Miracle-dz/UniFAR-FTUs huggingface dataset:
Improving Species Identification of Ancient Mammals Based on Next-Generation Sequencing Data

The taxonomical identification merely based on morphology is often difficult for ancient remains. Therefore, universal or specific PCR amplification followed by sequencing and BLAST (basic local alignment search tool) search has become the most frequently used genetic-based method for the species identification of biological samples, including ancient remains. However, it is challenging for these methods to process extremely ancient samples with severe DNA fragmentation and contamination. Here, we applied whole-genome sequencing data from 12 ancient samples with ages ranging from 2.7 to 700 kya to compare different mapping algorithms, and tested different reference databases, mapping similarities and query coverage to explore the best method and mapping parameters that can improve the accuracy of ancient mammal species identification. The selected method and parameters were tested using 152 ancient samples, and 150 of the samples were successfully identified. We further screened the BLAST-based mapping results according to the deamination characteristics of ancient DNA to improve the ability of ancient species identification. Our findings demonstrate a marked improvement to the normal procedures used for ancient species identification, which was achieved through defining the mapping and filtering guidelines to identify true ancient DNA sequences. The guidelines summarized in this study could be valuable in archaeology, paleontology, evolution, and forensic science. For the convenience of the scientific community, we wrote a software script with Perl, called AncSid, which is made available on GitHub.
Growth Hormone Deficiency Following Traumatic Brain Injury

Traumatic brain injury (TBI) is fairly common and annually affects millions of people worldwide. Post traumatic hypopituitarism (PTHP) has been increasingly recognized as an important and prevalent clinical entity. Growth hormone deficiency (GHD) is the most common pituitary hormone deficit in long-term survivors of TBI. The pathophysiology of GHD post TBI is thought to be multifactorial including primary and secondary mechanisms. An interplay of ischemia, cytotoxicity, and inflammation post TBI have been suggested, resulting in pituitary hormone deficits. Signs and symptoms of GHD can overlap with those of TBI and may delay rehabilitation/recovery if not recognized and treated. Screening for GHD is recommended in the chronic phase, at least six months to a year after TBI as GH may recover in those with GHD in the acute phase; conversely, it may manifest in those with a previously intact GH axis. Dynamic testing is the standard method to diagnose GHD in this population. GHD is associated with long-term poor medical outcomes. Treatment with recombinant human growth hormone (rhGH) seems to ameliorate some of these features. This review will discuss the frequency and pathophysiology of GHD post TBI, its clinical consequences, and the outcomes of treatment with GH replacement.
Is Transient and Persistent Poverty Harmful to Multimorbidity?: Model Testing Algorithms

Multimorbidity, the coexistence of two or more long-term medical conditions in one person, has been known to disproportionally affect the low-income population. Little is known about whether long-term income is more crucial for multimorbidity than income measured in one time point; whether persistent poverty is more harmful than transient one; how changes in wealth affect multimorbidity. This is a longitudinal study on a population representative dataset, the Korean Health Panel (KHP) survey (2010–2015). A multivariate analysis was conducted using logistic regressions. A variety of income and wealth variables was investigated. Low-income Koreans (lowest 20%) were more likely to have multiple disorders; average income was more significantly associated with multimorbidity than the yearly income measured for the same year; persistent episodes of poverty had a greater hazard than transient ones; and income changes appeared to be statistically insignificant. We found that long-term income and persistent poverty are important factors of multimorbidity. These findings support the importance of policies reducing the risk of persistent poverty. Policies to promote public investment in education and create jobs may be appropriate to address multimorbidity.
Best-Evidence Rehabilitation for Chronic Pain Part 2: Pain during and after Cancer Treatment

