bluuebunny/crossref_metadata_2025 huggingface dataset:
Thalamocortical Anatomical Connectivity in Schizophrenia and Psychotic Bipolar Disorder
Authors: Sheffield Julia M , Huang Anna S , Rogers Baxter P , Giraldo-Chica Monica , Landman Bennett A , Blackford Jennifer Urbano , Heckers Stephan , Woodward Neil D
Published: February 2020

Background

Anatomical connectivity between the thalamus and cortex, including the prefrontal cortex (PFC), is abnormal in schizophrenia. Overlapping phenotypes, including deficits in executive cognitive abilities dependent on PFC-thalamic circuitry, suggest dysrupted thalamocortical anatomical connectivity may extend to psychotic bipolar disorder. We tested this hypothesis and examined the impact of illness stage to inform when in the illness course thalamocortical dysconnectivity emerges.

Methods

Diffusion-weighted imaging data were collected on 70 healthy individuals and 124 people with a psychotic disorder (schizophrenia spectrum = 75; psychotic bipolar disorder = 49), including 62 individuals in the early stage of psychosis. Anatomical connectivity between major divisions of the cortex and thalamus was quantified using probabilistic tractography and compared between groups. Associations between PFC-thalamic anatomical connectivity and executive cognitive abilities were examined using regression analysis.

Results

Psychosis was associated with lower PFC-thalamic and elevated somatosensory-thalamic anatomical connectivity. Follow-up analyses established that lower PFC-thalamic and elevated somatosensory-thalamic anatomical connectivity were present in both schizophrenia and psychotic bipolar disorder. Lower PFC-thalamic anatomical connectivity was also present in early-stage and chronic psychosis. Contrary to expectations, lower PFC-thalamic anatomical connectivity was not associated with impaired executive cognitive abilities.

Conclusions

Altered thalamocortical anatomical connectivity, especially reduced PFC-thalamic connectivity, is a transdiagnostic feature of psychosis detectable in the early stage of illness. Further work is required to elucidate the functional consequences of the full spectrum of thalamocortical connectivity abnormalities in psychosis.
“We’d Rather Be Relevant than Theoretically Accurate”: The Translation and Commodification of Social Scientific Knowledge for Clinical Practice
Authors: Olsen Lauren D
Published: February 2020

At the turn of the 21st century, one of the ways in which the U.S. medical profession attempted to address the rampant health and healthcare disparities facing their patient populations was to pay more attention to a patient’s culture. Proving to be easier said than done, the operationalization of the social scientific concept of culture for clinical practice has been fraught with implementation difficulties—from clinician buy-in to stereotyping. I draw upon ethnographic data to detail how an interdisciplinary group of social scientists and clinicians work to translate a theoretically-complex, reflexive, and social-justice-oriented conceptualization of culture into a clinical intervention tool. As opposed to previous accounts of interdisciplinary collaboration that describe social science being ignored, marginalized, or non-commodifiable, I show how this group makes the anthropological concept of culture both clinically and commercially relevant and the importance of clinicians-as-consumers in the translational process.
Genetics and epigenetics of allergy
Authors: Agache Ioana , Cojanu Catalina , Laculiceanu Alexandru , Rogozea Liliana
Published: February 2020

Purpose of review

Allergic diseases are prototypic examples for gene × environment-wide interactions. This review considers the current evidence for genetic and epigenetic mechanisms in allergic diseases and highlights barriers and facilitators for the implementation of these novel tools both for research and clinical practice.

Recent findings

The value of whole-genome sequencing studies and the use of polygenic risk score analysis in homogeneous well characterized populations are currently being tested. Epigenetic mechanisms are known to play a crucial role in the pathogenesis of allergic disorders, especially through mediating the effects of the environmental factors, well recognized risk modifiers. There is emerging evidence for the immune-modulatory role of probiotics through epigenetic changes. Direct or indirect targeting of epigenetic mechanisms affect expression of the genes favouring the development of allergic diseases and can improve tissue biology. The ability to specifically edit the epigenome, especially using the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 technology, holds the promise of enhancing understanding of how epigenetic modifications function and enabling manipulation of cell phenotype for research or therapeutic purposes.

Additional research in the role of genetic and epigenetic mechanisms in relation to allergic diseases’ endotypes is needed. An international project characterizing the human epigenome in relation to allergic diseases is warranted.
Clinically significant differences in patient-reported outcomes evaluations in chronic spontaneous urticaria
Authors: Baiardini Ilaria , Canonica Giorgio W. , La Grutta Stefania , Braido Fulvio
Published: February 2020

Purpose of review

The aim of this review is to highlight the conceptual and practical knowledge for interpreting score changes in patient-reported outcomes (PROs) that have been validated for chronic spontaneous urticaria (CSU).

Recent findings

The urticaria guidelines recommends to assess PROs as Health-Related Quality of Life, disease activity and disease control, to detect the CSU impact and the overall treatment effect. To this aim it is crucial to determine the minimal important difference (MID) to assess if changes in questionnaire scores represent either perceived improvement or deterioration for patients. Methods for establishing the MID are well defined and are clustered into two broad categories: distribution-based and anchor-based.

