bluuebunny/crossref_metadata_2025 huggingface dataset:
Joint estimation of relaxation and diffusion tissue parameters for prostate cancer grading with relaxation-VERDICT MRI
Authors: Palombo Marco , Valindria Vanya , Singh Saurabh , Chiou Eleni , Giganti Francesco , Pye Hayley , Whitaker Hayley C. , Atkinson David , Punwani Shonit , Alexander Daniel C. , Panagiotaki Eleftheria
Published: July 2021

Purpose

The Vascular, Extracellular and Restricted Diffusion for Cytometry in Tumours (VERDICT) technique has shown promise discriminating normal from prostate cancer (PCa) tissue and Gleason grade 3+3 from 3+4. However, VERDICT currently doesn’t account for the inherent relaxation properties of the tissue that could add complementary information and potentially enhance its diagnostic power. The aim of this work is to introduce relaxation-VERDICT (rVERDICT) for prostate, a model for the joint estimation of diffusion and relaxation parameters.

Methods

72 men with suspected PCa underwent multiparametric MRI (mp-MRI) and VERDICT MRI. Among these, 44 underwent targeted biopsy and were analysed with rVERDICT using deep neural networks for fast fitting (∼60 times faster than non-linear least squares minimisation approach). A convolutional neural network classifier assessed the rVERDICT parameters in differentiating Gleason grades measured with accuracy, F1-score and Cohen’s kappa. To assess repeatability, five men were imaged twice.

Results

There were 37 cancer lesions: 6 Gleason 3+3, 18 Gleason 3+4, and 13 Gleason ≥4+3. The rVERDICT intracellular volume fraction fic discriminated between Gleason 3+3 and 3+4 (p=0.003); Gleason 3+4 and ≥4+3 (p=0.040); and between 5-class Gleason grades with (accuracy, F1-score,kappa)=(8,7,3) percentage points higher than classic VERDICT, and (12,13,24) percentage points higher than the ADC from mp-MRI. Repeatability of rVERDICT parameters was high (R2=0.79–0.98,CV=1%–7%,ICC=92%-98%). T2 values estimated with rVERDICT were not significantly different from those estimated with an independent multi-TE acquisition (p>0.05).

Conclusion

rVERDICT allows for accurate, fast and repeatable estimation of diffusion and relaxation properties of PCa and enables discriminating Gleason grade groups.
Communicating about COVID-19 vaccine development and safety
Authors: Thorpe Alistair , Fagerlin Angela , Butler Jorie , Stevens Vanessa , Drews Frank A. , Shoemaker Holly , Riddoch Marian , Scherer Laura D.
Published: July 2021

Purpose

Beliefs that the risks from the vaccine outweigh the risks from getting COVID-19 and concerns that the vaccine development process was rushed and lacking rigor have been identified as important drivers of hesitancy and refusal to get a COVID-19 vaccine. We tested whether messages designed to address these beliefs and concerns might promote intentions to get a COVID-19 vaccine.

Method

An online survey fielded between March 8-March 23, 2021 with US Veteran (n=688) and non-Veteran (n=387) respondents. In a between-subjects experiment, respondents were randomly assigned to a control group (with no message) or to read one of two intervention messages: 1. a fact-box styled message comparing the risks of getting COVID-19 compared to the vaccine, and 2. a timeline styled message describing the development process of the COVID-19 mRNA vaccines.

Results

Most respondents (60%) wanted a COVID-19 vaccine. However, 17% expressed hesitancy and 23% did not want to get a COVID-19 vaccine. The fact-box styled message and the timeline message did not significantly improve vaccination intentions, F(2,358)=0.86, p=.425, , or reduce the time respondents wanted to wait before getting vaccinated, F(2,306)=0.79, p=.453, , compared to no messages.

Discussion

We did not find an impact on vaccine intention based on providing information about vaccine risks and development. Further research is needed to identify how to effectively address concerns about the risks associated with COVID-19 vaccines and the development process and to understand additional factors that influence vaccine intentions.
Clinical management and impact of scarlet fever in the modern era: findings from a cross-sectional study of cases in London, 2018-2019
Authors: Herdman M. Trent , Cordery Rebecca , Karo Basel , Purba Amrit Kaur , Begum Lipi , Lamagni Theresa , Kee Chuin , Balasegaram Sooria , Sriskandan Shiranee
Published: July 2021

Background

Scarlet fever incidence has risen steeply in recent years, and is associated with wider outbreaks of severe Group A Streptococcal infections. Yet, few studies of its epidemiology, clinical features, and management have been undertaken in the antibiotic era.

Aim

To characterize symptomatology, management, and consequences of scarlet fever and identify associations with delayed diagnosis.

Design/Setting

Cross-sectional study of children with scarlet fever in London, 2018-2019.

Methods

online survey of parents/guardians of children with scarlet fever identified by Health Protection Teams, recording demographics, symptoms, care-seeking, and management; logistic regression for factors associated with delayed diagnosis; Cox’s regression for consequences of delayed diagnosis.

Results

Responses represented 412 cases in a period with 6828 notifications for children 0-14 years old, and 410 school/nursery outbreaks. 70% first sought care from general practice, and 31% had multiple consultations. For 28%, scarlet fever was not considered at first consultation: in these cases, symptoms were frequently attributed to viral infection (60%, 64/106). Delay in diagnosis beyond first consultation occurred more frequently among children aged 5+ who presented with sore throat (odds ratio 2.8 vs. 5+ without sore throat; 95%CI 1.3-5.8; P=0.006). On average, cases with delayed diagnosis took one day longer to return to baseline activities, and required one additional day off school versus those diagnosed at first consultation.

