Miracle-dz/UniFAR-FTUs huggingface dataset:
Dysfunctional peripheral T follicular helper cells dominate in people with impaired influenza vaccine responses: Results from the FLORAH study

Antigen-primed cluster of differentiation (CD) 4+ T follicular helper (Tfh) cells interact with B cells in the germinal centers (GCs) of lymph nodes to generate vaccine-induced antibody (Ab) responses. In the circulation, peripheral Tfh (pTfh) cells, a subset of memory CD4 T cells, serve as surrogates for GC Tfh because of several functional and phenotypic similarities between them. We investigated features of H1N1 influenza antigen-specific pTfh (Ag.pTfh) in virologically controlled HIV+ volunteers on antiretroviral therapy (ART) and healthy control (HC) participants selected from a seasonal influenza vaccine responsiveness study. Selection of the participants was made based on age, defined as young (18–40 y) and old (>60 y) and on their classification as a vaccine responder (VR) or vaccine nonresponder (VNR). VRs demonstrated expansion of CD40L+ and CD69+ Ag.pTfh, with induction of intracellular interleukin 21 (IL-21) and inducible costimulator (ICOS) post vaccination; these responses were strongest in young HC VRs and were less prominent in HIV+ individuals of all ages. Ag.pTfh in VNRs exhibited dramatically different characteristics from VRs, displaying an altered phenotype and a cytokine profile dominated by cytokines IL-2, tumor necrosis factor alpha (TNF-α), or IL-17 but lacking in IL-21. In coculture experiments, sorted pTfh did not support the B cell IgG production in VNRs and were predominantly an inflammatory T helper 1 (Th1)/T helper 17 (Th17) phenotype with lower ICOS and higher programmed cell death protein 1 (PD1) expression. Induction of IL-21 and ICOS on Ag.pTfh cells are negatively affected by both aging and HIV infection. Our findings demonstrate that dysfunctional Ag.pTfh cells with an altered IL-21/IL-2 axis contribute to inadequate vaccine responses. Approaches for targeting inflammation or expanding functional Tfh may improve vaccine responses in healthy aging and those aging with HIV infection.
Mannosidase Action, Independent of Glucose Trimming, Is Essential for Proteasome-Mediated Degradation of Unassembled Glycosylated Ig Light Chains

Abstract In order to study the role of N-glycans in the ER-associated degradation of unassembled immunoglobulin light (Ig L) chains, we introduced N-glycan acceptor sites into the variable domain of the murine Ig L chain κNS1, which is unfolded in unassembled molecules. We investigated the fate of κNS1 glycosylated at position 70 (κ70) and of a double mutant (κ/70) in stably transfected HeLa cells. Degradation of both chains was impaired by lactacystin, a specific inhibitor of the proteasome. The mannosidase inhibitor dMNJ also blocked degradation in a step preceding proteasome action, as did two protein synthesis inhibitors, cycloheximide and puromycin. In contrast, ER glucosidase inhibitors dramatically accelerated the degradation of the chains when added either pre- or posttranslationally. The accelerated degradation was sensitive to lactacystin, dMNJ and cycloheximide, too. None of these drugs, except lactacystin, affected the degradation of unglycosylated κNS1 chains. We conclude that ER mannosidases and proteasome activities, but not glucose trimming (and therefore, most likely not the calnexin/ calreticulin UDP:glucose glycoprotein glucosyl transferase cycle), are essential for ER-associated degradation (ERAD) of soluble glycoproteins. A role for a short-lived protein, acting before or simultaneously to ER mannosidases, is suggested.
Leishmania donovani Ornithine Decarboxylase Is Indispensable for Parasite Survival in the Mammalian Host

