bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exploring definitions of retention in care for people living with HIV in the United States in the modern treatment era
Authors: Lesko Catherine R. , Mugavero Michael J. , Shen Nicola M. , Fojo Anthony T. , Moore Richard D. , Keruly Jeanne C. , Cachay Edward R. , Napravnik Sonia , Mayer Kenneth H. , Christopoulos Katerina A. , Jacobson Jeffrey M. , Rebeiro Peter F. , Chander Geetanjali ,   for the CNICS
Published: June 2022

Objective:
To describe retention in HIV care based on various definitions of retention in the modern treatment era.

Design:
A cohort study of people enrolled in care at seven mostly urban HIV clinics across the United States, 2010–2018.

Methods:
We estimated retention based on missed visits, kept visits, kept encounters (clinical visits, CD4 counts, and viral loads), and HIV labs. We contrasted risk factors for retention by different definitions and estimated odds ratios for of viral suppression and hazard ratios for mortality in 2 years immediately following the year in which retention was defined (the study year).

Results:
Across 108 171 person-years (N = 21 481 people), in 71% of years people kept ≥75% of scheduled visits; in 78%, people kept ≥2 visits >90 days apart; in 74%, people had ≥2 HIV labs >90 days apart; and in 47%, people had no gaps >6 months in clinic visits. Missing >25% of scheduled visits despite attending ≥2 visits >90 days apart was associated with nonwhite non-Hispanic race/ethnicity, history of injection drug use, and prior AIDS diagnosis. In contrast, attending ≥75% of scheduled visits while not attending ≥2 visits >90 days apart was associated with male sex, white race, no injection drug use history, and no prior AIDS diagnosis. Subsequent viral nonsuppression was more strongly associated with missed- than kept-visit measures of retention; 2-year mortality was only associated with failure to be retained by missed-visit measures.

Discussion:
Missed and kept-visit definitions of retention capture different constructs. Missed-visit measures are more strongly associated with poor HIV outcomes.
Cognitive, Behavioural, Speech, Language and Developmental Outcomes Associated with Pathogenic Variants in the ERF Gene
Authors: Care Helen , Luscombe Carrie , Wall Steven A. , Dalton Louise , Johnson David , Wilkie Andrew O.M. 
Published: June 2022

Abstract:
Pathogenic variants of the ERF gene were previously associated with craniosynostosis, craniofacial dysmorphism and Chiari malformation. This study investigates cognitive, behavioural, speech, language, and developmental outcomes in the first 5 children identified at the Oxford Craniofacial Unit as having ERF-related craniosynostosis, together with three of their carrier parents.
There were no consistent findings related to overall intelligence. However, a pattern of cognitive difficulties is described, which includes poor attention, impulsivity and difficulties with functional fine motor skills, such as handwriting. A high frequency of speech, language and communication difficulties was evident, which was most often related to early language difficulties, speech sound difficulties, hyponasal resonance and concern regarding social communication skills and emotional immaturity.
It was common for these children to have needed input from ear, nose and throat services. Problems with tonsils and/or adenoids and/ or fluctuating conductive hearing loss were found which may be contributors to early speech, language and communication difficulties.
The authors make recommendations regarding the need for formal assessment of a range of developmental aspects upon diagnosis of a pathogenic variant in the ERF gene. The aim of this report is to give clinical guidance to anyone who may have care of patients with the ERF-related mutation.
Novel engineered chimeric engulfment receptors trigger T-cell effector functions against SIV infected CD4+ T cells
Authors: Corey Daniel , Haeseleer Francoise , Corey Lawrence 
Published: June 2022

