Miracle-dz/UniFAR-FTUs huggingface dataset:
Quantitative and Qualitative Perturbations of CD8+ MAITs in Healthy Mycobacterium tuberculosis–Infected Individuals

CD8 T cells are considered important contributors to the immune response against Mycobacterium tuberculosis, yet limited information is currently known regarding their specific immune signature and phenotype. In this study, we applied a cell population transcriptomics strategy to define immune signatures of human latent tuberculosis infection (LTBI) in memory CD8 T cells. We found a 41-gene signature that discriminates between memory CD8 T cells from healthy LTBI subjects and uninfected controls. The gene signature was dominated by genes associated with mucosal-associated invariant T cells (MAITs) and reflected the lower frequency of MAITs observed in individuals with LTBI. There was no evidence for a conventional CD8 T cell–specific signature between the two cohorts. We, therefore, investigated MAITs in more detail based on Vα7. 2 and CD161 expression and staining with an MHC-related protein 1 (MR1) tetramer. This revealed two distinct populations of CD8+Vα7. 2+CD161+ MAITs: MR1 tetramer+ and MR1 tetramer−, which both had distinct gene expression compared with memory CD8 T cells. Transcriptomic analysis of LTBI versus noninfected individuals did not reveal significant differences for MR1 tetramer+ MAITs. However, gene expression of MR1 tetramer− MAITs showed large interindividual diversity and a tuberculosis-specific signature. This was further strengthened by a more diverse TCR-α and -β repertoire of MR1 tetramer− cells as compared with MR1 tetramer+. Thus, circulating memory CD8 T cells in subjects with latent tuberculosis have a reduced number of conventional MR1 tetramer+ MAITs as well as a difference in phenotype in the rare population of MR1 tetramer− MAITs compared with uninfected controls.
Heart failure is associated with accelerated age related metabolic bone disease

Abstract Background The heart failure (HF)-syndrome is associated with neuro-hormonal activation, chronic kidney disease (CKD), inflammation and alterations in the phosphorus-metabolism, all of which are involved in regulation of mineral bone density. However, the role of HF as an independent factor associated with metabolic bone disease (MBD) remains unclear. Methods HF-patients undergoing dual X-ray absorptiometry (DEXA) were matched in a 1:2 fashion against age and gender matched controls without HF, to determine the proportion of osteoporosis (T-score < −2.5). HF-status was tested against known predictors of MBD. Correlation analysis and Z-score analysis were used to assess the impact of HF on age-related bone demineralisation. Results A total of 190 HF-patients (age = 80 ± 10 years, female = 61%) were age and gender matched to 380 controls. HF-patients had a higher proportion of osteoporosis (26 vs 17%; p = .007). HF patients had a lower averaged mineral bone density expressed in g/cm2 (p = .030), T-scores (p = .001) and Z-scores (p < .001). After adjusting for the individual osteoporosis risk-factors of the FRAX-score, difference in baseline features, kidney function and phosphorus-metabolism alterations, heart failure remained independently associated with a lower averaged T-score (Adjusted β = –0.189; p = .017). Heart failure was associated with an accelerated age-related decline in mineral bone density (p = .0418). Therapies with ACE-I or ARBs and beta-blockers associated with ameliorated bone demineralisation (p = .023, respectively p = .029), while loop diuretic associated with worsened bone demineralization (p < .001). Conclusion Heart failure independently associates with MBD and higher prevalence of osteoporosis. Heart failure aggravates the aged related loss in mineral bone density while treatment with neuro-hormonal blockers seemed to ameliorate this finding.
What Is the Impact of Intraoperative Microscope-Integrated OCT in Ophthalmic Surgery? Relevant Applications and Outcomes. A Systematic Review

