Miracle-dz/UniFAR-FTUs huggingface dataset:
Population Structure Limits Parallel Evolution in Sticklebacks

Abstract Population genetic theory predicts that small effective population sizes (Ne) and restricted gene flow limit the potential for local adaptation. In particular, the probability of evolving similar phenotypes based on shared genetic mechanisms (i.e., parallel evolution), is expected to be reduced. We tested these predictions in a comparative genomic study of two ecologically similar and geographically codistributed stickleback species (viz. Gasterosteus aculeatus and Pungitius pungitius). We found that P. pungitius harbors less genetic diversity and exhibits higher levels of genetic differentiation and isolation-by-distance than G. aculeatus. Conversely, G. aculeatus exhibits a stronger degree of genetic parallelism across freshwater populations than P. pungitius: 2,996 versus 379 single nucleotide polymorphisms located within 26 versus 9 genomic regions show evidence of selection in multiple freshwater populations of G. aculeatus and P. pungitius, respectively. Most regions involved in parallel evolution in G. aculeatus showed increased levels of divergence, suggestive of selection on ancient haplotypes. In contrast, haplotypes involved in freshwater adaptation in P. pungitius were younger. In accordance with theory, the results suggest that connectivity and genetic drift play crucial roles in determining the levels and geographic distribution of standing genetic variation, providing evidence that population subdivision limits local adaptation and therefore also the likelihood of parallel evolution.
Diverse RNA Viruses Discovered in Three Parasitoid Wasps of the Rice Weevil Sitophilus oryzae

The enormous diversity of RNA viruses in insects is continuously validated. Parasitoid wasps, as biocontrol insects which are widely used against insect pests in agroecosystems, may also carry many “good” RNA viruses. ABSTRACT In this study, many virus-like fragments were obtained from transcriptomes of three wasp species, including Anisopteromalus calandrae (8), Lariophagus distinguendus (3), and Theocolax elegans (18), which can parasitize and control rice weevil Sitophilus oryzae, a serious insect pest of farm-stored grains. By further bioinformatic analysis and sequencing, we identified six novel RNA viruses with complete genomes and named them WWPSRV-1, WWPSRV-2, AcPSRV-1, AcNSRV-1, AcNSRV-2, and LdNSRV-1. PCR-based detection revealed that WWPSRV-1 and WWPSRV-2 had the possibility of interspecies virus transmission, especially WWPSRV-2, which was also present in the rice weevil adults. Phylogenetically, three out of these six viruses appeared to be members of order Picornavirales: WWPSRV-1 belonged to unassigned virus families of this order, whereas WWPSRV-2 and AcPSRV-1 belonged to families Iflaviridae and Dicistroviridae, respectively. The conserved picornavirus-typical domains helicase, protease, and RNA-dependent RNA polymerase could be found in the nonstructural protein encoded by the three viruses, whose genomes consisted of the different numbers of open reading frames (ORFs). The other three RNA viruses could be classified to order Mononegavirales: AcNSRV-1 and AcNSRV-2 belonged to family Lispiviridae, whereas LdNSRV-1 belonged to a big family Rhabdoviridae. The genomes of the three viruses contained at least five ORFs, encoding deduced proteins in the following order: 3′-N-P-M-G-L-5′. All the ORFs were separated by conserved intergenic sequences which likely regulated the transcription termination and initiation. Our findings enhance the understanding of RNA viruses in weevil wasps and set the foundation for the future study of the association among weevils, weevil wasps, and RNA viruses. IMPORTANCE The enormous diversity of RNA viruses in insects is continuously validated. Parasitoid wasps, as biocontrol insects which are widely used against insect pests in agroecosystems, may also carry many “good” RNA viruses. Some RNA viruses in parasitoid wasps have been reported to affect the host wasps or the wasps’ host. Here, six novel RNA viruses with complete genomes were identified in three parasitoid wasps of the rice weevil. One of these viruses was also detected in the rice weevil adults. Phylogenetically, WWPSRV-1 was the first unambiguous detection of Nora-like virus in insect parasitoids. WWPSRV-2 and AcPSRV-1 belong to families Iflaviridae and Dicistroviridae, some viruses of which can result in lethal infections in silkworms and honeybees. The other three RNA viruses belong to order Mononegavirales, which comprises many well-known insect-associated viruses.
First Molecular Detection of Coxiella burnetii in Beef Cattle in West Java, Indonesia.

