bluuebunny/crossref_metadata_2025 huggingface dataset:
Clinical trial emulation can identify new opportunities to enhance the regulation of drug safety in pregnancy
Authors: Challa Anup P. , Niu Xinnan , Garrison Etoi A. , Van Driest Sara L. , Bastarache Lisa M. , Lippmann Ethan S. , Lavieri Robert R. , Goldstein Jeffery A. , Aronoff David M.
Published: November 2021

From the perspective of most regulatory agencies, it is usually unethical to perform interventional clinical trials on pregnant people. While this policy recognizes the vulnerability of an expectant mother and unborn child, it has created a public health emergency for millions of pregnant patients through a dearth of robust safety data for many common drugs. To address this problem, we harnessed an enterprise collection of 2.8M electronic health records (EHRs) originally collected from routine primary care, leveraging the data linkage between mothers and their babies to create a surrogate for randomized, controlled drug trials in this population. To demonstrate the feasibility of our clinical trial emulation platform to stimulate new hypotheses for post-market drug surveillance, we identified 1,054 drugs historically prescribed to pregnant patients and developed a medication history-wide association study and follow-up evidence synthesis platform—leveraging expert clinician review and real-world data analysis—to test the effects of maternal exposure to these drugs on the incidence of neurodevelopmental defects in their children. Our results replicate known teratogenic risks and existing knowledge on drug structure-related teratogenic risks. Herein, we highlight 5 common drug classes that we believe warrant further assessment of their safety in pregnancy. We also discuss our efforts to develop a discovery-to-regulatory framework that could allow for pragmatic translation of our results to enhanced regulatory policy. Collectively, our work presents a simple approach to evaluating the utility of EHRs in guiding new regulatory review programs focused on improving the delicate equipoise of accuracy and ethics inherent to assessing drug safety in an extremely vulnerable patient population.
Rationale and design of the Health Professional Students at the University of Illinois Chicago (HOLISTIC) Cohort Study
Authors: Dommaraju Sunil R. , Rivera Stephanie Gordon , Rocha Ethan G. , Bicknell Scott , Loizzo Daniel , Mohammad Ayesha , Rajan Priya , Seballos Alexandria , Datta Avisek , Ahmed Rashid , Krishnan Jerry A. , Keehn Mary
Published: November 2021

Objectives

The objectives of the HOLISTIC Cohort Study are to establish a 3-year prospective cohort study that characterizes the health of students within and across health professionals’ education programs during the coronavirus disease 2019 (COVID-19) pandemic, implement an interprofessional student research team, and inform initiatives to improve student health. This report describes the rationale and design of the HOLISTIC Cohort Study, including recruitment strategy, survey development, data management, and descriptive statistics of the first wave of study participants.

Methods

An interprofessional student research team was formed to continuously inform study design. The first wave of recruitment was conducted from April 14, 2021 to May 5, 2021 across seven health science colleges (applied health, dentistry, medicine, nursing, pharmacy, public health, social work) at the University of Illinois Chicago in Chicago, IL. Eligible students were sent an invitation via email to complete an online survey after providing electronic informed consent. The online survey was based on the U.S. Centers for Disease Control and Prevention’s Behavioral Risk Factor Surveillance System 2019 survey and the 2014 World Health Organization Report of the Strategic Advisory Group of Experts Working Group Questionnaire. Two additional recruitment waves are planned in the Spring 2022 and Spring 2023; follow-up of participants previously enrolled will occur during these second and third recruitment waves.

Results

Of 5,118 students invited to participate in the first wave, 553 (10.8%) completed the survey and includes participants from all seven health science colleges. The average age of participants is 27.3 years, 435 (78.8%) identify as female, and 137 (24.8%) identify as an underrepresented minority. Overall, 465 (84.6%) participants reported being currently employed for wages. Just over half (51%) reported no days with poor physical health within a month but only 11.2% reported no days with poor mental health within a month. Nearly one in ten (9.4%) reported having ever had a positive test for COVID-19.

Conclusion

The HOLISTIC Cohort Study of health professional students across seven health science colleges has completed the first of three waves of enrollment during the COVID-19 pandemic. Based on the first wave of study participants, increased attention to supporting the mental and physical health of health professional students is needed.
Movement ecology of vulnerable lowland tapirs across a gradient of human disturbance
Authors: Medici EP , Mezzini S , Fleming CH , Calabrese JM , Noonan MJ
Published: November 2021

Animal movement is a key ecological process that is tightly coupled to local environmental conditions. While agriculture, urbanisation, and transportation infrastructure are critical to human socio-economic improvement, these have spurred substantial changes in animal movement across the globe with potential impacts on fitness and survival. Notably, however, human disturbance can have differential effects across species, and responses to human activities are thus largely taxa and context specific. As human disturbance is only expected to worsen over the next decade it is critical to better understand how species respond to human disturbance in order to develop effective, case-specific conservation strategies. Here, we use an extensive telemetry dataset collected over 22 years to fill a critical knowledge gap in the movement ecology of lowland tapirs (Tapirus terrestris) across a gradient of human disturbance within three biomes in southern Brazil: the Pantanal, Cerrado, and Atlantic Forest.