Background: Optical coherence tomography (OCT) has recently been introduced in the operating theatre. The aim of this review is to present the actual role of microscope-integrated optical coherence tomography (MI-OCT) in ophthalmology. Method: A total of 314 studies were identified, following a literature search adhering to the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. After full-text evaluation, 81 studies discussing MI-OCT applications in ophthalmology were included. Results: At present, three microscope-integrated optical coherence tomography systems are commercially available. MI-OCT can help anterior and posterior segment surgeons in the decision-making process, providing direct visualization of anatomic planes before and after surgical manoeuvres, assisting in complex cases, and detecting or confirming intraoperative complications. Applications range from corneal transplant to macular surgery, including cataract surgery, glaucoma surgery, paediatric examination, proliferative diabetic retinopathy surgery, and retinal detachment surgery. Conclusion: The use of MI-OCT in ophthalmic surgery is becoming increasingly prevalent and has been applied in almost all procedures. However, there are still limitations to be overcome and the technology involved remains difficult to access and use.
Panenteric capsule endoscopy versus ileocolonoscopy plus magnetic resonance enterography in Crohn’s disease: a multicentre, prospective study

Introduction Crohn’s disease diagnosis and monitoring remains a great clinical challenge and often requires multiple testing modalities. Assessing Crohn’s disease activity in the entire gastrointestinal (GI) tract using a panenteric capsule endoscopy (CE) system could be used as an alternative to colonoscopy and cross-sectional imaging. This study assessed the accuracy and safety of panenteric CE in Crohn’s disease as compared with ileocolonoscopy (IC) and/or magnetic resonance enterography (MRE). Methods A prospective, multicentre study was performed in subjects with established Crohn’s disease. Individuals with proven small bowel patency underwent a standardised bowel preparation, followed by CE ingestion and IC either the same or following day. MRE, IC, and CE interpretations were performed by blinded central readers using validated scoring systems. The primary endpoint was the overall sensitivity of CE vs MRE and/or IC in Crohn’s disease subjects. Results Study enrolment included 158 subjects from 21 sites in the USA, Austria, and Israel. Of those, 99 were included in the analysis. Imaging modality scores indicated none to mild inflammation in the proximal small bowel and colon, but discrepant levels of inflammation in the terminal ileum. Overall sensitivity for active enteric inflammation (CE vs MRE and/or IC) was 94% vs 100% (p=0.125) and specificity was 74% vs 22% (p=0.001). Sensitivity of CE was superior to MRE for enteric inflammation in the proximal small bowel (97% vs 71%, p=0.021), and similar to MRE and/or IC in the terminal ileum and colon (p=0.500–0.625). There were seven serious adverse advents of which three were related to the CE device. Conclusion Panenteric CE is a reliable tool for assessing Crohn’s disease mucosal activity and extent compared with more invasive methods. This study demonstrates high performance of the panenteric CE as compared to MRE and/or IC without the need for multiple tests in non-stricturing Crohn’s disease. Trial registration number ClinicalTrials.gov NCT03241368
Dialysis Regret: Prevalence and Correlates.

BACKGROUND AND OBJECTIVES Although some patients regret the decision to start dialysis, modifiable factors associated with regret have rarely been studied. We aimed to identify factors associated with patients' regret to initiate dialysis. DESIGN, SETTING, PARTICIPANTS, & MEASUREMENTS A 41-item questionnaire was administered to adult patients receiving maintenance dialysis in seven dialysis units located in Cleveland, Ohio, and its suburbs. Of the 450 patients asked to participate in the study, 423 agreed and 397 provided data on decisional regret. We used multivariable logistic regression to identify predictors of regret, which was assessed using a single item, "Do you regret your decision to start dialysis? " We report adjusted odd ratios (ORs) and 95% confidence intervals (95% CIs) for the following candidate predictors: knowledge of CKD, attitudes toward CKD treatment, and preference for end-of-life care. RESULTS Eighty-two of 397 respondents (21%) reported decisional regret. There were no significant demographic correlates of regret. Regret was more common when patients reported choosing dialysis to please doctors or family members (OR, 2.34; 95% CI, 1.27 to 4.31; P<0.001). Patients who reported having a prognostic discussion about life expectancy with their doctors (OR, 0.42; 95% CI, 0.18 to 0.98; P=0.03) and those who had completed a living will (OR, 0.48; 95% CI, 0.25 to 0.95; P=0.03) were less likely to report regret with dialysis initiation. CONCLUSIONS Dialysis regret was common in this sample. Demographic factors (age, sex, marital status, race, or educational attainment) were not significantly associated with regret, but modifiable care processes were.
Long-term variation in common dolphin diet in relation to prey abundance

