bluuebunny/crossref_metadata_2025 huggingface dataset:
Occurrence of silver-containing particles in rat brains upon intranasal exposure of silver nanoparticles
Authors: Liu Nian , Qu Guangbo , Wen Ruoxi , Liu Xiaolei , Wang Yuanyuan , Gao Jie , Yin Yongguang , Shi Jianbo , Zhou Qunfang , He Bin , Hu Ligang , Jiang Guibin
Published: December 2021

The widespread application of silver (Ag) nanomaterials raises health concerns due to the adverse effects that can be associated with silver nanoparticles (AgNPs) exposure. AgNPs can be introduced into human bodies via inhalation, either intentionally (intranasal administration of AgNPs) or unintentionally (environmental pollution, accidental release, or occupational exposure). Recent studies have shown that intranasal exposure of experimental animals to AgNPs can lead to the accumulation of Ag in brain tissues. However, there is little information available concerning what forms of Ag (particulate and ionic) exist in brain tissues. This study aimed to investigate whether particulate Ag exists in rat brains following intranasal exposure of AgNPs at 1 mg/kg/day using multiple analytical techniques. The results demonstrated that Ag-containing particles were presented in AgNPs-exposed rat brains, accounting for 20.2–68.1% of the total Ag. The mass concentrations of Ag-containing particles in brain tissues increased with exposure time but only decreased by 37.5% after elimination for 4 weeks upon exposure cessation. The size of Ag-containing particles identified in rat brains was larger than the original AgNPs. The Ag-containing particles identified in the rat brain were composed of multiple elements, including Ag, sulfur, and selenium with atomic percentages of 45.8%, 37.5%, and 16.7%, respectively. The finding highlighted the occurrence and accumulation of transformed AgNPs containing S and Se in rat brains after intranasal exposure to AgNPs, implying potential risks for brain health.
Systematic review of determinants and interventions of areca nut cessation: curbing a public health menace
Authors: Gupta Ruchika , Nethan Suzanne T , Sinha Dhirendra N , Gupta Sanjay , Singh Shalini
Published: December 2021

Background

Areca nut (AN) is a proven human carcinogen and a global public health menace. There is yet no review providing comprehensive information on the determinants and interventions available for cessation of AN. This systematic review was aimed at summarizing the available literature on drivers and interventions for cessation of AN chewing habit and to highlight the research lacunae.

Methods

A systematic literature search (from 1990 till March 2021) was conducted for studies on AN cessation. Relevant data were extracted independently by two authors.

Results

A total of 16 studies were included, which highlighted the influence of socio-cultural factors, addictive nature of AN and withdrawal symptoms as barriers to quitting. However, the knowledge of ill-effects of AN use on health, absence of concurrent alcohol use or smoking and family pressure were associated with likelihood of AN cessation. The interventions utilized for AN cessation have been behavioural in majority of the studies except for one where antidepressants were used for this purpose.

Conclusions

The current review emphasizes the imperative need of appropriate cessation strategies for AN chewing habit including enhancing awareness of the harmful effects and research into additional behavioural and pharmacologic cessation therapies to control this significant public health problem.
Addressing infodemic through the comprehensive competency framework of media and information literacy
Authors: Toquero Cathy Mae D
Published: December 2021

As the world experiments with multiplex approaches to achieve a free pandemic society, infodemic pillages the online and offline realms, which exacerbates the spectrum of media fragilities, especially for particular age groups. Misinformation and disinformation related to health, political, and social issues, among others, deter the thin line that demarcates official reports from fake news. As a response to the COVID-19 infodemic, a curriculum and competency framework for media and information literacy can help promote a critical understanding of communications content for people to become media literate citizens. Incorporating the framework in the political and educational spheres enables the people, especially the dominant media users, to reinforce reliable information through responsible content-sharing on media platforms, which is essential for public health safety.
Effective Quantum Unique Ergodicity for Hecke–Maass Newforms and Landau–Siegel Zeros
Authors: Thorner Jesse
Published: December 2021

We show that Landau–Siegel zeros for Dirichlet L-functions do not exist or that quantum unique ergodicity for $\mathrm{GL}_2$ Hecke–Maass newforms holds with an effective rate of convergence. This follows from a more general result: Landau–Siegel zeros of Dirichlet L-functions repel the zeros of all other automorphic L-functions from the line $\mathrm{Re}(s)=1$.
Quadratic Twists of Central Values For GL(3)
Authors: Kuan Chan Ieong , Lesesvre Didier
Published: December 2021

We prove that a cuspidal automorphic representation of $\mathrm{GL}(3)$ over any number field is determined by the quadratic twists of its central value. In the case π is not a Gelbart–Jacquet lift, the result is conditional on the analytic behavior of a certain Euler product. We deduce the nonvanishing of infinitely many quadratic twists of central values. This generalizes a result of Chinta and Diaconu that was valid only over Q and explored only for Gelbart–Jacquet lifts.
RADIATION DOSE FOR PATIENTS WITH KAWASAKI DISEASE UNDERGOING FLUOROSCOPICALLY GUIDED CARDIAC CATHETERIZATION
Authors: Miranda Patricia , Vano Eliseo , Ubeda Carlos , Figueroa Ximena , Doggenweiller Paulina , Oliveira Marcus , Dalmazzo Dandaro
Published: December 2021

The goal of the present study was to estimate the radiation dose for a group of 45 Kawasaki disease (KD) patients undergoing fluoroscopically guided cardiac catheterization.