Coxiella burnetii (C. burnetii) is a bacterial agent causing Q fever which is widespread all over the world. Livestock such as cattle, goat, and sheep are the main sources of infection for this disease. Infection of C. burnetii causes abortion of livestock, resulting in economic damage. Q fever is zoonotic disease and potential public health hazard. To date, little is known about the infection of C. burnetii in livestock in Indonesia. The objective of this research is to screen the genome of C. burnetii bacteria in beef cattle in West Java, Indonesia. Organ tissue samples were collected from cattle slaughtered in slaughterhouses, West Java. C. burnetii genome was detected from cattle samples in all three samplings area by nested PCR (nPCR) targeting com1 gene of C. burnetii. Sequencing analysis of 16S rRNA gene revealed the amplicons showed 99.9% nucleotide identity to C. burnetii strains Heizberg, 1843, 2574, 701CbB1, and 14160-001. Our results indicate that the infection of C. burnetii occurs in Indonesian beef cattles and highlight the risk of exposure to C. burnetii infection in human.
IL-1R1-Dependent Signals Improve Control of Cytosolic Virulent Mycobacteria In Vivo

For decades, Mycobacterium tuberculosis has been one of the deadliest pathogens known. Despite infecting approximately one-third of the human population, no effective treatment or vaccine is available. ABSTRACT Mycobacterium tuberculosis infections claim more than a million lives each year, and better treatments or vaccines are required. A crucial pathogenicity factor is translocation from phagolysosomes to the cytosol upon phagocytosis by macrophages. Translocation from the phagolysosome to the cytosol is an ESX-1-dependent process, as previously shown in vitro. Here, we show that in vivo, mycobacteria also translocate to the cytosol but mainly when host immunity is compromised. We observed only low numbers of cytosolic bacilli in mice, armadillos, zebrafish, and patient material infected with M. tuberculosis, M. marinum, or M. leprae. In contrast, when innate or adaptive immunity was compromised, as in severe combined immunodeficiency (SCID) or interleukin-1 receptor 1 (IL-1R1)-deficient mice, significant numbers of cytosolic M. tuberculosis bacilli were detected in the lungs of infected mice. Taken together, in vivo, translocation to the cytosol of M. tuberculosis is controlled by adaptive immune responses as well as IL-1R1-mediated signals. IMPORTANCE For decades, Mycobacterium tuberculosis has been one of the deadliest pathogens known. Despite infecting approximately one-third of the human population, no effective treatment or vaccine is available. A crucial pathogenicity factor is subcellular localization, as M. tuberculosis can translocate from phagolysosome to the cytosol in macrophages. The situation in vivo is more complicated. In this study, we establish that high-level cytosolic escape of mycobacteria can indeed occur in vivo but mainly when host resistance is compromised. The IL-1 pathway is crucial for the control of the number of cytosolic mycobacteria. The establishment that immune signals result in the clearance of cells containing cytosolic mycobacteria connects two important fields, cell biology and immunology, which is vital for the understanding of the pathology of M. tuberculosis.
The many facets of miR‐223 in cancer: Oncosuppressor, oncogenic driver, therapeutic target, and biomarker of response

