bluuebunny/crossref_metadata_2025 huggingface dataset:
“Rapid Formation, Acute Rupture” Course of Intracranial Aneurysm
Authors: Bao Ming-Yue , Ye Lei , Cheng Hong-Wei , Zhang Xing
Published: October 2022

Intracranial aneurysm (IA) is a devastating cerebrovascular disease characterizing with a potential rupturing risk. In previous studies, the formation of IA was considered to be in a chronic manner, and the ruptured aneurysms might merely derived from the already formed unruptured IA. A 61-year-old male presented to the hospital complaining of a headache. The patient received neuroimage tests, including head computed tomography and digital substraction angiography, to examine the underlying cerebrovascular diseases. Interestingly, we found a newborn ruptured IA with 9-day intervals between 2 whole-cerebral digital subtraction angiography examinations. In summary, the case in our report provides a clue for the natural course that the IA is probably in a “rapid formation, acute rupture” manner.
Complexity of Online Facial Feminization Surgery Material Exceeds Patient Health Literacy
Authors: Cordero Justin , Frediani Tanner , Carre Antoine Lyonel , Lee James C. , Francis Stacey H. , Chu Michael W.
Published: October 2022

The increase in healthcare coverage for transgender populations has made facial feminization surgeries (FFS) more accessible. Majority of patients interested in surgery regularly check online medical information to help understand surgical procedures, risks, and recovery. National health organizations recommend that patient information material should be written at a sixth-grade-reading level, but online material often surpasses patient health literacy. This study evaluates the readability of online FFS resources. An Internet search of the top 100 Web sites was conducted using the keywords “facial feminization surgery.” Web sites were analyzed for relevant patient information articles on FFS and categorized into health care and nonhealth care groups. Readability examinations were performed for written text using the Automated Readability Index, Coleman-Liau Index, Flesch-Kincaid Grade Level, Gunning Fog Index, and Simple Measure of Gobbledygook Index. Statistical analysis was performed using 2-tailed z tests, with statistical significance set at P≤0.05. A total of 100 articles from 100 Web sites were examined. The average readability for all online FFS resources was at a 12th-grade-writing level. Articles from health care organizations were at a 13th-grade-reading level and nonhealth care organization articles were at a 12th-grade-reading level (P<0.01). Online patient information for FFS is more complex than nationally recommended writing levels, which may interfere with patient decision making and outcomes. Patient resources for FFS should be written at a lower reading level to promote patient education, satisfaction, and compliance.
Counterfactual curiosity: motivated thinking about what might have been
Authors: Fitzgibbon Lily , Murayama Kou
Published: October 2022

Counterfactual information, information about what might have been, forms the content of counterfactual thoughts and emotions like regret and relief. Recent research suggests that human adults and children, as well as rhesus monkeys, demonstrate ‘counterfactual curiosity’: they are motivated to seek out counterfactual information after making decisions. Based on contemporary theories of curiosity and information seeking and a broad range of empirical literature, we suggest multiple heterogeneous psychological processes that contribute to people's motivation for counterfactual information. This includes processes that are identified in the curiosity literature more generally—the potential use of counterfactual information for adaptive decision making (its long-term instrumental value) and the drive to reduce uncertainty. Additionally, we suggest that counterfactual information may be particularly alluring because of its role in causal reasoning; its relationship with prediction and decision making; and its potential to fulfil emotion regulation and self-serving goals. Some future directions have been suggested, including investigating the role of individual differences in counterfactual curiosity on learning and wellbeing.

This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
The pupillometry of the possible: an investigation of infants' representation of alternative possibilities
Authors: Cesana-Arlotti Nicolò , Varga Bálint , Téglás Ernő
Published: October 2022

Contrasting possibilities has a fundamental adaptive value for prediction and learning. Developmental research, however, has yielded controversial findings. Some data suggest that preschoolers might have trouble in planning actions that take into account mutually exclusive possibilities, while other studies revealed an early understanding of alternative future outcomes based on infants' looking behaviour. To better understand the origin of such abilities, here we use pupil dilation as a potential indicator of infants' representation of possibilities. Ten- and 14-month-olds were engaged in an object-identification task by watching video animations where three different objects with identical top parts moved behind two screens. Importantly, a target object emerged from one of the screens but remained in partial occlusion, revealing only its top part, which was compatible with a varying number of possible identities. Just as adults' pupil diameter grows monotonically with the amount of information held in memory, we expected that infants' pupil size would increase with the number of alternatives sustained in memory as candidate identities for the partially occluded object. We found that pupil diameter increased with the object's potential identities in 14- but not in 10-month-olds. We discuss the implications of these results for the foundation of humans' capacities to represent alternatives.