ABSTRACTAdoptive therapy with genetically engineered T cells offers potential for infectious disease treatment in immunocompromised persons. HIV/simian immunodeficiency virus (SIV) infected cells express phosphatidylserine (PS) early post-infection. We tested whether chimeric engulfment receptor (CER) T cells designed to recognize PS-expressing cells could eliminate SIV infected cells. Lentiviral CER constructs comprised of the extracellular domain of T-cell immunoglobulin and mucin domain containing 4 (TIM-4), the PS receptor, and engulfment signaling domains were transduced into primary rhesus macaque (RM) T cells. We measured PS binding and T-cell engulfment of RM CD4+ T cells infected with SIV expressing GFP. As chimeric antigen receptor (CAR) T cells induce PS and subsequent TIM-4 binding, we evaluated in vitro killing of CAR and CER T-cell combinations. We found that recombinant TIM-4 bound to SIV infected cells. In vitro, CER CD4+ T cells effectively killed SIV infected cells, which was dependent on TIM-4 binding to PS. Enhanced killing of SIV infected CD4+ T cells by CER and CAR T-cell combinations was observed. This installation of innate immune functions into T cells presents an opportunity to enhance elimination of SIV infected cells and offers potential to augment functional cure of SIV/HIV infection.
Bone Surface Mapping: a new method for recording detailed human bone surface variation
Authors: Paris Sarah E. , Foley Robert A. 
Published: June 2022

AbstractThis paper presents a new method for mapping surface features on bone (e.g. presence and distribution of ochre, surface cuts and scratches, pathologies, etc.). It is an accessible and quantifiable alternative to photogrammetry or three-dimensional scanning. It breaks each bone down into a number of two-dimensional geometric faces that can be utilised in statistical analyses. The number of faces differs depending on the skeletal development of the individual, with children having fewer faces. The recording method allows faces to be grouped by anatomical plane, bone type, side, and region of the body. These selective groupings facilitate flexible categories for hypothesis testing. The technique was developed to enable a detailed recording of ochre staining on human skeletal remains from Khok Phanom Di, Thailand, used in conjunction with a novel recording method to quantify pigment use across the body, and some exemplary results are presented here. While the technique was developed for recording bone surface staining it could also be used to map other variations on bone surfaces, such as in palaeopathological, forensic or taphonomic contexts.
Self-paced treadmill controller algorithm based on position and speed of centre of mass
Authors: Mokhtarzzadeh Hossein , Richards Rosie , Geijtenbeek Thomas 
Published: June 2022

AbstractBackgroundSelf-paced treadmills are increasingly used in clinical and research settings. Using self-paced (SP) treadmills, researchers can simulate overground walking while participants can walk with different but comfortable gait speeds in a controlled environment. Several algorithms have been designed for self-paced treadmills based on data from force plates, motion capture, and even marker-less systems such as 3D depth cameras.MethodsWe present a non-linear controller that implements a self-paced algorithm integrated with treadmills. This algorithm uses the subject’s centre-of-mass (CoM) position and velocity, relative to the front and back end of the treadmill as inputs. The controller continuously adjusts the treadmill’s belt speed via belt acceleration. The algorithm attempts to prevent the subject reaching the front and back of treadmill via minimal treadmill acceleration.FindingsThis method has been safely used in previous studies with over 410 subjects in various populations. We simulated the use of the SP algorithm with three different sensitivities (0.2, 1 and 2). The belt speed predicted by algorithm simulation in matched well with the belt speeds of experiments in (Gait Realtime Analysis Interactive Lab (GRAIL) system.InterpretationThis algorithm is integrated with a VR environment in which the subject can be immersed and even be mechanically perturbed. Additionally, this algorithm can be implemented in other treadmills where CoM position is known. We encourage researchers to use and build upon our well-established SP algorithm toward a more standardized SP algorithm in different gait scenarios across various instrumented treadmills with different populations.
Combining Backpropagation with Equilibrium Propagation to improve an Actor-Critic RL framework
Authors: Kubo Yoshimasa , Chalmers Eric , Luczak Artur 
Published: June 2022

