bluuebunny/crossref_metadata_2025 huggingface dataset:
Pre-Operative Assessment of Patients Undergoing Spinal Cord Stimulation for Refractory Angina Pectoris
Authors: Langford Brendan , Hunt Christine , Lerman Amir , Mauck William D
Published: March 2021

Spinal cord stimulation (SCS) is used to treat a variety of chronic pain conditions refractory to more conservative management including refractory angina pectoris. We identified 31 patients who underwent SCS implantation for the indication of refractory angina at a single institution from 2003 through 2018. Sixteen patients were male, and 15 were female. Average age was 53.9 years. Prior to SCS implantation, all patients had at least one coronary angiogram. Ten (32.3%) patients had undergone percutaneous coronary intervention, and four (12.9%) had undergone coronary artery bypass grafting. Thirty patients (96.7%) were currently using anti-angina medications. Twenty-six patients (83.9%) were on antiplatelet or anticoagulant agents at the time of SCS evaluation. Spinal cord stimulation implanters must perform a comprehensive evaluation incorporating appropriate multidisciplinary care particularly in patients with refractory angina given their cardiovascular comorbidities. It is important to have baseline data (e.g., pain scores, nitroglycerin consumption, frequency of angina episodes, and a questionnaire, such as the Seattle Angina Questionnaire) to compare with follow-up data to help define treatment success. We report a single institution’s pre-operative experience for patients undergoing SCS for refractory angina to illustrate unique pre-operative SCS considerations in this chronic pain population.
Collaborative Governance in Local Government: How State Law Shapes Community Problem-Solving through Intrastate Preemption
Authors: Amsler Lisa Blomgren , Vieilledent Thibault
Published: March 2021

How may local government, nested in state government as a creature of state law, effectively engage in collaborative governance? What if it finds itself thwarted by state legislation related to policy solutions that community stakeholders identify through collaborative governance as steps to mitigate climate change? This article examines how state legislation may limit or empower local government to use collaborative governance to address climate change. It uses Institutional Analysis and Development with a particular focus on state law as rules that shape municipal action arenas. Legal scholars term state legislation that limits local government action as state preemption or intrastate preemption. Using a 50-state review of state statutes regarding single use plastic bags, fracking, electricity supply, and broadband, this article identifies patterns of intrastate preemption of municipal government authority to adopt policies or ordinances related to the environment. It identifies patterns in states adopting intrastate preemption related to majority political party in the state legislature and governorship. It concludes intrastate preemption may inhibit collaborative governance and community problem-solving by limiting municipal policy choices. This research illustrates the importance of controlling for state law in research on municipal collaborative governance in policy-making.
Gene-activated matrix harboring a miR20a-expressing plasmid promotes rat cranial bone augmentation
Authors: Shido Rena , Sumita Yoshinori , Hara Masahito , Iwatake Mayumi , Narahara Shun , Umebayashi Mayumi , Miura Kei-ichiro , Kodama Yukinobu , Asahina Izumi
Published: March 2021

Gene-activated matrix (GAM) has a potential usefulness in bone engineering as an alternate strategy for the lasting release of osteogenic proteins but efficient methods to generate non-viral GAM remain to be established. In this study, we investigated whether an atelocollagen-based GAM containing naked-plasmid (p) DNAs encoding microRNA (miR) 20a, which may promote osteogenesis in vivo via multiple pathways associated with the osteogenic differentiation of mesenchymal stem/progenitor cells (MSCs), facilitates rat cranial bone augmentation. First, we confirmed the osteoblastic differentiation functions of generated pDNA encoding miR20a (pmiR20a) in vitro, and its transfection regulated the expression of several of target genes, such as Bambi1 and PPARγ, in rat bone marrow MSCs and induced the increased expression of BMP4. Then, when GAMs fabricated by mixing 100 μl of 2% bovine atelocollagen, 20 mg β-TCP granules and 0.5 mg (3.3 μg/μl) AcGFP plasmid-vectors encoding miR20a were transplanted to rat cranial bone surface, the promoted vertical bone augmentation was clearly recognized up to 8 weeks after transplantation, as were upregulation of VEGFs and BMP4 expressions at the early stages of transplantation. Thus, GAM-based miR delivery may provide an alternative non-viral approach by improving transgene efficacy via a small sequence that can regulate the multiple pathways.
Decellularized small intestine submucosa/polylactic-co-glycolic acid composite scaffold for potential application in hypopharyngeal and cervical esophageal tissue repair
Authors: Qiu Shijie , Liang Lijin , Zou Peng , Chen Qi
Published: March 2021

There has been an increase in the incidence of hypopharyngeal and cervical esophageal cancer worldwide, and hence growing needs for hypopharyngeal and cervical esophageal tissue repair. This work produced a bi-layer composite scaffold with decellularized small intestine submucosa and polylactic-co-glycolic acid, which resembled the layered architectures of its intended tissues. The decellularized small intestine submucosa contained minimal residual DNA (52.5 ± 1.2 ng/mg) and the composite scaffold exhibited satisfactory mechanical properties (a tensile modulus of 21.1 ± 4.8 MPa, an ultimate tensile strength of 14.0 ± 2.9 MPa and a failure strain of 26.9 ± 5.1%). The interactions between cells and the respective layers of the scaffold were characterized by CCK-8 assays, immunostaining and Western blotting. Desirable cell proliferation and phenotypic behaviors were observed. These results have provided an important basis for the next-step in vivo studies of the scaffold, and bode well for its future clinical applications.
Evaluating the potential of an amelogenin-derived peptide in tertiary dentin formation
Authors: Peng Xiu , Han Sili , Wang Kun , Ding Longjiang , Liu Zhenqi , Zhang Linglin
Published: March 2021

