bluuebunny/crossref_metadata_2025 huggingface dataset:
Neuroblastoma in Adults: A Scoping Review of Presentations, Genetics and Therapies
Authors: Alsaikhan Bader H. , Alwahhabi Basmah , Alshalan Abdullah , Koziarz Alex , Alkhayal Abdullah M. , Alrabeeah Khalid
Published: May 2024

Purpose

As a scoping review, evaluate the literature on the presentations, genetics, and therapies for neuroblastoma in adult patients.

Methods

We searched four databases for studies reporting adults with neuroblastoma. Cohort studies, case series, and case reports were synthesized qualitatively. Progression-free and overall survival were compared amongst cohort studies.

Results

Of 2287 unique records, 136 studies published in 141 articles were included. A total of 679 patients were included. On review of individual patient-level data, the adrenal gland and retroperitoneum were the most common primary site (47.3%).MYCNwas rarely amplified: seven studies reported zero patients with MYCN amplified, two studies with a single patient, and one study with 3/7 patients. Adult patients appear to show a high frequency of somatic mutations, specificallyALK(42%) andATRX(58%). Registry data of included studies showed 5- year overall survival to be 36.3% in adults aged ≥20 years.

Conclusion

Of nearly 700 cases of adult neuroblastoma published in the literature, the most common primary site is the adrenals or retroperitoneum. Relative to pediatric cases, adult cases demonstrate a considerable rate of somatic mutations such asALKandATRX. Registry data showed 5-year survival of 36%. Future studies evaluating targeted therapies in larger samples are needed.

Take home messages

679 cases of adult neuroblastoma have been published in the literature.

Compared to pediatrics, adult cases have more somatic mutations (eg: ALK, ATRX).

Registry data showed that adult neuroblastoma has a 5-year survival of 36%.
Prevalence, Concordance, and Related Factors of Four Cardiovascular Risk Calculators in the Peruvian Population: Analysis of a National Survey
Authors: Vera-Ponce Víctor Juan , Zuzunaga-Montoya Fiorella E. , Milagros Vásquez-Romero Luisa Erika , Loayza-Castro Joan A. , Vigil-Ventura Enrique , De Carrillo Carmen Inés Gutierrez
Published: May 2024

Introduction

Cardiovascular risk calculators (CVR) are essential for effectively preventing and managing cardiovascular diseases.

Objective

To determine the prevalence, the concordance among different CVR calculators, and the factors associated with these in the Peruvian population.

Methods

Analysis of data collected by the Food and Nutritional Surveillance Survey by Life Stages. The CVR calculators used were the AHA/ASCVD, World Health Organization (WHO) laboratory-based and non-laboratory-based, and Framingham. The percentage of risk for each individual in the study was calculated, categorizing the CVR of each calculator into low (<10%) vs moderate/high (≥10%). Concordance was analyzed through the kappa index.

Results

The level of moderate/high CVR risk according to the type of calculator used was 5.44%, 4.73%, 6.62%, and 23.88% for WHO laboratory-based, non-laboratory-based, AHA/ASCVD, and Framingham, respectively. Common related factors identified were male gender, age between 50–59 years, current smoker, hypertension, and diabetes. WHO laboratory-based and AHA/ASCVD showed higher concordance (kappa of 0.7289). In contrast, concordance between WHO laboratory-based and Framingham and between WHO non-laboratory-based and Framingham was relatively lower (kappa of 0.3098 and 0.2732, respectively).

Conclusions

There are discrepancies in CVR levels according to the different calculators evaluated, especially with Framingham, and common associated factors were identified. These variations suggest that prediction tools might not be universally applicable in their current form, making it essential to consider calibrating existing risk calculators or developing new tools that more accurately reflect the epidemiological and health profiles of the Peruvian population.
Universal Health Coverage – Exploring the What, How, and Why Using Realistic Review
Authors: Endalamaw Aklilu , Mengistu Tesfaye Setegn , Khatri Resham B. , Wolka Eskinder , Erku Daniel , Zewdie Anteneh , Assefa Yibeltal
Published: May 2024

Background

Universal health coverage (UHC) is a critical target in many health system strategies to achieve the ‘good health and wellbeing’. Evidence on the meaning and scope of UHC and the strategies required to achieve it are needed, as variations in its understanding and implementation have risen. We synthesised evidence on the meaning, components, significance, and strategies of UHC.

Methods

A review of evidence was conducted based on realist synthesis. We searched PubMed, EMBASE, Scopus, and Web of Science for published materials and websites for grey literature. We have followed some steps: define the scope of the review and develop initial programme theory, search for evidence, data extraction, and synthesis of evidence.

Results

Universal coverage, universal health, universal healthcare, universal access, and insurance coverage are used interchangeably with UHC. It is a legal notion that embodies a human rights-based and collaborative approach to ensure fair and comprehensive health care services. Universal health coverage is relevant for three macro reasons: first, it prevents and reduces the impact of diseases; second, it addresses inequality and promotes equity; and third, it is key for global health security. Various mechanisms involved to implement UHC, such as health insurance, social health protection, digital financing systems, value-based care, private sectors, civil societies, partnership, primary health care, and reciprocal health care systems.

