Miracle-dz/UniFAR-FTUs huggingface dataset:
Filopodia are dispensable for endothelial tip cell guidance

Actin filaments are instrumental in driving processes such as migration, cytokinesis and endocytosis and provide cells with mechanical support. During angiogenesis, actin-rich filopodia protrusions have been proposed to drive endothelial tip cell functions by translating guidance cues into directional migration and mediating new contacts during anastomosis. To investigate the structural organisation, dynamics and functional importance of F-actin in endothelial cells (ECs) during angiogenesis in vivo, we generated a transgenic zebrafish line expressing Lifeact-EGFP in ECs. Live imaging identifies dynamic and transient F-actin-based structures, such as filopodia, contractile ring and cell cortex, and more persistent F-actin-based structures, such as cell junctions. For functional analysis, we used low concentrations of Latrunculin B that preferentially inhibited F-actin polymerisation in filopodia. In the absence of filopodia, ECs continued to migrate, albeit at reduced velocity. Detailed morphological analysis reveals that ECs generate lamellipodia that are sufficient to drive EC migration when filopodia formation is inhibited. Vessel guidance continues unperturbed during intersegmental vessel development in the absence of filopodia. Additionally, hypersprouting induced by loss of Dll4 and attraction of aberrant vessels towards ectopic sources of Vegfa165 can occur in the absence of endothelial filopodia protrusion. These results reveal that the induction of tip cells and the integration of endothelial guidance cues do not require filopodia. Anastomosis, however, shows regional variations in filopodia requirement, suggesting that ECs might rely on different protrusive structures depending on the nature of the environment or of angiogenic cues.
FGF signaling sustains the odontogenic fate of dental mesenchyme by suppressing β-catenin signaling

Odontoblasts and osteoblasts develop from multipotent craniofacial neural crest cells during tooth and jawbone development, but the mechanisms that specify and sustain their respective fates remain largely unknown. In this study we used early mouse molar and incisor tooth germs that possess distinct tooth-forming capability after dissociation and reaggregation in vitro to investigate the mechanism that sustains odontogenic fate of dental mesenchyme during tooth development. We found that after dissociation and reaggregation, incisor, but not molar, mesenchyme exhibits a strong osteogenic potency associated with robustly elevated β-catenin signaling activity in a cell-autonomous manner, leading to failed tooth formation in the reaggregates. Application of FGF3 to incisor reaggregates inhibits β-catenin signaling activity and rescues tooth formation. The lack of FGF retention on the cell surface of incisor mesenchyme appears to account for the differential osteogenic potency between incisor and molar, which can be further attributed to the differential expression of syndecan 1 and NDST genes. We further demonstrate that FGF signaling inhibits intracellular β-catenin signaling by activating the PI3K/Akt pathway to regulate the subcellular localization of active GSK3β in dental mesenchymal cells. Our results reveal a novel function for FGF signaling in ensuring the proper fate of dental mesenchyme by regulating β-catenin signaling activity during tooth development.
Medical and Biological Physics.

One year of college physics is usually sufficient to satisfy the physics prerequisites of the admission offices of most medical schools in the United States. As a result, the beginning resident in radiology, surgery, anesthesiology, or other disciplines concerned with basic physical principles is often faced with the consideration of fairly sophisticated physical concepts with no more background than a course in sophomore physics taken perhaps seven years previously. This apparently is not true in the University of Queensland. This text, which attempts to present a general survey of physics which would have relevance to biophysics, was originally written for medical students at that university. Not only is this idea commendable but, in my opinion, may soon become a necessity. In the present era of patient monitoring, automated prosthetic devices, computer processing of clinical data, artificial organs, radioisotopes, and ultrasonics, all represent techniques of physics applied not to research but
Tethering Recombination Initiation Proteins in Saccharomyces cerevisiae Promotes Double Strand Break Formation

