Miracle-dz/UniFAR-FTUs huggingface dataset:
Emotion Regulation as a Time-Invariant and Time-Varying Covariate Predicts Outcome in an Internet-Based Psychodynamic Treatment Targeting Adolescent Depression

Objective Although psychodynamic psychotherapy is efficacious in the treatment of depression, research on mechanisms of change is still scarce. The aim of this study was to investigate if and how emotion regulation affects outcome both as a time-invariant and a lagged time-varying predictor. Method The sample consisted of 67 adolescents diagnosed with major depressive disorder, attending affect-focused psychodynamic internet-based treatment (IPDT). Linear mixed models were used to analyze emotion regulation as a baseline predictor and to assess the effect of within-person changes in emotion regulation on depression. Results Analyses suggested that emotion regulation at baseline was a significant predictor of outcome, where participants with relatively larger emotion regulation deficits gained more from IPDT. Further, the results showed a significant effect of improved emotion regulation on subsequent depressive symptomatology. When not controlling for time, increased emotion regulation explained 41.23% of the variance in subsequent symptoms of depression. When detrending the results were still significant, but the amount of explained variance was reduced to 8.7%. Conclusion The findings suggest that patients with relatively larger deficits in emotion regulation gain more from IPDT. Decreased emotion regulation deficits seem to act as a mechanism of change in IPDT as it drives subsequent changes in depression. Clinical Trial Registration International Standard Randomised Controlled Trial Number (ISRCTN) 16206254, https://doi.org/10.1186/ISRCTN16206254.
Investigating Waves and Temperature as Drivers of Kelp Morphology

Macroalgal morphological variation is determined to a large extent by a combination of environmental factors, with wave exposure and temperature perhaps the main influences, as they are key environmental properties to which a species becomes locally adapted. Macroalgae have shown to exhibit different responses to different magnitudes of exposure to waves, such as reduction in overall size and strength increasing traits. In terms of temperature, warmer environments have been shown to reduce the overall size of resident and transplanted species. However, none of the past studies have identified specific wave and temperature metrics responsible for the morphological adaptation macroalgae exhibit. Past research has often used simple or two-dimensional models of wave exposure, which do not take into account important aspects of the nearshore environment such as wave breaking, refraction and diffraction. Furthermore, past studies have often used satellite-derived datasets as sources for temperature data, however, such data have been shown to have large bias when applied to the nearshore environment. This study used in situ temperature data and wave power metrics calculated from a 3D-numerical model to identify specific temperature and wave metrics responsible for morphological adaptation of the kelp, Ecklonia maxima and Laminaria pallida. Between temperature and wave exposure, the results identify wave exposure as the main influencer of morphological adaptation while identifying specific wave metrics. Furthermore, the results show differences in wave metrics between species; and between deep and shallow populations.
Occupational Neuroplasticity in the Human Brain: A Critical Review and Meta-Analysis of Neuroimaging Studies

Many studies have revealed the structural or functional brain changes induced by occupational factors. However, it remains largely unknown how occupation-related connectivity shapes the brain. In this paper, we denote occupational neuroplasticity as the neuroplasticity that takes place to satisfy the occupational requirements by extensively professional training and to accommodate the long-term, professional work of daily life, and a critical review of occupational neuroplasticity related to the changes in brain structure and functional networks has been primarily presented. Furthermore, meta-analysis revealed a neurophysiological mechanism of occupational neuroplasticity caused by professional experience. This meta-analysis of functional neuroimaging studies showed that experts displayed stronger activation in the left precentral gyrus [Brodmann area (BA)6], left middle frontal gyrus (BA6), and right inferior frontal gyrus (BA9) than novices, while meta-analysis of structural studies suggested that experts had a greater gray matter volume in the bilateral superior temporal gyrus (BA22) and right putamen than novices. Together, these findings not only expand the current understanding of the common neurophysiological basis of occupational neuroplasticity across different occupations and highlight some possible targets for neural modulation of occupational neuroplasticity but also provide a new perspective for occupational science research.
The Isolation and Genome Sequencing of Five Novel Bacteriophages From the Rumen Active Against Butyrivibrio fibrisolvens