This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
The importance of thinking about the future in culture and cumulative cultural evolution
Authors: Vale G. L. , Coughlin C. , Brosnan S. F.
Published: October 2022

Thinking about possibilities plays a critical role in the choices humans make throughout their lives. Despite this, the influence of individuals' ability to consider what is possible on culture has been largely overlooked. We propose that the ability to reason about future possibilities or prospective cognition, has consequences for cultural change, possibly facilitating the process of cumulative cultural evolution. In particular, by considering potential future costs and benefits of specific behaviours, prospective cognition may lead to a more flexible use of cultural behaviours. In species with limited planning abilities, this may lead to the development of cultures that promote behaviours with future benefits, circumventing this limitation. Here, we examine these ideas from a comparative perspective, considering the relationship between human and nonhuman assessments of future possibilities and their cultural capacity to invent new solutions and improve them over time. Given the methodological difficulties of assessing prospective cognition across species, we focus on planning, for which we have the most data in other species. Elucidating the role of prospective cognition in culture will help us understand the variability in when and how we see culture expressed, informing ongoing debates, such as that surrounding which social learning mechanisms underlie culture.

This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Young children share imagined possibilities: evidence for an early-emerging human competence
Authors: Harris Paul L.
Published: October 2022

Children's ability to reason about junctures leading to two different destinations emerges slowly, with convergent evidence for a conceptual watershed at approximately 4 years. Young children and great apes misrepresent such junctures, planning for only one expected outcome. However, singular possibilities, as opposed to two mutually exclusive possibilities, are readily imagined, shared and acted upon by 2- and 3-year-olds. Analysis of three domains supports this claim. First, 2- and 3-year-olds respond appropriately to pretend spatial displacements enacted for them by a play partner. Second, they not only respond accurately to claims regarding an alleged but unwitnessed spatial displacement, they also ask their interlocutors about the possible whereabouts of missing objects and absent persons. Third, in ordinary conversation, they appropriately mark some of their assertions as possibilities rather than actualities. In summary, although the ability to reason about mutually inconsistent possibilities develops slowly in the preschool years, the ability to imagine and share information about possibilities is evident among 2- and 3-year-olds. Nothing comparable has been observed in great apes. Young children's ability to entertain shared possibilities diverges from that of non-human primates well before any potential watershed at 4 years with respect to the understanding of mutually exclusive possibilities.

This article is part of the theme issue ‘Thinking about possibilities: mechanisms, ontogeny, functions and phylogeny’.
Dysregulation of the PRUNE2/PCA3 genetic axis in human prostate cancer: From experimental discovery to validation in two independent patient cohorts
Authors: Lauer Richard C. , Barry Marc , Smith Tracey L. , Thomas Andrew Maltez , Wu Jin , Du Ruofei , Lee Ji-Hyun , Rao Arpit , Dobroff Andrey S. , Arap Marco A. , Nunes Diana N. , Silva Israel T. , Dias-Neto Emmanuel , Chen Isan , McCance Dennis J. , Cavenee Webster K. , Pasqualini Renata , Arap Wadih
Published: October 2022

BACKGROUND

We have previously shown that the long non-coding (lnc)RNAprostate cancer associated 3(PCA3; formerlyprostate cancer antigen 3) functions as a trans-dominant negative oncogene by targeting the previously unrecognized prostate cancer suppressor genePRUNE2(a homolog of theDrosophila prunegene), thereby forming a functional unit within a unique allelic locus in human cells. Here we investigated thePCA3/PRUNE2regulatory axis from early (tumorigenic) to late (biochemical recurrence) genetic events during human prostate cancer progression.

METHODS

The reciprocalPCA3andPRUNE2gene expression relationship in paired prostate cancer and adjacent normal prostate was analyzed in two independent retrospective cohorts of clinically-annotated cases post-radical prostatectomy: a single-institution discovery cohort (n=107) and a multi-institution validation cohort (n=497). We compared the tumor gene expression ofPCA3andPRUNE2to their corresponding expression in the normal prostate. We also serially examined clinical/pathological variables including time to disease recurrence.

RESULTS

We consistently observed increased expression ofPCA3and decreased expression ofPRUNE2in prostate cancer compared with the adjacent normal prostate across all tumor grades and stages. However, there was no association between the relative gene expression levels ofPCA3orPRUNE2and time to disease recurrence, independent of tumor grades and stages.

CONCLUSIONS

We concluded that upregulation of the lncRNAPCA3and targeted downregulation of the protein-codingPRUNE2gene in prostate cancer could be early (rather than late) molecular events in the progression of human prostate tumorigenesis but are not associated with biochemical recurrence. Further studies of PCA3/PRUNE2 dysregulation are warranted.

FUNDING

We received support from the Human Tissue Repository and Tissue Analysis Shared Resource from the Department of Pathology of the University of New Mexico School of Medicine and a pilot award from the University of New Mexico Comprehensive Cancer Center. RP and WA were supported by awards from the Levy-Longenbaugh Donor-Advised Fund and the Prostate Cancer Foundation. EDN reports research fellowship support from the Brazilian National Council for Scientific and Technological Development (CNPq), Brazil, and the Associação Beneficente Alzira Denise Hertzog Silva (ABADHS), Brazil. This work has been funded in part by the NCI Cancer Center Support Grants (CCSG; P30) to the University of New Mexico Comprehensive Cancer Center (CA118100) and the Rutgers Cancer Institute of New Jersey (CA072720).
Maternity and family leave experiences among female ophthalmologists
Authors: Daly Caroline M. , Kraus Courtney L. , Campbell Ashley A. , Kaleem Mona A. , Shukla Aakriti Garg , McGlumphy Elyse J.
Published: October 2022

Objective

To evaluate family and maternity leave policies and examine the social and professional impacts on female ophthalmologists

Participants

Participants were recruited through the Women in Ophthalmology online list-serv to complete a survey evaluating maternity leave policies and their impacts. Survey questions were repeated for each birth event after medical school for up to five birth events.