AbstractBackpropagation has been used to train neural networks for many years, allowing them to solve a wide variety of tasks like image classification, speech recognition, and reinforcement learning tasks. But the biological plausibility of backpropagation as a mechanism of neural learning has been questioned. Equilibrium Propagation (EP) has been proposed as a more biologically plausible alternative and achieves comparable accuracy on the CIFAR-10 image classification task. This study proposes the first EP-based reinforcement learning architecture: an actor-critic architecture with the actor network trained by EP. We show that this model can solve the basic control tasks often used as benchmarks for BP-based models. Interestingly, our trained model demonstrates more consistent high-reward behavior than a comparable model trained exclusively by backpropagation.
Spatial distribution and physicochemical properties of respirable volcanic ash from the 16-17 August 2006 Tungurahua eruption (Ecuador), and alveolar epithelium responsein-vitro
Authors: Eychenne Julia , Gurioli Lucia , Damby David , Belville Corinne , Schiavi Federica , Marceau Geoffroy , Szczepaniak Claire , Blavignac Christelle , Laumonier Mickael , Le Pennec Jean-Luc , Nedelec Jean-Marie , Blanchon Loïc , Sapin Vincent 
Published: June 2022

ABSTRACTBackgroundTungurahua volcano (Ecuador) intermittently emitted ash between 1999 and 2016, enduringly affecting the surrounding rural area and its population, but its health impact remains poorly documented.ObjectivesWe aim at assessing the respiratory health hazard posed by the 16-17 August 2006 most intense eruptive phase of Tungurahua.MethodsBased on detailed field surveys and grain size analyses, we mapped the spatial distribution of the health-relevant ash size fractions produced by the eruption in the area impacted by ash fallout. We used Scanning Electron Microscopy and Raman Spectroscopy to quantify the mineralogy, composition, surface texture and morphology of a respirable ash sample isolated by aerodynamic separation. The cytotoxicity and pro-inflammatory potential of this respirable ash towards lung tissues was assessedin-vitrousing A549 alveolar epithelial cells, by Electron Microscopy and biochemical assays (LDH assay, RT-qPCR, multiplex immunoassays).ResultsThe eruption produced a high amount of inhalable and respirable ash (12.0-0.04 kg/m2of sub-10 µm and 5.3-0.02 kg/m2of sub-4 µm ash deposited). Their abundance and proportion vary greatly across the deposit within the first 20 km from the volcano. The respirable ash is characteristic of an andesitic magma and no crystalline silica is detected. Morphological features and surface textures are complex and highly variable, with few fibres observed.In-vitroexperiments show that respirable volcanic ash are internalized by A549 cells and processed in the endosomal pathway, causing little cell damage, but some changes in cell morphology and membrane texture. The ash trigger a weak pro-inflammatory response.DiscussionThese data provide the first understanding of the respirable ash hazard near Tungurahua, and the extent to which it varies spatially in a fallout deposit. Given the long exposure duration of the surrounding population, the chronic effects of this inhalable, weakly bio-reactive ash on health could be further investigated.
Global epistasis and the emergence of ecological function
Authors: Diaz-Colunga Juan , Skwara Abigail , Vila Jean C. C. , Bajic Djordje , Sánchez Álvaro 
Published: June 2022

AbstractThe emergence of community functions is the result of a complex web of interactions between organisms and their environment. This complexity poses a significant obstacle in quantitatively predicting ecological function from the species-level composition of a community. In this study, we demonstrate that the collective impact of interspecies interactions leads to the emergence of simple linear models that predict ecological function. These predictive models mirror the patterns ofglobal epistasisreported in genetics, and they can be quantitatively interpreted in terms of pairwise ecological interactions between species. Our results illuminate an unexplored path to quantitatively linking the composition and function of ecological communities, bringing the tasks of predicting biological function at the genetic, organismal, and ecological scales under the same quantitative formalism.
Where does the rainbow end? A case study of self-sustaining rainbow troutOncorhynchus mykisspopulations in tropical rivers
Authors: Nevoux Marie , Marie Amandine D. , Raitif Julien , Baglinière Jean-Luc , Lorvelec Olivier , Roussel Jean-Marc 
Published: June 2022

