bluuebunny/crossref_metadata_2025 huggingface dataset:
Forseti: A mechanistic and predictive model of the splicing status of scRNA-seq reads
Authors: He Dongze , Gao Yuan , Chan Spencer Skylar , Quintana-Parrilla Natalia , Patro Rob
Published: February 2024

Motivation

Short-read single-cell RNA-sequencing (scRNA-seq) has been used to study cellular heterogeneity, cellular fate, and transcriptional dynamics. Modeling splicing dynamics in scRNA-seq data is challenging, with inherent difficulty in even the seemingly straightforward task of elucidating the splicing status of the molecules from which sequenced fragments are drawn. This difficulty arises, in part, from the limited read length and positional biases, which substantially reduce the specificity of the sequenced fragments. As a result, the splicing status of many reads in scRNA-seq is ambiguous because of a lack of definitive evidence. We are therefore in need of methods that can recover the splicing status of ambiguous reads which, in turn, can lead to more accuracy and confidence in downstream analyses.

Results

We developForseti, a predictive model to probabilistically assign a splicing status to scRNA-seq reads. Our model has two key components. First, we train a binding affinity model to assign a probability that a given transcriptomic site is used in fragment generation. Second, we fit a robust fragment length distribution model that generalizes well across datasets deriving from different species and tissue types.Forseticombines these two trained models to predict the splicing status of the molecule of origin of reads by scoring putative fragments that associate each alignment of sequenced reads with proximate potential priming sites. Using both simulated and experimental data, we show that our model can precisely predict the splicing status of reads and identify the true gene origin of multi-gene mapped reads.

Availability

Forsetiand the code used for producing the results are available athttps://github.com/COMBINE-lab/forsetiunder a BSD 3-clause license.
Characterizing and addressing error modes to improve sequencing accuracy
Authors: Kruglyak Semyon , Altomare Andrew , Ambroso Mark , Dien Vivian , Lajoie Bryan , Wiseman Kelly N. , Levy Shawn , Kellinger Matthew
Published: February 2024

The accuracy of a sequencing platform has traditionally been measured by the %Q30, or percentage of data exceeding a basecall accuracy of 99.9%. Improvements to accuracy beyond Q30 may be beneficial for certain applications such as the identification of low frequency alleles or the improvement of reference genomes. Here we demonstrate how we achieved over 70% Q50 (99.999% accuracy) data on the AVITI™ sequencer. This level of accuracy required us to not only improve sequencing quality but also to mitigate library preparation errors and analysis artifacts.
Effect of environmental conditions on the wing morphometric variation inAedes aegypti(Diptera: Culicidae) in India
Authors: Sharma Gaurav , Bhutiani Rakesh , Sarma Devojit Kumar
Published: February 2024

Aedes aegyptian efficient vector of different arboviral diseases, is a major concern for public health globally. Originating from Africa, this vector has now invaded most of the parts of the world, which shows its thriving adaptability against diverse ecological conditions. In India too,Ae. aegyptihas been found almost everywhere and along withAe. albopictus, it contributed more than 0.2 million cases of dengue in the year 2022. Due to heterogeneous environmental settings in India, this vector has shown various intraspecific variations including its behavioral, genetic, and physiological characteristics. Thus, the present study hypothesized that there will be some differences in wing morphometrics across the country for this species. Considering this, we have sampled adults and immatures ofAe. aegyptifrom 11 distinct locations, representing six varied climatic regions of India. The immatures were reared to adult and the right wing was used to score the morphometric variations. A significant variation in wing size and shape was observed. The Himalayan region (Srinagar CS: 1.92 ± 0.08 mm) supports the shortest (CS: 2.04 ± 0.09 mm) wing size mosquitoes while the Deccan Peninsular region (Nagpur CS: 4.48 ± 0.06 mm) exhibits the largest (CS: 4.46 ± 0.10 mm) wing size mosquito. After excluding the allometric effect, the semi-desert region (Kota) showed the greatest wide variety of wing shapes corresponding to a larger morphospace in CVA analysis. In addition, region-wise wing size was found positively correlated with temperature (64%) and altitude (82%) but no directional trend was detected for wing shape characteristics. Conclusively, the study suggests the existence of varied population structures ofAe. aegyptiin India based on wing morphometric analysis. This finding will be helpful towards focused actions and early measures to reduce the impact of these diseases carrying mosquitoes on public health.
HiCDiffusion - diffusion-enhanced, transformer-based prediction of chromatin interactions from DNA sequences
Authors: Chiliński Mateusz , Plewczynski Dariusz
Published: February 2024

Prediction of chromatin interactions from DNA sequence has been a significant research challenge in the last couple of years. Several solutions have been proposed, most of which are based on encoder-decoder architecture, where 1D sequence is convoluted, encoded into the latent representation, and then decoded using 2D convolutions into the Hi-C pairwise chromatin spatial proximity matrix. Those methods, while obtaining high correlation scores and improved metrics, produce Hi-C matrices that are artificial - they are blurred due to the deep learning model architecture. In our study, we propose the HiCDiffusion model that addresses this problem. We first train the encoder-decoder neural network and then use it as a component of the diffusion model - where we guide the diffusion using a latent representation of the sequence, as well as the final output from the encoder-decoder. That way, we obtain the high-resolution Hi-C matrices that not only better resemble the experimental results - improving the Fréchet inception distance by an average of 12 times, with the highest improvement of 35 times - but also obtain similar classic metrics to current state-of-the-art encoder-decoder architectures used for the task.
Fecundity Estimation of Atlantic mudskipperPeriophthalmus barbarusin Ogbo-Okolo mangrove Forest of Santa Barbara River, Bayelsa State Niger Delta, Nigeria
Authors: Nathaniel Ayibatonyo Markson , Soberekon Ilemi Jennifer , Gamage Igoniama Esau , Eli Akayinaboderi Augustus , Raimi Morufu Olalekan
Published: February 2024

Rationale

Fecundity estimation and reproductive biology of Atlantic mudskippers(Periophthalmus barbarus)in the Niger Delta region of Nigeria needs to be studied.

