bluuebunny/crossref_metadata_2025 huggingface dataset:
̃Evaluating reduction in CoViD-19 cases by isolation and protective measures in São Paulo State, Brazil, and scenarios of release
Authors: Yang Hyun Mo , Junior Luis Pedro Lombardi , Castro Fabio Fernandes Morato , Yang Ariana Campos
Published: May 2020

São Paulo State registered the first case of CoViD-19 on 26 February, the first death due to CoViD-19 on 16 March, and implemented the isolation of the population in non-essential activities on 24 March, which is programmed to end on 1 June. A mathematical model considering young (below 60 years old) and elder (above 60 years) subpopulations was formulated based on the natural history of CoViD-19 to study the transmission of the new coronavirus in São Paulo State, Brazil. This deterministic model used the data collected in São Paulo State to estimate the model parameters and to evaluate the effects of herd protection, that is, isolation and personal and collective protective measures. Based on the estimated parameters, we evaluated the scenarios of three releases divided in equal proportions elapsed by 14 days between releases, but beginning in three different times (the first release occurring on 1 and 23 June, and 6 July). We concluded that these three strategies of release are equivalent (little difference) in reducing the number of severe CoViD-19 if social behaviour does not change. However, if protective measures as using face mask and hygiene (washing hands, for instance) and social distancing could be massively disseminated in the population to decrease the transmission of CoViD-19 by 80%, we concluded that the health care system may not collapse with release.
Serologic responses to SARS-CoV-2 infection among hospital staff with mild disease in eastern France
Authors: Fafi-Kremer Samira , Bruel Timothee , Madec Yoann , Grant Rebecca , Tondeur Laura , Grzelak Ludivine , Staropoli Isabelle , Anna Francois , Souque Philippe , Mutter Catherine , Collongues Nicolas , Bolle Alexandre , Velay Aurelie , Lefebvre Nicolas , Mielcarek Marie , Meyer Nicolas , Rey David , Charneau Pierre , Hoen Bruno , De Seze Jerome , Schwartz Olivier , Fontanet Arnaud
Published: May 2020

Background: The serologic response of individuals with mild forms of SARS-CoV-2 infection is poorly characterized.
Methods: Hospital staff who had recovered from mild forms of PCR-confirmed SARS-CoV-2 infection were tested for anti-SARS-CoV-2 antibodies using two assays: a rapid immunodiagnostic test (99.4% specificity) and the S-Flow assay (~99% specificity).The neutralizing activity of the sera was tested with a pseudovirus-based assay.
Results: Of 162 hospital staff who participated in the investigation, 160 reported SARS-CoV- 2 infection that had not required hospital admission and were included in these analyses. The median time from symptom onset to blood sample collection was 24 days (IQR: 21-28, range 13-39). The rapid immunodiagnostic test detected antibodies in 153 (95.6%) of the samples and the S-Flow assay in 159 (99.4%), failing to detect antibodies in one sample collected 18 days after symptom onset (the rapid test did not detect antibodies in that patient). Neutralizing antibodies (NAbs) were detected in 79%, 92% and 98% of samples collected 13-20, 21-27 and 28-41 days after symptom onset, respectively (P=0.02).
Conclusion: Antibodies against SARS-CoV-2 were detected in virtually all hospital staff sampled from 13 days after the onset of COVID-19 symptoms. This finding supports the use of serologic testing for the diagnosis of individuals who have recovered from SARS-CoV-2 infection. The neutralizing activity of the antibodies increased overtime. Future studies will help assess the persistence of the humoral response and its associated neutralization capacity in recovered patients.
Detection of SARS-CoV-2 from raw patient samples by coupled high temperature reverse transcription and amplification
Authors: Kuiper Johannes W.P. , Baade Timo , Kremer Marcel , Kranaster Ramon , Irmisch Linda , Schuchmann Marcus , Zander Johannes , Marx Andreas , Hauck Christof R
Published: May 2020

The SARS-CoV-2 beta coronavirus is spreading globally with unprecedented consequences for modern societies. The early detection of infected individuals is a pre-requisite for all strategies aiming to contain the virus. Currently, purification of RNA from patient samples followed by RT-PCR is the gold standard to assess the presence of this single-strand RNA virus. However, these procedures are time consuming, require continuous supply of specialized reagents, and are prohibitively expensive in resource-poor settings. Here, we report an improved nucleic-acid-based approach to detect SARS-CoV-2, which alleviates the need to purify RNA, reduces handling steps, minimizes costs, and allows evaluation by non-specialized equipment. The use of unprocessed swap samples and the ability to detect as little as three viral genome equivalents is enabled by employing a heat-stable RNA- and DNA-dependent DNA polymerase, which performs the double task of stringent reverse transcription of RNA at elevated temperatures as well as PCR amplification of a SARS-CoV-2 specific target gene. As results are obtained within 2 hours and can be read-out by a hand-held LED-screen, this novel protocol will be of particular importance for large-scale virus surveillance in economically constrained settings.
Prevalence of Mental Health Problems During Virus Epidemics in the General Public, Health Care Workers and Survivors: A Rapid Review of the Evidence
Authors: Zuercher Simeon J , Kerksieck Philipp , Adamus Christine , Burr Christian , Lehmann Anja I , Huber Flavia K , Richter Dirk
Published: May 2020