Several novel biomaterials have been developed for dental pulp capping by inducing tertiary dentin formation. The aim of this study was to evaluate the effect of QP5, an amelogenin-based peptide, on the mineralization of dental pulp cells (DPCs) in vitro and in vivo. The cell viability of human DPCs (hDPCs) after treatment with QP5 was determined using the Cell Counting Kit-8 (CCK-8). Migration of hDPCs was assessed using scratch assays, and the pro-mineralization effect was determined using alkaline phosphatase (ALP) staining, alizarin red staining and the expression of mineralization-related genes and proteins. The results showed that QP5 had little effect on the cell viability, and significantly enhanced the migration capability of hDPCs. QP5 promoted the formation of mineralized nodules, and upregulated the activity of ALP, the expression of mRNA and proteins of mineralization-related genes. A pulp capping model in rats was generated to investigate the biological effect of QP5. The results of micro-computed tomography and haematoxylin and eosin staining indicated that the formation of tertiary dentin in QP5-capping groups was more prominent than that in the negative control group. These results indicated the potential of QP5 as a pulp therapy agent.
Characterization and evaluation of a femtosecond laser-induced osseointegration and an anti-inflammatory structure generated on a titanium alloy
Authors: Liu Yang , Rui Zhongying , Cheng Wei , Song Licheng , Xu Yunqiang , Li Ruixin , Zhang Xizheng
Published: March 2021

Cell–material interactions during early osseointegration of the bone–implant interface are critical and involve crosstalk between osteoblasts and osteoclasts. The surface properties of titanium implants also play a critical role in cell–material interactions. In this study, femtosecond laser treatment and sandblasting were used to alter the surface morphology, roughness and wettability of a titanium alloy. Osteoblasts and osteoclasts were then cultured on the resulting titanium alloy disks. Four disk groups were tested: a polished titanium alloy (pTi) control; a hydrophilic micro-dislocation titanium alloy (sandblasted Ti (STi)); a hydrophobic nano-mastoid Ti alloy (femtosecond laser-treated Ti (FTi)); and a hydrophilic hierarchical hybrid micro-/nanostructured Ti alloy [femtosecond laser-treated and sandblasted Ti (FSTi)]. The titanium surface treated by the femtosecond laser and sandblasting showed higher biomineralization activity and lower cytotoxicity in simulated body fluid and lactate dehydrogenase assays. Compared to the control surface, the multifunctional titanium surface induced a better cellular response in terms of proliferation, differentiation, mineralization and collagen secretion. Further investigation of macrophage polarization revealed that increased anti-inflammatory factor secretion and decreased proinflammatory factor secretion occurred in the early response of macrophages. Based on the above results, the synergistic effect of the surface properties produced an excellent cellular response at the bone–implant interface, which was mainly reflected by the promotion of early ossteointegration and macrophage polarization.
Fabrication of ulcer-adhesive oral keratin hydrogel for gastric ulcer healing in a rat
Authors: Cheng Zhongjun , Qing Rui , Hao Shilei , Ding Yi , Yin Haimeng , Zha GuoDong , Chen Xiaoliang , Ji Jingou , Wang Bochu
Published: March 2021

Hydrogel has been used for in suit gastric ulcer therapy by stopping bleeding, separating from ulcer from gastric fluids and providing extracellular matrix scaffold for tissue regeneration, however, this treatment guided with endoscopic catheter in most cases. Here, we developed an oral keratin hydrogel to accelerate the ulcer healing without endoscopic guidance, which can specially adhere to the ulcer because of the high-viscosity gel formation on the wound surface in vivo. Approximately 50% of the ulcer-adhesive keratin hydrogel can resident in ethanol-treated rat stomach within 12 h, while approximately 18% of them maintained in health rat stomach in the same amount of time. Furthermore, Keratin hydrogels accelerated the ethanol-induced gastric ulcer healing by stopping the bleeding, preventing the epithelium cells from gastric acid damage, suppressing inflammation and promoting re-epithelization. The oral administration of keratin hydrogel in gastric ulcer treatment can enhance the patient compliance and reduce the gastroscopy complications. Our research findings reveal a promising biomaterial-based approach for treating gastrointestinal ulcers.
Small Words That Matter: Linguistic Style and Conceptual Disorganization in Untreated First-Episode Schizophrenia
Authors: Silva Angelica , Limongi Roberto , MacKinley Michael , Palaniyappan Lena
Published: March 2021

