bluuebunny/crossref_metadata_2025 huggingface dataset:
Anatomical Reconstruction of Extensive Inferomedial Blow-Out Fractures Involving the Inferomedial Orbital Strut Using a Single Fan-shaped Titanium-Reinforced Porous Polyethylene Plate
Authors: Jeong Seong-Ho , Moon Kyung-Chul , Namgoong Sik , Dhong Eun-Sang , Han Seung-Kyu
Published: March 2023

Extensive inferomedial blow-out fractures involving the inferomedial orbit strut frequently result in severe ophthalmic complications. Therefore, anatomical reconstruction is essential but is still technically challenging. Thus, the authors have used a novel technique using a combination of single fan-shaped titanium-reinforced porous polyethylene (TR-PPE) implants and a bidirectionally extended transconjunctival approach. Herein, the authors describe our surgical technique and discuss its effectiveness. First, the transconjunctival approach was performed and was subsequently extended medially using the transcaruncular approach and laterally using lateral blepharotomy. After the origin of the inferior oblique muscle was identified, a trimmed fan-shaped TR-PPE implant was inserted into the orbital floor. It was subsequently rotated and bent at the site of origin of the IO muscle and moved upward to cover the superior bony ledge of the medial wall. Finally, the implant was fixed to the orbital rim. Anatomical orbital reconstruction was confirmed by a computed tomographic scan. The preoperative diplopia in 19 patients, resolved within 1 week in 16 patients and in 3 to 6 months in the remaining 3 patients. Preoperative enophthalmos >2 mm in all patients improved to <2 mm in 67 patients and 3 mm in 2 patients (>7 mm preoperatively). The postoperative course was uneventful, and no severe complications were observed. The authors believe that the placement of a fan-shaped TR-PEE implant into the orbit through the bidirectionally extended transconjunctival approach could be a viable option for the anatomical reconstruction of extensive inferomedial blow-out fractures involving the inferomedial orbital strut.
Flipped Nasal Bone Fracture: Peculiar Fracture Pattern in a Pediatric Patient
Authors: Shin Jong Weon , Kim Rah Yoon , Choi Jangyoun
Published: March 2023

Fractures to the facial bone in the pediatric population often show a different fracture pattern from that of the adult population. In this brief report, the authors share their experience with a nasal bone fracture in a 12-year-old child showing a bizarre fracture pattern, an inside-out displacement of the nasal bone. The authors share the detailed findings of this fracture and describe the method for reducing the fracture back to the proper position.
Diagnosis and Treatment of a Nonhealing Wound Secondary to a Reepithelialized Hair Tourniquet With Ultrasound
Authors: Chwa Emily S. , Reddy Narainsai K. , Rajeswaran Shankar , Yamada Akira
Published: March 2023

A 9-month-old girl presented with a chronic wound on the dorsal surface of her toe that failed 6 months of medical management. Due to the prolonged clinical course, there was a concern for a foreign body. Intraoperative ultrasound was utilized to identify linear echogenic structures, which were excised and consistent with reepithelialized hairs secondary to hair-thread tourniquet syndrome. There were also erosive changes to the underlying phalanx. Intraoperative ultrasound was also used to guide the incision size and confirm the complete removal of the hairs.
Beyond the Surgical Safety Checklist
Authors: Ramjaun Aliya , Hammond Mobilio Melanie , Wright Nicole , Masella Maria , Snyman Adam , Serrick Cyril , Moulton Carol-anne
Published: March 2023

Background:

The surgical safety checklist (SSC) has been credited with improving team situation awareness (SA) in the operating room. Although the SSC may support team SA at the outset of the operative case, intraoperative handoff provides an opportunity for either SA breakdown or, more preferably, SA reinforcement. High-functioning surgical teams demonstrate a high level of continued SA, whereas teams deficient in SA are more likely to be affected by surgical errors and adverse events. To date, no interprofessional intraoperative tools exist to support team SA beyond the SSC.

Methods:

This study was divided into 2 phases. The first used qualitative methods to (1) characterize intraoperative handoff processes across surgery, nursing, anesthesia, and perfusion, and (2) identify cultural factors that shaped handoff practices. Data for phase one were collected over 38 observation days and 41 brief interviews. Phase 2, informed by phase 1, used a modified Delphi process to create a tool for use during intraoperative handoff. Data were analyzed iteratively.

Results:

Handoff practices were not standardized and rarely involved the entire team. In addition we uncovered cultural factors—specifically assumptions held by participants—that hindered team communication during handoff. Assumptions included: (1) team members are interchangeable, (2) trained individuals are able to determine when it is appropriate to handoff without consulting the OR team. Despite claims of improved teamwork resulting from the SSC, many participants held a fragmented view of the OR team, resulting in communication challenges during handoff. Findings from both phases of our study informed the development of multidisciplinary intraoperative handoff tools to facilitate shared team situation awareness and a shared mental model.