Background: The swift spread of SARS-CoV-2 provides a challenge worldwide. As a consequence of restrictive public health measures like isolation, quarantine, and community containment, the provision of mental health services is a major challenge. Evidence from past virus epidemics and the current SARS-CoV-2 outbreak indicate high prevalence rates of mental health problems (MHP) as short- and long-term consequences. However, a broader picture of MHP among different populations is still lacking.
Methods: We conducted a rapid review on MHP prevalence rates published since 2000, during and after epidemics, including the general public, health care workers, and survivors. Any quantitative articles reporting on MHP rates were included. Out of 2855 articles screened, a total of 74 were included in this review.
Results: Most original studies on MHP were conducted in China in the context of SARS-CoV-1, and reported on anxiety, depression, post-traumatic stress symptoms/disorder, general psychiatric morbidity, and psychological symptoms. The MHP rates across studies, populations, and epidemics vary substantially. While some studies show high and persistent rates of MHP in populations directly affected by isolation, quarantine, threat of infection, infection, or life-threatening symptoms (e.g. health care workers), other studies report minor effects. Furthermore, even less affected populations (e.g. distant to epidemic epicenter, no contact history with suspected or confirmed cases) can show high rates of MHP.
Discussion: MHP vary largely across countries and risk-groups in reviewed studies. The results call attention to potentially high MHP during epidemics. Individuals affected directly by an epidemic might be at a higher risk of short or even long-term mental health impairments. This study delivers insights stemming from a wide range of psychiatric instruments and questionnaires. The results call for the use of validated and standardized instruments, reference norms, and pre-post measurements to better understand the magnitude of the MHP during and after the epidemics. Nevertheless, emerging MHP should be considered during epidemics including the provision of access to mental health care to mitigate potential mental impairments.
Susceptibility-adjusted herd immunity threshold model and potential R0 distribution fitting the observed Covid-19 data in Stockholm
Authors: Brennan Paul V , Brennan Luke Paul
Published: May 2020

The reproduction number, R0, is commonly used, and sometimes misused, in conjunction with the classic Kermack and McKindrick theory based on the assumption of homogeneity, in order to estimate herd immunity threshold (HIT). This provides a crude first estimate of HIT, with more elaborate modelling required to arrive at a more realistic value. Early estimates of HIT for Covid-19 were based on this simplistic homogeneous approach, yielding high HIT values that have since been revised downwards with more sophisticated network modelling taking account of R0 heterogeneity and with reference to the low HIT found from serological sampling in Stockholm County. The aim of this paper is to describe a simple model in which host susceptibility is directly linked to the heterogeneous R0 distribution, to shed further light on the mechanisms involved and to arrive at a bimodal R0 distribution consistent with the Covid-19 HIT observed in Stockholm County.
Cancer immunotherapy does not increase the risk of death by COVID-19 in melanoma patients
Authors: Gonzalez-Cao Maria , Antonazas-Basa Monica , Puertolas Teresa , Munoz-Couselo Eva , Manzano Jose Luis , Carrera Cristina , Marquez-Rodas Ivan , Lopez-Criado Pilar , Rodriguez-Moreno Juan Francisco , Garcia-Castano Almudena , Martin-Liberal Juan , Rodriguez-Jimenez Pedro , Puig Susana , Cerezuela Pablo , Feito-Rodriguez Marta , Rubio-Viqueira Belen , Crespo Guillermo , Luna-Fra Pablo , Aguayo Cristina , Ayala de Miguel Pablo , Feltes Rosa , Valles Lara , Drozdowskyj Ana , Soria Ainara , Maldonado Cayetana , Fernandez-Morales Luis , Rosell Rafael , Provencio Mariano , Berrocal Alfonso
Published: May 2020

Background: Covid-19 pandemic by the new coronavirus SARS-Cov-2 has produced devastating effects on the health care system, affecting also cancer patient care. Data about COVID-19 infection in cancer patients are scarce, and they point out a higher risk of complications due to the viral infection in this population. Moreover, cancer treatments could increase viral complications, specially those treatments based on the use of immunotherapy with checkpoints antibodies. There are no clinical data about the safety of immune check point antibodies in cancer patients when they become infected by SARS-CoV-2. As checkpoint inhibitors, mainly anti PD-1 and anti CTLA-4 antibodies, are an effective treatment for most melanoma patients, avoiding their use during the pandemic could lead to a decrease in the chances of curing melanoma.
Methods: In Spain we have started a national registry of melanoma patients infected by SARS-Cov-2 since April 1st, 2020. A retrospective analysis of patients included in the Spanish registery has been performed weekly since the activation of the study. Interim analysis shows unexpected findings about cancer treatment safety in SARS-Cov-2 infected melanoma patients, so a rapid communication to the scientific community is mandatory
Results: Fifty patients have been included as of May 17th, 2020. Median age is 69 years (range 6 to 94 years), 27 (54%) patients are males and 36 (70%) patients have stage IV melanoma. Twenty-two (44%) patients were on active anticancer treatment with anti PD-1 antibodies, 16 (32%) patients were on treatment with BRAF plus MEK inhibitors and 12 (24%) patients were not on active cancer treatment. COVID-19 episode has been resolved in 43 cases, including 30 (70%) patients cured, four (9%) patients that have died due to melanoma progression, and nine (21%) patients that have died from COVID-19. Mortality rates from COVID-19 according to melanoma treatment type were 16%, 15% and 36% for patients on immunotherapy, targeted drugs, and for those that were not undergoing active cancer treatment, respectively.
Conclusion: These preliminary findings show that the risk of death in those patients undergoing treatment with anti PD-1 antibodies does not exceed the global risk of death in this population. These results could be relevant in order to select melanoma therapy during the COVID-19 pandemic
A simple criterion to design optimal non-pharmaceutical interventions for epidemic outbreaks
Authors: Angulo Marco Tulio , Castaños Fernando , Moreno-Morton Rodrigo , Velasco-Hernández Jorge X. , Moreno Jaime A.
Published: May 2020

