rudyvdbrink/CitationDatabase huggingface dataset:
Optimising adjacent membrane segmentation and parameterisation in multicellular aggregates by piecewise active contours.
Journal of microscopy, 2020

In fluorescence microscopy imaging, the segmentation of adjacent cell membranes within cell aggregates, multicellular samples, tissue, organs, or whole organisms remains a challenging task. The lipid bilayer is a very thin membrane when compared to the wavelength of photons in the visual spectra. Fluorescent molecules or proteins used for labelling membranes provide a limited signal intensity, and light scattering in combination with sample dynamics during in vivo imaging lead to poor or ambivalent signal patterns that hinder precise localisation of the membrane sheets. In the proximity of cells, membranes approach and distance each other. Here, the presence of membrane protrusions such as blebs; filopodia and lamellipodia; microvilli; or membrane vesicle trafficking, lead to a plurality of signal patterns, and the accurate localisation of two adjacent membranes becomes difficult. Several computational methods for membrane segmentation have been introduced. However, few of them specifically consider the accurate detection of adjacent membranes. In this article we present ALPACA (ALgorithm for Piecewise Adjacent Contour Adjustment), a novel method based on 2D piecewise parametric active contours that allows: (i) a definition of proximity for adjacent contours, (ii) a precise detection of adjacent, nonadjacent, and overlapping contour sections, (iii) the definition of a polyline for an optimised shared contour within adjacent sections and (iv) a solution for connecting adjacent and nonadjacent sections under the constraint of preserving the inherent cell morphology. We show that ALPACA leads to a precise quantification of adjacent and nonadjacent membrane zones in regular hexagons and live image sequences of cells of the parapineal organ during zebrafish embryo development. The algorithm detects and corrects adjacent, nonadjacent, and overlapping contour sections within a selected adjacency distance d, calculates shared contour sections for neighbouring cells with minimum alterations of the contour characteristics, and presents piecewise active contour solutions, preserving the contour shape and the overall cell morphology. ALPACA quantifies adjacent contours and can improve the meshing of 3D surfaces, the determination of forces, or tracking of contours in combination with previously published algorithms. We discuss pitfalls, strengths, and limits of our approach, and present a guideline to take the best decision for varying experimental conditions for in vivo microscopy.
Cortical iron disrupts functional connectivity networks supporting working memory performance in older adults.
NeuroImage, 2020

Excessive brain iron negatively affects working memory and related processes but the impact of cortical iron on task-relevant, cortical brain networks is unknown. We hypothesized that high cortical iron concentration may disrupt functional circuitry within cortical networks supporting working memory performance. Fifty-five healthy older adults completed an N-Back working memory paradigm while functional magnetic resonance imaging (fMRI) was performed. Participants also underwent quantitative susceptibility mapping (QSM) imaging for assessment of non-heme brain iron concentration. Additionally, pseudo continuous arterial spin labeling scans were obtained to control for potential contributions of cerebral blood volume and structural brain images were used to control for contributions of brain volume. Task performance was positively correlated with strength of task-based functional connectivity (tFC) between brain regions of the frontoparietal working memory network. However, higher cortical iron concentration was associated with lower tFC within this frontoparietal network and with poorer working memory performance after controlling for both cerebral blood flow and brain volume. Our results suggest that high cortical iron concentration disrupts communication within frontoparietal networks supporting working memory and is associated with reduced working memory performance in older adults.
Introduction to knowledge and competency standards for specialized treatments for obsessive-compulsive disorder throughout the lifespan: Phase two series by the International Accreditation Task Force of the Canadian Institute for Obsessive Compulsive Disorders (CIOCD, www.ciocd.ca).
Psychiatry research, 2021

