A systematic approach to defining and verifying descriptors used in the Qualitative Behavioural Assessment of sows.

Qualitative Behaviour Assessment (QBA) is a welfare evaluation tool that uses a holistic approach to capturing an animal's emotional state. Lists of QBA descriptors validated to assess pig welfare exist, but their definitions are often not described in peer-reviewed literature and the processes used to develop definitions are lacking. The objective of this study is to detail a systematic approach to creating clear definitions for a pre-existing fixed list of QBA descriptors and test their application. A fixed list of 20 descriptors from the EU Welfare Quality® assessment protocol for pigs was modified, and ten pig experts were recruited to assist with defining these descriptors in a focus group-style discussion. Half of the experts involved in creating descriptor definitions partook in a subsequent step, where the newly developed definitions were tested by implementing QBA on a video library of post-weaned sows selected to capture the breadth of sow behaviour. Experts displayed excellent agreement in identifying a PCA dimension interpreted as the valence of descriptors and good agreement for another reflecting arousal. Inter-observer reliability was also measured for each descriptor. Only two descriptors exhibited less than moderate agreement between experts whereas half of the descriptors evoked substantial agreement or better. These findings support our process to delineate clear definitions for a fixed list of QBA descriptors in pigs. This study is the first of its kind detailing the in-depth process of creating and verifying descriptor definitions for future use in sow welfare assessment.

Erratum: Non-homeostatic body weight regulation through a brainstem-restricted receptor for GDF15.

This corrects the article DOI: 10.1038/nature24042.

Non-homeostatic body weight regulation through a brainstem-restricted receptor for GDF15.

Under homeostatic conditions, animals use well-defined hypothalamic neural circuits to help maintain stable body weight, by integrating metabolic and hormonal signals from the periphery to balance food consumption and energy expenditure. In stressed or disease conditions, however, animals use alternative neuronal pathways to adapt to the metabolic challenges of altered energy demand. Recent studies have identified brain areas outside the hypothalamus that are activated under these 'non-homeostatic' conditions, but the molecular nature of the peripheral signals and brain-localized receptors that activate these circuits remains elusive. Here we identify glial cell-derived neurotrophic factor (GDNF) receptor alpha-like (GFRAL) as a brainstem-restricted receptor for growth and differentiation factor 15 (GDF15). GDF15 regulates food intake, energy expenditure and body weight in response to metabolic and toxin-induced stresses; we show that Gfral knockout mice are hyperphagic under stressed conditions and are resistant to chemotherapy-induced anorexia and body weight loss. GDF15 activates GFRAL-expressing neurons localized exclusively in the area postrema and nucleus tractus solitarius of the mouse brainstem. It then triggers the activation of neurons localized within the parabrachial nucleus and central amygdala, which constitute part of the 'emergency circuit' that shapes feeding responses to stressful conditions. GDF15 levels increase in response to tissue stress and injury, and elevated levels are associated with body weight loss in numerous chronic human diseases. By isolating GFRAL as the receptor for GDF15-induced anorexia and weight loss, we identify a mechanistic basis for the non-homeostatic regulation of neural circuitry by a peripheral signal associated with tissue damage and stress. These findings provide opportunities to develop therapeutic agents for the treatment of disorders with altered energy demand.

Evidence for multi-copy Mega-NUMTs in the human genome.

