Miracle-dz/UniFAR-FTUs huggingface dataset:
Ultrasensitive Detection and Phenotyping of CD4+ T Cells with Optimized HLA Class II Tetramer Staining1

HLA class I tetramers have revolutionized the study of Ag-specific CD8+ T cell responses. Technical problems and the rarity of Ag-specific CD4+ Th cells have not allowed the potential of HLA class II tetramers to be fully realized. Here, we optimize HLA class II tetramer staining methods through the use of a comprehensive panel of HIV-, influenza-, CMV-, and tetanus toxoid-specific tetramers. We find rapid and efficient staining of DR1- and DR4-restricted CD4+ cell lines and clones and show that TCR internalization is not a requirement for immunological staining. We combine tetramer staining with magnetic bead enrichment to detect rare Ag-specific CD4+ T cells with frequencies as low as 1 in 250,000 (0.0004% of CD4+ cells) in human PBLs analyzed directly ex vivo. This ultrasensitive detection allowed phenotypic analysis of rare CD4+ T lymphocytes that had experienced diverse exposure to Ag during the course of viral infections. These cells would not be detectable with normal flow-cytometric techniques.
Monocyte‐derived dendritic cells from breast cancer patients are biased to induce CD4+CD25+Foxp3+ regulatory T cells

DCs orchestrate immune responses contributing to the pattern of response developed. In cancer, DCs may play a dysfunctional role in the induction of CD4+CD25+Foxp3+ Tregs, contributing to immune evasion. We show here that Mo‐DCs from breast cancer patients show an altered phenotype and induce preferentially Tregs, a phenomenon that occurred regardless of DC maturation stimulus (sCD40L, cytokine cocktail, TNF‐α, and LPS). The Mo‐DCs of patients induced low proliferation of allogeneic CD3+CD25negFoxp3neg cells, which after becoming CD25+, suppressed mitogen‐stimulated T cells. Contrastingly, Mo‐DCs from healthy donors induced a stronger proliferative response, a low frequency of CD4+CD25+Foxp3+ with no suppressive activity. Furthermore, healthy Mo‐DCs induced higher levels of IFN‐γ, whereas the Mo‐DCs of patients induced higher levels of bioactive TGF‐β1 and IL‐10 in cocultures with allogeneic T cells. Interestingly, TGF‐β1 blocking with mAb in cocultures was not enough to completely revert the Mo‐DCs of patientsˈ bias toward Treg induction. Altogether, these findings should be considered in immunotherapeutic approaches for cancer based on Mo‐DCs.
Modelling function‐valued stochastic processes, with applications to fertility dynamics

We introduce a simple and interpretable model for functional data analysis for situations where the observations at each location are functional rather than scalar. This new approach is based on a tensor product representation of the function‐valued process and utilizes eigenfunctions of marginal kernels. The resulting marginal principal components and product principal components are shown to have nice properties. Given a sample of independent realizations of the underlying function‐valued stochastic process, we propose straightforward fitting methods to obtain the components of this model and to establish asymptotic consistency and rates of convergence for the estimates proposed. The methods are illustrated by modelling the dynamics of annual fertility profile functions for 17 countries. This analysis demonstrates that the approach proposed leads to insightful interpretations of the model components and interesting conclusions.
Access Control for IoT Nodes With Energy and Fidelity Constraints

The presence of many battery-powered sensors in the Internet of Things paradigm calls for the design of energy-aware protocols. Source coding techniques make it possible to save some energy by compressing the packets sent over the network, but at the cost of poorer accuracy in the representation of the data. This paper addresses the problem of designing efficient policies to jointly perform processing and transmission tasks. In particular, we aim at defining a scheduling strategy with the twofold goal of extending the network lifetime and guaranteeing a low overall distortion of the transmitted data. We propose a time division multiple access-based access scheme that efficiently allocates resources to heterogeneous nodes. We use realistic rate-distortion curves to quantify the impact of compression on the data quality and propose a complete energy model that includes the energy spent for processing and transmitting the data, as well as the circuitry energy costs. We consider both full and statistical knowledge of the wireless channels and derive communication policies for the two cases. The overall problem is structured in modules and solved through convex and alternate programming techniques. Finally, we thoroughly evaluate the proposed algorithms and the influence of the design variables on the system performance adopting parameters taken from real sensors.
Effects of early life stress on depression, cognitive performance and brain morphology