Objectives

To estimate fecundity, gonadosomatic index, and condition factor ofP. barbarusand describe its reproductive biology.

Methods

P. barbarusspecimens were collected from Ogbo-Okolo mangrove forest in Bayelsa State, Nigeria. Length, weight, and gonad weight measurements were taken. Fecundity was estimated by the gravimetric method. Length-weight relationship, condition factor, and gonadosomatic index were calculated. Ovarian developmental stages were identified.

Results

Highest mean fecundity of 9612.7 eggs was observed in females of 10.1-12.0 cm standard length and 20.0-27.9 g weight. Length-weight relationship showed specimens were in good condition. Gonadosomatic index was higher in smaller individuals. Four ovarian developmental stages were identified.

Conclusion

P. barbarusexhibits high fecundity. Reproductive potential is greater in intermediate sized individuals compared to smaller or larger fish.

Recommendations

Sustainable management practices should be implemented to conserveP. barbarusstocks in the Niger Delta region. Further research into reproductive behavior and ecology is needed.
Spotiflow: accurate and efficient spot detection for fluorescence microscopy with deep stereographic flow regression
Authors: Mantes Albert Dominguez , Herrera Antonio , Khven Irina , Schlaeppi Anjalie , Kyriacou Eftychia , Tsissios Georgios , Skoufa Evangelia , Santangeli Luca , Buglakova Elena , Durmus Emine Berna , Manley Suliana , Kreshuk Anna , Arendt Detlev , Aztekin Can , Lingner Joachim , La Manno Gioele , Weigert Martin
Published: February 2024

Identifying spot-like structures in large and noisy microscopy images is a crucial step to produce high quality results in various life-science applications. Imaging-based spatial transcriptomics (iST) methods, in particular, critically depend on the precise detection of millions of transcripts in images with low signal-to-noise ratio. Despite advances in computer vision that have revolutionized many biological imaging tasks, currently adopted spot detection techniques are mostly still based on classical signal processing methods that often lack robustness to changing imaging conditions and thus require tedious manual tuning per dataset. In this work, we introduce Spotiflow, a deep learning method that achieves subpixel-accurate localizations by formulating the spot detection task as a multi-scale heatmap and stereographic flow regression problem. Spotiflow can be used for 2D images and 3D volumetric stacks and can be trained to generalize across different imaging conditions, tissue types and chemical preparations, while being substantially more time- and memory-efficient than existing methods. We show the efficacy of Spotiflow via extensive quantitative experiments on a variety of diverse datasets and demonstrate that the enhanced accuracy of Spotiflowleads to meaningful improvements in the biological insights obtained from iST and live imaging experiments. Spotiflow is available as an easy-to-use Python library as well as a napari plugin athttps://github.com/weigertlab/spotiflow.
INDIVIDUAL CONTRIBUTIONS TO NEST BUILDING AND INCUBATION BY COOPERATIVELY BREEDING AMERICAN CROWS
Authors: Caffrey Carolee , Peterson Charles C. , Hackler Tiffany W.
Published: February 2024

American Crows (Corvus brachyrhynchos brachyrhynchos) are long-lived birds with pair bonds that may last many years. Pairs in Stillwater, OK, nested singly or in groups with up to 10 auxiliaries (Caffrey and Peterson 2015). Breeders did most of the nest building. Pair members contributed at approximately equal rates, although the sexes differed slightly in details: males tended to carry sticks and hand off materials more often, and females spent more time at and in nests. Both sexes worked faster on second and third attempts than on first attempts of the season. We found no evidence that pair members were (sexually) signaling to each other via their contributions. Incubation periods were characterized by low levels of activity at nests, where females spent most of their time and were fed once every 3-4 hours, mostly by their mates. Contributions to both stages of nesting by auxiliaries varied widely and exhibited no patterns with respect to any measured phenotypic characteristics.
Short- and long-term effects of imatinib in patients hospitalised for COVID-19 infection: A randomised controlled trial
Authors: Halme Alex L. E. , Laakkonen Sanna , Rutanen Jarno , Nevalainen Olli P. O. , Sinisalo Marjatta , Horstia Saana , Mustonen Jussi M. J. , Pourjamal Negar , Vanhanen Aija , Investigators Solidarity Finland , Rosberg Tuomas , Renner Andreas , Perola Markus , Paukkeri Erja-Leena , Patovirta Riitta-Liisa , Parkkila Seppo , Paajanen Juuso , Nykänen Taina , Mäntylä Jarkko , Myllärniemi Marjukka , Mattila Tiina , Leinonen Maarit , Külmäsu Alvar , Kuutti Pauliina , Kuitunen Ilari , Kreivi Hanna-Riikka , Kilpeläinen Tuomas P. , Kauma Heikki , Kalliala Ilkka E. J. , Järvinen Petrus , Hankkio Riina , Hammarén Taina , Feuth Thijs , Ansakorpi Hanna , Ala-Karvia Riikka , Guyatt Gordon H. , Tikkinen Kari A. O.
Published: February 2024