Given their intrinsic pleiotropism, microRNAs (miR) play complex biological roles, in both normal and pathological conditions. Often the same miR can act as oncogene or oncosuppressor, depending on the biological process dysregulated in each specific tissue. miR‐223 does not represent an exception to this rule and its functions greatly differ in different contexts. miR‐223 has been widely studied in the hematopoietic compartment, where it plays a central role in innate immune response, regulating myeloid differentiation and granulocytes function. Accordingly, dysregulated expression of miR‐223 has been associated to different inflammatory disorders and tumors arising from the immune compartment. Most carcinomas, breast cancer being the most studied, display loss of miR‐223. However, in gastro‐esophageal cancers miR‐223 is frequently overexpressed and correlates with worse prognosis. A link between miR‐223 and response to CDK4/6‐inhibitors has been recently proposed, suggesting a role as biomarker of therapeutic response. The notion that one of the most commonly mutated protein in cancer, mutant p53, binds the promoter of miR‐223 and suppresses its transcription, adds a further level of complexity to the full understanding of miR‐223 in cancer. In this review, we will summarize the current knowledge on the molecular networks that alter or are altered by miR‐223, in different cancer types. We will discuss if the times are ready for the exploitation of miR‐223 as predictive biomarker of treatment response or, even, as therapeutic target, in specific settings. Finally, we will suggest which could be the next steps to be taken for a realistic clinical application of miR‐223.
Education and long-term outcomes in first episode psychosis: 10-year follow-up study of the PAFIP cohort

Abstract Background Lower levels of education have been associated with the development of psychosis. Investigating educational achievement in the first episode of psychosis (FEP) patients may shed light on the origins of the alterations and on the variability of outcomes in psychotic disorders. Methods Education achievement was explored in a large sample (n = 659) of FEP patients enrolled in programa de atención a fases iniciales de psicosis (PAFIP), a research and assistance program conducted in Spain. Patients were stratified according to the Spanish educational system according to their attendance in primary (low), secondary (medium) or university studies (high). The three groups were compared on available premorbid, clinical and neuropsychological variables. A subgroup of patients (n = 209), comprising the 10-year follow-up PAFIP cohort, were again compared. Results Overall, 49% and 37% of FEP patients had low and medium levels of education, respectively. In total, 13% of the patients with a higher level of education were more frequently women (64%) and older at illness onset (36 years old), reported better premorbid adjustment, presented less severe positive symptoms and better functioning; and showed higher premorbid intelligence quotient and better performance on all the explored cognitive domains. Ten years later the FEP patients in the medium- and high-education groups had good global functioning and a neurocognitive performance within the normal limits. Conclusions Higher education is associated with better initial conditions and more favourable outcomes after an FEP. Sharing this information with the world's educational systems is essential to targeting resources and designing innovative programs or strategies to compensate for student difficulties.
Emotion regulation therapy for social anxiety disorder: a single case series study.

BACKGROUND Despite the vast majority of evidence indicating the efficacy of traditional and recent cognitive behaviour therapy (CBT) therapies in treating social anxiety disorder (SAD), some individuals with SAD do not improve by these interventions, particularly when co-morbidity is present. AIMS It is not clear how emotion regulation therapy (ERT) can improve SAD co-morbid with symptoms of generalized anxiety disorder (GAD) and depression. This study investigated this gap. METHOD Treatment efficacy was assessed using a single case series methodology. Four clients with SAD co-occurring with GAD and depression symptoms received a 16-session version of ERT in weekly individual sessions. During the treatment, self-report measures and clinician ratings were used to assess the symptom intensity, model-related variables, and quality of life, work and social adjustment of participants every other week throughout the treatment. Follow-up was also conducted at 1, 2 and 3 months after treatment. Data were analysed using visual analysis, effect size (Cohen's d) and percentage of improvement. RESULTS SAD clients with depression and GAD symptoms demonstrated statistically and clinically significant improvements in symptom severity, quality of life, work, social adjustment and model-related measures (i.e. negative emotionality/safety motivation, emotion regulation strategies). The improvements were largely maintained during the follow-up period and increased for some variables. CONCLUSION These findings showed preliminary evidence for the role of emotion dysregulation and motivational factors in the aetiology and maintenance of SAD and the efficacy of ERT in the treatment of co-morbid SAD.
The effect of muscle blood flow restriction on hemodynamics, cerebral oxygenation and activation at rest.