For mitigating the COVID-19 pandemic, much emphasis is made on implementing non-pharmaceutical interventions to keep the reproduction number below one. However, using that objective ignores that some of these interventions, like bans of public events or lockdowns, must be transitory and as short as possible because of their significative economic and societal costs. Here we derive a simple and mathematically rigorous criterion for designing optimal transitory non-pharmaceutical interventions for mitigating epidemic outbreaks. We find that reducing the reproduction number below one is sufficient but not necessary. Instead, our criterion prescribes the required reduction in the reproduction number according to the desired maximum of disease prevalence and the maximum decrease of disease transmission that the interventions can achieve. We study the implications of our theoretical results for designing non-pharmaceutical interventions in 16 cities and regions during the COVID-19 pandemic. In particular, we estimate the minimal reduction of each region’s contact rate necessary to control the epidemic optimally. Our results contribute to establishing a rigorous methodology to guide the design of optimal non-pharmaceutical intervention policies.
Maturation of complex synaptic connections of layer 5 cortical axons in the posterior thalamic nucleus requires SNAP25
Authors: Hayashi Shuichi , Hoerder-Suabedissen Anna , Kiyokage Emi , Maclachlan Catherine , Toida Kazunori , Knott Graham , Molnár Zoltán
Published: May 2020

Synapses are able to form in the absence of neuronal activity, but how is their subsequent maturation affected in the absence of regulated vesicular release? We explored this question using 3D electron microscopy and immuno electron microscopy analyses in the large, complex synapses formed between cortical sensory efferent axons and dendrites in the posterior thalamic nucleus. Using aSnap25conditional knockout we found that during the first two postnatal weeks the axonal boutons emerge and increase in the size similar to the control animals. However, by P18, when an adult-like architecture should normally be established, axons were significantly smaller with 3D reconstructions showing that eachSnap25-cko bouton only forms a single synapse with the connecting dendritic shaft. No excrescences from the dendrites were formed, and none of the normally large glomerular axon endings were seen. These results show that activity mediated through regulated vesicular release from the presynaptic terminal is not necessary for the formation of synapses, but it is required for the maturation of the specialised synaptic structures between layer 5 corticothalamic projections in Po.
Massively parallel quantification of CRISPR editing in cells by TRAP-seq enables better design of Cas9, ABE, CBE gRNAs of high efficiency and accuracy
Authors: Xiang Xi , Qu Kunli , Liang Xue , Pan Xiaoguang , Wang Jun , Han Peng , Dong Zhanying , Liu Lijun , Zhong Jiayan , Ma Tao , Wang Yiqing , Yu Jiaying , Zhao Xiaoying , Li Siyuan , Xu Zhe , Wang Jinbao , Zhang Xiuqing , Jiang Hui , Xu Fengping , Zou Lijin , Teng Huajing , Liu Xin , Xu Xun , Wang Jian , Yang Huanming , Bolund Lars , Church George M. , Lin Lin , Luo Yonglun
Published: May 2020

The CRISPR RNA-guided endonucleases Cas9, and Cas9-derived adenine/cytosine base editors (ABE/CBE), have been used in both research and therapeutic applications. However, broader use of this gene editing toolbox is hampered by the great variability of efficiency among different target sites. Here we present TRAP-seq, a versatile and scalable approach in which the CRISPR gRNA expression cassette and the corresponding surrogate site are captured byTargetedReporterAnchoredPositionalSequencing in cells. TRAP-seq can faithfully recapitulate the CRISPR gene editing outcomes introduced to the corresponding endogenous genome site and most importantly enables massively parallel quantification of CRISPR gene editing in cells. We demonstrate the utility of this technology for high-throughput quantification of SpCas9 editing efficiency and indel outcomes for 12,000 gRNAs in human embryonic kidney cells. Using this approach, we also showed that TRAP-seq enables high throughput quantification of both ABE and CBE efficiency at 12,000 sites in cells. This rich amount of ABE/CBE outcome data enable us to reveal several novel nucleotide features (e.g. preference of flanking bases, nucleotide motifs, STOP recoding types) affecting base editing efficiency, as well as designing improved machine learning-based prediction tools for designing SpCas9, ABE and CBE gRNAs of high efficiency and accuracy (>70%). We have integrated all the 12,000 CRISPR gene editing outcomes for SpCas9, ABE and CBE into a CRISPR-centered portal: The Human CRISPR Atlas. This study extends our knowledge on CRISPR gene and base editing, and will facilitate the application and development of CRISPR in both research and therapy.
Fluctuation spectroscopy of giant unilamellar vesicles using confocal and phase contrast microscopy
Authors: Faizi Hammad A. , Reeves Cody J. , Georgiev Vasil N. , Vlahovska Petia M. , Dimova Rumiana
Published: May 2020