This study aimed to shed light on the linguistic style affecting the communication discourse in first-episode schizophrenia (FES) by investigating the analytic thinking index in relation to clinical scores of conceptual and thought disorganization (Positive and Negative Syndrome Scale, PANSS-P2 and Thought and Language Index, TLI). Using robust Bayesian modeling, we report three major findings: (1) FES subjects showed reduced analytic thinking, exhibiting a less categorical linguistic style than healthy control (HC) subjects (Bayes factor, BF10 > 1000), despite using the same proportion of function and content words as HCs; (2) the lower the analytic thinking score, the higher the symptoms scores of conceptual disorganization (PANSS-P2, BF = 22.66) and global disorganization of thinking (TLI, BF10 = 112.73); (3) the linguistic style is a better predictor of conceptual disorganization than the cognitive measure of processing speed in schizophrenia (SZ). These findings provide an objectively detectable linguistic style with a focus on Natural Language Processing Analytics of transcribed speech samples of patients with SZ that require no clinical judgment. These findings also offer a crucial insight into the primacy of linguistic structural disruption in clinically ascertained disorganized thinking in SZ. Our work contributes to an emerging body of literature on the psychopathology of SZ using a first-order lexeme-level analysis and a hypothesis-driven approach. At a utilitarian level, this has implications for improving educational and social outcomes in patients with SZ.
Intrahost speciations and host switches played an important role in the evolution of herpesviruses
Authors: Brito Anderson F , Baele Guy , Nahata Kanika D , Grubaugh Nathan D , Pinney John W
Published: March 2021

In times when herpesvirus genomic data were scarce, the cospeciation between these viruses and their hosts was considered to be common knowledge. However, as more herpesviral sequences were made available, tree reconciliation analyses started to reveal topological incongruences between host and viral phylogenies, indicating that other cophylogenetic events, such as intrahost speciation and host switching, likely played important roles along more than 200 million years of evolutionary history of these viruses. Tree reconciliations performed with undated phylogenies can identify topological differences, but offer insufficient information to reveal temporal incongruences between the divergence timing of host and viral species. In this study, we performed cophylogenetic analyses using time-resolved trees of herpesviruses and their hosts, based on careful molecular clock modelling. This approach enabled us to infer cophylogenetic events over time and also integrate information on host biogeography to better understand host–virus evolutionary history. Given the increasing amount of sequence data now available, mismatches between host and viral phylogenies have become more evident, and to account for such phylogenetic differences, host switches, intrahost speciations and losses were frequently found in all tree reconciliations. For all subfamilies in Herpesviridae, under all scenarios we explored, intrahost speciation and host switching were more frequent than cospeciation, which was shown to be a rare event, restricted to contexts where topological and temporal patterns of viral and host evolution were in strict agreement.
New SARS-CoV-2 lineages could evade CD8+ T-cells response
Authors: Pretti Marco Antonio M. , Galvani Rômulo G. , Farias Alessandro S , Boroni Mariana
Published: March 2021

Background

Many SARS-CoV-2 variants of concern have emerged since the Covid-19 outburst, notably the lineages detected in the UK, South Africa, and Brazil. Their increased transmissibility and higher viral load put them in the spotlight. Much has been investigated on the ability of those new variants to evade antibody recognition. However, not enough attention has been given to pre-existing and induced SARS-CoV-2-specific CD8+ T cell responses during the natural course of infection by new lineages.

Methods

In this work, we investigated the SARS-CoV-2-specific CD8+ T cell epitopes from the main variants of concern and the potential of associated mutations to trigger or hinder CD8+ T-cells response. We also estimated the population’s coverage of these different lineages, considering peptide binding predictions to class I HLA alleles from 29 countries to investigate differences in the fraction of individuals expected to respond to a given epitope set from new and previous lineages.

Results

We observed a lower populational coverage for 20B/S.484K (P.2 lineage) in contrast to an increased coverage found for 20H/501Y.V2 (B.1.351 Lineage) and 20J/501Y.V3 (P.1 lineage) compared to a reference lineage. Moreover, mutations such as Spike N501Y and Nucleocapsid T205I were predicted to have an overall higher affinity through HLA-I than the reference sequence.

Conclusions

In summary, the data in this work provided evidence for the existence of potentially immunogenic and conserved epitopes across new SARS-CoV-2 variants, but also highlights the reduced populational’s coverage for the Brazilian lineage P.2, suggesting its potential to evade from CD8+ T-cell responses. Our results also may guide efforts to characterize and validate relevant peptides to trigger CD8+ T-cell responses, and design new universal T-cell-inducing vaccine candidates that minimize detrimental effects of viral diversification and at the same time induce responses to a broad human population.
COVID-19 Vaccine Acceptance and Hesitancy in Low and Middle Income Countries, and Implications for Messaging
Authors: Solís Arce Julio S. , Warren Shana S. , Meriggi Niccoló F. , Scacco Alexandra , McMurry Nina , Voors Maarten , Syunyaev Georgiy , Malik Amyn Abdul , Aboutajdine Samya , Armand Alex , Asad Saher , Augsburg Britta , Bancalari Antonella , Nyqvist Martina Björkman , Borisova Ekaterina , Bosancianu Constantin Manuel , Cheema Ali , Collins Elliott , Farooqi Ahsan Zia , Fracchia Mattia , Guariso Andrea , Hasanain Ali , Kamwesigye Anthony , Kreps Sarah , Levine Madison , Littman Rebecca , Platas Melina , Ramakrishna Vasudha , Shapiro Jacob N. , Svensson Jakob , Vernot Corey , Vicente Pedro C. , Weissinger Laurin B , Zhang Baobao , Karlan Dean , Callen Michael , Teachout Matthieu , Humphreys Macartan , Omer Saad B. , Mobarak Ahmed Mushfiq
Published: March 2021

