Applying 3D Models of Giant Salamanders to Explore Form-function Relationships in Early Digit-bearing Tetrapods.

Extant salamanders are used as modern analogs of early digit-bearing tetrapods due to general similarities in morphology and ecology but the study species have been primarily terrestrial and relatively small when the earliest digit-bearing tetrapods were aquatic and an order of magnitude larger. Thus, we created a 3D computational model of underwater walking in extant Japanese giant salamanders (Andrias japonicus) using 3D photogrammetry and open-access graphics software (Blender) to broaden the range of testable hypotheses about the incipient stages of terrestrial locomotion. Our 3D model and software protocol represent the initial stages of an open-access pipeline that could serve as a "one-stop-shop" for studying locomotor function, from creating 3D models to analyzing the mechanics of locomotor gaits. While other pipelines generally require multiple software programs to accomplish the different steps in creating and analyzing computational models of locomotion, our protocol is built entirely within Blender and fully customizable with its Python scripting so users can devote more time to creating and analyzing models instead of navigating the learning curves of several software programs. The main value of our approach is that key kinematic variables (e.g., speed, stride length, elbow flexion) can be easily altered on the 3D model, allowing scientists to test hypotheses about locomotor function and conduct manipulative experiments (e.g., lengthening bones) that are difficult to perform in vivo. The accurate 3D meshes (and animations) generated through photogrammetry also provide exciting opportunities to expand the abundance and diversity of 3D digital animals available for researchers, educators, artists, conservation biologists, etc. to maximize societal impacts.

Cellular senescence in the pathogenesis of pulmonary arterial hypertension: the good, the bad and the uncertain.

Senescence refers to a cellular state marked by irreversible cell cycle arrest and the secretion of pro-inflammatory and tissue-remodeling factors. The senescence associated secretory phenotype (SASP) impacts the tissue microenvironment and provides cues for the immune system to eliminate senescent cells (SCs). Cellular senescence has a dual nature; it can be beneficial during embryonic development, tissue repair, and tumor suppression, but it can also be detrimental in the context of chronic stress, persistent tissue injury, together with an impairment in SC clearance. Recently, the accumulation of SCs has been implicated in the pathogenesis of pulmonary arterial hypertension (PAH), a progressive condition affecting the pre-capillary pulmonary arterial bed. PAH is characterized by endothelial cell (EC) injury, inflammation, and proliferative arterial remodeling, which leads to right heart failure and premature mortality. While vasodilator therapies can improve symptoms, there are currently no approved treatments capable of reversing the obliterative arterial remodeling. Ongoing endothelial injury and dysfunction is central to the development of PAH, perpetuated by hemodynamic perturbation leading to pathological intimal shear stress. The precise role of senescent ECs in PAH remains unclear. Cellular senescence may facilitate endothelial repair, particularly in the early stages of disease. However, in more advanced disease the accumulation of senescent ECs may promote vascular inflammation and occlusive arterial remodeling. In this review, we will examine the evidence that supports a role of endothelial cell senescence to the pathogenesis of PAH. Furthermore, we will compare and discuss the apparent contradictory outcomes with the use of interventions targeting cellular senescence in the context of experimental models of pulmonary hypertension. Finally, we will attempt to propose a framework for the understanding of the complex interplay between EC injury, senescence, inflammation and arterial remodeling, which can guide further research in this area and the development of effective therapeutic strategies.

Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.

Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.

Key quality parameter comparison of mesenchymal stem cell product cryopreserved in different cryopreservation solutions for clinical applications.

