bluuebunny/crossref_metadata_2025 huggingface dataset:
Disease Activity and Rate and Severity of Flares During Peripartum Period in Thai Patients With Systemic Lupus Erythematosus
Authors: Louthrenoo Worawit , Trongkamolthum Thananant , Kasitanon Nuntana , Wongthanee Antika
Published: June 2021

Background/Objective

The aim of this study was to compare disease activity and rate and severity of flares between pregnant and nonpregnant systemic lupus erythematosus (SLE) patients.

Methods

Medical records of pregnant SLE patients seen between January 1993 and June 2017 were reviewed. Nonpregnant SLE controls were matched by age at diagnosis and disease duration before pregnancy. Systemic lupus erythematosus disease activity and flares were determined by the cSLEDAI (clinical Systemic Lupus Erythematosus Disease Activity Index) and Safety of Estrogens in Lupus Erythematosus National Assessment–SLEDAI Flare Index, respectively. Disease activity was measured from 6 months before conception (−6 months) until the postpartum period. The repeated measures mixed model, Cox regression, and cumulative hazard plots were used for statistical analysis.

Results

Ninety pregnancies occurred in 77 patients. The cSLEDAI scores from −6 months to the postpartum period were comparable between the pregnancy and control group, but slightly yet significantly higher in the controls at conception (mean ± SEM, 3.57 ± 0.45 vs 1.90 ± 0.36; p = 0.019). When compared with the controls, during the pregnancy and postpartum period, the pregnancy group did not have significantly higher incidence of flare (41.11% vs 28.89%, p = 0.086 and 7.78% vs 11.11%, p = 0.445, respectively) or flare category (severe flare) (75.68% vs 53.85%, p = 0.070 and 85.71% vs 70.00%, p = 0.603, respectively). The flare incidence rate (95% confidence interval)/100 patient-months in the pregnancy and control group was 6.75 (4.89–9.32) and 4.34 (2.96–6.38), respectively, giving the adjusted hazards for flare (95% confidence interval) of 1.54 (0.91–2.61) (p = 0.110).

Conclusions

There was no overall significant increase in SLE disease activity, flare incidence, and flare severity in pregnant SLE patients when compared with their properly matched nonpregnant SLE controls.
Prevalence of Workforce Diversity Research Among Surgical Specialties in the United States
Authors: Reghunathan Meera , Blum Jessica , Gosman Amanda A. , Butler Paris D. , Chen Wendy
Published: June 2021

Background

Plastic surgeons are not as diverse as expected in relation to the increasingly diverse patient and medical student population. The authors assess the state of diversity in 8 primary surgical specialties in the United States and evaluate trends in research interest in diversity over the past 30 years.

Methods

Articles regarding diversity in surgery from 1990 to 2020 were systematically reviewed. The Association of American Medical Colleges Physician Specialty Data Reports and the Accreditation Council for Graduate Medical Education Data Resource Books provided resident/fellow and faculty data from 2011 to 2016. Trends were analyzed over time per specialty.

Results

From 1990 to 2020, a total of 199 publications related to diversity were identified among the various surgical specialties. Orthopedic surgery had significantly more publications per year compared with other specialties (P< 0.05). Every specialty demonstrated a significant increase in publications about diversity over time (P< 0.05). A majority of publications were related to sex rather than underrepresented in medicine topics. The proportion of female surgeons was significantly higher for plastic surgery than for orthopedic surgery and neurosurgery (P< 0.001). Plastic surgery exhibited the highest growth rate in female residents (+1.6% per year,P< 0.001). The proportion of underrepresented minorities composing surgical trainees has not significantly increased in any surgical specialty between 2011 and 2016 (P> 0.05).

Conclusions

Although diversity representation in surgery has somewhat improved, the rate is too slow to match the growing diversity of the US population. Outcomes have been disparate between specialties and demonstrate greater increases in sex equality relative to ethnic/racial equality. Evidence-based interventions need to be developed and implemented.
Joint Salvage and Biological Repair of Massive-Cavity Bone Defects After Extensive Curettage of Campanacci Grade II or III Giant Cell Tumor Around the Knee With Vascularized Fibular Autograft and Cancellous Allograft
Authors: Yang Yun-Fa , Wang Jian-Wei , Gao Xiao-Sheng , Huang Jian-Wen , Xu Zhong-He
Published: June 2021

Objective

The aim of the study was to report the clinical outcomes of repair of massive-cavity bone defects after extensive curettage of Campanacci grade II or III giant cell tumor (GCT) around knee with vascularized fibular autograft and cancellous allograft.

Methods

There were 12 consecutive patients with Campanacci grade II or III GCT around knee treated in our department between 2004 and 2016. All the patients underwent clinical evaluation, plain radiography, and/or magnetic resonance imaging of the knee right after admission. To preserve their knee function, we repaired the massive-cavity bone defects after extensive curettage of GCT by vascularized fibular autografts and cancellous allograft. All the patients were evaluated through clinical examinations, plain radiography of the knee and chest, and Musculoskeletal Tumor Society (MSTS) scores of the lower extremity in the follow-ups.

Results

The follow-up ranged from 1.5 to 12.0 years (mean, 4.2 years). There were no local recurrences or lung metastasis in any of the 12 patients at the last follow-up. Ten patients had no pain or experienced occasional pain, and 9 were able to resume their previous work. The mean range of motion of knee flexion was 117 degrees, and the extension was −6 degrees. The mean MSTS score was 24.7, and a total of 10 patients had excellent or good MSTS scores.