We analyze COVID-19 vaccine acceptance across 15 survey samples covering ten low- and middle-income countries (LMICs) in Asia, Africa, and South America, Russia (an upper-middle-income country), and the United States, using survey responses from 44,260 individuals. We find considerably higher willingness to take a COVID-19 vaccine in LMIC samples (80% on average) compared to the United States (65%) and Russia (30%). Vaccine acceptance was primarily explained by an interest in personal protection against COVID-19, while concern about side effects was the most commonly expressed reason for reluctance. Health workers were the most trusted sources of information about COVID-19 vaccines. Our findings suggest that prioritizing vaccine distribution to LMICs should yield high returns in promoting global immunization coverage, and that vaccination campaigns in these countries should focus on translating acceptance into uptake. Messaging highlighting vaccine efficacy and safety, delivered by healthcare workers, may be most effective in addressing remaining hesitancy.
Epigenetic clocks reveal a rejuvenation event during embryogenesis followed by aging
Authors: Kerepesi Csaba , Zhang Bohan , Lee Sang-Goo , Trapp Alexandre , Gladyshev Vadim N.
Published: March 2021

The notion that germline cells do not age goes back to the 19thcentury ideas of August Weismann. However, being in a metabolically active state, they accumulate damage and other age-related changes over time, i.e., they age. For new life to begin in the same young state, they must be rejuvenated in the offspring. Here, we developed a new multi-tissue epigenetic clock and applied it, together with other aging clocks, to track changes in biological age during mouse and human prenatal development. This analysis revealed a significant decrease in biological age, i.e. rejuvenation, during early stages of embryogenesis, followed by an increase in later stages. We further found that pluripotent stem cells do not age even after extensive passaging and that the examined epigenetic age dynamics is conserved across species. Overall, this study uncovers a natural rejuvenation event during embryogenesis and suggests that the minimal biological age (the ground zero) marks the beginning of organismal aging.
Spatial Prevalence and Determinants of Malaria among under-five Children in Ghana
Authors: Ejigu Bedilu Alamirie , Wencheko Eshetu
Published: March 2021

In Ghana malaria is an endemic disease and the incidence of malaria still accounts for 38.0% of all outpatient attendance with the most vulnerable groups being children under 5 years of age. In order to alleviate this problem, it is essential to design geographically targeted and cost-effective intervention mechanisms guided by up-to-date and reliable data and maps that show the spatial prevalence of the disease. The 2016 Ghana Malaria Indicator Survey data (N = 2,910 under-five children) were analyzed using model-based geostatistical methods with the two objectives to: (1) explore individual-, household-, and community-level determinant variables associated with malaria illness in U5 children, and (2) produce prevalence maps of malaria across the study locations in the country. The overall weighted prevalence of malaria by microscopy blood smear and rapid diagnostic tests were 20.63% (with 95% CI: 18.85% - 22.53%) and 27.82% (with 95% CI: 25.81% - 29.91%), respectively. Across regions of Ghana, the prevalence of malaria ranges from 5% in Greater Accra to 31% in Eastern region. Malaria prevalence was higher in rural areas, increased with child age, and decreased with better household wealth index and higher level of mother’s education. Given the high prevalence of childhood malaria observed in Ghana, there is an urgent need for effective and efficient public health interventions in hot spot areas. The determinant variables of malaria infection that have been identified in this study as well as the maps of parasitaemia risk could be used in malaria control program implementation to define priority intervention areas.
COVID-19 vaccine hesitancy among undergraduate medical students: results from a nationwide survey in India
Authors: Jain Jyoti , Saurabh Suman , Goel Akhil Dhanesh , Gupta Manoj Kumar , Bhardwaj Pankaj , Raghav Pankaja Ravi
Published: March 2021

COVID-19 vaccine was launched in India on 16 January 2021, prioritizing health care workers which included medical students. We aimed to assess vaccine hesitancy and factors related to it among undergraduate medical students in India. An online questionnaire was filled by 1068 medical students across 22 states and union territories of India from 2 February – 7 March 2021. Vaccine hesitancy was found among 10.6%. Concern regarding vaccine safety and efficacy, hurried testing of vaccines prior to launch and lack of trust in government agencies predicted COVID-19 vaccine hesitancy. Risk perception regarding contracting COVID-19 vaccine reduced COVID-19 vaccine hesitancy as well as hesitation in participating in COVID-19 vaccine trials. Choosing between the two available vaccines (Covishield and Covaxin) was considered important by medical students both for themselves and their future patients. Covishield was preferred to Covaxin by students. Majority of those willing to take the COVID-19 vaccine felt that it was important for them to resume their clinical posting, face-to-face classes and get their personal life back on track. Around three-fourths medical students viewed that COVID-19 vaccine should be made mandatory for both health care workers and international travellers. Prior adult vaccination didn’t have an effect upon COVID-19 vaccine hesitancy. Targeted awareness campaigns, regulatory oversight of vaccine trials and public release of safety and efficacy data and trust building activities could further reduce COVID-19 vaccine hesitancy among medical students.
Deep brain stimulation in the bed nucleus of the stria terminalis: a symptom provocation study in patients with obsessive-compulsive disorder
Authors: Luyck Kelly , Bervoets Chris , Deblieck Choi , Nuttin Bart , Luyten Laura
Published: March 2021

Background

Deep brain stimulation (DBS) is an emerging therapy for treatment-resistant obsessive-compulsive disorder (OCD), and several targets for electrode implantation and contact selection have been proposed, including the bed nucleus of the stria terminalis (BST). Selecting the active electrode contacts (patients typically have four to choose from in each hemisphere), and thus the main locus of stimulation, can be a taxing process. Here, we investigated whether contact selection based purely on their neuroanatomical position in the BST is a worthwhile approach. For the first time, we also compared the effects of uni- versus bilateral BST stimulation.