Conclusions

In assessing children with fever, rash, and sore throat, practitioners should be alert to the possibility of scarlet fever: it is frequently missed at first consultation, and prompt recognition speeds clinical recovery and public health management.

How this fits in [4 sentences summarising key messages of background and findings]

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In the five years leading up to the pandemic lockdown of 2020, scarlet fever incidence rose markedly in England and Wales, prompting this investigation of cases in London 2018-2019.

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Prompt recognition of the disease by carers and clinicians can direct timely antibiotic therapy, limit transmission in the household and community, and direct the identification and control of outbreaks.

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In this study, delayed diagnosis was more likely to occur among older children presenting with sore throat—perhaps reflecting a lower index of suspicion in this age group.

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Cases with delayed diagnosis took longer to return to normal activities, and required more time off from school than those diagnosed at the first consultation.
A Retrospective analysis of DIC score and SIC score in prediction of COVID-19 severity
Authors: Kapoor Mayank , Panda Prasan Kumar , Saini Lokesh Kumar , Bahurupi Yogesh Arvind
Published: July 2021

Background

The novel Disseminated Intravascular Coagulation (DIC) score [platelet count, prolonged prothrombin time, D-dimer, and fibrinogen] and Sepsis Induced Coagulopathy (SIC) score [platelet count, International normalized ratio, and Sequential organ failure assessment score] are markers of coagulopathy, which, for the first time, are explored in line with the COVID-19 disease outcomes. The correlation of D-dimer with these findings is also studied.

Patients and methods

A retrospective analysis of hospital-based records of 168 COVID-19 patients. Data including D-dimer, routine investigations, DIC and SIC scorings (all within three days of admission) were collected and correlated with the outcomes. The study was conducted in a tertiary care center catering to population of North India.

Results

Higher DIC score (1·59 ± 1·18 v/s 0·96 ± 1·18), SIC score (1·60 ± 0·89 v/s 0·63 ± 0·99), and D-dimer titers (1321·33 ± 1627·89 v/s 583·66 ± 777·71 ng/ml) were significantly associated with severe COVID-19 disease (P<0·05). DIC score and SIC score ≥ 1, and D-dimer ≥ 1315 ng/ml for severe disease; DIC score ≥ 1, SIC score ≥ 2, and D-dimer ≥ 600 ng/ml for Pulmonary Embolism (PE); and DIC score and SIC score ≥ 1, and D-dimer level ≥ 990 ng/ml for mortality were the respective cut-off values we found from our study.

Conclusion

Higher DIC scores, SIC scores, and D-dimer values are associated with severe COVID-19 disease, in-hospital mortality, and PE risk. They can serve as easily accessible early markers of severe disease and prioritize hospital admissions in the presently overburdened scenario, and may be used to develop prognostic prediction models.

Highlights

DIC scores, SIC scores, and D-dimer values are hereby studied in association with COVID-19 disease severity, in-hospital mortality, and PE risk. They serve as easily accessible early markers of severe disease and prioritize hospital admissions in the presently overburdened scenario, and may be used to develop prognostic prediction models.
SARS-CoV-2 Seroprevalence among First Responders in Northeastern Ohio
Authors: Zhang Xiaochun , Saade Elie , Noguez Jaime H , Schmotzer Christine
Published: July 2021

Objectives

First responders including firefighters, emergency medical technicians (EMT), paramedics, and police officers are working on the front lines to fight the COVID-19 pandemic and facing a higher risk of infection. This study assessed the seroprevalence among first responders in northeastern Ohio during May-September 2020.

Methods

A survey and IgG antibody test against SARS-CoV-2 were offered to University Hospitals Health System affiliated first responder departments.

Results

A total of 3080 first responders with diverse job assignments from more than 400 fire and police departments participated in the study. Among them, 73 (2.4%) were seropositive while only 0.8% had previously positive RT-PCR results. Asymptomatic infection accounts for 46.6% of seropositivity. By occupation, seropositive rates were highest among administration/support staff (3.8%), followed by paramedics (3.0%), EMTs (2.6%), firefighters (2.2%), and police officers (0.8%). Seroprevalence was not associated with self-reported exposure as work exposure rates were: paramedics 48.2%, firefighters 37.1%, EMTs 32.3%, police officers 7.7%, and administration/support staff 4.4%. Self-reported community exposure was strongly correlated with self-reported work exposure rate rather than seroprevalence suggesting a potential impact of risk awareness. Additionally, no significant difference was found among gender or age groups; however, black Americans have a higher positivity rate than other races although they reported lower exposure.

