Miracle-dz/UniFAR-FTUs huggingface dataset:
How Our Perception and Confidence Are Altered Using Decision Cues

Understanding how individuals utilize social information while making perceptual decisions and how it affects their decision confidence is crucial in a society. To date, very little has been known about perceptual decision-making in humans and the associated neural mediators under social influence. The present study provides empirical evidence of how individuals are manipulated by others' decisions while performing a face/car identification task. Subjects were significantly influenced by what they perceived as the decisions of other subjects, while the cues, in reality, were manipulated independently from the stimulus. Subjects, in general, tend to increase their decision confidence when their individual decision and the cues coincide, while their confidence decreases when cues conflict with their individual judgments, often leading to reversal of decision. Using a novel statistical model, it was possible to rank subjects based on their propensity to be influenced by cues. This was subsequently corroborated by an analysis of their neural data. Neural time series analysis revealed no significant difference in decision-making using social cues in the early stages, unlike neural expectation studies with predictive cues. Multivariate pattern analysis of neural data alludes to a potential role of the frontal cortex in the later stages of visual processing, which appeared to code the effect of cues on perceptual decision-making. Specifically, the medial frontal cortex seems to play a role in facilitating perceptual decision preceded by conflicting cues.
Treg Heterogeneity, Function, and Homeostasis

T-regulatory cells (Tregs) represent a unique subpopulation of helper T-cells by maintaining immune equilibrium using various mechanisms. The role of T-cell receptors (TCR) in providing homeostasis and activation of conventional T-cells is well-known; however, for Tregs, this area is understudied. In the last two decades, evidence has accumulated to confirm the importance of the TCR in Treg homeostasis and antigen-specific immune response regulation. In this review, we describe the current view of Treg subset heterogeneity, homeostasis and function in the context of TCR involvement. Recent studies of the TCR repertoire of Tregs, combined with single-cell gene expression analysis, revealed the importance of TCR specificity in shaping Treg phenotype diversity, their functions and homeostatic maintenance in various tissues. We propose that Tregs, like conventional T-helper cells, act to a great extent in an antigen-specific manner, which is provided by a specific distribution of Tregs in niches.
A Digital Hardware System for Spiking Network of Tactile Afferents

In the present research, we explore the possibility of utilizing a hardware-based neuromorphic approach to develop a tactile sensory system at the level of first-order afferents, which are slowly adapting type 1 (SA-I) and fast adapting type 1 (FA-I) afferents. Four spiking models are used to mimic neural signals of both SA-I and FA-I primary afferents. Next, a digital circuit is designed for each spiking model for both afferents to be implemented on the field-programmable gate array (FPGA). The four different digital circuits are then compared from source utilization point of view to find the minimum cost circuit for creating a population of digital afferents. In this way, the firing responses of both SA-I and FA-I afferents are physically measured in hardware. Finally, a population of 243 afferents consisting of 90 SA-I and 153 FA-I digital neuromorphic circuits are implemented on the FPGA. The FPGA also receives nine inputs from the force sensors through an interfacing board. Therefore, the data of multiple inputs are processed by the spiking network of tactile afferents, simultaneously. Benefiting from parallel processing capabilities of FPGA, the proposed architecture offers a low-cost neuromorphic structure for tactile information processing. Applying machine learning algorithms on the artificial spiking patterns collected from FPGA, we successfully classified three different objects based on the firing rate paradigm. Consequently, the proposed neuromorphic system provides the opportunity for development of new tactile processing component for robotic and prosthetic applications.
Cellular Metrology: Scoping for a Value Proposition in Extra- and Intracellular Measurements