Methods

Nine OCD patients currently receiving DBS participated in a double-blind, randomized symptom provocation study to compare no versus BST stimulation. Primary outcomes were anxiety and mood ratings in response to disorder-relevant trigger images, as well as ratings of obsessions, compulsions, tendency to avoid and overall wellbeing. Furthermore, we asked whether patients preferred the electrode contacts in the BST over their regular stimulation contacts as a new treatment setting after the end of the task.

Results

We found no statistically significant group differences between the four conditions (no, left, right and bilateral BST stimulation). Exploratory analyses, as well as follow-up data, did indicate that (bilateral) bipolar stimulation in the BST was beneficial for some patients, particularly for those who had achieved unsatisfactory effects through the typical contact selection procedure.

Conclusions

Despite its limitations, this study suggests that selection of stimulation contacts in the BST is a viable option for DBS in treatment-resistant OCD patients.
Mitochondrial Phenotypes Distinguish Pathogenic MFN2 Mutations by Pooled Functional Genomics Screen
Authors: Yenkin Alex L. , Bramley John C. , Kremitzki Colin L. , Waligorski Jason E. , Liebeskind Mariel J. , Xu Xinyuan E. , Vakaki Maria A. , Chandrasekaran Vinay D. , Mitra Robi D. , Milbrandt Jeffrey D. , Buchser William J.
Published: March 2021

Most human genetic variation is classified as VUS - variants of uncertain significance. While advances in genome editing have allowed innovation in pooled screening platforms, many screens deal with relatively simple readouts (viability, fluorescence) and cannot identify the complex cellular phenotypes that underlie most human diseases. In this paper, we present a generalizablefunctional genomicsplatform that combines high-content imaging, machine learning, and microraft isolation in a new method termed “Raft-Seq”. We highlight the efficacy of our platform by showing its ability to distinguish pathogenic point mutations of the mitochondrial regulatorMFN2, even when the cellular phenotype is subtle. We also show that our platform achieves its efficacy using multiple cellular features, which can be configured on-the-fly. Raft-Seq enables a new way to perform pooled screening on sets of mutations in biologically relevant cells, with the ability to physically capture any cell with a perturbed phenotype and expand it clonally, directly from the primary screen.

Graphical Abstract

Here, we address the need to evaluate the impact of numerous genetic variants. This manuscript depicts the methods of using machine learning on a biologically relevant phenotype to predict specific point mutations, followed by physically capturing those mutated cells.
GWAS associated Variants, Non-genetic Factors, and Transient Transcriptome in Multiple Sclerosis Etiopathogenesis: a Colocalization Analysis
Authors: Umeton Renato , Bellucci Gianmarco , Bigi Rachele , Romano Silvia , Buscarinu Maria Chiara , Reniè Roberta , Rinaldi Virginia , Umeton Raffaella Pizzolato , Morena Emanuele , Romano Carmela , Mechelli Rosella , Salvetti Marco , Ristori Giovanni
Published: March 2021

A clinically actionable understanding of multiple sclerosis (MS) etiology goes through GWAS interpretation, prompting research on new gene regulatory models. We previously suggested a stochastic etiologic model where small-scale random perturbations could reach a threshold for MS development. The recently described mapping of the transient transcriptome (TT), including intergenic and intronic RNAs, seems appropriate to verify this model through a rigorous colocalization analysis. We show that genomic regions coding for the TT were significantly enriched for MS-associated GWAS variants and DNA binding sites for molecular transducers mediating putative, non-genetic, etiopathogenetic factors for MS (e.g., vitamin D deficiency, Epstein Barr virus latent infection, B cell dysfunction). These results suggest a model whereby TT-coding regions are hotspots of convergence between genetic ad non-genetic factors of risk/protection for MS, and plausibly for other complex disorders. Our colocalization analysis also provides a freely available data resource (www.mscoloc.com) for future research on MS transcriptional regulation.
Ensemble Switching Unveils a Kinetic Rheostat Mechanism of the Eukaryotic Thiamine Pyrophosphate Riboswitch
Authors: Ma Junyan , Saikia Nabanita , Godar Subash , Hamilton George L. , Ding Feng , Alper Joshua , Sanabria Hugo
Published: March 2021