The sample of procedures corresponds to a single hospital and was collected in 10 years. Anthropometric characteristics and the quantities of air kerma-area product (PKA) among others were recorded for each procedure. Monte Carlo PCXMC 2.0 software was used to estimate organ and effective doses.

The PKA value of 7.2 Gy cm2 was proposed as the local Diagnostic Reference Level for KD. For organ absorbed doses, median values for thyroid, heart, lungs, esophagus, skin, active bone and breast were 1.2; 2.2; 4.6; 2.7; 1.1; 1.2 and 2.7 mGy, respectively. For effective dose, the mean value was 2.7 ± 2.5 mSv.

This paper presents the first patient dose values for the KD using catheterization techniques, in Latin America and the Caribbean Region.
The effect of adenotonsillectomy and rapid maxillary expansion on the upper airway in pediatric obstructive sleep apnea: a randomized crossover-controlled trial
Authors: Magalhães Maria Cecilia , Soares Carlos José , Araújo Eustáquio A , de Rezende Barbosa Gabriela , Novaes Ricardo Maurício O , Teodoro Vinicius Vasconcelos , Normando David , Kim Ki Beom , Almeida Guilherme A
Published: December 2021

Following the publication of the accepted manuscript, the current journal editorial staff raised concerns that the study had been registered after the study was initiated. Because of this, the authors later decided to withdraw the accepted manuscript from the journal due to the retrospective registration.
Application of Biochar on the runoff purification performance of porous asphalt pavement
Authors: Liu Jiawen , Li Hui , Harvey John , Zhang Hengji , Tian Yu
Published: December 2021

Biochar is currently applied in many low-impact development measures, such as biofilters and filter strips. However, its application in permeable pavement is limited. Due to the wide range of raw material sources, biochar may also contain nutrients and heavy metals. Whether its leachate will cause contamination during application remains unknown. Based on the static leachate contamination test, this study first evaluated the leachate contamination risks of three types of biochar and porous asphalt mixture (PA) with three biochar fillers. Through the pavement infiltration test, the purification performance of PA with biochar fillers and filter layers was further analysed. The results show that biochar contains nitrogen and phosphorus, and the leaching contamination of coconut shell is the most obvious; when the biochar is applied as a filler in PA, the leaching contamination decreases, while the pollutant purification performance is not obvious; when 3−5 mm rice straw biochar is used as a filter layer, the removal rate of total suspended solids can be 100%, but it is accompanied by more serious nitrogen and phosphorus leaching, and the greater the thickness, the more serious the degree of leaching. Deionized water cleaning can remove the phosphates contained in biochar, but have little effect on nitrogen. Therefore, before the application of biochar, cleaning measures should be taken to minimize its leaching contamination.
How is Exercise Prescribed for Hemodialysis Patients? A Scoping Review Protocol
Authors: Ribeiro Heitor S. , Andrade Francini P. , Leal Diogo V. , Oliveira Juliana S. , Wilund Kenneth R. , Viana João L.
Published: December 2021

Objective

The objective of this scoping review is to describe how exercise has been prescribed for hemodialysis patients.

Introduction

Exercise interventions have received more attention from the nephrology community in the last few years. Despite some limitations in the findings, there is currently robust evidence suggesting that exercise is clinically important and provides benefits to hemodialysis patients. Even so, there is little evidence precisely detailing and describing how exercise can be prescribed and delivered for this population.

Inclusion criteria

Based on the PCC framework, we will review and include evidence from hemodialysis patients (Participants); describing exercise interventions (Concept); in all settings and designs (Context). The evidence that included any other kidney replacement therapy other than hemodialysis will be excluded.

Methods

This review will follow the JBI methodology for scoping reviews and the PRISMA-ScR. We will perform a comprehensive literature search using MEDLINE, EMBASE, SPORTDiscuss, CINAHL, and LILACS databases without date or language restrictions from inception until December 2021. Websites, books, and guidelines from prominent societies and associations will also be searched. Experimental, quasi-experimental, observational, and protocol evidence from adults with chronic kidney disease (≥18 years) undergoing hemodialysis that prescribed exercise as an intervention will be considered. Two independent reviewers will screen title and abstract and perform the full-text review. Data extraction will be done by the main reviewer and checked by a second reviewer. Data characterizing the exercise interventions (e.g., type, setting, frequency, duration, intensity, volume, progression, periodization, professionals involved, etc.) will be extracted from selected evidence. The qualitative and quantitative results will be synthesized and presented in tables and figures along with a narrative summary.
Oral and gut microbiome biomarkers of susceptibility to respiratory tract infection in adults: a longitudinal cohort feasibility study
Authors: Woodall Claire A. , Hammond Ashley , Cleary David , Preston Andrew , Muir Peter , Pascoe Ben , Sheppard Samuel K. , Hay Alastair D.
Published: December 2021

Background and aim

Respiratory tract infections (RTIs) are common in the community. There is some evidence that microbial biomarkers can be used to identify individuals most susceptible to RTI acquisition. We investigated the feasibility of recruiting healthy adults to collect at-home self-reported socio-demographic data and biological samples, saliva (oral) and stool (gut) at three time points (TPs): baseline/start of the study (TP-A), during an RTI (TP-B) and end of study (TP-C).