A widely used method to measure the bending rigidity of bilayer membranes is fluctuation spectroscopy, which analyses the thermally-driven membrane undulations of giant unilamellar vesicles recorded with either phase-contrast or confocal microscopy. Here, we analyze the fluctuations of the same vesicle using both techniques and obtain consistent values for the bending modulus. We discuss the factors that may lead to discrepancies.
Traction Force Microscopy by Deep Learning
Authors: Wang Y.L. , Lin Y.-C.
Published: May 2020

Cells interact mechanically with their surrounding by exerting forces and sensing forces or force-induced displacements. Traction force microscopy (TFM), purported to map cell-generated forces or stresses, represents an important tool that has powered the rapid advances in mechanobiology. However, to solve the ill-posted mathematical problem, its implementation has involved regularization and the associated compromises in accuracy and resolution. Here we applied neural network-based deep learning as a novel approach for TFM. We modified a network for processing images to process vector fields of stress and strain. Furthermore, we adapted a mathematical model for cell migration to generate large sets of simulated stresses and strains for training the network. We found that deep learning-based TFM yielded results qualitatively similar to those from conventional methods but at a higher accuracy and resolution. The speed and performance of deep learning TFM make it an appealing alternative to conventional methods for characterizing mechanical interactions between cells and the environment.

Statement of Significance

Traction Force Microscopy has served as a fundamental driving force for mechanobiology. However, its nature as an ill-posed inverse problem has posed serious challenges for conventional mathematical approaches. The present study, facilitated by large sets of simulated stresses and strains, describes a novel approach using deep learning for the calculation of traction stress distribution. By adapting the UNet neural network for handling vector fields, we show that deep learning is able to minimize much of the limitations of conventional approaches to generate results with speed, accuracy, and resolution.
The Effect of Non-Pharmacologic Strategies on Prevention or Management of Intensive Care Unit Delirium: A Systematic Review
Authors: Hashemighouchani Haleh , Cupka Julie , Lipori Jessica , Ruppert Matthew M , Ozrazgat-Baslanti Tezcan , Rashidi Parisa , Bihorac Azra
Published: May 2020

Objective

The aim of this systematic review is to examine and report on recently available literature evaluating the relationship between non-pharmacologic management strategies and the reduction of delirium in the intensive care unit.

Methods

Six major research databases were systematically searched for articles analyzing the efficacy of non-pharmacologic delirium interventions in the past five years. Search results were restricted to adult human patients aged 18 years or older in the intensive care unit setting, excluding terminally ill subjects and withdrawal-related delirium. Following title, abstract, and full text review, 27 articles fulfilled the inclusion criteria and are included in this report.

Results

The 27 reviewed articles consist of 12 interventions with a single-component investigational approach, and 15 with multi-component bundled protocols. Delirium incidence was the most assessed outcome followed by duration. Family visitation was the most effective individual intervention and mobility interventions were the least effective. Two of the three family studies significantly reduced delirium incidence, while one in five mobility studies did the same. Multi-component bundle approaches were the most effective of all; of the reviewed studies, eight of 11 bundles significantly improved delirium incidence and seven of eight bundles decreased the duration of delirium.

Conclusions

Multi-component, bundled interventions were more effective at managing intensive care unit delirium than those utilizing an approach with a single interventional element. Although better management of this condition suggests a decrease in resource burden and improvement in patient outcomes, comparative research should be performed to identify the importance of specific bundle elements.
COVID-19 case forecasting model for Sri Lanka based on Stringency Index
Authors: Jayatilleke Achala Upendra , Dayarathne Sanjeewa , de Silva Padmal , Siribaddana Pandula , Abeygunawardana Rushan A B , Nieveras Olivia , de Silva Nilanthi , de Silva Janaka
Published: May 2020

Introduction
Sri Lanka has been able to contain COVID-19 transmission through very stringent suppression measures implemented from the onset. The country had been under a strict lockdown since 20 March 2020, and currently the lockdown is being relaxed gradually. The objective of this paper is to describe a projection model for COVID-19 cases in Sri Lanka applied to different scenarios after lockout, utilizing the stringency index as a proxy of total government response.

Methods
COVID-19 Stringency Index (C19SI) is published and updated real time by a research group from Oxford university on 17 selected mitigation and suppression measures employed by different countries. We have mapped and validated the stringency index for Sri Lanka and subsequently validated the projection model in two phases. Predictions for the base-case scenario, less stringent scenarios, advanced relaxation scenarios, and high-risk districts were done with 95% confidence intervals (95%CI) using the validated model, utilizing data up to 10th May.

Results
C19SI was able to accommodate all of the government responses. The model using validated C19SI could predict number of cases with 95% confidence for a period of two weeks. The model predicted base-case scenario of 815 (95%CI, 753-877) active cases by 17 May 2020 and 648 (95%CI, 599-696) cases for the high-risk districts by 18 May 2020. The model further predicted 3,159 (95%CI, 2,928-3,391) cases for 75% stringency and 928,824 (95%CI, 861,772-995,877) cases for 50% stringency. Advancing normalcy by three weeks resulted in the case load increasing to 4526 (95%CI, 4309-4744) by 30 June 2020.