Results

The survey was accessed 198 times, and 169 responses were unique. Most participants were practicing ophthalmologists (92.3%), with a minority in residency (5.3%), in fellowship (1.2%), on disability/leave (0.6%), or retired (0.6%). Most participants (78.3%) were within their first ten years of practice. Experiences were recorded for each leave event, with 169 responses for the first leave, 120 for the second, 28 for the third, and 2 for the fourth. Nearly half of participants reported the information they received about maternity leave to be somewhat or extremely inadequate (first: 49.7%; second: 42.1%; third: 40.9%). Many reported a greater sense of burnout after returning to work (first: 60.9%, second: 58.3%, third: 45.5%). A minority of participants received full pay during the first through third maternity leave events, 39%, 27%, and 33%, respectively. About a third of participants reported being somewhat or very dissatisfied with their maternity leave experience (first: 42.3%, second: 35.0%; third: 27.3%).

Conclusions

Female ophthalmologists have varying experiences with maternity leave, but many encounter similar challenges. This study demonstrates that many women receive inadequate information about family leave, desire more weeks of leave, experience a wide variation in pay practices, and lack support for breastfeeding. Understanding the shared experiences of women in ophthalmology identifies areas where improvements are needed in maternity leave practices within the field to create a more supportive environment for physician mothers.
Scenario modelling for diminished influenza seasons during 2020/2021 and 2021/2022 in England
Authors: Hill Edward M. , Keeling Matt J.
Published: October 2022

Background

There has been concern throughout the COVID-19 pandemic over highly stressed healthcare capacities being further pressured by seasonal influenza epidemics. Interventions to tackle the spread of SARS-CoV-2, the causative agent of COVID-19, have unsettled the respiratory pathogen landscape, including worldwide patterns of influenza activity. The implications of these disruptions for subsequent influenza seasons has been uncertain.

Methods

To conduct scenario analyses ahead of the 2020/2021 and 2021/2022 influenza seasons in England, we used a pre-existing age-structured, multi-strain compartmental model of influenza transmission and case severity, which included propagation of immunity between influenza seasons and had been previously fit to historical data. For the pre-2020/2021 influenza season, our scenarios varied the level of vaccine uptake and the inclusion/exclusion of nonpharmaceutical interventions (NPIs). We estimated the relative amount of health episode occurrences: symptomatic cases resulting in a GP consultation, hospital inpatient admissions, fatalities. In the pre-2021/2022 influenza season analysis, compared with a counterfactual case where influenza activity remained at historic levels in the 2020/2021 influenza season, we estimated the change in the same set of health episode occurrences in the 2021/2022 influenza season when assuming there was no influenza in circulation during the 2020/2021 influenza season.

Results

Attaining coverage of 75% in target groups for the 2020/2021 influenza season reduced health episode occurrences by 40–50% when compared to maintaining the 2019/2020 vaccination programme coverage and uptake levels. Having NPIs maintained throughout the entire influenza season saw 60-80% reductions in severe case outcomes. Combining an expanded vaccination programme and the use of NPIs could suppress the seasonal influenza epidemic, with reductions as much as 90–100%. In the absence of influenza transmission during the 2020/2021 influenza season, under our modelling assumption of mixing patterns returning to pre-2020 levels we projected a compensatory influenza epidemic with 1.2 to 2.2 times as many severe health episode occurrences in the subsequent 2021/2022 influenza season.

Conclusions

In the context of the time the work was originally conducted, the modelled scenarios indicated how bolstering vaccine coverage and reduction in contacts could likely allay resurgent seasonal influenza epidemics. Our analyses of the winter pressures that may be inflicted by other respiratory infections during the COVID-19 pandemic are one example of the modelling insights provided to the Scientific Pandemic Influenza Group on Modelling, Operational sub-group (SPI-M-O) for the Scientific Advisory Group for Emergencies (SAGE) in the UK.
A novel hospital-at-home model for patients with COVID-19 built by a team of local primary care clinics and clinical outcomes: A multi-center retrospective cohort study
Authors: Tsujimoto Yasushi , Kobayashi Masanori , Oku Tomohisa , Ogawa Takahisa , Yamadera Shinichi , Tsukamoto Masako , Matsuda Noriya , Nishihira Morikazu , Terauchi Yu , Tanaka Takahiro , Kawabata Yoshitaka , Miyamoto Yuki , Morikami Yoshiki
Published: October 2022

Background

Hospital-at-home (HaH) care has been proposed as an alternative to inpatient care for patients with COVID-19. Previous reports were hospital-led and involved patients triaged at the hospitals. To reduce the burden on hospitals, we constructed a novel HaH care model organised by a team of local primary care clinics.