This paper presents an introduction to the phase two series of papers by the 14 nation International Obsessive-Compulsive Disorders Task Force (ATF) of the Canadian Institute for Obsessive Compulsive Disorders. These papers present evidence-based knowledge and competency standards developed by the ATF for specialized treatments for obsessive-compulsive disorder (OCD) through the lifespan, operationalized as clinician abilities. Specialty standards for OCD do not currently exist and are deemed by experts to be foundational to transformative improvement globally in quality and accessibility of evidence-based treatments for this crippling disorder. Currently available guidelines for care are deemed to be essential but insufficient because of highly variable clinician knowledge and competencies specific to this disorder. The ATF standards encompass specialized cognitive behavior therapy, and pharmacotherapy, for pediatric and adult OCD. Evidence-based methodology with integration of expert opinion are described. Upcoming ATF phases three and four will involve development and implementation of training criteria and processes for certification (individual clinicians) and accreditation (clinical sites) based on the ATF standards. These standards will require periodic review and updating commensurate with advances in clinical research. We hope that this international initiative constitutes a significant step forward to inform and advance evidence-based specialized treatment and training for OCD.
Sex-and Region-Dependent Expression of the Autism-Linked ADNP Correlates with Social- and Speech-Related Genes in the Canary Brain.
Journal of molecular neuroscience : MN, 2020

The activity-dependent neuroprotective protein (ADNP) syndrome is an autistic-like disorder, instigated by mutations in ADNP. This syndrome is characterized by developmental delays, impairments in speech, motor function, abnormal hearing, and intellectual disabilities. In the Adnp-haploinsufficient mouse model, many of these impediments are evident, appearing in a sex-dependent manner. In zebra finch songbird (ZF; Taeniopygia guttata), an animal model used for song/language studies, ADNP mRNA most robust expression is observed in the cerebrum of young males, potentially corroborating with male ZF exclusive singing behavior and developed cerebral song system. Herein, we report a similar sex-dependent ADNP expression profile, with the highest expression in the cerebrum (qRT-PCR) in the brain of another songbird, the domesticated canary (Serinus canaria domestica). Additional analyses for the mRNA transcripts of the ADNP regulator, vasoactive intestinal peptide (VIP), sister gene ADNP2, and speech-related Forkhead box protein P2 (FoxP2) revealed multiple sex and brain region-dependent positive correlations between the genes (including ADNP). Parallel transcript expression patterns for FoxP2 and VIP were observed alongside specific FoxP2 increase in males compared with females as well as VIP/ADNP2 correlations. In spatial view, a sexually independent extensive form of expression was found for ADNP in the canary cerebrum (RNA in situ hybridization). The songbird cerebral mesopallium area stood out as a potentially high-expressing ADNP tissue, further strengthening the association of ADNP with sense integration and auditory memory formation, previously implicated in mouse and human.
Experience-driven remodeling of S1 digit representation in awake monkeys: the challenge of comparing active and passive touch.
Journal of neurophysiology, 2021

Many studies have compared active and passive touch to understand how motor action shapes touch perception. Current views emphasize the difficulties in making such a comparison and promote investigating how motor strategies enable the filtering out of sensory inputs to reshape touch perception. Cybulska-Klosowicz et al. (Cybulska-Klosowicz A, Tremblay F, Jiang W, Bourgeon S, Meftah E-M, Chapman CE.
Nicotine treatment buffers negative behavioral consequences induced by exposure to physical and emotional stress in adolescent male mice.
Psychopharmacology, 2020

