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Abstract The structure of cellular prion proteins encoded by the prion protein gene (PRNP) impacts susceptibility to transmissible spongiform encephalopathies, including chronic wasting disease (CWD) in deer. The recent emergence of CWD in Northern European reindeer (Rangifer tarandus), moose (Alces alces alces) and red deer (Cervus elaphus), in parallel with the outbreak in North America, gives reason to investigate PRNP variation in European deer, to implement risk assessments and adjust CWD management for deer populations under threat. We here report PRNP-sequence data from 911 samples of German red, roe (Capreolus capreolus), sika (Cervus nippon) and fallow deer (Dama dama) as well as additional data from 26 Danish red deer close to the German border and four zoo species not native to Germany. No PRNP sequence variation was observed in roe and fallow deer, as previously described for populations across Europe. In contrast, a broad PRNP variation was detected in red deer, with non-synonymous polymorphisms at codons 98, 226 and 247 as well as synonymous mutations at codons 21, 78, 136 and 185. Moreover, a novel 24 bp deletion within the octapeptide repeat was detected. In summary, 14 genotypes were seen in red deer with significant differences in their geographical distribution and frequencies, including geographical clustering of certain genotypes, suggesting “PRNP-linages” in this species. Based on data from North American CWD and the genotyping results of the European CWD cases, we would predict that large proportions of wild cervids in Europe might be susceptible to CWD once introduced to naive populations.

Este estudo avaliou, durante 671 dias, a remoção de demanda química de oxigênio (DQO) e de nitrogênio total (NT), em um reator de leito empacotado em escala piloto de 5,65 m3, tratando a mistura esgoto bruto: efluente de Upflow Anaerobic Sludge Blanket (UASB). O meio suporte usado no reator foi o Biobob® (espuma de poliuretano com estrutura externa de polipropileno). Foram testados tempos de retenção hidráulica (TRHs) de 12 e 10h; e taxa de reciclo: alimentação de 2:1. As condições de aeração do estudo foram: contínua, 60 min aerando/120 min sem aeração; e 120 min aerando/60 min sem aeração. A DQO afluente variou entre 317±53 e 599±129 mg.L-1; e a TKN, entre 35±10 e 56±10 mg.L-1. Não houve diferença estatística nas eficiências de redução de DQO (76 e 87%). A remoção de NT média foi de 68%. A nitrificação foi um fator limitante do processo e seu melhor desempenho ocorreu nas condições aeração contínua e 120 min de aeração, respectivamente. Concluiu-se que o reator estudado é eficiente na remoção simultânea de DQO e NT, sendo uma alternativa viável para o tratamento e pós-tratamento de esgoto sanitário.

Abstract Background Beta-cell monogenic forms of diabetes have strong support for precision medicine. We systematically analyzed evidence for precision treatments for GCK-related hyperglycemia, HNF1A-, HNF4A- and HNF1B-diabetes, and mitochondrial diabetes (MD) due to m.3243 A > G variant, 6q24-transient neonatal diabetes mellitus (TND) and SLC19A2-diabetes. Methods The search of PubMed, MEDLINE, and Embase for individual and group level data for glycemic outcomes using inclusion (English, original articles written after 1992) and exclusion (VUS, multiple diabetes types, absent/aggregated treatment effect measures) criteria. The risk of bias was assessed using NHLBI study-quality assessment tools. Data extracted from Covidence were summarized and presented as descriptive statistics in tables and text. Results There are 146 studies included, with only six being experimental studies. For GCK-related hyperglycemia, the six studies (35 individuals) assessing therapy discontinuation show no HbA1c deterioration. A randomized trial (18 individuals per group) shows that sulfonylureas (SU) were more effective in HNF1A-diabetes than in type 2 diabetes. Cohort and case studies support SU’s effectiveness in lowering HbA1c. Two cross-over trials (each with 15–16 individuals) suggest glinides and GLP-1 receptor agonists might be used in place of SU. Evidence for HNF4A-diabetes is limited. Most reported patients with HNF1B-diabetes (N = 293) and MD (N = 233) are on insulin without treatment studies. Limited data support oral agents after relapse in 6q24-TND and for thiamine improving glycemic control and reducing/eliminating insulin requirement in SLC19A2-diabetes. Conclusion There is limited evidence, and with moderate or serious risk of bias, to guide monogenic diabetes treatment. Further evidence is needed to examine the optimum treatment in monogenic subtypes.