Methods

We conducted a multi-center retrospective cohort study of the COVID-19 patients who received our HaH care from Jan 1stto Mar 31st, 2022. Patients who were not able to be triaged for the need for hospitalization by the Health Center solely responsible for the management of COVID-19 patients in Osaka City were included. The primary outcome was receiving medical care beyond the HaH care defined as a composite outcome of any medical consultation, hospitalization, or death within 30 days from the initial treatment.

Results

Of 382 eligible patients, 34 (9%) were triaged for hospitalization immediately after the initial visit. Of the remaining 348 patients followed up, 37 (11%) developed the primary outcome, while none died. Obesity, fever, and gastrointestinal symptoms at baseline were independently associated with an increased risk of needing medical care beyond the HaH care. A further 129 (37%) patients were managed online alone without home visit, and 170 (50%) required only one home visit in addition to online treatment.

Conclusions

The HaH care model with a team of primary care clinics was able to triage patients with COVID-19 who needed immediate hospitalization without involving hospitals, and treated most of the remaining patients at home.
The crucial role of titin in fetal development: recurrent miscarriages and bone, heart, and muscle anomalies characterize the severe end of titinopathies spectrum
Authors: Di Feo Maria Francesca , Lillback Victoria , Jokela Manu , McEntagart Meriel , Homfray Tessa , Giorgio Elisa , Casalis Cavalchini Guido C , Brusco Alfredo , Iascone Maria , Spaccini Luigina , D’Oria Patrizia , Savarese Marco , Udd Bjarne
Published: October 2022

Background

Titin truncating variants (TTNtv) have been associated with several forms of myopathies and/or cardiomyopathies. In homozygosity or in compound heterozygosity they cause a wide spectrum of recessive phenotypes with a congenital or childhood onset. Most recessive phenotypes showing a congenital or childhood onset have been described in subjects carrying biallelic TTNtv in specific exons. However,TTNis not yet included in many NGS panels for congenital musculoskeletal anomalies and dysmorphisms, and karyotype or chromosomal microarray analyses are often the only tests performed when prenatal anomalies are identified. Thereby, many cases caused byTTNdefects might be missed in the diagnostic evaluations. In this study, we aimed to dissect the most severe end of the titinopathies spectrum.

Methods

We performed a retrospective study analysing an international cohort of 93 published and 10 unpublished cases carrying biallelic TTNtv.

Results

We identified recurrent clinical features in antenatal and congenital recessive titinopathies, including fetal akinesia, arthrogryposis, facial dysmorphisms, joint, bone, and heart anomalies resembling complex, syndromic phenotypes.

Conclusion

We suggestTTNto be carefully evaluated in any diagnostic process involving patients with the mentioned signs. This step will be essential to improve diagnostic performance, expand our knowledge, and optimize prenatal genetic counseling.

Key message

Truncating variants in the titin gene (TTN) have been associated with a large spectrum of skeletal muscle diseases with or without cardiac involvement. The current work demonstrates that truncating biallelic variants in specific exons ofTTNresult in severe developmental anomalies, affecting not only the muscular systems but also bone, heart, and other organs, with a quite high rate of miscarriages and dysmorphisms. Thereby, we suggest TTN variants to be carefully evaluated in any diagnostic process involving patients with the mentioned signs.
Beyond social prescribing - the use of social return on investment (SROI) analysis in integrated health and social care interventions in England and Wales: a protocol for a systematic review
Authors: Hopkins Genevieve , Winrow Eira , Davies Ceryl , Seddon Diane
Published: October 2022

Introduction

With increasing costs of healthcare in England and Wales following the COVID-19 pandemic, finding alternatives to traditional medical interventions is more important than ever. Social prescribing provides a way of addressing health and well-being through using non-medical methods that may help relieve costs to the NHS.

Evaluating interventions, such as social prescribing, which have high social (but not easily quantifiable) value, can be problematic. Social return on investment (SROI) is a method of assigning monetary values to both social value as well as traditional assets, so provides a way of evaluating social prescribing initiatives.

Method

This protocol outlines the steps that will be taken in a systematic review of the SROI literature surrounding social prescribing-type integrated health and social care interventions based in the community in England and Wales.

Online academic databases such as PubMed Central, ASSIA and Web of Science will be searched, as will grey literature sources such as Google Scholar, the Wales School for Social Prescribing Research (WSSPR) and Social Value UK.

Titles and abstracts from the articles returned by the searches will be reviewed by one researcher. Those selected for full text review will be independently reviewed and compared by two researchers. Where the researchers disagree a third reviewer will help resolve any differences.

Information collected will include identifying stakeholder groups, assessing the quality of SROI analyses, identifying intended and unintended changes of social prescribing interventions, and comparing social prescribing initiatives in terms of SROI costs and benefits.

Quality assessment will be independently conducted on the selected papers by two researchers. The researchers will discuss to obtain consensus. Where there is disagreement, a third researcher will resolve these cases. A pre-existing quality framework will be developed and used to assess the quality of the literature.

