Miracle-dz/UniFAR-FTUs huggingface dataset:
Electronic health record and primary care physician self-reported quality of care: a multilevel study in China

ABSTRACT Background Health information technology is one of the building blocks of a high-performing health system. However, the evidence regarding the influence of an electronic health record (EHR) on the quality of care remains mixed, especially in low- and middle-income countries. Objective This study examines the association between greater EHR functionality and primary care physician self-reported quality of care. Methods A total of 224 primary care physicians from 38 community health centres (CHCs) in four large Chinese cities participated in a cross-sectional survey to assess CHC care quality. Each CHC director scored their CHC’s EHR functionality on the availability of ten typical features covering health information, data, results management, patient access, and clinical decision support. Data analysis utilised hierarchical linear modelling. Results The availability of five EHR features was positively associated with physician self-reported clinical quality: share records online with providers outside the practice (β = 0.276, p = 0.04), access records online by the patient (β = 0.325, p = 0.04), alert provider of potential prescription problems (β = 0.353, p = 0.04), send the patient reminders for care (β = 0.419, p = 0.003), and list patients by diagnosis or health risk (β = 0.282, p = 0.04). However, no association was found between specific features availability or total features score and physician self-reported preventive quality. Conclusions This study provides evidence that the availability of EHR systems, and specific features of these systems, was positively associated with physician self-reported quality of care in these 38 CHCs. Future longitudinal studies focused on standardised quality metrics, and designed to control known confounding variables, will further inform quality improvement efforts in primary care.
Design of Virtual Reality Exergames for Upper Limb Stroke Rehabilitation Following Iterative Design Methods: Usability Study

Background Since the early 2000s, there has been a growing interest in using exercise video games (exergames) and virtual reality (VR)–based interventions as innovative methods to enhance physical rehabilitation for individuals with multiple disabilities. Over the past decade, researchers and exercise professionals have focused on developing specialized immersive exercise video games for various populations, including those who have experienced a stroke, revealing tangible benefits for upper limb rehabilitation. However, it is necessary to develop highly engaging, personalized games that can facilitate the creation of experiences aligned with the preferences, motivations, and challenges communicated by people who have had an episode of stroke. Objective This study seeks to explore the customization potential of an exergame for individuals who have undergone a stroke, concurrently evaluating its usability as a technological tool in the realm of physical therapy and rehabilitation. Methods We introduce a playtest methodology to enhance the design of a VR exergame developed using a user-centered approach for upper limb rehabilitation in stroke survivors. Over 4 playtesting sessions, stroke survivors interacted with initial game versions using VR headsets, providing essential feedback for refining game content and mechanics. Additionally, a pilot study involving 10 stroke survivors collected data through VR-related questionnaires to assess game design aspects such as mechanics, assistance, experience, motion sickness, and immersion. Results The playtest methodology was beneficial for improving the exergame to align with user needs, consistently incorporating their perspectives and achieving noteworthy results. The pilot study revealed that users had a positive response. In the first scenario, a carpenter presents a game based on the flexion-extension movement of the elbow; the second scenario includes a tejo game (a traditional Colombian throwing game) designed around game mechanics related to the flexion-extension movement of the shoulder; and in the third scenario, a farmer challenges the player to perform a movement combining elbow flexion and extension with internal and external rotation of the shoulder. These findings suggest the potential of the studied exergame as a tool for the upper limb rehabilitation of individuals who have experienced a stroke. Conclusions The inclusion of exergames in rehabilitation for stroke-induced hemiparesis has significantly benefited the recovery process by focusing on essential shoulder and elbow movements. These interactive games play a crucial role in helping users regain mobility and restore practical use of affected limbs. They also serve as valuable data sources for researchers, improving the system’s responsiveness. This iterative approach enhances game design and markedly boosts user satisfaction, suggesting exergames have promising potential as adjunctive elements in traditional therapeutic approaches.
Task Context Modulates Feature-Selective Responses in Area V4