Abstract Differential diagnosis is a crucial aspect of medical practice, as it guides clinicians to accurate diagnoses and effective treatment plans. Traditional resources, such as medical books and services like UpToDate, are constrained by manual curation, potentially missing out on novel or less common findings. This paper introduces and analyzes two novel methods to mine etiologies from scientific literature. The first method employs a traditional Natural Language Processing (NLP) approach based on syntactic patterns. By using a novel application of human-guided pattern bootstrapping patterns are derived quickly, and symptom etiologies are extracted with significant coverage. The second method utilizes generative models, specifically GPT-4, coupled with a fact verification pipeline, marking a pioneering application of generative techniques in etiology extraction. Analyzing this second method shows that while it is highly precise, it offers lesser coverage compared to the syntactic approach. Importantly, combining both methodologies yields synergistic outcomes, enhancing the depth and reliability of etiology mining.

Abstract Introduction Aging is associated with a progressive decline in the capacity for physical activity. The objective of the current study was to evaluate the effect of an intermittent hyperbaric oxygen therapy (HBOT) protocol on maximal physical performance and cardiac perfusion in sedentary older adults. Methods A randomized controlled clinical trial randomized 63 adults (> 64yrs) either to HBOT (n = 30) or control arms (n = 33) for three months. Primary endpoint included the maximal oxygen consumption (VO2Max) and VO2Max/Kg, on an E100 cycle ergometer. Secondary endpoints included cardiac perfusion, evaluated by magnetic resonance imaging and pulmonary function. The HBOT protocol comprised of 60 sessions administered on a daily basis, for 12 consecutive weeks, breathing 100% oxygen at 2 absolute atmospheres (ATA) for 90 min with 5-minute air breaks every 20 min. Results Following HBOT, improvements were observed in VO2Max/kg, with a significant increase of 1.91 ± 3.29 ml/kg/min indicated by a net effect size of 0.455 (p = 0.0034). Additionally, oxygen consumption measured at the first ventilatory threshold (VO2VT1) showed a significant increase by 160.03 ± 155.35 ml/min (p

The effects of the supplier and the mass of pork thighs together with some production parameters including mass loss during ham production, mass of the final products and relative content of non-protein nitrogen (NPN) on the texture profile of Slovenian dry-cured ham – Kraški pršut were investigated to determine its optimal texture. The study included 32 dry-cured hams from two mass classes (heavy with thigh mass at salting of 11.7–12.1 kg and light with thigh mass at salting of 10.5–10.7 kg) and two different pork thigh suppliers from regular production. Slices cut transversally from the thigh at approximately 8 cm from the femur head were used for physicochemical parameter (pH, contents of moisture, total fat, protein, NaCl, and NPN) analysis, instrumental texture analysis profile analysis (TPA), and sensory analysis. Pork thigh mass had a significant effect on the TPA parameters; light samples were harder, chewier, springier, more cohesive and resilient compared to the heavy samples. NaCl content and sensory scores for saltiness were higher in the light Kraški pršut samples than in the heavy ones. Based on the median for hardness in the sensory analysis, the samples were classified into three ranks of texture using linear discriminant analysis (9 variables, 100% correct classification): optimal (median 4.0; 19% of samples), slightly too soft (median 3.5, 72% of samples), and soft (median 3.0; 9% of samples). Kraški pršut mass and hardness were significantly correlated to saltiness, pastiness, aroma, and all TPA parameters (p≤0.05). Positive correlation (p≤0.05) was also observed between NPN and pastiness. These findings indicate the importance of supplier, mass of pork thighs, and production parameters for optimizing the texture of Kraški pršut.