For the majority of the available questionnaires for CSU, an MID has been defined, according to the results of various approaches. In most of the studies in our review, anchor-based methods, either alone or in combination with distribution ones, were used. The available information regarding MIDs across validated tools for CSU patients helps to interpret measurement scores and allows the implementation of PROs in routine practices.
Scurvy as a Sequela of Avoidant-Restrictive Food Intake Disorder in Autism: A Systematic Review
Authors: Sharp William G. , Berry Rashelle C. , Burrell Lindsey , Scahill Lawrence , McElhanon Barbara O.
Published: February 2020

Objective:

To document the clinical presentation of scurvy in children with autism spectrum disorder (ASD) and summarize the contemporary approaches to assessment and management in this population. Scurvy is a disease caused by vitamin C deficiency most often detected in populations at high risk for nutrition insufficiency (e.g., extreme poverty). Children with ASD and severe food selectivity consistent with avoidant-restrictive food intake disorder may also be at risk for scurvy.

Method:

We searched MEDLINE, CINAHL, and PsycINFO databases (1990–2018) in peer-reviewed journals for studies of children with ASD and scurvy. Inclusion criteria required confirmed diagnosis of ASD and scurvy in children (birth to 18 years) with a clear description of restrictive dietary patterns. Cases of scurvy due to other causes were excluded. We used a standardized protocol to independently code information; agreement between coders was high.

Results:

The systematic search identified 20 case reports involving 24 children (mean age = 9 ± 3.5; 22 boys/2 girls). The eventual diagnosis of scurvy followed a wide range of negative diagnostic testing; treatment with ascorbic acid and/or a multivitamin resulted in rapid improvement.

Conclusions:

Symptoms of scurvy mimic other pediatric conditions (e.g., cancer). The range of diagnostic testing increased costs and healthcare risks (radiation, sedation) and delayed the diagnosis of scurvy. In children with ASD and severe food selectivity, a nutrition evaluation and laboratory testing are warranted before a more elaborate testing.
Video-assisted cardiopulmonary resuscitation via smartphone improves quality of resuscitation
Authors: Ecker Hannes , Lindacher Falko , Adams Niels , Hamacher Stefanie , Wingen Sabine , Schier Robert , Böttiger Bernd W. , Wetsch Wolfgang A.
Published: February 2020

BACKGROUND

Despite intensive research, cardiac arrest remains a leading cause of death. It is of paramount importance to undertake every possible effort to increase the overall quality of cardiopulmonary resuscitation (CPR) and improve patient outcome. CPR initiated by a bystander is one of the key factors in survival of such an incident. Telephone-assisted CPR (T-CPR) has proved to be an effective measure in improving layperson resuscitation.

OBJECTIVE

We hypothesised that adding video-telephony to the emergency call (video-CPR, V-CPR) enhances the quality of layperson resuscitation.

DESIGN

This randomised controlled simulation trial was performed from July to August 2018. Laypersons were randomly assigned to video-assisted (V-CPR), telephone-assisted (T-CPR) or control (unassisted CPR) groups. Participants were instructed to perform first aid on a mannequin during a simulated cardiac arrest.

SETTING

This study was conducted in the Skills Lab of the University Hospital of Cologne.

PARTICIPANTS

One hundred and fifty healthy adult volunteers.

INTERVENTION

The participants received a smartphone to call emergency services, with Emergency Eye video-call in V-CPR group, and normal telephone functionality in the other groups. T-CPR and V-CPR groups received standardised CPR assistance via phone.

MAIN OUTCOME MEASURES

Our primary endpoint was resuscitation quality, quantified by compression frequency and depth, and correct hand position.

RESULTS

Mean compression frequency of V-CPR group was 106.4 ± 11.7 min, T-CPR group 98.9 ± 12.3 min (NS), unassisted group 71.6 ± 32.3 min (P < 0.001). Mean compression depth was 55.4 ± 12.3 mm in V-CPR, 52.1 ± 13.3 mm in T-CPR (P < 0.001) and 52.9 ± 15.5 mm in unassisted (P < 0.001). Total percentage of correct chest compressions was significantly higher (P < 0.001) in V-CPR (82.6%), than T-CPR (75.4%) and unassisted (77.3%) groups.

CONCLUSION

V-CPR was shown to be superior to unassisted CPR, and was comparable to T-CPR. However, V-CPR leads to a significantly better hand position compared with the other study groups. V-CPR assistance resulted in volunteers performing chest compressions with more accurate compression depth. Despite reaching statistical significance, this may be of little clinical relevance.

TRIAL REGISTRATION

ClinicalTrials.gov (Identifier: NCT03527771)
Recent advances in genome editing for cardiovascular disease
Authors: Doerfler Alexandria M. , Walkey Christopher J. , Lagor William R.
Published: February 2020

Purpose of review

This review highlights recent progress in applying genome editing to the study and treatment of cardiovascular disease (CVD).

Recent findings

Recent work has shown that genome editing can be used to determine the pathogenicity of variants of unknown significance in patient-derived induced pluripotent stem cells. These cells can also be used to test therapeutic genome editing approaches in a personalized manner. Somatic genome editing holds great promise for the treatment of CVD, and important proof of concept experiments have already been performed in animal models. Here we briefly review recent progress in patient-derived cells, as well as the development of somatic genome-editing therapies for CVD, with a particular focus on liver and heart.

