Exploring transcription modalities from bimodal, single-cell RNA sequencing data.

There is a growing interest in generating bimodal, single-cell RNA sequencing (RNA-seq) data for studying biological pathways. These data are predominantly utilized in understanding phenotypic trajectories using RNA velocities; however, the shape information encoded in the two-dimensional resolution of such data is not yet exploited. In this paper, we present an elliptical parametrization of two-dimensional RNA-seq data, from which we derived statistics that reveal four different modalities.

Blood biomarker discovery for autism spectrum disorder: A proteomic analysis.

Autism spectrum disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social communication and social interaction and restricted, repetitive patterns of behavior, interests, or activities. Given the lack of specific pharmacological therapy for ASD and the clinical heterogeneity of the disorder, current biomarker research efforts are geared mainly toward identifying markers for determining ASD risk or for assisting with a diagnosis. A wide range of putative biological markers for ASD are currently being investigated.

Neural parameter calibration and uncertainty quantification for epidemic forecasting.

The recent COVID-19 pandemic has thrown the importance of accurately forecasting contagion dynamics and learning infection parameters into sharp focus. At the same time, effective policy-making requires knowledge of the uncertainty on such predictions, in order, for instance, to be able to ready hospitals and intensive care units for a worst-case scenario without needlessly wasting resources. In this work, we apply a novel and powerful computational method to the problem of learning probability densities on contagion parameters and providing uncertainty quantification for pandemic projections.

Epithelial Antimicrobial Peptide/Protein and Cytokine Expression Profiles Obtained from Nasopharyngeal Swabs of SARS-CoV-2-Infected and Non-Infected Subjects.

Immune responses of the epithelia of the upper respiratory tract are likely crucial in early inhibition of the viral replication and finally clearance of SARS-CoV-2. We aimed to compare the expression profiles of antimicrobial peptides/proteins (AMPs) and related cytokines observed in the nasopharynx of SARS-CoV-2-infected patients and non-infected controls and to assess the associations between these parameters and COVID-19 patients' outcomes. We included 45 subjects who had tested positive for SARS-CoV-2 and 22 control subjects who had tested negative for SARS-CoV-2.

A mathematical perspective on Romanisation: Modelling the Roman road activation process in ancient Tunisia.

Romanisation is a multi-faceted historical phenomenon with profound and lasting cultural impact on the ancient world. In the modern-day territory of Tunisia, this is particularly manifest during the first four centuries AD, under the reign of the Roman Empire. We derive a reduced, operational concept of Romanisation as a cultural diffusion process that is observable in the archaeological remains of the Roman era settlement system.

Interactional competencies in medical student admission- what makes a "good medical doctor"?

Doctors' interactional competencies play a crucial role in patient satisfaction, well-being, and compliance. Accordingly, it is in medical schools' interest to select candidates with strong interactional abilities. While Multiple Mini Interviews (MMIs) provide a useful context to assess such abilities, the evaluation of candidate performance during MMIs is not always based on a solid theoretical framework.

SGD-OD: investigating the potential oxygen demand of submarine groundwater discharge in coastal systems.

Submarine groundwater discharge (SGD) supplies nutrients, carbon, metals, and radionuclide tracers to estuarine and coastal waters. One aspect of SGD that is poorly recognized is its direct effect on dissolved oxygen (DO) demand in receiving waters, denoted here as SGD-OD. Sulfate-mediated oxidation of organic matter in salty coastal aquifers produces numerous reduced byproducts including sulfide, ammonia, dissolved organic carbon and nitrogen, methane, and reduced metals.

Characterising information gains and losses when collecting multiple epidemic model outputs.

Background: Collaborative comparisons and combinations of epidemic models are used as policy-relevant evidence during epidemic outbreaks. In the process of collecting multiple model projections, such collaborations may gain or lose relevant information. Typically, modellers contribute a probabilistic summary at each time-step.

Partial mean-field model for neurotransmission dynamics.