Conclusions

Despite the high work-associated exposure rate to SARS-CoV-2 infection, first responders with different roles demonstrated seroprevalence no higher than their administrative/supportive colleagues, which suggests infection control measures are effective in preventing work-related infection.
Enhancing epidemiological investigation of nosocomial SARS-CoV-2 infection with whole genome sequencing: A retrospective cohort study across four hospitals in the UK
Authors: Lumley Sheila F , Constantinides Bede , Sanderson Nicholas , Rodger Gillian , Street Teresa L , Swann Jeremy , Chau Kevin K , O’Donnell Denise , Warren Fiona , Hoosdally Sarah ,   OUH Microbiology laboratory,   OUH Infection Prevention and Control team, O’Donnell Anne-Marie , Walker Timothy M , Stoesser Nicole E , Butcher Lisa , Peto Tim EA , Crook Derrick W , Jeffery Katie , Matthews Philippa C , Eyre David W
Published: July 2021

Background

Despite robust efforts, patients and staff acquire SARS-CoV-2 infection in hospitals. In this retrospective cohort study, we investigated whether whole-genome sequencing (WGS) could enhance the epidemiological investigation of healthcare-associated SARS-CoV-2 acquisition.

Methods and findings

From 17-November-2020 to 5-January-2021, 803 inpatients and 329 staff were diagnosed with SARS-CoV-2 infection across four teaching hospitals in Oxfordshire, UK. We classified cases according to epidemiological definitions, sought epidemiological evidence of a potential source for each nosocomial infection, and evaluated if epidemiologically-linked cases had genomic evidence supporting transmission. We compared epidemiological and genomic outbreak identification.

Using national epidemiological definitions, 109/803 (14%) inpatient infections were classified as definite/probable nosocomial, 615 (77%) as community-acquired and 79 (10%) as indeterminate. There was strong epidemiological evidence to support definite/probable cases as nosocomial: 107/109 (98%) had a prior-negative PCR in the same hospital stay before testing positive, and 101(93%) shared time and space with known infected patients/staff. Many indeterminate cases were likely infected in hospital: 53/79 (67%) had a prior-negative PCR and 75 (95%) contact with a potential source. 89/615 (11% of all 803 patients) with apparent community-onset had a recent hospital exposure.

WGS highlighted SARS-CoV-2 is mainly imported into hospitals: within 764 samples sequenced 607 genomic clusters were identified (>1 SNP distinct). Only 43/607 (7%) clusters contained evidence of onward transmission (subsequent cases within ≤1 SNP). 20/21 epidemiologically-identified outbreaks contained multiple genomic introductions. Most (80%) nosocomial acquisition occurred in rapid super-spreading events in settings with a mix of COVID-19 and non-COVID-19 patients. Hospitals not routinely admitting COVID-19 patients had low rates of transmission. Undiagnosed/unsequenced individuals prevent genomic data from excluding nosocomial acquisition.

Conclusions

Our findings suggest current surveillance definitions underestimate nosocomial acquisition and reveal most nosocomial transmission occurs from a relatively limited number of highly infectious individuals.
A multi-level investigation of the genetic relationship between endometriosis and ovarian cancer histotypes
Authors: Mortlock Sally , Corona Rosario I. , Kho Pik Fang , Pharoah Paul , Seo Ji-Heui , Freedman Matthew L. , Gayther Simon A. , Siedhoff Matthew T. , Rogers Peter A.W. , Leuchter Ronald , Walsh Christine S. , Cass Ilana , Karlan Beth Y. , Rimel B.J. ,   Ovarian Cancer Association Consortium,   International Endometriosis Genetics Consortium, Montgomery Grant W. , Lawrenson Kate , Kar Siddhartha P.
Published: July 2021

Endometriosis is associated with increased risk of epithelial ovarian cancers (EOCs). Data from large endometriosis and EOC genome-wide association meta-analyses were used to estimate the genetic correlation and evaluate the causal relationship between genetic liability to endometriosis and major EOC histotypes, and to identify shared susceptibility loci. We estimated a significant genetic correlation (rg) between endometriosis and clear cell (rg=0.71), endometrioid (rg=0.48) and high-grade serous (rg=0.19) ovarian cancer, all supported by Mendelian randomization analyses. A bivariate meta-analysis identified 28 loci associated with endometriosis and EOC, including two novel risk loci, and 19 with evidence for a single underlying causal variant. Differences in the shared risk suggest different underlying pathways may contribute to the relationship between endometriosis and the different histotypes. Functional annotation using transcriptomic and epigenomic profiles of relevant tissues/cells highlighted several target genes. This comprehensive analysis reveals profound genetic overlap between endometriosis and EOC histotypes with valuable genomic targets for understanding the biological mechanisms linking the diseases.
The Role of CRP, Interleukin-6 and Their Derived Immune-Inflammatory Indices in Early Prediction of Severity and Mortality of COVID-19 Patients
Authors: Taha Sara I. , Shata Aalaa K. , El-Sehsah Eman M. , Fouad Shaimaa H. , Moussa Aya H. , Abdalgeleel Shaimaa A. , Moustafa Nouran M. , Youssef Mariam K.
Published: July 2021

Background

In coronavirus disease 2019 (COVID-19), finding sensitive biomarkers is critical for detecting severe cases early and intervening effectively.

Objectives

To compare and evaluate the predictive value of C-reactive protein (CRP), interleukin-6 (IL-6), and their derived immune-inflammatory indices (CRP/albumin (CRP/alb), lymphocyte/CRP (L/CRP), and lymphocyte/IL-6 (L/IL-6)) in COVID-19 patients.

Methods

On admission, 85 confirmed COVID-19 patients, their measured and collected laboratory data were obtained and compared.