Introduction: Cryopreservation is a critical process of cell products for achieving a commercial viability through wide scale adoption. By preserving cells in a lower temperature, cryopreservation enables a product to be off-the-shelf and ready for infusion. An optimized cryopreservation strategy can maintain the viability, phenotype, and potency of thawed mesenchymal stromal/stem cells (MSCs) while being regulatory compliant. We compared three clinical-ready formulations with one research cryopreservation solutions and evaluated key quality parameters of post thawed MSCs. Method and result: MSCs were cryopreserved at 3, 6, and 9 million cells/mL (M/mL) in four different cryopreservation solutions: NutriFreez (10% dimethyl sulfoxide [DMSO]), Plasmalyte A (PLA)/5% human albumin (HA)/10% DMSO (PHD10), CryoStor CS5 (5% DMSO), and CryoStor CS10 (10% DMSO). To establish post thaw viability, cells were evaluated with no dilution of DMSO (from 3 M/mL), 1:1 dilution (from 6 M/mL), or 1:2 dilution (from 9 M/mL) with PLA/5% HA, to achieve uniform concentration at 3 M/mL. Cell viability was measured at 0-, 2-, 4-, and 6-h post thaw with Trypan blue exclusion and Annexin V/PI staining. Dilution (1:2) of final cell products from 9M/mL resulted in an improvement of cell viability over 6 h but showed a trend of decreased recovery. MSCs cryopreserved in solutions with 10% DMSO displayed comparable viabilities and recoveries up to 6 h after thawing, whereas a decreasing trend was noted in cell viability and recovery with CS5. Cells from all groups exhibited surface marker characteristics of MSCs. We further evaluated cell proliferation after 6-day recovery in culture. While cells cryopreserved in NutriFreez and PHD10 presented similar cell growth post thaw, MSCs cryopreserved in CS5 and CS10 at 3 M/mL and 6M/mL showed 10-fold less proliferative capacity. No significant differences were observed between MSCs cryopreserved in NutriFreez and PHD10 in their potency to inhibit T cell proliferation and improve monocytic phagocytosis. Conclusion: MSCs can be cryopreserved up to 9 M/mL without losing notable viability and recovery, while exhibiting comparable post thaw potency with NutriFreez and PHD10. These results highlight the importance of key parameter testing for selecting the optimal cryopreservation solution for MSC-based therapy.

Multilocus sequence typing of pathogenic treponemes isolated from contagious ovine digital dermatitis stage five lesions: Implications for disease transmission dynamics.

Contagious ovine digital dermatitis (CODD) causes a severe, infectious foot disease and lameness of sheep, is common within the UK and is now also emerging in other countries. As well as causing severe animal welfare issues, huge economic losses emerge from the disease due to weight loss/lack of weight gain, and veterinary treatments. CODD lesion progress is measured, with a scoring system from 1 (early lesions) to 5 (healed). Here, using samples from an experimental flock infected by natural means, samples were taken from CODD stage 5 lesions, post treatment, and subjected to bacterial isolation and MLST using previously published methods. Sequences were compared to others from the same flock, and those from previous studies. All CODD 5 lesions produced viable Treponema spp. bacteria. High levels of variation of bacteria were seen, with 12 sequence types (STs) for T. medium phylogroup (11 new), 15 STs for T. phagedenis phylogroup (9 new) and six T. pedis STs, of which two were new. This study shows that CODD stage 5 lesions still contain viable bacteria, representing all three known pathogenic Treponema spp. phylogroups, and these may thus play a role in disease transmission and epidemiology despite appearing healed after treatment. The high level CODD treponeme variability within an infected flock where sheep were bought from different sources, as might occur in common agricultural practice, may suggest reasons as to why the bacterial disease is difficult to treat, control and eradicate, and adds further complexity to the polybacterial pathogenesis of these lesions.

A new interpretation of Pikaia reveals the origins of the chordate body plan.

Our understanding of the evolutionary origin of Chordata, one of the most disparate and ecologically significant animal phyla, is hindered by a lack of unambiguous stem-group relatives. Problematic Cambrian fossils that have been considered as candidate chordates include vetulicolians,1Yunnanozoon,2 and the iconic Pikaia.3 However, their phylogenetic placement has remained poorly constrained, impeding reconstructions of character evolution along the chordate stem lineage. Here we reinterpret the morphology of Pikaia, providing evidence for a gut canal and, crucially, a dorsal nerve cord-a robust chordate synapomorphy. The identification of these structures underpins a new anatomical model of Pikaia that shows that this fossil was previously interpreted upside down. We reveal a myomere configuration intermediate between amphioxus and vertebrates and establish morphological links between Yunnanozoon, Pikaia, and uncontroversial chordates. In this light, we perform a new phylogenetic analysis, using a revised, comprehensive deuterostome dataset, and establish a chordate stem lineage. We resolve vetulicolians as a paraphyletic group comprising the earliest diverging stem chordates, subtending a grade of more derived stem-group chordates comprising Yunnanozoon and Pikaia. Our phylogenetic results reveal the stepwise acquisition of characters diagnostic of the chordate crown group. In addition, they chart a phase in early chordate evolution defined by the gradual integration of the pharyngeal region with a segmented axial musculature, supporting classical evolutionary-developmental hypotheses of chordate origins4 and revealing a "lost chapter" in the history of the phylum.

