bluuebunny/crossref_metadata_2025 huggingface dataset:
Feasibility of 3T layer-dependent fMRI with GE-BOLD using NORDIC and phase regression
Authors: Knudsen Lasse , Bailey Christopher J. , Blicher Jakob U. , Yang Yan , Zhang Peng , Lund Torben E.
Published: June 2022

Introduction

Functional MRI with spatial resolution in the submillimeter domain enables measurements of activation across cortical layers in humans. This is valuable as different types of cortical computations, e.g., feedforward versus feedback related activity, take place in different cortical layers. Layer-dependent fMRI (L-fMRI) studies have almost exclusively employed 7T scanners to overcome the reduced signal stability associated with small voxels. However, such systems are relatively rare and only a subset of those are clinically approved. In the present study, we examined the feasibility of L-fMRI at 3T using NORDIC denoising.

Methods

5 healthy subjects were scanned on a Siemens MAGNETOM Prisma 3T scanner. To assess across-session reliability, each subject was scanned in 3-8 sessions on 3-4 consecutive days. A 3D gradient echo EPI (GE-EPI) sequence was used for BOLD acquisitions (voxel size 0.82 mm isotopic, TR = 2.2 s) using a block designed finger tapping paradigm. NORDIC denoising was applied to the magnitude and phase time series to overcome limitations in tSNR and the denoised phase time series were subsequently used to correct for large vein contamination through phase regression.

Results and conclusion

NORDIC denoising resulted in temporal signal-to-noise ratio (tSNR) values comparable to or higher than commonly observed at 7T. Layer-dependent activation profiles could thus be extracted robustly, within and across sessions, from regions of interest located in the hand knob of the primary motor cortex (M1). Phase regression led to substantially reduced superficial bias in obtained layer profiles, although residual macrovascular contribution remained. We believe the present results support the feasibility of L-fMRI at 3T, which might help make L-fMRI available to a much wider community.
Mutations in OsRZF1, encoding a zinc-finger protein, causes reduced magnesium uptake in roots and translocation to shoots in rice
Authors: Kobayashi Natsuko I. , Takagi Hiroki , Yang Xiaoyu , Nishizawa-Yokoi Ayako , Hoshina Tatsuaki , Oonishi Takayuki , Suzuki Hisashi , Iwata Ren , Toki Seiichi , Nakanishi Tomoko M. , Tanoi Keitaro
Published: June 2022

Magnesium (Mg) homeostasis is critical for maintaining many biological processes, but little information is available to comprehend the molecular mechanisms regulating Mg concentration in rice (Oryza sativa). To make up for the lack of information, we aimed to identify mutants defective in Mg homeostasis through a forward genetic approach. As a result of the screening of about 3,000 M2 seedlings mutated by ion-beam irradiation, we found a rice mutant that showed reduced Mg content in leaves and slightly increased Mg content in roots. Radiotracer 28Mg experiments showed that this mutant, named low magnesium content 1 (LMGC1), has decreased Mg2+ influx in the root and Mg2+ translocation from root to shoot. The MutMap method identified 7.4 kbp deletion in the LMGC1 genome leading to a loss of two genes. Genome editing using CRISPR-Cas9 further revealed that one of the two lost genes, a gene belonging to RanBP2-type zinc finger family, was the causal gene of the low-Mg phenotype. Considering this gene, named OsRZF1, has never been reported to be involved in ion transport, the phenotype of LMGC1 would be associated with a novel mechanism of Mg homeostasis in plants.
Error-suppression mechanism of PCR by blocker strands
Authors: Aoyanagi Hiroyuki , Pigolotti Simone , Ono Shinji , Toyabe Shoichi
Published: June 2022

The polymerase chain reaction (PCR) is a central technique in biotechnology. Its ability to amplify a specific target region of a DNA sequence has led to prominent applications, including virus tests, DNA sequencing, genotyping, and genome cloning. These applications rely on the specificity of the primer hybridization, and therefore require effective suppression of hybridization errors. A simple and effective method to achieve that is to add blocker strands, also called as clamp, to the PCR mixture. These strands bind to the unwanted target sequence, thereby blocking the primer mishybridization. Because of its simplicity, this method is applicable to a broad nucleic-acid-based biotechnology. However, the precise mechanism by which blocker strands suppress PCR error remains to be understood, limiting the applicability of this technique. Here, we combine experiments and theoretical modeling to reveal this mechanism. We find that the blocker strands both energetically destabilize the mishybridized complex and sculpt a kinetic barrier to suppress mishybridization. This combination of energetic and kinetic biasing extends the viable range of annealing temperatures, which reduces design constraint of the primer sequence and extends the applicability of PCR.
Data-driven machine learning for pattern recognition supports environmental quality prediction for irrigated rice in Brazil
Authors: Costa-Neto Germano , da Matta David Henriques , Kuivjogi Fernandes Igor , Stone Luís Fernando , Heinemann Alexandre Bryan
Published: June 2022