Conclusions

It is reliable to achieve knee joint salvage and repair massive-cavity bone defects after extensive curettage with vascularized fibular autograft and cancellous allograft in patients with Campanacci grade II or III GCT around the knee.
Standardized Patient Education for Decompensated Cirrhotic Patients and Impact on Clinician Satisfaction
Authors: Ignatiev Elena , Samardzija Melanie K. , Paul Sonali , Vuckovic Karen M. , Lockwood Mark B.
Published: June 2021

The development of ascites in patients with cirrhosis can cause numerous complications including abdominal discomfort, pain, respiratory distress, decreased mobility, diminished quality of life, and contributes to an increased mortality. Symptom self-monitoring that incorporates evidence-based treatments has been effective when used by patients with noncirrhotic chronic diseases. Guided by the theory of Self-Care of Chronic Illness, a self-monitoring guide was adapted from an existing validated tool. In the context of a pilot quality initiative, staff nurses educated patients with ascites and their caregivers, with the adapted symptom self-monitoring guide using a standardized process. Clinicians were surveyed regarding their satisfaction with the patient education pre- and post-implementation. Results indicated improved clinician satisfaction with the education provided to patients and their caregivers during the clinic visit. Implementation of self-monitoring may improve clinician and patient satisfaction and clinic workflows. Additional evaluation of the self-monitoring guide and its effect on patient satisfaction, impact on hospital admissions, and outpatient paracentesis is warranted.
Standardized Nursing Procedures for Fecal Microbiota Transplantation via Upper Endoscopy
Authors: Feng Juan , Tang Yun-Na , Zhou Li-Xiang , Pan Jin-Shui
Published: June 2021

Fecal microbiota transplantation is an emerging treatment option that lacks a standardized nursing procedure. In our department, fecal microbiota transplantation has been undertaken to treat chronic hepatitis B and inflammatory bowel diseases since 2015. The fecal microbiota transplantation process involves various nursing measures that are critical for the successful completion of the procedures. In our center, a set of standardized nursing procedures has been established and has proved effective and operable. Standardized nursing procedures enhance the efficacy of fecal microbiota transplantation and alleviate the risk of treatment-related complications.
Recent advances in biomedical, biosensor and clinical measurement devices for use in humans and the potential application of these technologies for the study of physiology and disease in wild animals
Authors: Macdonald Alexander , Hawkes Lucy A. , Corrigan Damion K.
Published: June 2021

The goal of achieving enhanced diagnosis and continuous monitoring of human health has led to a vibrant, dynamic and well-funded field of research in medical sensing and biosensor technologies. The field has many sub-disciplines which focus on different aspects of sensor science; engaging engineers, chemists, biochemists and clinicians, often in interdisciplinary teams. The trends which dominate include the efforts to develop effective point of care tests and implantable/wearable technologies for early diagnosis and continuous monitoring. This review will outline the current state of the art in a number of relevant fields, including device engineering, chemistry, nanoscience and biomolecular detection, and suggest how these advances might be employed to develop effective systems for measuring physiology, detecting infection and monitoring biomarker status in wild animals. Special consideration is also given to the emerging threat of antimicrobial resistance and in the light of the current SARS-CoV-2 outbreak, zoonotic infections. Both of these areas involve significant crossover between animal and human health and are therefore well placed to seed technological developments with applicability to both human and animal health and, more generally, the reviewed technologies have significant potential to find use in the measurement of physiology in wild animals.

This article is part of the theme issue ‘Measuring physiology in free-living animals (Part II)’.
DNA methylation changes in glial cells of the normal-appearing white matter in Multiple Sclerosis patients
Authors: Kular Lara , Ewing Ewoud , Needhamsen Maria , Kakhki Majid Pahlevan , Covacu Ruxandra , Gomez-Cabrero David , Brundin Lou , Jagodic Maja
Published: June 2021

Background

Multiple Sclerosis (MS), the leading cause of non-traumatic neurological disability in young adults, is a chronic inflammatory and neurodegenerative disease of the central nervous system (CNS). Due to the poor accessibility to the target organ, CNS-confined processes underpinning the later progressive form of MS remain elusive thereby limiting treatment options. We aim to examine DNA methylation, a stable epigenetic mark of genome activity, in glial cells to capture relevant molecular changes underlying MS neuropathology.

Methods

We profiled DNA methylation in nuclei of glial cells, isolated from 38 post-mortem normal-appearing white matter (NAWM) specimens of MS patients (n=8) in comparison to white matter of control individuals (n=14), using Infinium MethylationEPIC BeadChip.

Findings

We identified 1,226 significant (genome-wide adjusted P-value < 0.05) differentially methylated positions (DMPs) between MS patients and controls. Functional annotation of the altered DMP-genes uncovered alterations of processes related to cellular motility, cytoskeleton dynamics, metabolic processes, synaptic support, neuroinflammation and signaling, such as Wnt and TGF-β pathways. A fraction of the affected genes displayed transcriptional differences in the brain of MS patients, as reported by publically available transcriptomic data. Cell type-restricted annotation of DMP-genes attributed alteration of cytoskeleton rearrangement and extracellular matrix remodelling to all glial cell types, while some processes, including ion transport, Wnt/TGF-β signaling and immune processes were more specifically linked to oligodendrocytes, astrocytes and microglial cells, respectively.