Translating this technology into the clinic will require precise editing enzymes, efficient delivery systems, and mitigation of off-target events and immune responses. Further development of these technologies will improve diagnostics and enable permanent correction of some of the most severe forms of CVD.
Bowman Layer Onlay Transplantation to Manage Herpes Corneal Scar
Authors: Dapena Isabel , Musayeva Aytan , Dragnea Diana C. , Groeneveld-van Beek Esther A. , Ní Dhubhghaill Sorcha , Parker Jack S. , van Dijk Korine , Melles Gerrit R. J.
Published: February 2020

Purpose:

To introduce the concept of using a Bowman layer (BL) onlay graft to manage superficial herpetic corneal scarring and to describe the clinical outcomes of the first 2 cases undergoing this procedure.

Methods:

Two patients with a quiescent superficial corneal scar after herpes (varicella zoster virus [n = 1] and herpes simplex virus [n = 1]) keratitis underwent BL onlay transplantation. After the removal of the host epithelium and limited superficial keratectomy, an isolated BL graft was placed onto the host corneal surface. The cornea was then covered with an amniotic membrane and a bandage contact lens. Best spectacle-corrected visual acuity (VA) and/or best contact lens-corrected VA (BCLVA), biomicroscopy, corneal tomography, and anterior segment optical coherence tomography were recorded at 1 week, 1 month, and 3, 6, 9, 12, and 18 months postoperatively.

Results:

In both cases, the surgical and postoperative courses were uneventful. An improvement of the corneal clarity was observed at biomicroscopy, and no varicella zoster virus/herpes simplex virus reactivation occurred throughout the follow-up period. Biomicroscopy, Scheimpflug imaging, and anterior segment optical coherence tomography showed a completely epithelialized and well-integrated graft postoperatively. In case 1, BCLVA with a scleral lens improved from 20/100 (0.1) preoperatively to 20/32 (0.6) postoperatively. For case 2, no preoperative BCLVA was available, but a BCLVA of 20/36 (0.55) was achieved after the procedure.

Conclusions:

A BL onlay graft may be a feasible surgical procedure, which may have the potential to reduce superficial corneal scarring and/or anterior corneal irregularities without resorting to deeper keratoplasty in these complex cases.
Part I: Crossfit-Related Injury Characteristics Presenting to Sports Medicine Clinic
Authors: Stracciolini Andrea , Quinn Bridget , Zwicker Rebecca L. , Howell David R. , Sugimoto Dai
Published: February 2020

Objective:

To investigate CrossFit-related injuries presenting to a pediatric sports medicine clinic.

Design:

Retrospective review of pediatric CrossFit-related injuries from between January 1, 2003, and June 31, 2016.

Setting:

Pediatric sports medicine clinic at a tertiary-level academic medical center.

Patients:

Patients with injury related to CrossFit participation.

Independent Variables:

Sex, age, injury site, diagnosis, diagnostic imaging, and treatment.

Main Outcome Measures:

Annual CrossFit-related injury proportion (%) over time.

Results:

One hundred fifteen medical identified (N = 55 female; mean age, 25.2 ± 10.4 years). Proportion of CrossFit-related injuries presenting to clinic relative to overall clinic volume consistently increased over time (Pearson r = 0.825; P = 0.022). Injury location included head (0.08%), trunk/spine (25.2%), upper extremity (27.0%), and lower extremity (47.0%). Common injured joints included knee (27%), spine (24.3%), and shoulder (16.5%). Nearly half of patients had a single diagnostic imaging (49.6%; 57 of 115). Most common diagnostics included magnetic resonance imaging (60.0%; 69 of 115), plain radiographs (51.3%; 59 of 115), ultrasound (10.4%; 12 of 115), and computerized tomographic scan (9.6%; 11 of 115). Most commonly prescribed treatments included physical/occupational therapy (38.3%; 44 of 115), activity modification (19.1%; 22 of 115), crutches/brace/splinting/compression sleeve (13.0%; 15 of 115), and non–steroidal anti-inflammatory medications (10.4%; 12 of 115).

Conclusions:

CrossFit-related injury proportion presenting to a pediatric sports medicine clinic increased over time. A notable proportion of injuries occurred to the trunk and spine. Advanced imaging was obtained in approximately half of these youth athletes. Further research in youth CrossFit athletes is required surrounding mechanism of injury to prevent future injury in this mode of training for youth athletes.
Nutrition and health of edible insects
Authors: van Huis Arnold
Published: February 2020

Purpose of review

Elucidate the effect of insects as feed and food on nutrition and health of humans and animals.

Recent findings

A new sector is developing of insects as food and feed. The academic interest is growing exponentially. In addition to their high nutritional values, there are also health benefits. These relate to prebiotic effects of insect products, such as chitin on humans and animals. Insects have a large reservoir of antimicrobial peptides. Some insect species have shown to have antioxidant properties.