We report the short- and long-term results of the SOLIDARITY Finland on mortality and other patient-important outcomes in patients hospitalised for COVID-19. Between 08/2021 and 03/2023, we randomised 156 patients in 15 hospitals. In the imatinib group, 7.2% of patients had died at 30 days and 13.3% at 1 year and in the standard of care group 4.1% and 8.3% (adjusted HR at 30 days 1.09, 95% CI 0.23–5.07). In a meta-analysis of randomised trials of imatinib versus standard of care (n=732), allocation to imatinib was associated with a mortality risk ratio of 0.73 (95% CI 0.32–1.63). At 1-year, self-reported recovery occurred in 79.0% in imatinib and in 88.3% in standard of care (RR 0.91, 95% CI 0.78-1.06). Of the 21 potential long COVID symptoms, patients often reported moderate or major bother from fatigue (24%), sleeping problems (19%) and memory difficulties (17%). We found no convincing difference between imatinib and standard of care groups in quality of life or symptom outcomes. The evidence raises serious doubts regarding the benefit of imatinib in reducing mortality, improving recovery, and preventing potential long COVID symptoms when given to patients hospitalised for COVID-19.
Mapping uterine calcium dynamics during the ovulatory cycle in live mice
Authors: Combs David J. , Moult Eric M. , England Sarah K. , Cohen Adam E.
Published: February 2024

Uterine contraction patterns vary during the ovulatory cycle and throughout pregnancy but prior measurements have produced limited and conflicting information on these patterns. We combined a virally delivered genetically encoded calcium reporter (GCaMP8m) and ultra-widefield imaging in live nonpregnant mice to characterize uterine calcium dynamics at organ scale throughout the estrous cycle. Prior to ovulation (proestrus and estrus) uterine excitations primarily initiated in a region near the oviduct, but after ovulation (metestrus and diestrus), excitations initiated at loci homogeneously distributed throughout the organ. The frequency of excitation events was lowest in proestrus and estrus, higher in metestrus and highest in diestrus. These results establish a platform for mapping uterine activity, and show that the question of whether there is an anatomically localized trigger for uterine excitations depends on the estrous cycle phase.
Use of natural language understanding to facilitate surgical de-escalation of axillary staging in patients with breast cancer
Authors: Carleton Neil , Saadawi Gilan , McAuliffe Priscilla F. , Soran Atilla , Oesterreich Steffi , Lee Adrian V. , Diego Emilia J.
Published: February 2024

Natural language understanding (NLU) may be particularly well-equipped for enhanced data capture from the electronic health record (EHR) given its examination of both content- and context-driven extraction. We developed and applied a NLU model to examine rates of pathological node positivity (pN+) and rates of lymphedema to determine if omission of routine axillary staging could be extended to younger patients with ER+/cN0 disease. We found that rates of pN+ and arm lymphedema were similar between patients 55-69yo and ≥70yo, with rates of lymphedema exceeding rates of pN+ for clinical stage T1c and smaller disease. Data from our NLU model suggest that omission of SLNB might be extended beyond Choosing Wisely recommendations, limited to those over 70 years old, to all postmenopausal women with early-stage ER+/cN0 disease. These data support the recently-reported SOUND trial results and provide additional granularity to facilitate surgical de-escalation.
Prolonged airway explant culture enables study of health, disease, and viral pathogenesis
Authors: Lee-Ferris Rhianna E , Okuda Kenichi , Galiger Jacob R , Schworer Stephen A , Rogers Troy D , Dang Hong , Gilmore Rodney , Edwards Caitlin , Nakano Satoko , Cawley Anne M. , Pickles Raymond J , Gallant Samuel C , Crisci Elisa , Rivier Lauraine , Hagood James S , O’Neal Wanda K , Baric Ralph S , Grubb Barbara R , Boucher Richard C , Randell Scott H
Published: February 2024

In vitro models play a major role in studying airway physiology and disease. However, the native lung’s complex tissue architecture and non-epithelial cell lineages are not preserved in these models. Ex vivo tissue models could overcome in vitro limitations, but methods for long-term maintenance of ex vivo tissue has not been established. We describe methods to culture human large airway explants, small airway explants, and precision-cut lung slices for at least 14 days. Human airway explants recapitulate genotype-specific electrophysiology, characteristic epithelial, endothelial, stromal and immune cell populations, and model viral infection after 14 days in culture. These methods also maintain mouse, rabbit, and pig tracheal explants. Notably, intact airway tissue can be cryopreserved, thawed, and used to generate explants with recovery of function 14 days post-thaw. These studies highlight the broad applications of airway tissue explants and their use as translational intermediates between in vitro and in vivo studies.
Cardiovascular drugs approved for heart failure with reduced ejection fraction and/or post-myocardial infarction exert consistent effects in both populations: A meta-analysis and meta-regression of randomized controlled trials
Authors: Dasaro Christopher , Haslam Alyson , Prasad Vinay
Published: February 2024

Background

Heart failure (HF) following an acute myocardial infarction (post-MI HF) has been studied as an additional sub-type of HF to broaden the indications for HF drugs. Post-MI HF and HFrEF are pathophysiologically similar and share pharmacotherapies. In this meta-analysis, we examined the concordance between all-cause mortality data for drugs indicated for HFrEF and post-MI HF. We used our analysis to calculate the projected all-cause mortality hazard ratios (HRs) for the pending dapagliflozin (DAPA-MI) and empagliflozin (EMPACT-MI) post-MI HF trials.