From these data we found that the mean home range size across all monitored tapirs was 8.31 km2 (95% CI: 6.53 - 10.42), with no evidence that home range sizes differed between sexes nor age groups. Interestingly, although the Atlantic Forest, Cerrado, and Pantanal vary substantially in habitat composition, levels of human disturbance, and tapir population densities, we found that lowland tapir movement behaviour and space use were consistent across all three biomes. Human disturbance also had no detectable effect on lowland tapir movement. Lowland tapirs living in the most altered habitats we monitored exhibited movement behaviour that was comparable to that of tapirs living in a near pristine environment.

Contrary to our expectations, we observed very little individual variability in lowland tapir space use and movement, and human impacts on the landscape also had no measurable effect on their movement. Lowland tapir movement behaviour thus appears to exhibit very little phenotypic plasticity. Crucially, the lack of any detectable response to anthropogenic disturbance suggests that human modified habitats risk being ecological traps for tapirs and this information should be factored into conservation actions and species management aimed towards protecting lowland tapir populations.
ORYX-MRSI: A Fully-Automated Open-Source Software for Three-Dimensional Proton Magnetic Resonance Spectroscopic Imaging Data Analysis
Authors: Cengiz Sevim , Yildirim Muhammed , Bas Abdullah , Ozturk-Isik Esin
Published: November 2021

Proton magnetic resonance spectroscopic imaging (1H-MRSI) provides noninvasive evaluation of brain metabolism. However, there are some limitations of 1H-MRSI preventing its wider use in the clinics, including the spectral quality issues, partial volume effect and chemical shift artifact. Additionally, it is necessary to create metabolite maps for analyzing spectral data along with other MRI modalities. In this study, a MATLAB-based open-source data analysis software for 3D1H-MRSI, called Oryx-MRSI, which includes modules for visualization of raw1H-MRSI data and LCModel outputs, chemical shift correction, tissue fraction calculation, metabolite map production, and registration onto standard MNI152 brain atlas while providing automatic spectral quality control, is presented. Oryx-MRSI implements region of interest analysis at brain parcellations defined on MNI152 brain atlas. All generated metabolite maps are stored in NIfTI format. Oryx-MRSI is publicly available athttps://github.com/sevimcengiz/Oryx-MRSIalong with six example datasets.
Cortical-subcortical structural connections support transcranial magnetic stimulation engagement of the amygdala
Authors: Sydnor Valerie J. , Cieslak Matthew , Duprat Romain , Deluisi Joseph , Flounders Matthew W. , Long Hannah , Scully Morgan , Balderston Nicholas L. , Sheline Yvette I. , Bassett Dani S. , Satterthwaite Theodore D. , Oathes Desmond J.
Published: November 2021

The amygdala processes valenced stimuli, influences affective states, and exhibits aberrant activity across anxiety disorders, depression, and PTSD. Interventions that modulate amygdala activity hold promise for treating transdiagnostic affective symptoms. We investigated (N=45) whether transcranial magnetic stimulation (TMS) elicits indirect changes in amygdala activity when applied to ventrolateral prefrontal cortex (vlPFC), a region important for affect regulation. Harnessing in-scanner interleaved TMS/functional MRI (fMRI), we reveal that vlPFC neurostimulation evoked acute, dose-dependent modulations of amygdala fMRI BOLD signal. Larger TMS-evoked changes in amygdala fMRI signal were associated with higher fiber density in a vlPFC-amygdala white matter pathway, suggesting this pathway facilitated stimulation-induced communication between cortex and subcortex. This work provides evidence of amygdala engagement by TMS, highlighting stimulation of vlPFC-amygdala circuits as a candidate treatment for affective psychopathology. More broadly, it indicates that targeting cortical-subcortical connections may enhance the impact of TMS on subcortical neural activity and, by extension, subcortex-subserved behaviors.

Teaser

Individualized, connectivity-guided transcranial magnetic stimulation modulates the amygdala, demonstrating therapeutic potential.
Optimization algorithm for omic data subspace clustering
Authors: Ciortan Madalina , Defrance Matthieu
Published: November 2021

Subspace clustering identifies multiple feature subspaces embedded in a dataset together with the underlying sample clusters. When applied to omic data, subspace clustering is a challenging task, as additional problems have to be addressed: the curse of dimensionality, the imperfect data quality and cluster separation, the presence of multiple subspaces representative of divergent views of the dataset, and the lack of consensus on the best clustering method.

First, we propose a computational method (discover) to perform subspace clustering on tabular high dimensional data by maximizing the internal clustering score (i.e. cluster compactness) of feature subspaces. Our algorithm can be used in both unsupervised and semi-supervised settings. Secondly, by applying our method to a large set of omic datasets (i.e. microarray, bulk RNA-seq, scRNA-seq), we show that the subspace corresponding to the provided ground truth annotations is rarely the most compact one, as assumed by the methods maximizing the internal quality of clusters. Our results highlight the difficulty of fully validating subspace clusters (justified by the lack of feature annotations). Tested on identifying the ground-truth subspace, our method compared favorably with competing techniques on all datasets. Finally, we propose a suite of techniques to interpret the clustering results biologically in the absence of annotations. We demonstrate that subspace clustering can provide biologically meaningful sample-wise and feature-wise information, typically missed by traditional methods.

CCS Concepts: • Computing methodologies → Genetic algorithms; Mixture models; Cluster analysis.