Conclusion

Our findings strongly suggest that NAWM glial cells are highly altered, even in the absence of lesional insult, collectively exhibiting a multicellular reaction in response to diffuse inflammation.
Development and validation of blood-based prognostic biomarkers for severity of COVID disease outcome using EpiSwitch 3D genomic regulatory immuno-genetic profiling
Authors: Hunter Ewan , Koutsothanasi Christina , Wilson Adam , Santos Francisco C. , Salter Matthew , Westra Jurjen W. , Powell Ryan , Dring Ann , Brajer Paulina , Egan Benedict , Parnall Matthew , Williams Catriona , Katzinski Aemilia , Lavin Thomas , Ramadass Aroul , Messer William , Brunton Amanda , Lyski Zoe , Vancheeswaran Rama , Barlow Andrew , Pchejetski Dmitri , Robbins Peter A. , Mellor Jane , Akoulitchev Alexandre
Published: June 2021

The COVID-19 pandemic has raised several global public health challenges to which the international medical community have responded. Diagnostic testing and the development of vaccines against the SARS-CoV-2 virus have made remarkable progress to date. As the population is now faced with the complex lifestyle and medical decisions that come with living in a pandemic, a forward-looking understanding of how a COVID-19 diagnosis may affect the health of an individual represents a pressing need. Previously we used whole genome microarray to identify 200 3D genomic marker leads that could predict mild or severe COVID-19 disease outcomes from blood samples in a multinational cohort of COVID-19 patients. Here, we focus on the development and validation of a qPCR assay to accurately predict severe COVID-19 disease requiring intensive care unit (ICU) support and/or mechanical ventilation. From 200 original biomarker leads we established a classification model containing six markers. The markers were qualified and validated on 38 COVID-19 patients from an independent cohort. Overall, the six-marker model obtained a positive predictive value of 93% and balanced accuracy of 88% across 116 patients for the prognosis of COVID-19 severity requiring ICU care/ventilation support. The six-marker signature identifies individuals at the highest risk of developing severe complications in COVID-19 with high predictive accuracy and can assist in patient prognosis and clinical management decisions.
Rapid protocols to support Covid-19 clinical diagnosis based on hematological parameters
Authors: Gomes Juliana Carneiro , de Freitas Barbosa Valter Augusto , de Santana Maíra Araújo , de Lima Clarisse Lins , Calado Raquel Bezerra , Bertoldo Júnior Cláudio Roberto , de Almeida Albuquerque Jeniffer Emidio , de Souza Rodrigo Gomes , de Araújo Ricardo Juarez Escorel , Moreno Giselle Machado Magalhães , Soares Luiz Alberto Lira , Mattos Júnior Luiz Alberto Reis , de Souza Ricardo Emmanuel , dos Santos Wellington Pinheiro
Published: June 2021

Purpose

In December 2019, the Covid-19 pandemic began in the world. To reduce mortality, in addiction to mass vaccination, it is necessary to massify and accelerate clinical diagnosis, as well as creating new ways of monitoring patients that can help in the construction of specific treatments for the disease.

Objective

In this work, we propose rapid protocols for clinical diagnosis of Covid-19 through the automatic analysis of hematological parameters using Evolutionary Computing and Machine Learning. These hematological parameters are obtained from blood tests common in clinical practice.

Method

We investigated the best classifier architectures. Then, we applied the particle swarm optimization algorithm (PSO) to select the most relevant attributes: serum glucose, troponin, partial thromboplastin time, ferritin, D-dimer, lactic dehydrogenase, and indirect bilirubin. Finally, we used decision trees to build four rapid protocols for Covid-19 clinical diagnosis.

Results

We developed a web system for Covid-19 diagnosis support. Using a 100-tree Random Forest, we obtained results for accuracy, sensitivity and specificity superior to 99

Conclusion

By using a reduced set of hematological parameters common in clinical practice, it was possible to achieve results of accuracy, sensitivity and specificity comparable to those obtained with RT-PCR. It was also possible to automatically generate clinical decision protocols, allowing relatively accurate clinical diagnosis even without the aid of the web decision support system.
RIC3 variants are not associated with Parkinson’s Disease in large European, Latin American, or East Asian cohorts
Authors: Brolin Kajsa , Bandres-Ciga Sara , Leonard Hampton , Makarious Mary B. , Blauwendraat Cornelis , Mata Ignacio F , Foo Jia Nee , Pihlstrøm Lasse , Swanberg Maria , Gan-Or Ziv , Tan Manuela MX ,   International Parkinson’s Disease Genomics Consortium (IPDGC)
Published: June 2021

Parkinson’s disease (PD) is a complex neurodegenerative disorder in which both rare and common genetic variants contribute to disease risk. Multiple genes have been reported to be linked to monogenic PD, but these only explain a fraction of the observed familial aggregation. Rare variants in RIC3 have been suggested to be associated with PD in the Indian population. However, replication studies yielded inconsistent results. We further investigate the role of RIC3 variants in PD in European cohorts using individual-level genotyping data from 14,671 PD patients and 17,667 controls, as well as whole-genome sequencing data from 1,615 patients and 961 controls. We also investigated RIC3 using summary statistics from a Latin American cohort of 1,481 individuals, and from a cohort of 31,575 individuals of East Asian ancestry. We did not identify any association between RIC3 and PD in any of the cohorts. However, more studies of rare variants in non-European ancestry populations, in particular South Asian populations, are necessary to further evaluate the world-wide role of RIC3 in PD etiology.
Pre-activated anti-viral innate immunity in the upper airways controls early SARS-CoV-2 infection in children
Authors: Loske J , Röhmel J , Lukassen S , Stricker S , Magalhães VG , Liebig J , Chua RL , Thürmann L , Messingschlager M , Seegebarth A , Timmermann B , Klages S , Ralser M , Sawitzki B , Sander LE , Corman VM , Conrad C , Laudi S , Binder M , Trump S , Eils R , Mall M.A. , Lehmann I
Published: June 2021