Conclusions:

Intraoperative handoff occurs frequently, and offers the opportunity for either renewed or fractured team SA beyond the SSC.
Surgical Outcomes in Patients With Low-risk Papillary Thyroid Microcarcinoma From MAeSTro Study
Authors: Hwang Hyeonuk , Choi June Young , Yu Hyeong Won , Moon Jae Hoon , Kim Ji-hoon , Lee Eun Kyung , Kim Yeo Koon , Lee Chang Yoon , Cho Sun Wook , Chung Eun-Jae , Ryu Chang Hwan , Ryu Junsun , Yi Ka Hee , Park Do Joon , Lee Kyu Eun , Park Young Joo , Kim Su-jin , Jung Yuh-Seog
Published: March 2023

Objective:

To investigate surgical, and clinical outcomes in patients with low-risk papillary thyroid microcarcinoma (PTMC) according to treatment options [immediate operation (IOP) vs delayed operation after active surveillance (AS) (DOP)].

Background:

AS has been adopted as an alternative to immediate surgery in patients with low-risk PTMC. Although some patients undergo surgery during AS, there is little information on surgical, and clinical outcomes after delayed operation after AS.

Methods:

A multicenter prospective cohort study including 1177 patients was conducted at 3 tertiary hospitals in Korea from June 2016 to January 2020. Patients with low-risk PTMC were enrolled. The participants were self-assigned into AS or IOP, and during AS, the patients underwent surgery if there were signs of disease progression or if the patient’s choice changed.

Results:

A total of 516 patients underwent operation; 384 (74.4%) in the IOP group and 132 (25.6%) in the DOP group. Compared with the IOP group, the DOP group was significantly associated with a larger tumor size (P=0.002), higher rates of lymphatic invasion (P=0.002), and multifocality (P=0.008). However, the rates of total thyroidectomy, postoperative hypoparathyroidism and vocal cord palsy did not differ significantly between the groups (P= 0.283, P=0.184, and P=0.284, respectively). Of the 132 patients in the DOP group, disease progression was present in 39 (29.5%) patients. The DOP group with disease progression had a significantly higher rate of lymph node metastasis (P=0.021) and radioiodine therapy (P=0.025) than the DOP group without disease progression.

Conclusions:

These results suggest that AS might be considered an alternative treatment option for patients with low-risk PTMC regarding the extent of thyroidectomy and postoperative complications in the DOP group. To assess oncologic outcomes, long-term follow-up will be needed.

Trial registration:

ClinicalTrials.gov Identifier: NCT02938702.
Early mitochondrial dysfunction proceeds neuroinflammation, synaptic alteration, and autophagy impairment in hippocampus ofAppknock-in Alzheimer mouse models
Authors: Naia Luana , Shimozawa Makoto , Bereczki Erika , Li Xidan , Liu Jianping , Jiang Richeng , Leal Nuno Santos , Pinho Catarina Moreira , Berger Erik , Falk Victoria Lim , Dentoni Giacomo , Ankarcrona Maria , Nilsson Per
Published: March 2023

Increased amyloid β-peptide (Aβ) level is one of the drivers of Alzheimer’s disease (AD). Amyloid precursor protein (App) knock-in mice recapitulate the human Aβ pathology, allowing the elucidation of the downstream effects of Aβ and their temporal appearance upon disease progression. Here we have investigated the sequential onset of AD-like pathologies in theAppNL-FandAppNL-G-Fknock-in mouse models by time-course transcriptome analysis of the hippocampus, a region severely affected in AD. Energy metabolism emerged as one of the most significantly altered pathways at an early stage of the development of the pathologies. Functional experiments in mitochondria isolated fromAppNL-G-Fbrain subsequently identified upregulation of oxidative phosphorylation driven by the activity of mitochondrial complexes I, IV and V, combined with higher susceptibility to Ca2+-overload. This was followed by a strong neuroinflammatory response and impaired autophagy. Accumulation of autophagosomes and reduced number of mitochondria content in presynaptic terminals could account for the altered synapse morphology including increased number of synaptic vesicles and lowered thickness of post synaptic density inAppNL-G-Fmice. This shows that Aβ-induced pathways in theAppknock-in mice recapitulate some key pathologies observed in AD brain, and our data herein contributes to the understanding of their timewise appearance and potential role in new therapeutic approaches.
Post-progression survival in advanced non-small cell lung cancer treated with anti-PD-1/PDL-1 monotherapy: progression after durable clinical benefit versus primary resistance
Authors: Pourmir Ivan , Elaidi Reza , Maaradji Zineb , de Saint Basile Hortense , Ung Monivann , Gazeau Benoit , Fournier Laure , Rance Bastien , Gibault Laure , Ismaili Mohammed , Fabre Elizabeth
Published: March 2023

Aims

Anti-PD-1/PD-L1 can face the issue of tumor resistance in advanced non-small cell lung cancer (aNSCLC), mostly as primary resistance to the treatment. Still, disease progression (PD) also occurs after prior durable clinical benefit (DCB). Comparison of both situations and tools to evaluate residual benefit of PD-1/PD-L1 blockade are needed to understand and manage resistance.

Methods

We reviewed aNSCLCs with anti-PD-1/PD-L1 monotherapy, and disease progression per RECIST 1.1 (PD) in our center. Primary objective was comparison of post-progression survival (PPS) in primary resistance versus PD after DCB. Secondary objectives were to characterize patterns of PD after DCB; assess the feasibility and relevance of Tumor Growth Rate (TGR) in PD after DCB.

Results

148 patients were included. Median PPS were 5.2months (95% CI: 2.6-6.5) and 21.3months (95% CI: 18.5-36.3) (p<0.0001) for primary resistance and PD after DCB respectively. Multivariable hazard ratio for death in PD after DCB versus primary resistance was 0.14 (95% CI: 0.07-0.30). 76.7% of PD after DCB occurred in ≤3 lesions; 72.1% occurred only in preexisting lesions. TGR suggested a persistent benefit of PD-1/PD-L1 blockade in at least 44.2% of cases.