The maternal mode of mitochondrial DNA (mtDNA) inheritance is central to human genetics. Recently, evidence for bi-parental inheritance of mtDNA was claimed for individuals of three pedigrees that suffered mitochondrial disorders. We sequenced mtDNA using both direct Sanger and Massively Parallel Sequencing in several tissues of eleven maternally related and other affiliated healthy individuals of a family pedigree and observed mixed mitotypes in eight individuals. Cells without nuclear DNA, i.e. thrombocytes and hair shafts, only showed the mitotype of haplogroup (hg) V. Skin biopsies were prepared to generate ρ° cells void of mtDNA, sequencing of which resulted in a hg U4c1 mitotype. The position of the Mega-NUMT sequence was determined by fluorescence in situ hybridization and two different quantitative PCR assays were used to determine the number of contributing mtDNA copies. Thus, evidence for the presence of repetitive, full mitogenome Mega-NUMTs matching haplogroup U4c1 in various tissues of eight maternally related individuals was provided. Multi-copy Mega-NUMTs mimic mixtures of mtDNA that cannot be experimentally avoided and thus may appear in diverse fields of mtDNA research and diagnostics. We demonstrate that hair shaft mtDNA sequencing provides a simple but reliable approach to exclude NUMTs as source of misleading results.

A virtual reality paradigm with dynamic scene stimuli for use in memory research.

Episodic memory may essentially be memory for one's place within a temporally unfolding scene from a first-person perspective. Given this, pervasively used static stimuli may only capture one small part of episodic memory. A promising approach for advancing the study of episodic memory is immersing participants within varying scenes from a first-person perspective. We present a pool of distinct scene stimuli for use in virtual environments and a paradigm that is implementable across varying levels of immersion on multiple virtual reality (VR) platforms and adaptable to studying various aspects of scene and episodic memory. In our task, participants are placed within a series of virtual environments from a first-person perspective and guided through a virtual tour of scenes during a study phase and a test phase. In the test phase, some scenes share a spatial layout with studied scenes; others are completely novel. In three experiments with varying degrees of immersion, we measure scene recall, scene familiarity-detection during recall failure, the subjective experience of déjà vu, the ability to predict the next turn on a tour, the subjective sense of being able to predict the next turn on a tour, and the factors that influence memory search and the inclination to generate candidate recollective information. The level of first-person immersion mattered to multiple facets of episodic memory. The paradigm presents a useful means of advancing mechanistic understanding of how memory operates in realistic dynamic scene environments, including in combination with cognitive neuroscience methods such as functional magnetic resonance imaging and electrophysiology.

Opening a conceptual space for metamemory experience.

The experiences associated with remembering, including metamemory feelings about the act of remembering and attempts at remembering, are not often integrated into general accounts of memory. For example, David Rubin (2022) proposes a unified, three-dimensional conceptual space for mapping memory states, a map that does not systematically specify metamemory feelings. Drawing on Rubin's model, we define a distinct role for metamemory in relation to first-order memory content. We propose a fourth dimension for the model and support the proposal with conceptual, neurocognitive, and clinical lines of reasoning. We use the modified model to illustrate several cases, and show how it helps to conceptualize a new category of memory state: autonoetic knowing, exemplified by déjà vu. We also caution not to assume that memory experience is directly correlated with or caused by memory content, an assumption Tulving (1989) labeled the doctrine of concordance.

Daily Functionality in Adults with POTS: Predictive Factors.

Symptoms associated with postural orthostatic tachycardia syndrome (POTS) hinder overall functionality. This study examined factors that impacted daily life and contributed to overall daily functionality in adults with POTS (n = 958, ages 18-60). Descriptive and multiple linear regression analyses indicated that participants with fewer challenges in ADLs, IADLs, work, school, leisure, and socializing had overall better functionality. Furthermore, 'younger age with exercise tolerance', 'having a job', and 'no falls in the last year' were predictors of better functionality. A comprehensive approach to addressing physical, environmental, and psychological factors could help improve overall functionality and enhance quality of life in individuals with POTS.

Subjective distinguishability of seizure and non-seizure Déjà Vu: A case report, brief literature review, and research prospects.