Although the prokaryotic communities of the rumen microbiome are being uncovered through genome sequencing, little is known about the resident viral populations. Whilst temperate phages can be predicted as integrated prophages when analyzing bacterial and archaeal genomes, the genetics underpinning lytic phages remain poorly characterized. To the five genomes of bacteriophages isolated from rumen-associated samples sequenced and analyzed previously, this study adds a further five novel genomes and predictions gleaned from them to further the understanding of the rumen phage population. Lytic bacteriophages isolated from fresh ovine and bovine fecal and rumen fluid samples were active against the predominant fibrolytic ruminal bacterium Butyrivibrio fibrisolvens. The double stranded DNA genomes were sequenced and reconstructed into single circular complete contigs. Based on sequence similarity and genome distances, the five phages represent four species from three separate genera, consisting of: (1) Butyrivibrio phages Arian and Bo-Finn; (2) Butyrivibrio phages Idris and Arawn; and (3) Butyrivibrio phage Ceridwen. They were predicted to all belong to the Siphoviridae family, based on evidence in the genomes such as size, the presence of the tail morphogenesis module, genes that share similarity to those in other siphovirus isolates and phylogenetic analysis using phage proteomes. Yet, phylogenomic analysis and sequence similarity of the entire phage genomes revealed that these five phages are unique and novel. These phages have only been observed undergoing the lytic lifecycle, but there is evidence in the genomes of phages Arawn and Idris for the potential to be temperate. However, there is no evidence in the genome of the bacterial host Butyrivibrio fibrisolvens of prophage genes or genes that share similarity with the phage genomes.
Visualization of genomic relationships in allotetraploid hybrids between Chrysanthemum lavandulifolium X C. chanetii by fluorescence in situ hybridization and genomic in situ hybridization

Artificial cross between Chrysanthemum lavandulifolium (2n=18 diploid) and C. chanetii (2n=36, tetraploid) made succesfully interspecific F1 hybrid (2n=36 tetraploid instead of 2n=27 tripolid) for the first time. The F1 hybrid had 12 signals of 45S rDNA and and four signals of 5S rDNA by FISH. The chromosome complement of the F1 hybrid showed each set of the both parental chromosomes by GISH by using the biotin labeled probe of C. lavandulifolium mixed with approximately 20X blocking DNA of C. chanetii. Eighteen yellow-green colored chromosomes were hybridized with the probe of C. lavandulifolium, that could be involved with C. lavandulifolium, while the other 18 orange-red colored chromosomes were not GISH-hybridized chromosomes with the probe, that could be involved with C. chanetii. The extra nine chromosome set in the hybrids might be resulted due to duplication of the haploid chromosome set of C. lavandulifolium at/after fertilization.
In vitro Cytokine Responses to Virulent PRRS Virus Strains

Porcine reproductive and respiratory syndrome (PRRS) affects farmed swine causing heavy direct and indirect losses. The infections sustained by PRRS viruses (PRRSV-1 and PRRSV-2) may give rise to severe clinical cases. This highlights the issue of PRRSV pathogenicity and relevant markers thereof. Since PRRSV strains can be discriminated in terms of immunotypes, we aimed to detect possible correlates of virulence in vitro based on the profile of innate immune responses induced by strains of diverse virulence. To this purpose, 10 field PRRSV isolates were investigated in assays of innate immune response to detect possible features associated with virulence. Tumor necrosis factor-α, interleukin (IL)-1beta, IL-8, IL-10, and caspase-1 were measured in cultures of PRRSV-treated peripheral blood mononuclear cells of PRRS-naive pigs, unable to support PRRSV replication. Two reference PRRSV strains (highly pathogenic and attenuated, respectively), were included in the screening. The PRRSV strains isolated from field cases were shown to vary widely in terms of inflammatory cytokine responses in vitro, which were substantially lacking with some strains including the reference, highly pathogenic one. In particular, neither the field PRRSV isolates nor the reference highly pathogenic strain gave rise to an IL-1beta response, which was consistently induced by the attenuated strain, only. This pattern of response was reversed in an inflammatory environment, in which the attenuated strain reduced the ongoing IL-1beta response. Results indicate that some pathogenic PRRSV strains can prevent a primary inflammatory response of PBMCs, associated with reduced permissiveness of mature macrophages for PRRSV replication in later phases.
Peripheral Enthesitis Detected by Ultrasonography in Patients With Axial Spondyloarthritis—Anatomical Distribution, Morphology, and Response to Tumor Necrosis Factor-Inhibitor Therapy