The increasing demand for meat and the limited amount of land availability prompt the search for alternative protein sources. Insects require less land and have a lower environmental impact than meat products. In addition to having a high nutritional value, they have also health benefits. Several edible insect species can be grown on organic side streams, in this way contributing to a circular economy. The number of scientific articles increased exponentially, and more than 290 start-ups are now engaging in its production and marketing. Food safety issues are not a major issue but need to be carefully checked when organic waste streams are used. The main strategies related to consumer issues are disguising the insects in familiar products and making them tasty.
The establishment and application of sialoscintigraphic reference values from patients with obstructive sialadenitis
Authors: Chen Yen-Chun , Han Deng-Yu , Chang Chi-Ching , Su Chin-Hui , Hung Shih-Han , Hsu Chung-Huei
Published: February 2020

Aim

To evaluate feasibility of establishing a clinically applicable reference value through those unaffected salivary gland on sialoscintigraphic data obtained from patients presented with obstructive sialadenitis affected a single gland.

Materials and methods

Ninety-one patients suffered from single salivary gland swelling, pain/tenderness and received sialoscintigraphic examinations were retrospectively enrolled. The quantitative data parameters, including the uptake ratio, maximal accumulation, maximal excretion, time to maximal (T
max) and time to minimal (T
min) activity of the affected and unaffected glands, were calculated for analysis. Data were also obtained and recorded for comparison from 50 patients who fulfill the American–European criteria for the diagnosis of Sjogren’s syndrome.

Results

The maximal excretion appeared to be the best indicator for distinguishing affected and unaffected glands of obstructive diseases, for parotid and submandibular glands (P = 0.0002 and P < 0.0001, respectively). The area under the receiver-operating characteristic curve (AUC) is 0.82 for submandibular glands. In patients with Sjogren’s syndrome, the maximal excretion and T
min were the best parameters, for parotid (P = 0.002 and P < 0.0001, respectively) and submandibular glands (P < 0.0001 and P = 0.002, respectively). Uptake ratio was a good parameter for submandibular gland (P < 0.0001). The AUC of maximal excretion and uptake ratio for submandibular glands is 0.81 and 0.77, respectively.

Conclusion

Quantitative data obtained from the unaffected glands of patients with obstructive sialadenitis could be used as reference values for the functional evaluation of salivary gland disorders with maximal excretion as one of the reliable parameters.
The rise and fall of the model for end-stage liver disease score and the need for an optimized machine learning approach for liver allocation
Authors: Vagefi Parsia A. , Bertsimas Dimitris , Hirose Ryutaro , Trichakis Nikolaos
Published: February 2020

Purpose of review

The Model for End-Stage Liver Disease (MELD) has been used to rank liver transplant candidates since 2002, and at the time bringing much needed objectivity to the liver allocation process. However, and despite numerous revisions to the MELD score, current liver allocation still does not allow for equitable access to all waitlisted liver candidates.

Recent findings

An optimized prediction of mortality (OPOM) was developed utilizing novel machine-learning optimal classification tree models trained to predict a liver candidate's 3-month waitlist mortality or removal. When compared to MELD and MELD-Na, OPOM more accurately and objectively prioritized candidates for liver transplantation based on disease severity. In simulation analysis, OPOM allowed for more equitable allocation of livers with a resultant significant number of additional lives saved every year when compared with MELD-based allocation.

Machine learning technology holds the potential to help guide transplant clinical practice, and thus potentially guide national organ allocation policy.
Beta amyloid levels in cerebrospinal fluid of HIV-infected people vary by exposure to antiretroviral therapy
Authors: Fields Jerel Adam , Swinton Mary K. , Soontornniyomkij Benchawanna , Carson Aliyah , Achim Cristian L.
Published: February 2020

Background:

HIV-associated neurocognitive disorders (HAND) persist despite the widespread implementation of combined antiretroviral therapy (ART). As people with HIV (PWH) age on ART regimens, the risk of age-related comorbidities, such as Alzheimer's disease may increase. However, questions remain as to whether HIV or ART will alter such risks. Beta amyloid (Aβ) and phosphorylated-tau (p-tau) proteins are associated with Alzheimer's disease and their levels are altered in the CSF of Alzheimer's disease cases.

Methods:

To better understand how these Alzheimer's disease-related markers are affected by HIV infection and ART, postmortem CSF collected from 70 well characterized HIV+ decedents was analyzed for Aβ1–42, Aβ1–40, and p-tau levels.

Results:

Aβ1–42 and Aβ1–40 CSF levels were higher in cases that were exposed to ART. Aβ1–42 and Aβ1–40 CSF levels were also higher in cases on protease inhibitors compared with those with no exposure to protease inhibitors. Aβ1–42 and Aβ1–40 levels in CSF were lowest in HIV+ cases with HIV-associated dementia (HAD) and levels were highest in those diagnosed with asymptomatic neurocognitive impairment (ANI) and minor neurocognitive disorder (MND). Aβ1–42 and Aβ1–40 were inversely related with p-tau levels in all cases, as previously reported.