Roughly two-thirds of all people report having experienced déjà vu-the odd feeling that a current experience is both novel and a repeat or replay of a previous, unrecalled experience. Reports of an association between déjà vu and seizure aura symptomatology have accumulated for over a century, and frequent déjà vu is also now known to be associated with focal seizures, particularly those of a medial temporal lobe (MTL) origin. A longstanding question is whether seizure-related déjà vu has the same basis and is the same subjective experience as non-seizure déjà vu. Survey research suggests that people who experience both seizure-related and non-seizure déjà vu can often subjectively distinguish between the two. We present a case of a person with a history of focal MTL seizures who reports having experienced both seizure-related and non-seizure common déjà vu, though the non-seizure type was more frequent during this person's youth than it is currently. The patient was studied with a virtual tour paradigm that has previously been shown to elicit déjà vu among non-clinical, young adult participants. The patient reported experiencing déjà vu of the common non-seizure type during the virtual tour paradigm, without associated abnormalities of the intracranial EEG. We situate this work in the context of broader ongoing projects examining the subjective correlates of seizures. The importance for memory research of virtual scenes, spatial tasks, virtual reality (VR), and this paradigm for isolating familiarity in the context of recall failure are discussed.

Paradigm Shift Toward Digital Neuropsychology and High-Dimensional Neuropsychological Assessments: Review.

Neuropsychologists in the digital age have increasing access to emerging technologies. The National Institutes of Health (NIH) initiatives for behavioral and social sciences have emphasized these developing scientific and technological potentials (eg, novel sensors) for augmented characterization of neurocognitive, behavioral, affective, and social processes. Perhaps these innovative technologies will lead to a paradigm shift from disintegrated and data-poor behavioral science to cohesive and data-rich science that permits improved translation from bench to bedside. The 4 main advances influencing the scientific priorities of a recent NIH Office of Behavioral and Social Sciences Research strategic plan include the following: integration of neuroscience into behavioral and social sciences, transformational advances in measurement science, digital intervention platforms, and large-scale population cohorts and data integration. This paper reviews these opportunities for novel brain-behavior characterizations. Emphasis is placed on the increasing concern of neuropsychology with these topics and the need for development in these areas to maintain relevance as a scientific discipline and advance scientific developments. Furthermore, the effects of such advancements necessitate discussion and modification of training as well as ethical and legal mandates for neuropsychological research and praxes.

A Comparison of Virtual Reality Classroom Continuous Performance Tests to Traditional Continuous Performance Tests in Delineating ADHD: a Meta-Analysis.

Computerized continuous performance tests (CPTs) are commonly used to characterize attention in attention deficit-hyperactivity disorder (ADHD). Virtual classroom CPTs, designed to enhance ecological validity, are increasingly being utilized. Lacking is a quantitative meta-analysis of clinical comparisons of attention performance in children with ADHD using virtual classroom CPTs. The objective of the present systematic PRISMA review was to address this empirical void and compare three-dimensional (3D) virtual classroom CPTs to traditional two-dimensional (2D) CPTs. The peer-reviewed literature on comparisons of virtual classroom performance between children with ADHD and typically developing children was explored in six databases (e.g., Medline). Published studies using a virtual classroom to compare attentional performance between children with ADHD and typically developing children were included. Given the high heterogeneity with modality comparisons (i.e., computerized CPTs vs. virtual classroom CPTs for ADHD), both main comparisons included only population comparisons (i.e., control vs. ADHD) using each CPT modality. Meta-analytic findings were generally consistent with previous meta-analyses of computerized CPTs regarding the commonly used omission, commission, and hit reaction time variables. Results suggest that the virtual classroom CPTs reliably differentiate attention performance in persons with ADHD. Ecological validity implications are discussed pertaining to subtle meta-analytic outcome differences compared to computerized 2D CPTs. Further, due to an inability to conduct moderator analyses, it remains unclear if modality differences are due to other factors. Suggestions for future research using the virtual classroom CPTs are provided.

Impact of DNA degradation on massively parallel sequencing-based autosomal STR, iiSNP, and mitochondrial DNA typing systems.