Children are consistently reported to have reduced SARS-CoV-2 infection rates and a substantially lower risk for developing severe COVID-19. However, the molecular mechanisms underlying protection against COVID-19 in younger age groups remain widely unknown. Here, we systematically characterized the single-cell transcriptional landscape in the upper airways in SARS-CoV-2 negative and age-matched SARS-CoV-2 positive children (n=42) and corresponding samples from adults (n=44), covering an age range of four weeks to 77 years. Children displayed higher basal expression of the relevant pattern recognition receptor (PRR) pathways in upper airway epithelial cells, macrophages, and dendritic cells, resulting in stronger innate antiviral responses upon SARS-CoV-2 infection compared to adults. We further detected distinct immune cell subpopulations with an overall dominance of neutrophils and a population of cytotoxic T cells occurring predominantly in children. Our study provides evidence that the airway epithelial and mucosal immune cells of children are pre-activated and primed for virus sensing, resulting in a stronger early innate antiviral responses to SARS-CoV-2 infection compared to adults.
Ipsilesional motor cortex activation with high-force unimanual handgrip contractions of the less-affected limb in participants with stroke
Authors: Andrushko Justin W. , Gould Layla , Renshaw Doug W. , Forrester Shannon , Kelly Michael E. , Linassi Gary , Mickleborough Marla , Oates Alison , Hunter Gary , Borowsky Ron , Farthing Jonathan P.
Published: June 2021

Stroke is a leading cause of severe disability that often presents with unilateral motor impairment. Conventional rehabilitation approaches focus on motor practice of the affected limb and aim to suppress brain activity in the contralesional hemisphere to facilitate ipsilesional hemispheric neuroplasticity subserving motor recovery. Previous research has also demonstrated that exercise of the less-affected limb can promote motor recovery of the affected limb through the interlimb transfer of the trained motor task, termed cross-education. One of the leading theories for cross-education proposes that the interlimb transfer manifests from ipsilateral cortical activity during unimanual motor tasks, and that this ipsilateral cortical activity results in motor related neuroplasticity giving rise to contralateral improvements in motor performance. Conversely, exercise of the less-affected limb promotes contralesional brain activity which is typically viewed as contraindicated in stroke recovery due to the interhemispheric inhibitory influence onto the ipsilesional hemisphere. High-force unimanual handgrip contractions are known to increase ipsilateral brain activation in control participants, but it remains to be determined if this would be observed in participants with stroke. Therefore, this study aimed to determine how parametric increases in handgrip force during repeated contractions with the less-affected limb impacts brain activity bilaterally in participants with stroke and in a cohort of neurologically intact controls. In this study, higher force contractions were found to increase brain activation in the ipsilesional/ipsilateral hemisphere in both groups (p = .002), but no between group differences were observed. These data suggest that high-force exercise with the less-affected limb may promote ipsilesional cortical plasticity to promote motor recovery of the affected-limb in participants with stroke.
Chronic adolescent stress increases exploratory behavior but does not change the acute stress response in adult male C57BL/6 mice
Authors: Sturman Oliver , von Ziegler Lukas , Privitera Mattia , Waag Rebecca , Duss Sian , Vermeiren Yannick , de Deyn Peter , Bohacek Johannes
Published: June 2021

Chronic stress exposure in adolescence can lead to a lasting change in stress responsiveness later in life and is associated with increased mental health issues in adulthood. Here we investigate whether the Chronic Social Instability (CSI) paradigm in mice influences the behavioural and molecular responses to novel acute stressors, and whether it alters physiological responses influenced by the noradrenergic system. Using large cohorts of mice, we show that CSI mice display a persistent increase in exploratory behaviors in the open field test alongside small but widespread transcriptional changes in the ventral hippocampus. However, both the transcriptomic and behavioural responses to novel acute stressors are indistinguishable between groups. In addition, the pupillometric response to a tail shock, known to be mediated by the noradrenergic system, remains unaltered in CSI mice. Ultra-high performance liquid chromatography analysis of monoaminergic neurotransmitter levels in the ventral hippocampus also shows no differences between control or CSI mice at baseline or in response to acute stress. We conclude that CSI exposure during adolescence leads to persistent changes in exploratory behavior and gene expression in the hippocampus, but it does not alter the response to acute stress challenges in adulthood and is unlikely to alter the function of the noradrenergic system.
Feedback processing in attack and defense conflicts: a neurophysiological study
Authors: Paiva Tiago O. , Coelho Rui C. , Pasion Rita , Dias-Oliveira Eva , De Dreu Carsten K. W. , Barbosa Fernando
Published: June 2021