Methods

Using CenterWatch and UpToDate, we identified all FDA-approved drugs for NYHA Class II to IV HFrEF. We searched each of these drugs on FDALabel and ClinicalTrials.gov to identify their registration trials measuring all-cause mortality for HFrEF and, if available, in the post-MI setting—including trials where participants displayed a left ventricular ejection fraction of <40% (“post-MI HF”). For each of the included studies, we extracted the all-cause mortality HRs, their 95% confidence intervals, and the control-group used. For all drugs studied in both indications, we plotted the all-cause mortality HRs for HFrEF against those for post-MI (HF) and calculated the linear regressions.

Results

This meta-regression pooled data from 29 completed trials underlying 20 drugs. Two pending trials were also analyzed. Nine drugs (metoprolol, carvedilol, spironolactone, eplerenone, sacubitril-valsartan, lisinopril, enalapril, valsartan, losartan) had all-cause mortality data in both HFrEF and post-MI generally, with a linear coefficient of determination of 0.93. Five of these drugs (carvedilol, eplerenone, sacubitril-valsartan, valsartan, losartan) were studied in both HFrEF and non-acute post-MI HF, displaying a linear coefficient of determination of 0.99. Using our model, we predict the all-cause mortality HRs that will be observed in the EMPACT-MI and DAPA-MI trials will be 0.85 and 0.89, respectively.

Conclusions

In this meta-regression of registration trials for drugs studied in both HFrEF and post-MI (HF), all-cause mortality effects were highly concordant. We also find asymmetries in the assessment of HF drug indications, whereby drugs are seldom assessed for an all-cause mortality benefit in both HFrEF and in post-MI HF. Future studies may use these results to guide future HF RCT development.
Multicenter normative data for mesopic microperimetry
Authors: Pfau Maximilian , Jolly Jasleen K. , Charng Jason , von der Emde Leon , Müller Philipp L. , Ansari Georg , Pfau Kristina , Chen Fred K , Wu Zhichao
Published: February 2024

Purpose

To provide a large, multi-center normative dataset for the Macular Integrity Assessment (MAIA) microperimeter and compare the goodness-of-fit and prediction interval calibration-error for a panel of hill-of-vision models.

Methods

Microperimetry examinations from five independent study groups and one previously available dataset were included. Linear mixed models (LMMs) were fitted to the data to obtain interpretable hill-of-vision models. For predicting age-adjusted normative values, an array of regression models were compared using cross-validation with site-wise splits. The mean absolute error (MAE) and miscalibration area (area between the calibration curve and the ideal diagonal) were evaluated as the performance measures.

Results

1,052 tests from 531 eyes of 432 participants were included. Based on the parameters ‘participant age’, ‘eccentricity from the fovea’, ‘overlap with the central fixation target’ and ‘eccentricity along the four principal meridians’, a Bayesian mixed model had the lowest MAE (2.13 dB; 95% confidence interval [CI] = 1.86, 2.40 dB) and miscalibration area (0.14; 95% CI = 0.07, 0.20). However, a parsimonious linear model provided a comparable MAE (2.16 dB; 95% CI = 1.89, 2.43 dB) and a similar miscalibration area (0.14; 95% CI = 0.08, 0.20).

Conclusions

Normal variations in visual sensitivity on mesopic microperimetry can be effectively explained by a linear model that includes age and eccentricity. The dataset and a code vignette are provided for estimating normative values across a large range of retinal locations, applicable to customized testing patterns.
Public evidence on AI products for digital pathology
Authors: Matthews Gillian A. , McGenity Clare , Bansal Daljeet , Treanor Darren
Published: February 2024

Background

Novel products applying artificial intelligence (AI)-based approaches to digital pathology images have consistently emerged onto the commercial market, touting improvements in diagnostic accuracy, workflow efficiency, and treatment selection. However, publicly available information on these products can be variable, with few sources to obtain independent evidence.

Methods

Our objective was to identify and assess the public evidence on AI-based products for digital pathology. We compared key features of products on the European Economic Area/Great Britain (EEA/GB) markets, including their regulatory approval, intended use, and published validation studies. We included products that used haematoxylin and eosin (H&E)-stained tissue images as input, applied an AI-based method to support image interpretation, and received regulatory approval by September 2023.

Results

We identified 26 AI-based products that met our inclusion criteria. The majority (73%) were focused on breast pathology or uropathology, and their primary function was tumour or feature detection. Of the 26 products, 24 had received regulatory approval via the self-certification route as Generalin vitrodiagnostic (IVD) medical devices, which does not require independent review by a conformity assessment body. Furthermore, only 10 of the products (38%) were associated with peer-reviewed scientific publications describing their development and internal validation, while 11 products (42%) had peer-reviewed publications describing external validation (i.e., testing on data from a source distinct to that used in development).

Conclusions

The availability of public information on new products for digital pathology is struggling to keep up with the rapid pace of development. To support transparency, we gathered available public evidence on regulatory-approved AI products into an online register:https://resources.npic.uk/AI/ProductRegister. We anticipate this will provide an accessible resource on novel devices and support decisions on which products could bring benefit to patients.
Medical students in distress: a mixed methods approach to understanding the impact of debt on well-being
Authors: Yang Adrienne , Langness Simone , Chehab Lara , Rajapuram Nikhil , Zhang Li , Sammann Amanda
Published: February 2024

Background

Nearly three in four U.S. medical students graduate with debt in six-figure dollar amounts which impairs students emotionally and academically and impacts their career choices and lives long after graduation. Schools have yet to develop systems-level solutions to address the impact of debt on students’ well-being. The objectives of this study were to identify students at highest risk for debt-related stress, define the impact on medical students’ well-being, and to identify opportunities for intervention.