Methods

Healthy adults were recruited from two urban Bristol GP practices. To identify respiratory pathogens in all saliva samples and RTI-S stool samples reverse transcriptase PCR (RT-PCR) was applied. We compared oral and gut samples from participants who developed RTI symptoms (RTI-S) and those who remained healthy (no-RTI) using 16S rRNA profiling microbiome analysis to identify the core microbiome, alpha and beta diversity, and biomarkers for susceptibility to RTIs from baseline samples (TP-A) when all participants were healthy.

Results

We recruited 56 participants but due to the UK COVID-19 pandemic disruption we did not receive samples from 16 participants leaving 19 RTI-S and 21 no-RTI participants with socio-demographic and microbiome data. RT-PCR revealed coagulase-negative Staphylococcus carriage was significantly higher in RTI-S participants compared to those who remained healthy and RTI symptoms may have been due to viral influenzae and bacterial co-infection with Haemophilus influenzae. Core microbiomes of no-RTI participants contained a greater number of taxa compared to RTI-S participants. Microbial biomarkers of RTI susceptibility in the oral cavity were an increased abundance of the pathobiont Streptococcus sobrinus and decreased probiotic bacterium Lactobacillus salivarius whereas in the gut there was an increased abundance of the genus Veillonella and decreased abundance of Coprobacillus.

Conclusion

In our feasibility study we found oral and gut microbial biomarkers for susceptibility to RTI acquisition. Strategies to identify those most vulnerable to RTI in the community could lead to novel interventions to decrease respiratory infection and associated health services burden.
Cochlear implantation restores cortical processing for spatial hearing in asymmetric hearing loss
Authors: Karoui C. , Strelnikov K. , Payoux P. , Salabert A.-S. , James C. , Deguine O. , Barone P. , Marx M.
Published: December 2021

In asymmetric hearing loss (AHL), the normal pattern of contralateral hemispheric dominance for monaural stimulation is modified, with a shift towards the hemisphere ipsilateral to the better ear. The extent of this shift has been shown to relate to sound localisation deficits. In this study, we examined whether cochlear implantation to treat AHL can restore the normal functional pattern of auditory cortical activity and whether this relates to improved sound localisation. We recruited 10 subjects with a cochlear implant for AHL (AHL-CI) and 10 normally-hearing controls. The participants performed a voice/non-voice discrimination task with binaural and monaural presentation of the sounds, and the cortical activity was measured using positron emission tomography (PET) brain imaging with a H215O tracer. The auditory cortical activity was found to be lower in the AHL-CI participants for all of the conditions. A cortical asymmetry index was calculated and showed that a normal contralateral dominance was restored in the AHL-CI patients for the non-implanted ear, but not for the ear with the cochlear implant. It was found that the contralateral dominance for the non-implanted ear strongly correlated with sound localisation performance (rho = 0.8, p < 0.05). We conclude that the restoration of binaural mechanisms in AHL-CI subjects reverses the abnormal lateralisation pattern induced by the deafness, and that this leads to improved spatial hearing. Our results suggest that cochlear implantation fosters the rehabilitation of binaural excitatory/inhibitory cortical interactions, which could enable the reconstruction of the auditory spatial selectivity needed for sound localisation.
Age-related changes, influencing factors and crosstalk between vaginal and gut microbiota: a cross-sectional comparative study of pre- and postmenopausal women
Authors: Yoshikata Remi , Yamaguchi Michiko , Mase Yuri , Tatuzuki Ayano , Myint Khin Z. , Ohta Hiroaki
Published: December 2021

Objective

The ideal vaginal environment is maintained by Lactobacillus species, which keep the vagina clean and free of infections, including sexually transmitted diseases and human papilloma virus infection. Other reported health benefits of Lactobacillus include a favorable impact on fertility and immunity, leading to a reduced risk of gynecological malignancies. Age-related decline in estrogen affects the population of Lactobacillus, leading to dominance of pathogenic flora and increased diversity in vaginal microbiota. In this study, we compared the differences between the vaginal microbiota of premenopausal and postmenopausal women. In addition, we examined the relationships between vaginal and gut microbiota, as well as their relationships to sex hormones and equol producing ability.

Methods

This was a cross-sectional study of 35 premenopausal and 35 postmenopausal women, ranging from 27 to 76 years of age. We compared parameters such as the composition of the gut and vaginal microbiota, vaginal pH, sex hormones in the blood (estradiol and follicular stimulating hormone), and urinary equol concentration.

Results

In the vaginal microbiota of premenopausal women, Lactobacillus species constituted approximately 71.98%, and pathogenic flora constituted approximately 16.87%. They were 10.08% and 26.78%, respectively, in the vaginal microbiota of postmenopausal women. Therefore, the proportion of Lactobacillus was significantly low, whereas microbial diversity and vaginal pH were significantly high (p<0.0001) in postmenopausal women. The compositions of the vaginal microbiota were significantly different in pre- and postmenopausal women. However, such differences were not noticeable in the gut microbiota. Urinary equol production had no significant correlation with vaginal microbiota, although it had significant relationships with gut microbiota in postmenopausal women. There were significant correlations among bacterial species in the gut and vaginal microbiota, especially in postmenopausal women. In both groups, the proportions of vaginal Lactobacillus were inversely correlated with vaginal microbial diversity and vaginal pH.