This study tested the hypothesis that muscle blood flow restriction reduces muscle and cerebral oxygenation, at rest. In 26 healthy males, aged 33±2 yrs, physiological variables were continuously recorded during a 10-min period in two experimental conditions: a) with muscle blood flow restriction through thigh cuffs application inflated at 120 mmHg (With Cuffs, WC) and b) without restriction (No Cuffs, NC). Muscle and cerebral oxygenation were reduced by muscle blood flow restriction as suggested by the increase in both muscle and cerebral deoxygenated hemoglobin (Δ[HHb]; p<0.01) and the decrease of muscle and cerebral oxygenation index (Δ[HbDiff]; p<0.01). Hemodynamic responses were not affected by such muscle blood flow restriction, whereas baroreflex sensitivity was reduced (p=0.009). The perception of leg discomfort was higher (p<0.001) in the WC than in the NC condition. This study suggests that thigh cuffs application inflated at 120 mmHg is an effective method to reduce muscle oxygenation at rest. These changes at the muscular level seem to be sensed by the central nervous system, evoking alterations in cerebral oxygenation and baroreflex sensitivity. Novelty bullets: • Thigh cuffs application inflated at 120 mmHg effectively reduces muscle oxygenation at rest. • Limiting muscle oxygenation appears to reduce cerebral oxygenation, and baroreflex sensitivity, at rest. • Even in healthy subjects, limiting muscle oxygenation, at rest, affects neural integration.
Selectivity and the effect of mass extinctions on disparity and functional ecology

Fossils reveal that morphological disparity, ecology, and taxonomic richness can remain coupled across nonselective mass extinctions. Selectivity of mass extinctions is thought to play a major role in coupling or decoupling of taxonomic, morphological, and ecological diversity, yet these measures have never been jointly evaluated within a single clade over multiple mass extinctions. We investigate extinction selectivity and changes in taxonomic diversity, morphological disparity, and functional ecology over the ~160-million-year evolutionary history of diplobathrid crinoids (Echinodermata), which spans two mass extinctions. Whereas previous studies documented extinction selectivity for crinoids during background extinction, we find no evidence for selectivity during mass extinctions. Despite no evidence for extinction selectivity, disparity remains strongly correlated with richness over extinction events, contradicting expected patterns of disparity given nonselective extinction. Results indicate that (i) disparity and richness can remain coupled across extinctions even when selective extinction does not occur, (ii) simultaneous decreases in taxonomic diversity and disparity are insufficient evidence for extinction selectivity, and (iii) selectivity differs between background and mass extinction regimes.
Relationship between anthocyanins, proanthocyanidins, and cell wall polysaccharides in grapes and red wines. A current state-of-art review

Abstract Numerous research studies have evaluated factors influencing the nature and levels of phenolics and polysaccharides in food matrices. However, in grape and wines most of these works have approach these classes of compounds individually. In recent years, the number of publications interconnecting classes have increased dramatically. The present review relates the last decade’s findings on the relationship between phenolics and polysaccharides from grapes, throughout the entire winemaking process up to evaluating the impact of their relationship on the red wine sensory perception. The combination and interconnection of the most recent research studies, from single interactions in model wines to the investigation of the formation of complex macromolecules, brings the perfect story line to relate the relationship between phenolics and polysaccharides from the vineyard to the glass. Grape pectin is highly reactive toward grape and grape derived phenolics. Differences between grape cultivars or changes during grape ripeness will affect the extractability of these compounds into the wines. Therefore, the nature of the grape components will be crucial to understand the subsequent reactions occurring between phenolics and polysaccharide of the corresponding wines. It has been demonstrated that they can form very complex macromolecules which affect wine color, stability and sensory properties.
Isolation of Cellulose Nanofibres: Elucidation of a Novel Approach Utilizing Fungal Pretreatment