Conclusions

Universal health coverage is a multifaceted concept that can be expressed by various terms in different contexts. Universal health coverage is a political and ethical imperative that aims to promote health equity and protect human dignity across different levels of society. It is essential in preventing diseases and serving a crucial role in global health security. Practically, UHC is not truly universal, as it does not include all services under its scheme and varies across countries. This requires consistent advocacy, strategic and operational research as well as political will to ensure UHC.
Red flags to screen for tumors in patients with neck pain: a scoping review protocol
Authors: Occhetto Beatrice , Ballesio Martina , Mourad Firas , Trucco Marco , Maselli Filippo , Chiarotto Alessandro , Feller Daniel
Published: May 2024

Background

People with malignant (primary or metastatic) or benign tumors may present in clinical practice with neck pain, with or without other symptoms (e.g., radicular pain or headache). When not presenting as an emergency, neck pain is most often assessed by primary care clinicians such as general practitioners, physiotherapists, chiropractors or osteopaths. Therefore, primary care clinicians must be able to screen for tumors when evaluating patients with neck pain.

Despite clinical practice guidelines providing recommendations to triage serious conditions presenting as neck pain, there is a paucity of overviews on red flags for tumors in patients presenting with neck pain in primary care settings. The present scoping review aims to comprehensively map the existing literature on red flags for tumors in patients presenting with neck pain in primary care settings. Furthermore, we will aim to identify gaps in the literature to direct future research in this area.

Methods

We will search MEDLINE (via PubMed), Embase, CINHAL, and Scopus. In addition, we will use Web of Science to implement backward and forward citation tracking strategies. We will consider any primary study design written in English or Italian. No time or geographical restrictions will be applied to the search. Studies with a focus on the diagnostic pathway, considering patients of any age and gender with a diagnosis of tumor and a primary complaint of neck pain will be eligible for inclusion. Only studies conducted in primary care settings will be considered. Two authors will independently perform the study selection and data extraction phases. Results from the scoping review will be summarized descriptively through tables and diagrams. As a scoping review, we will highlight any gaps in the existing literature regarding our research questions.
Reporting standards for outbreak data: A systematic review
Authors: Grégoire Vanessa , Zhu Alex W , Haines Clint A. , Rivers Caitlin M
Published: May 2024

The current landscape of data reporting for outbreaks is ad hoc and inconsistent. Public health authorities have discretion to determine when, where, how, and what outbreak data to report. This uneven information flow hampers response efforts by decreasing the accountability and transparency needed to build public trust in the public health response. We performed a systematic literature review using the PubMed, EMBASE, MedLine Plus, and Google Scholar databases to identify existing guidelines that address timing, methodology and content of outbreak reporting. Our search strategy produced 46 manuscripts for initial screening to determine eligibility, after which we performed a full-text review of those selected for comprehensive evaluation. We identified four manuscripts that discuss minimum standards and expectations for outbreak reports. Included manuscripts highlight the absence of and the consequent need for minimum standards for what information should be reported to the public during outbreaks. Together, they suggest that the ideal outbreak report should contain information on disease severity, epidemic size and geographic extent, daily and total case count, demographics, transmissibility, signs and symptoms, probable disease transmission and exposure pathways, countermeasure status, and sources of uncertainty. This systematic review of existing guidelines is part of a larger effort to develop consensus guidelines for the public reporting of outbreak data.
COVID-19 vaccination atlas: an integrative systems vaccinology approach
Authors: Prates-Syed Wasim Aluísio , da Fonseca Dennyson Leandro Mathias , Pour Shahab Zaki , Schimke Lena F , Lira Aline , Cortes Nelson , Silva Jaqueline Dinis Queiroz , Carvalho Evelyn , Filgueiras Igor Salerno , Vinces Tania Geraldine Churascari , Chaves Lorena C. S. , Wunderlich Gerhard , Durães-Carvalho Ricardo , Câmara Niels O. S. , Dias Haroldo Dutra , Ochs Hans D. , Krieger José E. , Nakaya Helder I , Cabral-Marques Otávio , Cabral-Miranda Gustavo
Published: May 2024

The COVID-19 vaccinations have played a significant role in controlling the pandemic. To elucidate their impact on the immune system, a COVID-19 vaccination atlas was developed through an integrative systems vaccinology approach. The atlas includes both healthy individuals and those infected with or without prior vaccination, and covers the administration of five vaccines in different regimens: Covilo®, Zifivax®, Vaxzebria® or Covishield®, Spikevax®, and Comirnaty®. Critical markers were identified to discriminate the different types of vaccines and infection, in which infection was associated with GATA3, ZNF3, KMT2A, ASXL1, SP100, and GZMM, and vaccine types were marked by ITGAM, ACTG1, LGALS3, and STAT5B. Additionally, the immunological signatures of heterologous vaccination and infection were described, and it was also shown how a full vaccination regimen markedly limited the shift of immune responses during natural infection, thereby constraining disease progression. Finally, the common transcripts shared across COVID-19 vaccines and vaccines against other pathogens were described.
XplainScar: Explainable Artificial Intelligence to Identify and Localize Left Ventricular Scar in Hypertrophic Cardiomyopathy from 12-lead Electrocardiogram
Authors: Nezamabadi Kasra , Sivalokanathan Sanjay , Lee Ji Won , Tanriverdi Talha , Chen Meiling , Lu Daiyin , Abraham Jadyn , Sardaripour Neda , Li Pengyuan , Mousavi Parvin , Abraham M. Roselle
Published: May 2024