ACM Reference Format

Madalina Ciortan and Matthieu Defrance. 2021. Optimization algorithm for omic data subspace clustering. 1, 1 (September 2021), 40 pages. https://doi.org/10.1145/nnnnnnn.nnnnnnn
Formal meta-analysis of hypoxic gene expression profiles reveals a universal gene signature and cell type-specific effects
Authors: Puente-Santamaria Laura , Sanchez-Gonzalez Lucia , Gonzalez-Serrano Barbara P. , Pescador Nuria , Martinez-Costa Oscar H. , Ramos-Ruiz Ricardo , del Peso Luis
Published: November 2021

Background

Integrating transcriptional profiles results in the identification of gene expression signatures that are more robust than those obtained for individual datasets. However, direct comparison of datasets derived from heterogeneous experimental conditions is not possible and their integration requires the application of specific meta-analysis techniques. The transcriptional response to hypoxia has been the focus of intense research due to its central role in tissue homeostasis and in prevalent diseases. Accordingly, a large number of studies have determined the gene expression profile of hypoxic cells. Yet, in spite of this wealth of information, little effort have been done to integrate these dataset to produce a robust hypoxic signature.

Results

We applied a formal meta-analysis procedure to a dataset comprising 425 RNAseq samples derived from 42 individual studies including 33 different cell types, to derive a pooled estimate of the effect of hypoxia on gene expression. This approach revealed that a large proportion of the transcriptome (8556 genes out of 20888) is significantly regulated by hypoxia. However, only a small fraction of the differentially expressed genes (1265 genes, 15%) show an effect size that, according to comparisons to gene pathways known to be regulated by hypoxia, is likely to be biologically relevant. By focusing on genes ubiquitously expressed we identified a signature of 291 genes robustly and consistently regulated by hypoxia. Finally, by a applying a moderator analysis we found that endothelial cells show a characteristic gene expression pattern that is significantly different from other cell types.

Conclusion

By the application of a formal meta-analysis to hypoxic gene profiles, we have developed a robust gene signature that characterizes the transcriptomic response to low oxygen. In addition to identifying a universal set of hypoxia-responsive genes, we found a set of genes whose regulation is cell-type specific and suggest a unique metabolic response of endothelial cells to reduced oxygen tension.
Teaching a computer to assess hypnotic depth: A pilot study
Authors: Obukhov Nikita V. , L.N.Naish Peter , Solnyshkina Irina E. , Siourdaki Tatiana G. , Martynov Ilya A.
Published: November 2021

The therapeutic effects of hypnosis in some cases seem to be most marked when the patient has achieved sufficient hypnotic depth. It could be possible to monitor the deepening process using electrophysiological data to obtain information on depth changes throughout the session. However, although hypnosis is characterized by some common EEG patterns, significant differences between subjects are also observed. Therefore, an individualized approach is required to quantify the depth continuously during a session. To achieve this, we proposed the machine learning approach, using an EEG-based Brain-Computer interface, and tested it on video-EEG recordings of 8 outpatients. Based on the data from the first sessions, we trained the classification models to discriminate between conditions of wakefulness and deep hypnosis. Then, we applied them to subsequent sessions to predict the probability of deep hypnosis, i.e., to continuously measure depth level in real time. The models trained using frequency ranges of 1.5-14 and 4-15 Hz provided high accuracy. The applications and perspectives are discussed.
Transmembrane helices mediate the formation of a stable ternary complex of cyt b5 reductase, cyt b5, and SCD1
Authors: Shen Jiemin , Wu Gang , Tsai Ah-Lim , Zhou Ming
Published: November 2021

Mammalian cytochrome b5 (cyt b5) and cytochrome b5 reductase (b5R) are electron carrier proteins required for many membrane-embedded oxidoreductases. Both cyt b5 and b5R have a cytosolic domain anchored to the membrane by a single transmembrane helix (TM). It is not clear if b5R, cyt b5 and their partner oxidoreductases assemble as binary or ternary complexes. Here we show that b5R and cyt b5 form a stable binary complex, and that b5R, cyt b5 and a membrane-embedded oxidoreductase, stearoyl-CoA desaturase 1 (SCD1) form a stable ternary complex. The formation of the complexes significantly enhances electron transfer rates, and that the single TM of cyt b5 and b5R mediated assembly of the complexes. These results reveal a novel functional role of TMs in cyt b5 and b5R and suggest that an electron transport chain composed of a stable ternary complex may be a general feature in oxidoreductases that require the participation of cyt b5 and b5R.
Causation without correlation: parasite-mediated frequency-dependent selection and infection prevalence
Authors: Lively Curtis M. , Xu Julie , Ben-Ami Frida
Published: November 2021

Parasite-mediated selection is thought to maintain host genetic diversity for resistance. We might thus expect to find a strong positive correlation between host genetic diversity and infection prevalence across natural populations. Here we used computer simulations to examine host-parasite coevolution in 20 simi-isolated clonal populations across a broad range of values for both parasite virulence and parasite fecundity. We found that the correlation between host genetic diversity and infection prevalence can be significantly positive for intermediate values of parasite virulence and fecundity. But the correlation can also be weak and statistically non-significant, even when parasite-mediated frequency-dependent selection is the sole force maintaining host diversity. Hence correlational analyses of field populations, while useful, might underestimate the role of parasites in maintaining host diversity.