Conclusion:

These data suggest that ART exposure is associated with increased levels of Aβ1–42 and Aβ1–40 in the CSF. Also, HAD, but not ANI/MND diagnosis is associated with decreased levels of Aβ1–42 and Aβ1–40 in CSF, potentially suggesting impaired clearance. These data suggest that HIV infection and ART may impact pathogenic mechanisms involving Aβ1–42 and Aβ1–40, but not p-tau.
Assessing the validity of and factors that influence accurate self-reporting of HIV status after testing: a population-based study
Authors: Chasimpha Steady J.D. , Mclean Estelle M. , Dube Albert , McCormack Valerie , dos-Santos-Silva Isabel , Glynn Judith R.
Published: February 2020

Objectives:

To assess the validity of self-reported HIV status, and investigate factors that influence accurate reporting of HIV-positive status, in a population tested and informed of their HIV test result.

Design:

Prospective cohort study.

Methods:

We compared self-reported HIV status with biomarker-confirmed HIV test status among participants of Karonga Health and Demographic Surveillance Site in rural northern Malawi. We linked information on HIV test results to subsequent self-reported HIV status, and calculated sensitivity, specificity, positive predictive value and negative predictive value for self-reported HIV status (considered as a diagnostic test). We used Poisson regression with robust variance estimators to examine predictors of accurate self-reporting of HIV-positive status.

Results:

Among 17 445 adults who tested for HIV, were recorded as having received their HIV test results, and had a subsequent self-reported HIV status between 2007 and 2018: positive predictive value of self-reported HIV status was 98.0% (95% confidence interval: 97.3–98.7); negative predictive value was 98.3 (98.1–98.5); sensitivity was 86.1% (84.5–87.7); and specificity was 99.8% (99.7–99.9). Among true HIV-positive people, those who were younger, interviewed in community settings, and had tested for HIV longer ago were more likely to misreport their HIV-positive status.

Conclusion:

In this setting, self-report provides good estimates of test-detected HIV prevalence, suggesting that it can be used when HIV test results are not available. Despite frequent HIV testing, younger people and those interviewed in community settings were less likely to accurately report their HIV-positive status. More research on barriers to self-reporting of HIV status is needed in these subgroups.
The cognitive costs, contraindications and complications of epilepsy surgery in adults
Authors: Baxendale Sallie
Published: February 2020

Purpose of review

Access to epilepsy surgery is rapidly growing throughout the world. While it is an established and effective treatment for seizures, epilepsy surgery has the potential to exacerbate cognitive comorbidities of the condition.

Recent findings

Not all surgical patients experience a postoperative decline in cognitive function. Postoperative cognitive function depends upon the functional integrity of the tissue to be removed and the functional reserve of the structures that remainin situ. While developments in surgical technique can reduce the cognitive morbidity of epilepsy surgery, the same procedure may result in different cognitive outcomes for different candidates, depending on their preoperative characteristics and postoperative trajectories. Multivariate models can be used to identify those most at risk of cognitive decline. There remains a significant lack of research into clinical interventions aimed at reducing the impact of surgically induced cognitive deficits on the lives of the patients who experience them.

Accurate identification of the cognitive risks associated with surgery, based on an individual's personal risk profile rather than the generic risks associated with the procedure, is now recognized as a mandatory part of the preoperative evaluation and is one of the pillars of informed consent for the procedure.
An empirical assessment of transparency and reproducibility-related research practices in the social sciences (2014–2017)
Authors: Hardwicke Tom E. , Wallach Joshua D. , Kidwell Mallory C. , Bendixen Theiss , Crüwell Sophia , Ioannidis John P. A.
Published: February 2020

Serious concerns about research quality have catalysed a number of reform initiatives intended to improve transparency and reproducibility and thus facilitate self-correction, increase efficiency and enhance research credibility. Meta-research has evaluated the merits of some individual initiatives; however, this may not capture broader trends reflecting the cumulative contribution of these efforts. In this study, we manually examined a random sample of 250 articles in order to estimate the prevalence of a range of transparency and reproducibility-related indicators in the social sciences literature published between 2014 and 2017. Few articles indicated availability of materials (16/151, 11% [95% confidence interval, 7% to 16%]), protocols (0/156, 0% [0% to 1%]), raw data (11/156, 7% [2% to 13%]) or analysis scripts (2/156, 1% [0% to 3%]), and no studies were pre-registered (0/156, 0% [0% to 1%]). Some articles explicitly disclosed funding sources (or lack of; 74/236, 31% [25% to 37%]) and some declared no conflicts of interest (36/236, 15% [11% to 20%]). Replication studies were rare (2/156, 1% [0% to 3%]). Few studies were included in evidence synthesis via systematic review (17/151, 11% [7% to 16%]) or meta-analysis (2/151, 1% [0% to 3%]). Less than half the articles were publicly available (101/250, 40% [34% to 47%]). Minimal adoption of transparency and reproducibility-related research practices could be undermining the credibility and efficiency of social science research. The present study establishes a baseline that can be revisited in the future to assess progress.
Improved susceptible–infectious–susceptible epidemic equations based on uncertainties and autocorrelation functions
Authors: Nakamura Gilberto M. , Cardoso George C. , Martinez Alexandre S.
Published: February 2020