Conclusions

PD after DCB was an independent factor of longer post-progression survival, with specific patterns of progression. TGR is a promising tool to assess residual benefit of immunotherapy.

Highlights

Anti-PD-(L)1 immunotherapy still faces the problem of resistance in lung cancer

Resistance can be classified as primary or secondary (acquired)

Outcomes and mechanisms of both situations need to be characterized

This unique comparative study reveals diverging survival and progression patterns

Prior durable clinical benefit associates with longer post-progression survival

This data benefits our understanding and management of resistance to anti-PD-(L)1
How Images of Food Become Cravingly Salient in Obesity
Authors: Devoto F. , Ferrulli A. , Banfi G. , Luzi L. , Zapparoli L. , Paulesu E.
Published: March 2023

Background

Obesity is characterized by neurofunctional alterations within the mesocorticolimbic reward system, a brain network that originates from the midbrain ventral tegmental area (VTA). Here we tested the hypothesis that this system might be misconfigured in obesity, reflecting a bias for food-related visual stimuli and a predisposition for craving.

Methods

A group of normal weight and a group of obese patients underwent a resting-state fMRI scan and the assessment of impulsivity, food craving, appetite, and implicit bias for food and non-food pictures. The VTA was used as a seed to map, for each participant, the strength of its functional connections with the rest of the brain. We then computed the difference of such maps between the groups and performed brain-behavior correlations.

Results

Obese patients showed hyper-connectivity of the VTA with part of ventral occipitotemporal cortices (vOTC) recently found to be specialized for food images; there was also a hypo-connectivity with the left inferior frontal gyrus (IFG), devoted to cognitive control. The VTA-left vOTC connectivity was positively associated with food craving and bias for high-calories food; a reversed such correlation was seen for the IFG.

Interpretation

These findings reveal that, in obesity, food-related visual stimuli become cravingly salient through an imbalanced connectivity of the reward system with sensory-specific regions and the frontal cortex involved in cognitive control.
Extended regulation interface coupled to the allosteric network and disease mutations in the PP2A-B56δ holoenzyme
Authors: Wu Cheng-Guo , Balakrishnan Vijaya K. , Parihar Pankaj S. , Konovolov Kirill , Chen Yu-Chia , Merrill Ronald A , Wei Hui , Carragher Bridget , Sundaresan Ramya , Cui Qiang , Wadzinski Brian E. , Swingle Mark R. , Musiyenko Alla , Honkanen Richard , Chung Wendy K. , Suzuki Aussie , Strack Stefan , Huang Xuhui , Xing Yongna
Published: March 2023

An increasing number of mutations associated with devastating human diseases are diagnosed by whole-genome/exon sequencing. Recurrentde novomissense mutations have been discovered in B56δ (encoded byPPP2R5D), a regulatory subunit of protein phosphatase 2A (PP2A), that cause intellectual disabilities (ID), macrocephaly, Parkinsonism, and a broad range of neurological symptoms. Single-particle cryo-EM structures show that the PP2A-B56δ holoenzyme possesses closed latent and open active forms. In the closed form, the long, disordered arms of B56δ termini fold against each other and the holoenzyme core, establishing dual autoinhibition of the phosphatase active site and the substrate-binding protein groove. The resulting interface spans over 190 Å and harbors unfavorable contacts, activation phosphorylation sites, and nearly all residues with ID-associated mutations. Our studies suggest that this dynamic interface is close to an allosteric network responsive to activation phosphorylation and altered globally by mutations. Furthermore, we found that ID mutations perturb the activation phosphorylation rates, and the severe variants significantly increase the mitotic duration and error rates compared to the wild variant.
Epigenetic then genetic variations underpin rapid adaptation of oyster populations (Crassostrea gigas) to Pacific Oyster Mortality Syndrome (POMS)
Authors: Gawra Janan , Valdivieso Alejandro , Roux Fabrice , Laporte Martin , de Lorgeril Julien , Gueguen Yannick , Saccas Mathilde , Escoubas Jean-Michel , Montagnani Caroline , Destoumieux-Garzón Delphine , Lagarde Franck , Leroy Marc A. , Haffner Philippe , Petton Bruno , Cosseau Céline , Morga Benjamin , Dégremont Lionel , Mitta Guillaume , Grunau Christoph , Vidal-Dupiol Jeremie
Published: March 2023

Disease emergence is accelerating in response to human activity-induced global changes. Understanding the mechanisms by which host populations can rapidly adapt to this threat will be crucial for developing future management practices. Pacific Oyster Mortality Syndrome (POMS) imposes a substantial and recurrent selective pressure on oyster populations (Crassostrea gigas). Rapid adaptation to this disease may arise through both genetic and epigenetic mechanisms. In this study, we used a combination of whole exome capture of bisulfite-converted DNA, next-generation sequencing, and (epi)genome-wide association mapping, to show that natural oyster populations differentially exposed to POMS displayed signatures of selection both in their genome (single nucleotide polymorphisms) and epigenome (CG-context DNA methylation). Consistent with higher resistance to POMS, the genes targeted by genetic and epigenetic variations were mainly related to host immunity. By combining correlation analyses, DNA methylation quantitative trait loci, and variance partitioning, we revealed that a third of the observed phenotypic variation was explained by interactions between the genetic sequence and epigenetic information, ∼14% by the genetic sequence, and up to 25% by the epigenome alone. Thus, as well as genetic adaptation, epigenetic mechanisms governing immune responses contribute significantly to the rapid adaptation of hosts to emerging infectious diseases.
Genetic analysis ofrab7mutants in zebrafish
Authors: Heutschi Daniel , Schmelzer Etienne , Aydogan Vahap , Schmidt Alexander , Belting Heinz-Georg , Spang Anne , Affolter Markus , Kotini Maria P.
Published: March 2023