Conclusion
The proposed prediction model based on C19SI provides policy makers an evidence based scientific method for identifying suppression measures that can be relaxed at the most appropriate time.

Key words:
COVID-19, Projections, Stringency Index, SIR Model, Sri Lanka
The Probability of Choosing Both Hands Depends on an Interaction Between Motor Capacity and Limb-Specific Control in Chronic Stroke
Authors: Varghese Rini , Kutch Jason J , Schweighofer Nicolas , Winstein Carolee J
Published: May 2020

A goal of rehabilitation after stroke is to promote pre-stroke levels of arm use for everyday, frequently bimanual, functional activities. We reasoned that, after a stroke, the choice to use one or both hands for bimanual tasks might depend not only on residual motor capacity but also the specialized demands imposed by the task on the paretic hand. To capture spontaneous, task-specific choices, we covertly observed 50 pre-stroke right-handed chronic stroke survivors (25 left hemisphere damage, LHD) and recorded their hand use strategies for two pairs of bimanual tasks with distinct demands: one with greater precision requirements (photo-album tasks), and another with greater stabilization requirements (letter-envelope tasks). The primary outcome was the choice to use one or both hands. Logistic regression was used to test the hypothesis that the probability of choosing a bimanual strategy would be greater in those with less severe motor impairment and those with LHD. When collapsed across the four subtasks, we found support for this hypothesis. However, notably, the influence of these factors on bimanual choice varied based on task demands. For the photo-album task, the probability of a bimanual strategy was greater for those with LHD compared to RHD, regardless of the degree of motor impairment. For the letter-envelope task, we found a significant interaction between impairment and side of lesion in determining the likelihood of choosing both hands. Therefore, the manner in which side of lesion moderates the effect of impairment on hand use depends on the task.
Chromosome-level reference genome of the European wasp spiderArgiope bruennichi: a resource for studies on range expansion and evolutionary adaptation
Authors: Sheffer Monica M. , Hoppe Anica , Krehenwinkel Henrik , Uhl Gabriele , Kuss Andreas W. , Jensen Lars , Jensen Corinna , Gillespie Rosemary G. , Hoff Katharina J. , Prost Stefan
Published: May 2020

Background

Argiope bruennichi, the European wasp spider, has been studied intensively as to sexual selection, chemical communication, and the dynamics of rapid range expansion at a behavioral and genetic level. However, the lack of a reference genome has limited insights into the genetic basis for these phenomena. Therefore, we assembled a high-quality chromosome-level reference genome of the European wasp spider as a tool for more in-depth future studies.

Findings

We generated,de novo, a 1.67Gb genome assembly ofA. bruennichiusing 21.5X PacBio sequencing, polished with 30X Illumina paired-end sequencing data, and proximity ligation (Hi-C) based scaffolding. This resulted in an N50 scaffold size of 124Mb and an N50 contig size of 288kb. We found 98.4% of the genome to be contained in 13 scaffolds, fitting the expected number of chromosomes (n = 13). Analyses showed the presence of 91.1% of complete arthropod BUSCOs, indicating a high quality of the assembly.

Conclusions

We present the first chromosome-level genome assembly in the class Arachnida. With this genomic resource, we open the door for more precise and informative studies on evolution and adaptation inA. bruennichi, as well as on several interesting topics in Arachnids, such as the genomic architecture of traits, whole genome duplication and the genomic mechanisms behind silk and venom evolution.
BTP-7, a novel peptide for therapeutic targeting of malignant brain tumors
Authors: von Spreckelsen Niklas , Ghotmi Yarah , Fadzen Colin M. , Wolfe Justin M. , Hartrampf Nina , Farquhar Charlotte , Bergmann Sonja , Zdioruk Mykola , Wasserburg J. Roscoe , Murrell Emily , Bononi Fernanda C. , Luyt Leonard G. , Lamfers Martine L. M. , Ligon Keith L. , Chiocca E. Antonio , Viapiano Mariano S. , Pentelute Bradley L. , Lawler Sean E. , Cho Choi-Fong
Published: May 2020

Background

Targeted therapies for malignant brain cancer that are currently available have little clinical activity, highlighting an urgent need for the development of novel precision medicines. Brevican (Bcan), a central nervous system (CNS)-specific extracellular matrix protein is upregulated in glioma cells. A brevican isoform lacking glycosylation, dg-Bcan, is a unique glioma marker and thus represents a valuable target for anti-cancer therapy. In this study, we aimed to find a versatile dg-Bcan specific ligand to facilitate glioma targeting.

Methods

We screened a D-peptide library to identify dg-Bcan-TargetingPeptide (BTP) candidates, which were characterized extensively through binding kinetic analyses, cell uptake tests and animal studies.

Results

The top candidate, BTP-7 binds dg-Bcan with high affinity and specificity, is preferentially internalized by Bcan-expressing glioma cells and can cross the blood-brain barrierin vitroand in mice. Functionalization of camptothecin with BTP-7 led to increased drug delivery to intracranial glioblastoma and cytotoxicity in tumor tissues, as well as prolonged survival in tumor-bearing mice.

Conclusion

dg-Bcan is an attractive therapeutic target for high-grade gliomas, and BTP-7 represents a promising lead candidate for further development into novel targeted therapeutics.

Key points

BTP-7 is a high affinity peptide ligand for the dg-Bcan protein and Bcan-expressing cells.

