Innate immune activation in neurodegenerative diseases.

Activation of the innate immune system following pattern recognition receptor binding has emerged as one of the major pathogenic mechanisms in neurodegenerative disease. Experimental, epidemiological, pathological, and genetic evidence underscores the meaning of innate immune activation during the prodromal as well as clinical phases of several neurodegenerative disorders including Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and frontotemporal dementia. Importantly, innate immune activation and the subsequent release of inflammatory mediators contribute mechanistically to other hallmarks of neurodegenerative diseases such as aberrant proteostatis, pathological protein aggregation, cytoskeleton abnormalities, altered energy homeostasis, RNA and DNA defects, and synaptic and network disbalance and ultimately to the induction of neuronal cell death. In this review, we discuss common mechanisms of innate immune activation in neurodegeneration, with particular emphasis on the pattern recognition receptors (PRRs) and other receptors involved in the detection of damage-associated molecular patterns (DAMPs).

Nonunique UPGMA clusterings of microsatellite markers.

Agglomerative hierarchical clustering has become a common tool for the analysis and visualization of data, thus being present in a large amount of scientific research and predating all areas of bioinformatics and computational biology. In this work, we focus on a critical problem, the nonuniqueness of the clustering when there are tied distances, for which several solutions exist but are not implemented in most hierarchical clustering packages. We analyze the magnitude of this problem in one particular setting: the clustering of microsatellite markers using the Unweighted Pair-Group Method with Arithmetic Mean. To do so, we have calculated the fraction of publications at the Scopus database in which more than one hierarchical clustering is possible, showing that about 46% of the articles are affected. Additionally, to show the problem from a practical point of view, we selected two opposite examples of articles that have multiple solutions: one with two possible dendrograms, and the other with more than 2.5 million different possible hierarchical clusterings.

Triadic Approximation Reveals the Role of Interaction Overlap on the Spread of Complex Contagions on Higher-Order Networks.

Contagion processes relying on the exposure to multiple sources are prevalent in social systems, and are effectively represented by hypergraphs. In this Letter, we derive a mean-field model that goes beyond node- and pair-based approximations. We reveal how the stability of the contagion-free state is decided by either two- or three-body interactions, and how this is strictly related to the degree of overlap between these interactions. Our findings demonstrate the dual effect of increased overlap: it lowers the invasion threshold, yet produces smaller outbreaks. Corroborated by numerical simulations, our results emphasize the significance of the chosen representation in describing a higher-order process.

Study of pH and Thermodynamic Parameters via Circular Dichroism Spectroscopy of a Recombinant Human Lactoferrin.

The production of human recombinant proteins to be used for therapeutic or nutritional purposes must focus on obtaining a molecule that is as close as possible to the native human protein. This biotechnological tool has been documented in various studies published in recent decades, with lactoferrin being one of those that has generated the most interest, being a promising option for recombinant technology. However, stability studies including thermodynamic parameters have not been reported for recombinant lactoferrin (Lf). The objective of this work was to obtain the human recombinant protein using the yeast Komagataella phaffii to study structural changes modifying pH and temperature using circular dichroism spectroscopy (CD). Thermodynamic parameters such as ΔH, ΔS and Tm were calculated and compared with commercial human lactoferrin. We propose the potential use of CD and thermodynamic parameters as a criterion in the production of recombinant proteins to be used in the production of specialized recombinant proteins.

Comprehensive Automated Routine Implementation, Validation, and Benchmark of the Anisotropic Force Field (AUA4) Using Python and GROMACS.

Molecular simulation users are sometimes discouraged from using specific molecular models because of the inconvenience of finding the force field parameters and preparing and validating the topology files. To facilitate this process and make the accurate anisotropic force field AUA4 available to molecular dynamics users, we have created and validated an automated topology and coordinate file creation routine for the GROMACS molecular simulation software. In the present work, we describe the AUA4, explain its particularities and how it was implemented, thoroughly validating the implementation, and for the first time, perform a molecular dynamics benchmark for this transferable force field. Several properties were computed, namely, liquid density, vapor pressure, and vaporization enthalpy by conducting explicit vapor-liquid interface simulations. The results evidence the correct implementation showing slight deviations from the parametrization studies. The benchmark shows the superior predictive capability of the AUA4 in recreating liquid density (RMSD equal to 17.0 kg/m3) and vaporization enthalpy (RMSD equal to 1.3 kJ/mol) compared to other transferable force fields. In addition, its superior computational time performance doubles or even triples compared to an all-atom force field such as the OPLS, depending on whether the workstation counts with GPU.