Pain during, and especially after, cancer remains underestimated and undertreated. Moreover, both patients and health care providers are not aware of potential benefits of rehabilitation strategies for the management of pain during and following cancer treatment. In this paper, we firstly provided a state-of-the-art overview of the best evidence rehabilitation modalities for patients having (persistent) pain during and following cancer treatment, including educational interventions, specific exercise therapies, manual therapies, general exercise therapies and mind-body exercise therapies. Secondly, the findings were summarized from a clinical perspective and discussed from a scientific perspective. In conclusion, best evidence suggests that general exercise therapy has small pain-relieving effects. Supporting evidence for mind-body exercise therapy is available only in breast cancer patients. At this moment, there is a lack of high-quality evidence to support the use of specific exercises and manual therapy at the affected region for pain relief during and after cancer treatment. No clinically relevant results were found in favor of educational interventions restricted to a biomedical approach of pain. To increase available evidence these rehabilitation modalities should be applied according to, and within, a multidisciplinary biopsychosocial pain management approach. Larger, well-designed clinical trials tailored to the origin of pain and with proper evaluation of pain-related functioning and the patient’s pain experience are needed.
Theory-guided teaching: Implementation of a clinical reasoning curriculum in residents

Abstract Introduction: Educators have theorized that interventions grounded in dual process theory (DPT) and script theory (ST) may improve the diagnostic reasoning process of physicians but little empirical evidence exists. Methods: In this quasi-experimental study, we assessed the impact of a clinical reasoning (CR) curriculum grounded in DPT and ST on medicine residents participating in one of three groups during a 6-month period: no, partial, or full intervention. Residents completed the diagnostic thinking inventory (DTI) at baseline and 6 months. At 6 months, participants also completed a post-survey assessing application of concepts to cases. Results: There was a significant difference between groups in application of concepts (no intervention 1.6 (0.65) compared to partial 2.3 (0.81) and full 2.2 (0.91), p = 0.05), as well as describing cases in problem representation format (no intervention 1.2 (0.38) and partial 1.5 (0.55) compared to full 2.1 (0.93), p = 0.004). There was no significant difference in change in DTI scores (no intervention 7.0 (16.3), partial 8.8 (9.8), full 7.8 (12.0)). Conclusions: Residents who participated in a CR curriculum grounded in DPT and ST were effective in applying principles of CR in cases from their practice. To our knowledge, this is the first workplace-based CR educational intervention study showing differences in the reasoning process residents apply to patients.
High Prevalence of Multifocal Spine Infections Involving the Cervical and Thoracic Regions: A Case for Imaging the Entire Spine

Objective Pyogenic spinal infections account for 2%–4% of orthopaedic infections. They are often difficult to diagnose, resulting in a delay in diagnosis. Risk factors for orthopaedic and spinal infection are well-documented in the literature, yet there is a paucity of studies examining risk factors specifically for multifocal spinal infections. The objective of this study was to identify predictors of multifocal spinal infections in comparison to unifocal spinal infections. Methods The medical records, imaging studies, and bacteriology data of 20 patients treated surgically for pyogenic spinal infection over 6 years at a tertiary referral center were reviewed and analyzed after receiving Institutional Review Board approval. Univariate and multivariate analyses were performed to identify factors associated with a multifocal spinal infection. Results Seven patients (35%) had multifocal infections. Three were bifocal, and 4 were trifocal. Patients with surgically treated cervical or thoracic spinal infections had a high rate of concomitant multifocal spinal infections (71% and 83%, respectively). Other potential predictors (e.g., patient age, body mass index, magnetic resonance image findings, etc.) did not reach statistical significance. Each of the multifocal infections involved the lumbar spine. Conclusion In this study, the spinal region was the only statistically significant risk factor for multifocal infection. Patients who are diagnosed with a spinal infection that requires operative treatment should have their entire spine evaluated with magnetic resonance imaging to detect multifocal involvement promptly.
Searching for Potential Lipid Biomarkers of Parkinson’s Disease in Parkin-Mutant Human Skin Fibroblasts by HILIC-ESI-MS/MS: Preliminary Findings