Methods

This was a mixed methods, cross-sectional study that used quantitative survey analysis and human-centered design (HCD). We performed a secondary analysis on a national multi-institutional survey on medical student wellbeing, including univariate and multivariate logistic regression, a comparison of logistic regression models with interaction terms, and analysis of free text responses. We also conducted semi-structured interviews with a sample of medical student respondents and non-student stakeholders to develop insights and design opportunities.

Results

Independent risk factors for high debt-related stress included pre-clinical year (OR 1.75), underrepresented minority (OR 1.40), debt $20-100K (OR 4.85), debt >$100K (OR 13.22), private school (OR 1.45), West Coast region (OR 1.57), and consideration of a leave of absence for wellbeing (OR 1.48). Mental health resource utilization (p= 0.968) and counselors (p= 0.640) were not protective factors against debt-related stress. HCD analysis produced 6 key insights providing additional context to the quantitative findings, and associated opportunities for intervention.

Conclusions

We used an innovative combination of quantitative survey analysis and in-depth HCD exploration to develop a multi-dimensional understanding of debt-related stress among medical students. This approach allowed us to identify significant risk factors impacting medical students experiencing debt-related stress, while providing context through stakeholder voices to identify opportunities for system-level solutions.
Effects of excess phosphate on a coastal plankton community: a mesocosm experiment in the Baltic Sea
Authors: Spilling Kristian , Vanharanta Mari , Santoro Mariano , Villena-Alemany Cristian , Labrenz Matthias , Grossart Hans-Peter , Piwosz Kasia
Published: February 2024

Eutrophication in the Baltic Sea has caused an imbalance in the inorganic nitrogen (N) to phosphorus (P) ratio, leaving excess phosphate (PO4) after the phytoplankton spring bloom that terminates after N-depletion. Using monitoring data, we demonstrated that the PO4concentration has continued to increase in the outermost Gulf of Finland during past decades. We further investigated the fate of such excess PO4in a two-week mesocosm (1.2 m3) experiment. The starting concentration of PO4was 0.66 µM, and treatments included a non-treated control (control), nitrate addition (N-add; 3.6 µM), glucose addition (C-add; 25 µM) and combined nitrate and glucose addition (N+C-add). The addition of N both in N-add and N+C-add treatments stimulated nano- and microphytoplankton, while the picophytoplankton abundance increased only after N-depletion. Also, the copepod biomass was positively affected by the N-addition. N2-fixing cyanobacteria were present but in low abundance. Carbon addition did not enhance heterotrophic bacterial uptake of PO4contrary to our expectations, nor did it affect the phyto- or zooplankton community composition. The PO4concentration was reduced to ∼0.4 µM in the control and C-add treatments and to 0.16 µM in the two N-amended treatments, with an inorganic N:P uptake ratio of 6.7. These results underscore the role of picophytoplankton in reducing the excess PO4pool after the spring bloom, a function traditionally ascribed to bloom-forming diazotrophic cyanobacteria in the Baltic Sea.
APOLR3B-variant reveals a Pol III transcriptome response dependent on La protein/SSB
Authors: Mattijssen Sandy , Kerkhofs Kyra , Stephen Joshi , Yang Acong , Han Chen G. , Tadafumi Yokoyama , Iben James R. , Mishra Saurabh , Sakhawala Rima M. , Ranjan Amitabh , Gowda Mamatha , Gahl William A. , Gu Shuo , Malicdan May C. , Maraia Richard J.
Published: February 2024

RNA polymerase III (Pol III, POLR3) synthesizes tRNAs and other small non-coding RNAs. HumanPOLR3pathogenic variants cause a range of developmental disorders, recapitulated in part by mouse models, yet some aspects of POLR3 deficiency have not been explored. We characterized a humanPOLR3B:c.1625A>G;p.(Asn542Ser) disease variant that was found to cause mis-splicing ofPOLR3B. Genome-editedPOLR3B1625A>GHEK293 cells acquired the mis-splicing with decreases in multiple POLR3 subunits and TFIIIB, although display auto-upregulation of the Pol III termination-reinitiation subunitPOLR3E. La protein was increased relative to its abundant pre-tRNA ligands which bind via their U(n)U-3’-termini. Assays for cellular transcription revealed greater deficiencies for tRNA genes bearing terminators comprised of 4Ts than of ≥5Ts. La-knockdown decreased Pol III ncRNA expression unlinked to RNA stability. Consistent with these effects, small-RNAseq showed thatPOLR3B1625A>Gand patient fibroblasts express more tRNA fragments (tRFs) derived from pre-tRNA 3’-trailers (tRF-1) than from mature-tRFs, and higher levels of multiple miRNAs, relative to control cells. The data indicate that decreased levels of Pol III transcripts can lead to functional excess of La protein which reshapes small ncRNA profiles revealing new depth in the Pol III system. Finally, patient cell RNA analysis uncovered a strategy for tRF-1/tRF-3 asPOLR3-deficiency biomarkers.
Identification of transcriptional regulators using a combined disease module identification and prize-collecting Steiner tree approach
Authors: Galindez Gihanna , Lopez Ben Anthony , Blumenthal David B. , Kacprowski Tim
Published: February 2024