ABSTRACTThe great physiological, behavioral and morphological plasticity of salmonids contributed to the success of their introduction into a wide range of habitats. However, rainbow trout (Oncorhynchus mykiss) is the only salmonid species to live in the tropics. Like for any cold-water species, water temperature is assumed to be a major constraint to the presence and expansion of rainbow trout. In this study, we collected detailed records of the introduction history of rainbow trout at 35 sites across the island over 80 years, and we document the presence of self-sustainable trout at each site. We explored the linear relationship between water temperature and elevation.
Geometric constraints within tripeptides and the existence of tripeptide reconstructions
Authors: O’Donnell Timothée , Agashe Viraj , Cazals Frédéric 
Published: June 2022

AbstractDesigning movesets providing high quality protein conformations remains a hard problem, especially when it comes to deform a long protein backbone segment, and a key building block to do so is the so-called tripeptide loop closure (TLC). Consider a tripeptide whose first and last segments (N1Cα;1andCα;3C3) are fixed, and so are all internal coordinates except the six {(ϕ,ψ)}i=1,2,3dihedral angles associated to the threeCαcarbons. Under these conditions, the TLC algorithm provides all possible values for these six dihedral angles–there exists at most 16 solutions. TLC moves atoms up to ~ 5Å in one step and retains low energy conformations, whence its pivotal role to design move sets sampling protein loop conformations.In this work, we relax the previous constraints, allowing the last segment (Cα;3C3) to freely move in 3D space–or equivalently in a 5D configuration space. We exhibit necessary geometric constraints in this 5D space for TLC to admit solutions. Our analysis provides key insights on the geometry of solutions for TLC. Most importantly, when using TLC to sample loop conformations based onmconsecutive tripeptides along a protein backbone, we obtain an exponential gain in the volume of the 5m-dimensional configuration space to be explored.
Supplementation in vitamin B3 counteracts the negative effects of tryptophan deficiencies in bumble bees
Authors: Tissier M.L , Kraus S. , Gómez-Moracho T. , Lihoreau M. 
Published: June 2022

AbstractIncreasing evidence highlights the importance of diet content in 9 essential amino acids for bee physiological and behavioral performance. However, the tenth essential amino acid, tryptophan, has been overlooked as its experimental measurement requires a specific hydrolysis. Tryptophan is the precursor of serotonin and vitamin B3, which together modulate cognitive and metabolic functions in most animals. Here, we investigated how tryptophan deficiencies influence the longevity and behavior of bumble bees. Tryptophan-deficient diets led to a moderate increase in food intake, aggressiveness and mortality compared to the control diet. Vitamin B3 supplementation in tryptophan-deficient diets tended to buffer these effects on food intake and survival, and significantly reduced workers aggressiveness. Considering that the pollens of major crops and common plants, such as corn and dandelion, are deficient in tryptophan, these effects could have a strong impact on bee populations and their pollination service.
RetroFun-RVS: a retrospective family-based framework for rare variant analysis incorporating functional annotations
Authors: Mangnier Loïc , Ruczinski Ingo , Ricard Jasmin , Moreau Claudia , Girard Simon , Maziade Michel , Bureau Alexandre 
Published: June 2022