Subject Area. Evolution
Microfluidic system-based time-course tracking of physical proximity between cells and its effect on gene expression for elucidating live single cancer-immune cell interactions
Authors: Flores Bianca C. T. , Chawla Smriti , Ma Ning , Sanada Chad , Kujur Praveen Kumar , Chinen Ludmilla T. D. , Hukari Kyle , Lynch Mark , Ramalingam Naveen , Sengupta Debarka , Jeffrey Stefanie S.
Published: November 2021

Cell-cell communication and physical interactions play a vital role in cancer initiation, homeostasis, progression, and immune response. Here, we report a system that combines live capture of different cell types, co-incubation, time-lapse imaging, and gene expression profiling of doublets using a microfluidic integrated fluidic circuit (IFC) that enables measurement of physical distances between cells and the associated transcriptional profiles due to cell-cell interactions. The temporal variations in natural killer (NK) - triple-negative breast cancer (TNBC) cell distances were tracked and compared with terminally profiled cellular transcriptomes. The results showed the time-bound activities of regulatory modules and alluded to the existence of transcriptional memory. Our experimental and bioinformatic approaches serve as a proof of concept for interrogating live cell interactions at doublet resolution, which can be applied across different cancers and cell types.
Investigating Increased CO2 concentration on the pH of various plant species
Authors: Schafer Joshua , Puga Troy , Harris Pearce , Strasser Nora , Branum Gary , Agbedanu Prince N
Published: November 2021

The concept of bioremediation is quickly becoming the norm in the resolution of environmental issues. The steady increase in carbon dioxide (CO2) levels, as documented by NASA, inspired scientists to engineer plants to absorb excess CO2 from the atmosphere. Here, we have explored the consequences of the uptake of excess CO2 by select plants. Carbon dioxide dissolves in H2O to produce H2CO3, which dissociates to yield H+ ions. We hypothesized that increased CO2 absorption results in decrease in pH of plant sap. Three plants (Byophyllum pinnatum, Romaine Lettuce and Nevada Lettuce), exposed to increased CO2 concentrations (15%), demonstrated a consistent increase in pH towards alkalinity compared to control plants. Based on the outcome being opposite of what we have hypothesized, our results suggest Byophyllum pinnatum, Romaine lettuce and Nevada lettuce, all have a unique homeostatic system to prevent over-absorption of CO2 in a CO2-rich environment.
Single-sample proteome enrichment enables missing protein recovery and phenotype association
Authors: Wong Bertrand Jern Han , Kong Weijia , Goh Wilson Wen Bin
Published: November 2021

Proteomic studies characterize the protein composition of complex biological samples. Despite recent developments in mass spectrometry instrumentation and computational tools, low proteome coverage remains a challenge. To address this, we present Proteome Support Vector Enrichment (PROSE), a fast, scalable, and effective pipeline for scoring protein identifications based on gene co-expression matrices. Using a simple set of observed proteins as input, PROSE gauges the relative importance of proteins in the phenotype. The resultant enrichment scores are interpretable and stable, corresponding well to the source phenotype, thus enabling reproducible recovery of missing proteins. We further demonstrate its utility via reanalysis of the Cancer Cell Line Encyclopedia (CCLE) proteomic data, with prediction of oncogenic dependencies and identification of well-defined regulatory modules. PROSE is available as a user-friendly Python module from https://github.com/bwbio/PROSE.
Defining Innate Immune Responses to the Human Gut Microbiota from Phylum to Strain
Authors: Spindler Matthew P. , Siu Sophia S. , Mogno Ilaria , Li Zhihua , Yang Chao , Mehandru Saurabh , Britton Graham J. , Faith Jeremiah J.
Published: November 2021

The functional potential of the gut microbiota remains largely uncharacterized. Efforts to understand how the immune system responds to commensal organisms have been hindered by the large number of strains that comprise the human gut microbiota. We develop a screening platform to measure innate immune responses towards 277 bacterial strains isolated from the human gut microbiota. We find that innate immune responses to gut derived bacteria are as strong as responses towards pathogenic bacteria, and vary from phylum to strain. Myeloid cells differentially rely upon TLR2 or TLR4 to sense particular taxa, an observation that predicts in vivo function. These innate immune responses can be modeled using combinations of up to 8 TLR agonists. Furthermore, the immunogenicity of strains is stable over time and following transplantation into new humans. Collectively, we demonstrate a powerful high-throughput approach to determine how commensal microorganisms shape innate immune phenotypes.
Contribution of infection and vaccination to seroprevalence through two COVID waves in Tamil Nadu, India
Authors: Selvavinayagam T.S. , Somasundaram A. , Selvam Jerard Maria , Ramachandran Sabareesh , Sampath P. , Vijayalakshmi V. , Ajith Brabhu Kumar C. , Subramaniam Sudharshini , Parthipan K. , Raju S. , Avudaiselvi R. , Prakash V. , Yogananth N. , Subramanian Gurunathan , Roshini A. , Dhiliban D.N. , Imad Sofia , Tandel Vaidehi , Parasa Rajeswari , Sachdeva Stuti , Malani Anup
Published: November 2021

Four rounds of serological surveys were conducted, spanning two COVID waves (October 2020 and April-May 2021), in Tamil Nadu (population 72 million) state in India. Each round included representative populations in each district of the state, totaling ≥20,000 persons per round. State-level seroprevalence was 31.5% in round 1 (October-November 2020), after India’s first COVID wave. Seroprevalence fell to 22.9% in 2 (April 2021), consistent with waning of antibodies from natural infection. Seroprevalence rose to 67.1% by round 3 (June-July 2021), reflecting infections from the Delta-variant induced second COVID wave. Seroprevalence rose to 93.1% by round 4 (December 2021-January 2022), reflecting higher vaccination rates. Antibodies also appear to wane after vaccination. Seroprevalence in urban areas was higher than in rural areas, but the gap shrunk over time (35.7 v. 25.7% in round 1, 89.8% v. 91.4% in round 4) as the epidemic spread even in low-density rural areas.