Early life stress influences adult psychopathology and is associated with an increase in the propensity for drug use/seeking throughout the lifespan. Animal models corroborate that stress exposure exacerbates maladaptive reactivity to stressful stimuli while also shifting the rewarding properties of many drugs of abuse, including nicotine (NIC), a stimulant commonly misused by adolescents. Interestingly, NIC treatment can also normalize some stress-induced behavioral deficits in adult rodents; however, little is known about NIC's therapeutic efficacy following stress experienced during adolescence. The goal of the following experiments was to elucidate NIC's ability to buffer the negative consequences of stress exposure, and to further assess behavioral responsivity while on the drug. Given that stress often occurs in both physical and non-physical forms, we employed the vicarious social defeat stress (VSDS) model which allows for investigation of both physical (PS) and emotional stress (ES) exposure. After 10 days, exposure to PS and ES decreased interaction with a social target in the social interaction test (SIT), confirming social avoidance. Groups were further divided and given NIC (0.0 or 160 mg/L) in their drinking water. After 1 month of NIC consumption, the mice were exposed to the SIT, elevated plus maze (EPM), and the forced swim test (FST), respectively. NIC-treated mice showed a reversal of stress-induced deficits in the EPM and FST. Surprisingly, the mice did not show improvement in the SIT regardless of treatment condition. Together, these data confirm NIC's ability to normalize some stress-induced behavioral deficits; however, NIC's effects on social behavior need further investigation.
Social and affective neuroscience: an Australian perspective.
Social cognitive and affective neuroscience, 2020

While research in social and affective neuroscience has a long history, it is only in the last few decades that it has been truly established as an independent field of investigation. In the Australian region, despite having an even shorter history, this field of research is experiencing a dramatic rise. In this review, we present recent findings from a survey conducted on behalf of the Australasian Society for Social and Affective Neuroscience (AS4SAN) and from an analysis of the field to highlight contributions and strengths from our region (with a focus on Australia). Our results demonstrate that researchers in this field draw on a broad range of techniques, with the most common being behavioural experiments and neuropsychological assessment, as well as structural and functional magnetic resonance imaging. The Australian region has a particular strength in clinically driven research, evidenced by the types of populations under investigation, top cited papers from the region, and funding sources. We propose that the Australian region has potential to contribute to cross-cultural research and facilitating data sharing, and that improved links with international leaders will continue to strengthen this burgeoning field.
Predictive fat mass equations for spinal muscular atrophy type I children: Development and internal validation.
Clinical nutrition (Edinburgh, Scotland), 2021

Body composition assessment is paramount for spinal muscular atrophy type I (SMA I) patients, as weight and BMI have proven to be misleading for these patients. Despite its importance, no disease-specific field method is currently available, and the assessment of body composition of SMA I patients requires reference methods available only in specialized settings.
Common marmosets (Callithrix jacchus) cannot recognize global configurations of sound patterns but can recognize adjacent relations of sounds.
Behavioural processes, 2020

Processing the temporal configuration of discrete sounds to extract a regular pattern is fundamental to humans' faculties of perceiving words and musical phrases. To investigate such auditory pattern perception in monkeys, I trained two common marmosets to discriminate between AB-AB and AA-BB patterns under two training paradigms. One was an absolute discrimination task, in which the discrimination between these stimuli without reference cues was required. The other was a relative discrimination task, in which the detection of a change from one stimulus to the other was required. The marmosets failed in the absolute discrimination task but achieved the relative discrimination task. Failure in the absolute task indicated that the marmosets were unable to form a representation of the global sound patterns in their long-term memory stores. In contrast, success in the relative task indicated that the marmosets had short-term memory of ongoing sounds that enabled an online monitoring to detect deviations between incoming sounds and the anticipated upcoming sounds. Thus, the current findings imply that marmosets can at least perceive adjacent tone relations in an auditory stream regardless of the temporal configuration of the global sound patterns.
Modelling unitary fields and the single-neuron contribution to local field potentials in the hippocampus.
The Journal of physiology, 2020

We simulate the unitary local field potential (uLFP) generated in the hippocampus CA3, using morphologically detailed models. The model suggests that cancelling effects between apical and basal dendritic synapses explain the low amplitude of excitatory uLFPs. Inhibitory synapses around the soma do not cancel and could explain the high-amplitude inhibitory uLFPs. These results suggest that somatic inhibition constitutes a strong component of LFPs, which may explain a number of experimental observations.
Dispatches from the International Behavioral Neuroscience Society meeting 2014. Introduction.
Behavioural brain research, 2015