Objectives: To investigate the anatomical distribution, morphological abnormalities and response to adalimumab therapy of ultrasound(US)-detected peripheral enthesitis in patients with axial spondyloarthritis (SpA). Methods: In a randomized, placebo-controlled, double-blinded, investigator-initiated trial (NCT01029847), patients with axial SpA according to the Assessment of Spondyloarthritis International Society criteria were randomized to subcutaneous adalimumab 40 mg every other week or placebo from baseline to week 6. From week 6 to 24, all patients received adalimumab 40 mg every other week. Of 49 patients enrolled, 21 patients participated in our observational US sub-study. US assessment applying the OMERACT US definitions for enthesitis of 10 peripheral entheseal regions of the upper and lower extremities and clinical examination were performed at baseline, weeks 6 and 24. US was performed by one experienced investigator. Hypo-echogenicity, increased thickness and Doppler activity of the enthesis were considered signs of active inflammation, whereas insertional bone erosions, intratendinous calcifications, and enthesophytes were regarded as signs of structural lesions. Results: Enthesitis on US was mostly present in the lower limbs, especially in the Achilles tendon (81%), the quadriceps tendon (62%), and the greater femoral trochanter (52%). Structural lesions were predominant (38 vs. 12% of examined entheses with inflammatory changes), particularly in the entheses of the lower limbs, and exhibited no change during treatment. Conclusion: US-detected structural lesions were common while inflammatory lesions were relatively rare in patients initiating adalimumab due to axial SpA. Structural lesions did not appear to change during 24 weeks follow-up, suggesting that these lesions may not be helpful outcome measures in short-term clinical trials.
Fermentation Versus Meat Preservatives to Extend the Shelf Life of Mealworm (Tenebrio molitor) Paste for Feed and Food Applications

Freshly prepared pastes from blanched mealworms (Tenebrio molitor) are highly perishable and prone to microbial and chemical changes upon storage due to their high water activity, near–neutral pH, and their rich nutrient profile. Their shelf life is short unless preservation methods are used. In this study, the effects of preservatives (sodium nitrite and sodium lactate) and lactic acid fermentation (with the starter cultures Bactoferm® F-LC and Lactobacillus farciminis) on the microbiological and the chemical stability of mealworm pastes stored at 4°C were compared. During the storage experiment, the pH, water activity, color, microbial counts, and fat oxidation were monitored. In addition, the prevalence of the pathogens Bacillus cereus, Salmonella spp. , and Listeria monocytogenes were studied. Microbial quality evaluation of the mealworm pastes showed that the addition of preservatives did not inhibit microbial growth during refrigerated storage, reaching the upper limits for consumption between seven and 14 days. By contrast, the acid medium (pH < 4.50) created by fermentation stabilized all microbial populations investigated, indicating that these pastes could be consumed up to (at least) 8 weeks of refrigerated storage. L. monocytogenes, Salmonella, and B. cereus were not detected in any of the samples and lipid oxidation of the samples was minimal. Altogether, this study shows that lactic acid fermentation can be used successfully to inhibit microbial growth, to maintain chemical quality, and to extend the shelf life of mealworm pastes stored at 4°C.
Toward Emotion Recognition From Physiological Signals in the Wild: Approaching the Methodological Issues in Real-Life Data Collection