Protocol registration

Prospero registration number:CRD42022318911

https://www.crd.york.ac.uk/prospero/display_record.php?ID=CRD42022318911
A Step Towards Generalisability: Training a Machine Learning Scoring Function for Structure-Based Virtual Screening
Authors: Scantlebury Jack , Vost Lucy , Carbery Anna , Hadfield Thomas E. , Turnbull Oliver M. , Brown Nathan , Chenthamarakshan Vijil , Das Payel , Grosjean Harold , von Delft Frank , Deane Charlotte M.
Published: October 2022

Over the last few years, many machine learning-based scoring functions for predicting the binding of small molecules to proteins have been developed. Their objective is to approximate the distribution which takes two molecules as input and outputs the energy of their interaction. Only a scoring function that accounts for the interatomic interactions involved in binding can accurately predict binding affinity on unseen molecules. However, many scoring functions make predictions based on dataset biases rather than an understanding of the physics of binding. These scoring functions perform well when tested on similar targets to those in the training set, but fail to generalise to dissimilar targets. To test what a machine learning-based scoring function has learnt, input attribution—a technique for learning which features are important to a model when making a prediction on a particular data point—can be applied. If a model successfully learns something beyond dataset biases, attribution should give insight into the important binding interactions that are taking place. We built a machine learning-based scoring function that aimed to avoid the influence of bias via thorough train and test dataset filtering, and show that it achieves comparable performance on the CASF-2016 benchmark to other leading methods. We then use the CASF-2016 test set to perform attribution, and find that the bonds identified as important by PointVS, unlike those extracted from other scoring functions, have a high correlation with those found by a distance-based interaction profiler. We then show that attribution can be used to extract important binding pharmacophores from a given protein target when supplied with a number of bound structures. We use this information to perform fragment elaboration, and see improvements in docking scores compared to using structural information from a traditional, data-based approach. This not only provides definitive proof that the scoring function has learnt to identify some important binding interactions, but also constitutes the first deep learning-based method for extracting structural information from a target for molecule design.
The neural basis of cost-benefit trade-offs in effort investment: a quantitative activation likelihood estimation meta-analysis
Authors: Silva Castanheira Kevin da , Spreng R. Nathan , Vassena Eliana , Otto A. Ross
Published: October 2022

Prominent theories of cognitive effort-based decision-making posit that shared brain regions process both potential reward and task demand, supporting the idea that effort allocation are informed by a cost-benefit trade-off, weighing the expected benefits of successful control against the inherent costs of effort exertion. While the dorsal anterior cingulate cortex (dACC) has been proposed as a candidate region supporting this decision, it remains unclear whether dACC activity tracks rewards and costs as independent quantities, or it reflects the effort intensity worth the integrated costs and benefits. While recent accounts of dACC function posit a crucial role the region in negotiating cost-benefit trade-offs, empirical evidence for this account remains scarce across single studies. To address this, we conducted a systematic meta-analysis review of neuroimaging studies, using activation-likelihood estimation method to quantify brain activity across 45 studies (N = 1273 participants) investigating reward-guided effort. We found reliable recruitment of the dACC, putamen, and anterior insula for processing both larger rewards and increasing task demands. However, the dACC clusters sensitive to task demands and rewards were anatomically distinct with no significant overlap: caudal dACC activity tracked increasing task demands, while rostral dACC activity tracked increasing rewards. Critically, we also observed that caudal dACC activity tracked the integration of costs and benefits, compatible with mental effort intensity account. These findings suggest there are distinct signals for demand and effort in the dACC which are also integrated to support the decision to invest effort, supporting recent computational accounts of cost-benefit value integration in effort-based choice.
The Three Waves: Rethinking the Structure of the first Upper Paleolithic in Western Eurasia
Authors: Slimak Ludovic
Published: October 2022

The Neronian is a lithic tradition recognized in the Middle Rhône Valley of Mediterranean France now directly linked toHomo sapiensand securely dated to 54,000 years ago (ka), pushing back the arrival of modern humans in Europe by 10 ka. This incursion of modern humans into Neandertal territory and the relationships evoked between the Neronian and the Levantine Initial Upper Paleolithic (IUP) question the validity of concepts that define the firstH. sapiensmigrations and the very nature of the first Upper Paleolithic in western Eurasia. Direct comparative analyses between lithic technology from Grotte Mandrin and East Mediterranean archeological sequences, especially Ksar Akil, suggest that the three key phases of the earliest Levantine Upper Paleolithic have very precise technical and chronological counterparts in Western Europe, recognized from the Rhône Valley to Franco-Cantabria. These trans-Mediterranean technical connections suggest three distinct waves ofH. sapiensexpansion into Europe between 55-42 ka. These elements support an original thesis on the origin, structure, and evolution of the first moments of the Upper Paleolithic in Europe tracing parallel archaeological changes in the East Mediterranean region and Europe.
The neuropeptidergic connectome ofC. elegans
Authors: Ripoll-Sánchez Lidia , Watteyne Jan , Sun HaoSheng , Fernandez Robert , Taylor Seth R , Weinreb Alexis , Hammarlund Mark , Miller David M , Hobert Oliver , Beets Isabel , Vértes Petra E , Schafer William R
Published: October 2022