Understanding the effects of changes in prey abundance on predators is essential to predict responses of marine ecosystems to perturbation and ensure sustainable fishing. As abundant top predators feeding largely on commercially exploited fish, common dolphins Delphinus delphis are expected to be affected by fluctuations in fish abundance. Previous studies variously suggest that common dolphins show a preference for energy-rich species or that they are opportunistic predators. In the latter case, the intensity of predation on all prey species would be expected to vary in proportion to their abundances. If such relationships are seen for only a few prey species, and the importance of other species varies inversely with the abundance of these ‘preferred’ prey, this would indicate selective feeding. We suggest that studies on diet at the population level can provide insights into such individual-level foraging decisions. We analysed stomach contents from 514 stranded and by-caught common dolphins in Galicia (NW Spain), collected over 2 decades. The most important prey were sardine, blue whiting and hake. Using zeroinflated generalised additive models to deal with non-linear relationships and the high number of zeros in prey count data, we tested for evidence of ‘preference’ for the main prey species, as well as confirming the existence of ontogenetic, spatial and seasonal variation in diet. Relationships between diet and annual prey abundance do not conclusively confirm either opportunistic or selective predation, but there is more evidence for the former. Lack of evidence for selective predation on energy-rich sardine could be due to current low stock levels.
Serum concentrations of interleukin-6 (IL-6) in the general adult population: possible implications for anti-IL-6 therapy in SARS-Cov-2 infection and IL-6-related diseases.

J Investig Allergol Clin Immunol 2021; Vol. 31(1): 65-84 © 2021 Esmon Publicidad 2. McCall BP, Horwitz IB, Feldman SR, Balkrishnan R. Incidence rates, costs, severity, and work-related factors of occupational dermatitis: a workers’ compensation analysis of Oregon, 1990-1997. Arch Dermatol. 2005;141:713-8. 3. Subiabre-Ferrer D, Zaragoza-Ninet V, Ortiz-Salvador JM, Giacaman-von der Weth MM, Blasco-Encinas R, SierraTalamantes I. Dermatitis de contacto profesional, estudio clínico-epidemiológico entre los años 2011 y 2015. Med Segur Trab. 2016;62:318-26. 4. Holguín-Gómez L, Sastre Domínguez J. Occupational contact dermatitis in Spain. J Investig Allergol Clin Immunol. 2017;27:134-6. 5. Hervella-Garcés M, García-Gavín J, Silvestre-Salvador JF. The Spanish standard patch test series: 2016 update by the Spanish Contact Dermatitis and Skin Allergy Research Group (GEIDAC). Actas Dermosifiliogr. 2016;107:559-66. 6. Teo Y, McFadden JP, White IR, Lynch M, Banerjee P. Allergic contact dermatitis in atopic individuals: Results of a 30-year retrospective study. Contact Dermatitis. 2019;81:409-16. 7. Milam EC, Jacob SE, Cohen DE. Contact dermatitis in the patient with atopic dermatitis. J Allergy Clin Immunol Pract. 2019;7:18-26. 8. Bangsgaard N, Thyssen JP, Menné T, Andersen KE, Mortz CG, Paulsen E, et al. Contact allergy to epoxy resin: risk occupations and consequences. Contact Dermatitis. 2012;67:73-7. 9. Lárraga-Piñones G, Heras-Mendaza F, Conde-Salazar L. Occupational contact dermatitis in the wind energy industry. Actas Dermosifiliogr. 2012;103:905-9.
Fruit Availability and Peccary Frugivory in an Isolated Atlantic Forest Fragment: Effects on Peccary Ranging Behavior and Habitat Use

