Miracle-dz/UniFAR-FTUs huggingface dataset:
Variations in Chlorophyll Fluorescence Yields in Phytoplankton in the World Oceans

The ocean is optically thin and lends itself to large-scale measurements of in vivo chlorophyll fluorescence. In the open ocean, however, phytoplankton chlorophyll concentrations average only 0.2 μg L-1, and hence high sensitivity is required for precise measurements of the fluorescence yields. Over the past decade, we have developed two approaches to achieve the required sensitivity; these are the pump- and probe-technique and a fast repetition rate (FRR) method. Both methods have been adapted for in situ studies and are used to rapidly measure the maximum change in the quantum yield (ΔOmax) of photosystem II (PSII), as well as the effective absorption cross-section of PSII (σPSII). Sections of variable fluorescence across the Pacific and Atlantic Oceans reveal the influence of geophysical processes in controlling the quantum yields of phytoplankton photosynthesis. Areas of upwelling, such as off the coast of north-westem Africa, have Fv/Fm values of 0.65, which are close to the maximum achievable values in nutrient-replete cultures. Throughout most of the nutrient-deficient central ocean basins, this quantum efficiency is reduced by more than 50%. In high-nutrient, low- chlorophyll regions of the eastern Equatorial Pacific, the deliberate, large-scale addition of nanomolar iron directly to the ocean leads to a rapid increase in quantum efficiency of the natural phytoplankton community, thereby revealing that in these regions phytoplankton photosynthetic energy conversion efficiency is iron limited. Diel patterns of variation in the upper ocean display midday, intensity- dependent reductions in both upsII and AOmax. We interpret the former as indicative of non- photochemical quenching in the antenna, while the latter is a consequence of both rapidly reversible and slowly reversible damage to reaction centres. From knowledge of the incident spectral irradiance, ΔOmax, σPSII, and photochemical quenching, the absolute photosynthetic electron transport rate can be derived in real-time. Using unattended, moored continuous measurements of in vivo fluorescence parameters, the derived in situ electron transport rates can be related to satellite observations of the global ocean with basin-scale, seasonal estimates of phytoplankton carbon fixation. Thus, unlike any other photosynthetic parameter, chlorophyll fluorescence can be used to bridge the scales of biophysical responses to ecosystem dynamics.
Mitochondrial genomes of stick insects (Phasmatodea) and phylogenetic considerations

Phasmatodea represents an order of hemimetabolous insects. This group includes species with extreme forms of masquerade crypsis, whereby they imitate twigs, bark, lichen, moss, and leaves. In this study, we sequenced and annotated three mitochondrial genomes (mitogenomes) from Phasmatodea. The lengths of the novel mitogenomes range from 14,162 bp to 15,879 bp. The gene content and organization correspond to those inferred for the ancestral insect. We conducted phylogenetic analyses together with the existing mitogenomes of polyneopterans and mayflies. In most cases, the Phasmatodea was non-monophyletic, with Embioptera and Zoraptera nested inside. The mitogenome sequences from Embioptera and Zoraptera suffered from high substitution rates and displayed very long branches in phylogenetic trees. The monophyletic Phasmatodea was recovered only when the analysis employed the site-heterogeneous CAT-GTR model in PhyloBayes and used the nucleotide dataset PCG_nt. The Euphasmatodea was well established by various data types and inference methods. In addition, the clade Heteropterygidae and the subfamilies Lonchodinae and Necrosciinae were strongly supported. The Australasian clade Lanceocercata was recovered across analyses. However, the Clitumninae was non-monophyletic.
Material constancy in perception and working memory

A key challenge for the visual system entails the extraction of constant properties of objects from sensory information that varies moment by moment due to changes in viewing conditions. Although successful performance in constancy tasks requires cooperation between perception and working memory, the function of the memory system has been under-represented in recent material perception literature. Here, we addressed the limits of material constancy by elucidating if and how working memory is involved in constancy tasks by using a variety of material stimuli, such as metals, glass, and translucent objects. We conducted experiments with a simultaneous and a successive matching-to-sample paradigm in which participants matched the perceived material properties of objects with or without a temporal delay under varying illumination contexts. The current study combined a detailed analysis of matching errors, data on the strategy use obtained via a self-report questionnaire, and the statistical image analysis of diagnostic image cues used for material discrimination. We found a comparable material constancy between simultaneous and successive matching conditions, and it was suggested that, in both matching conditions, participants used similar information processing strategies for the discrimination of materials. The study provides converging evidence on the critical role of working memory in material constancy, where working memory serves as a shared processing bottleneck that constrains both simultaneous and successive material constancy.
Facing the Facets: No Association Between Dispositional Mindfulness Facets and Positive Momentary Stress Responses During Active Stressors