Summary

Efforts are currently ongoing to map synaptic wiring diagrams or connectomes in order to understand the neural basis of brain function. However, chemical synapses represent only one type of functionally important neuronal connection; in particular, extrasynaptic, “wireless” signaling by neuropeptides is widespread and plays essential roles in all nervous systems. By integrating single-cell anatomical and gene expression datasets with a biochemical analysis of receptor-ligand interactions, we have generated a draft connectome of neuropeptide signaling in theC. elegansnervous system. This connectome is characterized by a high connection density, extended signaling cascades, autocrine foci, and a decentralized topology, with a large, highly interconnected core containing three constituent communities sharing similar patterns of input connectivity. Intriguingly, several of the most important nodes in this connectome are little-studied neurons that are specialized for peptidergic neuromodulation. We anticipate that theC. elegansneuropeptidergic connectome will serve as a prototype to understand basic organizational principles of neuroendocrine signaling networks.
A model of the interactions between the FtsQLB and the FtsWI peptidoglycan synthase complex in bacterial cell division
Authors: Craven Samuel J. , Condon Samson G. F. , Senes Alessandro
Published: October 2022

InEscherichia coli, an important step in the divisome assembly pathway is the recruitment of the essential cell wall synthase complex FtsWI to the division site through interactions with the regulatory FtsQLB complex. Here, we investigate a key aspect of this recruitment by characterizing the structural organization of the FtsL-FtsW interaction. Mutations in the cytoplasmic and transmembrane regions of the two proteins result in cell division defects and loss of FtsW localization to division sites. We use thesein vivoresults to help validate the predicted interfaces from an AlphaFold2 model for the entire FtsQLBWI complex. Given the consistency between the predicted FtsQLBWI model and our current understanding of the structure and function of the complex, we further remodeled it, seeking insight into the potential structural transitions that may lead to activation of the FtsWI complex and PG synthesis. The model suggests that FtsLB serves as a support for FtsI, placing its periplasmic domain in an extended and possibly active conformation but it is also compatible with a proposed compact and possibly inactive conformation. Additionally, we reconfigure the model into an Fts[QLBWI]2diprotomeric state, which suggests that FtsLB may act as a central hub during assembly of the PG synthesis machinery. Finally, we propose a possible role for FtsQ in activation of this machinery, potentially by acting as a gatekeeper for the interaction between the FtsL AWI region and FtsI. We propose that this gatekeeping function depends on a hinge next to the FtsLB CCD region, which has implications for the mechanisms behind the FtsLBoff/ontransition that is central to cell division regulation.
Cross-Linking of Catalytically Essential Vicinal Thiols at Active Sites of the Cerebral Sodium Transporter Inactivates its Electrogenic Function
Authors: Ologunagba Titilayo Ibironke , Olorundare Bunmi Olaoluwa , Kade Ige Joseph
Published: October 2022

The inactivation of the electrogenic function of the transmembrane sodium transporter in oxidative stress conditions has been intrinsically linked with the oxidation of its catalytically essential thiols. However, the spatial proximity of these catalytically relevant thiols is yet to be fully elucidated and thus still open. Herein, the influence of a thiol cross-linking [diamide, DA (0.1-2mM)] and a thiol alkylating [iodoacetamide, IA (0.1-5mM)] agent on the activity of the synaptosomal Na+/K+-ATPase were determined. In addition, the ability of dithiothreitol to either prevent or reverse the inhibition imposed by the thiol modifiers on the enzyme activity was also evaluated. The results showed that the thiol cross-linker inactivates the electrogenic function of the synaptosomal Na+/K+-ATPase when exposed to the thiols located at either the nucleotide or cation-binding sites. Conversely, irrespective of the exposed active sites, the thiol alkylating agents have no overt effect on the activity of the pump. Furthermore, dithiothreitol markedly prevented but did not reverse the inactivation of the electrogenic pump caused by cross-linking of its critical thiols. Interestingly, both the thiol cross-linker and alkylating agents markedly oxidize dithiothreitol in a time and concentration-dependent fashion. Consequently, within the limit of the present data, it appears that the catalytically relevant thiols of the transmembrane electrogenic pump located at the cationic and nucleotide binding sites, are in close proximity sufficient enough to allow for their cross-linking.

Highlights

The presence of Na+/K+-ATPase catalytically important thiols at the nucleotide and cationic sites of the enzyme define its vulnerability to oxidative assault.

The spatial location of these thiols at vicinal positions at these domains favour the formation of disulphide linkages under oxidative conditions

The disulphide crosslinking of these thiols culminate in enzyme inactivation

The inactivation can be prevented but not reversed by exogenous thiol compound
Engineering transmembrane signal transduction in synthetic membranes using two-component systems
Authors: Peruzzi Justin A. , Galvez Nina R. , Kamat Neha P.
Published: October 2022

Cells use signal transduction across their membranes to sense and respond to a wide array of chemical and physical signals. Creating synthetic systems which can harness cellular signaling modalities promises to provide a powerful platform for biosensing and therapeutic applications. As a first step towards this goal, we investigated how bacterial two-component systems can be leveraged to enable transmembrane-signaling with synthetic membranes. Specifically, we demonstrate that a bacterial two-component nitrate-sensing system (NarX-NarL) can be reproduced outside of a cell using synthetic membranes and cell-free protein expression systems. We find that performance and sensitivity of the two-component system can be tuned by altering the biophysical properties of the membrane in which the histidine kinase (NarX) is integrated. Through protein engineering efforts, we modify the sensing domain of NarX to generate sensors capable of detecting an array of ligands. Finally, we demonstrate that these systems can sense ligands in relevant sample environments. By leveraging membrane and protein design, this work helps reveal how transmembrane sensing can be recapitulated outside of the cell, adding to the arsenal of deployable cell-free systems primed for real world biosensing.