The goal of this study was to examine seasonal frugivory by two sympatric peccary species (Tayassu pecari and T. tajacu) in a small (2178 ha), Atlantic Forest fragment on the inland plateau region of São Paulo State, Brazil. Fruit availability was determined with systematic ground surveys conducted over a 5‐yr period. Examining fruit availability trends for dry and wet seasons, we found that species diversity was greater in the wet season, but the total number and dry mass of fruits were higher in the dry season. Fruit abundance in the dry season was due to one palm, ‘jeriva’ (Syagrus romanzoffiana), which could be considered a keystone species at Caetetus Ecological Station as it also supported a diverse array of mammals, birds, reptiles, and insects. White‐lipped peccaries were the only ungulates that ate palmito fruits (Euterpe edulis) at Caetetus. They consumed ripe and unripe fruits and predated the seeds by chewing the pulp and seed. This occurred primarily during the dry season and was associated with a seasonal range shift and a preference for palmito habitat by the white‐lipped peccaries. The dominance of fruits in peccary diets (80% fruit items in scat) has management implications for other plateau forest fragments. Forest fragments with diminished fruit abundance or diversity, or lacking key species such as S. romanzoffiana or E. edulis, will not support the energetic requirements of the characteristically large and highly mobile white‐lipped peccary populations.
Relationship between risky behaviors and non-prescription opioid use among Asian American youth

Abstract Asian Americans (AA) are a highly understudied population and are often considered the “model minority” for health. However, there is a dearth of research on risky behaviors associated with opioid use in AA teens. Data among AA youth aged 12 to 16 was collected from the 2017 Youth Risk Behavior Surveillance System. Multivariate logistic regression models were run to determine associations between opioid use and risky behaviors, controlling for age and sex. Findings showed that opioid use is significantly associated with weapon carrying, risky sexual behavior, and body image. These conclusions inform public health practice on substance abuse treatment in AA teens.
In Vitro Antimicrobial and Antioxidant Activity of Ethanol Extract of Three Hypericum and Three Achillea Species From Turkey

The present study was conducted to determine the antimicrobial, antifungal and antioxidant activity of the ethanol extract of Hypericum scabrum L (HSm), Hypericum lysimachioides var. lysimachioides (HL), and Hypericum retusum Aucher (HR) and ethanol extracts of Achillea aleppica D.C. subsp. aleppica (AA), Achillea aleppica D.C. subsp. zederbaueri (Hayek) Hub. -Mor (AZ), and Achillea biebersteinii Afan. (AB). The antioxidant properties of extracts were evaluated using different antioxidants tests, including reducing power, free radical scavenging, deoxyribose assay, metal chelating activities and determination of total phenolic compounds. The extracts obtained from Hypericum and Achillea species showed high antioxidant properties. The protective effects of plant extracts were compared with a well known antioxidant, Butilated Hydroxytoluen (BHT) and α-tocopherol. Total antioxidant activity of ethanol extracts of plants were also tested by using ferric thiocyanate (FTC) and thiobarbituric acid (TBA) methods. Antioxidative activities of plant extracts were found to be comparable with Vitamin E. The results showed that the ethanol extracts of all tested plant exhibited different activity against tested microorganisms. Since most of the studied extracts have good antimicrobial and antioxidant activity, it might be possible to use them as natural food additives that act both as antioxidants and as spices.
The molecular chaperone Hsp90 regulates heterochromatin assembly through stabilizing multiple complexes in fission yeast

ABSTRACT In the fission yeast Schizosaccharomyces pombe, both RNAi machinery and RNAi-independent factors mediate transcriptional and posttranscriptional silencing and heterochromatin formation. Here, we show that the silencing of reporter genes at major native heterochromatic loci (centromeres, telomeres, mating-type locus and rDNA regions) and an artificially induced heterochromatin locus is alleviated in a fission yeast hsp90 mutant, hsp90-G84C. Also, H3K9me2 enrichment at heterochromatin regions, especially at the mating-type locus and subtelomeres, is compromised, suggesting heterochromatin assembly defects. We further discovered that Hsp90 is required for stabilization or assembly of the RNA-induced transcriptional silencing (RITS) and Argonaute siRNA chaperone (ARC) RNAi effector complexes, the RNAi-independent factor Fft3, the shelterin complex subunit Poz1 and the Snf2/HDAC-containing repressor complex (SHREC). Our ChIP data suggest that Hsp90 regulates the efficient recruitment of the methyltransferase/ubiquitin ligase complex CLRC by shelterin to chromosome ends and targeting of the SHREC and Fft3 to mating type locus and/or rDNA region. Finally, our genetic analyses demonstrated that increased heterochromatin spreading restores silencing at subtelomeres in the hsp90-G84C mutant. Thus, this work uncovers a conserved factor critical for promoting RNAi-dependent and -independent heterochromatin assembly and gene silencing through stabilizing multiple effectors and effector complexes. Summary: The molecular chaperone Hsp90 is involved in heterochromatic gene silencing and heterochromatin formation by facilitating stability and integrity of RNAi-dependent and -independent effectors in S. pombe.
Determinants of stigma among patients with hepatitis C virus infection