ABSTRACT Mutations within the polyamine biosynthetic pathway of Leishmania donovani, the etiological agent of visceral leishmaniasis, confer polyamine auxotrophy to the insect vector or promastigote form of the parasite. However, whether the infectious or amastigote form of the parasite requires an intact polyamine pathway has remained an open question. To address this issue, conditionally lethal Δodc mutants lacking ornithine decarboxylase (ODC), the rate-limiting enzyme in polyamine biosynthesis, were created by double targeted gene replacement within a virulent strain of L. donovani. ODC-deficient promastigotes and axenic amastigotes were auxotrophic for polyamines and capable of robust growth only when exogenous putrescine was supplied in the culture medium, confirming that polyamine biosynthesis is an essential nutritional pathway for L. donovani promastigotes. To assess whether the Δodc lesion also affected the ability of amastigotes to sustain a robust infection, macrophage and mouse infectivity experiments were performed. Parasite loads in murine macrophages infected with each of two independent Δodc knockout lines were decreased ∼80% compared to their wild-type counterpart. Furthermore, α-difluoromethylornithine, a suicide inhibitor of ODC, inhibited growth of wild-type L. donovani amastigotes and effectively cured macrophages of parasites, thereby preventing host cell destruction. Strikingly, however, parasitemias of both Δodc null mutants were reduced by 6 and 3 orders of magnitude, respectively, in livers and spleens of BALB/c mice. The compromised infectivity phenotypes of the Δodc knockouts in both macrophages and mice were rescued by episomal complementation of the genetic lesion. These genetic and pharmacological studies strongly implicate ODC as an essential cellular determinant that is necessary for the viability and growth of both L. donovani promastigotes and amastigotes and intimate that pharmacological inhibition of ODC is a promising therapeutic paradigm for the treatment of visceral and perhaps other forms of leishmaniasis.
Antioxidant and Cytoprotective Effect of Piper aduncum L. against Sodium Fluoride (NaF)-Induced Toxicity in Albino Mice

Piper aduncum, commonly known as matico, is a plant that grows in the mountainous and coastal regions of Peru, and is studied for its antimicrobial properties and various ethnopharmacological uses. The main objective of this study was to determine the cytoprotective and antioxidant effects of the methanolic extract of Piper aduncum leaves in Mus musculus previously administered with sodium fluoride (NaF) using the Micronucleus test and the Comet assay. The extract was administrated orally in four different concentrations: 150, 300, 600, and 1200 mg/Kg for ten days. At the 11th day, a single dose of NaF was administrated via intraperitoneal at 20 mg/Kg. The genotoxicity study was performed with mice from the strain BALB/c, using the Micronucleus test on bone marrow and the Comet assay on peripheral blood according to OECD guidelines 474 and 489, respectively. The statistical analysis was performed by median analysis with ANOVA. Significant differences were found in Micronucleus frequency between the highest concentrations of Piper aduncum and NaF. The Comet assay showed significant reduction of NaF-induced damage on erythrocytes depending on the different concentrations of the extract which were evaluated in this study. It is concluded that the methanolic extract of P. aduncum leaves has cytoprotective and antioxidant activity against sodium fluoride.
Regulatory T (Treg) cells in cancer: Can Treg cells be a new therapeutic target?

Regulatory T (Treg) cells suppress abnormal/excessive immune responses to self‐ and nonself‐antigens to maintain immune homeostasis. In tumor immunity, Treg cells are involved in tumor development and progression by inhibiting antitumor immunity. There are several Treg cell immune suppressive mechanisms: inhibition of costimulatory signals by CD80 and CD86 expressed by dendritic cells through cytotoxic T‐lymphocyte antigen‐4, interleukin (IL)‐2 consumption by high‐affinity IL‐2 receptors with high CD25 (IL‐2 receptor α‐chain) expression, secretion of inhibitory cytokines, metabolic modulation of tryptophan and adenosine, and direct killing of effector T cells. Infiltration of Treg cells into the tumor microenvironment (TME) occurs in multiple murine and human tumors. Regulatory T cells are chemoattracted to the TME by chemokine gradients such as CCR4‐CCL17/22, CCR8‐CCL1, CCR10‐CCL28, and CXCR3‐CCL9/10/11. Regulatory T cells are then activated and inhibit antitumor immune responses. A high infiltration by Treg cells is associated with poor survival in various types of cancer. Therefore, strategies to deplete Treg cells and control of Treg cell functions to increase antitumor immune responses are urgently required in the cancer immunotherapy field. Various molecules that are highly expressed by Treg cells, such as immune checkpoint molecules, chemokine receptors, and metabolites, have been targeted by Abs or small molecules, but additional strategies are needed to fine‐tune and optimize for augmenting antitumor effects restricted in the TME while avoiding systemic autoimmunity. Here, we provide a brief synopsis of these cells in cancer and how they can be controlled to achieve therapeutic outcomes.
Construct validity of the five-factor Strengths and Difficulties Questionnaire (SDQ) in pre-, early, and late adolescence.