Despite being extensively modelled to explore decision making processes in economic tasks, there are no studies exploring the neurophysiological correlates of the Predator-Prey Game, a game theory paradigm designed to operationalize attack and defence conflicts. In the present study, we explored the relationship between the ERP components associated with feedback, namely feedback-related negativity (FRN) and feedback -elated P3b, and investment in an adapted version of the Predator-Prey Game (PPG), operationalizing attack and defence. Forty-seven (28 female) community-dwelling volunteers without history of neurological disease were recruited. Participants played the PPG game both as attackers and defenders while EEG signal was recorded with a 128 channels sensor net. Behavioural results showed that individuals tend to invest more and decide faster when playing in defence, rather than in attack. Electrophysiological data showed FRN to be sensitive to the valence of feedback, with increased amplitudes of FRN loss feedbacks. On the other hand, the P3b amplitudes were sensitive to the role, with increased amplitude for attack when compared with defence. The integration of the behavioural and ERP findings supports the theoretical model positing that attack elicits more deliberate and less automatic brain processes than defence.
Fast 3D Clear: A Fast, Aqueous, Reversible Three-Day Tissue Clearing Method for Adult and Embryonic Mouse Brain and Whole Body
Authors: Kosmidis Stylianos , Negrean Adrian , Dranovsky Alex , Losonczy Attila , Kandel Eric R.
Published: June 2021

To date, a variety of optical clearing methods have emerged that serve as powerful tools to study intact organs and neuronal circuits. Here we describe a newly developed, aqueous clearing protocol named “Fast 3D Clear”, which relies on tetrahydrofuran (THF) for tissue delipidation, and iohexol (Histodenz) for clearing, such that tissues can be imaged under immersion oil in light sheet imaging systems. Fast 3D Clear requires three days to achieve high transparency of adult and embryonic mouse tissues, while maintaining their anatomical integrity, and preserving a vast array of transgenic and viral/dye fluorophores, such as GCaMP3/6, tdTomato, Fast Blue, and IRF670. A unique advantage of Fast 3D Clear is its complete reversibility and thus compatibility with tissue sectioning and immunohistochemistry. Fast 3D Clear can be easily and quickly applied to a wide range of biomedical studies, thereby greatly facilitating the acquisition of high-resolution, two - and three -dimensional images.
On Improving an Already Competitive Segmentation Algorithm for the Cell Tracking Challenge - Lessons Learned
Authors: Scherr Tim , Löffler Katharina , Neumann Oliver , Mikut Ralf
Published: June 2021

The virtually error-free segmentation and tracking of densely packed cells and cell nuclei is still a challenging task. Especially in low-resolution and low signal-to-noise-ratio microscopy images erroneously merged and missing cells are common segmentation errors making the subsequent cell tracking even more difficult. In 2020, we successfully participated as team KIT-Sch-GE (1) in the 5th edition of the ISBI Cell Tracking Challenge. With our deep learning-based distance map regression segmentation and our graph-based cell tracking, we achieved multiple top 3 rankings on the diverse data sets. In this manuscript, we show how our approach can be further improved by using another optimizer and by fine-tuning training data augmentation parameters, learning rate schedules, and the training data representation. The fine-tuned segmentation in combination with an improved tracking enabled to further improve our performance in the 6th edition of the Cell Tracking Challenge 2021 as team KIT-Sch-GE (2).
Relaxin/insulin-like family peptide receptor 4 (Rxfp4) expressing hypothalamic neurons modulate food intake and preference in mice
Authors: Lewis Jo E , Woodward Orla RM , Nuzzaci Danaé , Smith Christopher A , Adriaenssens Alice E , Billing Lawrence , Brighton Cheryl , Phillips Benjamin U , Tadross John A , Kinston Sarah J , Ciabatti Ernesto , Göttgens Berthold , Tripodi Marco , Hornigold David , Baker David , Gribble Fiona M , Reimann Frank
Published: June 2021

Relaxin/insulin-like-family peptide receptor-4 (RXFP4), the cognate receptor for insulin-like peptide 5 (INSL5), has been implicated in feeding behaviour as Rxfp4 knockout mice display shorter meal durations and reduced high fat diet (HFD) intake. Here, we generated transgenic Rxfp4-Cre mice to explore Rxfp4 expression and physiology. Using this model, we identified Rxfp4 expression in the central nervous system, including in the ventromedial hypothalamus (VMH). Intra-VMH infusion of INSL5 increased HFD and highly palatable liquid meal intake (HPM) of ad libitum fed wildtype mice. Single-cell RNA-sequencing of VMH Rxfp4-expressing cells (RXFP4VMH) defined a cluster of Rxfp4-labelled neurons expressing Esr1, Tac1 and Oxtr, alongside known appetite-modulating neuropeptide receptors (Mc4r, Cckar and Nmur2). Viral tracing demonstrated RXFP4VMH neural projections to the bed nucleus of the stria terminalis, paraventricular hypothalamus, paraventricular thalamus and central nucleus of the amygdala. Utilising designer receptors exclusively activated by designer drugs (DREADDs), we found that whole body chemogenetic inhibition (Di) of Rxfp4-expressing cells, mimicking native INSL5-RXFP4 signalling, increased intake of HFD and HPM, whilst activation (Dq), either at whole body level or specifically within the VMH, reduced HFD and HPM intake and altered food preference. Ablating VMH Rxfp4-expressing cells recapitulated the lower HFD intake phenotype of Rxfp4 knockout mice, resulting in reduced body weight. These findings identify a discrete Rxfp4-expressing neuronal population as a key regulator of food intake and preference and reveal hypothalamic RXFP4 signalling as a target for feeding behaviour manipulation.
Predicting and interpreting large scale mutagenesis data using analyses of protein stability and conservation
Authors: Høie Magnus H. , Cagiada Matteo , Frederiksen Anders Haagen Beck , Stein Amelie , Lindorff-Larsen Kresten
Published: June 2021