The symptomatic irreproducibility of data in biomedicine and biotechnology prompts the need for higher order measurements of cells in their native and near-native environments. Such measurements may support the adoption of new technologies as well as the development of research programs across different sectors including healthcare and clinic, environmental control and national security. With an increasing demand for reliable cell-based products and services, cellular metrology is poised to help address current and emerging measurement challenges faced by end-users. However, metrological foundations in cell analysis remain sparse and significant advances are necessary to keep pace with the needs of modern medicine and industry. Herein we discuss a role of metrology in cell and cell-related R&D activities to underpin growing international measurement capabilities. Relevant measurands are outlined and the lack of reference methods and materials, particularly those based on functional cell responses in native environments, is highlighted. The status quo and current challenges in cellular measurements are discussed in the light of metrological traceability in cell analysis and applications (e.g., a functional cell count). An emphasis is made on the consistency of measurement results independent of the analytical platform used, high confidence in data quality vs. quantity, scale of measurements and issues of building infrastructure for end-users.
Complement Receptor-Mediated Phagocytosis Induces Proinflammatory Cytokine Production in Murine Macrophages

Macrophages are professional phagocytes that are uniquely situated between the innate and adaptive arms of immunity with a high capacity for phagocytosis and proinflammatory cytokine production as well as antigen presentation. Phagocytosis is a critical process to eliminate microbes, apoptotic cells and other foreign particles and is accelerated by host-generated opsonins, such as antibodies and complement. Early phagocytosis studies established the paradigm that FcγR-mediated phagocytosis was more proinflammatory than Complement Receptor (CR)-mediated uptake in macrophages. Using qPCR, cytokine antibody arrays and ELISA, we revisited this research question in primary macrophages. Using qPCR we determined that CR-mediated phagocytosis increases levels of TNF-α, IL-1β, IL-6, and MMP-9, compared to FcγR-mediated phagocytosis and control unstimulated cells. We confirmed these findings at the protein level using cytokine antibody arrays and ELISAs. We next investigated the mechanism behind upregulated cytokine production during CR-mediated phagocytosis. IκBα protein levels were reduced after phagocytosis of both IgG- and C3bi-sRBCs indicating proteolytic degradation and implicating NF-κB activation. Inhibition of NF-κB activation impacted IL-6 production during phagocytosis in macrophages. Due to the roles of calpain in IκBα and integrin degradation, we hypothesized that CR-mediated phagocytosis may utilize calpain for proinflammatory mediator enhancement. Using qPCR and cytokine antibody array analysis, we saw significant reduction of cytokine expression during CR-mediated phagocytosis following the addition of the calpain inhibitor, PD150606, compared to untreated cells. These results suggest that the upregulation of proinflammatory mediators during CR-mediated phagocytosis is potentially dependent upon calpain-mediated activation of NF-κB.
Impacts of Temperature, CO2, and Salinity on Phytoplankton Community Composition in the Western Arctic Ocean

The Arctic Ocean has been experiencing rapid warming, which accelerates sea ice melt. Further, the increasing area and duration of sea ice-free conditions enhance ocean uptake of CO2. We conducted two shipboard experiments in September 2015 and 2016 to examine the effects of temperature, CO2, and salinity on phytoplankton dynamics to better understand the impacts of rapid environmental changes on the Arctic ecosystem. Two temperature conditions (control: <3 and 5°C above the control), two CO2 levels (control: ∼300 and 300/450 μatm above the control; i.e., 600/750 μatm), and two salinity conditions (control: 29 in 2015 and 27 in 2016, and 1.4 below the control) conditions were fully factorially manipulated in eight treatments. Higher temperatures enhanced almost all phytoplankton traits in both experiments in terms of chl-a, accessory pigments and diatom biomass. The diatom diversity index decreased due to the replacement of chain-forming Thalassiosira spp. by solitary Cylindrotheca closterium or Pseudo-nitzschia spp. under higher temperature and lower salinity in combination. Higher CO2 levels significantly increased the growth of small-sized phytoplankton (<10 μm) in both years. Decreased salinity had marginal effects but significantly increased the growth of small-sized phytoplankton under higher CO2 levels in terms of chl-a in 2015. Our results suggest that the smaller phytoplankton tend to dominate in the shelf edge region of the Chukchi Sea in the western Arctic Ocean under multiple environmental perturbations.
Minimum Time Dose in Nature to Positively Impact the Mental Health of College-Aged Students, and How to Measure It: A Scoping Review