Biological samples, including skeletal remains exposed to environmental insults for extended periods of time, exhibit increasing levels of DNA damage and fragmentation. Human forensic identification methods typically use a combination of mitochondrial (mt) DNA sequencing and short tandem repeat (STR) analysis, which target segments of DNA ranging from 80 to 500 base pairs (bps). Larger templates are often unavailable as skeletal samples age and the associated DNA degrades. Single-nucleotide polymorphism (SNP) loci target shorter templates and may serve as a solution to the problem. Recently developed assays for STR and SNP analysis using a massively parallel sequencing approach, such as the ForenSeq kit (Verogen, San Diego, CA), offer a means for generating results from degraded samples as they target templates down to 60 to 170 bps. We performed a modeling study that demonstrates that SNPs can increase the significance of an identification when analyzing DNA down to an average size of 100 bps for input amounts between 0.375 and 1 ng of nuclear DNA. Observations from this study were then compared with human skeletal material results (n = 14, ninth to eighteenth centuries), which further demonstrated the utility of the ForenSeq kit for degraded samples. The robustness of the Promega PowerSeq™ Mito System was also tested with human skeletal remains (n = 70, ninth to eighteenth centuries), resulting in successful coverage of 99.29% of the mtDNA control region at 50× coverage or more. This was accompanied by modifications to a mainstream DNA extraction technique for skeletal remains that improved recovery of shorter templates.

Critical role of histone tail entropy in nucleosome unwinding.

The nucleosome is the fundamental packaging unit for the genome. It must remain tightly wound to ensure genome stability while simultaneously being flexible enough to keep the DNA molecule accessible for genome function. The set of physicochemical interactions responsible for the delicate balance between these naturally opposed processes have not been determined due to challenges in resolving partially unwound nucleosome configurations at atomic resolution. Using a near atomistic protein-DNA model and advanced sampling techniques, we calculate the free energy cost of nucleosome DNA unwinding. Our simulations identify a large energetic barrier that decouples the outer and the inner DNA unwinding into two separate processes, occurring on different time scales. This dynamical decoupling allows the exposure of outer DNA at a modest cost to ensure accessibility while keeping the inner DNA and the histone core intact to maintain stability. We also reveal that this energetic barrier arises from a delayed loss of contacts between disordered histone tails and the DNA and is, surprisingly, largely offset by an entropic contribution from these tails. Implications of this enthalpy entropy compensation for the regulation of nucleosome stability and genome function are discussed.

The potential of function-led virtual environments for ecologically valid measures of executive function in experimental and clinical neuropsychology.

The assessment of executive functions is an integral task of neuropsychological assessment. Traditional measures of executive function are often based on hypothetical constructs that may have little relevance to real-world behaviours. In fact, some traditional tests utilised today were not originally developed for clinical use. Recently, researchers have been arguing for a new generation of "function-led" neuropsychological assessments that are developed from directly observable everyday behaviours. Although virtual environments (VEs) have been presented as potential aides in enhancing ecological validity, many were modelled on construct-driven approaches found in traditional assessments. In the current paper, we review construct-driven and function-led VE-based neuropsychological assessments of executive functions. Overall, function-led VEs best represent the sorts of tasks needed for enhanced ecological validity and prediction of real-world functioning.

Cellular plasticity induced by anti-α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor encephalitis antibodies.