BACKGROUND The Strengths and Difficulties Questionnaire (SDQ) is designed to measure psychological adjustment in children and adolescents. Psychometric evaluations of the instrument have shown satisfactory convergent and discriminant validity, while factor analysis studies have shown mixed results across countries. In the present study, the construct validity of the five-factor SDQ is evaluated in a large community sample of Norwegian pre-, early, and late adolescents. METHODS The sample consisted of 26,269 children and adolescents (10-19 years) with valid answers on all 25 items of the SDQ self-report. Complete parent/proxy data of respective pre-adolescent children was available for 6,645 cases. A Lisrel approach to Confirmatory Factor Analysis (CFA) was used to evaluate the five-factor model and the presence of a positive construal factor. In the sample of pre-adolescents and their parents/proxies, convergent and discriminant validity was evaluated by a CFA approach to multitrait-multimethods (MTMM). RESULTS Fit statistics for the hypothesized five-factor model were satisfactory, but introducing correlated error terms for some of the items led to significant model improvement in all age groups. All factor loadings were higher than . 30, except for item 11 (good friend). The loadings differed across age groups and differed markedly between the parent/proxy and self-report measures. The MTMM showed that the source of ratings made a difference on the validity of all subscale ratings, with self-reports discriminating more on ratings of emotional and peer problems, and parents/proxies discriminating more on hyperactivity symptoms. A positive construal factor was identified but had a modest effect compared with the original five traits. Results suggested an unclear construct and meaning of the Prosocial behaviour subscale. CONCLUSION The results of the present study indicated support for the proposed five-factor structure of the SDQ (Goodman, 2001) across a wide age range (10-19years), including older adolescents and different informants. However, some improvements should be considered to improve internal reliability and conceptual clarity.
Response Styles Theory: Downward Extension to Children

Describes partial support found for the downward extension of Nolen-Hoeksema's response styles theory of depression to preadolescents (N = 201). A self-report measure of response styles was developed. Evidence for the multidimensionality and independence of rumination and distraction is provided, as well as support for the reliability and validity of the new measure. Results supported 2 primary tenets of the theory: sex differences in ruminatory tendencies and associations between response styles and self-reported depressive symptoms. Implications of the findings for understanding depression in preadolescents are discussed, in addition to directions for advancing this knowledge area.
Porcine Dendritic Cells and Viruses: An Update

Several viral infections of swine are responsible for major economic losses and represent a threat to the swine industry worldwide. New tools are needed to prevent and control endemic, emerging, and re-emerging viral diseases. Dendritic cells (DC) play a central role in linking the innate and adaptive arms of the immune system, so knowledge regarding their interaction with pathogens is necessary to understand the mechanisms underlying diseases pathogenesis and protection. In the first part of this review, we provide an update on the heterogeneous cell subsets that comprise the porcine DC family. In the second part of this review, we provide an overview of how three viruses, affecting pork production at a global level, African swine fever virus (ASFV), classical swine fever virus (CSFV), and porcine circovirus 2 (PCV2), modulate DC function.
Activation of mammalian target of rapamycin in postmenopausal ovarian endometriosis

The purpose of this study was to determine whether Akt and mammalian target of rapamycin (mTOR), downstream targets of phosphatidylinositol 3-kinase, are activated in endometriosis and ovarian cancer specimens. We measured total and phosphorylated levels of Akt and mTOR from 17 frozen ovarian cancers and 15 benign endometriosis specimens (nine from premenopausal women and six from postmenopausal women) by quantitation of signals from western blots using antibodies against these proteins. Elevated phospho-Akt was detected in ovarian cancer versus endometriosis specimens from premenopausal women and endometriosis specimens from postmenopausal women (2.3 ± 0.45 versus 0.10 ± 0.06 and 0.17 ± 0.11; P < 0.05) when the western blot signal of activated kinase was normalized to total kinase levels. Elevated phospho-mTOR was detected in ovarian cancer and postmenopausal endometriosis versus premenopausal endometriosis (0.52 ± 0.19 and 0.46 ± 0.29 versus 0.13 ± 0.08; P < 0.05). Expression of total kinases (normalized to β-actin) was higher in carcinoma versus endometriosis specimens. Elevation of the active mTOR was specifically detected in postmenopausal endometriosis.
The GLFG Regions of Nup116p and Nup100p Serve as Binding Sites for Both Kap95p and Mex67p at the Nuclear Pore Complex*