BTP-7 targets human intracranial GBM xenografts in mice.

Functionalization of a toxic anti-cancer drug with BTP-7 enables targeted delivery of the therapeutic to intracranial GBM in mice

Importance of the Study

Targeted therapies for malignant brain cancer that are currently available have little clinical activity, highlighting an urgent need for the development of novel precision medicines that can selectively recognize and kill high-grade glioma tissues. A protein called dg-Bcan is an ideal target because it is present only in the extracellular matrix of high-grade glioma cells and is absent from normal brain tissues. Here, we describe the discovery of a novel dg-Bcan-TargetingPeptide, called BTP-7 that can bind specifically to high-grade glioma cells/tissues, and thus serve as a promising drug delivery vehicle.
Cis acting variation is common, can propagates across multiple regulatory layers, but is often buffered in developmental programs
Authors: Floc’hlay Swann , Wong Emily , Zhao Bingqing , Viales Rebecca R. , Thomas-Chollier Morgane , Thieffry Denis , Garfield David A. , Furlong Eileen EM
Published: May 2020

Precise patterns of gene expression are driven by interactions between transcription factors, regulatory DNA sequence, and chromatin. How DNA mutations affecting any one of these regulatory ‘layers’ is buffered or propagated to gene expression remains unclear. To address this, we quantified allele-specific changes in chromatin accessibility, histone modifications, and gene expression in F1 embryos generated from eightDrosophilacrosses, at three embryonic stages, yielding a comprehensive dataset of 240 samples spanning multiple regulatory layers. Genetic variation incis-regulatory elements is common, highly heritable, and surprisingly consistent in its effects across embryonic stages. Much of this variation does not propagate to gene expression. When it does, it acts through H3K4me3 or alternatively through chromatin accessibility and H3K27ac. The magnitude and evolutionary impact of mutations is influenced by a genes’ regulatory complexity (i.e. enhancer number), with transcription factors being most robust tocis-acting, and most influenced bytrans-acting, variation. Overall, the impact of genetic variation on regulatory phenotypes appears context-dependent even within the constraints of embryogenesis.
A new dual prokaryotic (E. coli) and mammalian expression system (pgMAXs)
Authors: Murakami Manabu , Murakami Agnieszka M. , Hirota Kazuyoshi , Itagaki Shirou
Published: May 2020

We introduce an efficient subcloning and expression plasmid system with two different modes (prokaryotic for expression inEscherichia coliwith lac promoter and mammalian modes with cytomegalovirus promoter). The efficient subcloning (DNA insertion) is based upon a DNA topoisomerase II toxin-originated gene for effective selection with isopropyl-β-D-thiogalactoside (IPTG) induction. The new pgMAXs system is manageable size (4452 bp) and has also various types of protein tags (flag, myc, poly-histidine, Human influenza hemagglutinin, strep, and v5) for expression analysis. With pgMAXs system, various types of fluorescent proteins were subcloned and prtein expressions were confirmed. We also tried to identify epitope amino acid sequences for anti-calcium channel β2 antibody, by constructing epitope-library with DNaseI-partial digestion and subcloning into EcoRV site in pgMAXs. The new pgMAXs plasmid system enables highly efficient subcloning, simple expression inE. coliand that it has a simple deletion step of rare 8-nucleotide rare-cutter blunt-end enzymes for mammalian expression plasmid construction. Taken together, the pgMAXs system simplifies prokaryotic and mammalian gene expression analyses.
Structural Features and Oligomeric Nature of Human Podocin Domain
Authors: Mulukala Sandeep KN , Irukuvajjula Shivkumar S , Kumar Krishan , Garai Kanchan , Venkatesu Pannuru , Vadrevu Ramakrishna , Pasupulati Anil K
Published: May 2020

Podocytes are crucial cells of the glomerular filtration unit and playing a vital role at the interface of the blood-urine barrier. Podocyte slit-diaphragm is a modified tight junction that facilitates size and shape-dependent permselectivity. Several proteins including podocin, nephrin, CD2AP, and TRPC6 form a macromolecular assembly and constitute the slit-diaphragm. Podocin is an integral membrane protein attached to the inner membrane of the podocyte via a short transmembrane region (101-125). The cytosolic N- and C-terminus help podocin to attain a hook-like structure. Podocin shares 44% homology with stomatin family proteins and similar to the stomatin proteins, podocin was shown to associate into higher-order oligomers at the site of slit-diaphragm. However, the stoichiometry of the homo-oligomers and how it partakes in the macromolecular assemblies with other slit-diaphragm proteins remains elusive. Here we investigated the oligomeric propensity of a truncated podocin construct (residues:126-350). We show that the podocin domain majorly homo-oligomerize into a 16mer. Circular dichroism and fluorescence spectroscopy suggest that the 16mer oligomer has considerable secondary structure and moderate tertiary packing.
The global proteome and phosphoproteome landscape of sepsis-induced kidney injury
Authors: Lin Yi-Han , Platt Maryann P. , Gonzalez-Juarbe Norberto , Zhou Dong , Yu Yanbao
Published: May 2020