Increasing control over biomineralization in conodont evolution.

Vertebrates use the phosphate mineral apatite in their skeletons, which allowed them to develop tissues such as enamel, characterized by an outstanding combination of hardness and elasticity. It has been hypothesized that the evolution of the earliest vertebrate skeletal tissues, found in the teeth of the extinct group of conodonts, was driven by adaptation to dental function. We test this hypothesis quantitatively and demonstrate that the crystallographic order increased throughout the early evolution of conodont teeth in parallel with morphological adaptation to food processing. With the c-axes of apatite crystals oriented perpendicular to the functional feeding surfaces, the strongest resistance to uniaxial compressional stress is conferred along the long axes of denticles. Our results support increasing control over biomineralization in the first skeletonized vertebrates and allow us to test models of functional morphology and material properties across conodont dental diversity.

Public transit mobility as a leading indicator of COVID-19 transmission in 40 cities during the first wave of the pandemic.

Background: The rapid global emergence of the COVID-19 pandemic in early 2020 created urgent demand for leading indicators to track the spread of the virus and assess the consequences of public health measures designed to limit transmission. Public transit mobility, which has been shown to be responsive to previous societal disruptions such as disease outbreaks and terrorist attacks, emerged as an early candidate. Methods: We conducted a longitudinal ecological study of the association between public transit mobility reductions and COVID-19 transmission using publicly available data from a public transit app in 40 global cities from March 16 to April 12, 2020. Multilevel linear regression models were used to estimate the association between COVID-19 transmission and the value of the mobility index 2 weeks prior using two different outcome measures: weekly case ratio and effective reproduction number. Results: Over the course of March 2020, median public transit mobility, measured by the volume of trips planned in the app, dropped from 100% (first quartile (Q1)-third quartile (Q3) = 94-108%) of typical usage to 10% (Q1-Q3 = 6-15%). Mobility was strongly associated with COVID-19 transmission 2 weeks later: a 10% decline in mobility was associated with a 12.3% decrease in the weekly case ratio (exp(ß) = 0.877; 95% confidence interval (CI): [0.859-0.896]) and a decrease in the effective reproduction number (ß = -0.058; 95% CI: [-0.068 to -0.048]). The mobility-only models explained nearly 60% of variance in the data for both outcomes. The adjustment for epidemic timing attenuated the associations between mobility and subsequent COVID-19 transmission but only slightly increased the variance explained by the models. Discussion: Our analysis demonstrated the value of public transit mobility as a leading indicator of COVID-19 transmission during the first wave of the pandemic in 40 global cities, at a time when few such indicators were available. Factors such as persistently depressed demand for public transit since the onset of the pandemic limit the ongoing utility of a mobility index based on public transit usage. This study illustrates an innovative use of "big data" from industry to inform the response to a global pandemic, providing support for future collaborations aimed at important public health challenges.

Dormant origin firing promotes head-on transcription-replication conflicts at transcription termination sites in response to BRCA2 deficiency.

BRCA2 is a tumor suppressor protein responsible for safeguarding the cellular genome from replication stress and genotoxicity, but the specific mechanism(s) by which this is achieved to prevent early oncogenesis remains unclear. Here, we provide evidence that BRCA2 acts as a critical suppressor of head-on transcription-replication conflicts (HO-TRCs). Using Okazaki-fragment sequencing (Ok-seq) and computational analysis, we identified origins (dormant origins) that are activated near the transcription termination sites (TTS) of highly expressed, long genes in response to replication stress. Dormant origins are a source for HO-TRCs, and drug treatments that inhibit dormant origin firing led to a reduction in HO-TRCs, R-loop formation, and DNA damage. Using super-resolution microscopy, we showed that HO-TRC events track with elongating RNA polymerase II, but not with transcription initiation. Importantly, RNase H2 is recruited to sites of HO-TRCs in a BRCA2-dependent manner to help alleviate toxic R-loops associated with HO-TRCs. Collectively, our results provide a mechanistic basis for how BRCA2 shields against genomic instability by preventing HO-TRCs through both direct and indirect means occurring at predetermined genomic sites based on the pre-cancer transcriptome.

The exciting potential and daunting challenge of using GPS human-mobility data for epidemic modeling.

