Miracle-dz/UniFAR-FTUs huggingface dataset:
Biodiversity conservation as infectious disease prevention: why a social-ecological perspective is essential

Non-technical summary Investing in stricter biodiversity conservation and wildlife protection to reduce the number of emerging diseases and, consequently, the risk of pandemics such as coronavirus disease-19 (COVID-19), must integrate a social-ecological perspective. Biodiversity conservation, in order to be effective as disease prevention, requires consideration of people's needs, knowledge and institutions within their locally specific contexts. To meet this goal, future biodiversity research and conservation policy should apply six social-ecological principles for shaping future practices of co-existence of societies and nature. Technical summary The COVID-19 pandemic, presumably originating in a spillover event from natural wildlife reservoirs into the human population, sets a new benchmark for the indirect cost of biodiversity exploitation. To reverse the trend of increasing pandemic risk, biodiversity conservation and wildlife protection must be strengthened globally. In this paper, we argue that such preventive measures explicitly need to employ a social-ecological approach. In particular, attention must be paid to the societal relations to nature to avoid falling for simplistic solutions that neglect regional and local particularities of both, biodiversity and local communities. We emphasize the importance of avoiding a Western-biased view and acknowledging the factors and causations of infectious disease emergence in industrialized countries. To reduce the emergence of zoonotic and vector-borne diseases in their specific contexts, we propose applying a social-ecological systems approach by integrating plural local knowledge and values, established practices, formal and informal institutions, as well as technology. We further introduce six social-ecological principles for shaping transformations in the Anthropocene to maintain and build more resilient and sustainable communities. By operationalizing these inter- and transdisciplinary principles, biodiversity conservation can be effectively implemented as infectious disease prevention. Social media summary A social-ecological approach to biodiversity conservation can pave the way for an effective and socially just reduction of future pandemic risks.
Mate value, intrasexual competition and sociosexual desire drive Brazilian women's well-being

Abstract Abstract Well-being (vs. ill-being) might function as an internal guide for approaching (vs. avoiding) situations, strategies, and achievements that ancestrally led to higher (vs. lower) reproductive success. Indeed, coupled individuals report higher well-being than singles, while depressive individuals report lower mate value and higher sociosexuality. Here we investigate associations between well-being, depression and evolutionary reproduction-related aspects (mate value, intrasexual competition, age, and sociosexuality). Overall, 1,173 predominantly heterosexual Brazilian women (mean = 31.89; standard deviation = 11.10) responded to online instruments measuring self-perceived happiness, life-satisfaction, depression, mate value, intrasexual competition, age, and sociosexuality. Multiple regression models indicated that higher well-being was positively predicted by mate value and negatively by intrasexual competition and sociosexual desire, while the opposite was true for depression. Although intrasexual competition and unrestricted sociosexuality can, under some circumstances, increase individual reproductive success, they are risky and suboptimally effective strategies, thus leading to feelings of ill-being. Contrarily, affective long-term bonds, higher mate-value, and lower intrasexual competition might increase feelings of well-being, because this would lead to a safer route towards ancestral reproductive advantages.
CHALLENGES OF THE FARS NEOLITHIC CHRONOLOGY: AN APPRAISAL