The Efficacy and Usability of an Unguided Web-Based Grief Intervention for Adults Who Lost a Loved One During the COVID-19 Pandemic: Randomized Controlled Trial.

BACKGROUND: The death of a loved one was a challenge many people faced during the COVID-19 pandemic within the context of extraordinary circumstances and great uncertainty. Grief is an unavoidable part of life, and for most people, feelings of grief decrease naturally over time. However, for some people, grieving can become a particularly painful process with clinical symptoms that may require professional help to resolve. To provide psychological support to people who had lost a loved one during the COVID-19 pandemic, an unguided web-based psychological intervention was developed. OBJECTIVE: The main objective of this study was to evaluate the efficacy of the web-based treatment, Grief COVID (Duelo COVID in Spanish; ITLAB), in reducing clinical symptoms of complicated grief, depression, posttraumatic stress, hopelessness, anxiety, and suicidal risk in adults. The secondary aim was to validate the usability of the self-applied intervention system. METHODS: We used a randomized controlled trial with an intervention group (IG) and a waitlist control group (CG). The groups were assessed 3 times (before beginning the intervention, upon completing the intervention, and 3 months after the intervention). The intervention was delivered on the web in an asynchronous format through the Duelo COVID web page. Participants created an account that could be used on their computers, smartphones, or tablets. The evaluation process was automated as part of the intervention. RESULTS: A total of 114 participants were randomly assigned to the IG or CG and met criteria for inclusion in the study (n=45, 39.5% completed the intervention and n=69, 60.5% completed the waitlist period). Most participants (103/114, 90.4%) were women. The results indicated that the treatment significantly reduced baseline clinical symptoms in the IG for all variables (P<.001 to P=.006), with larger effect sizes for depression, hopelessness, grief, anxiety, and risk of suicide (all effect sizes ≥0.5). The follow-up evaluation showed that symptom reduction was maintained at 3 months after the intervention. The results from the CG showed that participants experienced significantly decreased levels of hopelessness after completing the time on the waitlist (P<.001), but their suicidal risk scores increased. Regarding the usability of the self-applied intervention system, the results indicated a high level of satisfaction with the Grief COVID. CONCLUSIONS: The self-applied web-based intervention Grief COVID was effective in reducing symptoms of anxiety, depression, hopelessness, risk of suicide risk, posttraumatic stress disorder, and complicated grief disorder. Grief COVID was evaluated by the participants, who reported that the system was easy to use. These results affirm the importance of developing additional web-based psychological tools to help reduce clinical symptoms in people experiencing grief because of the loss of a loved one during a pandemic. TRIAL REGISTRATION: ClinicalTrials.gov NCT04638842; https://clinicaltrials.gov/ct2/show/NCT04638842.

A novel smartphone application for the tracking of procedural numbers and trainee experience in gastrointestinal endoscopy.

OBJECTIVES: The tracking and documentation of procedures in gastrointestinal endoscopy including therapeutic interventions is an essential but challenging process. The University of Alberta has developed a smartphone app to help facilitate this task. This study evaluated the functionality, usefulness, and user satisfaction of this app. METHODS: Four Gastroenterology (GI) residents and two therapeutic endoscopy fellows participated in the study. The trainees submitted all their data into the app from the procedures in which they participated hands-on for one year, data was collected and analyzed on the app and the website associated with it. RESULTS: Trainees were able to register the procedures immediately after each procedure without difficulty, this data was available to be reviewed at anytime in the app and associated website. Furthermore, the data collected was able to be transformed into tables and graphs on the app website. The total number of procedures and therapeutic interventions performed were easily accessed in the app and website at anytime. The app facilitated the calculation of the cecal intubation rate in colonoscopy and the cannulation rate in ERCP for the therapeutic endoscopy trainee. Trainees reported excellent experience with the app capabilities. CONCLUSIONS: A novel smartphone app was useful in collecting meaningful data submitted by gastrointestinal endoscopy trainees, furthermore, through an associated website, it was capable to create graphs and tables to show and facilitate the calculation of meaningful data such as key performance indicators.

On the number of stable solutions in the Kuramoto model.