Feature selectivity of visual cortical responses measured during passive fixation provides only a partial view of selectivity because it does not account for the influence of cognitive factors. Here we focus on primate area V4 and ask how neuronal tuning is modulated by task engagement. We investigated whether responses to colored shapes during active shape discrimination are simple, stimulus-agnostic, scaled versions of responses during passive fixation, akin to results from attentional studies. Alternatively, responses could be subject to stimulus-specific scaling, that is, responses to different stimuli are modulated differently, resulting in changes in underlying shape/color selectivity. Among 83 well-isolated V4 neurons in two male macaques, only a minority (16 of 83), which were weakly tuned to both shape and color, displayed responses during fixation and discrimination tasks that could be related by stimulus-agnostic scaling. The majority (67 of 83), which were strongly tuned to shape, color, or both, displayed stimulus-dependent response changes during discrimination. For some of these neurons (39 of 83), the shape or color of the stimulus dictated the magnitude of the change, and for others (28 of 83) it was the combination of stimulus shape and color. Importantly, for neurons with one strong and one weak tuning dimension, stimulus-dependent response changes during discrimination were associated with a relative increase in selectivity along the stronger tuning dimension, without changes in tuning peak. These results reveal that more strongly tuned V4 neurons may also be more flexible in their selectivity, and imbalances in selectivity are amplified during active task contexts. SIGNIFICANCE STATEMENT Tuning for stimulus features is typically characterized by recording responses during passive fixation, but cognitive factors, including attention, influence responses in visual cortex. To determine how behavioral engagement influences neuronal responses in area V4, we compared responses to colored shapes during passive fixation and active behavior. For a large fraction of neurons, differences in responses between passive fixation and active behavior depended on the identity of the visual stimulus. For a subgroup of strongly feature-selective neurons, this response modulation was associated with enhanced selectivity for one feature at the expense of selectivity for the other. Such flexibility in tuning strength could improve performance in tasks requiring active judgment of stimuli.
Breakthrough infections by SARS-CoV-2 variants boost cross-reactive hybrid immune responses in mRNA-vaccinated Golden Syrian hamsters

Hybrid immunity (vaccination + natural infection) to SARS-CoV-2 provides superior protection to re-infection. We performed immune profiling studies during breakthrough infections in mRNA-vaccinated hamsters to evaluate hybrid immunity induction. The mRNA vaccine, BNT162b2, was dosed to induce binding antibody titers against ancestral spike, but inefficient serum virus neutralization of ancestral SARS-CoV-2 or variants of concern (VoCs). Vaccination reduced morbidity and controlled lung virus titers for ancestral virus and Alpha but allowed breakthrough infections in Beta, Delta and Mu-challenged hamsters. Vaccination primed for T cell responses that were boosted by infection. Infection back-boosted neutralizing antibody responses against ancestral virus and VoCs. Hybrid immunity resulted in more cross-reactive sera, reflected by smaller antigenic cartography distances. Transcriptomics post-infection reflects both vaccination status and disease course and suggests a role for interstitial macrophages in vaccine-mediated protection. Therefore, protection by vaccination, even in the absence of high titers of neutralizing antibodies in the serum, correlates with recall of broadly reactive B- and T-cell responses.
Periodontal Disease Monitoring by Raman Spectroscopy of Phosphates: New Insights into Pyrophosphate Activity

(1) Background: The intent of this survey was to investigate the quality of the alveolar bone by revealing the different phases for calcified tissues independent of the medical history of the patient in relation to periodontal disease by means of Raman spectroscopy and then to correlate the results by suggesting a possible mechanism for the medical impairment; (2) Methods: The investigation was mainly based on Raman spectroscopy that was performed in vivo during surgery for the selected group of patients. The targeted peaks for the Raman spectra were according to the reference compounds (e.g., calcium phosphates, other phosphates); (3) Results: The variation in the intensity of the spectrum correlated to the specific bone constituents’ concentrations highlights the bone quality, while some compounds (such as pyrophosphate, PPi) are strongly related to the patient’s medical status, and they provide information regarding a physiological process that occurred in the calcified tissues. Moreover, bone sample fluorescence is related to the collagen (Col) content, enabling a complete evaluation of bone quality, revealing the importance of collagen matrix acting as a load-bearing element for Calcium phosphate (CaP) deposition during the complex bone mineralization process; (4) Conclusions: We highlight that Raman spectroscopy can be considered a viable investigative method for in vivo and rapid bone quality valuation through oral health monitoring.
The Teaching of Anthropogenic Climate Change and Earth Science via Technology-Enabled Inquiry Education

ABSTRACT A gap has existed between the tools and processes of scientists working on anthropogenic global climate change (AGCC) and the technologies and curricula available to educators teaching the subject through student inquiry. Designing realistic scientific inquiry into AGCC poses a challenge because research on it relies on complex computer models, globally distributed data sets, and complex laboratory and data collection procedures. Here we examine efforts by the scientific community and educational researchers to design new curricula and technology that close this gap and impart robust AGCC and Earth Science understanding. We find technology-based teaching shows promise in promoting robust AGCC understandings if associated curricula address mitigating factors such as time constraints in incorporating technology and the need to support teachers implementing AGCC and Earth Science inquiry. We recommend the scientific community continue to collaborate with educational researchers to focus on developing those inquiry technologies and curricula that use realistic scientific processes from AGCC research and/or the methods for determining how human society should respond to global change.
METTL17 is an Fe-S cluster checkpoint for mitochondrial translation