Results

Levels of CRP, IL-6, and CRP/alb were significantly higher (P=0.001) in severe patients and non-survivors, but L/CRP and L/IL-6 were significantly lower (P=0.001). We observed the best predictive performance for COVID-19 severity at 1.65 for CRP/alb and 260.86 for L/CRP with 84.7% diagnostic accuracy for both. The best diagnostic accuracy for COVID-19 in-hospital mortality was 87.1% by IL-6 at 120 pg/ml and 85.9% by L/IL-6 at 5.40. The multi-marker prediction surpassed the performance of a single biomarker prediction. IL-6 was an independent risk factor associated with severe disease development (odds ratio (OR): 1.033; 95% confidence interval (CI): 1.002-1.066).

Conclusions

Pretreatment values of CRP, IL-6, and their derived indices could be included in the diagnostic work-up of COVID-19 to determine the severity and predict the outcome.
Automated diagnosis of autism: State of the art
Authors: Valizadeh Amir , Moassefi Mana , Nakhostin-Ansari Amin , Some’eh Soheil Heidari , Hosseini-Asl Hossein , Torbati Mehrnush Saghab , Aghajani Reyhaneh , Ghorbani Zahra Maleki , Menbari-Oskouie Iman , Aghajani Faezeh , Mirzamohamadi Alireza , Ghafouri Mohammad , Faghani Shahriar , Memari Amir Hossein
Published: July 2021

Background

Autism spectrum disorder (ASD) represents a panel of conditions that begin during the developmental period and result in impairments of personal, social, academic, or occupational functioning. Early diagnosis is directly related to a better prognosis. Unfortunately, the diagnosis of ASD requires a long and exhausting subjective process.

Objective

To review the state of the art for the automated autism diagnosis.

Methods

In February 2022, we searched multiple databases and several sources of grey literature for eligible studies. We used an adapted version of the QUADAS-2 tool to assess the risk of bias in the studies. A brief report of the methods and results of each study is presented. Data were synthesized for each modality separately using the Split Component Synthesis (SCS) method. We assessed heterogeneity using the I2statistics and evaluated publication bias using trim and fill tests combined with ln DOR. Confidence in cumulative evidence was evaluated using the GRADE approach for diagnostic studies.

Results

We included 344 studies from 186020 participants (51129 are estimated to be unique) for nine different modalities in this review, from which 232 reported sufficient data for meta-analysis. The area under the curve was in the range of 0.71-0.90 for all the modalities. The studies on EEG data provided the best accuracy, with the area under the curve ranging between 0.85 to 0.93.

Conclusions

The literature is rife with bias and methodological/reporting flaws. Recommendations are provided for future research to provide better studies and fill in the current knowledge gaps.
Harnessing the Power of Sex Differences: What a Difference Ten Years Did Not Make
Authors: Rechlin Rebecca K. , Splinter Tallinn F.L. , Hodges Travis E. , Albert Arianne Y. , Galea Liisa A.M.
Published: July 2021

Sex differences exist in many neurological and psychiatric diseases. Mandates have been initiated across funding agencies for research to include males and females. What has been lacking in the literature is a detailed assessment of how sex is incorporated into the design (e.g. balanced design) and into the analyses (e.g. covariate). We surveyed papers in 2009 and 2019 across six journals in Neuroscience and Psychiatry. There was a 30% increase in the percentage of papers that included both sexes to 68% in 2019. Despite this increase, in 2019 only 19% of studies used an optimal design for discovery of possible sex differences and only 5% analyzed sex as a discovery variable. Here we show that little progress has been made in harnessing the power that sex differences can afford in research for discovery and therapeutic potential for neurological and psychiatric disease to improve the health of men, women and gender diverse individuals.

Highlights

68% of Neuroscience and Psychiatry papers reported the use of both sexes in 2019

Only 19% of studies in 2019 used sex consistently throughout the study analyses

Of the studies that used males and females, 59% did not include sex in the analyses

Only 5% of studies in 2019 used sex as a discovery variable in their analyses

Male only papers were 8.4 times more prevalent than female-only papers
Temporal and Spatial Niche Partitioning of Bumblebee Species (Apidae:Bombus) on a Himalayan Mountain
Authors: Moss Alan James , Camilo Gerardo R , Ren Zong-Xin , Bernhardt Peter
Published: July 2021

Background

Bumblebees are essential pollinators in many ecosystems. To maintain such ecosystem functions, bumblebee diversity remains an important concern. We measured abundance and diversity of bumblebee species along an elevational gradient over three flowering seasons. We hypothesized that co-occurring bumblebees partition niches over time and space.

Methods

We sampled bumblebees at six different meadows along Yulong Snow Mountain (Yunnan, SW China), a region known for high bumblebee diversity, over summer months (2017 – 2019). We analyzed the standardized abundances of the workers from different bumblebee species over 11 weeklong periods. We also analyzed the standardized abundances of the workers of each species at each of the six different meadows.

Results

Clear patterns of temporal niche partitioning were most apparent for the two, dominant species,B. friseanusandB. lepidus. Spatial niche partitioning was evident for rarer species which tended to be most abundant at lower elevations.

Conclusions

Temporal and spatial niche partitioning are among two of the ways that bumblebee diversity is maintained on Yulong Snow Mountain. This has future implications if changing climate conditions disrupt partitioning leading to increased interspecific competition.
Comprehensive transcriptomic analysis shows disturbed calcium homeostasis and deregulation of T lymphocyte apoptosis in inclusion body myositis
Authors: Johari Mridul , Vihola Anna , Palmio Johanna , Jokela Manu , Jonson Per Harald , Sarparanta Jaakko , Huovinen Sanna , Savarese Marco , Hackman Peter , Udd Bjarne
Published: July 2021

Objective

Inclusion body myositis (IBM) has an unclear molecular etiology due to the co-existence of characteristic cytotoxic T-cell activity and degeneration of muscle fibers. Using in-depth gene expression and splicing studies, we aimed at understanding the different components of the molecular pathomechanisms in IBM.