Thiamine pyrophosphate (TPP) riboswitches regulate thiamine metabolism by inhibiting the translation of enzymes essential to thiamine synthesis pathways upon binding to thiamine pyrophosphate in cells across all domains of life. Recent work on theArabidopsis thalianaTPP riboswitch suggests a multi-step TPP binding process involving multiple riboswitch conformational ensembles and that Mg2+dependence underlies the mechanism of TPP recognition and subsequent transition to the translation-inhibiting state of the switching sequence followed by changes in the expression platform. However, details of the relationship between TPP riboswitch conformational changes and interactions with TPP and Mg2+in the aptamer domain constituting this mechanism are unknown. Therefore, we integrated single-molecule multiparameter fluorescence and force spectroscopy with atomistic molecular dynamics simulations and found that conformational transitions within the aptamer domain associated with TPP and Mg2+ligand binding occurred between at least five different ensembles on timescales ranging from μs to ms. These dynamics are at least an order of magnitude faster than folding and unfolding kinetics associated with translation-state switching in the switching sequence. Moreover, we propose that two pathways exist for ligand recognition. Together, our results suggest a dynamic ensemble switching of the aptamer domain that may lead to the translation-inhibiting state of the riboswitch. Additionally, our results suggest that multiple configurations could enable inhibitory tuning manifested through ligand-dependent changes via ensemble switching and kinetic rheostat-like behavior of theArabidopsis thalianaTPP riboswitch.
DNA origami patterning of synthetic T cell receptors reveals spatial control of the sensitivity and kinetics of signal activation
Authors: Dong Rui , Aksel Tural , Chan Waipan , Germain Ronald N. , Vale Ronald D. , Douglas Shawn M.
Published: March 2021

T cell receptor clustering plays a key role in triggering cell activation, but the relationship between the spatial configuration of clusters and elicitation of downstream intracellular signals remains poorly understood. We developed a DNA-origami-based system that is easily adaptable to other cellular systems and enables rich interrogation of responses to a variety of spatially defined inputs. Using a chimeric antigen receptor (CAR) T cell model system with relevance to cancer therapy, we studied signaling dynamics at single cell resolution. We found that the spatial arrangement of receptors determines the ligand density threshold for triggering and encodes the temporal kinetics of signaling activities. We also showed that signaling sensitivity of a small cluster of high-affinity ligands is enhanced when surrounded by non-stimulating low-affinity ligands. Our results suggest that cells measure spatial arrangements of ligands and translates that information into distinct signaling dynamics, and provide insights into engineering new immunotherapies.
Familial thyroid follicular cell carcinomas in a large number of Dutch German longhaired pointers
Authors: Yu Yun , Krupa Adriana , Keesler Rebekah I. , Grinwis Guy C. M. , de Ruijsscher Mariska , de Vos Johan , Groenen Martien A. M. , Crooijmans Richard P. M. A.
Published: March 2021

Thyroid carcinomas originating from follicular cells of the thyroid gland occur in both humans and dogs and they have highly similar histomorphologic patterns. In dogs, thyroid carcinomas have not been extensively investigated, especially concerning the familial origin of thyroid carcinomas. Here we report familial thyroid follicular cell carcinomas confirmed by histology in 54 Dutch origin German longhaired pointers. From the pedigree, 45 of 54 histopathologically confirmed cases are closely related to a pair of first-half cousins in the past, indicating a familial disease. In addition, genetics contributed more to the thyroid follicular cell carcinoma than other factors by an estimated heritability of 0.62 based on pedigree. The age of diagnosis ranged between 4.5 and 13.5 years, and 76% of cases were diagnosed before 10 years of age, implying an early onset of disease. We observed a significant higher pedigree-based inbreeding coefficient in the affected dogs (meanF0.23) compared to unaffected dogs (meanF0.14), suggesting the contribution of inbreeding to tumour development. The unique occurrence of familial thyroid follicular cell carcinoma in this dog population and the large number of affected dogs make this population an important model to identify the genetic basis of familial thyroid follicular cell carcinoma in this breed and may contribute to the research into pathogenesis, prevention and treatment in humans.
FlywheelTools: Data Curation and Manipulation on the Flywheel Platform
Authors: Tapera Tinashe M. , Cieslak Matthew , Bertolero Max , Adebimpe Azeez , Aguirre Geoffrey K. , Butler Ellyn R. , Cook Philip A. , Davila Diego , Elliott Mark A. , Linguiti Sophia , Murtha Kristin , Tackett William , Detre John A. , Satterthwaite Theodore D.
Published: March 2021

The recent and growing focus on reproducibility in neuroimaging studies has led many major academic centers to use cloud-based imaging databases for storing, analyzing, and sharing complex imaging data. Flywheel is one such database platform that offers easily accessible, large-scale data management, along with a framework for reproducible analyses through containerized pipelines. The Brain Imaging Data Structure (BIDS) is a data storage specification for neuroimaging data, but curating neuroimaging data into BIDS can be a challenging and time-consuming task. In particular, standard solutions for BIDS curation are not designed for use on cloud-based systems such as Flywheel. To address these challenges, we developed “FlywheelTools”, a software toolbox for reproducible data curation and manipulation on Flywheel. FlywheelTools includes two elements:fw-heudiconv, for heuristic-driven curation of data into BIDS, andflaudit, which audits and inventories projects on Flywheel. Together, these tools accelerate reproducible neuroscience research on the widely used Flywheel platform.
Molecular Response to PARP1 Inhibition in Ovarian Cancer Cells as Determined by Mass Spectrometry Based Proteomics
Authors: Franz Alexandra , Coscia Fabian , Shen Ciyue , Charaoui Lea , Mann Matthias , Sander Chris
Published: March 2021