The International Behavioral Neuroscience Society (IBNS) was founded in 1992 to fill the need for a focused meeting of the international research community to discuss issues important for the development and progress of this scientific discipline. In the 20 plus years since its founding, IBNS has become a hub for the dissemination of new research, development of important research collaborations, support and networking for young investigators, and for outreach and education to the community. This work is covered in part by offering special sessions during the meeting for late-breaking scientific discoveries from a range of disciplines as well as background and seniority level of the presenters. This special issue is a culmination of the late-breaking research presented at the IBNS 2014 meeting. The manuscripts of this Special Issue cover a variety of themes, including, stress, depression, the intersection of monoamine systems and behavior, substance use disorders, attentional processes, and awareness and acceptance of brain training. This wide range of topics and interest as well as range in seniority of presenters demonstrate the driving interest of IBNS in advancing knowledge in behavioral neuroscience as well as supporting scientists at every level.
Effect of acute citalopram on self-referential emotional processing and social cognition in healthy volunteers.
BJPsych open, 2020

Depression is characterised by negative views of the self. Antidepressant treatment may remediate negative self-schema through increasing processing of positive information about the self. Changes in affective processing during social interactions may increase expression of prosocial behaviours, improving interpersonal communications.
An open-source toolbox for measuring dynamic video framerates and synchronizing video stimuli with neural and behavioral responses.
Journal of neuroscience methods, 2020

Researchers rely on the specified capabilities of their hardware and software even though, in reality, these capabilities are often not achieved. Considering that the number of experiments examining neural oscillations has increased steadily, easy-to-implement tools for testing the capabilities of hardware and software are necessary.
Tau is not necessary for amyloid-β-induced synaptic and memory impairments.
The Journal of clinical investigation, 2020

The amyloid hypothesis posits that the amyloid-beta (Aβ) protein precedes and requires microtubule-associated protein tau in a sort of trigger-bullet mechanism leading to Alzheimer's disease (AD) pathology. This sequence of events has become dogmatic in the AD field and is used to explain clinical trial failures due to a late start of the intervention when Aβ already activated tau. Here, using a multidisciplinary approach combining molecular biological, biochemical, histopathological, electrophysiological, and behavioral methods, we demonstrated that tau suppression did not protect against Aβ-induced damage of long-term synaptic plasticity and memory, or from amyloid deposition. Tau suppression could even unravel a defect in basal synaptic transmission in a mouse model of amyloid deposition. Similarly, tau suppression did not protect against exogenous oligomeric tau-induced impairment of long-term synaptic plasticity and memory. The protective effect of tau suppression was, in turn, confined to short-term plasticity and memory. Taken together, our data suggest that therapies downstream of Aβ and tau together are more suitable to combat AD than therapies against one or the other alone.
Glial cells and adaptive immunity in frontotemporal dementia with tau pathology.
Brain : a journal of neurology, 2021

Neuroinflammation is involved in the aetiology of many neurodegenerative disorders including Alzheimer's disease, Parkinson's disease and motor neuron disease. Whether neuroinflammation also plays an important role in the pathophysiology of frontotemporal dementia is less well known. Frontotemporal dementia is a heterogeneous classification that covers many subtypes, with the main pathology known as frontotemporal lobar degeneration. The disease can be categorized with respect to the identity of the protein that causes the frontotemporal lobar degeneration in the brain. The most common subgroup describes diseases caused by frontotemporal lobar degeneration associated with tau aggregation, also known as primary tauopathies. Evidence suggests that neuroinflammation may play a role in primary tauopathies with genome-wide association studies finding enrichment of genetic variants associated with specific inflammation-related gene loci. These loci are related to both the innate immune system, including brain resident microglia, and the adaptive immune system through possible peripheral T-cell involvement. This review discusses the genetic evidence and relates it to findings in animal models expressing pathogenic tau as well as to post-mortem and PET studies in human disease. Across experimental paradigms, there seems to be a consensus regarding the involvement of innate immunity in primary tauopathies, with increased microglia and astrocyte density and/or activation, as well as increases in pro-inflammatory markers. Whilst it is less clear as to whether inflammation precedes tau aggregation or vice versa; there is strong evidence to support a microglial contribution to the propagation of hyperphosphorylated in tau frontotemporal lobar degeneration associated with tau aggregation. Experimental evidence-albeit limited-also corroborates genetic data pointing to the involvement of cellular adaptive immunity in primary tauopathies. However, it is still unclear whether brain recruitment of peripheral immune cells is an aberrant result of pathological changes or a physiological aspect of the neuroinflammatory response to the tau pathology.
SOD1 regulates ribosome biogenesis in KRAS mutant non-small cell lung cancer.
Nature communications, 2021