Understanding and predicting the functional consequences of single amino acid is central in many areas of protein science. Here we collected and analysed experimental measurements of effects of >150,000 variants in 29 proteins. We used biophysical calculations to predict changes in stability for each variant, and assessed them in light of sequence conservation. We find that the sequence analyses give more accurate prediction of variant effects than predictions of stability, and that about half of the variants that show loss of function do so due to stability effects. We construct a machine learning model to predict variant effects from protein structure and sequence alignments, and show how the two sources of information are able to support one another. Together our results show how one can leverage large-scale experimental assessments of variant effects to gain deeper and general insights into the mechanisms that cause loss of function.
Macroscale structural changes of thylakoid architecture during high light acclimation in Chlamydomonas reinhardtii
Authors: Broderson Mimi , Niyogi Krishna K. , Iwai Masakazu
Published: June 2021

Photoprotection mechanisms are ubiquitous among photosynthetic organisms. The photoprotection capacity of the green alga Chlamydomonas reinhardtii is correlated with protein levels of stress-related light-harvesting complex (LHCSR) proteins, which are strongly induced by high light (HL). However, the dynamic response of overall thylakoid structure during acclimation to growth in HL has not been characterized. Here, we combined live-cell super-resolution microscopy and analytical membrane subfractionation to investigate macroscale structural changes of thylakoid membranes during HL acclimation in C. reinhardtii. Subdiffraction-resolution bioimaging revealed that overall thylakoid structures became thinned and shrunken during HL acclimation. The stromal space around the pyrenoid also became enlarged. Analytical density-dependent membrane fractionation indicated that the structural changes were partly a consequence of membrane unstacking. The analysis of both an LHCSR loss-of-function mutant, npq4 lhcsr1, and a regulatory mutant that over-expresses LHCSR, spa1-1, showed that structural changes occurred independently of LHCSR protein levels, demonstrating that LHCSR was neither necessary nor sufficient to induce the thylakoid structural changes associated with HL acclimation. In contrast, stt7-9, a mutant lacking a kinase of major light-harvesting antenna proteins, had a distinct thylakoid structural response during HL acclimation relative to all other lines tested. Thus, while LHCSR and the antenna protein phosphorylation are core features of HL acclimation, it appears that only the latter acts as a determinant for thylakoid structural rearrangements. These results indicate that two independent mechanisms occur simultaneously to cope with HL conditions. Possible scenarios for HL-induced thylakoid structural changes are discussed.
Evaluation of Host Defense Peptide (CaD23)-Antibiotic Interaction and Mechanism of Action: Insights from Experimental and Molecular Dynamics Simulations Studies
Authors: Ting Darren Shu Jeng , Li Jianguo , Verma Chandra S. , Goh Eunice T. L. , Nubile Mario , Mastropasqua Leonardo , Said Dalia G. , Beuerman Roger W. , Lakshminarayanan Rajamani , Mohammed Imran , Dua Harminder S.
Published: June 2021

Background/aim

Host defense peptides (HDPs) have the potential to provide a novel solution to antimicrobial resistance (AMR) in view of their unique and broad-spectrum antimicrobial activities. We had recently developed a novel hybrid HDP based on LL-37 and human beta-defensin-2, named CaD23, which was shown to exhibit good in vivo antimicrobial efficacy against Staphylococcus aureus in a bacterial keratitis murine model. This study aimed to examine the potential CaD23-antibiotic synergism and to evaluate the underlying mechanism of action of CaD23.

Methods

Antimicrobial efficacy was determined using minimum inhibitory concentration (MIC) assay with broth microdilution method. Peptide-antibiotic interaction was evaluated against S. aureus, methicillin-resistant S. aureus (MRSA), and Pseudomonas aeruginosa using established checkerboard assay and time-kill kinetics assay. Fractional inhibitory concentration index (FICI) was calculated and interpreted as synergistic (FICI<0.5), additive (FICI between 0.5-1.0), indifferent (FICI between >1.0 and ≤4), or antagonistic (FICI>4). SYTOX green uptake assay was performed to determine the membrane-permeabilising action of CaD23. Molecular dynamics (MD) simulations were performed to evaluate the interaction of CaD23 with bacterial and mammalian mimetic membranes.

Results

CaD23-amikacin and CaD23-levofloxacin combination treatment exhibited a strong additive effect against S. aureus SH1000 (FICI=0.56) and MRSA43300 (FICI=0.56) but a borderline additive-to-indifferent effect against P. aeruginosa (FIC=1.0-2.0). CaD23 (at 25 μg/ml; 2x MIC) was able to achieve complete killing of S. aureus within 30 mins. When used at sub-MIC concentration (3.1 μg/ml; 0.25x MIC), it was able to expedite the antimicrobial action of amikacin against S. aureus by 50%. The rapid antimicrobial action of CaD23 was attributed to the underlying membrane-permeabilising mechanism of action, evidenced by the SYTOX green uptake assay and MD simulations studies. MD simulations revealed that cationicity, alpha-helicity, amphiphilicity and hydrophobicity (related to the Trp residue at C-terminal) play important roles in the antimicrobial action of CaD23.