Emotion, mood, and stress recognition (EMSR) has been studied in laboratory settings for decades. In particular, physiological signals are widely used to detect and classify affective states in lab conditions. However, physiological reactions to emotional stimuli have been found to differ in laboratory and natural settings. Thanks to recent technological progress (e.g., in wearables) the creation of EMSR systems for a large number of consumers during their everyday activities is increasingly possible. Therefore, datasets created in the wild are needed to insure the validity and the exploitability of EMSR models for real-life applications. In this paper, we initially present common techniques used in laboratory settings to induce emotions for the purpose of physiological dataset creation. Next, advantages and challenges of data collection in the wild are discussed. To assess the applicability of existing datasets to real-life applications, we propose a set of categories to guide and compare at a glance different methodologies used by researchers to collect such data. For this purpose, we also introduce a visual tool called Graphical Assessment of Real-life Application-Focused Emotional Dataset (GARAFED). In the last part of the paper, we apply the proposed tool to compare existing physiological datasets for EMSR in the wild and to show possible improvements and future directions of research. We wish for this paper and GARAFED to be used as guidelines for researchers and developers who aim at collecting affect-related data for real-life EMSR-based applications.
Extracellular Vesicles in Fungi: Past, Present, and Future Perspectives

Extracellular vesicles (EVs) have garnered much interest in the cell biology and biomedical research fields. Many studies have reported the existence of EVs in all types of living cells, including in fifteen different fungal genera. EVs play diverse biological roles, from the regulation of physiological events and response to specific environmental conditions to the mediation of highly complex interkingdom communications. This review will provide a historical perspective on EVs produced by fungi and an overview of the recent discoveries in the field. We will also review the current knowledge about EV biogenesis and cargo, their role in cell-to-cell interactions, and methods of EV analysis. Finally, we will discuss the perspectives of EVs as vehicles for the delivery of biologically active molecules.
Diverse Microbial Composition of Sourdoughs From Different Origins

Hundreds of sourdoughs have been investigated in the last decades. However, many studies used a culture-dependent and/or culture-independent microbiological approach [mainly based on denaturing gradient gel electrophoresis (DGGE) of PCR amplicons], seldomly combined with a metabolite target analysis, to characterize the microbial species communities of the sourdoughs examined. Moreover, attention was mainly paid on lactic acid bacteria (LAB) and yeast species. In the present study, distinct household-scale (including an artisan lambic brewery) and artisan bakery-scale backslopped sourdoughs (17 in total), obtained from different regions (Belgium, France, United Kingdom, and USA), were examined through a multiphasic approach, encompassing a culture-dependent analysis [targeting LAB, acetic acid bacteria (AAB), and yeasts], different culture-independent techniques [rRNA-PCR-DGGE, metagenetics, and metagenomics (four bakery sourdoughs)], and metabolite target analysis. It turned out that the microbial species diversity of the sourdoughs was influenced by the house microbiota of the producer. Further, when the producer made use of different flours, the sourdoughs harbored similar microbial communities, independent of the flour used. AAB were only present in the Belgian sourdoughs, which might again be related to the processing environment. Fructilactobacillus sanfranciscensis (formerly known as Lactobacillus sanfranciscensis) was the prevalent LAB species of the eight sourdoughs produced by two of the three bakeries of different countries analyzed. These sourdoughs were characterized by the presence of either Saccharomyces cerevisiae or Kazachstania humilis. Moreover, the presence of Fl. sanfranciscensis was positively correlated with the production of mannitol and negatively correlated with the presence of other LAB or AAB species. Sourdoughs produced in an artisan lambic brewery were characterized by the presence of the yeast species Dekkera anomala and Pichia membranifaciens. One household sourdough was characterized by the presence of uncommon species, such as Pediococcus parvulus and Pichia fermentans. Metagenomic sequencing allowed the detection of many more LAB and AAB species than the other methods applied, which opened new frontiers for the understanding of the microbial communities involved during sourdough production processes.
Effects of Snow-Related Environmental Variation on Breeding Schedules and Productivity of a High-Altitude Population of Dusky Flycatchers (Empidonax oberholseri)