ABSTRACT Over the past few decades, several excavations that have been performed in the Fars Neolithic sites have resulted in the presentation of different chronologies for the region. Most of the research in Fars centered on the Kur River Basin (KRB). Fars has always had a different environment for the formation of different cultures over time, therefore, in order to reach a better understanding of the prehistoric cultures of the region it is necessary to make a brief review of the geographical zones of the plains and valleys of Fars province. Taking into account the existence of several questions and ambiguities regarding Neolithic Fars, the Hormangan site, located in the Bavant River Basin, was excavated. During the excavation, two settlement phases were identified that contained cultural materials relatively comparable to Tol-e Mushki, Tol-e Jari B, Kushk Hezar, and Rahmat Abad sequences. The goal of this paper is to explore the absolute chronology of the Hormangan site as well as other Neolithic sites located in the northern half of the Fars region with a special reference to the local cultural and technological sides of different Neolithic sites throughout the region. Bearing in mind the similarities of Bashi materials with Hormangan, Rahmat Abad, and Mushki regions and the absolute chronology of these regions, consideration of Bashi phase does not seem logical. Therefore, by comparing the cultural materials and absolute chronology done in other regions, a sequence chronology including Rahmat Abad (7500–7000 BC), formative Mushki (7000–6400 BC), Mushki (6400–6000 BC), Jari (6000–5600 BC), and Shams Abad (5600–5200 BC) for the Neolithic period of Fars can be presented. According to the excavation of Rahmatabad and Tal-e Sangi, it seems that Fars was inhabited in the middle of the 8th millennium BC and the Neolithic package entered this area, and there is no evidence of the Neolithization process. In the past, the Mushaki period was introduced as the oldest pottery Neolithic period, but with new excavations, it seems that the use of pottery had become common in Fars, as in many parts of Southwest Asia, around 7000 BC.
Influence of Non-canonical DNA Bases on the Genomic Diversity of Tevenvirinae

The Tevenvirinae viruses are some of the most common viruses on Earth. Representatives of this subfamily have long been used in the molecular biology studies as model organisms – since the emergence of the discipline. Tevenvirinae are promising agents for phage therapy in animals and humans, since their representatives have only lytic life cycle and many of their host bacteria are pathogens. As confirmed experimentally, some Tevenvirinae have non-canonical DNA bases. Non-canonical bases can play an essential role in the diversification of closely related viruses. The article performs a comparative and evolutionary analysis of Tevenvirinae genomes and components of Tevenvirinae genomes. A comparative analysis of these genomes and the genes associated with the synthesis of non-canonical bases allows us to conclude that non-canonical bases have a major influence on the divergence of Tevenvirinae viruses within the same habitats. Supposedly, Tevenvirinae developed a strategy for changing HGT frequency in individual populations, which was based on the accumulation of proteins for the synthesis of non-canonical bases and proteins that used those bases as substrates. Owing to this strategy, ancestors of Tevenvirinae with the highest frequency of HGT acquired genes that allowed them to exist in a certain niche, and ancestors with the lowest HGT frequency preserved the most adaptive of those genes. Given the origin and characteristics of genes associated with the synthesis of non-canonical bases in Tevenvirinae, one can assume that other phages may have similar strategies. The article demonstrates the dependence of genomic diversity of closely related Tevenvirinae on non-canonical bases.
Long-Term Recidivism of Mentally Disordered Offenders Considered “Dangerous to the Public” in Switzerland

Objectives: The commissions for risk assessment of offenders dangerous to the public were established in 1995 in Switzerland. The main goal was to reduce recidivism of offenders released into the community by means of identifying high-risk offenders and recommending measures for offender management. This study investigates long-term recidivism data of this high-risk cohort of offenders. Methods: Baseline data included risk assessment of one of the commissions, the type of index offense, and psychiatric disorders according to ICD-10 for the total cohort of offenders examined by the commissions between 1995 and 2009. Criminal records were drawn in 2019 for all offenders from the Swiss Federal Office of Justice. Results: From a total of 147 offenders 35 recidivated within a median time at risk of 9.1 years (31.8%), of which 10 (9.1%) recommitted a severe offense. Within the treatment status, sentences (imprisonment and preventive detention) were compared to court-ordered measures (in- or outpatient court ordered treatment, civil court mandated treatment, vocational training facility). There were no significant differences comparing treatment status, different diagnostic groups, type of index offense and other risk factors. Except of age at release (or relapse), which predicted recidivism with younger subjects showing higher recidivism rates (p = 0.014). Conclusion: Our study showed that over a long-term time at risk this high-risk cohort showed a similar recidivism rate as many other studies with different cohorts. With appropriate management recidivism rates in high-risk offenders can be lowered allowing them being consecutively reintegrated into society. The finding that younger subjects have higher recidivism rate was reproduced in this population.
Predicting Recurrent Venous Thromboembolism in Patients With Deep-Vein Thrombosis: Development and Internal Validation of a Potential New Prediction Model (Continu-8)