Poly (ADP)-ribose polymerase (PARP) inhibitors have entered routine clinical practice for the treatment of high-grade serous ovarian cancer (HGSOC), yet the molecular mechanisms underlying treatment response to PARP1 inhibition (PARP1i) are not fully understood. Here, we used unbiased mass spectrometry based proteomics with data-driven protein network analysis to systematically characterize how HGSOC cells respond to PARP1i treatment. We found that PARP1i leads to pronounced proteomic changes in a diverse set of cellular processes in HGSOC cancer cells, consistent with transcript changes in an independent perturbation dataset. We interpret decreases in the levels of the pro-proliferative transcription factors SP1 and β-catenin and in growth factor signaling as reflecting the anti-proliferative effect of PARP1i; and the strong activation of pro-survival processes NF-ϰB signaling and lipid metabolism as PARPi-induced adaptive resistance mechanisms. Based on these observations, we nominate several protein targets for therapeutic inhibition in combination with PARP1i. When tested experimentally, the combination of PARPi with an inhibitor of fatty acid synthase (TVB-2640) has a 3-fold synergistic effect and is therefore of particular pre-clinical interest. Our study improves the current understanding of PARP1 function, highlights the potential that the anti-tumor efficacy of PARP1i may not only rely on DNA damage repair mechanisms and informs on the rational design of PARP1i combination therapies in ovarian cancer.
Cdk8 directly regulates glycolysis via phosphorylation of Gcr2
Authors: Aristizabal Maria J. , O’Duibhir Eoghan , de Jonge Wim , Dever Kristy , Hawe Nicole , Koerkamp Marian Groot , Brok Mariel , van Leenen Dik , Lijnzaad Philip , Kobor Michael S. , Holstege Frank C.P. , Sadowski Ivan
Published: March 2021

CDK8encodes an evolutionarily conserved Mediator complex kinase subunit that functions in general and context-specific transcription regulation by phosphorylating core components of the transcription machinery and gene-specific transcription factors. To better understand the role Cdk8 in transcription regulation, we performed high-resolution gene expression time course analysis following nuclear depletion of Cdk8. Focusing on the earliest gene expression alterations revealed dysregulation of genes encoding glycolysis enzymes, suggesting a functional link to Gcr1 and Gcr2, key transcriptional activators of these genes. Consistently, we found that nuclear depletion of Cdk8 altered the mRNA levels of glycolysis genes as well as the promoter occupancy of Gcr2, but not Gcr1. Examination of the Gcr2 protein sequence revealed a putative Cdk8 phosphorylation site at serine 365, which we confirmed usingin vitroandin vivoassays. Importantly, phospho-mutantGCR2recapitulated the growth and gene expression defects of theGCR2deletion mutant, effects not observed with a phospho mimetic mutant. As such, our work highlights Gcr2 as a new Cdk8 substrate, revealing that its phosphorylation is critical for the activation of genes encoding glycolysis enzymes.
Mental health explains individual deviations from normative range in cognition-associated brain states
Authors: Zhang Wei , Vidaurre Diego , Bijsterbosch Janine Diane
Published: March 2021

Links between cognitive deficits and psychiatric disorders have been studied predominantly at the group level, leaving unique individual characteristics largely elusive. Here, we applied normative modeling to UK Biobank data (N=18,634) and estimated the individual-level interplay of large-scale brain networks over time (i.e., dynamic brain state) as a function of general cognitive ability. Abnormality in such brain states was linked to individual variation in mental health. Specifically, brain state measures including fractional occupancy that indicates the brain state probability over time were estimated using a Hidden Markov Model, followed by a Gaussian process regression to estimate the normative range of these brain state measures from general cognitive ability. Abnormality scores per participant were quantified to represent the degree of deviations relative to the estimated population norm. We found significant associations between the abnormality scores of several brain states and individuals’ overall mental health. Our findings suggest potential impact of mental health on dynamic brain states that subserve cognitive functions and shed light on the relevant brain mechanisms underlying cognitive deficits in mental illness.
Neuronal mechanisms of novelty seeking
Authors: Ogasawara Takaya , Sogukpinar Fatih , Zhang Kaining , Feng Yang-Yang , Pai Julia , Jezzini Ahmad , Monosov Ilya E.
Published: March 2021

Humans and other primates interact with the world by observing and exploring visual objects. In particular, they often seek out the opportunities to view novel objects that they have never seen before, even when they have no extrinsic primary reward value. However, despite the importance of novel visual objects in our daily life, we currently lack an understanding of how primate brain circuits control the motivation to seek out novelty. We found that novelty-seeking is regulated by a small understudied subcortical region, the zona incerta (ZI). In a task in which monkeys made eye movements to familiar objects to obtain the opportunity to view novel objects, many ZI neurons were preferentially activated by predictions of future novel objects and displayed burst excitations before gaze shifts to gain access to novel objects. Low intensity electrical stimulation of ZI facilitated gaze shifts, while inactivations of ZI reduced novelty-seeking. Surprisingly, additional experiments showed that this ZI-dependent novelty seeking behavior is not regulated by canonical neural circuitry for reward seeking. The habenula-dopamine pathway, known to reflect reward predictions that control reward seeking, was relatively inactive during novelty-seeking behavior in which novelty had no extrinsic reward value. Instead, high channel-count electrophysiological experiments and anatomical tracing identified a prominent source of control signals for novelty seeking in the anterior ventral medial temporal cortex (AVMTC), a brain region known to be crucially involved in visual processing and object memory. In addition to their well-known function in signaling the novelty or familiarity of objects in the current environment, AVMTC neurons reflected the predictions of future novel objects, akin to the way neurons in reward-circuitry predict future rewards in order to control reward-seeking. Our data uncover a network of primate brain areas that regulate novelty-seeking. The behavioral and neural distinctions between novelty-seeking and reward-processing highlight how the brain can accomplish behavioral flexibility, providing a mechanism to explore novel objects.
Confronting false discoveries in single-cell differential expression
Authors: Squair Jordan W. , Gautier Matthieu , Kathe Claudia , Anderson Mark A. , James Nicholas D. , Hutson Thomas H. , Hudelle Rémi , Qaiser Taha , Matson Kaya J. E. , Barraud Quentin , Levine Ariel J. , La Manno Gioele , Skinnider Michael A. , Courtine Grégoire
Published: March 2021