Background Childhood early life stress (ELS) increases risk of adulthood major depressive disorder (MDD) and is associated with altered brain structure and function. It is unclear whether specific ELSs affect depression risk, cognitive function and brain structure. Method This cross-sectional study included 64 antidepressant-free depressed and 65 never-depressed individuals. Both groups reported a range of ELSs on the Early Life Stress Questionnaire, completed neuropsychological testing and 3T magnetic resonance imaging (MRI). Neuropsychological testing assessed domains of episodic memory, working memory, processing speed and executive function. MRI measures included cortical thickness and regional gray matter volumes, with a priori focus on the cingulate cortex, orbitofrontal cortex (OFC), amygdala, caudate and hippocampus. Results Of 19 ELSs, only emotional abuse, sexual abuse and severe family conflict independently predicted adulthood MDD diagnosis. The effect of total ELS score differed between groups. Greater ELS exposure was associated with slower processing speed and smaller OFC volumes in depressed subjects, but faster speed and larger volumes in non-depressed subjects. In contrast, exposure to ELSs predictive of depression had similar effects in both diagnostic groups. Individuals reporting predictive ELSs exhibited poorer processing speed and working memory performance, smaller volumes of the lateral OFC and caudate, and decreased cortical thickness in multiple areas including the insula bilaterally. Predictive ELS exposure was also associated with smaller left hippocampal volume in depressed subjects. Conclusions Findings suggest an association between childhood trauma exposure and adulthood cognitive function and brain structure. These relationships appear to differ between individuals who do and do not develop depression.
A review of research on human-computer interfaces for online information retrieval systems

Purpose – The purpose of this article is to review the research on human‐computer interfaces for library‐based commercial online information retrieval (IR) systems.Design/methodology/approach – The review first focuses on basic interface issues for information retrieval such as interface style, end‐user searching, query formulation, relevance feedback and browsing. The second part deals with cognitive engineering in IR including mental models and individual differences. Finally, the topics on user interface engineering are covered. These include user interface guidelines, usability evaluation methods and interface engineering techniques.Findings – The review shows that user interface design has received a limited attention from IR researchers. There is a need for adopting human‐computer interaction (HCI) techniques into IR interface designs, but this issue has not yet been fully recognised by the commercial database vendors and distributors. The paper recommends that applying HCI techniques could help in .
Effects of arbuscular mycorrhizal fungi on growth and nitrogen uptake of Chrysanthemum morifolium under salt stress

Soil salinity is a common and serious environmental problem worldwide. Arbuscular mycorrhizal fungi (AMF) are considered as bio-ameliorators of soil salinity tolerance in plants. However, few studies have addressed the possible benefits of AMF inoculation for medicinal plants under saline conditions. In this study, we examined the effects of colonization with two AMF, Funneliformis mosseae and Diversispora versiformis, alone and in combination, on the growth and nutrient uptake of the medicinal plant Chrysanthemum morifolium (Hangbaiju) in a greenhouse salt stress experiment. After 6 weeks of a non-saline pretreatment, Hangbaiju plants with and without AMF were grown for five months under salinity levels that were achieved using 0, 50 and 200 mM NaCl. Root length, shoot and root dry weight, total dry weight, and root N concentration were higher in the mycorrhizal plants than in the non-mycorrhizal plants under conditions of moderate salinity, especially with D. versiformis colonization. As salinity increased, mycorrhizal colonization and mycorrhizal dependence decreased. The enhancement of root N uptake is probably the main mechanism underlying salt tolerance in mycorrhizal plants. These results suggest that the symbiotic associations between the fungus D. versiformis and C. morifolium plants may be useful in biotechnological practice.
Logics of Redistribution