Meiotic recombination in Saccharomyces cerevisiae is initiated by the creation of DNA double strand breaks (DSBs), an event requiring 10 recombination initiation proteins. Published data indicate that these 10 proteins form three main interaction subgroups [(Spo11-Rec102-Rec104-Ski8), (Rec114-Rec107-Mei4), and (Mre11-Rad50-Xrs2)], but certain components from each subgroup may also interact. Although several of the protein–protein interactions have been defined, the mechanism for DSB formation has been challenging to define. Using a variation of the approach pioneered by others, we have tethered 8 of the 10 initiation proteins to a recombination coldspot and discovered that in addition to Spo11, 6 others (Rec102, Rec104, Ski8, Rec114, Rec107, and Mei4) promote DSB formation at the coldspot, albeit with different frequencies. Of the 8 proteins tested, only Mre11 was unable to cause DSBs even though it binds to UASGAL at GAL2. Our results suggest there may be several ways that the recombination initiation proteins can associate to form a functional initiation complex that can create DSBs.
A conserved role for non-neural ectoderm cells in early neural development

During the early steps of head development, ectodermal patterning leads to the emergence of distinct non-neural and neural progenitor cells. The induction of the preplacodal ectoderm and the neural crest depends on well-studied signalling interactions between the non-neural ectoderm fated to become epidermis and the prospective neural plate. By contrast, the involvement of the non-neural ectoderm in the morphogenetic events leading to the development and patterning of the central nervous system has been studied less extensively. Here, we show that the removal of the rostral non-neural ectoderm abutting the prospective neural plate at late gastrulation stage leads, in mouse and chick embryos, to morphological defects in forebrain and craniofacial tissues. In particular, this ablation compromises the development of the telencephalon without affecting that of the diencephalon. Further investigations of ablated mouse embryos established that signalling centres crucial for forebrain regionalization, namely the axial mesendoderm and the anterior neural ridge, form normally. Moreover, changes in cell death or cell proliferation could not explain the specific loss of telencephalic tissue. Finally, we provide evidence that the removal of rostral tissues triggers misregulation of the BMP, WNT and FGF signalling pathways that may affect telencephalon development. This study opens new perspectives on the role of the neural/non-neural interface and reveals its functional relevance across higher vertebrates.
Regulation of ECM degradation and axon guidance by growth cone invadosomes

Invadopodia and podosomes, collectively referred to as invadosomes, are F-actin-rich basal protrusions of cells that provide sites of attachment to and degradation of the extracellular matrix. Invadosomes promote the invasion of cells, ranging from metastatic cancer cells to immune cells, into tissue. Here, we show that neuronal growth cones form protrusions that share molecular, structural and functional characteristics of invadosomes. Growth cones from all neuron types and species examined, including a variety of human neurons, form invadosomes both in vitro and in vivo. Growth cone invadosomes contain dynamic F-actin and several actin regulatory proteins, as well as Tks5 and matrix metalloproteinases, which locally degrade the matrix. When viewed using three-dimensional super-resolution microscopy, F-actin foci often extended together with microtubules within orthogonal protrusions emanating from the growth cone central domain. Finally, inhibiting the function of Tks5 both reduced matrix degradation in vitro and disrupted motoneuron axons from exiting the spinal cord and extending into the periphery. Taken together, our results suggest that growth cones use invadosomes to target protease activity during axon guidance through tissues. Highlighted article: Growth cones from multiple neuronal types form F-actin-rich protrusions called invadosomes, which are necessary for axonal growth as motor neurons exit the spinal cord.
A Robust and Powerful Set-Valued Approach to Rare Variant Association Analyses of Secondary Traits in Case-Control Sequencing Studies