Mindfulness has been associated with enhanced coping with stress. However, it remains unclear how dispositional mindfulness impacts the nature and valence of experiences during active stressors. Across 1,001 total participants, we used cardiovascular responses from the biopsychosocial model of challenge/threat to assess the degree to which individuals cared about a stressor in the moment and had a positive versus negative psychological experience. Although we found a small association between mindfulness—particularly the acting with awareness facet—and responses consistent with caring more about the stressor (i.e., greater task engagement), we found no evidence that mindfulness was associated with exhibiting a more positive psychological response (i.e., greater challenge) during the stressor. Despite no differences in the valence of momentary experiences as a function of mindfulness, individuals higher in mindfulness self-reported more positive experiences afterward. These findings suggest that dispositional mindfulness may benefit responses to active stressors only after they have passed.
B-vitamins and metabolic syndrome in Mesoamerican children and their adult parents

Abstract Objective: To examine the associations between vitamins of the methionine-homocysteine (Hcys) cycle (B6, B12 and folate) and Hcys with metabolic syndrome (MetS) among Mesoamerican children and their adult parents. Design: We conducted a cross-sectional study. Exposures were plasma vitamins B6 and B12 concentrations, erythrocyte folate and plasma Hcys. In children, the outcome was a continuous metabolic risk score calculated through sex- and age standardisation of waist circumference, the homoeostatic model assessment for insulin resistance, mean arterial pressure (MAP), serum HDL-cholesterol and serum TAG. In parents, the outcome was the prevalence of MetS according to the Adult Treatment Panel III Criteria. We estimated mean differences in the metabolic risk score and prevalence ratios of MetS between quartiles of the exposures using multivariable-adjusted linear and Poisson regression models, respectively. Setting: Capital cities of Belize, Guatemala, El Salvador, the Dominican Republic, Honduras, Nicaragua, Panama, Costa Rica and Chiapas State in Mexico. Participants: In total, 237 school-aged children and 524 parents. Results: Among children, vitamin B12 was inversely associated with the metabolic risk score (quartiles 4–1 adjusted difference = –0·13; 95 % CI: –0·21, –0·04; P trend = 0·008) through MAP, HDL-cholesterol and TAG. In contrast, folate was positively associated with the metabolic risk score (quartiles 4–1 adjusted difference = 0·11; 95 % CI: 0·01, 0·20; P trend = 0·02). In adults, vitamin B6 was inversely associated with MetS prevalence, whereas vitamin B12 and folate were positively related to this outcome. Conclusions: Vitamins of the methionine-Hcys cycle are associated with MetS in different directions. The associations differ between children and adults.
Chicken Infectious Anemia Status in Commercial Broiler Chickens Flocks in Assiut-upper Egypt: Occurrence, Molecular Analysis Using PCR-RFLP and Apoptosis Effect on Affected Tissues

Chicken infectious anemia virus is ubiquitous virus of chickens causing disease in young chickens and immunosuppression in all birds. In the present study, the presence of chicken anemia virus CAV infection using PCR, genetic variability of isolated strains based on restriction of VP1 gene by Mbo1 and apoptotic changes in the CAV positive broiler chickens in Assiut region, Upper of Egypt, were investigated. The history of problem showed that the clinical features were depression, increased susceptibility to various diseases, vaccination failure and mortalities ranged from 4-21%. Postmortem findings were pale liver, atrophy of thymus and hemorrhages subcutaneously. These findings strongly suggested that CIAV may be the cause of the problem. DNA was extracted from thymus and bursa of fabricius of the collected birds and exposed to PCR assay. A total of 44 Chicken Infectious Anemia Virus (CIAV)DNA was detected genetically from 165 broiler chickens of age up to 7 weeks with a percentage 26.6%, which can be considered high and thus, reflects an attention demanding situation. The data show that restriction endonuclease analysis performed with the 1350-bp PCR product and the Mbo I enzyme indicated genetic variations among examined field isolates that two variants of the viruses having differences at genomic level were causing the disease in closely related regions of the province. Twenty five thymuses were collected and processed for DNA extraction. Cellular DNA was subjected to electrophoresis on 1.5% agarose gel and stained with ethidium bromide. Internucleosomal DNA fragmentation was detected in CIAV-infected tissues. These data indicated that infection with CIAV induced apoptosis in lymphoid cells that may affect solely on cellular immunity. Present findings thus highlights the significance of CIAV, therefore, focus should be made on CIAV epidemiology in the Upper Egypt and to further develop and apply reliable diagnostic tools as well as molecular studies so as to advise suitable prevention strategies for this economical important avian pathogen.
‘Diabetes doesn’t matter as long as we’re keeping traditions alive’: a qualitative study exploring the knowledge and awareness of Type 2 diabetes and related risk factors amongst the young Punjabi Sikh population in the UK