The sustainability of irrigated rice (Oryza sativa L.) production systems in Brazilian tropical region highly depends on the success of developing stable cultivars. To achieve this goal, many steps in product development must address the environmental variability and genotype by environment interactions (GE), which makes difficult the design and development of local-specific adapted cultivars. Thus, the adoption of new strategies for characterizing environmental-phenotype relations are the key for optimizing this process. In addition, it could also benefit post-breeding stages of seed production. To overcome this situation, we implemented a data-driven approach to link environmental characterization to yield clustering using historical data (1982-2017, 31 locations, 471 genotypes), 42 envirotyping covariables and machine learning (ML), combining two unsupervised (K-means and decision tree models, DTC) algorithms. Additionally, linear mixed models (LMM) were applied to explore the relations between the outcomes of our approach and GE analysis for irrigated rice yield in Brazilian tropical region. Four environments were identified: Very Low Yield (1.7 Mg.ha-1), Low Yield (5.1 Mg.ha-1), High Yield (7.2 Mg.ha-1), and Very High Yield (9.0 Mg.ha-1), considering all genotypes and regions. Our approach allows the prediction of environments (yield clusters) for a diverse set of growing conditions and revealed geographic and climatic causes of environmental quality, which differ according to each region and genotype group. From the LMM analysis, we found that the current relation between genetics (G), environmental variation (E), and GE for rainfed rice in Brazil is 1:6:2, but when we introduced our data-driven clusters (ME), the ratio decreased to 1:5:1. Consequently, the selection reliability for local adaptability across an extensive region increases. Our approach helps to identify mega-environments in Brazil that could be used as a target population of environments (TPE) of breeding programs. Additionally, it helps to identify more productive and stable seed production fields.

Highlights

A nationwide environmental characterization and its relation to the genotype by environment interaction (GE) for grain yield of rainfed rice growing regions in Brazil.

A data-driven approach capable to identifying clusters of yield levels and a machine learning approach to relate those clusters with environmental typologies.

Unrevealed geographic and climatic causes of environmental quality for a group of genotypes or cultivar-specific predictions.

The strategy benefits diverse stages of breeding (multiple environmental trial analysis) and post-breeding (selection of fields for seed production) as an alternative approach to reduce costs and support decisions on cultivar planting locations.
600+ insect genomes reveal repetitive element dynamics and highlight biodiversity-scale repeat annotation challenges
Authors: Sproul John S. , Hotaling Scott , Heckenhauer Jacqueline , Powell Ashlyn , Marshall Dez , Larracuente Amanda M. , Kelley Joanna L. , Pauls Steffen U. , Frandsen Paul B.
Published: June 2022

Repetitive elements (REs) are integral to the composition, structure, and function of eukaryotic genomes, yet remain understudied in most taxonomic groups. We investigated REs across 601 insect species and report wide variation in REs dynamics across groups. Analysis of associations between REs and protein-coding genes revealed dynamic evolution at the interface between REs and coding regions across insects, including notably elevated RE-gene associations in lineages with abundant long interspersed nuclear elements (LINEs). We leveraged this large, empirical data set to quantify impacts of long-read technology on RE detection and investigate fundamental challenges to RE annotation in diverse groups. In long-read assemblies we detected ∼36% more REs than short-read assemblies, with long terminal repeats (LTRs) showing 162% increased detection, while DNA transposons and LINEs showed less respective technology-related bias. In most insect lineages, 25–85% of repetitive sequences were “unclassified” following automated annotation, compared to only ∼13% inDrosophilaspecies. Although the diversity of available insect genomes has rapidly expanded, we show the rate of community contributions to RE databases has not kept pace, preventing efficient annotation and high-resolution study of REs in most groups. We highlight the tremendous opportunity and need for the biodiversity genomics field to embrace REs and suggest collective steps for making progress towards this goal.
Ploidy variation and spontaneous haploid-diploid switching of Candida glabrata clinical isolates
Authors: Zheng Qiushi , Liu Jing , Qin Juanxiu , Wang Bingjie , Bing Jian , Du Han , Li Min , Yu Fangyou , Huang Guanghua
Published: June 2022

The human fungal pathogen Candida glabrata is phylogenetically closely related to Saccharomyces cerevisiae, a model eukaryotic organism. Unlike S. cerevisiae with both haploid and diploid forms and a complete sexual cycle, C. glabrata has long been considered a haploid and asexual species. In this study, we analyzed the ploidy states of 500 clinical isolates of C. glabrata from four Chinese hospitals and found that approximately 4% of the isolates were in or able to spontaneously switch to an aneuploidy (genomic DNA: 1N-2N), diploidy (2N), or hyperdiploid (>2N) form under in vivo or in vitro conditions. Stable diploid-form cells were identified in 3% of the isolates (15/500). Of particular interest, one clinical strain only existed in the diploid form. Multilocus sequence typing (MLST) assays revealed two major genetic clusters (A and B) of C. glabrata isolates. Most of the isolates (70%) from China belonged to the A cluster, whereas most of the isolates from other countries (such as Iran, Japan, USA, and European countries) belonged to the B cluster. Further investigation indicated that C. glabrata cells of different ploidy forms differed in a number of aspects, including morphologies, antifungal susceptibility, virulence, and global gene expression profiles. Additionally, C. glabrata could undergo spontaneous switching between the diploid and haploid form under both in vitro and in vivo conditions. Given the absence of an apparent sexual phase, one would expect that the ploidy shifts could function as an alternative strategy that promotes genetic diversity and benefits the ability of the fungus to rapidly adapt to the changing environment.