In many case-control designs of genome-wide association (GWAS) or next generation sequencing (NGS) studies, extensive data on secondary traits that may correlate and share the common genetic variants with the primary disease are available. Investigating these secondary traits can provide critical insights into the disease etiology or pathology, and enhance the GWAS or NGS results. Methods based on logistic regression (LG) were developed for this purpose. However, for the identification of rare variants (RVs), certain inadequacies in the LG models and algorithmic instability can cause severely inflated type I error, and significant loss of power, when the two traits are correlated and the RV is associated with the disease, especially at stringent significance levels. To address this issue, we propose a novel set-valued (SV) method that models a binary trait by dichotomization of an underlying continuous variable, and incorporate this into the genetic association model as a critical component. Extensive simulations and an analysis of seven secondary traits in a GWAS of benign ethnic neutropenia show that the SV method consistently controls type I error well at stringent significance levels, has larger power than the LG-based methods, and is robust in performance to effect pattern of the genetic variant (risk or protective), rare or common variants, rare or common diseases, and trait distributions. Because of the SV method’s striking and profound advantage, we strongly recommend the SV method be employed instead of the LG-based methods for secondary traits analyses in case-control sequencing studies.
To Break or Not To Break: Sex Chromosome Hemizygosity During Meiosis in Caenorhabditis

Meiotic recombination establishes connections between homologous chromosomes to promote segregation. Hemizygous regions of sex chromosomes have no homologous chromosome to recombine with, yet must be transmitted through meiosis. An extreme case of hemizygosity exists in the genus Caenorhabditis, where males have a single X chromosome that completely lacks a homologous partner. To determine whether similar strategies have evolved to accommodate hemizygosity of the X during male meiosis in Caenorhabditis with distinct modes of sexual reproduction, we examined induction and processing of meiotic double strand breaks (DSBs) in androdioecious (hermaphrodite/male) Caenorhabditis elegans and C. briggsae, and gonochoristic (female/male) C. remanei and C. brenneri. Analysis of the recombinase RAD-51 suggests more meiotic DSBs are induced in gonochoristic vs. androdioecious species. However, in late prophase in all species, chromosome pairs are restructured into bivalents around a single axis, suggesting that the holocentric nature of Caenorhabditis chromosomes dictates a single crossover per bivalent regardless of the number of DSBs induced. Interestingly, RAD-51 foci were readily observed on the X chromosome of androdioecious male germ cells, while very few were detected in gonochoristic male germ cells. As in C. elegans, the X chromosome in C. briggsae male germ cells undergoes transient pseudosynapsis and flexibility in DSB repair pathway choice. In contrast, in C. remanei and C. brenneri male germ cells, the X chromosome does not undergo pseudosynapsis and appears refractory to SPO-11-induced breaks. Together our results suggest that distinct strategies have evolved to accommodate sex chromosome hemizygosity during meiosis in closely related Caenorhabditis species.
Avian haemosporidians in the cattle egret (Bubulcus ibis) from central-western and southern Africa: High diversity and prevalence

We described the geographic distribution of 82 haemosporidian lineages (Plasmodium, Haemoproteus, and Leucocytozoon) in the cattle egret sampled in five countries in central-western and southern Africa. Seventy-three lineages have not previously been reported. We determined the prevalence of three haemosporidians in the samples. We investigated the influence of the internal environment of the host and environmental variables on the Plasmodium diversity and whether environmental variables may explain spatial variations in the prevalence of Plasmodium. We screened DNA from 509 blood samples from nestlings in 15 African colonies for infection by sequencing the cytochrome b gene of parasites. The molecular phylogenetic analysis was performed using Bayesian methods and including sequences from the MalAvi and GeneBank databases. We found 62 new Plasmodium lineages in a clade with MYCAME02, which is a lineage described in waterbirds and recently identified in birds of prey as Plasmodium paranucleophilum. Two Haemoproteus lineages identified in cattle egret formed a distinct group with Haemoproteus catharti and MYCAMH1 (Haemoproteus spp.). Seven Leucocytozoon lineages found in the cattle egret clustered with Leucocytozoon californicus. We found different Plasmodium diversities among the colonies sampled, demonstrating that the internal environment of the host is not the primary determinant of diversity. A linear mixed-effects multivariate model showed that precipitation was positively associated with Plasmodium diversity when controlling for the effects of temperature, colony composition (mixed and non-mixed species) and country. Moreover, a generalized mixed model showed that temperature was positively associated with the prevalence of Plasmodium when controlling for precipitation, elevation and country. We conclude that the cattle egret is a good model for future haemosporidian studies, as we found a significant number of new lineages in this host, which occupies regions with different climate characteristics where environmental variables exert an influence on the diversity and prevalence of Plasmodium.
Repository of Enriched Structures of Proteins Involved in the Red Blood Cell Environment (RESPIRE)