Background: Previous prediction models for recurrent thromboembolism (VTE) are often complicated to apply and have not been implemented widely. Aim: To develop and internally validate a potential new prediction model for recurrent VTE that can be used without stopping anticoagulant treatment for D-dimer measurements in patients with provoked and unprovoked DVT. Methods: Cohort data of 479 patients treated in a clinical care pathway at Maastricht University Medical Center were used. Predictors for the Cox proportional hazards model (unprovoked DVT, male gender, factor VIII levels) were derived from literature and using forward selection procedure. The scoring rule was internally validated using bootstrapping techniques and the predictive ability was compared to existing prediction models. Results: Patients were followed for a median of 3.12 years after stopping anticoagulation treatment (IQR 0.78, 3.90). Sixty-four of 479 patients developed recurrent VTE (13%). The scoring rule consisted of unprovoked DVT (yes: 2 points), male sex (yes: 1 point), and factor VIII > 213 % (yes: 2 points) and was categorized into three groups [i.e., low risk (score 0), medium risk (scores 1, 2, or 3) and high risk (scores 4 and 5)]. The concordance statistic was 0.68 (95% CI: 0.61, 0.75). Conclusion: The discriminative ability of the new Continu-8 score was adequate. Future studies shall verify this score in an independent setting without stopping anticoagulation treatment.
Abnormal Glycosylation of Cancer Stem Cells and Targeting Strategies

Cancer stem cell (CSCs) are deemed as one of the main reasons of tumor relapse due to their resistance to standard therapies. Numerous intracellular signaling pathways along with extracellular features are crucial in regulating CSCs properties, such as heterogeneity, plasticity and differentiation. Aberrant glycosylation of these cellular signaling pathways and markers of CSCs have been directly correlated with maintaining survival, self-renewal and extravasation properties. In this review, we highlight the importance of glycosylation in promoting stemness character of CSCs, and present strategies for targeting abnormal glycosylation to eliminate the resistant CSC population.
Diversity of Chemical Structures and Biosynthesis of Polyphenols in Nut-Bearing Species

Nuts, such as peanut, almond, and chestnut, are valuable food crops for humans being important sources of fatty acids, vitamins, minerals, and polyphenols. Polyphenols, such as flavonoids, stilbenoids, and hydroxycinnamates, represent a group of plant-specialized (secondary) metabolites which are characterized as health-beneficial antioxidants within the human diet as well as physiological stress protectants within the plant. In food chemistry research, a multitude of polyphenols contained in culinary nuts have been studied leading to the identification of their chemical properties and bioactivities. Although functional elucidation of the biosynthetic genes of polyphenols in nut species is crucially important for crop improvement in the creation of higher-quality nuts and stress-tolerant cultivars, the chemical diversity of nut polyphenols and the key biosynthetic genes responsible for their production are still largely uncharacterized. However, current technical advances in whole-genome sequencing have facilitated that nut plant species became model plants for omics-based approaches. Here, we review the chemical diversity of seed polyphenols in majorly consumed nut species coupled to insights into their biological activities. Furthermore, we present an example of the annotation of key genes involved in polyphenolic biosynthesis in peanut using comparative genomics as a case study outlining how we are approaching omics-based approaches of the nut plant species.
Cardiac Energetics Before, During, and After Anthracycline-Based Chemotherapy in Breast Cancer Patients Using 31P Magnetic Resonance Spectroscopy: A Pilot Study