Methods

We performed RNA-seq on RNA extracted from skeletal muscle biopsies of clinically and histopathologically defined IBM (n=24), tibial muscular dystrophy (n=6), and histopathologically normal group (n=9). In a comprehensive transcriptomics analysis, we analyzed the differential gene expression, differential splicing and exon usage, downstream pathway analysis, and the interplay between coding and non-coding RNAs (micro RNAs and long non-coding RNAs).

Results

We observe dysregulation of genes involved in calcium homeostasis, particularly affecting the T-cell activity and regulation, causing disturbed Ca2+ induced apoptotic pathway of T cells in IBM muscles. Additionally, LCK/p56, which is an essential gene in regulating the fate of T-cell apoptosis, shows altered expression and splicing usage in IBM muscles

Interpretation

Our analysis provides a novel understanding of the molecular mechanisms in IBM by showing a detailed dysregulation of genes involved in calcium homeostasis and its effect on T-cell functioning in IBM muscles. Loss of T-cell regulation is hypothesized to be involved in the consistent observation of no response to immune therapies in IBM patients. Our results show that loss of apoptotic control of cytotoxic T cells could indeed be one component of their abnormal cytolytic activity in IBM muscles.
Inverse Density of Iba1 and Glutamine Synthetase Expressing Glia in Rat Inferior Colliculus
Authors: Orton Llwyd David
Published: July 2021

Microglia and astrocytes undertake numerous essential roles in nervous systems but we know little of their anatomical distribution within numerous nuclei. In the principal nuclei of the mammalian auditory midbrain, the inferior colliculi (IC), the cellular density and relative distribution of glutamate synthetase (GS) expressing astrocytes and ionized calcium-binding adapter molecule 1 (Iba1) expressing microglia is unknown. To address this, the IC of young adult, male Wistar rats were immunohistochemically labelled for GS and Iba1, using chromogenic methods. Sub-regions of imaged IC sections were demarked and soma density of both cell types determined. GS labelled somata were twice more densely packed as Iba1 labelled somata throughout IC parenchyma and peri-vascular regions. Furthermore, GS labelled somata density was significantly lower in dorsal cortex than external cortex or central nucleus. Iba1 labelled somata density exhibited the opposite trend, revealing an inverse density of these glial cell types between IC sub-regions. GS labelled neuropil was strongest in the cortices with and a gradual transition of lighter labelling towards central nucleus. These data provide the first detailed descriptions of GS labelling in IC and demonstrate sub-regional differences in IC glial cell density. Taken together, these findings suggest neurochemical specialization of glia in IC sub-regions, likely related to local physiological and metabolic demands, with implications for IC function.
The Ventral Midline Thalamus Mediates Successful Deliberation by Coordinating Prefrontal and Hippocampal Neural Activity
Authors: Stout John J. , Hallock Henry L. , Adiraju Suhaas S. , Griffin Amy L.
Published: July 2021

When faced with difficult choices, the possible outcomes are considered through a process known as deliberation. In rats, deliberation can be reflected by pause-and-reorienting behaviors, better known as Vicarious Trial and Errors (VTEs). While VTEs are thought to require medial prefrontal cortex (mPFC) and dorsal hippocampal (dHPC) interactions, no work has demonstrated such a dual requirement. The nucleus reuniens (Re) of the ventral midline thalamus is anatomically connected with both the mPFC and dHPC, is required for HPC-dependent spatial memory tasks, and is critical for mPFC-dHPC neural synchronization. Currently, it is unclear if, or how, the Re is involved in deliberation. Therefore, by examining the role of the Re on VTE behaviors, we can better understand the anatomical and physiological mechanisms supporting deliberation. Here, we examined the impact of Re suppression on VTE behaviors and mPFC-dHPC theta synchrony during well-learned performance of a HPC-dependent delayed alternation (DA) task. Pharmacological suppression of the Re increased VTE behaviors that resulted in erroneous choices. These errors were best characterized as perseverative behaviors, where at the decision-point, some rats repeatedly turned in the direction that previously yielded no reward, while simultaneously deliberating. These ‘failed’ deliberations were associated with a reduction in mPFC-dHPC theta coherence at the choice-point. Importantly, the reduction in mPFC-dHPC theta synchrony observed during VTE behaviors was almost entirely driven by Re-suppression induced changes to the mPFC theta oscillation. Our findings suggest that the Re is important for successful deliberation, and mPFC-dHPC interactions, by coordinating local theta oscillations in the mPFC.
Organization of the catecholaminergic system in the short-lived fish Nothobranchius furzeri
Authors: Borgonovo Janina , Ahumada-Galleguillos Patricio , Oñate-Ponce Alejandro , Allende-Castro Camilo , Henny Pablo , Concha Miguel L.
Published: July 2021