Vascular network formation requires the fusion of newly formed blood vessels and the emergence of a patent lumen between the newly established connections so that blood flow can start. Lumen formation has been shown to depend on the late endosomal/lysosomal pathway in various organs of animal tubular systems. Here, we identified a late endosomal/lysosomal vesicular fraction (Rab7/Lamp2) in early zebrafish angiogenic sprouts, which appears to contribute to apical membrane growth during lumen formation. To study the effect of the late endocytic pathway on vascular development, we generated mutant alleles for all threerab7genes in zebrafish (rab7a, rab7ba, rab7bb). Allrab7genes are expressed in wild-type zebrafish and we did not detect any compensatory effects by the otherrab7isoforms in single knockout mutants, which were all viable. Only the triple mutant was lethal suggesting some functional redundancy. However, the differentrab7isoforms fulfil also at least partially independent functions because eggs laid from mothers lacking tworab7(rab7a and/or rab7bb). showed reduced survival and contained enlarged yolk granules, suggesting maternal contribution of these tworab7. Finally, we observed minor effects on lumen formation in embryos which still express one copy ofrab7. Our results support the notion that the late endocytic/lysosomal compartment contributes to lumen expansion.
Topography modulates climate sensitivity of multidecadal trends of holm oak decline
Authors: López-Ballesteros Ana , Rodríguez-Caballero Emilio , Moreno Gerardo , Escribano Paula , Hereş Ana María , Curiel-Yuste Jorge
Published: March 2023

Forest decline events have increased worldwide over the last decades, being holm oak one of the tree species with the most worrying trends across Europe. Previous research identified drought and soil pathogens as the main causes behind holm oak decline. However, despite tree health loss is a multifactorial phenomenon where abiotic and biotic factors interact in time and space, there are some abiotic factors whose influence has been commonly overlooked. Here, we evaluate how land use (forests versus savannas), topography, and climate extremes jointly relate to spatiotemporal patterns of holm oak defoliation over almost three decades (1987-2014) in Spain, where holm oak represents the 25% of the national forested area. We found an increasing defoliation trend in 119 of the total 134 holm oak plots evaluated, being this increase rate significantly higher in forests compared to savannas. Moreover, we have detected that the interaction between topography and summer drought can explain trends of holm oak decline across the Mediterranean region. While a higher occurrence of dry summers increases defoliation trends in complex terrains where forests dominate, an inverse relationship was found at flatter terrains where savannas are located. Our results contribute to growing evidence of the influence of local topography, tightly linked to potential soil water availability, on forest functioning, as it can shape forest vulnerability against climate extremes. The present work could assist the identification of potential tree decline hotspots over the Mediterranean region. Moreover, our findings suggest that forest adaptive management will be key to guarantee the health and future stability of Mediterranean oak ecosystems, especially in the topographically more complex areas where tree vulnerability to climate extremes may be greater.
Multiplex single-cell chemical genomics reveals the kinase dependence of the response to targeted therapy
Authors: McFaline-Figueroa José L. , Srivatsan Sanjay , Hill Andrew J. , Gasperini Molly , Jackson Dana L. , Saunders Lauren , Domcke Silvia , Regalado Samuel G. , Lazarchuck Paul , Alvarez Sarai , Monnat Raymond J. , Shendure Jay , Trapnell Cole
Published: March 2023

Chemical genetic screens are a powerful tool for exploring how cancer cells’ response to drugs is shaped by their mutations, yet they lack a molecular view of the contribution of individual genes to the response to exposure. Here, we present sci-Plex-Gene-by-Environment (sci-Plex-GxE), a platform for combined single-cell genetic and chemical screening at scale. We highlight the advantages of large-scale, unbiased screening by defining the contribution of each of 522 human kinases to the response of glioblastoma to different drugs designed to abrogate signaling from the receptor tyrosine kinase pathway. In total, we probed 14,121 gene-by-environment combinations across 1,052,205 single-cell transcriptomes. We identify an expression signature characteristic of compensatory adaptive signaling regulated in a MEK/MAPK-dependent manner. Further analyses aimed at preventing adaptation revealed promising combination therapies, including dual MEK and CDC7/CDK9 or NF-kB inhibitors, as potent means of preventing transcriptional adaptation of glioblastoma to targeted therapy.
vcfdist: Accurately benchmarking phased small variant calls in human genomes
Authors: Dunn Tim , Narayanasamy Satish
Published: March 2023