Compartmental equations are primary tools in the study of disease spreading processes. They provide accurate predictions for large populations but poor results whenever the integer nature of the number of agents is evident. In the latter instance, uncertainties are relevant factors for pathogen transmission. Starting from the agent-based approach, we investigate the role of uncertainties and autocorrelation functions in the susceptible–infectious–susceptible (SIS) epidemic model, including their relationship with epidemiological variables. We find new differential equations that take uncertainties into account. The findings provide improved equations, offering new insights on disease spreading processes.
Epistasis between cultural traits causes paradigm shifts in cultural evolution
Authors: Pascual Ignacio , Aguirre Jacobo , Manrubia Susanna , Cuesta José A.
Published: February 2020

Every now and then the cultural paradigm of a society changes. While current models of cultural shifts usually require a major exogenous or endogenous change, we propose that the mechanism underlying many paradigm shifts may just be an emergent feature of the inherent congruence among different cultural traits. We implement this idea through a population dynamics model in which individuals are defined by a vector of cultural traits that changes mainly through cultural contagion, biased by a ‘cultural fitness’ landscape, between contemporary individuals. Cultural traits reinforce or hinder each other (through a form of cultural epistasis) to prevent cognitive dissonance. Our main result is that abrupt paradigm shifts occur, in response to weak changes in the landscape, only in the presence of epistasis between cultural traits, and regardless of whether horizontal transmission is biased by homophily. A relevant consequence of this dynamics is the irreversible nature of paradigm shifts: the old paradigm cannot be restored even if the external changes are undone. Our model puts the phenomenon of paradigm shifts in cultural evolution in the same category as catastrophic shifts in ecology or phase transitions in physics, where minute causes lead to major collective changes.
Learning partial differential equations for biological transport models from noisy spatio-temporal data
Authors: Lagergren John H. , Nardini John T. , Michael Lavigne G. , Rutter Erica M. , Flores Kevin B.
Published: February 2020

We investigate methods for learning partial differential equation (PDE) models from spatio-temporal data under biologically realistic levels and forms of noise. Recent progress in learning PDEs from data have used sparse regression to select candidate terms from a denoised set of data, including approximated partial derivatives. We analyse the performance in using previous methods to denoise data for the task of discovering the governing system of PDEs. We also develop a novel methodology that uses artificial neural networks (ANNs) to denoise data and approximate partial derivatives. We test the methodology on three PDE models for biological transport, i.e. the advection–diffusion, classical Fisher–Kolmogorov–Petrovsky–Piskunov (Fisher–KPP) and nonlinear Fisher–KPP equations. We show that the ANN methodology outperforms previous denoising methods, including finite differences and both local and global polynomial regression splines, in the ability to accurately approximate partial derivatives and learn the correct PDE model.
Mimicking the active cochlea with a fluid-coupled array of subwavelength Hopf resonators
Authors: Ammari Habib , Davies Bryn
Published: February 2020

We present a design for an acoustic metamaterial that mimics the behaviour of the active cochlea. This material is composed of a size-graded array of cylindrical subwavelength resonators, has similar dimensions to the cochlea and is able to per- form frequency separation of audible frequencies. Nonlinear amplification is introduced to the model in order to replicate the behaviour of the cochlear amplifier. This formulation takes the form of a fluid-coupled array of Hopf resonators. We seek solutions in the form of a modal decomposition, so as to retain the physically derived coupling between resonators.
Accelerated landing in a stingless bee and its unexpected benefits for traffic congestion
Authors: Tichit Pierre , Alves-dos-Santos Isabel , Dacke Marie , Baird Emily
Published: February 2020

To land, flying animals must simultaneously reduce speed and control their path to the target. While the control of approach speed has been studied in many different animals, little is known about the effect of target size on landing, particularly for small targets that require precise trajectory control. To begin to explore this, we recorded the stingless beesScaptotrigona depilislanding on their natural hive entrance—a narrow wax tube built by the bees themselves. Rather than decelerating before touchdown as most animals do,S. depilisaccelerates in preparation for its high precision landings on the narrow tube of wax. A simulation of traffic at the hive suggests that this counterintuitive landing strategy could confer a collective advantage to the colony by minimizing the risk of mid-air collisions and thus of traffic congestion. If the simulated size of the hive entrance increases and if traffic intensity decreases relative to the measured real-world values, ‘accelerated landing' ceases to provide a clear benefit, suggesting that it is only a useful strategy when target cross-section is small and landing traffic is high. We discuss this strategy in the context ofS. depilis' ecology and propose that it is an adaptive behaviour that benefits foraging and nest defence.
Speedy revelations: how alarm calls can convey rapid, reliable information about urgent danger
Authors: McLachlan Jessica R. , Magrath Robert D.
Published: February 2020