Background: Across the U.S., college and university students exhibit high levels of stress, anxiety, depression, and other mental health issues. While counseling, medications and, in more severe cases, hospitalization are all appropriate treatments for such conditions, an increasing body of evidence has demonstrated that spending time in nature can provide tangible benefits for mental health and well-being. The aim of this study was to define a “dose” of time in nature that could be prescribed to college-age students, as a preventative and supportive mental health and well-being intervention. The specific objectives of this scoping review were thus: to define the minimum amount of time in nature that results in positive impact on mental health and well-being for college-aged students; to describe the types of engagement with nature that elicited the impact; and to describe and explore the most commonly used measure of effect pre- and post-time in nature. Methods: This scoping review was conducted following the PRISMA-ScR Checklist. A review protocol was developed but not registered. Fourteen bibliographic databases were searched and all results were blindly screened using established inclusion criteria. All titles and abstracts were screened by at least two reviewers, a third being used as a tie-breaker if needed. Studies were included if: subjects were of average college age; they examined a treatment of time (hours or minutes) in nature; they examined change in measures of mental health and well-being pre- and post-exposure; they compared participants across at least two environments; the study was published in English or French; and if the study was <20 years old. Results: Initially, 11,799 titles were identified and once de-duplicated, 10,917 titles were screened. One hundred fifty-five papers were given full text reviews, of which 14 studies were included in this review. In summary, 13 of the 14 papers explicitly noted that the participants were college students. Two-thirds of the studies (n = 10) took place in Japan. One study took place in Sweden, and the remaining studies took place in the United States (n = 3). These studies show that, when contrasted with equal durations spent in urbanized settings, as little as 10 min of sitting or walking in a diverse array of natural settings significantly and positively impacted defined psychological and physiological markers of mental well-being for college-aged individuals. Within the included studies, 22 different measures were used to assess the effects of nature doses on mental health and well-being. Conclusions: This review provides time-dose and activity-type evidence for programs looking to use time in nature as a preventative measure for stress and mental health strain, and also demonstrates opportunities in six specific foci for more research in this area.
Prebiotic Driven Increases in IL-17A Do Not Prevent Campylobacter jejuni Colonization of Chickens

Worldwide Campylobacter jejuni is a leading cause of foodborne disease. Contamination of chicken meat with digesta from C. jejuni-positive birds during slaughter and processing is a key route of transmission to humans through the food chain. Colonization of chickens with C. jejuni elicits host innate immune responses that may be modulated by dietary additives to provide a reduction in the number of campylobacters colonizing the gastrointestinal tract and thereby reduce the likelihood of human exposure to an infectious dose. Here we report the effects of prebiotic galacto-oligosaccharide (GOS) on broiler chickens colonized with C. jejuni when challenged at either an early stage in development at 6 days of age or 20 days old when campylobacters are frequently detected in commercial flocks. GOS-fed birds had increased growth performance, but the levels of C. jejuni colonizing the cecal pouches were unchanged irrespective of the age of challenge. Dietary GOS modulated the immune response to C. jejuni by increasing cytokine IL-17A expression at colonization. Correspondingly, reduced diversity of the cecal microbiota was associated with Campylobacter colonization in GOS-fed birds. In birds challenged at 6 days-old the reduction in microbial diversity was accompanied by an increase in the relative abundance of Escherichia spp. Whilst immuno-modulation of the Th17 pro-inflammatory response did not prevent C. jejuni colonization of the intestinal tract of broiler chickens, the study highlights the potential for combinations of prebiotics, and specific competitors (synbiotics) to engage with the host innate immunity to reduce pathogen burdens.
Negotiation of Parental Duties in Chick-Rearing Common Murres (Uria aalge) in Different Foraging Conditions