Our previous studies have focused on a family ofSaccharomyces cerevisiae nuclear pore complex (NPC) proteins that contain domains composed of repetitive tetrapeptide glycine-leucine-phenylalanine-glycine (GLFG) motifs. We have previously shown that the GLFG regions of Nup116p and Nup100p directly bind the karyopherin transport factor Kap95p during nuclear protein import. In this report, we have further investigated potential roles for the GLFG region in mRNA export. The subcellular localizations of green fluorescent protein (GFP)-tagged mRNA transport factors were individually examined in yeast cells overexpressing the Nup116-GLFG region. The essential mRNA export factors Mex67-GFP, Mtr2-GFP, and Dbp5-GFP accumulated in the nucleus. In contrast, the localizations of Gle1-GFP and Gle2-GFP remained predominantly associated with the NPC, as in wild type cells. The localization of Kap95p was also not perturbed with GLFG overexpression. Coimmunoprecipitation experiments from yeast cell lysates resulted in the isolation of a Mex67p-Nup116p complex. Soluble binding assays with bacterially expressed recombinant proteins confirmed a direct interaction between Mex67p and the Nup116-GLFG or Nup100-GLFG regions. Mtr2p was not required for in vitro binding of Mex67p to the GLFG region. To map the Nup116-GLFG subregion(s) required for Kap95p and/or Mex67p association, yeast two-hybrid analysis was used. Of the 33 Nup116-GLFG repeats that compose the domain, a central subregion of nine GLFG repeats was sufficient for binding either Kap95p or Mex67p. Interestingly, the first 12 repeats from the full-length region only had a positive interaction with Mex67p, whereas the last 12 were only positive with Kap95p. Thus, the GLFG domain may have the capacity to bind both karyopherins and an mRNA export factor simultaneously. Taken together, our in vivo and in vitro results define an essential role for a direct Mex67p-GLFG interaction during mRNA export.
OF THE EXPERIMENTAL ANALYSIS OF BEHAVIOR OPTIMAL CHOICE

We present a classification and theoretical analysis of discrete-trial and free-operant choice procedures in which reinforcement is assigned to one alternative only, or independently to both, is either always available or conditionally available, and is either "held" or not from trial to trial. Momentary-maximizing and (globally) optimal choice sequences are defined in terms of initializing and marker events. Free-operant choice is analyzed in terms of a clock space whose axes are the times since the last A and B choices. The analysis shows that most molar matching data are derivable from momentary maximizing, and that the momentary-maximizing hypothesis has not been adequately rested in either discrete-trial or free-operant situations.
Health outcomes and services in children with sickle cell trait, sickle cell anemia, and normal hemoglobin.

The health effects of sickle cell trait among children are unknown. We compared select health outcomes and health services utilization among children with sickle cell trait, sickle cell anemia (SCA), and normal hemoglobin. Newborn screening records were used to identify children with sickle cell trait and SCA born in Michigan (1997-2014) who were enrolled in Michigan Medicaid for ≥1 year from 2012 to 2014. Each select health outcome (acute otitis media, acute respiratory infections, fever, invasive pneumococcal disease, pneumonia and influenza, renal complications, spleen problems, stroke) was defined as ≥1 claim with a diagnosis code for the respective outcome within a study year. Health services utilization was summarized as counts of emergency department, inpatient, and outpatient encounters. The relationship between hemoglobin status and each health outcome or utilization was assessed by logistic or negative binomial regression with generalized estimating equations. The study population consisted of 18 257 children with sickle cell trait, 368 with SCA, and 74 523 with normal hemoglobin (227 188 total person-years). Compared with those with normal hemoglobin, children with sickle cell trait had lower odds of acute otitis media (odds ratio [OR], 0.88; 95% confidence interval [CI], 0.84-0.91), acute respiratory infections (OR, 0.94; 95% CI, 0.92-0.97), pneumonia and influenza (OR, 0.93; 95% CI, 0.87-0.99), and outpatient visits (incidence rate ratio, 0.95; 95% CI, 0.93-0.97). Children with SCA had higher or nonsignificant odds of all outcomes and types of health services utilization. These results indicate that children with sickle cell trait may not be at additional health risk for these outcomes. However, additional case-control studies may be necessary to identify rare events.
Re‐examination of accelerometer data processing and calibration for the assessment of physical activity intensity