Conclusion

Postmenopausal women had significantly low Lactobacillus and high pathogenic flora in their vaginal flora, whereas such age-related differences were not identified in gut microbiota. There were significant correlations among the bacterial species inhabiting the gut and vaginal microbiota, especially in postmenopausal women, indicating potential crosstalk between each other.
Complete genomic profiles of 1,496 Taiwanese reveal curated medical insights
Authors: Wu Dung-Chi , Hsu Jacob Shu-Jui , Chen Chien-Yu , Shih Shang-Hung , Liu Jen-Feng , Tsai Ya-Chen , Lee Tung-Lin , Chen Wei-An , Tseng Yi-Hsuan , Lo Yi-Chung , Lin Hong-Ye , Chen Yi-Chieh , Chen Jing-Yi , Chang Darby Tien-Hao , Guo Wei-Hong , Mao Hsin-Hsiang , Chen Pei-Lung
Published: December 2021

Background

Taiwan Biobank (TWB) project has built a nationwide database to facilitate the basic and clinical collaboration within the island and internationally, which is one of the valuable public datasets of the East Asian population. This study provided comprehensive genomic medicine findings from 1,496 WGS data from TWB.

Methods

We reanalyzed 1,496 Illumina-based whole genome sequences (WGS) of Taiwanese participants with at least 30X depth of coverage by Sentieon DNAscope, a precisionFDA challenge winner method. All single nucleotide variants (SNV) and small insertions/deletions (Indel) have been jointly called and recalibrated as one cohort dataset. Multiple practicing clinicians have reviewed clinically significant variants.

Results

We found that each Taiwanese has 6,870.7 globally novel variants and classified all genomic positions according to the recalibrated sequence qualities. The variant quality score helps distinguish actual genetic variants among the technical false-positive variants, making the accurate variant minor allele frequency (MAF). All variant annotation information can be browsed at TaiwanGenomes (https://genomes.tw). We detected 54 PharmGKB-reported Cytochrome P450 (CYP) genes haplotype-drug pairs with MAF over 10% in the TWB cohort and 39.8% (439/1103) Taiwanese harbored at least one PharmGKB-reported human leukocyte antigen (HLA) risk allele. We also identified 23 variants located at ACMG secondary finding V3 gene list from 25 participants, indicating 1.67% of the population is harboring at least one medical actionable variant. For carrier status of all known pathogenic variants, we estimated one in 22 couples (4.52%) would be under the risk of having offspring with at least one pathogenic variant, which is in line with Japanese (JPN) and Singaporean (SGN) populations. We also detected 6.88% and 2.02% of carrier rates for alpha thalassemia and spinal muscular atrophy (SMA) for copy number pathogenic variants, respectively.

Conclusion

As WGS has become affordable for everyone, a person only needs to test once for a lifetime; comprehensive WGS data reanalysis of the genomic profile will have a significant clinical impact. Our study highlights the overall picture of a complete genomic profile with medical information for a population and individuals.
An experimental feasibility study evaluating the adequacy of sportswear-type wearables for recording physical exercise intensity
Authors: Marutani Yoshihiro , Konda Shoji , Ogasawara Issei , Yamasaki Keita , Yokoyama Teruki , Maeshima Etsuko , Nakata Ken
Published: December 2021

Sportswear-type wearables with integrated inertial sensors and electrocardiogram (ECG) electrodes, have been developed. We examined the feasibility of using sportswear-type wearables to evaluate exercise intensity within a controlled laboratory setting. Six male college athletes were asked to wear a sportswear-type wearable while performing a treadmill test that reached up to 20 km/h. The magnitude of the filtered tri-axial acceleration signal, recorded by the inertial sensor, was used to calculate the acceleration index. The R-R intervals of ECG were used to determine heart rate; the external validity of the heart rate was then evaluated according to oxygen uptake, which is the gold standard physiological exercise intensity. Single regression analyses between treadmill speed and the acceleration index in each participant showed that the slope of the regression line was significantly greater than zero with a high coefficient of determination (walking, 0.95; jogging, 0.96; running, 0.90). Another single regression analyses between heart rate and oxygen uptake showed that the slope of the regression line was significantly greater than zero, with a high coefficient of determination (0.96). Together, these results indicate that sportswear-type wearables are a feasible technology for evaluating physical and physiological exercise intensity across a wide range of physical activities and sport performances.
Method versatility in RNA extraction-free PCR detection of SARS-CoV-2 in saliva samples
Authors: Allicock Orchid M. , Yolda-Carr Devyn , Earnest Rebecca , Breban Mallery I. , Vega Noel , Ott Isabel M. , Kalinich Chaney , Alpert Tara , Petrone Mary E. , Wyllie Anne L.
Published: December 2021

Early in the pandemic, a simple, open-source, RNA extraction-free RT-qPCR protocol for SARS-CoV-2 detection in saliva was developed and made widely available. This simplified approach (SalivaDirect) requires only sample treatment with proteinase K prior to PCR testing. However, feedback from clinical laboratories highlighted a need for a flexible workflow that can be seamlessly integrated into their current health and safety requirements for the receiving and handling of potentially infectious samples. To address these varying needs, we explored additional pre-PCR workflows. We built upon the original SalivaDirect workflow to include an initial incubation step (95°C for 30 minutes, 95°C for 5 minutes or 65°C for 15 minutes) with or without addition of proteinase K. The limit of detection for the workflows tested did not significantly differ from that of the original SalivaDirect workflow. When tested on de-identified saliva samples from confirmed COVID-19 individuals, these workflows also produced comparable virus detection and assay sensitivities, as determined by RT-qPCR analysis. Exclusion of proteinase K did not negatively affect the sensitivity of the assay. The addition of multiple heat pretreatment options to the SalivaDirect protocol increases the accessibility of this cost-effective SARS-CoV-2 test as it gives diagnostic laboratories the flexibility to implement the workflow which best suits their safety protocols.
Amplicon-based nanopore minion sequencing of patients with COVID-19 omicron variant from India
Authors: Kumar Somesh , Lomash Avinash , Faruq Mohammed , Siddiqui Oves , Kumar Suresh , Kapoor Seema , Suravajhala Prashanth , Polipalli Sunil K ,   SCOG_MAMC_ LNH
Published: December 2021