Mates of biparental species share parental care but they are also predicted to try, within limits, to push for more offspring care from their partners. Here we test (a) whether mates will attempt to exploit their partners less often when resources are scarce so as to not push their partners to their abandonment threshold and (b) whether there are differences in exploitation and compensation strategies of low and high quality partners where the quality assessment is based on within-pair differences in chick-provisioning rates. The same 14 pairs of common murres were observed in a year when capelin fish (the main prey species) were abundant (match year) and in a second year when capelin did not arrive inshore to spawn until the second week after hatching (mismatch year). One murre parent always attends the chick and, in the most common type of interaction, the returning parent feeds the chick, and takes over the brooding role. We consider nest relief interactions to be irregular if they did not follow this sequence for determining which parent will continue or take on the lower-energy brooder role. Two types of irregular nest reliefs were examined: (a) the returning bird does not bring a fish and (b) the brooding bird does not allow a brooding changeover even when the returner brings a fish. Rates of irregular nest reliefs and total visit time increased in the mismatch year after capelin arrived inshore, suggesting that longer co-attendance in good conditions reflects negotiation, rather than the increased resting or “loafing” time as previously proposed. High provisioners initiated fewer irregular nest reliefs than their low provisioning partners during favorable conditions but increased to comparable levels when resources were scarce. Partners' attempts to brood without provisioning were less often refused during unfavorable feeding conditions, suggesting that murres compensated for their mates when they could. The observation that rates of irregular nest reliefs changed with resource availability suggests that negotiation occurs throughout chick rearing and is not a set “sealed bid” at the onset.
Visceral Adiposity and Diet Quality Are Differentially Associated With Cognitive Abilities and Early Academic Skills Among Preschool-Age Children

Background: Visceral adipose tissue (VAT) and diet quality influence cognitive health in preadolescents; however, these relationships remain understudied among preschool-age children. Objectives: Investigate the relationship between VAT, diet quality, academic skills, and cognitive abilities among preschool-age children. Methods: Children between 4 and 5 years (N = 57) were enrolled in a cross-sectional study. Woodcock Johnson Early Cognitive and Academic Development Test (ECAD™) was utilized to assess General Intellectual Ability, Early Academic Skills, and Expressive Language. DXA was used to assess VAT. Diet quality was measured using the Healthy Eating Index-2015 (HEI-2015) based on 7-day food records. Results: Greater VAT was associated with poorer Early Academic Skills (r = −0.28, P = 0.03) whereas a diet pattern that included Fatty Acids, Whole Grains, Saturated Fats, Seafood and Plant Proteins, Total Vegetables, and Dairy was positively associated with General Intellectual Ability (r = 0.26, P = 0.04). Conclusions: Higher VAT is negatively related to Early Academic Skills whereas diet quality was positively and selectively related to intellectual abilities among preschool-age children. These findings indicate that the negative impact of abdominal adiposity on academic skills is evident as early as preschool-age while providing preliminary support for the potentially beneficial role of diet quality on cognitive abilities in early childhood.
Metabolomic Analysis Reveals Contributions of Citric and Citramalic Acids to Rare Earth Bioleaching by a Paecilomyces Fungus