Abstract Background Adult muscle-resident myogenic stem cells, satellite cells (SCs), that play non-redundant role in muscle regeneration, are intrinsically impaired in Duchenne muscular dystrophy (DMD). Previously we revealed that dystrophic SCs express low level of anti-inflammatory and anti-oxidative heme oxygenase-1 (HO-1, HMOX1). Here we assess whether targeted induction of HMOX1 affect SC function and alleviates hallmark symptoms of DMD. Methods We generated double-transgenic mouse model (mdx;HMOX1 Pax7Ind) that allows tamoxifen (TX)-inducible HMOX1 expression in Pax7 positive cells of dystrophic muscles. Mdx;HMOX1 Pax7Ind and control mdx mice were subjected to 5-day TX injections (75 mg/kg b.w.) followed by acute exercise protocol with high-speed treadmill (12 m/min, 45 min) and downhill running to worsen skeletal muscle phenotype and reveal immediate effects of HO-1 on muscle pathology and SC function. Results HMOX1 induction caused a drop in SC pool in mdx;HMOX1 Pax7Ind mice (vs. mdx counterparts), while not exaggerating the effect of physical exercise. Upon physical exercise, the proliferation of SCs and activated CD34− SC subpopulation, was impaired in mdx mice, an effect that was reversed in mdx;HMOX1 Pax7Ind mice, however, both in vehicle- and TX-treated animals. This corresponded to the pattern of HO-1 expression in skeletal muscles. At the tissue level, necrotic events of selective skeletal muscles of mdx mice and associated increase in circulating levels of muscle damage markers were blunted in HO-1 transgenic animals which showed also anti-inflammatory cytokine profile (vs. mdx). Conclusions Targeted expression of HMOX1 plays protective role in DMD and alleviates dystrophic muscle pathology.

Abstract We show that correlations in strongly interacting many-particle systems can create quantum decoherence, leading to a mechanism of dissipation that does not rely on an external source. Using analytical methods, we study a bosonic many body system in two dimensions, with extended interactions between particles. We show that, as expected, the system can be driven out of a coherent state. Surprisingly, when the interaction strength is sufficiently large, the system reenters the superfluid phase even after coherence is lost. The breakdown of quantum coherence is a certainty, but interpreting the process correctly relies on understanding and preserving the nature of the coupling between the constituents of the many particle system. The methods used provide a natural cutoff point at the critical temperature, where superfluidity breaks down.

Abstract The modification of the surgical polypropylene mesh and the polytetrafluoroethylene vascular prosthesis with cecropin A (small peptide) and puromycin (aminonucleoside) yielded very stable preparations of modified biomaterials. The main emphasis was placed on analyses of their antimicrobial activity and potential immunomodulatory and non-cytotoxic properties towards the CCD841 CoTr model cell line. Cecropin A did not significantly affect the viability or proliferation of the CCD 841 CoTr cells, regardless of its soluble or immobilized form. In contrast, puromycin did not induce a significant decrease in the cell viability or proliferation in the immobilized form but significantly decreased cell viability and proliferation when administered in the soluble form. The covalent immobilization of these two molecules on the surface of biomaterials resulted in stable preparations that were able to inhibit the multiplication of Staphylococcus aureus and S. epidermidis strains. It was also found that the preparations induced the production of cytokines involved in antibacterial protection mechanisms and stimulated the immune response. The key regulator of this activity may be related to TLR4, a receptor recognizing bacterial LPS. In the present study, these factors were produced not only in the conditions of LPS stimulation but also in the absence of LPS, which indicates that cecropin A- and puromycin-modified biomaterials may upregulate pathways leading to humoral antibacterial immune response.

Slavic populations, such as those in Poland, are considered to have a low prevalence of giant cell arteritis (GCA), although epidemiological data are sparse. The study aimed to compare the reported frequency of GCA in various regions of Poland and analyze the differences between them. We conducted a multicenter, retrospective study of all GCA patients included in the POLVAS registry—the first large multicenter database of patients with vasculitis in Poland. The data from the POLVAS registry were compared with the reported prevalence provided by national insurers from the corresponding regions. A 10-fold increase in the diagnostic rates of GCA was observed in Poland between 2008 and 2019, reaching 8.38 per 100,000 population > 50 years old. It may be attributed to increased interest accompanied by improved diagnostic modalities with the introduction of ultrasound-based, fast-track diagnostic pathways in some centers. However, regional inequities are present, resulting in 10-fold differences (from 2.57 to 24.92) in reported prevalence between different regions. Corticosteroid (CS) monotherapy was the main stem of treatment. Further cooperation and education are needed to minimize regional inequities. This observational study suggests some potential for further increase of the recognizability of GCA and wider use of other than CS monotherapy treatment regimens. We hope that the Polish experience might be interesting and serve as some guidance for the populations where GCA is underdiagnosed.