Transcription factors play important roles in maintaining normal biological function, and their dys-regulation can lead to the development of diseases. Identifying candidate transcription factors involved in disease pathogenesis is thus an important task for deriving mechanistic insights from gene expression data. We developed Transcriptional Regulator Identification using Prize-collecting Steiner trees (TRIPS), a workflow for identifying candidate transcriptional regulators from case-control expression data. In the first step, TRIPS combines the results of differential expression analysis with a disease module identification step to retrieve perturbed subnetworks comprising an expanded gene list. TRIPS then solves a prize-collecting Steiner tree problem on a gene regulatory network, thereby identifying candidate transcriptional modules and transcription factors. We compare TRIPS to relevant methods using publicly available disease datasets and show that the proposed workflow can recover known disease-associated transcription factors with high precision. Network perturbation analyses demonstrate the reliability of TRIPS results. We further evaluate TRIPS on Alzheimer’s disease, diabetic kidney disease, and prostate cancer single-cell omics datasets. Overall, TRIPS is a useful approach for prioritizing transcriptional mechanisms for further downstream analyses.
Unprocessed Genomic Uracil as a Source of DNA Replication Stress in Cancer Cells
Authors: Saxena Sneha , Patel Parasvi S. , Nabel Christopher S. , Kawale Ajinkya S. , Crosby Caroline R. , Heiden Matthew G. Vander , Hata Aaron N. , Zou Lee
Published: February 2024

Alterations of bases in DNA constitute a major source of genomic instability. It is believed that base alterations trigger base excision repair (BER), generating DNA repair intermediates interfering with DNA replication. Here, we show that genomic uracil, a common base alteration, induces DNA replication stress (RS) without being processed by BER. In the absence of uracil DNA glycosylase (UNG), genomic uracil accumulates to high levels, DNA replication forks slow down, and PrimPol-mediated repriming is enhanced, generating single-stranded gaps in nascent DNA. ATR inhibition in UNG-deficient cells blocks repair of uracil-induced gaps, increasing replication fork collapse and cell death. Notably, a subset of cancer cells harboring high levels of genomic uracil upregulate UNG2 to limit RS, and these cancer cells are hypersensitive to co-treatment with ATR inhibitors and drugs increasing genomic uracil. These results reveal unprocessed genomic uracil as an unexpected source of RS and a targetable vulnerability of cancer cells.
Large-scale multi-omics analyses identified root-microbiome associations underlying plant nitrogen nutrition
Authors: Li Nannan , Li Guoliang , Wang Danning , Ma Lige , Huang Xiaofang , Bai Zhen , Wang Yongfeng , Luo Meng , Luo Yu , Zhu Yantao , Cao Xulv , Feng Qirui , Xu Ying , Mu Jianxin , An Ran , Yang Cuiling , Chen Hao , Li Xiaodan , Dong Yachen , Zhao Jianhua , Jiang Lixi , Jiang Yong , Reif Jochen C. , Hochholdinger Frank , Chen Xinping , Wang Daojie , Zhang Yanfeng , Bai Yang , Yu Peng
Published: February 2024

The microbiome determines the performance and fitness of the host plant. Nevertheless, the causal interaction between host genetic variation, gene regulation and the impact of the microbiome on the host phenotype remain unknown. Here we generated 1,341 paired root transcriptome, rhizosphere microbiome and root ionome samples and performed a multi-omics analyses of the host-microbe association at the root-soil interface using 175 rapeseeds (Brassica napusL.) resequenced ecotypes at two field environments. We observed the highest statistically explained variance for root nitrogen uptake among natural ionomic variation by overall transcriptome-wide gene expression and microbial abundance variation. Moreover, we identified significant genome-wide associations for 203 highly heritable amplicon sequence variants (ASVs) at multiple genetic loci regulated by eQTL hotspots associated with nitrogen metabolism components. These associations involved a central bacterial genus (Sphingopyxis), which plays a dominant role on gene regulatory effect on its variation regulated by eQTL hotspots. In addition, we performed high-throughput bacterial cultivation from rapeseed roots and subjectedSphingopyxisto whole genome sequencing. Finally, targeted metabolite profiling and confocal imaging assays demonstrated a host-microbiome regulatory effect onSphingopyxisestablished by lateral root development and plant nitrogen nutrition. In summary, our integrative approach reveals the genetic basis of host-microbiome trait associations in the transcriptional, nutritional and environmental domains and suggests that the microbiome might have causal effects on root development with implications towards the breeding of nutrient-efficient crops.
Autorepression of Yeast Hsp70 co-chaperones by intramolecular interactions involving their J-domains
Authors: Rebeaud Mathieu E. , Tiwari Satyam , Fauvet Bruno , Mohr Adelaïde , De Los Rios Paolo , Goloubinoff Pierre
Published: February 2024

The Hsp70 chaperones control protein homeostasis in all ATP-containing cellular compartments. J-domain proteins (JDPs) co-evolved with Hsp70s to trigger ATP-hydrolysis and catalytically upload various substrate polypeptides in need to be structurally modified by the chaperone. Here, we measured the protein disaggregation and refolding activities of the main yeast cytosolic Hsp70, Ssa1, in the presence of its most abundant JDPs, Sis1 and Ydj1, and two swap mutants, in which the J-domains have been interchanged. The observed differences by which the four constructs differently cooperate with Ssa1 and cooperate with each other, as well as their observed intrinsic ability to bind misfolded substrates and trigger Ssa1’s ATPase, indicates the presence of yet uncharacterized intra-molecular dynamic interactions between the J-domains and their remaining C-terminal domains. Taken together, the data suggest an auto-regulatory role to these intra-molecular interactions within both type A and B JDPs, which might have evolved to reduce energy-costly ATPase cycles by the Ssa1-4 chaperones that are the most abundant Hsp70s in the yeast cytosol.Graphical abstract:

Lower panel: autoinhibited DnaJA or DnaJB dimers, drawn here as Swiss army knives with sequestered J-domains as folded blades, can bind misfolded polypeptides (violet). Upper panel: DnaJA or DnaJB become active when their J-domains are exposed and can bind ATP-Hsp70s, and transfer the misfolded polypeptides, respectively, onto Hsp70’s nucleotide binding (Cyan) and protein binding domains (Orange and Green). Hsp70’s interdomain linker (DLLLLDV, Magenta).
Restraining Wnt activation and intestinal tumorigenesis by a Rab35 dependent GTPase relay
Authors: Redhai Siamak , Wang Tianyu , Boonekamp Kim. E , Reuter Saskia , Capraz Tümay , Leible Svenja , Bahaguna Shivohum , Port Fillip , Pavlović Bojana , Holzem Michaela , Doll Roman M. , Rindtorff Niklas , Valentini Erica , Schmitt Barbara , Richter Karsten , Engel Ulrike , Huber Wolfgang , Boutros Michael
Published: February 2024

Maintenance of homeostatic processes ensure curtailment of intestinal tumorigenesis. Inactivating mutations to Adenomatous Polyposis Coli (Apc) result in aberrantly activated Wnt signalling and initiates colorectal cancer (CRC) in approx. 80% of cases, yet our understanding of the subcellular mechanisms that modulate dysregulated pathway activity is limited. Here, using a conditionalin vivogenetic screen, we identify Rab35 GTPase as a novel tumour suppressor that modulates regional Wnt activity after loss ofApcin progenitor cells. Single cell analysis revealed that progenitor cells respond toApcdepletion by increasing the expression of a GTPase activating protein, which we namedblackbelt, and triggering Rab35 disassociation from the plasma membrane. Mechanistically, we demonstrate that Rab35 controls the localisation and activation of the Rho GTPase, Cdc42, which functions as a relay to regulate JNK signalling. This in turn tunes the Wnt pathway upstream of β-catenin to direct proliferation and differentiation of progenitor cells. Importantly, we show that maintaining active JNK signalling is important for the propagation ofApcmutant mouse colon organoids. Our findings highlight a novel GTPase cascade that sustains aberrant Wnt activity in specific segments of the intestine and provides impetus to therapeutically exploit this pathway to target CRC.
CD40 Expression by B cells is Required for Optimal Immunity to MurinePneumocystisInfection
Authors: Sassi Monica , Curran Shelly J. , Bishop Lisa R. , Liu Yueqin , Kovacs Joseph A.
Published: February 2024

CD40-CD40L interactions are critical for controllingPneumocystisinfection. However, which CD40-expressing cell populations are important for this interaction have not been well-defined. We used a cohousing mouse model ofPneumocystisinfection, combined with flow cytometry and qPCR, to examine the ability of different populations of cells from C57BL/6 mice to reconstitute immunity in CD40 knockout (KO) mice. Unfractionated splenocytes, as well as purified B cells, were able to controlPneumocystisinfection, while B cell depleted splenocytes and unstimulated bone-marrow derived dendritic cells (BMDCs) were unable to control infection in CD40 KO mice.Pneumocystisantigen-pulsed BMDCs showed early, but limited, control of infection. Consistent with recent studies that have suggested a role for antigen presentation by B cells, using cells from immunized animals, B cells were able to presentPneumocystisantigens to induce proliferation of T cells. Thus, CD40 expression by B cells appears necessary for robust immunity toPneumocystis.
Insights into ontogenetic scaling and morphological variation in sharks from near-term brown smooth-hound (Mustelus henlei) embryos
Authors: Gayford Joel H. , Sternes Phillip C. , Seamone Scott G. , Godfrey Hana , Whitehead Darren A.
Published: February 2024

Elasmobranchs (sharks and rays) exhibit a wide range of body forms adapted to various ecological niches. Body form differs not only between species, but between life stages of individual species as a result of ontogenetic allometry. In sharks, it has been proposed that these ontogenetic shifts in body form result from shifts in trophic and/or spatial ecology (the allometric niche shift hypothesis). Alternatively, it has been suggested that ontogenetic allometry may result from intrinsic morphological constraints associated with increasing body size – e.g. to counteract shifts in form-function relationships that occur as a function of size and could compromise locomotory performance. One major limitation affecting our understanding of ontogenetic scaling in sharks is that existing studies focus on postpartum ontogeny – ignoring the period of growth that occurs prior to birth/hatching. In this study, we report ontogenetic growth trajectories from 39 near-term brown smooth hound (Mustelus henlei) embryos taken from manually collected measurements. We found that unlike most other species and later ontogenetic stages ofM. henlei, these embryos predominantly grow isometrically, and appear to display relatively high levels of morphological disparity. These results provide rudimentary support for the allometric niche shift hypothesis (as in the absence of ontogenetic niche shifts isometry dominates body-form scaling) and provide important insight into early shark ontogeny and morphological/developmental evolution.
The dimensionality of neural coding for cognitive control is gradually transformed within the lateral prefrontal cortex
Authors: Chiou Rocco , Duncan John , Jefferies Elizabeth , Lambon Ralph Matthew A.
Published: February 2024