Large-scale GPS location datasets hold immense potential for measuring human mobility and interpersonal contact, both of which are essential for data-driven epidemiology. However, despite their potential and widespread adoption during the COVID-19 pandemic, there are several challenges with these data that raise concerns regarding the validity and robustness of its applications. Here we outline two types of challenges-some related to accessing and processing these data, and some related to data quality-and propose several research directions to address them moving forward.

Misunderstanding the harms of online misinformation.

The controversy over online misinformation and social media has opened a gap between public discourse and scientific research. Public intellectuals and journalists frequently make sweeping claims about the effects of exposure to false content online that are inconsistent with much of the current empirical evidence. Here we identify three common misperceptions: that average exposure to problematic content is high, that algorithms are largely responsible for this exposure and that social media is a primary cause of broader social problems such as polarization. In our review of behavioural science research on online misinformation, we document a pattern of low exposure to false and inflammatory content that is concentrated among a narrow fringe with strong motivations to seek out such information. In response, we recommend holding platforms accountable for facilitating exposure to false and extreme content in the tails of the distribution, where consumption is highest and the risk of real-world harm is greatest. We also call for increased platform transparency, including collaborations with outside researchers, to better evaluate the effects of online misinformation and the most effective responses to it. Taking these steps is especially important outside the USA and Western Europe, where research and data are scant and harms may be more severe.

Domain general frontoparietal regions show modality-dependent coding of auditory and visual rules.

A defining feature of human cognition is our ability to respond flexibly to what we see and hear, changing how we respond depending on our current goals. In fact, we can rapidly associate almost any input stimulus with any arbitrary behavioural response. This remarkable ability is thought to depend on a frontoparietal "multiple demand" circuit which is engaged by many types of cognitive demand and widely referred to as domain general. However, it is not clear how responses to multiple input modalities are structured within this system. Domain generality could be achieved by holding information in an abstract form that generalises over input modality, or in a modality-tagged form, which uses similar resources but produces unique codes to represent the information in each modality. We used a stimulus-response task, with conceptually identical rules in two sensory modalities (visual and auditory), to distinguish between these possibilities. Multivariate decoding of functional magnetic resonance imaging data showed that representations of visual and auditory rules recruited overlapping neural resources but were expressed in modality-tagged non-generalisable neural codes. Our data suggest that this frontoparietal system may draw on the same or similar resources to solve multiple tasks, but does not create modality-general representations of task rules, even when those rules are conceptually identical between domains.

In transfusion-dependent, angiodysplasia-related anemia, adding octreotide to usual care reduced transfusions at 1 y.

SOURCE CITATION: Goltstein LC, Grooteman KV, Bernts LH, et al. Standard of care versus octreotide in angiodysplasia-related bleeding (the OCEAN study): a multicenter randomized controlled trial. Gastroenterology. 2024;166:690-703. 38158089.

Spontaneous Intragastric Balloon Hyperinflation: Two Cases and Outcomes.

Endoscopic bariatric therapies can provide treatment options for obesity in non-surgical candidates, as a part of combination or serial treatment plans, and for the reduction of obesity-related comorbidities. Several complications of intragastric balloons have been documented, but spontaneous hyperinflation is a risk that has not been well reported previously. We describe two cases of spontaneous intragastric balloon hyperinflation and their outcomes.

Deciphering complexity in Pd-catalyzed cross-couplings.

Understanding complex reaction systems is critical in chemistry. While synthetic methods for selective formation of products are sought after, oftentimes it is the full reaction signature, i.e., complete profile of products/side-products, that informs mechanistic rationale and accelerates discovery chemistry. Here, we report a methodology using high-throughput experimentation and multivariate data analysis to examine the full signature of one of the most complicated chemical reactions catalyzed by palladium known in the chemical literature. A model Pd-catalyzed reaction was selected involving functionalization of 2-bromo-N-phenylbenzamide and multiple bond activation pathways. Principal component analysis, correspondence analysis and heatmaps with hierarchical clustering reveal the factors contributing to the variance in product distributions and show associations between solvents and reaction products. Using robust data from experiments performed with eight solvents, for four different reaction times at five different temperatures, we correlate side-products to a major dominant N-phenyl phenanthridinone product, and many other side products.

Quantifying the impact of misinformation and vaccine-skeptical content on Facebook.