OBJECTIVE: Autoimmune-mediated anti-α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) encephalitis is a severe but treatment-responsive disorder with prominent short-term memory loss and seizures. The mechanisms by which patient antibodies affect synapses and neurons leading to symptoms are poorly understood. METHODS: The effects of patient antibodies on cultures of live rat hippocampal neurons were determined with immunostaining, Western blot, and electrophysiological analyses. RESULTS: We show that patient antibodies cause a selective decrease in the total surface amount and synaptic localization of GluA1- and GluA2-containing AMPARs, regardless of receptor subunit binding specificity, through increased internalization and degradation of surface AMPAR clusters. In contrast, patient antibodies do not alter the density of excitatory synapses, N-methyl-D-aspartate receptor (NMDAR) clusters, or cell viability. Commercially available AMPAR antibodies directed against extracellular epitopes do not result in a loss of surface and synaptic receptor clusters, suggesting specific effects of patient antibodies. Whole-cell patch clamp recordings of spontaneous miniature postsynaptic currents show that patient antibodies decrease AMPAR-mediated currents, but not NMDAR-mediated currents. Interestingly, several functional properties of neurons are also altered: inhibitory synaptic currents and vesicular γ-aminobutyric acid transporter (vGAT) staining intensity decrease, whereas the intrinsic excitability of neurons and short-interval firing increase. INTERPRETATION: These results establish that antibodies from patients with anti-AMPAR encephalitis selectively eliminate surface and synaptic AMPARs, resulting in a homeostatic decrease in inhibitory synaptic transmission and increased intrinsic excitability, which may contribute to the memory deficits and epilepsy that are prominent in patients with this disorder.

Real space electrostatics for multipoles. III. Dielectric properties.

In Papers I and II, we developed new shifted potential, gradient shifted force, and Taylor shifted force real-space methods for multipole interactions in condensed phase simulations. Here, we discuss the dielectric properties of fluids that emerge from simulations using these methods. Most electrostatic methods (including the Ewald sum) require correction to the conducting boundary fluctuation formula for the static dielectric constants, and we discuss the derivation of these corrections for the new real space methods. For quadrupolar fluids, the analogous material property is the quadrupolar susceptibility. As in the dipolar case, the fluctuation formula for the quadrupolar susceptibility has corrections that depend on the electrostatic method being utilized. One of the most important effects measured by both the static dielectric and quadrupolar susceptibility is the ability to screen charges embedded in the fluid. We use potentials of mean force between solvated ions to discuss how geometric factors can lead to distance-dependent screening in both quadrupolar and dipolar fluids.

Chemoenzymatic Synthesis of a Phosphorylated Glycoprotein.

The majority of lysosomal enzymes are targeted to the lysosome by post-translational tagging with N-glycans terminating in mannose-6-phosphate (M6P) residues. Some current enzyme replacement therapies (ERTs) for lysosomal storage disorders are limited in their efficacy by the extent to which the recombinant enzymes bear the M6P-terminated glycans required for effective trafficking. Chemical synthesis was combined with endo-ß-N-acetylglucosaminidase (ENGase) catalysis to allow the convergent synthesis of glycosyl amino acids bearing M6P residues. This approach can be extended to the remodeling of proteins, as exemplified by RNase. The powerful synergy of chemical synthesis and ENGase-mediated biocatalysis enabled the first synthesis of a glycoprotein bearing M6P-terminated N-glycans in which the glycans are attached to the peptide backbone by entirely natural linkages.

Optimal Synthetic Glycosylation of a Therapeutic Antibody.

Glycosylation patterns in antibodies critically determine biological and physical properties but their precise control is a significant challenge in biology and biotechnology. We describe herein the optimization of an endoglycosidase-catalyzed glycosylation of the best-selling biotherapeutic Herceptin, an anti-HER2 antibody. Precise MS analysis of the intact four-chain Ab heteromultimer reveals nonspecific, non-enzymatic reactions (glycation), which are not detected under standard denaturing conditions. This competing reaction, which has hitherto been underestimated as a source of side products, can now be minimized. Optimization allowed access to the purest natural form of Herceptin to date (≥90 %). Moreover, through the use of a small library of sugars containing non-natural functional groups, Ab variants containing defined numbers of selectively addressable chemical tags (reaction handles at Sia C1) in specific positions (for attachment of cargo molecules or "glycorandomization") were readily generated.

Acute mechanisms underlying antibody effects in anti-N-methyl-D-aspartate receptor encephalitis.