Early diagnosis of neural changes causing cerebral impairment is critical for proposing preventive therapies for Parkinson’s disease (PD). Biomarkers currently available cannot be informative of PD onset since they are characterized by analysing post-mortem tissues from patients with severe degeneration of the substantia nigra. Skin fibroblasts (SF) are now recognized as a useful model of primary human cells, capable of reflecting the chronological and biological aging of the subjects. Here a lipidomic study of easily accessible primary SF is presented, based on hydrophilic interaction liquid chromatography coupled to electrospray ionization and mass spectrometry (HILIC/ESI-MS). Phospholipids (PL) from dermal fibroblasts of five PD patients with different parkin mutations and healthy control SF were characterized by single and tandem MS measurements using a hybrid quadrupole-Orbitrap and a linear ion trap mass analysers. The proposed approach enabled the identification of more than 360 PL. Univariate statistical analyses highlight abnormality of PL metabolism in the PD group, suggesting down- or up-regulation of certain species according to the extent of disease progression. These findings, although preliminary, suggest that the phospholipidome of human SF represents a source of potential biomarkers for the early diagnosis of PD. The dysregulation of ethanolamine plasmalogens in the circulatory system, especially those containing polyunsaturated fatty acids (PUFA), might be likely associated with neurodegeneration.
Earth’s radiative imbalance from the Last Glacial Maximum to the present

Significance Earth’s radiative imbalance determines whether energy is flowing into or out of the ocean–atmosphere system. The present, anthropogenic, positive imbalance drives global warming. This study reconstructs the radiative imbalance for the last deglaciation, ∼20,000 to 10,000 y ago. During the deglaciation, a positive imbalance was maintained for several thousand years, which brought the climate system from the last ice age into the Holocene warm period. We show that the imbalance varied significantly during this time, possibly due to changes in ocean circulation that affect the radiative energy fluxes, highlighting the importance of internal variability in Earth’s energy budget. The energy imbalance at the top of the atmosphere determines the temporal evolution of the global climate, and vice versa changes in the climate system can alter the planetary energy fluxes. This interplay is fundamental to our understanding of Earth’s heat budget and the climate system. However, even today, the direct measurement of global radiative fluxes is difficult, such that most assessments are based on changes in the total energy content of the climate system. We apply the same approach to estimate the long-term evolution of Earth’s radiative imbalance in the past. New measurements of noble gas-derived mean ocean temperature from the European Project for Ice Coring in Antarctica Dome C ice core covering the last 40,000 y, combined with recent results from the West Antarctic Ice Sheet Divide ice core and the sea-level record, allow us to quantitatively reconstruct the history of the climate system energy budget. The temporal derivative of this quantity must be equal to the planetary radiative imbalance. During the deglaciation, a positive imbalance of typically +0.2 W⋅m−2 is maintained for ∼10,000 y, however, with two distinct peaks that reach up to 0.4 W⋅m−2 during times of substantially reduced Atlantic Meridional Overturning Circulation. We conclude that these peaks are related to net changes in ocean heat uptake, likely due to rapid changes in North Atlantic deep-water formation and their impact on the global radiative balance, while changes in cloud coverage, albeit uncertain, may also factor into the picture.
Marine Bacterial Exopolymers-Mediated Green Synthesis of Noble Metal Nanoparticles with Antimicrobial Properties

A straightforward and green method for the synthesis of gold, silver, and silver chloride nanoparticles (Au NPs and Ag/AgCl NPs) was developed using three different microbial exopolymers (EP) as reducing and stabilizing agents. The exopolysaccharides EPS B3-15 and EPS T14 and the poly-γ-glutamic acid γ-PGA-APA were produced by thermophilic bacteria isolated from shallow hydrothermal vents off the Eolian Islands (Italy) in the Mediterranean Sea. The production of metal NPs was monitored by UV−Vis measurements by the typical plasmon resonance absorption peak and their antimicrobial activity towards Gram-positive and Gram- negative bacteria (Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa), as well as fungi (Candida albicans) was investigated. The biological evaluation showed no activity for EP-Au NPs, except against E. coli, whereas EP-Ag NPs exhibited a broad-spectrum of activity. The chemical composition, morphology, and size of EP-Ag NPs were investigated by UV–Vis, zeta potential (ζ), dynamic light scattering (DLS) measurements and transmission electron microscopy (TEM). The best antimicrobial results were obtained for EPS B3-15-Ag NPs and EPS T14-Ag NPs (Minimum Inhibitory Concentration, MIC: 9.37–45 µg/mL; Minimum Bactericidal Concentration/Minimum Fungicidal Concentration, MBC/MFC: 11.25–75 µg/mL).
Responses of tundra soil microbial communities to half a decade of experimental warming at two critical depths