Importance

The human fungal pathogen Candida glabrata has long been thought to be a haploid organism. Here we report the population structure and ploidy states of 500 clinical isolates of C. glabrata from China. To our surprise, we found that the ploidy of a subset of clinical isolates varied dramatically. Some isolates were in or able to switch to an aneuploid, diploid, or hyperdiploid form. C. glabrata cells with different ploidy differed in a number of biological aspects, including morphologies, antifungal susceptibility, virulence, and global gene expression profiles. Given the absence of an apparent sexual phase in this fungus, we propose that ploidy switching could be a rapid adaption strategy to environmental changes and could function as an alternative strategy of sexual reproduction.
Pseudomonas aeruginosa strains from both clinical and environmental origins readily adopt a stable small colony variant (SCV) phenotype resulting from single mutations in c-di-GMP pathways
Authors: Besse Alison , Groleau Marie-Christine , Trottier Mylène , Vincent Antony T. , Déziel Eric
Published: June 2022

A subpopulation of Small Colony Variants (SCVs) is a frequently observed feature of Pseudomonas aeruginosa isolated from colonized cystic fibrosis lungs. Since most SCVs have until now been isolated from clinical samples, it remains unclear how widespread is the ability of P. aeruginosa to develop this phenotype and the genetic mechanism(s) behind SCVs emergence according to the origin of the isolate. In the present work, we investigated the ability of 22 P. aeruginosa isolates from various environmental origins to, under laboratory culture conditions, spontaneously adopt a SCV-like smaller alternative morphotype distinguishable from the ancestral parent strain. We found that all the P. aeruginosa strains tested could adopt a SCV phenotype, regardless of their origin. Whole genome sequencing of SCVs obtained from clinical and environmental sources revealed single mutations exclusively in two distinct c-di-GMP signaling pathways, Wsp and YfiBNR. We conclude that the ability to switch to a SCV phenotype is a conserved feature of P. aeruginosa and results from the acquisition of a stable genetic mutation, regardless of the origin of the strain.

IMPORTANCE

P. aeruginosa is an opportunistic pathogen that thrives in many environments. It poses a significant health concern, notably because this bacterium is the most prevalent pathogen found in the lungs of people with cystic fibrosis. In infected hosts, its persistence is considered related to the emergence of an alternative small colony variant (SCV) phenotype. By reporting the distribution of P. aeruginosa SCVs in various non-clinical environments and the involvement of c-di-GMP in SCV emergence from both clinical and environmental strains, this work contributes to understanding a conserved adaptation mechanism used by P. aeruginosa to adapt readily in all environments. Hindering this adaptation strategy could help control P. aeruginosa persistent infection.
Gargle sample is an effective option in a novel fully automated molecular point-of-care test for influenza: a multicenter study
Authors: Kaku Norihito , Urabe Tomohito , Iida Tetsuya , Yun Chyuns , Nishida Yoshiyuki , Onitsuka Yasunori , Hashiguchi Kohji , Hirose Kiyoto , Tomonaga Akimitsu , Izumikawa Koichi , Mukae Hiroshi , Yanagihara Katsunori
Published: June 2022

Background

We conducted a multicenter study to evaluate the performance of a novel fully automated molecular point-of-care test using transcription-reverse transcription concerted reaction that can detect influenza A and B within 15 minutes in nasopharyngeal swabs and gargle samples (TRCsatFLU).

Methods

Patients who visited or were hospitalized at eight clinics and hospitals with influenza-like illnesses between December 2019 and March 2020 participated in this study. We collected nasopharyngeal swabs from all patients and gargle samples from patients whom the physician judged fit to perform gargling. The result of TRCsatFLU was compared to a conventional reverse transcription-polymerase chain reaction (RT-PCR). If the results of TRCsatFLU and conventional RT-PCR were different, the samples were analyzed by sequencing.

Results

We evaluated 233 nasopharyngeal swabs and 213 gargle samples from 244 patients.. The average age of the patients was 39.3 ± 21.2. Of the patients, 68.9% visited a hospital within 24 h of symptom onset. The most common symptoms were fever (93.0%), fatigue (79.5%), and nasal discharge (64.8%). All patients in whom the gargle sample was not collected were children. Influenza A or B was detected in 98 and 99 patients in nasopharyngeal swabs and gargle samples using TRCsatFLU, respectively. Four and five patients in nasopharyngeal swabs and gargle samples, respectively, with different TRCsatFLU and conventional RT-PCR results. Influenza A or B was detected using sequencing in all samples with different results. Based on the combined conventional RT-PCR and sequencing results, the sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of TRCsatFLU for influenza detection in nasopharyngeal swabs were 0.990, 1.000, 1.000, and 0.993, respectively. In the gargle samples, the sensitivity, specificity, PPV, and NPV of the TRCsatFLU for detecting influenza were 0.971, 1.000, 1.000, and 0.974, respectively.

Conclusions

The TRCsatFLU showed great sensitivity and specificity for the detection of influenza in nasopharyngeal swabs and gargle samples.

Trial registration

This study was registered in the UMIN Clinical Trials Registry (reference number: UMIN000038276) on October 11, 2019. Before sample collection, written informed consent for the participation and publication of this study was obtained from all participants.
The use of data for planning and service improvement in Tanzanian Primary healthcare facilities: Experience from Star Rating Assessment
Authors: German Chrisogone C. , Yahya Talhiya A. , Hokororo Joseph C. , Kinyenje Erick S. , Nungu Saumu I. , Mohamed Mohamed A. , Degeh Mbwana M. , Nassoro Omary A. , Mwaisengela Syabo M. , Bahegwa Radenta P. , Msigwa Yohanes S. , Ngowi Ruth R. , Marandu Laura E. , Eliakimu Eliudi S.
Published: June 2022

Background

The use of data for planning and improving healthcare delivery is sub-optimal among developing countries. In 2015, Tanzania started to implement Star Rating Assessment (SRA) process for primary health care (PHC) facilities to improve various dimensions of quality of services, including the use of data. We aimed at assessing the extent and predictors of data use in Tanzanian PHC facilities.

