Miracle-dz/UniFAR-FTUs huggingface dataset:
Cryo-ET of Toxoplasma parasites gives subnanometer insight into tubulin-based structures

Significance Tubulin polymers are essential for a variety of cellular functions. Using cryo-ET, we reveal the 3D organization of the apical complex in Toxoplasma gondii, an intracellular eukaryote with tubulin-based structures, including an apical “conoid” involved in host cell invasion. Our development of an advanced subtomogram averaging protocol for filamentous structures enabled us to accurately assign tubulins in cellular context. At the subnanometer resolution achieved, tubulins were confirmed to assemble into two major forms: canonical subpellicular microtubules (SPMTs) and noncanonical conoid fibrils (CFs). The data further revealed associated proteins in both structures, a dominant orientation of SPMTs, and a unique patterning of the CFs. This work demonstrates an approach that can be used to determine cellular filamentous structures at multiscale resolutions. Tubulin is a conserved protein that polymerizes into different forms of filamentous structures in Toxoplasma gondii, an obligate intracellular parasite in the phylum Apicomplexa. Two key tubulin-containing cytoskeletal components are subpellicular microtubules (SPMTs) and conoid fibrils (CFs). The SPMTs help maintain shape and gliding motility, while the CFs are implicated in invasion. Here, we use cryogenic electron tomography to determine the molecular structures of the SPMTs and CFs in vitrified intact and detergent-extracted parasites. Subvolume densities from detergent-extracted parasites yielded averaged density maps at subnanometer resolutions, and these were related back to their architecture in situ. An intralumenal spiral lines the interior of the 13-protofilament SPMTs, revealing a preferred orientation of these microtubules relative to the parasite’s long axis. Each CF is composed of nine tubulin protofilaments that display a comma-shaped cross-section, plus additional associated components. Conoid protrusion, a crucial step in invasion, is associated with an altered pitch of each CF. The use of basic building blocks of protofilaments and different accessory proteins in one organism illustrates the versatility of tubulin to form two distinct types of assemblies, SPMTs and CFs.
Evolutionary velocity with protein language models

Predicting the order of biological homologs is a fundamental task in evolutionary biology. For protein evolution, this order is often determined by first arranging sequences into a phylogenetic tree, which has limiting assumptions and can suffer from substantial ambiguity. Here, we demonstrate how machine learning algorithms called language models can learn mutational likelihoods that predict the directionality of evolution, thereby enabling phylogenetic analysis that addresses key limitations of existing methods. Our main conceptual advance is to construct a “vector field” of protein evolution through local evolutionary predictions that we refer to as evolutionary velocity (evo-velocity). We show that evo-velocity can successfully predict evolutionary order at vastly different timescales, from viral proteins evolving over years to eukaryotic proteins evolving over geologic eons. Evo-velocity also yields new evolutionary insights, predicting strategies of viral-host immune escape, resolving conflicting theories on the evolution of serpins, and revealing a key role of horizontal gene transfer in the evolution of eukaryotic glycolysis. In doing so, our work suggests that language models can learn sufficient rules of natural protein evolution to enable evolutionary predictability.
Operationalizing Community Assessment Results to Enhance Preparedness for a Radiological Emergency

Objective: A radiological emergency such as the detonation of a radiological dispersal device would have catastrophic health, environmental, and economic consequences. Community assessments can provide useful information about radiological and other emergency preparedness at the household level. Tools such as logic models can be applied to link data collected in a community assessment to planned activities and targeted outcomes. This study sought to answer how public health departments can use the results of a community assessment to improve preparedness for radiological and other types of emergencies and to present a sample logic model demonstrating how questions asked in a community assessment can be used to drive intended outcomes. Design: Surveys were fielded in 2019 to professionals with experience in radiological emergency preparedness, state and local health and emergency management, and journalism. Questions included the role of health departments in radiological emergency preparedness, the operationalization of results from a community assessment for preparedness, and information sharing in a radiological emergency. Descriptive statistics and a modified framework approach were used for open-ended questions. Results: Nearly three-fourths of state/local officials reported that it would be at least somewhat difficult (73%; 11 of 15 state/local officials) for a local health department to operationalize the results of a community health assessment for radiological emergency preparedness. Potential barriers included competing priorities, lack of funds, and limited staff. Resources such as pretested communication materials, tailored messaging, and technical tools and training can assist health departments and emergency management agencies in using the information collected from a community assessment. Conclusions: To address implementation challenges in operationalizing the results of a community assessment, officials can use tools such as logic models to illustrate how the information gathered from a community health assessment will create an intended preparedness outcome and to advocate for funds for this type of assessment.
Seroprevalence and risk factors of brucellosis in Arabian horses