Purpose: To explore the utility of phosphorus magnetic resonance spectroscopy (31P MRS) in identifying anthracycline-induced cardiac toxicity in patients with breast cancer. Methods: Twenty patients with newly diagnosed breast cancer receiving anthracycline-based chemotherapy had cardiac magnetic resonance assessment of left ventricular ejection fraction (LVEF) and 31P MRS to determine myocardial Phosphocreatine/Adenosine Triphosphate Ratio (PCr/ATP) at three time points: pre-, mid-, and end-chemotherapy. Plasma high sensitivity cardiac troponin-I (cTn-I) tests and electrocardiograms were also performed at these same time points. Results: Phosphocreatine/Adenosine Triphosphate did not change significantly between pre- and mid-chemo (2.16 ± 0.46 vs. 2.00 ± 0.56, p = 0.80) and pre- and end-chemo (2.16 ± 0.46 vs. 2.17 ± 0.86, p = 0.99). Mean LVEF reduced significantly by 5.1% between pre- and end-chemo (61.4 ± 4.4 vs. 56.3 ± 8.1 %, p = 0.02). Change in PCr/ATP ratios from pre- to end-chemo correlated inversely with changes in LVEF over the same period (r = −0.65, p = 0.006). Plasma cTn-I increased progressively during chemotherapy from pre- to mid-chemo (1.35 ± 0.81 to 4.40 ± 2.64 ng/L; p = 0.01) and from mid- to end-chemo (4.40 ± 2.64 to 18.33 ± 13.23 ng/L; p = 0.001). Conclusions: In this small cohort pilot study, we did not observe a clear change in mean PCr/ATP values during chemotherapy despite evidence of increased plasma cardiac biomarkers and reduced LVEF. Future similar studies should be adequately powered to take account of patient drop-out and variable changes in PCr/ATP and could include T1 and T2 mapping.
Analyzing the Loss and the Recovery of Consciousness: Functional Connectivity Patterns and Changes in Heart Rate Variability During Propofol-Induced Anesthesia

The analysis of the central and the autonomic nervous systems (CNS, ANS) activities during general anesthesia (GA) provides fundamental information for the study of neural processes that support alterations of the consciousness level. In the present pilot study, we analyzed EEG signals and the heart rate (HR) variability (HRV) in a sample of 11 patients undergoing spinal surgery to investigate their CNS and ANS activities during GA obtained with propofol administration. Data were analyzed during different stages of GA: baseline, the first period of anesthetic induction, the period before the loss of consciousness, the first period after propofol discontinuation, and the period before the recovery of consciousness (ROC). In EEG spectral analysis, we found a decrease in posterior alpha and beta power in all cortical areas observed, except the occipital ones, and an increase in delta power, mainly during the induction phase. In EEG connectivity analysis, we found a significant increase of local efficiency index in alpha and delta bands between baseline and loss of consciousness as well as between baseline and ROC in delta band only and a significant reduction of the characteristic path length in alpha band between the baseline and ROC. Moreover, connectivity results showed that in the alpha band there was mainly a progressive increase in the number and in the strength of incoming connections in the frontal region, while in the beta band the parietal region showed mainly a significant increase in the number and in the strength of outcoming connections values. The HRV analysis showed that the induction of anesthesia with propofol was associated with a progressive decrease in complexity and a consequent increase in the regularity indexes and that the anesthetic procedure determined bradycardia which was accompanied by an increase in cardiac sympathetic modulation and a decrease in cardiac parasympathetic modulation during the induction. Overall, the results of this pilot study showed as propofol-induced anesthesia caused modifications on EEG signal, leading to a “rebalance” between long and short-range cortical connections, and had a direct effect on the cardiac system. Our data suggest interesting perspectives for the interactions between the central and autonomic nervous systems for the modulation of the consciousness level.
GAMER-MRI in Multiple Sclerosis Identifies the Diffusion-Based Microstructural Measures That Are Most Sensitive to Focal Damage: A Deep-Learning-Based Analysis and Clinico-Biological Validation