Social policy scholars disagree about which factors best predict U.S. welfare state generosity. We argue that this disagreement is an artifact of study designs. Researchers usually study either the totality of a state’s social expenditures or one specific program. These approaches overlook the fact that individual social programs were born of different circumstances and serve different constituencies. Comparing state-level policies for Temporary Assistance for Needy Families (TANF), the Children’s Health Insurance Program (CHIP), and the Supplemental Nutrition Assistance Program (SNAP), our findings suggest that these programs are governed by distinct logics of redistribution. Racial characteristics drive TANF generosity. Economic forces best predict CHIP generosity. SNAP generosity is a function of political factors. Qualitative data from Congressional hearings confirm these findings. These results adjudicate between conflicting accounts of the contemporary welfare state and also highlight which aspects of a program’s design make it most susceptible to the effects of racial bias and to partisan politics.
A Comparison of Food Habits Between Japanese Marten and Raccoon Dog in Western Tokyo with Reference to Fruit Use

We studied the food habits of the Japanese marten (Martes melampus) and the raccoon dog (Nyctereutes procionoides) at the Tama Forest Science Garden, western Tokyo, Japan by fecal analysis in 2014/15. Martens were dependent on fruits throughout the year and showed less marked seasonal changes. Raccoon dogs were less dependent on fruits than martens were, and more dependent on mammals in spring, insects in summer and winter, and seeds throughout the year. Martens fed on more fruits containing tiny seeds, such as Actinidia arguta and Stachyurus praecox, whereas raccoon dogs fed on more large-seeded fruits, such as Ginkgo biloba and Diospyros kaki. Martens fed on more fruits that grew at the forest edges, whereas raccoon dogs fed on more fruits growing inside the forest.
Protective effect of APOE epsilon 2 on intrinsic functional connectivity of the entorhinal cortex is associated with better episodic memory in elderly individuals with risk factors for Alzheimer's disease

The apolipoprotein E (APOE) ε4 allele associates with accelerating the conversion from amnestic mild cognitive impairment (aMCI) to Alzheimer's disease (AD), whereas the protectiveAPOEε2 allele appears to be against the disease. Moreover, entorhinal cortex (ERC) is one of the earliest brain regions of AD pathology that disrupts the formation of episodic memory. To investigate the effects of APOE ε2 and ε4alleles on functional connectivity (FC) of ERC and cognition in aMCI. Methods The FC analyses of ERC were performed in 83 aMCI (9 ε2-carrier, 44 ε3ε3, and 30 ε4-carrier) and 88 healthy controls (HC, 15 ε2-carrier, 40 ε3ε3, and 33 ε4-carrier). Multiple linear regression model was performed between the altered ERC connectivities and cognition. In the ERC network, aMCI with ε4-carriers showed decreased FC in the bilateral middle temporal gyrus (MTG), right precuneus, and right precentral gyrus (PreCG), while ε2-carriers showed increased FC in these regions (except the right PreCG) compared to HC. The altered FC between ERC and right MTG correlated with episodic memory performance in aMCI carried ε2 and ε4 alleles. These results suggest that the effects ofAPOEon the ERC network are closely linked to the role of this gene on AD risk, which aMCI with ε4-carriers can accelerate the pathological progression of network-based mechanisms while ε2-carriers may play a protective role in contributing to a compensatory mechanism. It further suggests that APOE can appear to directly affect the ERC-MTG neural pathway associated with the impairment of episodic memory in aMCI.
Conformational dynamics of individual antibodies using computational docking and AFM