SARS-CoV-2 infection has been playing havoc with emerging omicron variants of concern (VoC). Here, we report sequencing of the omicron variant in 13 patients from India using Oxford Nanopore Technology (ONT) Minion, wherein a rapid amplicon based sequence analysis was performed to assess and compare with existing 34 mutations in spike glycoprotein. We highlight and discuss the nature of these mutations that are unique and common to other populations. This is perhaps the first report on omicron variants from India using a long read sequencing chemistry.
Detection of the omicron variant in international travellers and their family contacts in India
Authors: Potdar Varsha A. , Yadav Pragya D. , Lole Kavita , Cherian Sarah , Shastri Jayanti , Malhotra Bharati , Bharadwaj Sumit , Razdan Alpana , Choudhary M L , Gupta Nivedita , Abraham Priya ,   NIC team,   Bioinformatics team,   BSL4 team,   The Indian SARS-CoV-2 Genomics Consortium (INSACOG)
Published: December 2021

Highlights

With the emergence of the Variant of Concern, omicron (B.1.1.529), India has enhanced genomic surveillance in international travellers. The omicron variant was detected in 59 cases from different States; 40 from Maharashtra, 17 from Rajasthan and one each from Gujrat and Tamil Nadu. The positive cases and their contacts were asymptomatic and genomic surveillance could identify two clusters, one from Maharashtra and another from Rajasthan.
Structural basis of SARS-CoV-2 Omicron immune evasion and receptor engagement
Authors: McCallum Matthew , Czudnochowski Nadine , Rosen Laura E. , Zepeda Samantha K. , Bowen John E. , Dillen Josh R. , Powell Abigail E. , Croll Tristan I. , Nix Jay , Virgin Herbert W. , Corti Davide , Snell Gyorgy , Veesler David
Published: December 2021

The SARS-CoV-2 Omicron variant of concern evades antibody mediated immunity with an unprecedented magnitude due to accumulation of numerous spike mutations. To understand the Omicron antigenic shift, we determined cryo-electron microscopy and X-ray crystal structures of the spike and RBD bound to the broadly neutralizing sarbecovirus monoclonal antibody (mAb) S309 (the parent mAb of sotrovimab) and to the human ACE2 receptor. We provide a structural framework for understanding the marked reduction of binding of all other therapeutic mAbs leading to dampened neutralizing activity. We reveal electrostatic remodeling of the interactions within the spike and those formed between the Omicron RBD and human ACE2, likely explaining enhanced affinity for the host receptor relative to the prototypic virus.
Single-nuclei isoform RNA sequencing reveals combination patterns of transcript elements across human brain cell types
Authors: Hardwick Simon A , Hu Wen , Joglekar Anoushka , Fan Li , Collier Paul G , Foord Careen , Balacco Jennifer , Belchikov Natan , Jarroux Julien , Prjibelski Andrey , Mikheenko Alla , Luo Wenjie , Milner Teresa A , Ndhlovu Lishomwa C , Trojanowski John Q , Lee Virginia MY , Fedrigo Olivier , Tombácz Dóra , Ross M Elizabeth , Jarvis Erich , Boldogkői Zsolt , Gan Li , Tilgner Hagen U
Published: December 2021

Single-nuclei RNA-Seq is being widely employed to investigate cell types, especially of human brain and other frozen samples. In contrast to single-cell approaches, however, the majority of single-nuclei RNA counts originate from partially processed RNA leading to intronic cDNAs, thus hindering the investigation of complete isoforms. Here, using microfluidics, PCR-based artifact removal, target enrichment, and long-read sequencing, we developed single-nuclei isoform RNA-sequencing (‘SnISOr-Seq’), and applied it to the analysis of human adult frontal cortex samples. We found that exons associated with autism exhibit coordinated and more cell-type specific inclusion than exons associated with schizophrenia or ALS. We discovered two distinct modes of combination patterns: first, those distinguishing cell types in the human brain. These are enriched in combinations of TSS-exon, exon-polyA site, and distant (non-adjacent) exon pairs. Second, those with all isoform combinations found within one neural cell type, which are enriched in adjacent exon pairs. Furthermore, adjacent exon pairs are predominantly mutually associated, while distant pairs are frequently mutually exclusive. Finally, we observed that human-specific exons are as tightly coordinated as conserved exons, pointing to an efficient evolutionary mechanism underpinning coordination. SnISOr-Seq opens the door to single-nuclei long-read isoform analysis in the human brain, and in any frozen, archived or hard-to-dissociate sample.
Comparative proteomic analysis of Fusarium oxysporum f. sp. cubense strains (Foc R1 and Foc TR4) provides better insights into mechanisms of their virulence, habitat adaptation and pathogenesis
Authors: Raman Thangavelu , Kalaimughilan Kalaiponmani , Esack Edwin Raj
Published: December 2021