Low uptake of the COVID-19 vaccine in the US has been widely attributed to social media misinformation. To evaluate this claim, we introduce a framework combining lab experiments (total N = 18,725), crowdsourcing, and machine learning to estimate the causal effect of 13,206 vaccine-related URLs on the vaccination intentions of US Facebook users (N ≈ 233 million). We estimate that the impact of unflagged content that nonetheless encouraged vaccine skepticism was 46-fold greater than that of misinformation flagged by fact-checkers. Although misinformation reduced predicted vaccination intentions significantly more than unflagged vaccine content when viewed, Facebook users' exposure to flagged content was limited. In contrast, unflagged stories highlighting rare deaths after vaccination were among Facebook's most-viewed stories. Our work emphasizes the need to scrutinize factually accurate but potentially misleading content in addition to outright falsehoods.

Single-Cell RNA Sequencing Reveals Repair Features of Human Umbilical Cord Mesenchymal Stromal Cells.

RATIONALE: The chronic lung disease bronchopulmonary dysplasia (BPD) is the most severe complication of extreme prematurity. BPD results in impaired lung alveolar and vascular development and long-term respiratory morbidity, for which only supportive therapies exist. Umbilical cord-derived mesenchymal stromal cells (UC-MSCs) improve lung structure and function in experimental BPD. Results of clinical trials with MSCs for many disorders do not yet match the promising preclinical studies. A lack of specific criteria to define functionally distinct MSCs persists. OBJECTIVES: To determine and correlate single-cell UC-MSC transcriptomic profile with therapeutic potential. METHODS: UC-MSCs from five term donors and human neonatal dermal fibroblasts (HNDFs, control cells of mesenchymal origin) transcriptomes were investigated by single-cell RNA sequencing analysis (scRNA-seq). The lung-protective effect of UC-MSCs with a distinct transcriptome and control HNDFs was tested in vivo in hyperoxia-induced neonatal lung injury in rats. MEASUREMENTS AND MAIN RESULTS: UC-MSCs showed limited transcriptomic heterogeneity, but were different from HNDFs. Gene ontology enrichment analysis revealed distinct - progenitor-like and fibroblast-like - UC-MSC subpopulations. Only the treatment with progenitor-like UC-MSCs improved lung function and structure and attenuated pulmonary hypertension in hyperoxia-exposed rat pups. Moreover, scRNA-seq identified major histocompatibility complex class I as a molecular marker of non-therapeutic cells and associated with decreased lung retention. CONCLUSIONS: UC-MSCs with a progenitor-like transcriptome, but not with a fibroblast-like transcriptome, provide lung protection in experimental BPD. High expression of major histocompatibility complex class I is associated with reduced therapeutic benefit. scRNA-seq may be useful to identify subsets of MSCs with superior repair capacity for clinical application.

Minimally invasive anterior cervical foraminotomy for unilateral radiculopathy.

Anterior cervical foraminotomy (ACF) is an alternative surgical option for the treatment of refractory unilateral radiculopathy due to disc herniation or spondylosis. The efficacy and adverse event rate in experienced practitioners are comparable to those of anterior cervical discectomy and fusion, total disc arthroplasty, and posterior foraminotomy. However, this technique has not been widely adopted, likely because of the proximity of the working zone and the vertebral artery. The authors present a detailed operative video of a patient successfully treated with an ACF. They also present a review of the ACF literature. The video can be found here: https://stream.cadmore.media/r10.3171/2024.1.FOCVID23196.

High-Density, Conformable Conducting Polymer-Based Implantable Neural Probes for the Developing Brain.

Neurologic and neuropsychiatric disorders substantially impact the pediatric population, but there is a lack of dedicated devices for monitoring the developing brain in animal models, leading to gaps in mechanistic understanding of how brain functions emerge and their disruption in disease states. Due to the small size, fragility, and high water content of immature neural tissue, as well as the absence of a hardened skull to mechanically support rigid devices, conventional neural interface devices are poorly suited to acquire brain signals without inducing damage. Here, the authors design conformable, implantable, conducting polymer-based probes (NeuroShanks) for precise targeting in the developing mouse brain without the need for skull-attached, rigid mechanical support structures. These probes enable the acquisition of high spatiotemporal resolution neurophysiologic activity from superficial and deep brain regions across unanesthetized behavioral states without causing tissue disruption or device failure. Once implanted, probes are mechanically stable and permit precise, stable signal monitoring at the level of the local field potential and individual action potentials. These results support the translational potential of such devices for clinically indicated neurophysiologic recording in pediatric patients. Additionally, the role of organic bioelectronics as an enabling technology to address questions in developmental neuroscience is revealed.