Article Summary Line

Antibodies waned after India’s first COVID wave and both vaccination and infection contributed its roughly 90% seroprevalence after its second wave.
Determination of nuclear position by the arrangement of actin filaments using deep generative networks
Authors: Vasudevan Jyothsna , Zheng Chuanxia , Wan James G. , Cham Tat-Jen , Teck Lim Chwee , Fernandez Javier G.
Published: November 2021

The cell nucleus is a dynamic structure that changes locales during cellular processes such as proliferation, differentiation, or migration1, and its mispositioning is a hallmark of several disorders2,3. As with most mechanobiological activities of adherent cells, the repositioning and anchoring of the nucleus are presumed to be associated with the organization of the cytoskeleton, the network of protein filaments providing structural integrity to the cells4. However, this correlation between cytoskeleton organization and nuclear position has not, to date, been demonstrated, as it would require the parameterization of the extraordinarily intricate cytoskeletal fiber arrangements. Here, we show that this parameterization and demonstration can be achieved outside the limits of human conceptualization, using generative network and raw microscope images, relying on machine-driven interpretation and selection of parameterizable features. The developed transformer-based architecture was able to generate high-quality, completed images of more than 8,000 cells, using only information on actin filaments, predicting the presence of a nucleus and its exact localization in more than 70 per cent of instances. Our results demonstrate one of the most basic principles of mechanobiology with a remarkable level of significance. They also highlight the role of deep learning as a powerful tool in biology beyond data augmentation and analysis, capable of interpreting—unconstrained by the principles of human reasoning—complex biological systems from qualitative data.
Liver ductal organoids reconstruct intrahepatic biliary trees in decellularized liver grafts
Authors: Tomofuji Katsuhiro , Fukumitsu Ken , Kondo Jumpei , Horie Hiroshi , Makino Kenta , Wakama Satoshi , Ito Takashi , Oshima Yu , Ogiso Satoshi , Ishii Takamichi , Inoue Masahiro , Hatano Etsuro
Published: November 2021

Three-dimensional scaffolds decellularized from native organs are a promising technique to establish engineered liver grafts and overcome the current shortage of donor organs. However, limited sources of bile duct cells and inappropriate cell distribution in bioengineered liver grafts have hindered their practical application. Organoid technology is anticipated to be an excellent tool for the advancement of regenerative medicine. In the present study, we reconstructed intrahepatic bile ducts in a rat decellularized liver graft by recellularization with liver ductal organoids. Using an ex vivo perfusion culture system, we demonstrated the biliary characteristics of repopulated mouse liver organoids, which maintained bile duct markers and reconstructed biliary tree-like networks with luminal structures. We also established a method for the co-recellularization with engineered bile ducts and primary hepatocytes, revealing the appropriate cell distribution to mimic the native liver. We then utilized this model in human organoids to demonstrate the reconstructed bile ducts. Our results show that liver ductal organoids are a potential cell source for bile ducts from bioengineered liver grafts using three-dimensional scaffolds.
Global landscape of replicative DNA polymerase usage in the human genome
Authors: Koyanagi Eri , Kakimoto Yoko , Yoshifuji Fumiya , Natsume Toyoaki , Higashitani Atsushi , Ogi Tomoo , Carr Antony M. , Kanemaki Masato T. , Daigaku Yasukazu
Published: November 2021

The division of labour among DNA polymerase underlies the accuracy and efficiency of replication. However, the roles of replicative polymerases have not been directly established in human cells. We developed polymerase usage sequence (Pu-seq) in HCT116 cells and mapped Polε and Polα usage genome wide. The polymerase usage profiles show Polε synthesises the leading strand and Polα contributes mainly to lagging strand synthesis. Combining the Polε and Polα profiles, we accurately predict the genome-wide pattern of fork directionality plus zones of replication initiation and termination. We confirm that transcriptional activity contributes to the pattern of initiation and termination and, by separately analysing the effect of transcription on both co-directional and converging forks, demonstrate that coupled DNA synthesis of leading and lagging strands in both co- directional and convergent forks is compromised by transcription. Polymerase uncoupling is particularly evident in the vicinity of large genes, including the two most unstable common fragile sites, FRA3B and FRA3D, thus linking transcription-induced polymerase uncoupling to chromosomal instability.
Tomographic Volumetric Bioprinting of Heterocellular Bone-like Tissues in Seconds
Authors: Gehlen Jenny , Qiu Wanwan , Schädli Gian Nutal , Müller Ralph , Qin Xiao-Hua
Published: November 2021