Abstract

Accurately benchmarking small variant calling accuracy is critical for the continued improvement of human whole genome sequencing. In this work, we show that current variant calling evaluations are biased towards certain variant representations and may misrepresent the relative performance of different variant calling pipelines. We propose solutions, first exploring the affine gap parameter design space for complex variant representation and suggesting a standard. Next, we present our tool “vcfdist” and demonstrate the importance of enforcing local phasing for evaluation accuracy. We then introduce the notion of partial credit for mostly-correct calls and present an algorithm for clustering dependent variants. Lastly, we motivate using alignment distance metrics to supplement precision-recall curves for understanding variant calling performance. We evaluate the performance of 64 phased “Truth Challenge V2” submissions and show that vcfdist improves measured (SNP, INDEL) performance consistency across variant representations fromR2= (0.14542, 0.97243)for baseline vcfeval to(0.99999, 0.99996)for vcfdist.
Methodological Considerations When Using Polygenic Scores to Explore Parent-Offspring Genetic Nurturing Effects
Authors: Chuong M. , Adams M.J. , Kwong A.S.F. , Haley C.S. , Amador C. , McIntosh A.M.
Published: March 2023

Background

Research has begun to explore the effects of parental genetic nurturing on offspring outcomes using polygenic scores (PGSs). However, there are concerns regarding potential biases due to confounding when mediating parental phenotypes are included.

Methods

Depression, educational attainment and height PGSs were generated for 2680 biological parent-offspring trios using genome-wide association study (GWAS) meta-analysis summary statistics in a large population study: Generation Scotland. Regression and pathway models were estimated incorporating PGSs for both parents and offspring to explore direct (offspring PGS) and genetic nurturing (parental PGS) effects on psychological distress, educational attainment and height. Genetic nurturing via parental phenotypes were incorporated into the models. To explore sources of bias we conducted simulation analyses of 10,000 trios using combinations of PGS predictive accuracy and accounted variance.

Results

Models incorporating both offspring and parental PGSs suggested positive parental genetic nurturing effects on offspring educational attainment, but not psychological distress or height. In contrast, models additionally incorporating parental phenotypic information suggested positive parent phenotype mediated genetic nurturing effects were at play for all phenotypes explored as well as negative residual genetic nurturing effects for height. 10,000 parent-offspring trio effects (without genetic nurturing effects) were simulated. Simulations demonstrated that models incorporating parent and offspring PGSs resulted in genetic nurturing effects that were unbiased. However, adding parental phenotypes as mediating variables results in biased positive estimates of parent phenotype mediated genetic nurturing effects and negative estimates of residual genetic nurturing effects. Biased effects increased in magnitude as PGS accuracy and accounted variance decreased. These biases were only eliminated when PGSs were simulated to capture the entirety of trait genetic variance.

Conclusion

Results suggest that in the absence of PGSs that capture all genetic variance, parental phenotypes act as colliders in the same way as heritable environments. Relatively simple models combining parental and offspring PGSs can be used to detect genetic nurturing effects in complex traits. However, our findings suggest alternative methods should be utilised when aiming to identify mediating phenotypes and potentially modifiable parental nurturing effects.
Phylogenetic relatedness of plant species co-occurring with an invasive alien plant species (Anthemis cotulaL.) varies with elevation
Authors: Afshana  , Pinto-Ledezma Jesús N. , Reshi Zafar A.
Published: March 2023

Darwin’s naturalization conundrum, which posits that the alien species either succeed in the introduced region because being phylogenetically related to the native species hence being pre-adapted, or are phylogenetically dissimilar to native species and thus occupy unfilled niches, has received a lot of attention but the results have been contradictory. Instead of the usual phylogenetic comparison between native and introduced species to address this conundrum, we followed a novel approach of studying the phylogenetic relationship of a highly widespread and invasive species, Anthemis cotula L. (focal species) separately with the native species and all its co-occurring species (including native and non-native species) along an elevation gradient. The abundance of A. cotula declined continuously with an increase in elevation and species richness. The phylogenetic relationship between the focal species and all the co-occurring species using abundance-weighted mean pair-wise distance (MPDaw) showed an increase with an increase in elevation and species richness. A similar but slightly weaker relationship was noticed when the non-abundance weighted mean pair-wise distance (MPDpa) was used. Interestingly, the phylogenetic distance between the focal species and the native species based on MPDaw declined with elevation as well as species richness, but such a decline was seen when MPDpa was used. Our study also revealed that soil nutrients influence the abundance of A. cotula and the phylogenetic distance between the focal and other species, thereby indicating the role of micro-ecological factors and spatial heterogeneity in community assembly.
DANGER ANALYSIS: RISK-AVERSE ON/OFF-TARGET ASSESSMENT FOR CRISPR EDITING WITHOUT A REFERENCE GENOME
Authors: Nakamae Kazuki , Bono Hidemasa
Published: March 2023