Fusarium oxysporum f. sp. cubense (Foc), a devastative soil-borne fungal pathogen causing vascular wilt (i.e. Panama disease) which leads to severe crop losses in most of the banana-growing regions of the world. As there is no single source of effective management practices available so far, understand the pathogenicity of the organism may help in designing effective control measures through molecular approaches. The study aims to compare the proteome of the two pathogenic Foc virulent strains, Race 1 (Foc R1) and tropical race 4 (Foc TR4) that are capable of infecting the Cavendish group of bananas using 2-dimensional (2-D) gel electrophoresis, MALDI-TOF/MS and MS/MS analysis. The results of the study revealed that the proteins, peroxiredoxins, NAD-aldehyde dehydrogenase (NAD-ALDH), MAPK protein, pH-response regulator protein palA/rim-20 and isotrichodermin C15 hydroxylase have shared homology with the fungal proteins, which regulate the osmotic stress response, signal transduction, root colonization and toxin biosynthesis. These are the important functions for the pathogen survival in an unfavourable environment, and successful establishment and infection of the banana host. The present study also identified several putative pathogenicity related proteins in both Foc R1 and Foc TR4. Specifically, certain Foc TR4 specific putative pathogenicity related proteins, phytotoxins biosynthesis gene, fructose 1,6-bisphosphate aldolase class II, Synembryn-like proteins found to contribute strong virulence. Overexpression or knockout of the elective genes could help in devising better control measures for the devastative pathogens in the future. To the best of our knowledge, this is the first report on the proteomics of Foc R1 and Foc TR4 strains of Indian origin that infect Cavendish bananas.
Pronounced sequence specificity of the TET enzyme catalytic domain guides its cellular function
Authors: Ravichandran Mirunalini , Rafalski Dominik , Ortega-Recalde Oscar , Davies Claudia I. , Glanfield Cassandra R. , Kotter Annika , Misztal Katarzyna , Wang Andrew H. , Wojciechowski Marek , Rażew Michał , Mayyas Issam M. , Kardailsky Olga , Schwarz Uwe , Zembrzycki Krzysztof , Morison Ian M. , Helm Mark , Weichenhan Dieter , Jurkowska Renata Z. , Krueger Felix , Plass Christoph , Zacharias Martin , Bochtler Matthias , Hore Timothy A. , Jurkowski Tomasz P.
Published: December 2021

TET (ten-eleven translocation) enzymes catalyze the oxidation of 5-methylcytosine bases in DNA, thus driving active and passive DNA demethylation. Here, we report that the catalytic cores of mammalian TET enzymes favor CpGs embedded within bHLH and bZIP transcription factor binding sites, with 250-fold preference in vitro. Crystal structures and molecular dynamics calculations show that sequence preference is caused by intra-substrate interactions and CpG flanking sequence indirectly affecting enzyme conformation. TET sequence preferences are physiologically relevant as they explain the rates of DNA demethylation in TET-rescue experiments in culture and in vivo within the zygote and germline. Most and least favorable TET motifs represent DNA sites that are bound by methylation-sensitive immediate-early transcription factors and OCT4, respectively, illuminating TET function in transcriptional responses and pluripotency support.

One-Sentence Summary

The catalytic domains of the enzymes that facilitate passive and drive active DNA demethylation have intrinsic sequence preferences that target DNA demethylation to bHLH and bZIP transcription factor binding sites.
High density single-unit human cortical recordings using the Neuropixels probe
Authors: Chung JE , Sellers KK , Leonard MK , Gwilliams L , Xu D , Dougherty M , Kharazia V , Welkenhuysen M , Dutta B , Chang EF
Published: December 2021

A fundamental unit of neural computation is the action potential. While significant advances have been made in the ability to sample action potentials of large numbers of individual neurons in animal models, translation of these methodologies to humans has been lacking due to clinical time constraints, electrical noise in the operating room, and reliability of the methodology. Here we present a reliable method for intraoperative recording of dozens of neurons in humans using the Neuropixels probe, yielding up to ∼100 simultaneously-recorded single-units (n=596 across 11 recordings in 8 participants). Most single-units were active within 1 minute of reaching target depth, compatible with clinical time constraints. Cell pairs active close in time were spatially closer in most recordings, demonstrating the power to resolve complex cortical dynamics. Altogether, this approach provides access to population single-unit activity across the depth of human neocortex at scales previously only accessible in animal models.

Highlights

Single units in 8 patients, yielding 596 putative single units across 11 recordings

The majority of putative neurons fire at least 1 spike within one minute after reaching target depth

Putative neurons take longer to fire at least one spike in anesthetized compared to awake participants

Cell-pairs that fire action potentials close in time are spatially closer together than those fire further apart in time
TXNRD3 supports male fertility via the redox control of spermatogenesis
Authors: Dou Qianhui , Turanov Anton A. , Mariotti Marco , Hwang Jae Yeon , Wang Huafeng , Lee Sang-Goo , Paulo Joao A. , Yim Sun Hee , Gygi Stephen P. , Chung Jean-Ju , Gladyshev Vadim N.
Published: December 2021