Stigma around hepatitis C virus (HCV) infection is an important and understudied barrier to HCV treatment and elimination. The determinants of HCV‐related stigma, including the impacts of stage of HCV treatment (ie spontaneously cleared; diagnosed, untreated; previously treated, not cured; currently being treated; and treated, cured) and coinfection with human immunodeficiency virus (HIV), remain unknown. To address these gaps, we conducted a cross‐sectional study among patients with a history of HCV infection (n = 270) at outpatient clinics in Philadelphia from July 2018 to May 2019. We evaluated stigma using the validated HCV Stigma Scale, adapted from the Berger HIV Stigma Scale. Associations among HCV‐related stigma and hypothesized demographic, behavioural, and clinical risk factors were evaluated by multivariable linear regression. Most participants (95.5%) experienced HCV‐related stigma. Mean stigma scores did not differ significantly between HCV‐monoinfected and HIV/HCV‐coinfected participants (P = .574). However, we observed significant interactions between HIV status and multiple determinants; therefore, we stratified analyses by HIV status. Among HIV/HCV‐coinfected participants, previous HCV treatment without cure, female gender, Hispanic/Latinx ethnicity and some college education were significantly associated with higher HCV‐stigma scores. An annual income of $10 000‐$40 000 was associated with significantly lower stigma scores. No significant associations were observed among HCV‐monoinfected participants. We found that most participants experienced stigma associated with HCV diagnosis. While stigma scores were similar between HCV‐monoinfected and HIV/HCV‐coinfected participants, the determinants associated with HCV stigma differed by HIV status. Understanding how experiences of stigma differ between HCV‐monoinfected and HIV/HCV‐coinfected patients may aid in the development of targeted interventions to address the HCV epidemic.
Effect of Isomixing on Grape Must Fermentations of ATF1–Overexpressing Wine Yeast Strains

Speeding up grape must fermentation would be of great economic benefit. We subjected Saccharomyces cerevisiae VIN13 and two recombinant VIN13-strains expressing ATF1 alleles under two different promoters (either PGK1 or HXT7) to four styles of grape must fermentations; we then assessed the effect of constantly stirring a must fermentation (isomixing). The four different fermentation setups were as follows: isomixed, closed in an ANKOM Rf Gas productions system; isomixed, open in a stirred tall tube cylinder; static, closed constituting a conventional fermentation in a wine bottle equipped with an airlock and static; and static, open in a tall tube cylinder (without stirring). We report on major fermentation parameters and the volatile aroma compositions generated in the finished wines. The primary fermentations of the strains subjected to constant stirring finished after 7 days, whereas the static fermentations reached dryness after 19 days. The wines derived from isomixed fermentations produced approximately 0.7% less ethanol compared to the unstirred fermentations. The speed that the isomixed fermentation took to reach completion may provide an alternative to static fermentations in the preparation of base wines for sparkling wine production. The observed increase of volatiles of isomixed fermentations merits further investigation.
Grammaticalization

This article presents the study of grammaticalization within the fields of language change and variation, and historical linguistics. Grammaticalization has to do with the diachronic relationship between the lexicon and grammar and with stages of relatively greater and lesser grammaticality. The major effects of grammaticalization, e.g. phonological reduction, semantic generalization, and fusion (or bondedness) are reviewed. The various roles that reanalysis, analogy, and frequency play in grammaticalization are also discussed. The paper further presents the role that grammaticalization studies has played in establishing diachronic universals and discusses metaphor and metonymy in motivating those universals. Finally, the controversies concerning the exceptional status of grammaticalization, the unidirectionality hypothesis, and the legitimacy of grammaticalization as ‘process’ and ‘theory’ are addressed.