Significance Ongoing permafrost thaw is expected to stimulate microbial release of greenhouse gases, threatening to further exacerbate climate change (cause positive feedback). In this study, a unique field warming experiment was conducted in Interior Alaska to promote surface permafrost degradation while maintaining uniform hydraulic conditions. After 5 winters of experimental warming by ∼1 °C, microbial community shifts were observed at the receded permafrost/active layer boundary, which reflected more reduced conditions, including increased methanogenesis. In contrast, increased carbohydrate utilization (respiration) was observed at the surface layer. These shifts were relatable to observed increases in CO2 and CH4 release from this study site and the surrounding ecosystem. Collectively, our results demonstrate that microbial responses to warming are rapid and identify potential biomarkers that could be important in modeling. Northern-latitude tundra soils harbor substantial carbon (C) stocks that are highly susceptible to microbial degradation with rising global temperatures. Understanding the magnitude and direction (e.g., C release or sequestration) of the microbial responses to warming is necessary to accurately model climate change. In this study, Alaskan tundra soils were subjected to experimental in situ warming by ∼1.1 °C above ambient temperature, and the microbial communities were evaluated using metagenomics after 4.5 years, at 2 depths: 15 to 25 cm (active layer at outset of the experiment) and 45 to 55 cm (transition zone at the permafrost/active layer boundary at the outset of the experiment). In contrast to small or insignificant shifts after 1.5 years of warming, 4.5 years of warming resulted in significant changes to the abundances of functional traits and the corresponding taxa relative to control plots (no warming), and microbial shifts differed qualitatively between the two soil depths. At 15 to 25 cm, increased abundances of carbohydrate utilization genes were observed that correlated with (increased) measured ecosystem carbon respiration. At the 45- to 55-cm layer, increased methanogenesis potential was observed, which corresponded with a 3-fold increase in abundance of a single archaeal clade of the Methanosarcinales order, increased annual thaw duration (45.3 vs. 79.3 days), and increased CH4 emissions. Collectively, these data demonstrate that the microbial responses to warming in tundra soil are rapid and markedly different between the 2 critical soil layers evaluated, and identify potential biomarkers for the corresponding microbial processes that could be important in modeling.
Immunomodulatory potential of Nisin A with application in wound healing

Antimicrobial peptides can have a dual role with both antimicrobial activity against a broad range of bacteria and immunomodulatory effect, making them attractive as therapeutic treatment of difficult wounds. Nisin A is widely known for its antimicrobial activity, and a preliminary study demonstrated that it increased wound closure, but the mechanism behind its effect is unknown. The aim of this study is to elucidate the wound healing potential of Nisin A and the mechanism behind. First, an epithelial and endothelial cell line, human keratinocyte (HaCaT) and human umbilical vein endothelial cell, were used to demonstrate migration and proliferation effects in vitro. From HaCaT cells and peripheral blood mononuclear cell, changes in cytokine levels were shown by quantitative polymerase chain reaction and enzyme‐linked immunosorbent assay. Second, the ex vivo porcine wound healing model was used to investigate the re‐epithelization potential of Nisin A. Finally, the model Galleria mellonella was used to confirm antimicrobial activity and to investigate potential immunomodulatory effects in vivo. Here, we demonstrated that Nisin A affected migration significantly of both human umbilical vein endothelial cell and HaCaT cells (p < 0.05) but not proliferation, potentially by decreasing the levels of proinflammatory cytokines tumor necrosis factor‐α, interleukin‐6, and interleukin‐8 (p < 0.001). Furthermore, Nisin A treatment diminished lipopolysaccharide‐induced tumor necrosis factor‐α levels from peripheral blood mononuclear cells and monocyte chemoattractant protein‐1 from HaCaT cells (p < 0.001). Furthermore, Nisin A did not affect proliferation ex vivo either but increased re‐epithelization of the porcine skin. Nisin A improved survival of G. mellonella significantly from Staphylococcus epidermidis (p < 0.001) but not from Escherichia coli, indicating that Nisin A did not help the larvae to survive the infection in a different than direct antimicrobial way. All together this makes Nisin A a potential treatment to use in wound healing, as it increases the mobility of skin cells, dampens the effect of lipopolysaccharide and proinflammatory cytokines, and decreases bacterial growth.
The role of chaperone‐mediated autophagy in neurotoxicity induced by alpha‐synuclein after methamphetamine exposure