The CRISPR-Cas9 system has successfully achieved site-specific gene editing in organisms ranging from humans to bacteria. The technology efficiently generates mutants, allowing for phenotypic analysis of the on-target gene. However, some conventional studies did not investigate whether deleterious off-target effects partially affect the phenotype. Herein, we present a novel phenotypic assessment of CRISPR-mediated gene editing: Deleterious and ANticipatable Guides Evaluated by RNA-sequencing (DANGER) analysis. Using RNA-seq data, this bioinformatics pipeline can elucidate genomic on/off-target sites on mRNA-transcribed regions related to expression changes and then quantify phenotypic risk at the gene ontology (GO) term level. We demonstrated the risk-averse on/off-target assessment in RNA-seq data from gene-edited samples of human cells and zebrafish brains. Our DANGER analysis successfully detected off-target sites, and it quantitatively evaluated the potential contribution of deleterious off-targets to the transcriptome phenotypes of the edited mutants. Notably, DANGER analysis harnessedde novotranscriptome assembly to perform risk-averse on/off-target assessments without a reference genome. Thus, our resources would help assess genome editing in non-model organisms, individual human genomes, and atypical genomes from diseases and viruses. In conclusion, DANGER analysis facilitates the safer design of genome editing in all organisms with a transcriptome.
A systematic search for RNA structural switches across the human transcriptome
Authors: Khoroshkin Matvei , Asarnow Daniel , Navickas Albertas , Winters Aidan , Yu Johnny , Zhou Simon K. , Zhou Shaopu , Palka Christina , Fish Lisa , Ansel K. Mark , Cheng Yifan , Gilbert Luke A. , Goodarzi Hani
Published: March 2023

RNA structural switches are key regulators of gene expression in bacteria, yet their characterization in Metazoa remains limited. Here we present SwitchSeeker, a comprehensive computational and experimental approach for systematic identification of functional RNA structural switches. We applied SwitchSeeker to the human transcriptome and identified 245 putative RNA switches. To validate our approach, we characterized a previously unknown RNA switch in the 3’UTR of the RORC transcript.In vivoDMS-MaPseq, coupled with cryogenic electron microscopy, confirmed its existence as two alternative structural conformations. Furthermore, we used genome-scale CRISPR screens to identifytransfactors that regulate gene expression through this RNA structural switch. We found that nonsense-mediated mRNA decay acts on this element in a conformation-specific manner. SwitchSeeker provides an unbiased, experimentally-driven method for discovering RNA structural switches that shape the eukaryotic gene expression landscape.
Towards bone-remodeling-on-a-chip: self-assembling 3D osteoblast-osteoclast coculture in a microfluidic chip
Authors: Vis M.A.M. , Zhao F. , Bodelier E.S.R. , Bood C.M. , Bulsink J. , van Doeselaar M. , Amirabadi H. Eslami , Ito K. , Hofmann S.
Published: March 2023

Healthy bone is maintained by the process of bone remodeling. An unbalance in this process can lead to pathologies such as osteoporosis which are often studied with animal models. However, data from animals have limited power in predicting the results that will be obtained in human clinical trials. In search for alternatives to animal models, humanin vitromodels are emerging as they address the principle of reduction, refinement, and replacement of animal experiments (3Rs). At the moment, no completein vitromodel for bone-remodeling exists. Microfluidic chips offer great possibilities, particularly because of the dynamic culture options, which are crucial forin vitrobone formation. In this study, a scaffold free, fully human, 3D microfluidic coculture model of bone remodeling is presented. A bone-on-a-chip coculture system was developed in which human mesenchymal stromal cells differentiated into osteoblasts and self-assembled into scaffold free bone-like tissues with the shape and dimensions of human trabeculae. Human monocytes were able to attach to these tissues and to fuse into multinucleated osteoclast-like cells, establishing the coculture. Furthermore, a set-up was developed allowing for long-term (35 days) on-chip cell culture with benefits including continuous fluid-flow, low bubble formation risk, easy culture medium exchange inside the incubator and live cell imaging options. This on-chip coculture is a crucial advance towards developingin vitrobone remodeling models to facilitate drug testing.
In-silico Discovery of Genetic Diversity inCucumis sativusvar. hardwickii: A Wild Relative of Cultivated Cucumber
Authors: Rawat Suniti , Kaushik Prashant
Published: March 2023

Genome-wide sequencing data play an important role in evaluating the genomic level differences between superior and poor-quality crop plants and improving our understanding of molecular association with desired traits. We analyzed the obtained 92,921,066 raw reads from genome-wide resequencing ofCucumis sativusvar. hardwickii through in-silico approaches and mapped to the reference genome of Cucumis sativus to identify the genome-wide single nucleotide polymorphisms (SNPs) and Single nucleotide variations (SNV). Here, we report 19, 74,213 candidate SNPs including 1,33,468 insertions and 1,43,237 deletions and 75 Indels genome-wide. A total of 2228224 identified variants were classified into four classes including 0.01% sequence alteration, 5.94% insertion, 6.37% deletion and 87.66% SNV respectively. These variations can be a major source of phenotypic diversity and sequence variation within the species. Overall, the discovery of SNPs and genomic variants may help predict the plant response to certain environmental factors and can be utilized to improve crop plants’ economically important traits.
Finite Sample Corrections for Average Equivalence Testing
Authors: Boulaguiem Younes , Quartier Julie , Lapteva Maria , Kalia Yogeshvar N , Victoria-Feser Maria-Pia , Guerrier Stéphane , Couturier Dominique-Laurent
Published: March 2023