The Red Blood Cell (RBC) is a metabolically-driven cell vital for processes such a gas transport and homeostasis. RBC possesses at its surface exposing antigens proteins that are critical in blood transfusion. Due to their importance, numerous studies address the cell function as a whole but more and more details of RBC structure and protein content are now studied using massive state-of-the art characterisation techniques. Yet, the resulting information is frequently scattered in many scientific articles, in many databases and specialized web servers. To provide a more compendious view of erythrocytes and of their protein content, we developed a dedicated database called RESPIRE that aims at gathering a comprehensive and coherent ensemble of information and data about proteins in RBC. This cell-driven database lists proteins found in erythrocytes. For a given protein entry, initial data are processed from external portals and enriched by using state-of-the-art bioinformatics methods. As structural information is extremely useful to understand protein function and predict the impact of mutations, a strong effort has been put on the prediction of protein structures with a special treatment for membrane proteins. Browsing the database is available through text search for reference gene names or protein identifiers, through pre-defined queries or via hyperlinks. The RESPIRE database provides valuable information and unique annotations that should be useful to a wide audience of biologists, clinicians and structural biologists. Database URL: http://www.dsimb. inserm.fr/respire
Effects of person-centered care at the organisational-level for people with dementia. A systematic review

The aim of the systematic review was to determine the effectiveness of organizational-level person-centered care for people living with dementia in relation to their quality of life, mood, neuropsychiatric symptoms and function. ALOIS, the Cochrane Dementia and Cognitive Improvement Group Specialised Register databases, were searched up to June 2018 using the terms dementia OR cognitive impairment OR Alzheimer AND non-pharmacological AND personhood OR person-centered care. Reviewed studies included randomized controlled trials (RCTs), cluster-randomized trials (CRTs) and quasi-experimental studies that compared outcomes of person-centered care and usual (non-person-centered) care, for people with a diagnosis of dementia. The search yielded 12 eligible studies with a total of 2599 people living with dementia in long-term care homes, 600 receiving hospital care and 293 living in extra-care community housing. Random-effects models were used to pool adjusted risk ratios and standard mean differences from all studies; the findings were assessed followed the PRISMA guidelines and GRADE criteria. Statistical heterogeneity was assessed using the I2 method and Chi2 P value; studies with low statistical heterogeneity were analyzed using a random-effects model with restricted maximum likelihood estimation in R. Analyses of pre/post data within 12 months identified: a significant effect for quality of life (standardized mean difference (SMD) 0.16 and 95% CI 0.03 to 0.28; studies = 6; I2 = 22%); non-significant effects for neuropsychiatric symptoms (SMD 0.06, 95% CI -0.08 to 0.19; studies = 4; I2 = 0%) and well-being (SMD 0.15, 95% CI -0.15 to 0.45; studies = 4; I2 = 77%); and no effects for agitation (SMD -0.05 (95% CI -0.17 to -0.07; studies 5; I2 = 0%) and depression (SMD -0.06 and 95% CI -0.27 to 0.15, studies = 5; I2 = 53%). The evidence from this review recommends implementation of person-centered care at the organizational-level to support the quality of life of people with living with dementia.
Myoinositol CEST signal in animals with increased Iba-1 levels in response to an inflammatory challenge—Preliminary findings