This article addresses reaction networks in which spatial and stochastic effects are of crucial importance. For such systems, particle-based models allow us to describe all microscopic details with high accuracy. However, they suffer from computational inefficiency if particle numbers and density get too large.

Practical Guide to Measuring Wetland Carbon Pools and Fluxes.

Unlabelled: Wetlands cover a small portion of the world, but have disproportionate influence on global carbon (C) sequestration, carbon dioxide and methane emissions, and aquatic C fluxes. However, the underlying biogeochemical processes that affect wetland C pools and fluxes are complex and dynamic, making measurements of wetland C challenging. Over decades of research, many observational, experimental, and analytical approaches have been developed to understand and quantify pools and fluxes of wetland C.

Modelling opinion dynamics under the impact of influencer and media strategies.

Digital communication has made the public discourse considerably more complex, and new actors and strategies have emerged as a result of this seismic shift. Aside from the often-studied interactions among individuals during opinion formation, which have been facilitated on a large scale by social media platforms, the changing role of traditional media and the emerging role of "influencers" are not well understood, and the implications of their engagement strategies arising from the incentive structure of the attention economy even less so. Here we propose a novel framework for opinion dynamics that can accommodate various versions of opinion dynamics as well as account for different roles, namely that of individuals, media and influencers, who change their own opinion positions on different time scales.

Novel multi-objective affinity approach allows to identify pH-specific μ-opioid receptor agonists.

Opioids are essential pharmaceuticals due to their analgesic properties, however, lethal side effects, addiction, and opioid tolerance are extremely challenging. The development of novel molecules targeting the [Formula: see text]-opioid receptor (MOR) in inflamed, but not in healthy tissue, could significantly reduce these unwanted effects. Finding such novel molecules can be achieved by maximizing the binding affinity to the MOR at acidic pH while minimizing it at neutral pH, thus combining two conflicting objectives.

Studying additive effects of combining rTMS with cognitive control training: a pilot investigation.

Background: Repetitive transcranial magnetic stimulation (rTMS) on the dorsolateral prefrontal cortex (DLPFC) is an effective treatment for depression that has been proposed to work via the enhancement of cognitive control. Cognitive control training (CCT) can also alleviate depression by relying on DLPFC activation. As the additive effects of rTMS and CCT are unclear, we set out to conduct a within-subject pilot study in healthy controls.

Autoimmune encephalitis: Epidemiology, pathophysiology and clinical spectrum (part 2).

Autoimmune encephalitis (AE) represents a growing number of severe autoimmune-inflammatory diseases affecting both the white and grey matter of the brain. In part 1 of this series we focused on the epidemiology, pathophysiology and clinical presentation of this condition, with two illustrative cases. In this part, we will introduce the clinical criteria for AE, particularly for the diagnosis of anti-N-methyl-D-aspartate (NMDA) receptor encephalitis, which were developed to facilitate immune treatment in suspected cases before antibody results are available.

Rate-limiting recovery processes in neurotransmission under sustained stimulation.

At active zones of chemical synapses, an arriving electric signal induces the fusion of vesicles with the presynaptic membrane, thereby releasing neurotransmitters into the synaptic cleft. After a fusion event, both the release site and the vesicle undergo a recovery process before becoming available for reuse again. Of central interest is the question which of the two restoration steps acts as the limiting factor during neurotransmission under high-frequency sustained stimulation.

Guest editorial.

Since the identification of anti-N-methyl-D-aspartate (NMDA) receptor antibodies about 15 years ago, many patients with rapidly progressing psychiatric symptoms, abnormal movements, seizures or unexplained coma, have been diagnosed with autoimmune encephalitis (AE). The symptom onset is often unspecific and might mimic psychiatric disease, but the later course is frequently characterized by severe disease, often requiring intensive care. Clinical and immunological criteria are helpful in identifying the patients, but no biomarkers exist to guide the clinician in therapy or predict outcome.

Autoimmune encephalitis : Part 1 (Epidemiology, Pathophysiology and Clinical spectrum).