Background & Aims: Tacrolimus has been associated with recurrence of primary biliary cholangitis (PBC) after liver transplantation (LT), which in turn may reduce survival. This study aimed to assess the association between the type of calcineurin inhibitor used and long-term outcomes following LT in patients with PBC. Methods: Survival analyses were used to assess the association between immunosuppressive drugs and graft or patient survival among adult patients with PBC in the European Liver Transplant Registry. Patients who received a donation after brain death graft between 1990 and 2021 with at least 1 year of event-free follow-up were included. Results: In total, 3,175 patients with PBC were followed for a median duration of 11.4 years (IQR 5.9–17.9) after LT. Tacrolimus (Tac) was registered in 2,056 (64.8%) and cyclosporin in 819 (25.8%) patients. Following adjustment for recipient age, recipient sex, donor age, and year of LT, Tac was not associated with higher risk of graft loss (adjusted hazard ratio [aHR] 1.07, 95% CI 0.92-1.25, p = 0.402) or death (aHR 1.06, 95% CI 0.90-1.24, p = 0.473) over cyclosporin. In this model, maintenance mycophenolate mofetil (MMF) was associated with a lower risk of graft loss (aHR 0.72, 95% CI 0.60-0.87, p

Online education is a type of distance education in which the entire teaching process is mediated by technology. There are many benefits and challenges to online education, like time management, maintaining social interactions, and motivation. Studying itself is full of challenges that arise from academic activities, which can lead to academic stress. The ability to adapt and respond to such challenges is known as academic resilience. Since the pandemic pushed universities online, there was no time to adapt to such circumstances. Therefore, the first aim of this study was to investigate the similarities and differences between online and in-class education in time management, assessments and group tasks, social interactions, and motivation from the perspective of students in higher education in Croatia. Our second aim was to identify the role of these factors in predicting academic stress and academic resilience. The study was conducted online, and 704 students participated. Most of them believe that they have learned less during online courses, they were less motivated to learn, and they have cheated more during online compared to in-class courses. Time flexibility and lower tendency for procrastination, satisfaction with assessments and group tasks, and higher motivation were highlighted as important factors contributing to lower academic stress and higher academic resilience. There were no associations between social support and changes in academic stress or resilience. Recommendations for online courses and stakeholders in education who care about the mental health of students are discussed.

ABSTRACT Currently, tuberculosis immunoprophylaxis is based solely on Bacillus Calmette-Guérin (BCG) vaccination, and some of the new potential tuberculosis vaccines are based on the BCG genome. Therefore, it is reasonable to analyze the genomes of individual BCG substrains. The aim of this study was the genetic characterization of the BCG-Moreau Polish (PL) strain used for the production of the BCG vaccine in Poland since 1955. Sequencing of different BCG lots showed that the strain was stable over a period of 59 years. As a result of comparison, BCG-Moreau PL with BCG-Moreau Rio de Janeiro (RDJ) 143 single nucleotide polymorphisms (SNPs) and 32 insertion/deletion mutations (INDELs) were identified. However, the verification of these mutations showed that the most significant were accumulated in the BCG-Moreau RDJ genome. The mutations unique to the Polish strain genome are 1 SNP and 2 INDEL. The strategy of combining short-read sequencing with long-read sequencing is currently the most optimal approach for sequencing bacterial genomes. With this approach, the only available genomic sequence of BCG-Moreau PL was obtained. This sequence will primarily be a reference point in the genetic control of the stability of the vaccine strain in the future. The results enrich knowledge about the microevolution and attenuation of the BCG vaccine substrains.IMPORTANCEThe whole genome sequence obtained is the only genomic sequence of the strain that has been used for vaccine production in Poland since 1955. Sequencing of different BCG lots showed that the strain was stable over a period of 59 years. The comprehensive genomic analysis performed not only enriches knowledge about the microevolution and attenuation of the BCG vaccine substrains but also enables the utilization of identified markers as a reference point in the genetic control and identity tests of the stability of the vaccine strain in the future.

Abstract Background The long-term consequences of prematurity are often not sufficiently recognized. To address this gap, a prospective cohort study, which is a continuation of the multicenter Polish study PREMATURITAS, was conducted, utilizing unique clinical data from 20 years ago. Objective The main goal was to evaluate lung function, detect any structural abnormalities using lung ultrasound, and assess psychological well-being in young adults born between 24 and 34 weeks of gestational age (GA). Additionally, the study aimed to investigate potential associations between perinatal risk factors and abnormalities observed in pulmonary function tests (PFTs) during adulthood. Methods The young survivors underwent a comprehensive set of PFTs, a lung ultrasound, along with the quality of life assessment. Information regarding the neonatal period and respiratory complications was obtained from the baseline data collected in the PREMATURITAS study. Results A total of 52 young adults, with a mean age of 21.6 years, underwent PFTs. They were divided into two groups based on GA: 24–28 weeks (n = 12) and 29–34 weeks (n = 40). The subgroup born more prematurely had significantly higher lung clearance index (LCI), compared to the other subgroup (p = 0.013). LCI ≥ 6.99 was more frequently observed in the more premature group (50% vs. 12.5%, p = 0.005), those who did not receive prenatal steroids (p = 0.020), with a diagnosis of Respiratory Distress Syndrome (p = 0.034), those who received surfactant (p = 0.026), and mechanically ventilated ≥ 7 days (p = 0.005). Additionally, elevated LCI was associated with the diagnosis of asthma (p = 0.010). Conclusions The findings suggest pulmonary effects due to prematurity persist into adulthood and their insult on small airway function. Regular follow-up evaluations of young survivors born preterm should include assessments of PFTs. Specifically, the use of LCI can provide valuable insights into long-term pulmonary impairment.