Abstract

Average (bio)equivalence tests are used to assess if a parameter, like the mean difference in treatment response between two conditions for example, lies within a given equivalence interval, hence allowing to conclude that the conditions have ‘equivalent’ means. TheTwo One-Sided Tests(TOST) procedure, consisting in testing whether the target parameter is respectively significantly greater and lower than some pre-defined lower and upper equivalence limits, is typically used in this context, usually by checking whether the confidence interval for the target parameter lies within these limits. This intuitive and visual procedure is however known to be conservative, especially in the case of highly variable drugs, where it shows a rapid power loss, often reaching zero, hence making it impossible to conclude for equivalence when it is actually true. Here, we propose a finite sample correction of the TOST procedure, theα-TOST, which consists in a correction of the significance level of the TOST allowing to guarantee a test size (or type-I error rate) ofα. This new procedure essentially corresponds to a finite sample and variability correction of the TOST procedure. We show that this procedure is uniformly more powerful than the TOST, easy to compute, and that its operating characteristics outperform the ones of its competitors. A case study about econazole nitrate deposition in porcine skin is used to illustrate the benefits of the proposed method and its advantages compared to other available procedures.
Small Molecule Inhibitors Targeting Methyltransferase-Like (METTL) Proteins Against Hepatocellular Carcinoma: A Comprehensive Drug Repurposing Approach
Authors: Morshed Md Niaz , Parvez Md Sorwer Alam , Akanda Rakibul Islam , Saha Manash Kumar , Fardous Jannatul , Hosen Mohammad Jakir
Published: March 2023

An efficient and durable multi-targeted therapeutic drug against hepatocellular carcinoma (HCC) has recently been a growing concern for tackling the chemoresistance of approved anti-HCC drugs. Recent studies indicated that methyltransferase-like (METTL) proteins including METTL1, METTL3, METTL6, METTL16, and METTL18, have overexpressed and associated with the progression of HCC malignancy, and making them excellent biomarkers. Here, we present a series of bioinformatics study including novel compound repurposing approach, molecular docking, pharmacophore modeling, and molecular dynamic simulation, which revealed two first-in-class highly potent catalytic multi-target inhibitors (ZINC70666503 and ZINC13000658 with 87% and 82% drug scores, respectively) of methyltransferase-like proteins. Comparatively, these two inhibitors showed a notable binding affinity against studied METTL proteins. Furthermore, ADME and toxicity analysis suggested that these two commercially available compounds have good drug-likeliness properties with no potent toxic effects. Of note, the molecular dynamics study supported their conformational stability and high selectivity at the pocket of proteins’ adenosine moiety of S-Adenosyl Methionine. However, this comprehensive analysis needsin vivovalidation to facilitate multi-targeting therapeutic development against hepatocellular carcinoma.
Ocular following eye movements in marmosets follow complex motion trajectories
Authors: Pattadkal Jagruti J. , Barr Carrie , Priebe Nicholas J.
Published: March 2023

Ocular following eye movements help stabilize images on the retina and offer a window to study motion interpretation by visual circuits. We use these ocular following eye movements to study motion integration behavior in the marmosets. We characterize ocular following responses in the marmosets using different moving stimuli such as dot patterns, gratings, and plaids. The marmosets can accurately track motion along different directions and exhibit spatial frequency and speed sensitivity that closely matches the sensitivity reported in neurons from their motion selective area MT. Marmosets are also able to track the integrated motion of plaids, with tracking direction consistent with intersection of constraints model of motion integration. Marmoset ocular following responses are similar to responses in macaques and humans with certain species-specific differences in peak sensitivities. Such motion sensitive eye movement behavior in combination with direct access to cortical circuitry makes the marmoset model well suited to study the neural basis of motion integration.

Significance statement

Ocular following is a reflexive eye tracking behavior in response to large visual field motion. It reflects the properties of underlying motion sensing circuits. One of the primary motion sensing areas in primates is area MT. In the primate species of marmosets, this and other cortical areas are easily accessible due to their lissencephalic brain. We demonstrate ocular following behavior in the marmosets for simple and complex motion trajectories and describe its characteristics. We then use ocular following to distinguish between different motion integration models. Our results show the utility of ocular following to study the neural basis for motion sensing in marmosets.
A Pillar and Perfusion Plate Platform for Robust Human Organoid Culture and Analysis
Authors: Kang Soo-Yeon , Kimura Masaki , Shrestha Sunil , Lewis Phillip , Lee Sangjoon , Cai Yuqi , Joshi Pranav , Acharya Prabha , Liu Jiafeng , Yang Yong , Sanchez J. Guillermo , Ayyagari Sriramya , Alsberg Eben , Wells James M. , Takebe Takanori , Lee Moo-Yeal
Published: March 2023

Human organoids have potential to revolutionizein vitrodisease modeling by providing multicellular architecture and function that are similar to thosein vivo. This innovative and evolving technology, however, still suffers from assay throughput and reproducibility to enable high-throughput screening (HTS) of compounds due to cumbersome organoid differentiation processes and difficulty in scale-up and quality control. Using organoids for HTS is further challenged by lack of easy-to-use fluidic systems that are compatible with relatively large organoids. Here, we overcome these challenges by engineering “microarray three-dimensional (3D) bioprinting” technology and associated pillar and perfusion plates for human organoid culture and analysis. High-precision, high-throughput stem cell printing and encapsulation techniques were demonstrated on a pillar plate, which was coupled with a complementary deep well plate and a perfusion well plate for static and dynamic organoid culture. Bioprinted cells and spheroids in hydrogels were differentiated into liver and intestine organoids forin situfunctional assays. The pillar/perfusion plates are compatible with standard 384-well plates and HTS equipment, and thus may be easily adopted in current drug discovery efforts.
BOLD Moments: modeling short visual events through a video fMRI dataset and metadata
Authors: Lahner Benjamin , Dwivedi Kshitij , Iamshchinina Polina , Graumann Monika , Lascelles Alex , Roig Gemma , Gifford Alessandro Thomas , Pan Bowen , Jin SouYoung , Ratan Murty N. Apurva , Kay Kendrick , Oliva Aude , Cichy Radoslaw
Published: March 2023