Neuroinflammation plays an important role in the pathogenesis of a range of brain disorders. Non-invasive imaging of neuroinflammation is critical to help improve our understanding of the underlying disease mechanisms, monitor therapies and guide drug development. Generally, MRI lacks specificity to molecular imaging biomarkers, but molecular MR imaging based on chemical exchange saturation transfer (CEST) can potentially detect changes of myoinositol, a putative glial marker that may index neuroinflammation. In this pilot study we aimed to investigate, through validation with immunohistochemistry and in vivo magnetic resonance spectroscopy (MRS), whether CEST imaging can reflect the microglial response to a mild inflammatory challenge with lipopolysaccharide (LPS), in the APPSwe/ PS1 mouse model of Alzheimer’s disease and wild type controls. The response to the immune challenge was variable and did not align with genotype. Animals with a strong response to LPS (Iba1+, n = 6) showed an increase in CEST contrast compared with those who did not (Iba1-, n = 6). Changes of myoinositol levels after LPS were not significant. We discuss the difficulties of this mild inflammatory model, the role of myoinositol as a glial biomarker, and the technical challenges of CEST imaging at 0.6ppm.
Fast Prototyping a Dialogue Comprehension System for Nurse-Patient Conversations on Symptom Monitoring

Data for human-human spoken dialogues for research and development are currently very limited in quantity, variety, and sources; such data are even scarcer in healthcare. In this work, we investigate fast prototyping of a dialogue comprehension system by leveraging on minimal nurse-to-patient conversations. We propose a framework inspired by nurse-initiated clinical symptom monitoring conversations to construct a simulated human-human dialogue dataset, embodying linguistic characteristics of spoken interactions like thinking aloud, self-contradiction, and topic drift. We then adopt an established bidirectional attention pointer network on this simulated dataset, achieving more than 80% F1 score on a held-out test set from real-world nurse-to-patient conversations. The ability to automatically comprehend conversations in the healthcare domain by exploiting only limited data has implications for improving clinical workflows through red flag symptom detection and triaging capabilities. We demonstrate the feasibility for efficient and effective extraction, retrieval and comprehension of symptom checking information discussed in multi-turn human-human spoken conversations.
Fast Video Retargeting Based on Seam Carving with Parental Labeling

Seam carving is a state-of-the-art content-aware image resizing technique that effectively preserves the salient areas of an image. However, when applied to video retargeting, not only is it time intensive, but it also creates highly visible frame-wise discontinuities. In this paper, we propose a novel video retargeting method based on seam carving. First, for a single frame, we locate and remove several seams instead of one seam at once. Second, we use a dynamic spatiotemporal buffer of energy maps and a standard deviation operator to carve out the same seams in a temporal cube of frames with low variation in energy. Last but not least, an improved energy function that considers motions detected through difference method is employed. During testing, these enhancements result in a 93 percent reduction in processing time and a higher frame-wise consistency, thus showing superior performance compared to existing video retargeting methods.
Penalizing Side Effects using Stepwise Relative Reachability

How can we design safe reinforcement learning agents that avoid unnecessary disruptions to their environment? We show that current approaches to penalizing side effects can introduce bad incentives, e.g. to prevent any irreversible changes in the environment, including the actions of other agents. To isolate the source of such undesirable incentives, we break down side effects penalties into two components: a baseline state and a measure of deviation from this baseline state. We argue that some of these incentives arise from the choice of baseline, and others arise from the choice of deviation measure. We introduce a new variant of the stepwise inaction baseline and a new deviation measure based on relative reachability of states. The combination of these design choices avoids the given undesirable incentives, while simpler baselines and the unreachability measure fail. We demonstrate this empirically by comparing different combinations of baseline and deviation measure choices on a set of gridworld experiments designed to illustrate possible bad incentives.
Efficient Video Scene Text Spotting: Unifying Detection, Tracking, and Recognition

This paper proposes an unified framework for efficiently spotting scene text in videos. The method localizes and tracks text in each frame, and recognizes each tracked text stream one-time. Specifically, we first train a spatial-temporal text detector for localizing text regions in the sequential frames. Secondly, a well-designed text tracker is trained for grouping the localized text regions into corresponding cropped text streams. To efficiently spot video text, we recognize each tracked text stream one-time with a text region quality scoring mechanism instead of identifying the cropped text regions one-by-one. Experiments on two public benchmarks demonstrate that our method achieves impressive performance.