Abstract Background Brucellosis, as a zoonotic disease, mainly occurs in horses by Brucella abortus, Brucella canis and Brucella suis. The disease in equines is often asymptomatic, but the clinical signs in horses are mostly characterized by bursitis, arthritis and tenosynovitis. Objectives This study, thus, aimed to determine the seroprevalence of brucellosis and its associated risk factors in the Arabian horses of Khuzestan province, South‐west Iran. Methods To that end, the blood samples randomly collected from 180 Arabian horses were analyzed for the presence of anti‐Brucella antibodies by Rose Bengal plate test (RBPT), serum agglutination test (SAT), 2‐mercaptoethanol test (2‐ME) and a commercial i‐ELISA kit. Results The ROC curve analysis showed that the best cut‐off point for S/P values in i‐ELISA turned out to be 26.25%. The results showed that the overall seroprevalence of brucellosis based on parallel interpretation of the test results was 12.22% (Positive/Tested = 22/180). The prevalence of acute and chronic brucellosis was 8.3 and 3.9%, respectively. The seroprevalence of brucellosis with RBPT and i‐ELISA methods was 1.11% (2/180) and 7.22% (13/180), respectively. According to what SAT revealed, 9.44% (17/180) of sera had a titer of 40 or greater, and at 2‐ME, 7.22% of samples (13 out of 180 samples) depicted a titer of 40. The results of i‐ELISA, SAT and 2‐ME were significantly different from those of RBPT (p < 0.01); however, there was no significant difference between i‐ELISA, SAT and 2‐ME in findings (p > 0.05). Conclusions The results of this study recommend that i‐ELISA be used for screening purposes of brucellosis in horses. The findings confirmed that Arabian horses are natural hosts for the Brucellae. It is, thus, necessary to adopt appropriate prevention and control programs by health authorities and horse owners so as to reduce the distribution and transmission of the infection in the regions where brucellosis is prevalent.
Adaptive Joint Optimization for 3D Reconstruction with Differentiable Rendering

Due to inevitable noises introduced during scanning and quantization, 3D reconstruction via RGB-D sensors suffers from errors both in geometry and texture, leading to artifacts such as camera drifting, mesh distortion, texture ghosting, and blurriness. Given an imperfect reconstructed 3D model, most previous methods have focused on refining either geometry, texture, or camera pose. Consequently, different optimization schemes and objectives for optimizing each component have been used in previous joint optimization methods, forming a complicated system. In this paper, we propose a novel optimization approach based on differentiable rendering, which integrates the optimization of camera pose, geometry, and texture into a unified framework by enforcing consistency between the rendered results and the corresponding RGB-D inputs. Based on the unified framework, we introduce a joint optimization approach to fully exploit the inter-relationships among the three objective components, and describe an adaptive interleaving strategy to improve optimization stability and efficiency. Using differentiable rendering, an image-level adversarial loss is applied to further improve the 3D model, making it more photorealistic. Experiments on synthetic and real data using quantitative and qualitative evaluation demonstrated the superiority of our approach in recovering both fine-scale geometry and high-fidelity texture.
A multisynaptic pathway from the ventral midbrain toward spinal motoneurons in monkeys

Motivation boosts motor performance. Activity of the ventral midbrain (VM), consisting of the ventral tegmental area (VTA), the substantia nigra pars compacta (SNc) and the retrorubral field (RRF), plays an important role in processing motivation. However, little is known about the neural substrate bridging the VM and the spinal motor output. We hypothesized that the VM might exert a modulatory influence over the descending motor pathways. By retrograde transneuronal labelling with rabies virus, we demonstrated the existence of multisynaptic projections from the VM to the cervical enlargement in monkeys. The distribution pattern of spinal projection neurons in the VM exhibited a caudorostral gradient, in that the RRF and the caudal part of the SNc contained more retrogradely labelled neurons than the VTA and the rostral part of the SNc. Electrical stimulation of the VM induced muscle responses in the contralateral forelimb with a delay of a few milliseconds following the responses of the ipsilateral primary motor cortex (M1). The magnitude and number of evoked muscle responses were associated with the stimulus intensity and number of pulses. The muscle responses were diminished during M1 inactivation. Thus, the present study has identified a multisynaptic VM–spinal pathway that is mediated, at least in part, by the M1 and might play a pivotal role in modulatory control of the spinal motor output.
Weld defect detection in industrial radiography based on image segmentation