The catecholaminergic system has received much attention based on its regulatory role in a wide range of brain functions and its relevance in aging and neurodegenerative diseases. In the present study, we analyzed the neuroanatomical distribution of catecholaminergic neurons based on tyrosine hydroxylase (TH) immunoreactivity in the brain of adult Nothobranchius furzeri. In the telencephalon, numerous TH+ neurons were observed in the olfactory bulbs and the ventral telencephalic area, arranged as strips extending through the rostrocaudal axis. We found the largest TH+ groups in the diencephalon at the preoptic region level, the ventral thalamus, the pretectal region, the posterior tuberculum, and the caudal hypothalamus. In the dorsal mesencephalic tegmentum, we identified a particular catecholaminergic group. The rostral rhombencephalon housed TH+ cells in the locus coeruleus and the medulla oblongata, distributing in a region dorsal to the inferior reticular formation, the vagal lobe, and the area postrema. Finally, scattered TH+ neurons were present in the ventral spinal cord and the retina. From a comparative perspective, the overall organization of catecholaminergic neurons is consistent with the general pattern reported for other teleosts. However, Nothobranchius furzeri shows some particular features, including the presence of catecholaminergic cells in the midbrain. This work provides a detailed neuroanatomical map of the catecholaminergic system of Nothobranchius furzeri, a powerful aging model, also contributing to the phylogenetic understanding of one of the most ancient neurochemical systems.
Intrinsic Network Activity Reflects the Ongoing Experience of Chronic Pain
Authors: Jahn Pauline , Deak Bettina , Mayr Astrid , Stankewitz Anne , Keeser Daniel , Griffanti Ludovica , Witkovsky Viktor , Irving Stephanie , Schulz Enrico
Published: July 2021

Analyses of intrinsic network activity have been instrumental in revealing cortical processes that are altered in chronic pain patients. However, such studies have not accounted for variable time courses of network activity and subjective pain experience. In a novel approach, we aimed to elucidate how intrinsic functional networks evolve in regard to the fluctuating intensity of the experience of chronic pain.

In a longitudinal study with 156 fMRI sessions, 20 chronic back pain patients and 20 chronic migraine patients were asked to continuously rate the intensity of their endogenous pain. Using group independent component analysis and dual-regression, we extracted the time courses of 100 independent components separately for chronic back pain and chronic migraine. We investigated the relationship between the fluctuation of intrinsic network activity with the time course of subjective pain ratings.

For chronic back pain, we found increased cortical network activity for the salience network and a local pontine network, as well as decreased network activity in the anterior and posterior default mode network for higher pain intensities. Higher pain intensities in chronic migraine were accompanied with lower activity in a prefrontal cortical network.

By taking the perspective of the individual, we focused on the processes that matter for each patient, which are phases of relatively low pain and more straining phases of relatively high pain. The present design of ongoing assessment of the endogenous pain can be a powerful and promising tool to assess the signature of a patient’s endogenous pain encoding over weeks and months.
The influence of adaptation to life at high-altitude on condition dependent sexual shape and size dimorphism in Drosophila melanogaster
Authors: Pesevski Maria , Dworkin Ian
Published: July 2021

Sexual dimorphism is common despite factors such as inter-sex genetic correlations and sex-specific patterns of selection that might limit its evolution. Sexual dimorphism can be phenotypically plastic and condition dependent, that themselves may be targets of selection. However, it remains unclear how sexual dimorphism, its plasticity and condition dependence evolves, in particular during rapid adaptation to a new environment. Furthermore, the interplay between SSD and other forms of dimorphism, such as shape dimorphism co-evolves. Using Sub-Saharan populations of Drosophila melanogaster that vary for size and shape as a result of adaptation to high altitude environments, we examined sex specific patterns of developmental plasticity. We raised strains of Drosophila from low (Zambia) and high (Ethiopia) altitude populations varying for food quality or rearing temperature. We observed expected differences in wing size and shape due to population, sex and plasticity. While larval mass showed substantial evolved changes for sex specific condition dependence, effects on wing size and shape were modest. We examined shape-size allometric effects between groups. Allometric effects were generally similar across sexes, but differed substantially due to population of origin and plasticity. We discuss findings within the context of the evolution of plasticity for SSD, condition dependence and allometric relationships.
Acquisition of cancer stem cell properties during EMT requires cell division
Authors: den Hollander Petra , Vasaikar Suhas , Castaneda Maria , Joseph Robiya , Deshmukh Abhijeet P. , Zhou Tieling , Pietila Mika , Fu Chunxiao , Symmans William F. , Soundararajan Rama , Mani Sendurai A.
Published: July 2021

Cancer cells acquire stem cell and mesenchymal properties during epithelial-to-mesenchymal transition (EMT), facilitating metastasis and chemoresistance [1-6]. In this study, we find that mammary epithelial cells quickly develop mesenchymal phenotype in response to EMT-inducing signals; however, acquiring stemness takes several days and always requires a preceding mesenchymal program. In addition, we observe that carcinoma cells, over a period of time, switch their cell division from symmetrical differentiated type to symmetrical self-renewal type. Importantly, epithelial cells can gain mesenchymal properties without undergoing cell division, but cell disivion is vital for these cells to gain stem cell properties during EMT. The EMT-induced stemness signature (SC-sig) is capable of predicting progression-free and overall-survival of breast cancer patients but not the EMT-induced mesenchymal signature (M-sig). Collectively, our findings demonstrate that the use of mesenchymal markers alone is insufficient to identify tumors with metastatic and chemoresistance potential and emphasize that the markers of EMT-induced stem cell program are central for clinical prediction. Most importantly, our data, for the first time, demonstrate that acquisition of stem cell properties during EMT depends on cell division but not the mesenchymal program.
Conversion of mammalian cell culture media waste to microbial fermentation feed efficiently supports production of recombinant protein by Escherichia coli
Authors: Lynch Ciara D , O’Connell David J
Published: July 2021