In the perpetual struggle between high-speed predators and their prey, individuals need to react in the blink of an eye to avoid capture. Alarm calls that warn of danger therefore need to do so sufficiently rapidly that listeners can escape in time. Paradoxically, many species produce more elements in their alarm calls when signalling about more immediate danger, thereby increasing the reliability of transmission of critical information but taking longer to convey the urgent message. We found that New Holland honeyeaters,Phylidonyris novaehollandiae, incorporated more elements in alarm calls given to more dangerous predators, but video analysis revealed that listeners responded in 100 ms, after only the first element. Consistent with this rapid response, the acoustic structure of the first element varied according to the danger, and playbacks confirmed that birds need hear only the first element to assess risk. However, birds hid for longer and were more likely to flee, after calls with more elements. The dual mechanisms of varying both element structure and number may provide a widespread solution to signalling rapidly and reliably about immediate danger.
Global multi-environment resistance QTL for foliar late blight resistance in tetraploid potato with tropical adaptation
Authors: Lindqvist-Kreuze Hannele , de Boeck Bert , Unger Paula , Gemenet Dorcus , Li Xianping , Pan Zhechao , Sui Qinjun , Qin Junhong , Woldegjorgis Gebremedhin , Negash Kassaye , Seid Ibrahim , Hirut Betaw , Gastelo Manuel , De Vega Jose , Bonierbale Merideth
Published: February 2020

The identification of environmentally stable and globally predictable resistance to potato late blight is challenged by the crop’s clonal and polyploid nature and the pathogen’s rapid evolution. Genome-wide analysis (GWA) of multi-environment trials can add precision to breeding for complex traits. A diversity panel of tetraploid potato germplasm bread for multiple resistance and quality traits was genotyped by genotyping by sequencing (GBS) and phenotyped for late blight resistance in a trait observation network spanning three continents addressed by the International Potato Center’s (CIP’s) breeding program. The aims of this study were to (i) identify QTL underlying resistance in and across environments and (ii) develop prediction models to support the global deployment and use of promising resistance sources in local breeding and variety development programs. Health-indexedin vitroplants of 380 clones and varieties were distributed from CIP headquarters in Peru to China and Ethiopia and tuber seed was produced centrally in each country. Phenotypes were recorded as rAUDPC following field exposure to local isolates ofPhytophthora infestans, Stringent filtering for individual read depth >60 resulted in 3,239 tetraploid SNPs. Meanwhile, 55,748 diploid SNPs were identified using diploidized data and individual read depth>17. The kinship matrix was utilized to obtain BLUP and identify best performing germplasm in each and all environments. Genotypes with high levels of resistance in all environments were identified from the B3, LBHT and B3-LTVR populations. GWA identified stable QTL for late blight resistance in chromosome 9 and environment specific QTL in chromosomes 3, 5, 6 and 10.
phyr: An R package for phylogenetic species-distribution modelling in ecological communities
Authors: Li Daijiang , Dinnage Russell , Nell Lucas , Helmus Matthew R. , Ives Anthony
Published: February 2020

Model-based approaches are increasingly popular in ecological studies. A good example of this trend is the use of joint species distribution models to ask questions about ecological communities. However, most current applications of model-based methods do not include phylogenies despite the well-known importance of phylogenetic relationships in shaping species distributions and community composition. In part, this is due to lack of accessible tools allowing ecologists to fit phylogenetic species distribution models easily.

To fill this gap, the R packagephyr(pronounced fire) implements a suite of metrics, comparative methods and mixed models that use phylogenies to understand and predict community composition and other ecological and evolutionary phenomena. Thephyrworkhorse functions are implemented in C++ making all calculations and model estimations fast.

phyrcan fit a variety of models such as phylogenetic joint-species distribution models, spatiotemporal-phylogenetic autocorrelation models, and phylogenetic trait-based bipartite network models.phyralso estimates phylogenetically independent trait correlations with measurement error to test for adaptive syndromes and performs fast calculations of common alpha and beta phylogenetic diversity metrics. Allphyrmethods are united under Brownian motion or Ornstein-Uhlenbeck models of evolution and phylogenetic terms are modelled as phylogenetic covariance matrices.

The functions and model formula syntax we propose inphyrserves as a simple and unified framework that ignites the use of phylogenies to address a variety of ecological questions.
ErrorX: automated error correction for immune repertoire sequencing datasets
Authors: Sevy Alexander M
Published: February 2020

Motivation

Recent advances in DNA sequencing technology have allowed deep profiling of B- and T-cell receptor sequences on an unprecedented scale. However, sequencing errors pose a significant challenge in expanding the scope of these experiments. Errors can arise both by PCR during library preparation and by miscalled bases on the sequencing instrument itself. These errors compromise the validity of biological conclusions drawn from the data.

Results

To address these concerns I have developed ErrorX, a software for automated error correction of B- and T-cell receptor NGS datasets. ErrorX uses deep learning to automatically identify bases that have a high probability of being erroneous. In benchmark studies, ErrorX reduced the overall error rate of public datasets by up to 36% with a false positive rate of 0.05% or less. Since ErrorX is a pure bioinformatics approach, it can be directly applied to any existing antibody or T-cell receptor sequencing datasets to infer sites of probable error without any changes in library preparation.