Chaperone‐mediated autophagy (CMA) is an autophagy–lysosome pathway (ALP) that is different from the other two lysosomal pathways, namely, macroautophagy and microautophagy, and can selectively degrade cytosolic proteins in lysosomes without vesicle formation. CMA activity declines in neurodegenerative diseases such as Parkinson's disease, and similar neurotoxicity can occur after methamphetamine (METH) treatment. The relationship between CMA and METH‐induced neurotoxicity is not clear.
Genome-wide association study of piscine myocarditis virus (PMCV) resistance in Atlantic salmon (Salmosalar).

Cardiomyopathy syndrome is a severe, viral disease of Atlantic salmon that mostly affects farmed animals during their late production stage at sea. Caused by piscine myocarditis virus (PMCV), over the past few years outbreaks due to this disease have resulted in significant losses to the aquaculture industry. However, there is currently no vaccine that has proven effective against this virus. In this study, using a challenge model, we investigated the genetic variation for resistance to PMCV, by screening a large number of animals using a 55 K SNP array. In particular, we aimed to identify genetic markers that are tightly linked to higher disease resistance and can potentially be used in breeding programs. Using genomic information, we estimated a heritability of 0.51 ± 0.06, suggesting that resistance against this virus, to a great extent, is controlled by genetic factors. Through association analysis, we identified a significant quantitative trait locus (QTL) on chromosome 27, explaining approximately 57% of the total additive genetic variation. The region harbouring this QTL contains various immune-related candidate genes, many of which have previously been shown to have a different expression profile between the naïve and infected animals. We also identified a suggestive association on chromosome 12, with the QTL linked markers located in two putatively immune-related genes. These results are of particular interest, as they can readily be implemented into breeding programs, can further assist in fine-mapping the causative mutations, and help in better understanding the biology of the disease and the immunological mechanisms underlying resistance against PMCV.
Cross-sectional Association between Walking and Sunburn: A Potential Trade-off between Cancer Prevention and Risk Factors.

BACKGROUND The positive association between physical activity and sunburn is a health behavior trade-off between the health benefits of physical activity and increased risk of skin cancer. PURPOSE We assessed walking, which is a common source of physical activity, and the prevalence of sunburn. METHODS This research used the 2015 National Health Interview Survey of adults (N = 26,632), age ≥ 18 years. We defined four exclusive categories of walking: (a) those who reported not walking; (b) only transportation (to get some place, such as work, a store, or public transit stop); (c) only leisure (such as for fun, relaxation, or exercise); and (d) both categories. We estimated the adjusted prevalence of sunburn by walking category and separately for walking duration; we stratified by gender and sun sensitivity. RESULTS The adjusted sunburn prevalence was not different between walking categories for women, but it was for men. Specifically, prevalence was lower for men who reported not walking, 34.1% (95% confidence interval [CI]: 32.2%-36.1%) compared to 38.8% (95% CI: 36.5%-41.2%) who walked for both purposes (p = .003). Walking duration was not associated with sunburn prevalence. CONCLUSION We could not determine whether sunburn occurred during walking trips because the questions were not asked as such. However, the results suggest that walking, unlike leisure-time physical activity (such as exercise, sports, or physically active hobbies), may not generally be associated with sunburn, except for the higher sunburn prevalence for men who walked for both leisure and transportation purposes.