Abstract In computational pathology, automatic nuclei instance segmentation plays an essential role in whole slide image analysis. While many computerized approaches have been proposed for this task, supervised deep learning (DL) methods have shown superior segmentation performances compared to classical machine learning and image processing techniques. However, these models need fully annotated datasets for training which is challenging to acquire, especially in the medical domain. In this work, we release one of the biggest fully manually annotated datasets of nuclei in Hematoxylin and Eosin (H&E)-stained histological images, called NuInsSeg. This dataset contains 665 image patches with more than 30,000 manually segmented nuclei from 31 human and mouse organs. Moreover, for the first time, we provide additional ambiguous area masks for the entire dataset. These vague areas represent the parts of the images where precise and deterministic manual annotations are impossible, even for human experts. The dataset and detailed step-by-step instructions to generate related segmentation masks are publicly available on the respective repositories.

Abstract In our previous randomized controlled trial, we documented significant improvements in cognitive, psychiatric, fatigue, sleep, and pain symptoms among long Coronavirus disease 2019 (COVID) patients who underwent hyperbaric oxygen therapy (HBOT). The primary objective of the present study was to evaluate the enduring 1 year long term effects of HBOT on long COVID syndrome. This longitudinal long-term follow-up included 31 patients with reported post COVID-19 cognitive symptoms, who underwent 40 daily sessions of HBOT. Participants were recruited more than one year (486 ± 73) after completion of the last HBOT session. Quality of life, assessed using the short form-36 (SF-36) questionnaire revealed, that the long-term results exhibited a similar magnitude of improvement as the short-term outcomes following HBOT across most domains. Regarding sleep quality, improvements were observed in global score and across five sleep domains with effect sizes of moderate magnitude during the short-term evaluation, and these improvements persisted in the long-term assessment (effect size (ES1) = 0.47–0.79). In the realm of neuropsychiatric symptoms, as evaluated by the brief symptom inventory-18 (BSI-18), the short-term assessment following HBOT demonstrated a large effect size, and this effect persisted at the long-term evaluation. Both pain severity (ES1 = 0.69) and pain interference (ES1 = 0.83), had significant improvements during the short-term assessment post HBOT, which persisted at long term. The results indicate HBOT can improve the quality of life, quality of sleep, psychiatric and pain symptoms of patients suffering from long COVID. The clinical improvements gained by HBOT are persistent even 1 year after the last HBOT session.

Abstract There has been a growing effort to replace manual extraction of data from research papers with automated data extraction based on natural language processing, language models, and recently, large language models (LLMs). Although these methods enable efficient extraction of data from large sets of research papers, they require a significant amount of up-front effort, expertise, and coding. In this work, we propose the ChatExtract method that can fully automate very accurate data extraction with minimal initial effort and background, using an advanced conversational LLM. ChatExtract consists of a set of engineered prompts applied to a conversational LLM that both identify sentences with data, extract that data, and assure the data’s correctness through a series of follow-up questions. These follow-up questions largely overcome known issues with LLMs providing factually inaccurate responses. ChatExtract can be applied with any conversational LLMs and yields very high quality data extraction. In tests on materials data, we find precision and recall both close to 90% from the best conversational LLMs, like GPT-4. We demonstrate that the exceptional performance is enabled by the information retention in a conversational model combined with purposeful redundancy and introducing uncertainty through follow-up prompts. These results suggest that approaches similar to ChatExtract, due to their simplicity, transferability, and accuracy are likely to become powerful tools for data extraction in the near future. Finally, databases for critical cooling rates of metallic glasses and yield strengths of high entropy alloys are developed using ChatExtract.