This review re‐examines the use of accelerometer and oxygen uptake data for the assessment of activity intensity. Accelerometers capture mechanical work, while oxygen uptake captures the energy cost of this work. Frequency filtering needs to be considered when processing acceleration data. A too restrictive filter attenuates the acceleration signal for walking and, to a higher degree, for running. This measurement error affects shorter (children) more than taller (adults) individuals due to their higher movement frequency. Less restrictive filtering includes more movement‐related signals and provides measures that better capture mechanical work, but may include more noise. An optimal filter cut‐point is determined where most relevant acceleration signals are included. Further, accelerometer placement affects what part of mechanical work being captured. While the waist placement captures total mechanical work and therefore contributes to measures of activity intensity equivalent by age and stature, the thigh and wrist placements capture more internal work and do not provide equivalent measures. Value calibration of accelerometer measures is usually performed using measured oxygen uptake with the metabolic equivalent of task (MET) as reference measure of activity intensity. However, the use of MET is not stringent and is not a measure of activity intensity equivalent by age and stature. A candidate measure is the mass‐specific net oxygen uptake, VO2net (VO2tot − VO2stand). To improve measurement of physical activity intensity using accelerometers, research developments are suggested concerning the processing of accelerometer data, use of energy expenditure as reference for activity intensity, and calibration procedure with absolute versus relative intensity.
Chiral Sign Induction by Vortices During the Formation of Mesophases in Stirred Solutions

Achiral diprotonated porphyrins, forming homoassociates in aqueous solution, lead to spontaneous chiral symmetry breaking. The unexpected result is that the chirality sign of these homoassociates can be selected by vortex motion during the aggregation process. This result is confirmed by means of circular dichroism spectra. These experimental findings are rationalized in terms of the asymmetric influence of macroscopic forces on bifurcation scenarios and by considering the specific binding characteristics of the porphyrin units to form the homoassociates.
Microsecond and millisecond dynamics in the photosynthetic protein LHCSR1 observed by single-molecule correlation spectroscopy

Significance Protein flexibility is essential for the robustness of biological systems, yet the dynamics underlying this flexibility are difficult to observe, because they are small, fast, and stochastic. Photoprotection in plants is critical for robust growth under highly variable sunlight, but the complexity of photosynthetic proteins means that identifying conformational states and dynamics responsible is challenging. Here, we develop a method using the correlation function of the fluorescence lifetime to characterize multiple dynamical processes in single proteins. By applying this method to the protein Light-Harvesting Complex Stress Related 1 (LHCSR1), we identify two local protein motions that control quenching of excess sunlight, which is a photoprotective effect. Our analytical approach enables a structure-based understanding of the photoprotective mechanisms in green plants. Biological systems are subjected to continuous environmental fluctuations, and therefore, flexibility in the structure and function of their protein building blocks is essential for survival. Protein dynamics are often local conformational changes, which allows multiple dynamical processes to occur simultaneously and rapidly in individual proteins. Experiments often average over these dynamics and their multiplicity, preventing identification of the molecular origin and impact on biological function. Green plants survive under high light by quenching excess energy, and Light-Harvesting Complex Stress Related 1 (LHCSR1) is the protein responsible for quenching in moss. Here, we expand an analysis of the correlation function of the fluorescence lifetime by improving the estimation of the lifetime states and by developing a multicomponent model correlation function, and we apply this analysis at the single-molecule level. Through these advances, we resolve previously hidden rapid dynamics, including multiple parallel processes. By applying this technique to LHCSR1, we identify and quantitate parallel dynamics on hundreds of microseconds and tens of milliseconds timescales, likely at two quenching sites within the protein. These sites are individually controlled in response to fluctuations in sunlight, which provides robust regulation of the light-harvesting machinery. Considering our results in combination with previous structural, spectroscopic, and computational data, we propose specific pigments that serve as the quenching sites. These findings, therefore, provide a mechanistic basis for quenching, illustrating the ability of this method to uncover protein function.