Sepsis-induced acute kidney injury (S-AKI) is the most common complication in hospitalized and critically ill patients, highlighted by a rapid decline of kidney function occurring a few hours or days after sepsis onset. Systemic inflammation elicited by microbial infections is believed to lead to kidney damage under immunocompromised conditions. However, while AKI has been recognized as a disease with long-term sequelae, partly due to the associated higher risk of chronic kidney disease (CKD), the understanding of kidney pathophysiology at the molecular level and the global view of dynamic regulationsin situafter S-AKI, including transition to CKD, remains limited. Existing studies of S-AKI mainly focus on deriving sepsis biomarkers from body fluids. In the present study, we constructed a mid-severity septic murine model using cecal ligation and puncture (CLP), and examined the temporal changes to the kidney proteome and phosphoproteome at day 2 and day 7 after CLP surgery, corresponding to S-AKI and the transition to CKD, respectively by employing an ultrafast and economical filter-based sample processing method combined with the label-free quantitation approach. Collectively, we identified 2,119 proteins and 2,950 phosphosites through multi-proteomics analyses. Here we denote the pathways that are specifically responsive to S-AKI and its transition to CKD, which include regulation of cell metabolism regulation, oxidative stress, and energy consumption in the diseased kidneys. Our data can serve as an enriched resource for the identification of mechanisms and biomarkers for sepsis-induced kidney diseases.
A kinetic model improves off-target predictions and reveals the physical basis ofSpCas9 fidelity
Authors: Eslami-Mossallam Behrouz , Klein Misha , Smagt Constantijn v.d. , Sanden Koen v.d. , Jones Stephen K. , Hawkins John A. , Finkelstein Ilya J. , Depken Martin
Published: May 2020

TheS. pyogenes (Sp)Cas9 endonuclease is an important gene-editing tool.SpCas9 is directed to target sites via a single guide RNA (sgRNA). However, SpCas9 also binds and cleaves genomic off-target sites that are partially matched to the sgRNA. Here, we report a microscopic kinetic model that simultaneously captures binding and cleavage dynamics forSpCas9 andSp-dCas9 in free-energy terms. This model not only outperforms state-of-the-art off-target prediction tools, but also details howSp-Cas9’s structure-function relation manifests itself in binding and cleavage dynamics. Based on the biophysical parameters we extract, our model predictsSpCas9’s open, intermediate, and closed complex configurations and indicates that R-loop progression is tightly coupled with structural changes in the targeting complex. We show thatSpCas9 targeting kinetics are tuned for extended sequence specificity while maintaining on-target efficiency. Our extensible approach can characterize any CRISPR-Cas nuclease – benchmarking natural and future high-fidelity variants againstSpCas9; elucidating determinants of CRISPR fidelity; and revealing pathways to increased specificity and efficiency in engineered systems.
CD45 pre-exclusion from the tips of microvilli establishes a phosphatase-free zone for early TCR triggering
Authors: Jung Yunmin , Wen Lai , Altman Amnon , Ley Klaus
Published: May 2020

The tyrosine phosphatase CD45 is a major gatekeeper for restraining T cell activation. Its exclusion from the immunological synapse (IS) is crucial for TCR signal transduction. Here, we used expansion super-resolution microscopy to reveal that CD45 is pre-excluded from the tips of microvilli on primary T cells prior to antigen encounter. This pre-exclusion was diminished by depleting cholesterol or by engineering the transmembrane domain of CD45 to increase its membrane integration length, but was independent of the CD45 extracellular domain. We further show that brief microvilli-mediated contacts can induce Ca2+influx in mouse antigen-specific T cells engaged by antigen-pulsed APCs. We propose that the absence of CD45 phosphatase activity at the tips of microvilli enables or facilitates TCR triggering from brief T cell-APC contacts before formation of a stable IS, and that these microvilli-mediated contacts represent the earliest step in the initiation of a T cell adaptive immune response.

Graphical abstract
Visual acuity and egg spatial chromatic contrast predict egg rejection behavior of American robins
Authors: Luro Alec B. , Fernández-Juricic Esteban , Baumhardt Patrice , Hauber Mark E.
Published: May 2020

Color and spatial vision are critical for recognition and discrimination tasks affecting fitness, including finding food and mates and recognizing offspring. For example, as a counter defense to avoid the cost of raising the unrelated offspring of obligate interspecific avian brood parasites, many host species routinely view, recognize, and remove the foreign egg(s) from their nests. Recent research has shown that host species visually attend to both chromatic and spatial pattern features of eggs; yet how hosts simultaneously integrate these features together when recognizing eggs remains an open question. Here, we tested egg rejection responses of American robins (Turdus migratorius) using a range of 3D-printed model eggs covered with blue and yellow checkered patterns differing in relative square sizes. We predicted that robins would reject a model egg if they could visually resolve the blue and yellow squares as separate features or accept it if the squares blended together and appeared similar in color to the natural blue-green color of robin eggs as perceived by the avian visual system. As predicted, the probability of robins rejecting a model egg increased with greater sizes of its blue and yellow squares. Our results suggest that chromatic visual acuity and viewing distance have the potential to limit the ability of a bird to recognize a foreign egg in its nest, thus providing a limitation to host egg recognition that obligate interspecific avian brood parasites may exploit.
From Hi-C Contact Map to Three-dimensional Organization of Interphase Human Chromosomes
Authors: Shi Guang , Thirumalai D.
Published: May 2020