Conclusions

CaD23 is a novel membrane-active synthetic HDP that can enhance and expedite the antimicrobial action of antibiotics against Gram-positive bacteria when used in combination. MD simulation serves as a useful tool in dissecting the mechanism of action and guiding the design and optimisation of HDPs.
Multiple reproductive females in family groups of smooth-coated otters
Authors: Bungum Haaken Zhong , Yee Mei-Mei Tan Heng , Borker Atul , Hsu Chia Da , Johns Philip
Published: June 2021

Smooth-coated otters (Lutrogale perspicillata) are inhabitants of the waterways of India and Singapore. Otter families typically consist of a single mating pair with mature, nonbreeding siblings living in family groups, or “romps”. We note here the presence of multiple reproductive female otters within some romps, as well as the possible existence of simultaneous litters by different mothers. This phenomenon has not been recorded amongL. perspicillatabefore. Here we address possible influences leading to multiple reproductive females within romps of smooth-coated otters, including inclusive fitness, incomplete suppression of reproduction, and existing in an urban environment. The numerous, recurring observations of multiple reproductive females warrant further investigation; while uncommon, this phenomenon is not as rare as once thought.
In Vivo Simultaneous Nonlinear Absorption Raman and Fluorescence (SNARF) Imaging of Mouse Brain Cortical Structures
Authors: Francis Andrew T. , Manifold Bryce , Thomas Elena C. , Hu Ruoqian , Hill Andrew H. , Men Shuaiqian , Fu Dan
Published: June 2021

Abstract

Two-photon excited fluorescence (TPEF) microscopy is a widely used optical imaging technique that has revolutionized neurophotonics through a diverse palette of dyes, specialized transgenic models, easy implementation, and straightforward data analysis. However, in vivo TPEF imaging is often limited in the number of contrasts available to distinguish different cells, structures, or functions. We propose using two label-free multiphoton microscopy techniques – stimulated Raman scattering (SRS) microscopy and transient absorption microscopy (TAM) – as complementary and orthogonal imaging modalities to TPEF for in vivo brain imaging. In this study, we construct a simultaneous nonlinear absorption, Raman, and fluorescence (SNARF) microscope and image several cortical structures up to 250-300 μm below the pial surface, the highest reported in vivo imaging depth for SRS or TAM. We further demonstrate the capabilities of our SNARF microscope through the quantification of age-dependent myelination, hemodynamics, vessel structure, cell density, and cell identity in vivo. Using machine learning, we report the use of label-free SRS and TAM features to predict capillary-lining cell identities with 90% accuracy. The SNARF microscope and methodology outlined herein provide a powerful platform to study several research topics, including neurovascular coupling, blood-brain barrier, neuronal and axonal degeneration in aging, and neurodegenerative diseases.
The role of temporal coherence and temporal predictability in the build-up of auditory grouping
Authors: Sollini Joseph , Poole Katarina C , Blauth-Muszkowski Dominic , Bizley Jennifer K.
Published: June 2021

The cochlea decomposes sounds into separate frequency channels, from which the auditory brain must reconstruct the auditory scene. To do this the auditory system must make decisions about which frequency information should be grouped together, and which should remain distinct. Two key cues for grouping are temporal coherence, resulting from coherent changes in power across frequency, and temporal predictability, resulting from regular or predictable changes over time. To test how these cues contribute to the construction of a sound scene we present listeners with a range of precursor sounds, which act to prime the auditory system by providing information about each sounds structure, followed by a fixed masker in which participants were required to detect the presence of an embedded tone. By manipulating temporal coherence and/or temporal predictability in the precursor we assess how prior sound exposure influences subsequent auditory grouping. In Experiment 1, we measure the contribution of temporal predictability by presenting temporally regular or jittered precursors, and temporal coherence by using either narrow or broadband sounds, demonstrating that both independently contribute to masking/unmasking. In Experiment 2, we measure the relative impact of temporal coherence and temporal predictability and ask whether the influence of each in the precursor signifies an enhancement or disruption of unmasking. We observed that interfering precursors produced the largest changes to thresholds.
Cryo-EM structures of human TMEM120A and TMEM120B
Authors: Ke Meng , Yu Yue , Zhao Changjian , Lai Shirong , Su Qiang , Yuan Weidan , Yang Lina , Deng Dong , Wu Kun , Zeng Weizheng , Geng Jia , Wu Jianping , Yan Zhen
Published: June 2021

TMEM120A (Transmembrane protein 120A) was recently identified as a mechanical pain sensing ion channel named as TACAN, while its homologue TMEM120B has no mechanosensing property1. Here, we report the cryo-EM structures of both human TMEM120A and TMEM120B. The two structures share the same dimeric assembly, mediated by extensive interactions through the transmembrane domain (TMD) and the N-terminal coiled coil domain (CCD). However, the nearly identical structures cannot provide clues for the difference in mechanosensing between TMEM120A and TMEM120B. Although TMEM120A could mediate conducting currents in a bilayer system, it does not mediate mechanical-induced currents in a heterologous expression system, suggesting TMEM120A is unlikely a mechanosensing channel. Instead, the TMDs of TMEM120A and TMEM120B resemble the structure of a fatty acid elongase, ELOVL7, indicating their potential role of an enzyme in lipid metabolism.
A universal probabilistic spike count model reveals ongoing modulation of neural variability
Authors: Liu David , Lengyel Máté
Published: June 2021