Significance Statement

Cells detect and respond to environmental and chemical information by using a combination of membrane proteins and genetic polymers. Recapitulation of this behavior in synthetic systems holds promise for engineering biosensors and therapeutics. Using the nitrate-sensing bacterial two-component system as a model, we demonstrate methods to reproduce and tune transmembrane signaling in synthetic lipid membranes, leading to the synthesis of genetically programmed proteins. Through this study, we gain insight into how membrane augmented cell-free systems can be used as a platform to characterize membrane-receptor interactions and engineer new biosensors.
Structural basis for ion selectivity in potassium-selective channelrhodopsins
Authors: Tajima Seiya , Kim Yoon Seok , Fukuda Masahiro , Byrne Eamon F.X. , Wang Peter Y. , Paggi Joseph M. , Kishi Koichiro E. , Ramakrishnan Charu , Takaramoto Syunki , Nagata Takashi , Konno Masae , Sugiura Masahiro , Katayama Kota , Matsui Toshiki E. , Yamashita Keitaro , Ikeda Hisako , Inoue Masatoshi , Kandori Hideki , Dror Ron O. , Inoue Keiichi , Deisseroth Karl , Kato Hideaki E.
Published: October 2022

The KCR channelrhodopsins are recently-discovered light-gated ion channels with high K+selectivity, a property that has attracted broad attention among biologists– due to intense interest in creating novel inhibitory tools for optogenetics leveraging this K+selectivity, and due to the mystery of how this selectivity is achieved in the first place. Indeed, the molecular and structural mechanism for K+selectivity in KCRs has remained especially puzzling since these 7-transmembrane retinal-binding proteins completely lack structural similarity with known K+channels, which generally coordinate K+in a precisely symmetric conduction pathway formed by a tight interface among multiple small monomeric channel subunits (presumably not an accessible mechanism for the large KCR rhodopsin proteins). Here we present the cryo-electron microscopy structures of two KCRs fromHyphochytrium catenoideswith distinct spectral properties for light absorption and channel actuation,HcKCR1, andHcKCR2, at resolutions of 2.6 and 2.5 Å, respectively. Structural comparison revealed first an unusually-shaped retinal binding pocket which induces rotation of the retinal inHcKCR2, explaining the large spectral difference betweenHcKCR1 and 2. Next, our combined structural, electrophysiological, computational, and spectroscopic analyses revealed a new solution to the challenging problem of K+-selective transport. KCRs indeed do not exhibit the canonical tetrameric K+selectivity filter that specifically coordinates dehydrated K+; instead, single KCR monomers form a size exclusion filter using aromatic residues at the extracellular side of the pore which inhibits passage of bulky hydrated ions. This unique feature allows KCRs to function as K+channels under relevant physiological conditions, providing not only a novel mechanism for achieving high K+permeability ratios in biological ion channels, but also a framework for designing the next generation of inhibitory optogenetic tools.

In Brief

The first structures of K+-selective channelrhodopsins (HcKCR1 and 2) are determined, revealing a K+selectivity mechanism distinctly different from canonical K+channels.

Highlights

The cryo-EM structures of K+-selective channelrhodopsins,HcKCR1 and 2, in nanodisc

Conditions under which naturally-occurring microbial rhodopsins have a 6-s-cisretinal

Identification of key residues for high K+permeability ratios

The unique K+selectivity mechanism of KCRs
SHIP2 controls matrix mineralization by regulation of the RhoA/ROCK pathway and remodeling of the actin cytoskeleton
Authors: Fradet Anais , Fitzgerald Jamie
Published: October 2022

Mutations inINPPL1, the gene coding for SH2 Domain-Containing Inositol 5’-Phosphatase 2 (SHIP2), cause Opsismodysplasia, a severe chondrodysplasia characterized by delayed bone maturation. The mechanism by which the loss of an inositol phosphatase causes a major skeletal developmental defect is unclear. To investigate the role of SHIP2 in mineralization, theINPPL1gene was deletedin vitroin chondrocyte and osteoblast differentiation models and the effect of the loss of SHIP2 on cell differentiation, subsequent mineralization, and on actin cytoskeleton formation was investigated. The loss of SHIP2 does not impact differentiation but, consistent with the disease phenotype, induces a significant reduction in extracellular matrix mineralization in both cell types. Absence of SHIP2 also altered the actin cytoskeleton to increase cell adhesion and focal adhesion formation. Furthermore, inhibition of actin polymerization in SHIP2-deficient cells rescued the mineralization phenotype. RhoA/ROCK, Cdc42 and Rac1 are the three main RhoGTPases responsible for actin cytoskeleton regulation in bone cells. Specific inhibitors of these RhoGTPases were used to determine the pathways involved in SHIP2-mediated mineralization. Since only the ROCK pathway inhibitor rescued the mineralization phenotype, it is concluded that SHIP2 regulates actin cytoskeleton remodeling and consequently extracellular matrix mineralization by inhibiting the RhoA/ROCK pathway.
Morphoelastic modeling of pattern development in the petal epidermal cell cuticle
Authors: Lugo Carlos A. , Airoldi Chiara , Chen Chao , Crosby Alfred J. , Glover Beverley J.
Published: October 2022