ABSTRACT Objectives: It is well known that Sikhs are at an increased risk of Type 2 Diabetes (T2DM) due to a genetic predisposition. High level of education is associated with lower incidence of T2DM. Young Sikhs are well educated compared to other South Asian sub-groups. Despite this, T2DM rates remain high in Sikhs. The uptake of preventative services is also low within Sikhs. At present, no research has been conducted with the young Punjabi Sikh population on diabetes awareness in the UK. To address this gap, this study explores the knowledge and awareness of T2DM and related modifiable risk factors in the UK Punjabi Sikh community. Views surrounding T2DM health-seeking behaviours are also explored. Design: A qualitative design comprising of 1-to-1 semi-structured interviews was adopted. Thirteen Punjabi Sikh participants between the ages of 18–30 took part. Participants were recruited through a Sikh temple and University of Manchester Sikh Society using purposive and snowball sampling in West Yorkshire and North West England. Data were analysed using inductive thematic analysis taking a critical realist stance. Results: Three themes were identified: (1) Perceptions of the causes of T2DM, (2) Perceptions of factors impacting physical activity and diet, and (3) Attitudes towards health-seeking behaviours. Conclusions: The findings show that although well educated, participants overlooked physical activity as contributing factor towards T2DM onset. Additionally, gender and cultural norms influenced physical activity and diet, as these are passed through generations to preserve the collectivist Sikh culture. Exploration of health seeking behaviours also found young Punjabi Sikhs perceived the internet to be the preferred tool to seek T2DM information. These findings hold implications for health professionals, as the information and preventative services provided to Sikhs can be tailored to be culturally appropriate and in line with cultural and gender norms, such as bhangra dancing for physical activity.
Intracranial vessel wall lesions on 7T MRI and MRI features of cerebral small vessel disease: The SMART-MR study

The etiology of cerebral small vessel disease (CSVD) is the subject of ongoing research. Although intracranial atherosclerosis (ICAS) has been proposed as a possible cause, studies on their relationship remain sparse. We used 7 T vessel wall magnetic resonance imaging (MRI) to study the association between intracranial vessel wall lesions—a neuroimaging marker of ICAS—and MRI features of CSVD. Within the SMART-MR study, cross-sectional analyses were performed in 130 patients (68 ± 9 years; 88% male). ICAS burden—defined as the number of vessel wall lesions—was determined on 7 T vessel wall MRI. CSVD features were determined on 1.5 T and 7 T MRI. Associations between ICAS burden and CSVD features were estimated with linear or modified Poisson regression, adjusted for age, sex, vascular risk factors, and medication use. In 125 patients, ≥1 vessel wall lesions were found (mean 8.5 ± 5.7 lesions). ICAS burden (per + 1 SD) was associated with presence of large subcortical and/or cortical infarcts (RR = 1.65; 95%CI: 1.12–2.43), lacunes (RR = 1.45; 95% CI: 1.14–1.86), cortical microinfarcts (RR = 1.48; 95%CI: 1.13–1.94), and total white matter hyperintensity volume (b = 0.24; 95%CI: 0.02–0.46). Concluding, patients with a higher ICAS burden had more CSVD features, although no evidence of co-location was observed. Further longitudinal studies are required to determine if ICAS precedes development of CSVD.
Lack of airway submucosal glands impairs respiratory host defenses