Left ventricular (LV) scar is a risk factor for sudden cardiac death and heart failure in hypertrophic cardiomyopathy (HCM). LV scar is frequent in HCM and evolves over time. Hence there is a need for LV scar detection and longitudinal monitoring. The current gold standard for LV scar detection is late gadolinium enhancement (LGE) on magnetic resonance imaging (MRI), which is limited by high cost and susceptibility to artifacts from implanted defibrillators. We introduceXplainScar, the first explainable machine learning method for LV scar detection and localization in HCM, using 12-lead electrocardiogram (ECG) data, which is not influenced by implanted devices. We use 500 patients from the JH-HCM Registry for model development, and 248 patients from the UCSF-HCM-Registry for validation.XplainScarcombines unsupervised and self-supervised ECG representation learning, resulting in high precision (90%), sensitivity (95%), specificity (80%) and F1-score (90%) for scar detection in the basal, mid, and apical LV myocardium, with a processing time of <1 minute per 10 patients. Basal LV scar prediction byXplainScaris dominated by QRS features, and mid/apical LV scar by T wave features.XplainScargeneralizes well to the held-out test UCSF data, with 88% precision, 90% sensitivity, 78% specificity, and F1-score of 89%. In summary,XplainScardemonstrates good performance for LV scar detection, and provides ECG signatures of basal, mid, and apical LV scar in HCM.

XplainScaris publicly available athttps://github.com/KasraNezamabadi/XplainScar
Approximation of bone mineral density and subcutaneous adiposity using T1-weighted images of the human head
Authors: Kalc Polona , Hoffstaedter Felix , Luders Eileen , Gaser Christian , Dahnke Robert
Published: May 2024

Bones and brain are intricately connected and scientific interest in their interaction is growing. This has become particularly evident in the framework of clinical applications for various medical conditions, such as obesity and osteoporosis. The adverse effects of obesity on brain health have long been recognised, but few brain imaging studies provide sophisticated body composition measures. Here we propose to extract the following bone- and adiposity-related measures from T1-weighted MR images of the head: an approximation of skull bone mineral density (BMD), skull bone thickness, and two approximations of subcutaneous fat (i.e., the intensity and thickness of soft non-brain head tissue). The measures pertaining to skull BMD, skull bone thickness, and intensi-ty-based adiposity proxy proved to be reliable (r=.93/.83/.74,p<.001) and valid, with high correlations to DXA-de-rived head BMD values (rho=.70,p<.001) and MRI-derived abdominal subcutaneous adipose volume (rho=.62,p<.001). Thickness-based adiposity proxy had only a low retest reliability (r=.58,p<.001).The outcomes of this study constitute an important step towards extracting relevant non-brain features from available brain scans.
Associating EEG Functional Networks and the Effect of Sleep Deprivation as Measured Using Psychomotor Vigilance Tests
Authors: Mason Sophie L. , Junges Leandro , Woldman Wessel , Ftouni Suzanne , Anderson Clare , Terry John R. , Bagshaw Andrew P.
Published: May 2024

People are routinely forced to undertake cognitive challenges under the effect of sleep deprivation, due to professional and social obligations forcing them to ignore their circadian clock. However, low intra-individual and high inter-individual differences in behavioural outcomes are known to occur when people are sleep deprived, leading to the conclusion that trait-like differences to sleep deprivation could explain the differing levels of resilience. Within this study we consider if trait-like resilience to sleep deprivation, measured using psychomotor vigilance tests over a 40h constant routine protocol, could be associated with graph metrics (mean node strength, clustering coefficient, characteristic path length and stability) calculated from EEG functional networks acquired when participants are well rested (baseline). Furthermore, we investigated how stability (the consistency of a participant’s functional network over time measured using 2-D correlation) changed over the constant routine. We showed evidence of strong significant correlations between high mean node strength, low characteristic path length and high stability at baseline with a general resilience to extended sleep deprivation, although the same features lead to vulnerability during the period of natural sleep onset, highlighting non-uniform correlations over time. We also show significant differences in the levels of stability between resilient and vulnerable groups.
An event-driven neural network for monitoring of epileptic seizures on low-power neuromorphic hardware
Authors: Bartels Jim , Gallou Olympia , Ito Hiroyuki , Cook Matthew , Sarnthein Johannes , Indiveri Giacomo , Ghosh Saptarshi
Published: May 2024

Long-term monitoring of biomedical signals is essential for the modern clinical management of neurological conditions such as epilepsy. However, developing wearable systems, able to monitor, analyze, and detect epileptic seizures with long-lasting operation times, using current technologies is still an open challenge. Brain-inspired spiking neural networks (SNNs) represent a promising signal processing and computing framework as they can be deployed on ultra-low power neuromorphic computing systems, for this purpose. Here, we introduce a foundational SNN architecture, co-designed and validated on a mixed-signal neuromorphic chip, for always-on monitoring of epileptic activity. We demonstrate how the hardware implementation of this SNN captures the phenomenon of partial synchronization within neural activity during seizure periods. We benchmark the network using a full-custom asynchronous mixed-signal neuromorphic platform, processing analog signals in real-time from an Electroencephalographic (EEG) seizure dataset. The neuromorphic chip comprises an analog front-end (AFE) signal conditioning stage and an asynchronous delta modulation (ADM) circuit directly integrated on the same die, which can produce the stream of spikes as input to the SNN, directly from the EEG electrodes. A linear classifier in a post processing stage is sufficient to reliably classify and detect seizures, from the local features extracted by the SNN. This research marks a significant advancement toward developing embedded intelligent “wear and forget” units for resource-constrained environments. These units could autonomously detect and log relevant EEG events of interest in out-of-hospital environments, offering new possibilities for patient care and management of neurological disorders.
A single-cell eQTL atlas of the human cerebellum reveals vulnerability of oligodendrocytes in essential tremor
Authors: Castonguay Charles-Etienne , Aboasali Farah , Medeiros Miranda , Becret Théodore , Schmilovich Zoe , Khayachi Anouar , Rajput Alex , Dion Patrick A. , Rouleau Guy A
Published: May 2024