The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experiments. How to go from the contact map, a matrix listing the mean contact probabilities between a large number of pairs of loci, to an ensemble of three-dimensional structures is an open problem. A solution to this problem, without assuming an assumed energy function, would be the first step in understanding the way nature has solved the packaging of chromosomes in tight cellular spaces. We created a theory, based on polymer physics characteristics of chromosomes and the maximum entropy principles, referred to as HIPPS (Hi-C-Polymer-Physics-Structures) method, that allows us to calculate the 3D structures solely from Hi-C contact maps. The first step in the HIPPS method is to relate the mean contact probabilitybetween lociiandjand the average spatial distance,. This is a difficult problem to solve because the cell population is heterogeneous, which means that a given contact exists only in a small unknown fraction of cells. Despite the population heterogeneity, we first prove that there is a theoretical lower bound connecting 〈pij〉 andvia a power-law relation. We show, using simulations of a precisely solvable model, that the overall organization is accurately captured by constructing the distance map from the contact map even when if the cell population is highly heterogeneous, thus justifying the use of the lower bound. In the second step, the mean distance matrix, with elements, is used as a constraint in the maximum entropy principle to obtain the joint distribution of spatial positions of the loci. Using the two steps, we created an ensemble of 3D structures for the 23 chromosomes from lymphoblastoid cells using the measured contact maps as inputs. The HIPPS method shows that conformations of chromosomes are heterogeneous even in a single cell type. The differences in the conformational heterogeneity of the same chromosome in different cell types (normal as well as cancerous cells) can also be quantitatively discerned using our theory. We validate the method by showing that the calculated volumes of the 23 chromosomes from the predicted 3D structures are in good agreement with experimental estimates. Because the method is general, the 3D structures for any species may be calculated directly from the contact map without the need to assume a specific polymer model, as is customarily done.
Stretched-Exponential Modeling of Anomalous T1ρand T2Relaxation in the Intervertebral DiscIn Vivo
Authors: Wilson Robert L. , Bowen Leah , Kim Woong , Reiter David A. , Neu Corey P.
Published: May 2020

Purpose

Intervertebral disc degeneration (IVDD), resulting in the depletion of hydrophilic glycosaminoglycans (GAGs) located in the nucleus pulposus (NP), can lead to debilitating neck and back pain. Magnetic Resonance Imaging (MRI) is a promising means of IVD assessment due to the sensitivity of MRI tissue relaxation properties to matrix composition. Furthermore, anomalous (i.e. non-monoexponential) relaxation models have shown higher sensitivity to specific matrix components compared to conventional monoexponential models. Here, we extend the use of the stretched exponential model, an anomalous relaxation model, to IVD relaxometry data.

Theory and Methods

T1ρand T2relaxation data were measured in the cervical IVDs of healthy volunteers and IVDs adjacent to cervical fusion, and analyzed using both conventional and stretched-exponential (SE) models. Model differences were evaluated via goodness of fit in the healthy data. Normalized histograms of the resultant quantitative MRI (qMRI) maps were described using stable distributions, and data were compared across adjacent disc segments.

Results

In the healthy IVDs, we found lower mean squared error in the SE relaxation model fitting behavior compared to monoexponential models, supporting anomalous relaxation behavior in healthy IVDs. SE model parameter αT1ρincreased level-wise in the caudal direction, especially in the nucleus pulposus, while conventional T1ρand T2monoexponential measures did not vary. For IVDs adjacent to cervical fusion, SE parameters deviated near the fusion site compared with those in the healthy population.

Conclusion

SE modeling of T1ρrelaxation provides greater sensitivity to level-wise variation in IVD matrix properties compared with conventional relaxation modeling, and could provide improved sensitivity to early stages of IVD degeneration. The improved model fit and correlation between the SE αT1ρparameter with IVD level suggests SE modeling may be a more sensitive method for detection of GAG content variation.
Multimodal and multisensory coding in theDrosophilalarval peripheral gustatory center
Authors: Maier G. Larisa , Biočanin Marjan , Bues Johannes , Meyenhofer Felix , Avalos Clarisse Brunet , Kwon Jae Young , Deplancke Bart , Sprecher Simon G.
Published: May 2020

The ability to evaluate food palatability is innate in all animals, ensuring their survival. The external taste organ inDrosophilalarvae is composed of only few sensory neurons but enables discrimination between a wide range of chemicals and displays high complexity in receptor gene expression and physiological response profile. It remains largely unknown how the discrepancy between a small neuronal number and the perception of a large sensory space is genetically and physiologically resolved. We tackled dissection of taste sensory coding at organ level with cellular resolution in the fruit fly larva by combining whole-organ calcium imaging and single-cell transcriptomics to map physiological properties and molecular features of individual neurons. About one third of gustatory sense neurons responded to multiple tastants, showing a rather large degree of multimodality within the taste organ. Further supporting the notion of signal integration at the periphery, we observed neuronal deactivation events within simultaneous neighboring responses, suggesting inter-cellular communication through electrical coupling and thus providing an additional level in how neurons may encode taste sensing. Interestingly, we identified neurons responding to both mechanical and taste stimulation, indicating potential multisensory integration. On a molecular level, chemosensory cells show heterogeneity in neuromodulator expression. In addition to a broad cholinergic profile, markers on dopaminergic, glutamatergic or neuropeptidergic pathways are present either in distinct cell populations or are seemingly co-expressed. Our data further extend the sensory capacity of the larval taste system pointing towards an unanticipated degree of multimodal and multisensory coding principles.