We consider a system of n coupled oscillators described by the Kuramoto model with the dynamics given by θ˙=ω+Kf(θ). In this system, an equilibrium solution θ∗ is considered stable when ω+Kf(θ∗)=0, and the Jacobian matrix Df(θ∗) has a simple eigenvalue of zero, indicating the presence of a direction in which the oscillators can adjust their phases. Additionally, the remaining eigenvalues of Df(θ∗) are negative, indicating stability in orthogonal directions. A crucial constraint imposed on the equilibrium solution is that |Γ(θ∗)|≤π, where |Γ(θ∗)| represents the length of the shortest arc on the unit circle that contains the equilibrium solution θ∗. We provide a proof that there exists a unique solution satisfying the aforementioned stability criteria. This analysis enhances our understanding of the stability and uniqueness of these solutions, offering valuable insights into the dynamics of coupled oscillators in this system.

Creatine Kinase MB Isoenzyme Is a Complementary Biomarker in Amyotrophic Lateral Sclerosis.

Amyotrophic lateral sclerosis (ALS) is an invariably fatal neurodegenerative disease with limited therapeutic options. There is an urgent need for novel biomarkers to be used as surrogates for new therapeutic trials and disease monitoring. In this study, we sought to systematically study creatine kinase isoenzyme MB (CK-MB) in a real-world cohort of ALS patients, assess the diagnostic performance, and evaluate its association with other laboratory and clinical parameters. We reviewed data from 194 consecutive patients that included 130 ALS patients and 64 disease control patients (primary lateral sclerosis [PLS], benign fasciculations syndrome [BFS], Huntington's disease [HD] and Alzheimer's disease [AD]). CK-MB was elevated in the sera of more than half of all patients with ALS. In patients with spinal-onset ALS, CK-MB levels were significantly higher than in patients with other neurodegenerative diseases. Patients with slower rates of functional decline had a significantly higher baseline CK-MB. Furthermore, CK-MB elevations correlated with cardiac troponin T (cTnT) and with revised ALS Functional Rating Scale (ALSFRS-R) bulbar subcategory. We posit that measuring CK-MB in ALS patients in a complimentary fashion could potentially aid in the diagnostic workup of ALS and help discriminate the disease from some ALS mimics and other neurodegenerative diseases. CK-MB levels also may provide valuable prognostic information regarding disease aggressiveness as well as correlations with specific phenotypic presentations.

Autophagy Modulation as a Potential Therapeutic Strategy in Osteosarcoma: Current Insights and Future Perspectives.

Autophagy, the process that enables the recycling and degradation of cellular components, is essential for homeostasis, which occurs in response to various types of stress. Autophagy plays an important role in the genesis and evolution of osteosarcoma (OS). The conventional treatment of OS has limitations and is not always effective at controlling the disease. Therefore, numerous researchers have analyzed how controlling autophagy could be used as a treatment or strategy to reverse resistance to therapy in OS. They highlight how the inhibition of autophagy improves the efficacy of chemotherapeutic treatments and how the promotion of autophagy could prove positive in OS therapy. The modulation of autophagy can also be directed against OS stem cells, improving treatment efficacy and preventing cancer recurrence. Despite promising findings, future studies are needed to elucidate the molecular mechanisms of autophagy and its relationship to OS, as well as the mechanisms underlying the functioning of autophagic modulators. Careful evaluation is required as autophagy modulation may have adverse effects on normal cells, and the optimization of autophagic modulators for use as drugs in OS is imperative.

Advances on Cellulose Manufacture in Biphasic Reaction Media.

Cellulose is produced industrially by the kraft and sulfite processes. The evolution of these technologies in biorefineries is driven by the need to obtain greater added value through the efficient use of raw materials and energy. In this field, organosolv technologies (and within them, those using liquid phases made up of water and one partly miscible organic solvent, known as "biphasic fractionation" in reference to the number of liquid phases) represent an alternative that is receiving increasing interest. This study considers basic aspects of the composition of lignocellulosic materials, describes the fundamentals of industrial cellulose pulp production processes, introduces the organosolv methods, and comprehensively reviews published results on organosolv fractionation based on the use of media containing water and an immiscible solvent (1-butanol, 1-pentanol or 2-methyltetrahydrofuran). Special attention is devoted to aspects related to cellulose recovery and fractionation selectivity, measured through the amount and composition of the treated solids.

Study of brine-halite phase separation through optical constringence and molecular dynamics.

This work presents a study of the reciprocal dispersive power, also known as constringence or Abbe number of an aqueous solution of NaCl in a wide range of concentrations. The constringence exhibited a distinct behavior in the region close to the phase transition between a phase containing exclusively brine and a phase containing brine+halite. Molecular dynamics simulations of this system indicated the existence of halite formation below the known saturation curve, which agreed with the experimental measurements, indicating a crystal growth in the unsaturated region.