AbstractA large proportion of genetic variations involved in complex diseases are rare and located within non-coding regions, making the interpretation of underlying biological mechanisms a daunting task. Although technical and methodological progresses have been made to annotate the genome, current disease - rare-variant association tests incorporating such annotations suffer from two major limitations. Firstly, they are generally restricted to case-control designs of unrelated individuals, which often require tens or hundreds of thousands of individuals to achieve sufficient power. Secondly, they were not evaluated with region-based annotations needed to interpret the causal regulatory mechanisms. In this work we propose RetroFun-RVS, a new retrospective family-based score test, incorporating functional annotations. One of the critical features of the proposed method is to aggregate genotypes while measuring rare variant sharing among affected family members to compute the test statistic. Through extensive simulations, we have demonstrated that RetroFun-RVS integrating networks based on 3D genome contacts as functional annotations reaches greater power over the region-wide test, other strategies to include sub-regions and competing methods. Also, the proposed framework shows robustness to non-informative annotations, keeping a stable power when causal variants are spread across regions. We provide recommendations when dealing with different types of annotations or family structures commonly encountered in practice. Application of RetroFun-RVS is illustrated on whole genome sequence in the Eastern Quebec Schizophrenia and Bipolar Disorder Kindred Study with networks constructed from 3D contacts and epigenetic data on neurons. In summary we argue that RetroFun-RVS, by allowing integration of functional annotations corresponding to regions or networks with transcriptional impacts, is a useful framework to highlight regulatory mechanisms involved in complex diseases.
Clearance of defective muscle stem cells by senolytics reduces the expression of senescence-associated secretory phenotype and restores myogenesis in myotonic dystrophy type 1
Authors: Conte Talita C. , Duran-Bishop Gilberto , Orfi Zakaria , Mokhtari Inès , Deprez Alyson , Roussel Marie-Pier , Côté Isabelle , Pellerito Ornella , Maggiorani Damien , Benabdallah Basma , Leclerc Severine , Feulner Lara , Mathieu Jean , Gagnon Cynthia , Andelfinger Gregor , Beauséjour Christian , McGraw Serge , Duchesne Elise , Dumont Nicolas A. 
Published: June 2022

ABSTRACTMuscle weakness and atrophy are clinical hallmarks of myotonic dystrophy type 1 (DM1). Muscle stem cells, which contribute to skeletal muscle growth and repair, are also affected in this disease. However, the molecular mechanisms leading to this defective activity and the impact on the disease severity are still elusive. Here, we explored through an unbiased approach the molecular signature leading to myogenic cell defects in DM1. Single cell RNAseq data revealed the presence of a specific subset of DM1 myogenic cells expressing a senescence signature, characterized by the high expression of genes related to senescence-associated secretory phenotype (SASP). This profile was confirmed using different senescence markers in vitro and in situ. Accumulation of intranuclear RNA foci in senescent cells, suggest that RNA-mediated toxicity contribute to senescence induction. High expression of IL-6, a prominent SASP cytokine, in the serum of DM1 patients was identified as a biomarker correlating with muscle weakness and functional capacity limitations. Drug screening revealed that the BCL-XL inhibitor (A1155463), a senolytic drug, can specifically target senescent DM1 myoblasts to induce their apoptosis and reduce their SASP. Removal of senescent cells re-established the myogenic function of the non-senescent DM1 myoblasts, which displayed improved proliferation and differentiation capacity in vitro; and enhanced engraftment following transplantation in vivo. Altogether this study presents a well-defined senescent molecular signature in DM1 untangling part of the pathological mechanisms observed in the disease; additionally, we demonstrate the therapeutic potential of targeting these defective cells with senolytics to restore myogenesis.
A comparative study of the human, mouse, and zebrafish eye after staining with RGB trichrome
Authors: de la Torre Antonio Prieto , Gaytán Francisco 
Published: June 2022

AbstractEyesight plays essential roles for the survival of most animal species, and diseases leading to blindness or partial vision loss in humans have an enormous impact in life quality. The complex structure of the eye makes it ideal for the study of structure-function relationships, and to accomplish integration of histology with other disciplines, connecting basic anatomical sciences to clinical medicine. The RGB trichrome consists of the sequential staining with three dyes, fast green (as a general protein stain), picrosirius red and alcian blue (for two main components of the extracellular matrix, collagen and glycosaminoglycans respectively). Notably, this combination of primary colors matches the physiological color detection capacity of the human trichromatic eye. Application of RGB stain to human eye samples and to the eye of two widely used animal models, the mouse and the zebrafish (Danio rerio), gives rise to brilliant staining of eye connective tissues, with a range of colors from red to magenta depending on the extracellular matrix composition, and producing highly contrasted tissue interfaces, facilitating the observation of tissue structures, as well as histomorphometric analysis. Interestingly, staining of the retina resulted in differential staining of the retinal layers in the three species analyzed. These results support the effectiveness of RGB as a reliable general staining method, complementary to routine basic hematoxylin and eosin (H&E), applicable to the study of the eye in human pathology, basic preclinical research, as well as in histo(patho)logy teaching.