Implementing cognitive control relies on neural representations that are inherently high-dimensional and distribute across multiple subregions in the prefrontal cortex (PFC). Traditional approaches tackle prefrontal representations by reducing them into a unidimensional measure (univariate amplitude) or using them to distinguish a limited number of alternatives (pattern classification). By contrast, representational similarity analysis (RSA) enables flexibly formulating various hypotheses about informational contents underlying the neural codes, explicitly comparing hypotheses, and examining the representational alignment between brain regions. Here, we used a multifaceted paradigm wherein the difficulty of cognitive control was manipulated separately for five cognitive tasks. We used RSA to unveil representational contents, measure the representational alignment between regions, and quantify representational generalityvs.specificity. We found a graded transition in the lateral PFC: The dorsocaudal PFC was tuned to the information about behavioural effort, preferentially connected with the parietal cortex, and representationally generalisable across domains. The ventrorostral PFC was tuned to the abstract structure of tasks, preferentially connected with the temporal cortex, and representationally specific. The middle PFC (interposed between dorsocaudal and ventrorostral PFC) was tuned to individual task-sets, ranked in the middle in terms of connectivity and generalisability. Furthermore, whether a region was dimensionally rich or thin co-varied with its functional profile: Low dimensionality (only gist) in the dorsocaudal PFC dovetailed with better generality, whereas high dimensionality (gist plus details) in the ventrorostral PFC corresponded with better ability to encode subtleties. Our findings, collectively, demonstrate how cognitive control is decomposed into distinct facets that transition steadily along prefrontal subregions.

Significance

Cognitive control is known to be a high-dimensional construct, implemented along the dorsocaudal-ventrorostral subregions of PFC. However, it remains unclear how prefrontal representations could be dissected in a multivariate fashion to reveal (1) what information is encoded in each subregion, (2) whether information systematically transforms across contiguous PFC subregions as a gradient, (3) how this transformation is affected by functional connectivity. Here we shed light on these issues by using RSA to decode informational composition in the PFC while using participant-specific localisers to facilitate individually-tailored precision. Our findings elucidate the functional organisation of PFC by revealing how a trade-off between dimensionality and generalisability unfolds in the PFC and highlight the strength of RSA in deciphering the coding of cognitive control.
A Functional and Non-Homuncular Representation of the Larynx in the Primary Motor Cortex of Mice, a Vocal Non-Learner
Authors: Vargas César D. M. , Agravat Rajvi K. , Waidmann Elena N. , Bochalis Christodoulos , Bermudez Hector , Giannakopoulos Theodoros , Jarvis Erich D.
Published: February 2024

Vocalization is a complex behavior ranging from fully innate to advanced vocal learning. Vocal learning species possess a vocal primary motor cortex (M1) region that makes direct projections to brainstem vocal motor neurons, which are thought to facilitate learning and fine modulation of vocalizations. Surprisingly, a similar, albeit sparse, direct projection from M1 was found in mice. Mice produce ultrasonic vocalizations (USV) which appear to be mostly innate. Modulation of these USVs is impacted by lesions to this M1 region, but genetic ablation of the cortex leads to few, if any, changes to USVs. It remained unclear whether M1 has any control over the vocal organ in a vocal non-learning species. In the current study, we found that stimulation in different parts of M1 in mice can generate contractions in laryngeal and jaw muscles, with different latencies suggestive of both direct and indirect projections to brainstem vocal motor neurons. Viral tracing reveals both single- and double-labeled populations of cortical neurons that simultaneously innervate laryngeal, jaw, and forelimb motor circuits. Chemical lesions reveal that an anterolateral orofacial region of M1 regulates the number of syllables in vocal sequences. Our results provide evidence that M1 in a vocal non-learner has some influence on vocal musculature, consistent with the continuum hypothesis of vocal learning. They also reveal that the representations of muscles for different behaviors across mouse M1 are more intermixed than previously considered. We discuss how these results impact hypotheses on the evolution of cortical vocal control and motor cortex organization.
Electric field characteristics of rotating permanent magnet stimulation
Authors: Robins Pei L. , Makaroff Sergey N. , Dib Michael , Lisanby Sarah H. , Deng Zhi-De
Published: February 2024

Neurostimulation devices that use rotating permanent magnets are being explored for their potential therapeutic benefits in patients with psychiatric and neurological disorders. This study aims to characterize the electric field (E-field) for ten configurations of rotating magnets using finite element analysis and phantom measurements. Various configurations were modeled, including single or multiple magnets, bipolar or multipolar magnets, rotated at 10, 13.3, and 400 Hz. E-field strengths were also measured using a hollow sphere (r= 9.2 cm) filled with a 0.9% sodium chloride solution and with a dipole probe. The E-field spatial distribution is determined by the magnets’ dimensions, number of poles, direction of the magnetization, and axis of rotation, while the E-field strength is determined by the magnets’ rotational frequency and magnetic field strength. The induced E-field strength on the surface of the head ranged between 0.0092 and 0.59 V/m. At the range of rotational frequencies applied, the induced E-field strengths were approximately an order or two of magnitude lower than those delivered by conventional transcranial magnetic stimulation. The impact of rotational frequency on E-field strength represents a previously unrecognized confound in clinical trials that seek to personalize stimulation frequency to individual neural oscillations and may represent a mechanism to explain some clinical trial results.