Molecular recognition between a receptor and a ligand requires a certain level of flexibility in macromolecules. In this study, we aimed at analyzing the conformational variability of receptors portrayed by monoclonal antibodies that have been individually imaged using atomic force microscopy (AFM). Individual antibodies were chemically coupled to activated mica surface, and they have been imaged using AFM in ambient conditions. The resulting topographical surface of antibodies was used to assemble the three subunits constituting antibodies: two antigen‐binding fragments and one crystallizable fragment using a surface‐constrained computational docking approach. Reconstructed structures based on 10 individual topographical surfaces of antibodies are presented for which separation and relative orientation of the subunits were measured. When compared with three X‐ray structures of antibodies present in the protein data bank database, results indicate that several arrangements of the reconstructed subunits are comparable with those of known structures. Nevertheless, no reconstructed structure superimposes adequately to any particular X‐ray structure consequence of the antibody flexibility. We conclude that high‐resolution AFM imaging with appropriate computational reconstruction tools is adapted to study the conformational dynamics of large individual macromolecules deposited on mica. Copyright © 2013 John Wiley & Sons, Ltd.
Antioxidant‐rich foods and response to altitude training: A randomized controlled trial in elite endurance athletes

High doses of isolated antioxidant supplements such as vitamin C and E have demonstrated the potential to blunt cellular adaptations to training. It is, however, unknown whether intake of high doses of antioxidants from foods has similar effects. Hence, the aim of the study was to investigate whether intake of antioxidant‐rich foods affects adaptations to altitude training in elite athletes. In a randomized controlled trial, 31 national team endurance athletes (23 ± 5 years) ingested antioxidant‐rich foods (n = 16) or eucaloric control foods (n = 15) daily during a 3‐week altitude training camp (2320 m). Changes from baseline to post‐altitude in hemoglobin mass (Hbmass; optimized CO rebreathing), maximal oxygen uptake (VO2max; n = 16) or 100 m swimming performance (n = 10), and blood parameters were compared between the groups. The antioxidant group significantly increased total intake of antioxidant‐rich foods (~118%) compared to the control group during the intervention. The total study population improved VO2max by 2.5% (1.7 mL/kg/min, P = .006) and Hbmass by 4.7% (48 g, P < .001), but not 100 m swimming performance. No difference was found between the groups regarding changes in Hbmass, VO2max or swimming performance. However, hemoglobin concentration increased more in the antioxidant group (effect size = 0.7; P = .045) with a concomitantly larger decrease in plasma and blood volumes compared to control group. Changes in ferritin and erythropoietin from pre‐ to post‐altitude did not differ between the groups. Doubling the intake of antioxidant‐rich foods was well tolerated and did not negatively influence the adaptive response to altitude training in elite endurance athletes.
Psychiatric Disorders and Treatment in Adoptees: A Meta-Analytic Comparison with Non-Adoptees

ABSTRACT This meta-analysis integrates the results of 85 studies on psychiatric disorders and treatment in adoptees and non-adoptees. The risk of adoptees experiencing psychiatric disorders, contact with mental health services, or treatment in a psychiatric hospital was approximately twice as high as that of non-adoptees. Elevated risks were observed for attention-deficit/hyperactivity disorders, anxiety disorders, conduct disorders/oppositional defiant disorders, depression, substance use disorders, and psychoses. Larger effect sizes were, in part, found in clinical studies than in community-based studies, in studies with a higher percentage of individuals adopted after the age of three years and international adoptees, and in older studies.
Development of voltage-activated potassium currents in cultured cerebellar granule neurons under different growth conditions.

1. The functional expression of two potassium currents in cultured cerebellar granule cells was investigated with the whole cell patch-clamp technique in relation to development and growth condition. Cells were grown in medium containing different concentrations of potassium: 25 mM (K25) and 40 mM (K40), together referred to as "high K+"; 10 mM (K10) or "low K+"; and K10 with 100 microM N-methyl-D-aspartate (KNMDA). All conditions are known to influence maturation and survival of granule cells in culture. 2. At 2 days in vitro (DIV) the membrane capacitance, taken as index of membrane surface area, was the same for cells grown in each growth condition. At 7-9 DIV it had increased in each condition, but to a substantially larger extent in cells grown in KNMDA, K25, and K40 than in cells grown in K10. During development the input resistance only decreased in cells grown in KNMDA and high K+. 3. A delayed potassium current (IK) and a fast transient potassium current (IA) could both be recorded at 2 DIV in each growth condition, although a few neurons only expressed the IK. The IK was partially suppressed by tetraethylammonium (5 mM), whereas IA was predominantly sensitive to 4-aminopyridine (5 mM). 4. Normalized for cell capacitance, the specific IA conductance hardly changed during development in cells grown in high K+ and KNMDA. Cells in K10, however, displayed an IA with totally different properties in 23 of 24 cells; the specific IA conductance in these cells was considerably smaller at 7-9 DIV, suggesting a deletion of these channels during development. (ABSTRACT TRUNCATED AT 250 WORDS)
Children's memory for location and object properties in vision and haptics: automatic or attentional processing?