Thioredoxin/glutathione reductase (TGR, TXNRD3) is a thiol oxidoreductase of unknown function composed of thioredoxin reductase and glutaredoxin domains. This NADPH-dependent enzyme evolved by gene duplication within the Txnrd family, is expressed in the testes and can reduce both thioredoxin and glutathione in vitro. To characterize the function of TXNRD3 in vivo, we generated a strain of mice with the deletion of Txnrd3 gene. We show that Txnrd3 knockout mice are viable and without discernable gross phenotypes, but TXNRD3 deficiency leads to fertility impairment in male mice. Txnrd3 knockout animals exhibit a lower fertilization rate in vitro, a sperm movement phenotype and an altered redox status of thiols. Proteomic analyses revealed a broad range of substrates reduced by TXNRD3 during sperm maturation, presumably as a part of quality control. The results show that TXNRD3 plays a critical role in male reproduction via the thiol redox control of spermatogenesis.
Kinetics Of Interferon-λ And Receptor Expression In Response To In Vitro Respiratory Viral Infection
Authors: Lozhkov Alexey A , Yolshin Nikita D , Baranovskaya Irina L , Plotnikova Marina A , Sergeeva Mariia V. , Gyulikhandanova Natalia E , Klotchenko Sergey A , Vasin Andrey V
Published: December 2021

The major protective immune response against viruses is production of type I and III interferons (IFNs). IFNs induce the expression of hundreds of IFN-stimulated genes (ISGs) that block viral replication and further viral spread. The ability of respiratory viruses to suppress induction of IFN-mediated antiviral defenses in infected epithelial cells may be a factor contributing to the particular pathogenicity of several strains. In this report, we analyzed expression of IFNs and some ISGs in an alveolar epithelial cell subtype (A549) in response to infection with: influenza A viruses (A/California/07/09pdm (H1N1), A/Texas/50/12 (H3N2)); influenza B virus (B/Phuket/3073/13); adenovirus type 5 and 6; or respiratory syncytial virus (strain A2). IFNL and ISGs expression significantly increased in response to infection with all RNA viruses 24 hpi. Nevertheless, only IBV led to early increase in IFNL and ISGs mRNA level. IBV and H1N1 infection led to elevated proinflammatory cytokine production. We speculate that augmented IFN-α, IFN-β, IL-6 levels negatively correlate to SOCS1 expression. Importantly, we showed a decrease in IFNLR1 mRNA in case of IBV infection that implies the existence of negative ISGs expression regulation at IFNλR level. It could be either a specific feature of IBV or a consequence of early IFNL expression.
Work and oxygen consumption of isolated right ventricular papillary muscle in experimental pulmonary hypertension
Authors: van der Laarse Willem J. , Bogaards Sylvia J.P. , Schalij Ingrid , Noordegraaf Anton Vonk , Vaz Frédéric M. , van Groen Duncan
Published: December 2021

Right-sided myocardial mechanical efficiency (work output/metabolic energy input) in pulmonary hypertension can be severely reduced. We determined the contribution of intrinsic myocardial determinants of efficiency using papillary muscle preparations from monocrotaline-induced pulmonary hypertensive (MCT-PH) rats. The hypothesis was tested that efficiency is reduced by mitochondrial dysfunction in addition to increased activation heat reported previously. Right ventricular (RV) muscle preparations were subjected to 5 Hz sinusoidal length changes at 37°C. Work and suprabasal oxygen consumption (VO2) were measured before and after cross-bridge inhibition by blebbistatin. Cytosolic cytochrome c concentration, myocyte cross-sectional area, proton permeability of the inner mitochondrial membrane (PP IMM), and monoamine oxidase (MAO)-A and glucose 6-phosphate dehydrogenase (G-6-PDH) activities and phosphatidylglycerol (PG) and cardiolipin (CL) contents were determined. Mechanical efficiency ranged from 23 to 11% in control (n = 6) and from 22 to 1% in MCT-PH (n = 15) and correlated with work (r2 = 0.68, P < 0.0001) but not with VO2 (r2 = 0.004, P = 0.7919). VO2 for cross-bridge cycling was proportional to work (r2 = 0.56, P = 0.0005). Blebbistatin-resistant VO2 (r2 = 0.32, P = 0.0167) and IMM PP (r2 = 0.36, P = 0.0110) correlated inversely with efficiency. Together, these variables explained the variance of efficiency (coefficient of multiple determination R2 = 0.79, P = 0.0001). Cytosolic cytochrome c correlated inversely with work (r2 = 0.28, P = 0.0391), but not with efficiency (r2 = 0.20, P = 0.0867). G-6-PDH, MAO-A and PG/CL increased in the RV wall of MCT-PH but did not correlate with efficiency. Reduced myocardial efficiency in MCT-PH is due to activation processes and mitochondrial dysfunction. The variance of work and the ratio of activation heat reported previously and blebbistatin-resistant VO2 are discussed.

Key points

Mechanical efficiency of right ventricular myocardium is reduced in pulmonary hypertension. Increased energy use for activation processes has been demonstrated previously, but the contribution of mitochondrial dysfunction is unknown.

Work and oxygen consumption is determined during work loops. Oxygen consumption for activation and cross-bridge cycling confirm the previous heat measurements.

Cytosolic cytochrome c concentration, proton permeability of the mitochondrial inner membrane and phosphatidylglycerol/cardiolipin are increased in experimental pulmonary hypertension.

Mitochondrial dysfunction in right ventricular myocytes is related to reduced work and mechanical efficiency in experimental pulmonary hypertension.