Since the identification of anti-N-methyl-D-aspartate (NMDA) receptor antibodies about 15 years ago, many patients with rapidly progressing psychiatric symptoms, abnormal movements, seizures or unexplained coma, have been diagnosed with autoimmune encephalitis (AE). The symptom onset is often unspecific and might mimic psychiatric disease, but the later course is frequently characterized by severe disease, often requiring intensive care. Clinical and immunological criteria are helpful in identifying the patients, but no biomarkers exist to guide the clinician in therapy or predict outcome.

Late-onset efavirenz toxicity: A descriptive study from Pretoria, South Africa.

Background: The neuropsychiatric side effects of efavirenz occur mainly early during treatment and are usually mild. A lesser-known and serious complication is late-onset efavirenz toxicity causing ataxia and encephalopathy. Data regarding this condition are limited.

Modelling altered signalling of G-protein coupled receptors in inflamed environment to advance drug design.

We previously reported the successful design, synthesis and testing of the prototype opioid painkiller NFEPP that does not elicit adverse side effects. The design process of NFEPP was based on mathematical modelling of extracellular interactions between G-protein coupled receptors (GPCRs) and ligands, recognizing that GPCRs function differently under pathological versus healthy conditions. We now present an additional and novel stochastic model of GPCR function that includes intracellular dissociation of G-protein subunits and modulation of plasma membrane calcium channels and their dependence on parameters of inflamed and healthy tissue (pH, radicals).

Efficacy of deep brain stimulation of the anterior-medial globus pallidus internus in tic and non-tic related symptomatology in refractory Tourette syndrome.

Introduction: Although refractory Tourette Syndrome (TS) is rare, it poses great challenges in clinical practice. Co-morbid psychiatric symptoms often occur, negatively impacting quality of life. Deep brain stimulation (DBS) targeting different brain structures seems effective for tics, but specific literature regarding response of psychiatric symptoms is more limited.

Integration of machine learning with complex industrial mining systems for reduced energy consumption.

The deep-level mining industry is experiencing narrowing profit margins due to increasing operating costs and decreasing production. The industry is known for its lack of dynamic control across complex integrated systems running deep underground, making IoT technologies difficult to implement. An important integrated system in a typical underground mine is the refrigeration-ventilation system.

Update of the CHIP (CT in Head Injury Patients) decision rule for patients with minor head injury based on a multicenter consecutive case series.

Objective: To update the existing CHIP (CT in Head Injury Patients) decision rule for detection of (intra)cranial findings in adult patients following minor head injury (MHI).

Methods: The study is a prospective multicenter cohort study in the Netherlands. Consecutive MHI patients of 16 years and older were included.

Cost of Delivering Tetanus Toxoid and Tetanus-Diphtheria Vaccination in Vietnam and the Budget Impact of Proposed Changes to the Schedule.

Introduction: In 2017, aligned with global World Health Organization tetanus guidelines, Vietnam prepared evidence to support a recommendation to introduce the tetanus-diphtheria (Td) vaccine into routine immunization. This study aimed to provide evidence on the costs and budgetary impact of the potential replacement of the tetanus-toxoid (TT) vaccine with the Td vaccine, considering different possible delivery strategies.

Method: We used an activity-based ingredients costing approach to estimate the 2017 program costs of providing TT vaccination to girls aged 15-16 years and conducting Td campaigns in outbreak areas.

TOR1A mutation-related isolated childhood-onset generalised dystonia in South Africa.

Background: Childhood-onset generalised dystonia is commonly caused by TOR1A mutations and is known to respond well to pallidal deep-brain stimulation (DBS) surgery. The incidence and prevalence of monogenic dystonia in individuals from Africa and specifically of African ancestry are unknown, and no local cases of TOR1A mutation dystonia are found in the literature.

Objectives: To describe our experience with the outcome of TOR1A mutation-positive patients with isolated generalised dystonia (IGD) of childhood onset who were treated with pallidal DBS.