Tomographic volumetric bioprinting (VBP) has recently emerged as a powerful tool for rapid solidification of cell-laden hydrogel constructs within seconds. However, its practical applications in tissue engineering requires a detailed understanding of how different printing parameters (concentration of resins, laser dose) affect cell activity and tissue formation. Herein, we explore a new application of VBP in bone tissue engineering by merging a soft gelatin methacryloyl (GelMA) bioresin (<5 kPa) with 3D endothelial co-culture to generate heterocellular bone-like constructs with enhanced functionality. To this, a series of bioresins with varying concentrations of GelMA and lithium Phenyl(2,4,6-trimethylbenzoyl)phosphinate (LAP) photoinitiator were formulated and characterized in terms of photo-reactivity, printability and cell-compatibility. A bioresin with 5% GelMA and 0.05% LAP was identified as the optimal formulation for VBP of complex perfusable constructs within 30 s at high cell viability (>90%). The fidelity was validated by micro-computed tomography and confocal microscopy. Compared to 10% GelMA, this bioresin provided a softer and more permissive environment for osteogenic differentiation of human mesenchymal stem cells (hMSCs). The expression of osteoblastic markers (collagen-I, ALP, osteocalcin) and osteocytic markers (podoplanin, Dmp1) was monitored for 42 days. After 21 days, early osteocytic markers were significantly increased in 3D co-cultures with human umbilical vein endothelial cells (HUVECs). Additionally, we demonstrate VBP of a perfusable, pre-vascularized model where HUVECs self-organized into an endothelium-lined channel. Altogether, this work leverages the benefits of VBP and 3D co-culture, offering a promising platform for fast scaled biofabrication of 3D bone-like tissues with unprecedented functionality.

Graphical abstract

Statement of significance

This study explores new strategies for ultrafast bio-manufacturing of bone tissue models by leveraging the advantages of tomographic volumetric bioprinting (VBP) and endothelial co-culture. After screening the properties of a series of photocurable gelatin methacryloyl (GelMA) bioresins, a formulation with 5% GelMA was identified with optimal printability and permissiveness for osteogenic differentiation of human mesenchymal stem cells (hMSC). We then established 3D endothelial co-cultures to test if the heterocellular interactions may enhance the osteogenic differentiation in the printed environments. This hypothesis was evidenced by increased gene expression of early osteocytic markers in 3D co-cultures after 21 days. Finally, VBP of a perfusable cell-laden tissue construct is demonstrated for future applications in vascularized tissue engineering.
Detection, not mortality, constrains the evolution of virulence
Authors: Kennedy David A.
Published: November 2021

Why would a pathogen evolve to kill its hosts when killing a host ends a pathogen’s own opportunity for transmission? A vast body of scientific literature has attempted to answer this question using “trade-off theory,” which posits that host mortality persists due to its cost being balanced by benefits of other traits that correlate with host mortality. The most commonly invoked trade-off is the mortality-transmission trade-off, where increasingly harmful pathogens are assumed to transmit at higher rates from hosts while the hosts are alive, but the pathogens truncate their infectious period by killing their hosts. Here I show that costs of mortality are too small to plausibly constrain the evolution of disease severity except in systems where survival is rare. I alternatively propose that disease severity can be much more readily constrained by a cost of behavioral change due to the detection of infection, whereby increasingly harmful pathogens have increasing likelihood of detection and behavioral change following detection, thereby limiting opportunities for transmission. Using a mathematical model, I show the conditions under which detection can limit disease severity. Ultimately, this argument may explain why empirical support for trade-off theory has been limited and mixed.
Mechanism of glycogen synthase inactivation and interaction with glycogenin
Authors: Marr Laura , Biswas Dipsikha , Daly Leonard A. , Browning Christopher , Vial Sarah , Maskell Daniel P. , Hudson Catherine , Pollard John , Bertrand Jay , Ranson Neil A. , Khatter Heena , Eyers Claire E. , Sakamoto Kei , Zeqiraj Elton
Published: November 2021

Glycogen is the major glucose reserve in eukaryotes, and defects in glycogen metabolism and structure lead to disease. Glycogenesis involves interaction of glycogenin (GN) with glycogen synthase (GS), where GS is activated by glucose-6-phosphate (G6P) and inactivated by phosphorylation. We describe the 2.6 Å resolution cryo-EM structure of phosphorylated human GS revealing an autoinhibited GS tetramer flanked by two GN dimers. Phosphorylated N- and C-termini from two GS protomers converge near the G6P-binding pocket and buttress against GS regulatory helices. This keeps GS in an inactive conformation mediated by phospho-Ser641 interactions with a composite “arginine cradle”. Structure-guided mutagenesis perturbing interactions with phosphorylated tails led to increased basal/unstimulated GS activity. We propose that multivalent phosphorylation supports GS autoinhibition through interactions from a dynamic “spike” region, allowing a tuneable rheostat for regulating GS activity. This work therefore provides new insights into glycogen synthesis regulation and facilitates studies of glycogen-related diseases.
Correlational selection and genetic architecture promote the leaf economics spectrum in a perennial grass
Authors: Heckman Robert W. , Bonnette Jason E. , Campitelli Brandon E. , Fay Philip A. , Juenger Thomas E.
Published: November 2021

The leaf economics spectrum (LES) is hypothesized to result from a trade-off between resource acquisition and conservation. Yet few studies have examined the evolutionary mechanisms behind the LES, perhaps because most species exhibit relatively specialized leaf economics strategies. In a genetic mapping population of the phenotypically diverse grassPanicum virgatum, we evaluate two interacting mechanisms that may drive LES evolution: 1) genetic architecture, where multiple traits are coded by the same gene (pleiotropy) or by genes in close physical proximity (linkage), and 2) correlational selection, where selection acts non-additively on combinations of multiple traits. We found evidence suggesting that shared genetic architecture (pleiotropy) controls covariation between two pairs of leaf economics traits. Additionally, at five common gardens spanning 17 degrees of latitude, correlational selection favored particular combinations of leaf economics traits. Together, these results demonstrate how the LES can evolve within species.
Deep Learning-based Automated Rare Sperm Identification from Testes Biopsies
Authors: Lee Ryan , Witherspoon Luke , Robinson Meghan , Lee Jeong Hyun , Duffy Simon P. , Flannigan Ryan , Ma Hongshen
Published: November 2021