Conventional methods for extracting rare earth elements from monazite ore require high energy inputs and produce environmentally damaging waste streams. Bioleaching offers a potentially more environmentally friendly alternative extraction process. In order to better understand bioleaching mechanisms, we conducted an exo-metabolomic analysis of a previously isolated rare earth bioleaching fungus from the genus Paecilomyces (GenBank accession numbers KM874779 and KM 874781) to identify contributions of compounds exuded by this fungus to bioleaching activity. Exuded compounds were compared under two growth conditions: growth with monazite ore as the only phosphate source, and growth with a soluble phosphate source (K2HPO4) added. Overall metabolite profiling, in combination with glucose consumption and biomass accumulation data, reflected a lag in growth when this organism was grown with only monazite. We analyzed the relationships between metabolite concentrations, rare earth solubilization, and growth conditions, and identified several metabolites potentially associated with bioleaching. Further investigation using laboratory prepared solutions of 17 of these metabolites indicated statistically significant leaching contributions from both citric and citramalic acids. These contributions (16.4 and 15.0 mg/L total rare earths solubilized) accounted for a portion, but not all, of the leaching achieved with direct bioleaching (42 ± 15 mg/L final rare earth concentration). Additionally, citramalic acid released significantly less of the radioactive element thorium than did citric acid (0.25 ± 0.01 mg/L compared to 1.18 ± 0.01 mg/L), suggesting that citramalic acid may have preferable leaching properties for a monazite bioleaching process.
Conversion Surgery for Pancreatic Cancer—The Impact of Neoadjuvant Treatment

Pancreatic ductal adenocarcinoma (PDAC) has still a dismal prognosis, mainly because only 15–20% of all patients present with resectable tumor stages at the time of diagnosis. Due to locally extended tumor growth or distant metastases upfront resection is not reasonable in the majority of patients. Considerably, PDAC will be the 2nd most frequent cause of cancer-related deaths within the next 10 years for both men and women. While there is currently no convincing evidence for the use of neoadjuvant therapy in resectable PDAC, there are controversial results from studies investigating neoadjuvant treatment concepts in borderline resectable PDAC (BR-PDAC). However, the definition of BR-PDAC is a topic of debate. While BR-PDAC has originally been defined on merely anatomical criteria, the International Association of Pancreatology (IAP) has recently suggested a broader definition based on a combination of anatomical (A) findings, biological (B) criteria (which reflect tumor aggressiveness), and conditional (C) aspects (which respect host-related condition). In case of BR-PDAC with venous invasion alone, upfront resection is generally recommended whenever technically possible in patients fit for surgery and without evidence for lymph node metastases. In contrast, in case of arterial invasion neoadjuvant therapy is regarded as the treatment of choice. The same accounts for high CA 19-9 levels, suspected or proven lymph node involvement and poor performance status. In locally advanced PDAC (LA-PDAC), neoadjuvant treatment represents the standard of care resulting in proportionally high rates of secondary resection. This “conversion” surgery offers the chance for improved survival times in an otherwise palliative situation. Herein, we summarize the current evidence of different treatment strategies for pancreatic cancer with a focus on conversion surgery and the impact of neoadjuvant treatment in this setting.
Chitinases of Bacillus thuringiensis: Phylogeny, Modular Structure, and Applied Potentials

The most important bioinsecticide used worldwide is Bacillus thuringiensis and its hallmark is a rich variety of insecticidal Cry protein, many of which have been genetically engineered for expression in transgenic crops. Over the past 20 years, the discovery of other insecticidal proteins and metabolites synthesized by B. thuringiensis, including chitinases, antimicrobial peptides, vegetative insecticidal proteins (VIP), and siderophores, has expanded the applied value of this bacterium for use as an antibacterial, fungicidal, and nematicidal resource. These properties allow us to view B. thuringiensis not only as an entity for the production of a particular metabolite, but also as a multifaceted microbial factory. In particular, chitinases of B. thuringiensis are secreted enzymes that hydrolyze chitin, an abundant molecule in the biosphere, second only to cellulose. The observation that chitinases increase the insecticidal activity of Cry proteins has stimulated further study of these enzymes produced by B. thuringiensis. Here, we provide a review of a subset of our knowledge of B. thuringiensis chitinases as it relates to their phylogenetic relationships, regulation of expression, biotechnological potential for controlling entomopathogens, fungi, and nematodes, and their use in generating chitin-derived oligosaccharides (ChOGs) that possess antibacterial activities against a number of clinically significant bacterial pathogens. Recent advances in the structural organization of these enzymes are also discussed, as are our perspective for future studies.