Upregulation of the pentose phosphate pathway and a potential gap in the energy balance suggest mitochondrial dysfunction in right ventricular overload is due to excessive production of reactive oxygen species.
Diffusion of small molecule drugs is affected by surface interactions and crowder proteins
Authors: Dey Debabrata , Nunes-Alves Ariane , Wade Rebecca C , Schreiber Gideon
Published: December 2021

Crowded environments are known to affect the diffusion of macromolecules but their effects on the diffusion of small molecules, such as drugs, are largely uncharacterized. Here, we investigate how three macromolecular protein crowders, bovine serum albumin (BSA), hen egg-white lysozyme and myoglobin, influence the translational diffusion rates and interactions of four low molecular-weight compounds: the diagnostic marker fluorescein, and three drugs, doxorubicin, glycogen synthase kinase-3 inhibitor SB216763 and quinacrine. Using Fluorescence Recovery After Photo-bleaching in Line mode (Line- FRAP), Brownian dynamics simulations and molecular docking, we find that the diffusive behavior of the small molecules is highly affected by self-aggregation, interactions with the proteins, and surface adhesion. The diffusion of fluorescein is decreased by protein crowders due to its interactions with the proteins and their surface adsorption. In contrast, the presence of protein crowders increases the diffusion rate of doxorubicin by reducing surface interactions. SB216763 shows a third scenario, where BSA, but not lysozyme or myoglobin , reduces self-aggregation, resulting in faster diffusion. Quinacrine was the only compound whose diffusion was not affected by the presence of protein crowders. The mechanistic insights gained here into the effects of interactions of small molecules with proteins and surfaces on the translational diffusion of small molecules can assist in optimizing the design of compounds for higher mobility and lower occlusion in complex macromolecular environments.
pixOL: pixel-wise dipole-spread function engineering for simultaneously measuring the 3D orientation and 3D localization of dipole-like emitters
Authors: Wu Tingting , Lu Jin , Lew Matthew D.
Published: December 2021

Interactions between biomolecules are characterized by both where they occur and how they are organized, e.g., the alignment of lipid molecules to form a membrane. However, spatial and angular information are mixed within the image of a fluorescent molecule–the microscope’s dipolespread function (DSF). We demonstrate the pixOL algorithm for simultaneously optimizing all pixels within a phase mask to produce an engineered Green’s tensor–the dipole extension of point-spread function engineering. The pixOL DSF achieves optimal precision for measuring simultaneously the 3D orientation and 3D location of a single molecule, i.e., 1.14° orientation, 0.24 sr wobble angle, 8.17 nm lateral localization, and 12.21 nm axial localization precisions over an 800-nm depth range using 2500 detected photons. The pixOL microscope accurately and precisely resolves the 3D positions and 3D orientations of Nile red within a spherical supported lipid bilayer, resolving both membrane defects and differences in cholesterol concentration, in 6 dimensions.
Bioprinting the Tumor Microenvironment with an Upgraded Consumer Stereolithographic 3D Printer
Authors: Breideband Louise , Wächtershäuser Kaja N. , Hafa Levin , Wieland Konstantin , Frangakis Achilleas , Stelzer Ernst H. K. , Pampaloni Francesco
Published: December 2021

A widespread application of three-dimensional (3D) bioprinting in basic and translational research requires the accessibility to affordable printers able to produce physiologically relevant tissue models. To facilitate the use of bioprinting as a standard technique in biology, an open-source device based on a consumer-grade 3D stereolithographic (SL) printer was developed. This SL bioprinter can produce complex constructs that preserve cell viability and recapitulate the physiology of tissues. The detailed documentation of the modifications apported to the printer as well as a throughout performance analysis allow for a straightforward adoption of the device in other labs and its customization for specific applications. Given the low cost, several modified bioprinters could be simultaneously operated for a highly parallelized tissue production.

To showcase the capability of the bioprinter, we produced constructs consisting of patient-derived cholangiocarcinoma organoids encapsulated in a gelatin methacrylate (GelMA)/polyethylene glycol diacrylate (PEGDA) hydrogel. A thorough characterization of different GelMA/PEGDA ratios revealed that the mechanical properties of the bioprinted tumor model can be accurately fine-tuned to mimic a specific tumor micro-environment. Immunofluorescence and gene expression analyses of tumor markers confirmed that the bioprinted synthetic hydrogel provides a flexible and adequate replacement of animal-derived reconstituted extracellular matrix.
A nanopore interface for high bandwidth DNA computing
Authors: Zhang Karen , Chen Yuan-Jyue , Doroschak Kathryn , Strauss Karin , Ceze Luis , Seelig Georg , Nivala Jeff
Published: December 2021

DNA has emerged as a powerful substrate for programming information processing machines at the nanoscale. Among the DNA computing primitives used today, DNA strand displacement (DSD) is arguably the most popular, with DSD-based circuit applications ranging from disease diagnostics to molecular artificial neural networks. The outputs of DSD circuits are generally read using fluorescence spectroscopy. However, due to the spectral overlap of typical small-molecule fluorescent reporters, the number of unique outputs that can be detected in parallel is limited, requiring complex optical setups or spatial isolation of reactions to make output bandwidths scalable. Here, we present a multiplexable sequencing-free readout method that enables real-time, kinetic measurement of DSD circuit activity through highly parallel, direct detection of barcoded output strands using nanopore sensor array technology (Oxford Nanopore Technologies’ MinION device). We show that engineered reporter probes can be detected and classified with high accuracy at the single-molecule level directly from raw nanopore signals using deep learning. We then demonstrate this method’s utility in multiplexed detection of clinically relevant microRNA sequences. These results increase DSD output bandwidth by an order of magnitude over what is possible with fluorescence spectroscopy, laying the foundations for a new paradigm in DNA circuit readout and programmable multiplexed molecular diagnostics using portable nanopore devices.