Neural responses are variable: even under identical experimental conditions, single neuron and population responses typically differ from trial to trial and across time. Recent work has demonstrated that this variability has predictable structure, can be modulated by sensory input and behaviour, and bears critical signatures of the underlying network dynamics and computations. However, current methods for characterising neural variability are primarily geared towards sensory coding in the laboratory: they require trials with repeatable experimental stimuli and behavioural covariates. In addition, they make strong assumptions about the parametric form of variability, rely on assumption-free but data-inefficient histogram-based approaches, or are altogether ill-suited for capturing variability modulation by covariates. Here we present a universal probabilistic spike count model that eliminates these shortcomings. Our method builds on sparse Gaussian processes and can model arbitrary spike count distributions (SCDs) with flexible dependence on observed as well as latent covariates, using scalable variational inference to jointly infer the covariate-to-SCD mappings and latent trajectories in a data efficient way. Without requiring repeatable trials, it can flexibly capture covariate-dependent joint SCDs, and provide interpretable latent causes underlying the statistical dependencies between neurons. We apply the model to recordings from a canonical non-sensory neural population: head direction cells in the mouse. We find that variability in these cells defies a simple parametric relationship with mean spike count as assumed in standard models, its modulation by external covariates can be comparably strong to that of the mean firing rate, and slow low-dimensional latent factors explain away neural correlations. Our approach paves the way to understanding the mechanisms and computations underlying neural variability under naturalistic conditions, beyond the realm of sensory coding with repeatable stimuli.
Candida albicans Isolates 529L and CHN1 Exhibit Stable Colonization of the Murine Gastrointestinal Tract
Authors: McDonough Liam , Mishra Animesh Anand , Tosini Nicholas , Kakade Pallavi , Penumutchu Swathi , Liang Shen-Huan , Maufrais Corrine , Zhai Bing , Taur Ying , Belenky Peter , Bennett Richard J. , Hohl Tobias M. , Koh Andrew Y. , Ene Iuliana V.
Published: June 2021

Candida albicans is a pathobiont that colonizes multiple niches in the body including the gastrointestinal (GI) tract, but is also responsible for both mucosal and systemic infections. Despite its prevalence as a human commensal, the murine GI tract is generally refractory to colonization with the C. albicans reference isolate SC5314. Here, we identify two C. albicans isolates, 529L and CHN1, that stably colonize the murine GI tract in three different animal facilities under conditions where SC5314 is lost from this niche. Analysis of the bacterial microbiota did not show notable differences between mice colonized with the three C. albicans strains. We compared the genotypes and phenotypes of these three strains and identified thousands of SNPs and multiple phenotypic differences, including their ability to grow and filament in response to nutritional cues. Despite striking filamentation differences under laboratory conditions, however, analysis of cell morphology in the GI tract revealed that the three isolates exhibited similar filamentation properties in this in vivo niche. Notably, we found that SC5314 is more sensitive to the antimicrobial peptide CRAMP, and the use of CRAMP-deficient mice increased the ability of SC5314 to colonize the GI tract relative to CHN1 and 529L. These studies provide new insights into how strain-specific differences impact C. albicans traits in the host and advance CHN1 and 529L as relevant strains to study C. albicans pathobiology in its natural host niche.

IMPORTANCE

Understanding how fungi colonize the GI tract is increasingly recognized as highly relevant to human health. The animal models used to study Candida albicans commensalism commonly rely on altering the host microbiome (via antibiotic treatment or defined diets) to establish successful GI colonization by the C. albicans reference isolate SC5314. Here, we characterize two C. albicans isolates that can colonize the murine GI tract without antibiotic treatment and can therefore be used as tools for studying fungal commensalism. Importantly, experiments were replicated in three different animal facilities and utilized three different mouse strains. Differential colonization between fungal isolates was not associated with alterations in the bacterial microbiome but rather with distinct responses to CRAMP, a host antimicrobial peptide. This work emphasizes the importance of C. albicans intra-species variation as well as host anti-microbial defense mechanisms in defining commensal interactions.
Tracking and Measuring Local Protein Synthesis In Vivo
Authors: Kays Ibrahim , Chen Brian E.
Published: June 2021

Detecting when and how much a protein molecule is synthesized is important for understanding cell function, but current methods have poor cellular or temporal resolution or are destructive to cells (Dahm et al., 2008). Here, we developed a technique to detect and quantify subcellular protein synthesis events in real time in vivo. This Protein Translation Reporting (PTR) technique uses a genetic tag that produces a stoichiometric ratio of a small peptide portion of a split fluorescent protein and the protein of interest during protein synthesis. We show that the split fluorescent protein peptide can generate fluorescence within milliseconds upon binding the larger portion of the fluorescent protein, and that the fluorescence intensity is directly proportional to the number of molecules of the protein of interest synthesized. Using PTR, we tracked and measured protein synthesis events in single cells over time in vivo. We use split red fluorescent protein to detect multiple genes or alleles in single cells simultaneously. We also split a photoswitchable fluorescent protein to photoconvert the reconstituted fluorescent protein to a different channel and arbitrarily reset the time of detection of synthesis events, continually over time.