Friedreich’s ataxia (FA) is the most common monogenic mitochondrial disease. FA is caused by a depletion of the mitochondrial protein frataxin (FXN), an iron-sulfur (Fe-S) cluster biogenesis factor. To better understand the cellular consequences of FA, we performed quantitative proteome profiling of human cells depleted for FXN. Nearly every known Fe-S cluster-containing protein was depleted in the absence of FXN, indicating that as a rule, cluster binding confers stability to Fe-S proteins. Proteomic and genetic interaction mapping identified impaired mitochondrial translation downstream of FXN loss, and specifically highlighted the methyltransferase-like protein METTL17 as a candidate effector. Using comparative sequence analysis, mutagenesis, biochemistry and cryogenic electron microscopy we show that METTL17 binds to the mitoribosomal small subunit during late assembly and harbors a previously unrecognized [Fe4S4]2+ cluster required for its stability on the mitoribosome. Notably, METTL17 overexpression rescued the mitochondrial translation and bioenergetic defects, but not the cellular growth, of FXN null cells. Our data suggest that METTL17 serves as an Fe-S cluster checkpoint: promoting the translation and assembly of Fe-S cluster rich OXPHOS proteins only when Fe-S cluster levels are replete.
Malacofaune du Pliocène marin du Roussillon: taphonomie et paléoécologie

In this paper, the taphonomic study of the main Zanclean outcrops of Roussillon (France) are made, on the basis of the lithology, the molluscan fauna, the ichnology and the presence of other taxa (barnacles, .). The outcrops are composed by blue clays and (or) yellow sands. Six paleocommunities are identified in the blue clays, which have been analysed from the paleoecological point of view. The trophic characteristics of the bivalve associations and the estimation of the faunistic (molluscan) affinity index between those paleocommunities are considered
Fetal programming effect of rumen-protected methionine on primiparous Angus × Simmental offspring’s performance and skeletal muscle gene expression

Abstract Primiparous Angus × Simmental dams (n = 22) with an average body weight (BW) of 449 ± 32 kg of BW were divided based on two nutritional treatments: control (CTRL) and rumen-protected methionine (RPM). The control group received bermudagrass hay, corn gluten, and soybean hulls pellets supplementation (base diet); whereas the RPM group received the base diet in addition to 0.07% of DM of RPM at a fixed rate during the last trimester of gestation and the first ~80 d of lactation, in which calves (n = 17) were early weaned. Only male calves were included in this study. After weaning, calves born to RPM dams also received RPM from weaning (day 1) to day 100. Blood sampling and skeletal muscle biopsies for subsequent quantitative polymerase chain reaction (PCR) analysis were conducted on days 1, 25, 50, and 100 on calves. Quantitative PCR data were analyzed using GLIMMIX, and blood metabolites concentrations, BW, and body condition score (BCS) were analyzed using the MIXED procedure of SAS. There was no difference in maternal BW and BCS between treatments. Glucose and blood metabolites that served as biomarkers for liver health (e.g., aspartate transaminase, albumin, alkaline phosphatase, and alanine transaminase) were in the normal levels for all calves (P > 0.40). Calves in the RPM group had a greater expression of adipogenic genes (e.g., PPARG, LPL, and CEBPD) at day 100 compared with CTRL (P < 0.01). In addition, DNA methylation (DNMT1) and oxidative stress-related genes (SOD2 and NOS3) in the RPM group were upregulated at day 100 compared with CTRL (P < 0.01). These results may suggest that calves born to primiparous dams exposed to RPM supplementation are more prone to develop greater adipose tissue than CTRL calves. Furthermore, RPM supplementation may improve methylation processes, as shown by the upregulation of DNMT1. The results shown in our study aim at expanding the knowledge on fetal programming and early-life growth and development of beef cattle under supplementation with RPM.
Impact of coal-carrying trains on particulate matter concentrations in the Lower Mainland region of British Columbia, Canada

The transport of coal by train through residential neighbourhoods in Metro Vancouver, British Columbia, Canada is a growing concern for many residents living near the railway. This study aimed to identify and quantify any potential particulate matter (PM) increase caused by the presence of rail tra c adjacent to John Oliver Park in Delta, BC. Field work was carried out during August and September 2014, using a GRIMM optical particle counter that measured PM concentration at various size ranges. A select number of passing trains were confirmed visually, while the majority of passages were identified with audio data recorded by a microphone. A horizontally operating mini-micropulse lidar system was also set up at the park on three individual days to make intensive backscatter measurements. Wind data were recorded by collocated instruments maintained by Metro Vancouver. Finally, the Corporation of Delta had a dustfall measurement campaign during the same time period. Trains carrying coal are associated with a 5.28, 4.11, and 2.55 μg/m3 average increase in concentration over a 15 minute period, compared to control conditions for PM3, PM10, and PM20, respectively. These increases are all statistically significant at ↵ = 0.01. PM concentrations during train passages of all types were not found to be significantly di↵erent from PM concentrations during control conditions. The presence of coal dust particles at the site was confirmed by the dustfall measurements carried out by the Corporation of Delta. Lidar backscatter imagery provided individual snapshots of train passages. However, it is clear that not every train passage causes an increase in PM concentration, and the e↵ect appears to be highly dependent on wind direction and local meteorology. ii Preface This thesis consists of original, unpublished, and independent work completed by the author. Input on research design and analysis was provided by Dr. Ian McKendry. All wind data and some PM concentration data used in Chapters 3 and 4 were provided by Metro Vancouver’s Air Quality group. The dustfall observations in Section 3.4 were provided by the Corporation of Delta’s Climate Action & Environment department. The lidar backscatter images in Chapter 4 were created by Paul Cottle.
Expression of RNautophagy/DNautophagy-related genes is regulated under control of an innate immune receptor