National survey regarding the timing of endoscopic procedures during the COVID-19 pandemic.

BACKGROUND: During the COVID-19 pandemic, several questions have arisen about which endoscopic procedures (EPs) must be performed and which ones can be postponed. The aim of this study was to conduct a nationwide survey regarding the appropriate timing of EPs during the COVID-19 pandemic. METHODS: This prospective study was performed through a nationwide electronic survey. The survey consisted of 15 questions divided into three sections. The first evaluated the agreement for EPs classified as "time sensitive" and "not time sensitive". Two other sections assessed "high-priority" and "low-priority" scenarios. Agreement was considered when > 75% of respondents answered a question in the same direction. RESULTS: The response rate was 27.2% (214/784). Among the respondents, agreement for the need to perform EP in < 72 h was only reached for variceal bleeding (93.4%). Dysphagia with alarm symptoms was the scenario in which the highest percentage of physicians (95.9%) agreed that an EP needed to be performed within a month. Less than 30% of endoscopists would perform an EP within the first 72 h for patients with mild cholangitis, non-variceal upper gastrointestinal bleeding without hemodynamic instability, or severe anaemia without overt bleeding. In time-sensitive clinical scenarios suggestive of benign disease, none of the scenarios reached agreement in any sense. Among the time-sensitive clinical scenarios suggestive of malignancy, > 90% of the surveyed respondents considered that EP could not be postponed for > 8 weeks. CONCLUSIONS: There was no consensus among endoscopists about the timing of EPs in patients with pathologies considered time sensitive or in those with high-priority pathologies. Agreement was only reached in five (17%) of the evaluated clinical scenarios.

Estimation of the QTc interval in the presence of right bundle branch block: A comparative study using validated formulae for left bundle branch block.

BACKGROUND: Adequate measurement of the QT interval is of clinical importance in order to identify patients at higher risk for ventricular arrhythmias. Previous studies have described different methods to estimate baseline QT in patients with left bundle branch block (LBBB). However, the evidence regarding the assessment of the QT in patients with right bundle branch block (RBBB) is scarce. AIM: To analyze the feasibility and reliability of the different formulae described for LBBB in the estimation of the baseline QT in the presence of RBBB. METHODS: We performed an observational study including patients who underwent electrophysiology study and/or ablation. Two types of RBBB were considered: 1) pacing-induced and 2) transient true RBBB. QRS, JT and QT intervals were measured during baseline and RBBB. Estimated QTc was calculated using LBBB formulae: Bogossian, Rautaharju, Tabatabaei, Tang-Rabkin, Yankelson, Wang. Linear correlation and intraclass correlation coefficients (ICC) were used to assess the reliability of these formulae for the estimation of baseline QTc. RESULTS: We finally included a total of 100 patients. Correlations between baseline and estimated QTc were strong (R > 0.7) for all the formulae except for Tabatabaei. Yankelson and Wang showed the highest reliability (ICC = 0.775 and 0.727, respectively). Yankelson appeared to be the most accurate formula, with a mean estimated QTc closest to baseline values. CONCLUSION: Previously described formulae for LBBB exhibited marked differences regarding reliability in the estimation of the QTc interval in the presence of RBBB. According to our results, Yankelson showed the most consistent and accurate agreement in this setting.

Interrelations of Alzheimer´s disease candidate biomarkers neurogranin, fatty acid-binding protein 3 and ferritin to neurodegeneration and neuroinflammation.

There is growing evidence that promising biomarkers of inflammation in Alzheimer´s disease (AD) and other neurodegenerative diseases correlate strongest to levels of tau or neurofilament, indicating an inflammatory response to neuronal damage or death. To test this hypothesis, we investigated three AD candidate markers (ferritin, fatty acid binding protein 3 (FABP-3), and neurogranin) in interrelation to established AD and inflammatory protein markers. We further aimed to determine if such interrelations would be evident in pathological subjects only or also under non-pathological circumstances. Cerebrospinal fluid levels of the three proteins were quantified in samples from the University Clinic of Bonn (UKB) Department of Neurodegenerative Diseases & Geriatric Psychiatry, Germany. Data were analyzed based on clinical or biomarker-defined stratification of subjects with adjustment for covariates age, sex, and APOE status. Levels of ferritin, FABP-3 and neurogranin were elevated in subjects with pathological levels of t-tau independent of beta-amyloid status. The three markers correlated with each other, tau isoforms, age, and those inflammatory markers previously described as related to neurodegeneration, predominantly sTREM2, macrophage migration inhibitory factor, soluble vascular endothelial growth factor receptor, soluble vascular cell adhesion molecule 1 (sVCAM-1), and C1q. These interrelations existed in subjects with pathological and sub-pathological tau levels, in particular for FABP-3 and neurogranin. Relations to ferritin were independent of absolute levels of tau, too, but showed differing trajectories between pathological and non-pathological subjects. A specific set of inflammatory markers is highly related to markers of neuronal damage such as tau, neurogranin, or FABP-3. These proteins could be used as readouts of the inflammatory response during the neurodegeneration phase of AD.