Deriving new value from waste streams through secondary processes is a central aim of the circular bioeconomy. In this study we investigate whether chemically defined spent media (CDSM) waste from cell culture bioprocess can be recycled and used as a feed in secondary microbial fermentation to produce new recombinant protein products. Our results show that CDSM supplemented with 2% glycerol supported a specific growth rate of E. coli cultures equivalent to that achieved using a nutritionally rich microbiological media (LB). The titre of recombinant protein produced following induction in a 4-hour expression screen was approximately equivalent in the CDSM fed cultures to that of baseline, and this was maintained in a 16-hr preparative fermentation. To understand the protein production achieved in CDSM fed culture we performed a quantitative analysis of proteome changes in the E. coli using mass spectrometry. This analysis revealed significant upregulation of protein synthesis machinery enzymes and significant downregulation of carbohydrate metabolism enzymes. We conclude that spent cell culture media, which represents 100s of millions of litres of waste generated by the bioprocessing industry annually, may be valorized as a feed resource for the production of recombinant proteins in secondary microbial fermentations.
Bayesian inference of clonal expansions in a dated phylogeny
Authors: Helekal David , Ledda Alice , Volz Erik , Wyllie David , Didelot Xavier
Published: July 2021

Microbial population genetics models often assume that all lineages are constrained by the same population size dynamics over time. However, many neutral and selective events can invalidate this assumption, and can contribute to the clonal expansion of a specific lineage relative to the rest of the population. Such differential phylodynamic properties between lineages result in asymmetries and imbalances in phylogenetic trees that are sometimes described informally but which are difficult to analyse formally. To this end, we developed a model of how clonal expansions occur and affect the branching patterns of a phylogeny. We show how the parameters of this model can be inferred from a given dated phylogeny using Bayesian statistics, which allows us to assess the probability that one or more clonal expansion events occurred. For each putative clonal expansion event we estimate their date of emergence and subsequent phylodynamic trajectories, including their long-term evolutionary potential which is important to determine how much effort should be placed on specific control measures. We demonstrate the applicability of our methodology on simulated and real datasets.
Nanobodies restore stability to cancer-associated mutants of tumor suppressor protein p16INK4a
Authors: Burbidge Owen , Pastok Martyna W , Hodder Samantha L , Zenkeviciute Grasilda , Noble Martin EM , Endicott Jane A , Itzhaki Laura
Published: July 2021

We describe the generation and characterization of camelid single-domain antibodies (nanobodies) raised against tumor suppressor protein p16INK4a (p16). p16 plays a critical role in the cell cycle by inhibiting cyclin-dependent kinases CDK4 and CDK6, and it is inactivated in sporadic and familial cancers. The majority of the p16 missense mutations cause loss of function by destabilizing the protein structure. We show that the nanobodies bind p16 with nanomolar affinities and restore the stability of a range of different cancer-associated p16 mutations located at sites throughout the protein. The nanobodies also bind and stabilize p16 in a cellular setting. The crystal structure of a nanobody-p16 complex reveals that the nanobody binds to the opposite face of p16 to the CDK-binding interface permitting formation of a ternary complex. These findings indicate that nanobodies could be used as pharmacological chaperones to determine the consequences of restoring the function of p16 in the cell.
A Plasmodium falciparum lysophospholipase regulates fatty acid acquisition for membrane biogenesis to enable schizogonic asexual division
Authors: Sheokand Pradeep Kumar , Yamaryo-Botte Yoshiki , Thakur Vandana , Banday Mudassir M , Asad Mohd , Botte Cyrille Y , Mohmmed Asif
Published: July 2021

Phospholipid metabolism is crucial for membrane biogenesis and homeostasis during the intracellular life cycle of Plasmodium falciparum. To generate large amounts of phospholipids required during blood stages, the parasite massively scavenge, recycle and reassemble host lipids. P. falciparum possesses an unusual large number of lysophospholipases. However, their functional roles and importance remain to be elucidated. Here, we functionally characterized one of P. falciparum lysophospholipase (PfLPL3) (Gene ID PF3D7_1476800), to reveal its critical role in parasite propagation during asexual blood stages. We generated a transgenic parasite line using GFP-glmS C-terminal tagging approach, for localization as well as inducible knockdown of PfLPL3. PfLPL3 displayed a dynamic localization throughout asexual stages, mainly localizing in the host parasite interface: parasitophorous vacuole space and expanding into the tubulovesicular network within the host cell. Inducible knock-down of PfLPL3 hindered normal intraerythrocytic cycle, specifically causing disruption in parasite development from trophozoites to schizont, as well as reduction in number of merozoites progenies. Thus, down-regulation of PfLPL3 significantly inhibited parasite growth suggesting its critical role for proper parasite propagation during blood stages. Detailed lipidomic analyses showed that PfLPL3 generates fatty-acids for the synthesis of neutral lipids DAG and TAG, whilst controlling the timely synthesis of phospholipids that are crucial for membrane biogenesis required for merozoite development during asexual cycle. Setting up an in vitro activity based screening of Malaria Box allowed identification of specific inhibitors of PfLPL3 having potent parasitical efficacies. These compounds are pertinent both as anti-malarial drug candidates and chemical tools specifically targeting membrane biogenesis during asexual blood stages.
The versatile regulation of K2P channels by polyanionic lipids of the phosphoinositide (PIP2) and fatty acid metabolism (LC-CoA)
Authors: Riel Elena B. , Jürs Björn C. , Cordeiro Sönke , Musinszki Marianne , Schewe Marcus , Baukrowitz Thomas
Published: July 2021