ABSTRACT Double-stranded RNA (dsRNA) is a molecular pattern uniquely produced in cells infected with various viruses as a product or byproduct of replication. Cells detect such molecules, which indicate non-self invasion, and induce diverse immune responses to eliminate them. The degradation of virus-derived molecules can also play a role in the removal of pathogens and suppression of their replication. RNautophagy and DNautophagy are cellular degradative pathways in which RNA and DNA are directly imported into a hydrolytic organelle, the lysosome. Two lysosomal membrane proteins, SIDT2 and LAMP2C, mediate nucleic acid uptake via this pathway. Here, we showed that the expression of both SIDT2 and LAMP2C is selectively upregulated during the intracellular detection of poly(I:C), a synthetic analog of dsRNA that mimics viral infection. The upregulation of these two gene products upon poly(I:C) introduction was transient and synchronized. We also observed that the induction of SIDT2 and LAMP2C expression by poly(I:C) was dependent on MDA5, a cytoplasmic innate immune receptor that directly recognizes poly(I:C) and induces various antiviral responses. Finally, we showed that lysosomes can target viral RNA for degradation via RNautophagy and may suppress viral replication. Our results revealed a novel degradative pathway in cells as a downstream component of the innate immune response and provided evidence suggesting that the degradation of viral nucleic acids via RNautophagy/DNautophagy contributes to the suppression of viral replication.
Beyond the Bioclimatic Law

Almost a century ago, observed geographic patterns of plant phenology (such as leaf-out and flowering) were summarized in Hopkins’ Bioclimatic Law. This law describes phenology as varying along climatic gradients by latitude, longitude, and altitude. Yet phenological patterns are not only affected by contemporary climatic differences across space, but also by underlying geographic variations in plant genetics that arise from long-term climatic adaptation. The latter influence on geographic patterns in phenology has been undervalued to this day, mainly due to the difficulty of quantifying it. This study outlines a methodology for bridging this knowledge gap through delineating geographic adaption patterns using common garden and cloned plant phenology. Through synthesizing existing literature, typical geographic adaptation patterns in both spring and autumn phenology of many temperate tree species are identified. Under uniform environment, spring leaf-out of colder climate-adapted populations of a certain species is either earlier than warmer climate-adapted ones due to lower thermal requirements, or later because of higher chilling (for dormancy release) demands. The former leads to a countergradient pattern as it is opposite to an in situ observation, while the latter leads to a cogradient pattern. Autumn leaf senescence, on the other hand, expresses a consistent cogradient pattern that is related to latitude and constrained by the populations’ varied photoperiod requirements. These geographic adaptation patterns allow a clearer understanding of geographical variations in phenological responses to climate change, and provide a theoretical basis for spatially explicit phenological models. In addition, given that these adaptive patterns reveal genotype-based variabilities, they are potentially useful for more accurately tracking phenology-dependent ecosystem processes (e.g. species distribution) and non-weather-related vegetation changes. As a unique subfield of physical geography with broad environmental implications, this line of research needs to be further developed by furnishing a stronger and more explicit spatial structure into current phenological studies.
Enhanced Stability in Quantum Optimal Transport Pseudometrics: From Hartree to Vlasov-Poisson

In this paper we establish almost-optimal stability estimates in quantum optimal transport pseudometrics for the semiclassical limit of the Hartree dynamics to the Vlasov-Poisson equation, in the regime where the solutions have bounded densities. We combine Golse and Paul's method from [Arch. Ration. Mech. Anal. 223:57-94, 2017], which uses a semiclassical version of the optimal transport distance and which was adapted to the case of the Coulomb and gravitational interactions by the second author in [J. Stat. Phys. 177:20-60, 2019], with a new approach developed by the first author in [Arch. Ration. Mech. Anal. 244:27-50, 2022] to quantitatively improve stability estimates in kinetic theory.