ii Chapter 1 Introduction . 1 1.1 Cellulose and Cellulose Microfibrils . 1 1.2 Cellulose Nanofibres . 1 1.3 Why Cellulose Nanofibres? 2 1.4 Applications . 3 1.5 Cellulose Nanofibre Isolation and Application Challenges . 8 1.6 Isolation of Cellulose Nanofibres . 10 1.7 Research Significance . 18 Chapter 2 Scientific Background . 20 2.1 Structure of Cellulose . 20 2.2 Biodegradation of Cellulosic Materials . 36 2.3 Research Rationale . 47 2.4 The Choice of Ophiostoma Ulmi . 49 Chapter 3 Research Hypothesis and Objectives . 51 3.1 Hypothesis. 51 3.2 Research Objectives . 51 Chapter 4 Approach . 52 Chapter 5 Experimental . 55 5.1 Materials . 55 5.2 Methods. 55 vi Chapter 6 Results and Discussion . 70 Bio-treatment of Natural Fibres: Effect on Fibres and Yield of Cellulose Nanofibres . 70 6.1 Introduction . 70 6.2 Bleached Kraft Fibre Characterization . 70 6.3 Effect of Ophiostoma Ulmi Bio-treatment of Fibres on Cellulose Nanofibres Yield and Fibre Diameter Distribution . 71 6.4 Conclusions . 82 Chapter 7 Results and Discussion . 83 Bio-Treatment of Natural Fibres: Impact of Pre-refining of Fibres on Bio-treatment Efficiency and Nanofibre Yield . 83 7.1 Introduction . 83 7.2 Pre-Refining of Wood Fibres and Its Effect on Bio-treatment . 83 7.3 Cellulose Nanofibres Overall Yield and Diameter Distribution . 85 7.4 Conclusions . 90 Chapter 8 Results and Discussion . 91 Bio-treatment of Natural Fibres: Effect on Hydrogen Bonding Network . 91 8.1 Introduction . 91 8.2 Determination of Relative Intensity of Hydrogen Bonding by FT-IR . 92 8.3 Effect of Bio-treatment on the Hydroxyl Chemistry of Cellulose Fibres . 95 8.4 Decrease in the Relative Intensity of Hydrogen Bond Network . 97 8.5 Solid State C Nuclear Magnetic Resonance Spectroscopy . 107 8.6 Isolation and Identification of Fungal Protein Secreted by Ophiostoma Ulmi . 112 8.7 Conclusions . 117
Thromboembolic Complications of Vascular Catheters Used for Pediatric Continuous Renal Replacement Therapy: Prevalence in a Single-Center, Retrospective Cohort*

OBJECTIVES: Pediatric venous thromboembolic events are commonly associated with in situ central venous catheters. The risk for severe venous thromboembolism increases if a larger portion of the vessel lumen is occupied by the central venous catheter. A functioning vascular catheter is required when the continuous renal replacement therapy is used in critically ill children. Due to the high blood flow required for continuous renal replacement therapy, the external diameter of the catheter needs to be larger than a conventional central venous catheter used for venous access, potentially increasing the risk of venous thromboembolism. However, children on continuous renal replacement therapy often receive systemic anticoagulation to prevent filter clotting, possibly also preventing venous thromboembolism. The frequency of catheter-related venous thromboembolic events in this setting has not been described. Our main objective was to determine the prevalence of catheter-related venous thromboembolism in pediatric continuous renal replacement therapy. DESIGN: Retrospective cohort study. SETTING: Tertiary multidisciplinary academic pediatric hospital. PATIENTS: Patients 0–18 years old with a vascular catheter used for continuous renal replacement therapy. INTERVENTIONS: None. MEASUREMENTS AND MAIN RESULTS: In our series of 80 patients, we used 105 vascular catheters. The median age of the patients was 10 months and PICU mortality rate was 21%. Venous thromboembolic events were considered to be catheter related if located in the same vein as the vascular catheter and radiologically verified. Six (5.7%) catheter-related venous thromboembolic events were found. The clinically relevant complications of venous thromboembolism included superior vena cava syndrome and catheter dysfunction. In one patient, severe and life-threatening pulmonary embolism occurred. In comparison with patients without venous thromboembolism, venous thromboembolic events were associated with lower body weight (p = 0.03) and longer durations of continuous renal replacement therapy (p < 0.01), mechanical ventilation (p = 0.03), and PICU stay (p < 0.01). Five out of six venous thromboembolisms appeared in neonates. CONCLUSIONS: Catheter-related venous thromboembolism is a clinically relevant complication of pediatric continuous renal replacement therapy, with a prevalence of 5.7% in our cohort. Clinicians involved in pediatric continuous renal replacement therapy need to be vigilant for symptoms of venous thromboembolisms and initiate appropriate treatment as soon as possible.