Non-obstructive azoospermia (NOA), the most severe form of male infertility, is currently treated using microsurgical sperm extraction (microTESE) to retrieve sperm cells for in vitro fertilization via intracytoplasmic sperm injection (IVF-ICSI). The success rate of this procedure for NOA patients is currently limited by the ability of andrologists to identify a few rare sperm cells among millions of background testis cells. To improve this success rate, we developed a convolution neural network (CNN) to detect rare sperm from low-resolution microscopy images of microTESE samples. Our CNN uses the U-Net architecture to perform pixel-based classification on image patches from brightfield microscopy, which is followed by morphological analysis to detect individual sperm instances. This CNN is trained using microscopy images of fluorescently labeled sperm, which is fixed to eliminate their motility, and doped into testis biopsies obtained from NOA patients. We initially tested this algorithm using purified sperm samples at different imaging magnifications in order to determine the upper bounds of performance. We then tested this algorithm by doping rare sperm cells into testis biopsy samples from NOA patients and found a sperm detection F1 score of 85.2%. These results demonstrate the potential to use automated microscopy to dramatically increase the amount of testis biopsy tissue that could be comprehensively examined, which greatly increases the chance of finding rare viable sperm, and thereby increases the success rates of IVF-ICSI for couples with NOA.
Patterns of regulatory divergence and gene expression in hybrids are associated with molecular evolution in species undergoing gene flow
Authors: Díaz Fernando , Wolf Jason , de Brito Reinaldo
Published: November 2021

The extent to which hybridization disrupts a gene’s pattern of expression likely governs its propensity for introgression, while its extent of molecular divergence can itself underlie such disruption. Together, these phenomena shape the landscape of sequence and transcriptional divergence across the genome as species diverge. To understand this process, we examine gene expression inheritance, regulatory and molecular divergences in the reproductive transcriptomes of species linked by gene flow. The fruit flies Anastrepha fraterculus and A. obliqua show evidence of gene flow despite clear evolutionary divergence and incomplete reproductive isolation. We find that their transcriptional patterns are a mosaic between those typically observed within and between allopatric species. Genes showing transgressive expression in hybrids or cis-regulatory divergence between species are associated with greater molecular divergence. This may reflect pleiotropic constraints that make them more resistant to gene flow or they may be more likely to experience divergent selection. However, while these highly divergent genes are likely to be important contributors to species differences, they are relatively rare. Instead, most differentially regulated genes, including those linked to reproduction, show high degrees of dominance in hybrids and trans-regulated divergence between species, suggesting widespread genetic compatibility that allowed for the identified introgression. These findings provide insights into how postzygotic isolating mechanisms might evolve in the presence of gene flow: regions showing cis-regulatory divergence or transgressive expression contribute to reproductive isolation, while regions with dominant expression and trans-regulatory divergence act as a buffer of hybrid breakdown, facilitating introgression, and leading to a genomic mosaic of expression and sequence divergence.
Ca2+-inactivation of the mammalian ryanodine receptor type 1 in a lipidic environment revealed by cryo-EM
Authors: Nayak Ashok R. , Samsó Montserrat
Published: November 2021

Activation of the intracellular Ca2+channel ryanodine receptor (RyR) triggers a cytosolic Ca2+surge, while elevated cytosolic Ca2+inhibits the channel in a negative feedback mechanism. Cryo-EM carried out under partially inactivating Ca2+conditions revealed two conformations of RyR1, an open state and an inactivated state, resolved at 4.0 and 3.3 Å resolution, respectively. RyR1s were embedded in nanodiscs with two lipids resolved at each inter-subunit crevice. Ca2+binding to the high affinity site engages the central (CD) and C-terminal domains (CTD) into a quasi-rigid unit, which separates the S6 four-helix bundle and opens the channel. Further out-of-plane rotation of the quasi-rigid unit pushes S6 towards the central axis, closing (inactivating) the channel. The inactivated conformation is characterized by a downward conformation of the cytoplasmic assembly, a tightly-knit subunit interface contributed by a fully occupied and partially remodeled Ca2+activation site, and two salt bridges between the EF hand domain and the S2-S3 loop of the neighboring subunit validated by naturally-occurring diseasecausing mutations. Ca2+also bound to ATP, mediating a tighter interaction between S6 and CTD. Our study suggests that theclosed-inactivatedis a distinctive state of the RyR1 and its transition to theclosed-activablestate is not a simple reverse of the Ca2+mediated activation pathway.
pGlycoQuant with a deep residual network for precise and minuscule-missing-value quantitative glycoproteomics enabling the functional exploration of site-specific glycosylation
Authors: Cao Weiqian , Kong Siyuan , Zeng Wenfeng , Gong Pengyun , Jiang Biyun , Hou Xinhang , Zhang Yang , Zhao Huanhuan , Liu Mingqi , Qiao Xihua , Wu Mengxi , Yan Guoquan , Liu Chao , Yang Pengyuan
Published: November 2021