Methodology

We used the most current national SRA data available in DHIS2 that was collected in 2017/2018 from all 7,289 PHC facilities. A facility was considered using data if gained 80% of the allocated scores. Other dependent variables were the three components that together contribute to the use of data [If PHC facility has Health Management Information systems (HMIS) functional, disseminate information, and has proper medical records]. We determined the association between data use and facility ownership status (public or private), location of the facility (rural or urban) and facility service level (dispensary, health centre or hospital). Results are presented as proportions of facilities that qualified for data use and the three components. The associations are reported in Adjusted odds ratio (AOR) with a 95% confidence interval (CI).

Results

A total of 6,663(91.4%) PHC facilities met our inclusion criteria for analysis. Among the facilities: 1,198(18.0%) had used data for planning and services improvement; 3,792(56.9%) had functional HMIS; 1,752(26.3%) had disseminated data; and 631(9.5%) had proper medical records. PHC facilities that are publicly owned (AOR 1.25; 95% CI: 1.05–1.48) and those at higher service level [hospitals (AOR 1.77; 95% CI: 1.27–2.46) and health centres (AOR 1.39; 95% CI: 1.15–1.68) compared to dispensaries] were more likely to use data.

Conclusion

The use of facility data for planning and services improvement in Tanzanian PHC facilities is low, and much effort needs to be targeted at privately-owned and low-level PHC facilities.
Waning of two-dose BNT162b2 and mRNA-1273 vaccine effectiveness against symptomatic SARS-CoV-2 infection is robust to depletion-of-susceptibles bias
Authors: Andrejko Kristin L. , Pry Jake , Myers Jennifer F. , Mehrotra Megha , Lamba Katherine , Lim Esther , Fukui Nozomi , DeGuzman Jennifer L. , Openshaw John , Watt James , Jain Seema , Lewnard Joseph A.
Published: June 2022

Concerns about the duration of protection conferred by COVID-19 vaccines have arisen in postlicensure evaluations. However, “depletion of susceptibles” bias driven by differential accrual of infection among vaccinated and unvaccinated individuals may contribute to the appearance of waning vaccine effectiveness (VE) in epidemiologic studies, potentially hindering interpretation of estimates. We enrolled California residents who received molecular SARS-CoV-2 tests in a matched, test-negative design case-control study to estimate VE of mRNA-based COVID-19 vaccines between 23 February and 5 December 2021. We analyzed waning protection following 2 vaccine doses using conditional logistic regression models. Additionally, we used data from case-based surveillance along with estimated case-to-infection ratios from a population-based serological study to quantify the potential contribution of the “depletion-of-susceptibles” bias to time-varying VE estimates for 2 doses. We also estimated VE for 3 doses relative to 0 doses and 2 doses, by time since second dose receipt. Pooled VE of BNT162b2 and mRNA-1273 against symptomatic SARS-CoV-2 infection was 91.3% (95% confidence interval: 83.8-95.4%) at 14 days after second-dose receipt and declined to 50.8% (31.2-75.6%) at 7 months. Accounting for differential depletion-of-susceptibles among vaccinated and unvaccinated individuals, we estimated VE was 53.2% (23.6-71.2%) at 7 months among individuals who had completed the primary series (2 doses). With receipt of a third dose of BN162b2 or mRNA-1273, VE increased to 95.0% (82.8-98.6%), compared with zero doses. These findings confirm that observed waning of protection is not attributable to epidemiologic bias and support ongoing efforts to administer additional vaccine doses to mitigate burden of COVID-19.
Genetic Diversity and Evolutionary Convergence of Cryptic SARS-CoV-2 Lineages Detected Via Wastewater Sequencing
Authors: Gregory Devon A. , Trujillo Monica , Rushford Clayton , Flury Anna , Kannoly Sherin , San Kaung Myat , Lyfoung Dustin , Wiseman Roger W. , Bromert Karen , Zhou Ming-Yi , Kesler Ellen , Bivens Nathan , Hoskins Jay , Lin Chung-Ho , O’Connor David H. , Wieberg Chris , Wenzel Jeff , Kantor Rose S. , Dennehy John J. , Johnson Marc C.
Published: June 2022

Wastewater-based epidemiology (WBE) is an effective way of tracking the appearance and spread of SARS-COV-2 lineages through communities. Beginning in early 2021, we implemented a targeted approach to amplify and sequence the receptor binding domain (RBD) of SARS-COV-2 to characterize viral lineages present in sewersheds. Over the course of 2021, we reproducibly detected multiple SARS-COV-2 RBD lineages that have never been observed in patient samples in 9 sewersheds located in 3 states in the USA. These cryptic lineages contained between 4 to 24 amino acid substitutions in the RBD and were observed intermittently in the sewersheds in which they were found for as long as 14 months. Many of the amino acid substitutions in these lineages occurred at residues also mutated in the Omicron variant of concern (VOC), often with the same substitution. One of the sewersheds contained a lineage that appeared to be derived from the Alpha VOC, but the majority of the lineages appeared to be derived from pre-VOC SARS-COV-2 lineages. Specifically, several of the cryptic lineages from New York City appeared to be derived from a common ancestor that most likely diverged in early 2020. While the source of these cryptic lineages has not been resolved, it seems increasingly likely that they were derived from immunocompromised patients or animal reservoirs. Our findings demonstrate that SARS-COV-2 genetic diversity is greater than what is commonly observed through routine SARS-CoV-2 surveillance. Wastewater sampling may more fully capture SARS-CoV-2 genetic diversity than patient sampling and could reveal new VOCs before they emerge in the wider human population.