Essential tremor (ET) is a movement disorder characterized by an upper-limb postural and action tremor. It is one of the most common neurological disorders, affecting 1% of the worldwide population. Despite strong evidence for genetic factors driving the aetiology of ET, the underlying pathophysiology remains poorly understood. To understand the effects of genetic risk factors in ET on the cerebellum, the brain region thought to be affected by the disease, we built a population-scale single-cell atlas of the human cerebellar cortex comprised of over 1 million cells from 109 individuals. Using single-cell expression quantitative trait loci and mendelian randomization, we found evidence of ET-associated variants in theBACE2locus causally linked to its downregulation in cerebellar oligodendrocytes. We highlight a genetically vulnerable population ofBACE2-expressing immature oligodendrocytes, suggestive of demyelination. We also find dysfunctional processes affecting interactions between Golgi cells, Purkinje layer interneurons, and oligodendrocytes in ET. Our study suggests a crucial role for cerebellar oligodendrocytes in the pathogenesis of ET.
Exploring the dynamics and interactions of the N-myc transactivation domain through solution NMR
Authors: Rejnowicz Ewa , Batchelor Matthew , Leen Eoin , Ahangar Mohd Syed , Richards Mark W. , Kalverda Arnout P. , Bayliss Richard
Published: May 2024

The myc family of proteins (c-, N- and L-myc) are transcription factors (TFs) responsible for maintaining the proliferative program in cells. They consist of a C-terminal domain that mediates heterodimerisation with Max and DNA binding, and an N-terminal disordered region culminating in the transactivation domain (TAD). The TAD participates in many protein–protein interactions, notably with kinases that promote stability (Aurora-A) or degradation (ERK1, GSK3) via the ubiquitin-proteasome system. Structural characterization of the TAD of N-myc, is very limited, with the exception of a crystal structure of Aurora-A bound to a helical region of N-myc. We probed the structure, dynamics and interactions of N-myc TAD using nuclear magnetic resonance (NMR) spectroscopy following its complete backbone assignment enabled by a truncation approach. Chemical shift analysis revealed that N-myc has two regions with clear helical propensity: one region within Trp77–Glu86 and the second between Ala122–Glu132. These regions also have more restricted ps–ns motions than the rest of the TAD, and, along with another known interaction site (myc box I), have comparatively high transverse (R2)15N relaxation rates, indicative of slower timescale dynamics and/or chemical exchange. Collectively these features suggest differential propensities for structure and interaction, either internal or with binding partners, across the TAD. Solution studies on the interaction between N-myc and Aurora-A revealed a previously uncharacterised binding site. The specificity and kinetics of sequential phosphorylation of N-myc by ERK1 and GSK3 were characterised using NMR and showed no significant structural changes through the rest of the TAD. When doubly phosphorylated on residues Ser62 and Thr58, N-myc formed a robust interaction with the Fbxw7–Skp1 complex. Our study provides foundational insights into N-myc TAD dynamics and a backbone assignment that will underpin future work on the structure, dynamics, interactions and regulatory post-translational modifications of this key oncoprotein.
The impact of various microplastics on bacterial community and antimicrobial resistance genes in Norwegian and South African wastewater
Authors: Tran Tam Thanh , Stenger Kabelo Stephans , Strømmen Marte , Bezuidenhout Cornelius Carlos , Wikmark Odd-Gunnar
Published: May 2024

Wastewater treatment plants (WWTPs) may serve as hotspots for pathogens and promote antimicrobial resistance (AMR). Plastic debris in wastewater could further contribute to AMR dissemination. The aim of this study is to investigate the impact of various microplastic types on bacterial communities and AMR gene abundance in Norwegian and South African wastewater. Microcosm experiments were designed as follows: Five manufactured microplastic pellet types were used for testing and two rock aggregate types were used as controls. In addition, each material type was subjected to artificial aging treatments using either ultra-violet light or hydrogen peroxide. Each material was incubated in flasks containing inlet/outlet wastewater obtained from Norwegian/South African WWTPs. Nucleic acids were extracted after a one-week incubation period. The detection of theblaFOXand blaMOXgenes was performed using quantitative PCR. Extracted DNA was sequenced using a MinION device. Non-metric multi-dimensional scaling plot on full-length 16S sequencing data at the species level showed samples were clustered into distinct material groups. These results were in line with the ANOSIM test showing significant p-values in both Norwegian and South African WWTP settings. Indicator species analysis showed a strong association between many Acinetobacter species with the plastic group than the rock group. Aging treatment using hydrogen peroxide showed some effects on microbial. The abundance ofblaFOXandblaMOXgenes in the Norwegian wastewater outlet were generally lower compared to those in the inlet, though results were contrary in South African wastewater samples. The relative abundance of AMR genes seemed to be increased on several plastic types (PET, PE, PLA) but decreased on PVC-A. WWTP treatments in this study did not effectively reduce the abundance of AMR genes. In addition, plastic categories were shown to play a pivotal role in developing distinct bacterial communities and AMR profiles.
TelAP2 links TelAP1 to the telomere complex inTrypanosoma brucei
Authors: Weisert Nadine , Majewski Verena , Hartleb Laura , Luko Katarina , Lototska Liudmyla , Krapoth Nils Christian , Ulrich Helle D. , Janzen Christian J. , Butter Falk
Published: May 2024