Differential expression analysis in single-cell transcriptomics enables the dissection of cell-type-specific responses to perturbations such as disease, trauma, or experimental manipulation. While many statistical methods are available to identify differentially expressed genes, the principles that distinguish these methods and their performance remain unclear. Here, we show that the relative performance of these methods is contingent on their ability to account for variation between biological replicates. Methods that ignore this inevitable variation are biased and prone to false discoveries. Indeed, the most widely used methods can discover hundreds of differentially expressed genes in the absence of biological differences. Our results suggest an urgent need for a paradigm shift in the methods used to perform differential expression analysis in single-cell data.
Learning accurate path integration in a ring attractor model of the head direction system
Authors: Vafidis Pantelis , Owald David , D’Albis Tiziano , Kempter Richard
Published: March 2021

Ring attractor models for angular path integration have recently received strong experimental support. To function as integrators, head-direction (HD) circuits require precisely tuned connectivity, but it is currently unknown how such tuning could be achieved. Here, we propose a network model in which a local, biologically plausible learning rule adjusts synaptic efficacies during development, guided by supervisory allothetic cues. Applied to theDrosophilaHD system, the model learns to path-integrate accurately and develops a connectivity strikingly similar to the one reported in experiments. The mature network is a quasi-continuous attractor and reproduces key experiments in which optogenetic stimulation controls the internal representation of heading, and where the network remaps to integrate with different gains. Our model predicts that path integration requires supervised learning during a developmental phase. The model setting is general and also applies to architectures that lack the physical topography of a ring, like the mammalian HD system.
Face processing of social cognition in patients with first episode psychosis: Its deficits and association with the right subcallosal anterior cingulate cortex
Authors: Narita Zui , Kuga Hironori , Piancharoen Peeraya , Faria Andreia , Mihaljevic Marina , Longo Luisa , Etyemez Semra , Namkung Ho , Coughlin Jennifer , Nestadt Gerald , Nucifora Frederik , Sedlak Thomas , Schaub Rebecca , Crawford Jeff , Schretlen David , Ishizuka Koko , Miyata Jun , Yang Kun , Sawa Akira
Published: March 2021

The clinical importance of social cognition is well acknowledged in patients with psychosis, in particular those with first episode psychosis (FEP). Nevertheless, its brain substrates and circuitries remain elusive, lacking precise analysis between multimodal brain characteristics and behavioral sub-dimensions within social cognition. In the present study, we examined face processing of social cognition in 79 FEP patients and 80 healthy controls (HCs). We looked for a possible correlation between face processing and multimodal MRI characteristics such as resting-state functional connectivity (rsFC) and brain volume. We observed worse recognition accuracy, longer recognition response time, and longer memory response time in FEP patients when compared with HCs. Of these, memory response time was selectively correlated with specific rsFCs, which included the right subcallosal sub-region of BA24 in the ACC (scACC), only in FEP patients. The volume of this region was also correlated with memory response time in FEP patients. The scACC is functionally and structurally important in FEP-associated abnormalities of face processing measures in social cognition.
Altered cortico-subcortical network after adolescent alcohol exposure mediates behavioral deficits in flexible decision-making
Authors: Gómez-A Alexander , Dannenhoffer Carol A. , Elton Amanda , Lee SungHo , Ban Woomi , Shih Yen-Yu Ian , Boettiger Charlotte A. , Robinson Donita L.
Published: March 2021

Behavioral flexibility, the ability to modify behavior according to changing conditions, is essential to optimize decision-making. Deficits in behavioral flexibility that persist into adulthood are one consequence of adolescent alcohol exposure, and another is decreased functional connectivity in brain structures involved in decision-making; however, a link between these two outcomes has not been established. We assessed effects of adolescent alcohol and sex on both Pavlovian and instrumental behaviors and functional connectivity in adult animals to determine associations between behavioral flexibility and resting-state functional connectivity. Alcohol exposure impaired attentional set reversals and decreased functional connectivity among cortical and subcortical regions-of-interest that underlie flexible behavior. Moreover, mediation analyses indicated that adolescent alcohol-induced reductions in functional connectivity within a subnetwork of affected brain regions mediated errors committed during reversal learning. These results provide a novel link between persistent reductions in brain functional connectivity and deficits in behavioral flexibility resulting from adolescent alcohol exposure.