Incidental versus intentional memorization of visually coded and haptically coded location (Eperimenr 1), haptically coded texture (Experiment 2A), and visually coded color (Experiment 2B) were studied in children aged 7 and 9 years. The objective was to determine wherther the same mode of processing (automatic vs attentional) is at work in vision and in haptics. In addition to age effects, the results showed that (1) location was well memorized incidentally in both modalities suggestin g automaticity; 2) haptic texture was recalled only under intentional learning instructions, suggesting effortful processing, while (visual) color was well memorized under both incidental and intentional learnin g conditions. The comparison between the visual and haptic modes of object property processing is discussed in relation to Hasher and Zacks' (1979) definition of automaticity and to Klatzky and Lederman's studies of haptic exploratory procedures (1987; Klatzky, Lederman, & Reed, 1989)
Testing the predictions of energy allocation decisions in the evolution of life‐history trade‐offs

Summary 1. Allocating a greater amount of limited resources, such as energy, to current reproduction can reduce the amount of energy available for somatic maintenance and can ultimately impair future breeding success or maternal survival (i.e. cost of reproduction hypothesis). Although there is some support for the cost of reproduction hypothesis in birds, few empirical studies of mammals have demonstrated a trade-off between current and future reproduction. More importantly, most studies testing ultimate costs have neglected to confirm that the proximate costs of reproduction are high. 2. We experimentally manipulated litter size in a wild population of Columbian ground squirrels for 2 years to examine both the proximate energetic and ultimate fitness (i.e. survival and breeding) costs of reproduction. We predicted that females raising augmented litters would have the highest rates of daily energy expenditure and as a result would experience lower survival rates or future fecundity. 3. Females raising augmented litters weaned more pups, had the highest litter masses at weaning, and had field metabolic rates that were almost 15 times greater than females raising control or reduced litters. Contrary to our prediction, there were no negative impacts of greater maternal investment and higher energy expenditure on the probability of maternal survival or future reproduction. 4. Pups from augmented litters grew more slowly during the lactation period were smaller at weaning and had a lower probability of survival over-winter. Thus, although females were capable of raising more young than they gave birth to without short-term costs of reduced survival or fecundity, our observations suggest that limitations to litter size are not due to a trade-off in the allocation of energy, but rather due to the reduced survival of offspring from larger litters. 5. Examining the proximate mechanisms hypothesized to underlie life-history trade-offs can be challenging but is critical for a comprehensive understanding of the evolution of life histories.
Interactions between care-giving and paid work hours among European midlife women, 1994 to 1996

This paper uses data from the European Community Household Panel surveys of 1994 and 1996 to study the association between changes in care-giving and changes in weekly work hours. Our sample comprises women aged 45–59 years who participated in the labour force in at least one of the two years studied. Controlling for country variation, we find significant relationships between starting or increasing informal care-giving and changes in weekly work hours. No such association is found however among women terminating a care-giving commitment or reducing their care hours. Starting care-giving significantly reduces work hours for women in northern European countries (except Ireland). By contrast, women in southern Europe and Ireland respond to an increase in care-giving hours by a smaller increase or a higher decrease in work hours than non care-givers. In summary, our results show that the impact of care-giving on adjustments of weekly work hours is asymmetrical and that it differs in southern and northern Europe.