The extracellular parasiteTrypanosoma bruceievades the immune system of the mammalian host by periodically exchanging its variant surface glycoprotein (VSG) coat. Hereby, only one VSG gene is transcribed from one of 15 subtelomeric so-called bloodstream form expression sites (BES) at any given timepoint, while all other BESs are silenced. VSG gene expression is altered by homologous recombination using a large VSG gene repertoire or by a so-calledin situswitch, which activates a previously silent BES. Transcriptional activation, VSG switching and VSG silencing during developmental differentiation from the bloodstream form to the procyclic form present in the tsetse fly vector are tightly regulated. Due to their subtelomeric position, telomere-associated proteins are involved in the regulation of VSG expression. Three functional homologs of mammalian telomere complex proteins have been characterized thus far, and novel telomere-interacting proteins, such as telomere-associated protein 1 (TelAP1), have recently been identified. Here, we used mass spectrometry-based proteomics and interactomics approaches, telomere pull-down assays with recombinant material and immunofluorescence analysis to elucidate the interactions of 21 other putative TelAPs. We investigated the influence on VSG expression and showed that depletion of TelAPs does not ultimately lead to changes in VSG expression. Additionally, we examined the interaction patterns of four TelAPs with theTbTRF/TbTIF2/TbRAP1 telomere complex by reciprocal affinity purification. We further propose that TelAP1 interacts with Tb927.6.4330, now called TelAP2, and that TelAP1 depends on this interaction to form a complex with the telomeric proteinsTbTRF,TbTIF2 andTbRAP1.
Neuron-level Prediction and Noise can Implement Flexible Reward-Seeking Behavior
Authors: Li Chenguang , Brenner Jonah , Boesky Adam , Ramanathan Sharad , Kreiman Gabriel
Published: May 2024

We show that neural networks can implement reward-seeking behavior using only local predictive updates and internal noise. These networks are capable of autonomous interaction with an environment and can switch between explore and exploit behavior, which we show is governed by attractor dynamics. Networks can adapt to changes in their architectures, environments, or motor interfaces without any external control signals. When networks have a choice between different tasks, they can form preferences that depend on patterns of noise and initialization, and we show that these preferences can be biased by network architectures or by changing learning rates. Our algorithm presents a flexible, biologically plausible way of interacting with environments without requiring an explicit environmental reward function, allowing for behavior that is both highly adaptable and autonomous. Code is available athttps://github.com/ccli3896/PaN.
Plasticity of sex-biased aggression in response to the sex of territory intruders in an African cichlid fish, Julidochromis marlieri
Authors: Dennis Ry , Wood Kelsey J , Renn Suzy C.P. , Anderson Andrew P
Published: May 2024

Behavior is often linked to gonadal sex; however, ecological or social environments can induce plasticity in sex-biased behaviors. In biparental species, pairs may divide offspring care into two parental roles, in which one parent specializes in territory defense and the other in nest care. The African cichlid fish Julidochromis marlieri displays plasticity in sex-biased behaviors. In Lake Tanganyika, J. marlieri form female-larger pairs in which the female is more aggressive than the male who performs more nest care, but under laboratory conditions, male-larger pairs can be formed in which these sex-biased behaviors are reversed. We investigated the influence of social environment on behavior by observing how individuals in both pair-types respond to conspecific intruders of either sex. We examined behavioral responses to three factors: sex of the subject, relative size of the subject, and the sex of the intruder. We confirm that relative size is a factor in behavior. The larger fish in the pair is more aggressive than the smaller fish is towards an intruder. While neither fish in the female-larger pairs varied their behaviors in response to the sex of the intruder, both members of the male-larger pairs were sensitive to intruder sex. Both individuals in the male-larger pairs engaged in more biting behaviors towards the intruder. Intruder biting behaviors strongly correlated with the biting behavior of the larger individual in the pair and occurred more frequently when encountering pairs with same sex as the larger fish when compared to pairs with the same sex as the smaller fish. Our results support the role of the social environment as a contributor in the expression of sex-biased behavior.
Robustly encoding certainty in a metastable neural circuit model
Authors: Cihak Heather L , Kilpatrick Zachary P
Published: May 2024