Constructive Neutral Evolution 20 Years Later.

Evolution has led to a great diversity that ranges from elegant simplicity to ornate complexity. Many complex features are often assumed to be more functional or adaptive than their simpler alternatives. However, in 1999, Arlin Stolzfus published a paper in the Journal of Molecular Evolution that outlined a framework in which complexity can arise through a series of non-adaptive steps. He called this framework Constructive Neutral Evolution (CNE). Despite its two-decade-old roots, many evolutionary biologists still appear to be unaware of this explanatory framework for the origins of complexity. In this perspective piece, we explain the theory of CNE and how it changes the order of events in narratives that describe the evolution of complexity. We also provide an extensive list of cellular features that may have become more complex through CNE. We end by discussing strategies to determine whether complexity arose through neutral or adaptive processes.

Spatio-temporal variation in the wintering associations of an alpine bird.

Many animals make behavioural changes to cope with winter conditions, being gregariousness a common strategy. Several factors have been invoked to explain why gregariousness may evolve during winter, with individuals coming together and separating as they trade off the different costs and benefits of living in groups. These trade-offs may, however, change over space and time as a response to varying environmental conditions. Despite its importance, little is known about the factors triggering gregarious behaviour during winter and its change in response to variation in weather conditions is poorly documented. Here, we aimed at quantifying large-scale patterns in wintering associations over 23 years of the white-winged snowfinch Montifringilla nivalis nivalis. We found that individuals gather in larger groups at sites with harsh wintering conditions. Individuals at colder sites reunite later and separate earlier in the season than at warmer sites. However, the magnitude and phenology of wintering associations are ruled by changes in weather conditions. When the temperature increased or the levels of precipitation decreased, group size substantially decreased, and individuals stayed united in groups for a shorter time. These results shed light on factors driving gregariousness and points to shifting winter climate as an important factor influencing this behaviour.

MONET: a toolbox integrating top-performing methods for network modularization.

SUMMARY: We define a disease module as a partition of a molecular network whose components are jointly associated with one or several diseases or risk factors thereof. Identification of such modules, across different types of networks, has great potential for elucidating disease mechanisms and establishing new powerful biomarkers. To this end, we launched the 'Disease Module Identification (DMI) DREAM Challenge', a community effort to build and evaluate unsupervised molecular network modularization algorithms. Here, we present MONET, a toolbox providing easy and unified access to the three top-performing methods from the DMI DREAM Challenge for the bioinformatics community. AVAILABILITY AND IMPLEMENTATION: MONET is a command line tool for Linux, based on Docker and Singularity containers; the core algorithms were written in R, Python, Ada and C++. It is freely available for download at https://github.com/BergmannLab/MONET.git. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Evaluation of the diagnostic performance of nine commercial RT-PCR kits for the detection of SARS-CoV-2 in Colombia.

The ongoing severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic has led to the design and development of multiple reverse-transcription polymerase chain reaction kits aimed to facilitate the rapid scale-up of molecular testing for massive screening. We evaluated the diagnostic performance of nine commercial kits, which showed optimal performance and high discriminatory power. However, we observed differences in terms of sensitivity, specificity, and E gene Ct Values and discuss these results in light of the influence of SARS-CoV-2 genetic variability and its potential impact in current molecular diagnostic assays.

The arrival and spread of SARS-CoV-2 in Colombia.

We performed phylogenomic analysis of severe acute respiratory syndrome coronavirus-2 from 88 infected individuals across different regions of Colombia. Eleven different lineages were detected, suggesting multiple introduction events. Pangolin lineages B.1 and B.1.5 were the most frequent, with B.1 being associated with prior travel to high-risk areas.