Submucosal glands (SMGs) are a prominent structure that lines human cartilaginous airways. Although it has been assumed that SMGs contribute to respiratory defense, that hypothesis has gone without a direct test. Therefore, we studied pigs, which have lungs like humans, and disrupted the gene for ectodysplasin (EDA-KO), which initiates SMG development. EDA-KO pigs lacked SMGs throughout the airways. Their airway surface liquid had a reduced ability to kill bacteria, consistent with SMG production of antimicrobials. In wild-type pigs, SMGs secrete mucus that emerges onto the airway surface as strands. Lack of SMGs and mucus strands disrupted mucociliary transport in EDA-KO pigs. Consequently, EDA-KO pigs failed to eradicate a bacterial challenge in lung regions normally populated by SMGs. These in vivo and ex vivo results indicate that SMGs are required for normal antimicrobial activity and mucociliary transport, two key host defenses that protect the lung.
Effect of RvD1/FPR2 on inflammatory response in chorioamnionitis

Chorioamnionitis (CAM), as a common intrauterine infectious disease, is the leading cause of premature birth, stillbirth, neonatal infection and sepsis. The formyl peptide receptor 2 (FPR2) is a member of GPCRs widely distributed in a variety of tissues and is associated with many inflammatory diseases. With the discovery of FPR2 in human placenta, the possibility of exploring the function of FPR2 in obstetrics is evolving. The Resolvin D1 (RvD1) plays an important role in the resolution of inflammation by combining with FPR2. In this study, we evaluated the role of FPR2 and RvD1 in CAM, not only in the human placenta but also in mouse models. The expression of FPR2 increased in the placenta of CAM patients and the downstream PPARγ/NF‐κB signalling changed accordingly. Moreover, Fpr2−/− mice were highly susceptible to LPS, displaying a worse CAM symptom, compared with WT mice. By establishing a model of trophoblast inflammation in vitro, it was confirmed that RvD1 rescued the effect of LPS on inflammation by combining with FPR2 and its downstream PPARγ/NF‐κB pathway. Otherwise, RvD1 improved the preterm labour in a mouse model of CAM induced by LPS. Altogether, these findings show that RvD1 alleviated the inflammation of trophoblast in vivo and in vitro through FPR2/PPARγ/NF‐κB pathway, suggesting RvD1/FPR2 might be a novel therapeutic strategy to alleviate CAM.
Actions of FTY720 (Fingolimod), a Sphingosine-1-Phosphate Receptor Modulator, on Delayed-Rectifier K+ Current and Intermediate-Conductance Ca2+-Activated K+ Channel in Jurkat T-Lymphocytes

FTY720 (fingolimod), a modulator of sphingosine-1-phosphate receptors, is known to produce the immunomodulatory actions and to be beneficial for treating the relapsing multiple sclerosis. However, whether it exerts any effects on membrane ion currents in immune cells remains largely unknown. Herein, the effects of FTY720 on ionic currents in Jurkat T-lymphocytes were investigated. Cell exposure to FTY720 suppressed the amplitude of delayed-rectifier K+ current (IK(DR)) in a time- and concentration-dependent manner with an IC50 value of 1.51 μM. Increasing the FTY720 concentration not only decreased the IK(DR) amplitude but also accelerated the inactivation time course of the current. By using the minimal reaction scheme, the effect of FTY720 on IK(DR) inactivation was estimated with a dissociation constant of 3.14 μM. FTY720 also shifted the inactivation curve of IK(DR) to a hyperpolarized potential with no change in the slope factor, and recovery from IK(DR) became slow during the exposure to this compound. Cumulative inactivation for IK(DR) in response to repetitive depolarizations was enhanced in the presence of FTY720. In SEW2871-treated cells, FTY720-induced inhibition of IK(DR) was attenuated. This compound also exerted a stimulatory action on the activity of intermediate-conductance Ca2+-activated K+ channels in Jurkat T-lymphocytes. However, in NSC-34 neuronal cells, FTY720 did not modify the inactivation kinetics of KV3.1-encoded IK(DR), although it suppressed IK(DR) amplitude in these cells. Collectively, the perturbations by FTY720 on different types of K+ channels may contribute to the functional activities of immune cells, if similar findings appear in vivo.
Gender differences in response to an opportunistic brief intervention for obesity in primary care: Data from the BWeL trial