Studying the neural basis of human dynamic visual perception requires extensive experimental data to evaluate the large swathes of functionally diverse brain neural networks driven by perceiving visual events. Here, we introduce the BOLD Moments Dataset (BMD), a repository of whole-brain fMRI responses to over 1,000 short (3s) naturalistic video clips of visual events across ten human subjects. We use the videos’ extensive metadata to show how the brain represents word- and sentence-level descriptions of visual events and identify correlates of video memorability scores extending into the parietal cortex. Furthermore, we reveal a match in hierarchical processing between cortical regions of interest and video-computable deep neural networks, and we showcase that BMD successfully captures temporal dynamics of visual events at second resolution. With its rich metadata, BMD offers new perspectives and accelerates research on the human brain basis of visual event perception.
Manipulation of the nucleoscaffold potentiates cellular reprogramming kinetics
Authors: Yang Benjamin A. , da Rocha André Monteiro , Newton Isabel , Shcherbina Anna , Wong Sing-Wan , Fraczek Paula M. , Larouche Jacqueline A. , Hiraki Harrison L. , Baker Brendon M. , Shin Jae-Won , Takayama Shuichi , Thouless M. D. , Aguilar Carlos A.
Published: March 2023

Somatic cell fate is an outcome set by the activities of specific transcription factors and the chromatin landscape and is maintained by gene silencing of alternate cell fates through physical interactions with the nuclear scaffold. Here, we evaluate the role of the nuclear scaffold as a guardian of cell fate in human fibroblasts by comparing the effects of transient loss (knockdown) and mutation (progeria) of functional Lamin A/C, a core component of the nuclear scaffold. We observed that Lamin A/C deficiency or mutation disrupts nuclear morphology, heterochromatin levels, and increases access to DNA in lamina-associated domains. Changes in Lamin A/C were also found to impact the mechanical properties of the nucleus when measured by a microfluidic cellular squeezing device. We also show that transient loss of Lamin A/C accelerates the kinetics of cellular reprogramming to pluripotency through opening of previously silenced heterochromatin domains while genetic mutation of Lamin A/C into progerin induces a senescent phenotype that inhibits the induction of reprogramming genes. Our results highlight the physical role of the nuclear scaffold in safeguarding cellular fate.
A Bayesian model for genomic prediction using metabolic networks
Authors: Onogi Akio
Published: March 2023

Motivation

Genomic prediction is now an essential technique in breeding and medicine, and it is interesting to see how omics data can be used to improve prediction accuracy. Precedent work proposed a metabolic network-based method in biomass prediction of Arabidopsis; however, the method consists of multiple steps that possibly degrade prediction accuracy

Results

We proposed a Bayesian model that integrates all steps and jointly infers all fluxes of reactions related to biomass production. The proposed model showed higher accuracies than methods compared both in simulated and real data. The findings support the previous excellent idea that metabolic network information can be used for prediction.

Availability and implementation

All R and stan scripts to reproduce the results of this study are available athttps://github.com/Onogi/MetabolicModeling.

Contact

onogiakio@gmail.com

Supplementary information

This study provides no supplementary information
Length estimation of fish detected as non-occluded using a smartphone application and deep learning techniques
Authors: Shibata Yasutoki , Iwahara Yuka , Manano Masahiro , Kanaya Ayumi , Sone Ryota , Tamura Satoko , Kakuta Naoya , Nishino Tomoya , Ishihara Akira , Kugai Shungo
Published: March 2023

Uncertainty in stock assessment can be reduced if accurate and precise length composition of catch is available. Length data are usually manually collected, although this method is costly and time-consuming. Recently, some studies have estimated fish species and length from images using deep learning by installing camera systems in fishing vessels or a fish auction center. Once the deep learning model is properly trained, it does not require expensive and time-consuming manual labor. However, several previous studies have focused on monitoring fishing practices using an electronic monitoring system (EMS); therefore, it is necessary to solve many challenges, such as counting the total number of fish in the catch. In this study, we proposed a new deep learning-based method to estimate fish length using images. Species identification was not performed by the model, and images were taken manually by the measurers; however, length composition was obtained only for non-occluded fish detected by the model. A smartphone application was developed to calculate scale information (cm/pixel) from a known size fish box in fish images, and the Mask R-CNN (Region-based convolutional neural networks) model was trained using 76,161 fish to predict non-occluded fish. Two experiments were conducted to confirm whether the proposed method resulted in errors in the length composition. First, we manually measured the total length (TL) for each of the five fish categories and estimated the TL using deep learning and calculated the bias. Second, multiple fish in a fish box were photographed simultaneously, and the difference between the mean TL estimated from the non-occluded fish and the true TL from all fish was calculated. The results indicated that the biases of all five species categories were within ± 3%. Moreover, the difference was within ± 1.5% regardless of the number of fish in the fish box. In the proposed method, deep learning was used not to replace the measurer but to increase their measurement efficiency. The proposed method is expected to increase opportunities for the application of deep learning-based fish length estimation in areas of research that are different from the scope of conventional EMS.