OBJECTIVE: A severe but treatable form of immune-mediated encephalitis is associated with antibodies in serum and cerebrospinal fluid (CSF) against the GluN1 subunit of the N-methyl-D-aspartate receptor (NMDAR). Prolonged exposure of hippocampal neurons to antibodies from patients with anti-NMDAR encephalitis caused a reversible decrease in the synaptic localization and function of NMDARs. However, acute effects of the antibodies, fate of the internalized receptors, type of neurons affected, and whether neurons develop compensatory homeostatic mechanisms were unknown and are the focus of this study. METHODS: Dissociated hippocampal neuron cultures and rodent brain sections were used for immunocytochemical, physiological, and molecular studies. RESULTS: Patient antibodies bind to NMDARs throughout the rodent brain, and decrease NMDAR cluster density in both excitatory and inhibitory hippocampal neurons. They rapidly increase the internalization rate of surface NMDAR clusters, independent of receptor activity. This internalization likely accounts for the observed decrease in NMDAR-mediated currents, as no evidence of direct blockade was detected. Once internalized, antibody-bound NMDARs traffic through both recycling endosomes and lysosomes, similar to pharmacologically induced NMDAR endocytosis. The antibodies are responsible for receptor internalization, as their depletion from CSF abrogates these effects in hippocampal neurons. We find that although anti-NMDAR antibodies do not induce compensatory changes in glutamate receptor gene expression, they cause a decrease in inhibitory synapse density onto excitatory hippocampal neurons. INTERPRETATION: Our data support an antibody-mediated mechanism of disease pathogenesis driven by immunoglobulin-induced receptor internalization. Antibody-mediated downregulation of surface NMDARs engages homeostatic synaptic plasticity mechanisms, which may inadvertently contribute to disease progression.

Refractoriness enhances temporal coding by auditory nerve fibers.

A universal property of spiking neurons is refractoriness, a transient decrease in discharge probability immediately following an action potential (spike). The refractory period lasts only one to a few milliseconds, but has the potential to affect temporal coding of acoustic stimuli by auditory neurons, which are capable of submillisecond spike-time precision. Here this possibility was investigated systematically by recording spike times from chicken auditory nerve fibers in vivo while stimulating with repeated pure tones at characteristic frequency. Refractory periods were tightly distributed, with a mean of 1.58 ms. A statistical model was developed to recapitulate each fiber's responses and then used to predict the effect of removing the refractory period on a cell-by-cell basis for two largely independent facets of temporal coding: faithful entrainment of interspike intervals to the stimulus frequency and precise synchronization of spike times to the stimulus phase. The ratio of the refractory period to the stimulus period predicted the impact of refractoriness on entrainment and synchronization. For ratios less than ∼0.9, refractoriness enhanced entrainment and this enhancement was often accompanied by an increase in spike-time precision. At higher ratios, little or no change in entrainment or synchronization was observed. Given the tight distribution of refractory periods, the ability of refractoriness to improve temporal coding is restricted to neurons responding to low-frequency stimuli. Enhanced encoding of low frequencies likely affects sound localization and pitch perception in the auditory system, as well as perception in nonauditory sensory modalities, because all spiking neurons exhibit refractoriness.

Rationally designed short polyisoprenol-linked PglB substrates for engineered polypeptide and protein N-glycosylation.

The lipid carrier specificity of the protein N-glycosylation enzyme C. jejuni PglB was tested using a logical, synthetic array of natural and unnatural C10, C20, C30, and C40 polyisoprenol sugar pyrophosphates, including those bearing repeating cis-prenyl units. Unusual, short, synthetically accessible C20 prenols (nerylnerol 1d and geranylnerol 1e) were shown to be effective lipid carriers for PglB sugar substrates. Kinetic analyses for PglB revealed clear K(M)-only modulation with lipid chain length, thereby implicating successful in vitro application at appropriate concentrations. This was confirmed by optimized, efficient in vitro synthesis allowing >90% of Asn-linked ß-N-GlcNAc-ylated peptide and proteins. This reveals a simple, flexible biocatalytic method for glycoconjugate synthesis using PglB N-glycosylation machinery and varied chemically synthesized glycosylation donor precursors.