Author Summary

During the COVID-19 pandemic, wastewater-based epidemiology has become an effective public health tool. Because many infected individuals shed SARS-CoV-2 in feces, wastewater has been monitored to reveal infection trends in the sewersheds from which the samples were derived. Here we report novel SARS-CoV-2 lineages in wastewater samples obtained from 3 different states in the USA. These lineages appeared in specific sewersheds intermittently over periods of up to 14 months, but generally have not been detected beyond the sewersheds in which they were initially found. Many of these lineages may have diverged in early 2020. Although these lineages share considerable overlap with each other, they have never been observed in patients anywhere in the world. While the wastewater lineages have similarities with lineages observed in long-term infections of immunocompromised patients, animal reservoirs cannot be ruled out as a potential source.
Investigating Causal Relationships between Inflammatory Bowel Disease and Autism Spectrum Disorder: A Bidirectional Two-sample Mendelian Randomization Study
Authors: Zeng Ruijie , Jiang Rui , Wang Jinghua , Yang Jie , Wu Huihuan , Zhuo Zewei , Yang Qi , Li Jingwei , Liao Songyan , Tse Hung-Fat , Sha Weihong , Chen Hao
Published: June 2022

Background and aims

Inflammatory bowel disease (IBD) is usually comorbid with psychological disorders. Emerging observational studies have indicated the association between autism spectrum disorder (ASD) and IBD, including Crohn’s disease (CD) and ulcerative colitis (UC), whereas the causality remains unknown. Our study aimed to explore the causal association between IBD and ASD using bidirectional two-sample Mendelian randomization (MR) design.

Methods

Summary-level data from large-scale genome-wide association (GWAS) studies of IBD (International Inflammatory Bowel Disease Genetics Consortium, Ncases=25,042, Ncontrols=34,915) and ASD (Integrative Psychiatric Research-Psychiatric Genomics Consortium, Ncases=18,382, Ncontrols=27,969) were retrieved. Gene variants for IBD and ASD were selected as instrumental variables. MR analyses were performed mainly including the inverse-variance-weighted method with a series of sensitivity tests.

Results

Genetic predisposition to IBD was associated with a high risk of ASD (odds ratio [OR] = 1.03, 95% confidence interval [CI] = 1.01-1.06, P = 0.01; OR [95% CI]: 1.03 [1.01-1.05], P = 0.02 for CD; OR [95% CI]: 1.03 [1.01-1.07], P = 0.04 for UC). In contrast, no causal association was found for the genetic liability to ASD on IBD.

Conclusions

Our findings reveal that genetically predicted IBD is causally related to ASD, whereas the causal association of ASD on IBD is not supported. Our study highlights the early screening and surveillance of psychological symptoms, as well as sustaining support for patients with IBD. Further investigations on age-specific groups are warranted.
Bayesian multi-level calibration of a process-based maize phenology model
Authors: Viswanathan Michelle , Scheidegger Andreas , Streck Thilo , Gayler Sebastian , Weber Tobias KD
Published: June 2022

Plant phenology models are important components in process-based crop models, which are used to assess the impact of climate change on food production. For reliable model predictions, parameters in phenology models have to be accurately known. They are usually estimated by calibrating the model to observations. However, at regional scales in which different cultivars of a crop species may be grown, not accounting for inherent differences in phenological development between cultivars in the model and the presence of model deficits lead to inaccurate parameter estimates. To account for inherent differences between cultivars and to identify model deficits, we used a Bayesian multi-level approach to calibrate a phenology model (SPASS) to observations of silage maize grown across Germany between 2009 and 2017. We evaluated four multi-level models of increasing complexity, where we accounted for different combinations of ecological, weather, and year effects, as well as the hierarchical classification of cultivars nested within ripening groups of the maize species. We compared the calibration quality from this approach to the commonly used pooled approach in which none of these factors are considered. Our approach proved successful in improving calibration quality by incorporating the hierarchical classification of cultivars within ripening groups of maize. Our findings have implications for regional model calibration and data-gathering studies, since it emphasizes that ripening group and cultivar information is essential. Furthermore, we found that if this information is not available, at least weather, ecological regions and year effects should be taken into account. Our results can facilitate model improvement studies since we identified possible model limitations related to temperature effects in the reproductive (post-flowering) phase and to soil-moisture. We demonstrate that Bayesian multi-level calibration of a phenology model facilitates the incorporation of hierarchical dependencies and the identification of model limitations. Our approach can be extended to full crop models at different spatial scales.
Localized Leishmania major infection causes systemic iron deficiency that can be controlled by oral iron supplementation
Authors: Banerjee Sourav , Datta Rupak
Published: June 2022