Interpreting large-scale glycoproteomic data for intact glycopeptide identification has been tremendously advanced by software tools. However, software tools for quantitative analysis of intact glycopeptides remain lagging behind, which greatly hinders exploring the differential expression and functions of site-specific glycosylation in organisms. Here, we report pGlycoQuant, a generic software tool for accurate and convenient quantitative intact glycopeptide analysis, supporting both primary and tandem mass spectrometry quantitation for multiple quantitative strategies. pGlycoQuant enables intact glycopeptide quantitation with very low missing values via a deep residual network, thus greatly expanding the quantitative function of several powerful search engines, currently including pGlyco 2.0, pGlyco3, Byonic and MSFragger-Glyco. The pGlycoQuant-based site-specific N-glycoproteomic study conducted here quantifies 6435 intact N-glycopeptides in three hepatocellular carcinoma cell lines with different metastatic potentials and, together with in vitro molecular biology experiments, illustrates core fucosylation at site 979 of the L1 cell adhesion molecule (L1CAM) as a potential regulator of HCC metastasis. pGlycoQuant is freely available at https://github.com/expellir-arma/pGlycoQuant/releases/. We have demonstrated pGlycoQuant to be a powerful tool for the quantitative analysis of site-specific glycosylation and the exploration of potential glycosylation-related biomarker candidates, and we expect further applications in glycoproteomic studies.
WITHDRAWN: In Silico Prediction and Comparison of Resistomes in Model Pseudomonas Strains by Resistance Gene Identifier (RGI)
Authors: Kwatra Bharat BK
Published: November 2021

Withdrawal Statement

This manuscript has been removed owing to an apparent copyright violation resulting from a fraudulent submission.
Essential role for Max in early embryonic growth and development
Authors: Shen-Li Hong , O'Hagan Rónán C. , Hou Harry , Horner James W. , Lee Han-Woong , DePinho Ronald A.
Published: November 2021

Loss of Max function in the mouse resulted in generalized developmental arrest of both embryonic and extraembryonic tissues at early postimplantation (∼E5.5–6.5), coincident with loss or dilution of maternal Max stores in the expanding embryo in vivo and in blastocyst outgrowths in vitro. Developmentally arrested embryos were reduced in size and exhibited widespread cytological degeneration and feeble BrdU incorporation. Max and, by extension, the Myc superfamily, serve essential roles in early mammalian development and a maternal reservoir of Max exists in sufficient amount to sustain Myc superfamily function through preimplantation stages of development.
Nuclear receptor corepressors partner with class II histone deacetylases in a Sin3-independent repression pathway
Authors: Huang Eric Y. , Zhang Jinsong , Miska Eric A. , Guenther Matthew G. , Kouzarides Tony , Lazar Mitchell A.
Published: November 2021

Transcriptional repression mediated by corepressors N-CoR and SMRT is a critical function of nuclear hormone receptors, and is dysregulated in human myeloid leukemias. At the present time, these corepressors are thought to act exclusively through an mSin3/HDAC1 complex. Surprisingly, however, numerous biochemical studies have not detected N-CoR or SMRT in mSin3- and HDAC1-containing complexes. Each corepressor contains multiple repression domains (RDs), the significance of which is unknown. Here we show that these RDs are nonredundant, and that one RD, which is conserved in N-CoR and SMRT, represses transcription by interacting directly with class II HDAC4 and HDAC5. Endogenous N-CoR and SMRT each associate with HDAC4 in a complex that does not contain mSin3A or HDAC1. This is the first example of a single corepressor utilizing distinct domains to engage multiple HDAC complexes. The alternative HDAC complexes may mediate specific repression pathways in normal as well as leukemic cells.
Wnt signaling maintains the hair-inducing activity of the dermal papilla
Authors: Kishimoto Jiro , Burgeson Robert E. , Morgan Bruce A.
Published: November 2021

The formation of the hair follicle and its cyclical growth, quiescence, and regeneration depend on reciprocal signaling between its epidermal and dermal components. The dermal organizing center, the dermal papilla (DP), regulates development of the epidermal follicle and is dependent on signals from the epidermis for its development and maintenance. GFP specifically expressed in DP cells of a transgenic mouse was used to purify this population and study the signals required to maintain it. We demonstrate that specific Wnts, but not Sonic hedgehog (Shh), maintain anagen-phase gene expression in vitro and hair inductive activity in a skin reconstitution assay.
Two protein tyrosine phosphatases, Ptp2 and Ptp3, modulate the subcellular localization of the Hog1 MAP kinase in yeast
Authors: Mattison Christopher P. , Ota Irene M.
Published: November 2021

The MAP kinase Hog1 transiently accumulates in the nucleus upon activation. Although Hog1 nuclear export correlates with its dephosphorylation, we find that dephosphorylation is not necessary for export. Unexpectedly, a strain lacking the nuclear protein tyrosine phosphatase, Ptp2, showed decreased Hog1 nuclear retention, while a strain lacking the cytoplasmic Ptp3 showed prolonged Hog1 nuclear accumulation, consistent with Ptp2 being a nuclear tether for Hog1 and Ptp3 being a cytoplasmic anchor. In support of this result PTP2overexpression sequestered Hog1 in the nucleus while PTP3overexpression restricted Hog1 to the cytoplasm. Thus, Ptp2 and Ptp3 regulate Hog1 localization by binding Hog1.