Work of the past three decades provided tremendous insight into the regulation of K+ channels - in particular Kir channels - by polyanionic lipids of the phosphoinositide (e.g. PIP2) and fatty acid metabolism (e.g. oleoyl-CoA). However, comparatively little is known regarding the phosphoinositide regulation in the K2P channel family and the effects of long-chain fatty acid CoA esters (LC-CoA, e.g. oleoyl-CoA) are so far unexplored. By screening most mammalian K2P channels (12 in total), we report strong effects of polyanionic lipids (activation and inhibition) for all tested K2P channels. In most cases the effects of PIP2 and oleoyl-CoA were similar causing either activation or inhibition depending on the respective subgroup. Activation was observed for members of the TREK, TALK and THIK subfamily with the strongest activation by PIP2 seen for TRAAK (~110-fold) and by oleoyl-CoA for TALK-2 (~90-fold). In contrast, inhibition was observed for members of the TASK and TRESK subfamilies up to ~85 %. In TASK-2 channels our results indicated an activatory as well as an inhibitory PIP2 site with different affinities. Finally, we provided evidence that PIP2 inhibition in TASK-1 and TASK-3 channels is mediated by closure of the recently identified lower X-gate as critical mutations within the gate (i.e. L244A, R245A) prevent PIP2 induced inhibition. Our results disclosed K2P channels as a family of ion channels highly sensitive to polyanionic lipids (PIP2 and LC-CoA), extended our knowledge on the mechanisms of lipid regulation and implicate the metabolisms of these lipids as possible effector pathways to regulate K2P channel activity.
The method of choice to knock-in large inserts via CRISPR
Authors: Marks David , Bachmann Lisa , Villarejo Lucia Gallego , Geidies Alexander , Heinen Natalie , Anstatt Jannis , Müller Thorsten
Published: July 2021

CRISPR/Cas9 gene editing is a revolutionary method used to study gene function by transcript silencing, knock-out, or activation. The knock-in of DNA fragments to endogenous genes of interest is another promising approach to study molecular pathways but is technically challenging. Many approaches have been suggested, but the proof of correct integration has often been relied on less convenient validation experiments. Within this work, we investigated homology-directed repair (HDR), non-homologous end joining (NHEJ), and PCRextension (PCRext) based approaches as three different methods to knock-in large DNA fragments (>1000 bp), and compared feasibility, cost effectiveness, and reliability. As a knock-in fragment, we used a fluorescent reporter sequence in order to directly assess successful integration by microscopy, subsequently proven by sequencing. For NHEJ and PCRext, we demonstrate that it is insufficient to rely on the fluorescent reporter due to false positive results. Both NHEJ and PCRext failed to reliably knock-in large DNA sequences, they were accompanied by massive generation of InDels driving the methodology cost-intensive and non-reliable. In contrast, combination of CRISPR/Cas9 and HDR revealed correct integration, proven by correct fluorescence of the subcellular localization and sequencing, and thus, corresponds to the method of choice for large fragment integration. Next to HEK293T, we demonstrate successful HDR based knock-in in human induced pluripotent stem cells (hiPSCs). Subsequent differentiation of gene-edited hiPSCs into cerebral organoids showed relevance of the approach to study subcellular protein localization and abundance in 3D tissue.
Thiol-based mucolytics exhibit antiviral activity against SARS-CoV-2 through allosteric disulfide disruption in the spike glycoprotein
Authors: Shi Yunlong , Zeida Ari , Edwards Caitlin E. , Mallory Michael L. , Sastre Santiago , Machado Matías R. , Pickles Raymond J. , Fu Ling , Liu Keke , Yang Jing , Baric Ralph S. , Boucher Richard C. , Radi Rafael , Carroll Kate S.
Published: July 2021

Small molecule therapeutics targeting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have lagged far behind the development of vaccines in the fight to control the COVID-19 pandemic. Here, we show that thiol-based mucolytic agents, P2119 and P2165, potently inhibit infection by human coronaviruses, including SARS-CoV-2, and decrease the binding of spike glycoprotein to its receptor, angiotensin-converting enzyme 2 (ACE2). Proteomics and reactive cysteine profiling link the antiviral activity of repurposed mucolytic agents to the reduction of key disulfides, specifically, by disruption of the Cys379–Cys432 and Cys391–Cys525 pairs distal to the receptor binding motif (RBM) in the receptor binding domain (RBD) of the spike glycoprotein. Computational analyses provide insight into conformation changes that occur when these disulfides break or form, consistent with an allosteric role, and indicate that P2119/P2165 target a conserved hydrophobic binding pocket in the RBD with the benzyl thiol warhead pointed directly towards Cys432. These collective findings establish the vulnerability of human coronaviruses to repurposed thiol-based mucolytics and lay the groundwork for developing these compounds as a potential treatment, preventative and/or adjuvant against infection.