ABSTRACT. Reproductive schedules of Dusky Flycatchers (Empidonax oberholseri) at Tioga Pass, in the central Sierra Nevada of California, varied considerably among years. Dates of earliest laying ranged from 29 May to 1 July and varied with snow depth, melt dates, and other factors associated with snowpack. A small apparent advance in laying date over the course of the study (0.52 days year-1 over 15 years) was associated with extremes in winter snowpack and spring melt that were related to wet—dry cycles in the Sierra Nevada. Spring snowpack acted on reproductive timing through direct and indirect effects of temperature, melt schedule, and phenological changes in habitat availability. The influence of these variables on laying dates was greatest on the first females to lay (most in early June) and declined through mid-July, when breeding terminated. Clutch size and fledgling production varied between years of heavy and light snowpack as a direct consequence of delayed egg laying in years of heavy snow. In years of light snowpack, females that laid eggs by mid-June produced larger clutches, fledged more young per nest, and were more likely to renest if nest failure occurred. Only two females attempted two broods in a single season, and both were among the first to breed. Seasonal declines in sensitivity to local environmental conditions may constrain the ability of Dusky Flycatchers to adjust breeding schedules to match phenological delays produced by changes in winter temperature, precipitation, and snowpack, and may limit range expansion to areas with arid winters and earlier spring melt.
Occupational Physical Stress Is Negatively Associated With Hippocampal Volume and Memory in Older Adults

Our jobs can provide intellectually and socially enriched environments but also be the source of major psychological and physical stressors. As the average full-time worker spends >8 h at work per weekday and remains in the workforce for about 40 years, occupational experiences must be important factors in cognitive and brain aging. Therefore, we studied whether occupational complexity and stress are associated with hippocampal volume and cognitive ability in 99 cognitively normal older adults. We estimated occupational complexity, physical stress, and psychological stress using the Work Design Questionnaire (Morgeson and Humphrey, 2006), Quantitative Workload Inventory and Interpersonal Conflict at Work Scale (Spector and Jex, 1998). We found that physical stress, comprising physical demands and work conditions, was associated with smaller hippocampal volume and poorer memory performance. These associations were independent of age, gender, brain size, socioeconomic factors (education, income, and job title), duration of the job, employment status, leisure physical activity and general stress. This suggests that physical demands at work and leisure physical activity may have largely independent and opposite effects on brain and cognitive health. Our findings highlight the importance of considering midlife occupational experiences, such as work physical stress, in understanding individual trajectories of cognitive and brain aging.
Glucose Oxidase/Nano-ZnO/Thin Film Deposit FTO as an Innovative Clinical Transducer: A Sensitive Glucose Biosensor

In the present research, a new biocompatible electrode is proposed as a rapid and direct glucose biosensing technique that improves on the deficiencies of fast clinical devices in laboratory investigations. Nano-ZnO (nanostructured zinc oxide) was sputtered by reactive direct current magnetron sputtering system on a precovered fluorinated tin oxide (FTO) conductive layer. Spin-coated polyvinyl alcohol (PVA) at optimized instrumental deposition conditions was applied to prepare the effective medium for glucose oxidase enzyme (GOx) covalent immobilization through cyanuric chloride (GOx/nano-ZnO/PVA/FTO). The electrochemical behavior of glucose on the fabricated GOx/nano-ZnO/PVA/FTO biosensor was investigated by I-V techniques. In addition, field emission scanning electron microscopy and electrochemical impedance spectroscopy were applied to assess the morphology of the modified electrode surface. The I-V results indicated good sensitivity for glucose detection (0.041 mA per mM) within 0.2–20 mM and the limit of detection was 2.0 μM. We believe that such biodevices have good potential for tracing a number of biocompounds in biological fluids along with excellent accuracy, selectivity, and precise analysis. The fast response time of the fabricated GOx/nano-ZnO/PVA/FTO biosensor (less than 3 s) could allow most types of real-time analysis.