Localized persistent neural activity has been shown to serve delayed estimation of continuous variables. Common experiments require that subjects store and report the feature value (e.g., orientation) of a particular cue (e.g., oriented bar on a screen) after a delay. Visualizing recorded activity of neurons according to their feature tuning reveals activitybumpswhose centers wander stochastically, degrading the estimate over time. Bump position therefore represents the remembered estimate. Recent work suggests that bump amplitude may represent estimate certainty reflecting a probabilistic population code for a Bayesian posterior. Idealized models of this type are fragile due to the fine tuning common to constructed continuum attractors in dynamical systems. Here we propose an alternative metastable model for robustly supporting multiple bump amplitudes by extending neural circuit models to includequantizednonlinearities. Asymptotic projections of circuit activity produce low-dimensional evolution equations for the amplitude and position of bump solutions in response to external stimuli and noise perturbations. Analysis of reduced equations accurately characterizes phase variance and the dynamics of amplitude transitions between stable discrete values. More salient cues generate bumps of higher amplitude which wander less, consistent with the experimental finding that greater certainty correlates with more accurate memories.
Cyclic di-GMP as an Antitoxin Regulates Bacterial Genome Stability and Antibiotic Persistence in Biofilms
Authors: Liao Hebin , Yan Xiaodan , Wang Chenyi , Huang Chun , Zhang Wei , Xiao Leyi , Jiang Jun , Bao Yongjia , Huang Tao , Zhang Hanbo , Guo Chunming , Zhang Yufeng , Pu Yingying
Published: May 2024

Biofilms are complex bacterial communities characterized by a high persister prevalence, which contributes to chronic and relapsing infections. Historically, persister formation in biofilms has been linked to constraints imposed by their dense structures. However, we observed an elevated persister frequency accompanying the stage of cell adhesion, marking the onset of biofilm development. Subsequent mechanistic studies uncovered a comparable type of toxin-antitoxin (TA) module (TA-like system) triggered by cell adhesion, which is responsible for this elevation. In this module, the toxin HipH acts as a genotoxic deoxyribonuclease, inducing DNA double strand breaks and genome instability. While the second messenger c-di-GMP functions as the antitoxin, exerting control over HipH expression and activity. The dynamic interplay between c-di-GMP and HipH levels emerges as a crucial determinant governing genome stability and persister generation within biofilms. These findings unveil a unique TA system, where small molecules act as the antitoxin, outlining a biofilm-specific molecular mechanism influencing genome stability and antibiotic persistence, with potential implications for treating biofilm infections.
Metabolic engineering of yeast forde novoproduction of kratom monoterpene indole alkaloids
Authors: Holtz Maxence , Rago Daniela , Nedermark Ida , Hansson Frederik G. , Lehka Beata J. , Hansen Lea G. , Marcussen Nils E. J. , Veneman Wouter J. , Ahonen Linda , Wungsintaweekul Juraithip , Dirks Ron P. , Acevedo-Rocha Carlos G. , Zhang Jie , Keasling Jay D. , Jensen Michael K.
Published: May 2024

Monoterpene indole alkaloids (MIAs) fromMitragyna speciosa(“kratom”), such as mitragynine and speciogynine, are promising novel scaffolds for opioid receptor ligands for treatment of pain, addiction, and depression. While kratom leaves have been used for centuries in South-East Asia as stimulant and pain management substance, the biosynthetic pathway of these psychoactives have only recently been partially elucidated. Here, we demonstrate thede novoproduction of mitragynine and speciogynine inSaccharomyces cerevisiaethrough the reconstruction of a five-step synthetic pathway from common MIA precursor strictosidine comprising fungal tryptamine 4-monooxygenase to bypass an unknown kratom hydroxylase. Upon optimizing cultivation conditions, a titer of ∼290 µg/L kratom MIAs from glucose was achieved. Untargeted metabolomics analysis of lead production strains led to the identification of numerous shunt products derived from the activity of strictosidine synthase (STR) and dihydrocorynantheine synthase (DCS), highlighting them as candidates for enzyme engineering to further improve kratom MIAs production in yeast. Finally, by feeding fluorinated tryptamine and expressing a human tailoring enzyme, we further demonstrate production of fluorinated and hydroxylated mitragynine derivatives with potential applications in drug discovery campaigns. Altogether, this study introduces a yeast cell factory platform for the biomanufacturing of complex natural and new-to-nature kratom MIAs derivatives with therapeutic potential.
Tango-seq: overlaying transcriptomics on connectomics to identify neurons downstream ofDrosophilaclock neurons
Authors: Ehrlich Alison , Xu Angelina A. , Luminari Sofia , Kidd Simon , Treiber Christoph D. , Russo Jordan , Blau Justin
Published: May 2024

Knowing how neural circuits change with neuronal plasticity and differ between individuals is important to fully understand behavior. Connectomes are typically assembled using electron microscopy, but this is low throughput and impractical for analyzing plasticity or mutations. Here, we modified thetrans-Tango genetic circuit-tracing technique to identify neurons synaptically downstream ofDrosophilas-LNv clock neurons, which show 24hr plasticity rhythms. s-LNv target neurons were labeled specifically in adult flies using a nuclear reporter gene, which facilitated their purification and then single cell sequencing. We call this Tango-seq, and it allows transcriptomic data – and thus cell identity – to be overlayed on top of anatomical data. We found that s-LNvs preferentially make synaptic connections with a subset of the CNMa+ DN1p clock neurons, and that these are likely plastic connections. We also identified synaptic connections between s-LNvs and mushroom body Kenyon cells. Tango-seq should be a useful addition to the connectomics toolkit.
Green Jackfruit Flour Prevents Metabolic Dysfunction-Associated Steatohepatitis and Progression to Hepatocellular Carcinoma via the AMPK and MAPK Signaling Pathways
Authors: Suresh Diwakar , Gunaseelan Bharathwaaj , Srinivas Akshatha N. , Bharadwaj Amith , Joseph James , Megha  , Varghese Thomas , Satish Suchitha , Suvarna Deepak , Santhekadur Prasanna K. , Chidambaram Saravana Babu , Duseja Ajay , Kumar Divya P.
Published: May 2024