Leishmania major (L. major) and its related parasitic species infection causes human cutaneous leishmaniasis that results into disfiguring skin lesion. Although L. major infection has been found to alter macrophage iron homeostasis we have limited understanding on whether it can also manipulate the same at systemic level. In fact, localized L. major infection found to promote iron deficiency anemia in children by an unknown mechanism. To address these unresolved issues, Balb/c mouse were infected with L. major and iron status in different organs were monitored systematically with the development of cutaneous lesion. At week 10 post infection when there was maximum lesion development in the parasite infected left hind footpad, the iron content increased significantly in this tissue with the concomitant increase in parasite burden. L. major infection mediated iron accumulation in infected mouse footpad was found to be due to transferrin receptor upregulation and natural resistance-associated macrophage protein 1 (Nramp1) downregulation. Surge in iron level was found to be associated with the reduced hepatic iron storage that resulted increased serum iron. Limited iron storage in liver and bone-marrow of infected mice caused reduced hemoglobin level and production of deformed erythrocytes. Interestingly, L. major infected mice developed splenomegaly with significant upregulation of erythroid related genes. Importantly, oral iron supplementation post infection rescued the development of cutaneous lesion in infected mice. Together, our study unravelled a comprehensive mechanism behind developing iron deficiency anemia during cutaneous leishmaniasis and a novel therapeutic route of treating this infection by delivering iron.
Label-Free Hyperspectral Imaging and Deep-Learning Prediction of Retinal Amyloid β-Protein and Phosphorylated Tau
Authors: Du Xiaoxi , Koronyo Yosef , Mirzaei Nazanin , Yang Chengshuai , Fuchs Dieu-Trang , Black Keith L. , Koronyo-Hamaoui Maya , Gao Liang
Published: June 2022

Alzheimer’s disease (AD) is a major risk for the aging population. The pathological hallmarks of AD—an abnormal deposition of amyloid β-protein (Aβ) and phosphorylated tau (pTau)—have been demonstrated in the retinas of AD patients, including in prodromal patients with mild cognitive impairment (MCI). Aβ pathology, especially the accumulation of the amyloidogenic 42-residue long alloform (Aβ42), is considered an early and specific sign of AD, and together with tauopathy, confirms AD diagnosis. To visualize retinal Aβ and pTau, state-of-the-art methods use fluorescence. However, administering contrast agents complicates the imaging procedure. To address this problem, we developed a label-free hyperspectral imaging method to detect the spectral signatures of Aβ42 and pS396-Tau and predicted their abundance in retinal cross sections. For the first time, we reported the spectral signature of pTau and demonstrated an accurate prediction of Aβ and pTau distribution powered by deep learning. We expect our finding will lay the groundwork for label-free detection of AD at its very earliest roots.

Significance Statement

The pathological hallmarks of Alzheimer’s disease (AD), amyloid β-protein (Aβ) and hyperphosphorylated (p)Tau protein have been characterized by a hyperspectral camera in terms of spectral signatures. The unique optical properties of the hallmark proteins on the broad visible light range enable label-free and high-resolution detection and virtual staining of abnormal deposition in the retina tissue, which will lay the groundwork for AD early diagnosis and AD development quantification.
Extrinsic control of the early postnatal CA1 hippocampal circuits
Authors: Leprince Erwan , Dard Robin F. , Mortet Salomé , Filippi Caroline , Giorgi-Kurz Marie , Lenck-Santini Pierre-Pascal , Picardo Michel A. , Bocchio Marco , Baude Agnès , Cossart Rosa
Published: June 2022

The adult CA1 region of the hippocampus produces coordinated neuronal dynamics with minimal reliance on its extrinsic inputs. In contrast, the neonatal CA1 is tightly linked to externally-generated sensorimotor activity but the circuit mechanisms underlying early synchronous activity in CA1 remain unclear. Here, using a combination ofin vivoandex vivocircuit mapping, calcium imaging and electrophysiological recordings in mouse pups, we show that early dynamics in the ventro-intermediate CA1 are under the mixed influence of entorhinal (EC) and thalamic (VMT) inputs. Both VMT and EC can drive internally-generated synchronous eventsex vivo. However, movement-related population bursts detectedin vivoare exclusively driven by the EC. These differential effects on synchrony reflect the different intrahippocampal targets of these inputs. Hence, cortical and subcortical pathways act differently on the neonatal CA1, implying distinct contributions to the development of the hippocampal microcircuit and related cognitive maps.
Non-invasive auditory brainstem responses to FM sweeps in awake big brown bats
Authors: Simmons Andrea Megela , Tuninetti Amaro , Yeoh Brandon M. , Simmons James A.
Published: June 2022

We introduce two EEG techniques, one based on conventional monopolar electrodes and one based on a novel tripolar electrode, to record for the first time auditory brainstem responses (ABRs) from the scalp of unanesthetized, unrestrained big brown bats. Stimuli were frequency-modulated (FM) sweeps varying in sweep direction, sweep duration, and harmonic structure. As expected from previous invasive ABR recordings, upward-sweeping FM signals evoked larger amplitude responses (peak-to-trough amplitude in the latency range of 3-5 ms post-stimulus onset) than downward-sweeping FM signals. Scalp-recorded responses displayed amplitudelatency trading effects as expected from invasive recordings. These two findings validate the reliability of our noninvasive recording techniques. The feasibility of recording noninvasively in unanesthetized, unrestrained bats will energize future research uncovering electrophysological signatures of perceptual and cognitive processing of biosonar signals in these animals, and allows for better comparison with ABR data from echolocating cetaceans, where invasive experiments are heavily restricted. Because experiments can be repeated in the same animal over time without confounds of stress or anesthesia, our technique requires fewer captures of wild bats, thus helping to preserve natural populations and addressing the goal of reducing animal numbers used for research purposes.
A probabilistic successor representation for context-dependent prediction
Authors: Geerts Jesse P. , Gershman Samuel J. , Burgess Neil , Stachenfeld Kimberly L.
Published: June 2022