We use the model systemHibiscus trionumas a vehicle to study the origin and propagation of surface nano-ridges in plant petal epidermal cells by tracking the development of the cell shape and the cuticle. In this system, the cuticle develops two distinct subdomains, (i) an uppermost layer which increases in thickness and in-plane extension and (ii) a substrate. We quantify the pattern formation and geometrical changes and then postulate a mechanical model assuming that the cuticle behaves as a growing bi-layer. The model is a quasi-static morpho-elastic system and it is numerically investigated in two and three dimensional settings, using different laws of film and substrate expansion and boundary conditions. We recreate several features of the observed developmental trajectories in petals. We establish the respective roles of the layers’ stiffness mismatch, the underlying cell-wall curvature, the cell in-plane expansion and the thickness growth rates of the layers in determining the observed pattern features, such as the variance observed in amplitude and wavelength. Our observations provide evidence which justify the growing bi-layer description, and provide valuable insights into why some systems develop surface patterns and others do not.
Epigenetically silencing gluconeogenic enzyme PCK1 by EZH2 promotes renal tubulointerstitial fibrosis
Authors: Wu Ming , Chen Dongping , Wang Yanzhe , Lin Pinglan , Yang Feng , Lin Junyan , Tan Bo , Sheng Guangyu , Yang Xuejun , Huang Di , Ye Chaoyang
Published: October 2022

Renal fibrosis is the common pathological pathway of various chronic kidney diseases (CKD) in progression to the end stage of renal failure. Impaired renal gluconeogenesis has been recently identified as a hallmark of CKD. The role of gluconeogenesis in renal fibrosis is currently unknown. Through RNA sequencing and cleavage under targets and tagmentation (CUT&Tag) sequencing analysis, we found that the phosphoenolpyruvate carboxykinase 1 (PCK1), a critical enzyme in gluconeogenesis, is negatively regulated by the methyltransferase enhancer of zeste homolog 2 (EZH2) in fibrotic kidneys, which was further confirmed by quantitative PCR, CUT&Tag and Western blotting analysis in unilateral ureteral obstruction (UUO) kidneys and renal cells. We further showed that pharmaceutical inhibition or conditional knockout of EZH2 increased PCK1 expression and attenuated renal fibrosis in two other mouse models. Moreover, the concentration of lactate, a glucogenic metabolic intermediate, was increased in mouse fibrotic kidneys, which was reduced by EZH2 inhibition. We further showed that glucose production was impaired in folic acid induced nephrotic mice and restored by EZH2 inhibition as assessed by pyruvate tolerance test. Importantly, the direct anti-gluconeogenesis effect of EZH2 on renal proximal epithelial cells was shown in human HK2 cells by analysis of gluconeogenic gene expression and production of glucose or lactate. Finally, inhibition of PCK1 by 3-mercaptopropionic acid abrogated the anti-fibrotic effect of EZH2 inhibitor in UUO kidneys. We conclude that EZH2 promotes renal tubulointerstitial fibrosis through epigenetic inhibition of PCK1. Our study suggests that therapeutic restoration of the impaired renal gluconeogenesis is beneficial to CKD patients.

Translational Statement

Renal fibrosis is the common pathological pathway of various chronic kidney diseases (CKD) in progression to the end stage of renal failure. Impaired renal gluconeogenesis has been recently identified as a hallmark of CKD. In this study, we found that the methyltransferase EZH2 is negatively correlated with the expression of the gluconeogenic enzyme PCK1 in fibrotic kidneys. Epigenetic inhibition of PCK1 by EZH2 promotes renal tubulointerstitial fibrosis. Our study indicates that renal gluconeogenesis in CKD can be epigenetically regulated and therapeutically targeted. Epigenetic restoration of renal gluconeogenesis is a potential therapeutic strategy to treat CKD patients with tubulointerstitial fibrosis.
Slice-PASEF: fragmenting all ions for maximum sensitivity in proteomics
Authors: Szyrwiel Lukasz , Sinn Ludwig , Ralser Markus , Demichev Vadim
Published: October 2022

We present Slice-PASEF, a novel mass spectrometry technology based on trapped ion mobility separation of ions. Slice-PASEF allows to achieve the theoretical maximum of MS/MS sensitivity and boosts proteomics of low sample amounts. Leveraging Slice-PASEF, we show, for the first time, that comprehensive profiling of single cell-level peptide amounts is possible using ultra-fast microflow chromatography and a general-purpose mass spectrometer, allowing quantification of 1417 proteins from 200 picograms of a HeLa cell peptide standard on an Evosep One LC system coupled to a timsTOF Pro 2, at a 200 samples per day throughput. We implemented a Slice-PASEF module in our DIA-NN data processing software, to make it readily available for the proteomics community.