SOD1 is known as the major cytoplasmic superoxide dismutase and an anticancer target. However, the role of SOD1 in cancer is not fully understood. Herein we describe the generation of an inducible Sod1 knockout in KRAS-driven NSCLC mouse model. Sod1 knockout markedly reduces tumor burden in vivo and blocks growth of KRAS mutant NSCLC cells in vitro. Intriguingly, SOD1 is enriched in the nucleus and notably in the nucleolus of NSCLC cells. The nuclear and nucleolar, not cytoplasmic, form of SOD1 is essential for lung cancer cell proliferation. Moreover, SOD1 interacts with PeBoW complex and controls its assembly necessary for pre-60S ribosomal subunit maturation. Mechanistically, SOD1 regulates co-localization of PeBoW with and processing of pre-rRNA, and maturation of cytoplasmic 60S ribosomal subunits in KRAS mutant lung cancer cells. Collectively, our study unravels a nuclear SOD1 function essential for ribosome biogenesis and proliferation in KRAS-driven lung cancer.
Cajal's first steps in scientific research.
Neuroscience, 2012

More than 125 years ago, Santiago Ramón y Cajal was able to draft and prove the neuron doctrine, and later, to develop prophetic theories about neural function and plasticity, many of which have been proven by current neuroscience. It was chance that made Cajal, during his doctorate studies, have his first contact with histology and force him to study the then current theories about pathogenesis of inflammation. Thus, he gained knowledge of the vascular hypothesis, by Julius Cohnheim, a German pathologist who, opposing the opinion of his teacher and father of cellular pathology, Rudolf Virchow, made leukocytes the protagonists of inflammation, given their ability to develop ameboid movements directed by chemical signals. Cohnheim's chemotactic theory deeply influenced Cajal's conception of biology. So, the basic postulates of chemotaxis can be identified at different moments in Cajal's research, from the description of the "growth cone" in embryonic neuroblasts, the origin of the neurotrophic theory, to the proposal of the pathophysiological mechanisms of neuronal plasticity. From Cajal's point of view, the neurons move during their development and also adapt to different external circumstances. Chemical endogenous substances can stimulate this movement in a similar way to leukocytes during the process of inflammation.
Study protocol of comprehensive risk evaluation for anorexia nervosa in twins (CREAT): a study of discordant monozygotic twins with anorexia nervosa.
BMC psychiatry, 2020

Anorexia nervosa (AN) is a severe disorder, for which genetic evidence suggests psychiatric as well as metabolic origins. AN has high somatic and psychiatric comorbidities, broad impact on quality of life, and elevated mortality. Risk factor studies of AN have focused on differences between acutely ill and recovered individuals. Such comparisons often yield ambiguous conclusions, as alterations could reflect different effects depending on the comparison. Whereas differences found in acutely ill patients could reflect state effects that are due to acute starvation or acute disease-specific factors, they could also reflect underlying traits. Observations in recovered individuals could reflect either an underlying trait or a "scar" due to lasting effects of sustained undernutrition and illness. The co-twin control design (i.e., monozygotic [MZ] twins who are discordant for AN and MZ concordant control twin pairs) affords at least partial disambiguation of these effects.