Weight loss programmes appeal mainly to women, prompting calls for gender‐specific programmes. In the United Kingdom, general practitioners (GPs) refer nine times as many women as men to community weight loss programmes. GPs endorsement and offering programmes systematically could reduce this imbalance. In this trial, consecutively attending patients in primary care with obesity were invited and 1882 were enrolled and randomized to one of two opportunistic 30‐second interventions to support weight loss given by GPs in consultations unrelated to weight. In the support arm, clinicians endorsed and offered referral to a weight loss programme and, in the advice arm, advised that weight loss would improve health. Generalized linear mixed effects models examined whether gender moderated the intervention. Men took effective weight loss action less often in both arms (support: 41.6% vs 60.7%; advice: 12.1% vs 18.3%; odds ratio (OR) = 0.38, 95% confidence interval (CI), 0.27, 0.52, P < . 001) but there was no evidence that the relative effect differed by gender (interaction P = .32). In the support arm, men accepted referral and attended referral less often, 69.3% vs 82.4%; OR = 0.48, 95% CI, 0.35, 0.66, P < . 001 and 30.4% vs 47.6%; OR = 0.48, 95% CI, 0.36, 0.63, P < . 001, respectively. Nevertheless, the gender balance in attending weight loss programmes closed to 1.6:1. Men and women attended the same number of sessions (9.7 vs 9.1 sessions, P = .16) and there was no evidence weight loss differed by gender (6.05 kg men vs 4.37 kg women, P = .39). Clinician‐delivered opportunistic 30‐second interventions benefits men and women equally and reduce most of the gender imbalance in attending weight loss programmes.
Imbalanced cellular metabolism compromises cartilage homeostasis and joint function in a mouse model of mucolipidosis type III gamma

ABSTRACT Mucolipidosis type III (MLIII) gamma is a rare inherited lysosomal storage disorder caused by mutations in GNPTG encoding the γ-subunit of GlcNAc-1-phosphotransferase, the key enzyme ensuring proper intracellular location of multiple lysosomal enzymes. Patients with MLIII gamma typically present with osteoarthritis and joint stiffness, suggesting cartilage involvement. Using Gnptg knockout (Gnptgko) mice as a model of the human disease, we showed that missorting of a number of lysosomal enzymes is associated with intracellular accumulation of chondroitin sulfate in Gnptgko chondrocytes and their impaired differentiation, as well as with altered microstructure of the cartilage extracellular matrix (ECM). We also demonstrated distinct functional and structural properties of the Achilles tendons isolated from Gnptgko and Gnptab knock-in (Gnptabki) mice, the latter displaying a more severe phenotype resembling mucolipidosis type II (MLII) in humans. Together with comparative analyses of joint mobility in MLII and MLIII patients, these findings provide a basis for better understanding of the molecular reasons leading to joint pathology in these patients. Our data suggest that lack of GlcNAc-1-phosphotransferase activity due to defects in the γ-subunit causes structural changes within the ECM of connective and mechanosensitive tissues, such as cartilage and tendon, and eventually results in functional joint abnormalities typically observed in MLIII gamma patients. This idea was supported by a deficit of the limb motor function in Gnptgko mice challenged on a rotarod under fatigue-associated conditions, suggesting that the impaired motor performance of Gnptgko mice was caused by fatigue and/or pain at the joint. This article has an associated First Person interview with the first author of the paper. Summary: Analyses of Gnptg knockout mice indicate that functional joint abnormalities observed in mucolipidosis type III gamma patients are caused by imbalanced metabolism, leading to structural extracellular matrix changes in cartilage and tendons.
Fresh-market Tomato Production in a Low-input Alternative System Using Cover-crop Mulch

A low-input sustainable agricultural system for the production of staked, fresh-market field tomatoes (Lycopersicon esculentum Mill.) is described. The system uses winter annual cover crops to fix N, recycle leftover nutrients, produce biomass, and prevent soil erosion throughout the winter and spring. Yields of tomato plants grown in hairy vetch (Vicia villosa Roth), crimson clover (Trifolium incarnatum L.), and rye (Secale cereale L.) plus hairy vetch mulches were higher than those grown in the conventional black polyethylene (BP) mulch system in 2 of 3 years. Fruit were heavier with the plant mulches than with BP mulch. Eight weeks after transplanting, N levels in tomato leaves were higher with plant than with BP mulch, although the plant mulch plots received only 50% of the N applied to the BP plots. The cover crops had no effect on populations of five phytoparasitic nematode species.