The different strategies that animals use for predicting reward are often classified as model-based or model-free reinforcement learning (RL) algorithms. Model-based RL involves explicit simulation the future to make decisions while model-free strategies rely on learning associations between stimuli and predicted reward by trial and error. An alternative, intermediate strategy for RL is based on the “successor representation” (SR), an encoding of environmental states in terms of predicted future states. A recent theoretical proposal suggests that the hippocampus encodes the SR in order to facilitate prediction of future reward. However, this proposal does not take into account how learning should adapt under uncertainty and switches of context. Here, we introduce a theory of learning SRs using prediction errors which includes optimally balancing uncertainty in new observations versus existing knowledge. We then generalise that approach to a multi-context setting, allowing the model to learn and maintain multiple task-specific SRs and infer which one to use at any moment based on the accuracy of its predictions. Thus, the context used for predictions can be determined by both the contents of the states themselves and the distribution of transitions between them. This probabilistic SR model captures animal behaviour in tasks which require contextual memory and generalisation, and unifies previous SR theory with hippocampal-dependent contextual decision making.
Doxorubicin induces prolonged DNA damage signal in cells overexpressing DEK isoform-2
Authors: Özçelik Emrah , Kalaycı Ahmet , Çelik Büşra , Avcı Açelya , Akyol Hasan , Baki Kılıç İrfan , Güzel Türkan , Çetin Metin , Tuzlakoğlu Öztürk Merve , Çalışkaner Zihni Onur , Tombaz Melike , Yoleri Dilan , Konu Özlen , Kandilci Ayten
Published: June 2022

DEK has a short isoform (DEK isoform-2; DEK2) that lacks amino acid residues between 49-82. The full-length DEK (DEK isoform-1; DEK1) is ubiquitously expressed and plays a role in different cellular processes but whether DEK2 is involved in these processes remains elusive. We stably overexpressed DEK2 in human bone marrow stromal cell line HS-27A, in which endogenous DEKs were intact or suppressed via short hairpin RNA (sh-RNA). We have found that contrary to ectopic DEK1, DEK2 locates in the nucleus and nucleolus, causes persistent γH2AX signal upon doxorubicin treatment, and couldn’t functionally compensate for the loss of DEK1. In addition, DEK2 overexpressing cells were more sensitive to doxorubicin than DEK1-cells. Expressions of DEK1 and DEK2 in cell lines and primary tumors exhibit tissue specificity. DEK1 is upregulated in cancers of the colon, liver, and lung compared to normal tissues while both DEK1 and DEK2 are downregulated in subsets of kidney, prostate, and thyroid carcinomas. Interestingly, only DEK2 was downregulated in a subset of breast tumors suggesting that DEK2 can be modulated differently than DEK1 in specific cancers. In summary, our findings show distinct expression patterns and subcellular location and suggest non-overlapping functions between the two DEK isoforms.
Analysis of SMAD1/5 target genes in a sea anemone reveals ZSWIM4-6 as a novel BMP signaling modulator
Authors: Knabl Paul , Schauer Alexandra , Pomreinke Autumn Penecilla , Zimmermann Bob , Rogers Katherine W. , Müller Patrick , Genikhovich Grigory
Published: June 2022

BMP signaling has a conserved function in patterning the dorsal-ventral body axis in Bilateria and the directive axis in anthozoan cnidarians. So far, cnidarian studies have focused on the role of different BMP signaling network components in regulating pSMAD1/5 gradient formation. Much less is known about the target genes downstream of BMP signaling. To address this, we generated a genome-wide list of direct pSMAD1/5 target genes in the anthozoan Nematostella vectensis, several of which were conserved in Drosophila and Xenopus. Our ChIP-Seq analysis revealed that many of the regulatory molecules with documented bilaterally symmetric expression in Nematostella are directly controlled by BMP signaling. Among the so far uncharacterized BMP-dependent transcription factors and signaling molecules we identified several, whose bilaterally symmetric expression may be indicative of their involvement in secondary axis patterning. One of these molecules, zswim4-6, encodes a novel nuclear modulator of the pSMAD1/5 gradient potentially promoting BMP-dependent gene repression. Strikingly, overexpression of the zebrafish homologue zswim5 suggests that its effect on the pSMAD1/5 gradient is conserved between anthozoan Cnidaria and Bilateria.
Improving T-cell mediated immunogenic epitope identification via machine learning: the neoIM model
Authors: Pfitzer Lena , Lybaert Lien , Bogaert Cedric , Fant Bruno
Published: June 2022

The identification of immunogenic peptides that will elicit a CD8+ T cell-specific immune response is a critical step for various immunotherapeutic strategies such as cancer vaccines. Significant research effort has been directed towards predicting whether a peptide is presented on class I major histocompatibility complex (MHC I) molecules. However, only a small fraction of the peptides predicted to bind to MHC I turn out to be immunogenic. Prediction of immunogenicity, i.e. the likelihood for CD8+ T cells to recognize and react to a peptide presented on MHC I, is of high interest to reduce validation costs, de-risk clinical studies and increase therapeutic efficacy especially in a personalized setting where in vitro immunogenicity pre-screening is not possible.