Availability

ErrorX is free for non-commercial use, with both a command-line interface and GUI available for Mac, Linux, and Windows operating systems, and full documentation available. Pre-compiled binaries are available athttps://endeavorbio.com/downloads/.
Basal forebrain-derived acetylcholine encodes valence-free reinforcement prediction error
Authors: Sturgill JF , Hegedus P , Li SJ , Chevy Q , Siebels A , Jing M , Li Y , Hangya B , Kepecs A
Published: February 2020

Acetylcholine (Ach) is released by the cholinergic basal forebrain (CBF) throughout the cortical mantle and is implicated in behavioral functions ranging from arousal to attention to learning. Yet what signal ACh provides to cortex remains unresolved, hindering our understanding of its functional roles. Here we demonstrate that the CBF signals unsigned reinforcement prediction error, in contrast to dopamine (DA) neurons that encode reward prediction error. We show that both CBF neuronal activity and acetylcholine (ACh) release at cortical targets signal reinforcement delivery, acquire responses to predictive stimuli and show diminished responses to expected outcomes, hallmarks of a prediction error. To compare ACh with DA, we simultaneously monitored the activity of both neuromodulators during a serial reversal learning task. ACh tracked learning as swiftly as DA during acquisition but lagged slightly during extinction, suggesting that these neuromodulators play complementary roles in reinforcement as their patterns of innervation, cellular targets, and signaling mechanisms are themselves complementary. Through retrograde viral tracing we show that the cholinergic and dopaminergic systems engage overlapping upstream circuits, accounting for their coordination during learning. This predictive and valence-free signal explains how ACh can proactively and retroactively improve the processing of behaviorally important stimuli, be they good or bad.
Live cell imaging of single neurotrophin receptor molecules on human neuron in Alzheimer’s disease
Authors: Barabás Klaudia , Kobolák Julianna , Godó Soma , Ernszt Dávid , Kecskés Miklós , Varga Csaba , Kardos József , Jánosi Tibor Z. , Fujiwara Takahiro , Kusumi Akihiro , Téglási Annamária , Dinnyés András , Ábrahám István M.
Published: February 2020

The changes in the receptor dynamics such as the surface movement of the receptor molecules on the plasma membrane are essential to receptor function. However, whether the receptor dynamics are affected by disease conditions is unknown. Neurotrophin receptors such as TrkA and p75NTRplay a critical role in neuronal survival and their functions are highly affected in Alzheimer’s disease (AD). Using live-cell single-molecule imaging of neurotrophin receptors we examined the surface trafficking of TrKA and p75NTRmolecules on human induced pluripotent stem cells (hiPSCs) derived live neurons from presenilin 1 (PSEN1) mutant AD patients and healthy subjects. Here we report that surface trafficking of p75NTRmolecules on neurites is faster than that of TrkA molecules in healthy controls. The surface dynamics of TrkA molecules were elevated in AD patients compared to healthy individuals. In contrast, the surface movement of p75NTRwas significantly smaller in AD patients compared to healthy individuals. Interestingly, amyloid beta1-42(Aβ1-42) administration increased the surface trafficking of both TrkA and p75NTRin healthy hiPSCs neurons. These findings provides the first evidence that the surface diffusion of TrkA and p75NTRmolecules are altered in patients suffering from AD. Our data also suggest that Aβ1-42may responsible for the alteration of the surface movements of TrkA but not for p75NTR.

One Sentence Summary

The surface movements of neurotrophin receptors such as TrkA and p75NTRare altered in neurons derived from patients suffering from familial Alzheimer’s disease.
Systematic review protocol: Quantitative susceptibility mapping of brain iron accumulation in neurodegenerative diseases
Authors: Ravanfar Parsa , Loi Samantha , Van Rheenen Tamsyn , Bush Ashley , Desmond Patricia , Cropley Vanessa , Moffat Bradford , Velakoulis Dennis , Pantelis Christos
Published: February 2020

Iron has been found to play an important role in neurodegeneration. Quantitative susceptibility mapping (QSM) is a relatively new – and the most accurate - MRI technique available for assessment of iron deposition in the brain. There is a rapidly growing number of studies using QSM to investigate brain iron distribution in neurodegenerative diseases including but not limited to Alzheimer’s disease, Parkinson’s disease, Amyotrophic lateral sclerosis, Huntington disease and Wilson’s disease. These studies have shown increased iron deposition in the brain regions that are associated with the pathology of the disease. Additionally, QSM is found to be accurate in differential diagnosis of neurodegenerative diseases where clinical presentations are indistinguishable. Structural changes evidenced by QSM are reported to precede the onset of clinical manifestation of neurodegenerative diseases suggesting its benefit in early diagnosis. To our knowledge, no systematic review of QSM findings in neurodegenerative diseases has been published before. A systematic synthesis and conclusion of the existing evidence can improve our understanding of the pathophysiology of neurodegeneration, describe the clinical and research utility of QSM, and point out the direction for future studies in neuropsychiatric disorders.

This document is a systematic review protocol developed in accordance with Preferred reporting items for systematic review and meta-analysis protocols (PRISMA-P) guideline. This protocol is prepared as a guide for conducting a systematic review of studies investigating brain iron and microstructural changes in neurodegenerative diseases using quantitative susceptibility mapping (QSM). This protocol has also been submitted to Prospective Register of Systematic Reviews (PROSPERO) for registration. By publishing this protocol, we aim to enhance clarity and transparency of our systematic review and minimise the risk of bias in the process of its development.