Conventional magnetic resonance imaging (cMRI) in multiple sclerosis (MS) patients provides measures of focal brain damage and activity, which are fundamental for disease diagnosis, prognosis, and the evaluation of response to therapy. However, cMRI is insensitive to the damage to the microenvironment of the brain tissue and the heterogeneity of MS lesions. In contrast, the damaged tissue can be characterized by mathematical models on multishell diffusion imaging data, which measure different compartmental water diffusion. In this work, we obtained 12 diffusion measures from eight diffusion models, and we applied a deep-learning attention-based convolutional neural network (CNN) (GAMER-MRI) to select the most discriminating measures in the classification of MS lesions and the perilesional tissue by attention weights. Furthermore, we provided clinical and biological validation of the chosen metrics—and of their most discriminative combinations—by correlating their respective mean values in MS patients with the corresponding Expanded Disability Status Scale (EDSS) and the serum level of neurofilament light chain (sNfL), which are measures of disability and neuroaxonal damage. Our results show that the neurite density index from neurite orientation and dispersion density imaging (NODDI), the measures of the intra-axonal and isotropic compartments from microstructural Bayesian approach, and the measure of the intra-axonal compartment from the spherical mean technique NODDI were the most discriminating (respective attention weights were 0.12, 0.12, 0.15, and 0.13). In addition, the combination of the neurite density index from NODDI and the measures for the intra-axonal and isotropic compartments from the microstructural Bayesian approach exhibited a stronger correlation with EDSS and sNfL than the individual measures. This work demonstrates that the proposed method might be useful to select the microstructural measures that are most discriminative of focal tissue damage and that may also be combined to a unique contrast to achieve stronger correlations to clinical disability and neuroaxonal damage.
Cerebrospinal Fluid Neurofilament Light Chain (NfL) Predicts Disease Aggressiveness in Amyotrophic Lateral Sclerosis: An Application of the D50 Disease Progression Model

Amyotrophic lateral sclerosis (ALS) is a relentlessly progressive neurodegenerative disorder. As previous therapeutic trials in ALS have been severely hampered by patients’ heterogeneity, the identification of biomarkers that reliably reflect disease progression represents a priority in ALS research. Here, we used the D50 disease progression model to investigate correlations between cerebrospinal fluid (CSF) neurofilament light chain (NfL) levels and disease aggressiveness. The D50 model quantifies individual disease trajectories for each ALS patient. The value D50 provides a unified measure of a patient’s overall disease aggressiveness (defined as time taken in months to lose 50% of functionality). The relative D50 (rD50) reflects the individual disease covered and can be calculated for any time point in the disease course. We analyzed clinical data from a well-defined cohort of 156 patients with ALS. The concentration of NfL in CSF samples was measured at two different laboratories using the same procedure. Based on patients’ individual D50 values, we defined subgroups with high (<20), intermediate (20–40), or low (>40) disease aggressiveness. NfL levels were compared between these subgroups via analysis of covariance, using an array of confounding factors: age, gender, clinical phenotype, frontotemporal dementia, rD50-derived disease phase, and analyzing laboratory. We found highly significant differences in NfL concentrations between all three D50 subgroups (p < 0.001), representing an increase of NfL levels with increasing disease aggressiveness. The conducted analysis of covariance showed that this correlation was independent of gender, disease phenotype, and phase; however, age, analyzing laboratory, and dementia significantly influenced NfL concentration. We could show that CSF NfL is independent of patients’ disease covered at the time of sampling. The present study provides strong evidence for the potential of NfL to reflect disease aggressiveness in ALS and in addition proofed to remain at stable levels throughout the disease course. Implementation of CSF NfL as a potential read-out for future therapeutic trials in ALS is currently constrained by its demonstrated susceptibility to (pre-)analytical variations. Here we show that the D50 model enables the discovery of correlations between clinical characteristics and CSF analytes and can be recommended for future studies evaluating potential biomarkers.