To address this, we present neoIM, a random forest classifier specifically trained to classify short peptides as immunogenic or non-immunogenic. This first-in-class algorithm was trained using a positive dataset of more than 8000 non-self immunogenic peptide sequences, and a negative dataset consisting of MHC I-presented peptides with one or two mismatches to the human proteome for a closer resemblance to a background of mutated but non-immunogenic peptides. Peptide features were constructed by performing principal component analysis on amino acid physicochemical properties and stringing together the values of the ten main principal components for each amino acid in the peptide, combined with a set of peptide-wide properties. The neoIM algorithm outperforms the currently publicly available methods and is able to predict peptide immunogenicity with high accuracy (AUC=0.88). neoIM is MHC-allele agnostic, and in vitro validation through ELISPOT experiments on 33 cancer-derived neoantigens have confirmed its predictive power, showing that 71% of all immunogenic peptides are contained within the top 30% of neoIM predictions and all immunogenic peptides were included when selecting the top 55% of peptides with the highest neoIM score. Finally, neoIM results can help to better predict the response to checkpoint inhibition therapy, especially in low TMB tumors, by focusing on the number of immunogenic variants in a tumor.

Overall, neoIM enables significantly improved identification of immunogenic peptides allowing the development of more potent vaccines and providing new insights into the characteristics of immunogenic peptides.
Nanopore sequencing for N1-methylpseudouridine in RNA reveals sequence-dependent discrimination of the modified nucleotide triphosphate during transcription
Authors: Fleming Aaron M. , Burrows Cynthia J.
Published: June 2022

Direct RNA sequencing with a commercial nanopore platform was used to sequence RNA containing uridine (U), pseudouridine (Ψ), or N1-methylpseudouridine (m1Ψ) generated by in vitro transcription (IVT). The base calling data as well as the ionic currents and dwell times for U, Ψ, or m1Ψ as they translocated through the helicase and nanopore proteins identified diagnostic signatures for Ψ and m1Ψ; however, the two modifications yielded similar patterns although both were different from U. Understanding the nanopore signatures for Ψ and m1Ψ enabled a running start T7 RNA polymerase assay to study how competing mixtures of UTP with ΨTP or m1ΨTP lead to nucleotide selection in all possible adjacent sequence contexts. For UTP vs. ΨTP, ΨTP was favorably incorporated in singly-modified contexts, while doubly-modified contexts found high yields of ΨTP insertion on the 5′ side and lower yields on the 3′ side. For UTP vs. m1ΨTP, UTP was favorably selected except in 5′-XA (X = U or m1Ψ) where the ratio was determined by their relative NTP concentrations. Experiments with chemically-modified triphosphates and DNA templates designed based on the structure of T7 RNA polymerase provide a model to explain the observations. These results may aid in future efforts that employ IVT to make therapeutic mRNAs with sub-stochiometric amounts of m1Ψ.
Inter-layer and inter-subject variability of circadian gene expression in human skin
Authors: del Olmo Marta , Spörl Florian , Korge Sandra , Jürchott Karsten , Felten Matthias , Grudziecki Astrid , de Zeeuw Jan , Nowozin Claudia , Reuter Hendrik , Blatt Thomas , Herzel Hanspeter , Kunz Dieter , Kramer Achim , Ananthasubramaniam Bharath
Published: June 2022

The skin is the largest human organ with a circadian clock that regulates its function. Although circadian rhythms in specific functions are known, rhythms in the proximal clock output, gene expression, in human skin have not been thoroughly explored. This work reports circadian gene expression in two skin layers, epidermis and dermis, in a cohort of young, healthy adults, who maintained natural, regular sleep schedules. 10% of the expressed genes showed rhythms at the population level, of which only a third differed between the two layers. Broadly, expression magnitudes of circadian genes were consistent across subjects in each layer. Amplitude and phases of circadian gene expression, however, varied more across subjects than layers, with amplitude being more variable than phases. Expression amplitudes in the epidermis were larger and more subject-variable, while they were smaller and more consistent in the dermis. Core clock gene expression was similar across layers at the population-level, but were heterogeneous in the their variability across subjects. We used this data to identify small sets of biomarkers for internal clock phase in each layer, which consisted of layer-specific non-core clock genes. This work provides a valuable resource to advance our understanding of human skin to realize the potential of circadian medicine as well as a novel methodology to quantify sources of variability in human circadian rhythms.
Laser particle barcoding for multi-pass high-dimensional flow cytometry
Authors: Kwok Sheldon J.J. , Forward Sarah , Fahlberg Marissa D. , Cosgriff Sean , Lee Seung Hyung , Abbott Geoffrey , Zhu Han , Minasian Nicolas H. , Vote A. Sean , Martino Nicola , Yun Seok-Hyun
Published: June 2022

Flow cytometry is a standard technology in life science and clinical laboratories used to characterize the phenotypes and functional status of cells, especially immune cells. Recent advances in immunology and immuno-oncology as well as drug and vaccine discovery have increased the demand to measure more parameters. However, the overlap of fluorophore emission spectra and one-time measurement nature of flow cytometry are major barriers to meeting the need. Here, we present multi-pass flow cytometry, in which cells are tracked and measured repeatedly through barcoding with infrared laser-emitting microparticles. We demonstrate the benefits of this approach on several pertinent assays with human peripheral blood mononuclear cells (PBMCs). First, we demonstrate unprecedented time-resolved flow characterization of T cells before and after stimulation. Second, we show 33-marker deep immunophenotyping of PBMCs, analyzing the same cells in 3 back-to-back cycles. This workflow allowed us to use only 10-13 fluorophores in each cycle, significantly reducing spectral spillover and simplifying panel design. Our results open a new avenue in multi-dimensional single-cell analysis based on optical barcoding of individual cells.