Metabolic dysfunction-associated steatotic liver disease (MASLD), encompassing metabolic-dysfunction associated steatotic liver (MAFL) and steatohepatitis (MASH), which further progresses to hepatocellular carcinoma (HCC), is a serious public health concern. Given the paucity of approved therapeutic strategies for this lifestyle disorder, dietary interventions may prove effective. We evaluated how green jackfruit flour (JF) prevents MASH and progression to HCC and its underlying mechanisms. The study utilized two murine models that mimicked human MASLD disease: (i) a diet-induced MASH model; (ii) a MASH-HCC model induced by diet and a very low dose of CCl4. C57Bl/6 mice were fed with chow (CD) or western diet (WD) with normal (NW) or sugar water (SW) for 12 weeks, then randomized to receive either 5 kcal% green jackfruit flour (JF) or an equal volume of placebo flour (PB). The biochemical, histological, and molecular analyses were assessed. JF significantly reduced body weight, liver injury, insulin resistance, and alleviated obesity, steatosis, inflammation, fibrosis, and tumor development in WDSW or WDSW/CCl4mice compared to placebo groups. Furthermore, JF activated AMPK (AMP-activated protein kinase) and inhibited MAPK (mitogen-activated protein kinase) signaling pathways in MASH and MASH-HCC experimental models, respectively. This was supported by sodium propionate treatment, the primary short-chain fatty acid entering the liver from JF’s soluble fiber microbial fermentation, which also regulated AMPK and MAPK signaling in cellular models of MASH and HCC, respectively. Hence, our findings present strong evidence of JF’s therapeutic potential in the prevention of MASH and MASH-HCC, warranting further investigation of JF’s efficacy as a dietary intervention in clinical trials.
Lipid oxidation alters membrane mechanics favoring permeabilization
Authors: Lotfipour Nasudivar Sara , Pedrera Lohans , García-Sáez Ana J.
Published: May 2024

Ferroptosis is a form of regulated necrosis characterized by the iron-dependent accumulation of lipid peroxides in cell membranes. However, how lipid oxidation affects biophysical properties of cellular membranes and how these changes contribute to the opening of membrane pores are major questions in the field. Therefore, understanding the interplay between oxidized phospholipids and alterations in membrane biophysical properties is essential to unravel the underlying mechanisms of ferroptosis. Here, we characterized membrane alterations upon lipid oxidation inin vitromodel membrane systems using lipid vesicles and supported lipid bilayers (SLBs) in which lipid oxidation was induced by Fenton reactions. We find that vesicle permeabilization kinetically correlates with the appearance of malondialdehyde (MDA), a product of lipid oxidation. Lipid oxidation also alters the lateral organization of SLBs exhibiting liquid-ordered (Lo)/liquid-disordered (Ld) phase coexistence, reducing the lipid mismatch between domains and decreasing the circularity of Lo domains, indicating a decrease in line tension at the phase boundaries. Further characterization of SLBs by force spectroscopy reveals a significant reduction in the average membrane breakthrough force upon oxidation, indicating changes in lipid bilayer organization that make it more susceptible to permeabilization. Our findings suggest that lipid oxidation induces strong changes in membrane lipid interactions and in the mechanical properties of membranes leading to reduced tension in the permeabilized state of the bilayer, which promotes membrane pore formation.
Structural Survey of Antigen Recognition by Synthetic Human Antibodies
Authors: Gorelik Maryna , Miersch Shane , Sidhu Sachdev S.
Published: May 2024

Synthetic antibody libraries have been used extensively to isolate and optimize antibodies. To generate these libraries, the immunological diversity and the antibody framework(s) that supports it outside of the binding regions are carefully designed/chosen to ensure favorable functional and biophysical properties. In particular, minimalist, single-framework synthetic libraries pioneered by our group have yielded a vast trove of antibodies to a broad array of antigens. Here, we review their systematic and iterative development to provide insights into the design principles that make them a powerful tool for drug discovery. In addition, the ongoing accumulation of crystal structures of antigen-binding fragment (Fab)–antigen complexes generated with synthetic antibodies enables a deepening understanding of the structural determinants of antigen recognition and usage of immunoglobulin sequence diversity, which can assist in developing new strategies for antibody and library optimization. Toward this, we also survey here the structural landscape of a comprehensive and unbiased set of 50 distinct complexes derived from these libraries and compare it to a similar set of natural antibodies with the goal of better understanding how each achieves molecular recognition and whether opportunities exist for iterative improvement of synthetic libraries. From this survey, we conclude that despite the minimalist strategies used for design of these synthetic antibody libraries, the overall structural interaction landscapes are highly similar to natural repertoires. We also found, however, some key differences that can help guide the iterative design of new synthetic libraries via the introduction of positionally tailored diversity.
Principles of Affinity Selection
Authors: Smith George P.
Published: May 2024

