforced concrete structures exposed to marine environment often sustain high levels of chloride-induced reinforcement corrosion, which causes reinforcement corrosion and resulting in degraded performance under cyclic service loading. This article studied the dynamic bond performance between corroded reinforcing and concrete under force controlled loading. Tests were carried out to evaluate the cyclic bond-slip degradation with different reinforcement corrosion levels. A series of 30 specimens with various corrosion levels of rebar and stirrup were made. The specimen was cast as concrete cube with the dimension of 200 mm, and a steel rebar was centrally embedded with two stirrups around. The embedded steel rebar and stirrups were corroded using an electrochemical accelerated corrosion technique. The corrosion crack opening width and length were recorded after completion of artificial corrosion. Then, cyclic loading test was carried out; three different force levels of 24, 36, and 48 kN were adopted. The effects of reinforcement corrosion rate on crack opening, maximum slip, energy dissipation, and unloading stiffness were discussed in detail. It was found that both reinforcement corrosion rate and crack opening would have significant effects on cyclic bond performance. Further studies are urgently needed to quantify these effects to the cyclic bond performance.