The most common application of phage-display technology is the discovery of peptides or proteins that specifically bind some molecule or other substance of interest—for example, antibodies that specifically bind an antigen. The discovery process starts with a library encompassing a very large array of proteins or peptides with a great diversity of binding specificities—for example, single-chain antibodies with a great diversity of antigen-binding sites. Each member of the array is displayed on the surface of hundreds to billions of identical virus particles (virions) belonging to a single-phage clone; the library as a whole comprises millions to billions of such clones, all mixed together in a single vessel. Affinity selection is the process by which a molecule or substance of interest—generically called the selector—is used to select very rare clones in the library displaying proteins or peptides that happen to bind the selector with high affinity and selectivity. Here, I explain general principles guiding a successful affinity-selection project—principles grounded in phage biology, kinetics of reversible binding, technological advances, and the practical experience of thousands of investigators around the globe.
Performing Quantitative PCR after Chromatin Immunoprecipitation (ChIP) ofDrosophilaAntennal and Brain Samples
Authors: Du Chengcheng , Volkan Pelin
Published: May 2024

Chromatin immunoprecipitation (ChIP) is a technique used to study specific protein–DNA interaction. Briefly, in this technique, antibodies to proteins of interest are used to isolate regions of DNA where these proteins bind. ChIP samples can be processed and analyzed in different ways. One of the approaches for assessing the results of ChIP experiments is quantitative PCR (qPCR). qPCR is used to quantitatively measure the amount of DNA fragments that have been isolated, reflecting the signal of specific proteins interacting with these fragments. This protocol describes both the “percent input” method and the “fold enrichment” method for ChIP-qPCR data analysis usingDrosophilatissues as an example. The “percent input” method measures signals of DNA fragments against the input measurement. In contrast, the “fold enrichment” method quantifies the amplified signal strength relative to a background control. Because the quality of primers is critical for the reliability of ChIP-qPCR results, this protocol also describes how to measure primer amplification efficiency usingDrosophilagenomic DNA.
Generating and Validating Transgenic Mosquitoes with Transposon-Mediated Transgenesis
Authors: Bottino-Rojas Vanessa , James Anthony A.
Published: May 2024

Transposon-mediated transgenesis has revolutionized both basic and applied studies of mosquito vectors of disease. Currently, techniques such as enhancer traps and transposon tagging, which rely on remobilizable insertional mutagenesis, are only possible with transposon-based vector systems. Here, we provide general descriptions of methods and applications of transposon-based mosquito transgenesis. The exact procedures must be adapted to each mosquito species and comparisons of some differences among different mosquito species are outlined. A number of excellent publications showing detailed and specific protocols and methods are featured and referenced.
Identification of Mosquito Eggshell Proteins fromAedes aegyptiby Liquid Chromatography with Tandem Mass Spectrometry (LC–MS/MS) Proteomic Analysis
Authors: Isoe Jun , Parsawar Krishna , David Cynthia L. , Riehle Michael A. , Miesfeld Roger L.
Published: May 2024

The insect eggshell is a multifunctional structure with several important roles, including generating an entry point for sperm via the micropyle before oviposition, serving as an oviposition substrate attachment surface, and functioning as a protective layer during embryo development. Eggshell proteins play major roles in eggshell tanning and hardening following oviposition and provide molecular cues that define dorsal–ventral axis formation. Precise eggshell formation during ovarian follicle maturation is critical for normal embryo development and the synthesis of a defective eggshell often gives rise to inviable embryos. Therefore, simple and accurate methods for identifying eggshell proteins will facilitate our understanding of the molecular pathways regulating eggshell formation and the mechanisms underlying normal embryo development. This protocol describes how to isolate and enrich eggshells from mature oocytes ofAedes aegyptimosquitoes and how to extract their eggshell proteins for liquid chromatography with tandem mass spectrometry (LC–MS/MS) proteomic analysis. Although this methodology was developed for studying mosquito eggshells, it may be applicable to eggs from a variety of insects. Mosquitoes are ideal model organisms for this study as their ovarian follicle development and eggshell formation are meticulously regulated by blood feeding and their follicles develop synchronously throughout oogenesis in a time-dependent manner.
Extracting DNA from Preserved Mosquito Blood Meals
Authors: Reeves Lawrence E. , Burkett-Cadena Nathan D.
Published: May 2024

Mosquito species vary in their host associations. Although some species are relative generalists, most specialize, to varying extents, on particular types of host animals. Mosquito host associations are among the most important factors that influence the transmission dynamics of mosquito-vectored pathogens, and understanding these associations can provide insight on how such pathogens move within ecosystems. Characterization of the host associations of mosquito species requires applying blood meal analysis to the largest possible sample size of mosquito blood meals. Processing large samples of mosquito blood meals can be time-consuming, especially when chain-termination sequencing is used, necessitating individual processing of each specimen. Various methods and commercially available kits and products are available for extracting DNA from mosquito blood meals. The hot sodium hydroxide and Tris (HotSHOT) method is a rapid and inexpensive method of DNA extraction that is compatible with the recovery of DNA from mosquito blood meals preserved on QIAcard Flinders Technology Associates (FTA) Classic Cards (FTA cards). FTA cards allow nucleic acids found in blood meals to be preserved easily, even in field conditions. DNA prepared using this method is suitable for polymerase chain reaction (PCR)-based blood meal analysis.