Radiographic testing is one of the most important non-destructive testing techniques for welding inspection. In this paper, a novel approach is proposed for welding defect detection on radiographic images based on a multi-scale segmentation strategy, where the initial partition is obtained using the minimal cut algorithm. The linear diffusion and an improved boundary trace method are then applied to implement multi-scale segmentation and extraction of the regions, which is followed by an energy-based evaluation model applied as stopping criteria to control the segmentation iteration. Therefore, the segmented sizes of defects obtained can be controlled by setting diffusion parameters according to the requirement of a special application. The proposed approach has been demonstrated by numerical experiments.
CDX2 expression in malignant peripheral nerve sheath tumour: a potential diagnostic pitfall associated with PRC2 inactivation

Malignant peripheral nerve sheath tumour (MPNST) is a soft tissue sarcoma that exhibits features of Schwann cell differentiation. Heterologous, often mesenchymal‐type differentiation occurs in a subset of MPNST, while glandular morphology also is encountered in rare cases. We observed in MPNST unanticipated expression of CDX2, a transcription factor that regulates intestinal epithelial differentiation, and aimed to further characterize this phenomenon.
Effectiveness of electronic drug monitoring feedback to increase adherence in patients with RA initiating a biological DMARD: a randomised clinical trial

Objective Medication non-adherence in rheumatoid arthritis (RA) is associated with disease flares, increased disability and increased costs. This study assessed the effectiveness of electronic monitoring feedback (EMF) on medication adherence in patients with RA starting with or switching to a new biological disease-modifying antirheumatic drug (bDMARD). Methods In this randomised controlled trial, bDMARD starters were assigned to the intervention or control group and followed for 1 year. The intervention group received a needle container with a Medication Event Monitoring System (MEMS) cap registering patient’s adherence to injections. Scores were calculated every 3 months with MEMS and motivational interviewing feedback was given. The control group received usual care. Effectiveness of EMF on adherence was measured with the medication possession ratio (MPR). Results 104 consecutive intervention patients were included and 102 controls. MPR was 0.95 (SD: 0.10) and 0.90 (0.16) after 12 months (B: 0.036, 95% CI: 0.001 to 0.007, p=0.045). bDMARD-naive patients receiving EMF achieved low disease activity (LDA) sooner compared with the control group, adjusted for baseline DAS (HR: 1.68, 95% CI: 1.00 to 2.81, p=0.050). Side effects and DAS28 were similar. Conclusion EMF increased adherence for patients with RA starting with or switching to a bDMARD. Especially bDMARD-naive patients achieved LDA sooner compared with the control group, which holds promise for the future.
PIPS: A Parallel Planning Model of Sentence Production

Subject-verb agreement errors are common in sentence production. Many studies have used experimental paradigms targeting the production of subject-verb agreement from a sentence preamble (The key to the cabinets) and eliciting verb errors (… *were shiny). Through reanalysis of previous data (50 experiments; 102,369 observations), we show that this paradigm also results in many errors in preamble repetition, particularly of local noun number (The key to the *cabinet). We explore the mechanisms of both errors in parallelism in producing syntax (PIPS), a model in the Gradient Symbolic Computation framework. PIPS models sentence production using a continuous-state stochastic dynamical system that optimizes grammatical constraints (shaped by previous experience) over vector representations of symbolic structures. At intermediate stages in the computation, grammatical constraints allow multiple competing parses to be partially activated, resulting in stable but transient conjunctive blend states. In the context of the preamble completion task, memory constraints reduce the strength of the target structure, allowing for co-activation of non-target parses where the local noun controls the verb (notional agreement and locally agreeing relative clauses) and non-target parses that include structural constituents with contrasting number specifications (e.g., plural instead of singular local noun). Simulations of the preamble completion task reveal that these partially activated non-target parses, as well the need to balance accurate encoding of lexical and syntactic aspects of the prompt, result in errors. In other words: Because sentence processing is embedded in a processor with finite memory and prior experience with production, interference from non-target production plans causes errors.
Questing Ixodes ricinus ticks and Borrelia spp. in urban green space across Europe: A review

For more than three decades, it has been recognized that Ixodes ricinus ticks occur in urban green space in Europe and that they harbour multiple pathogens linked to both human and animal diseases. Urban green space use for health and well‐being, climate mitigation or biodiversity goals is promoted, often without consideration for the potential impact on tick encounters or tick‐borne disease outcomes. This review synthesizes the results of over 100 publications on questing I. ricinus and Borrelia spp. infections in ticks in urban green space in 24 European countries. It presents data on several risk indicators for Lyme borreliosis and highlights key research gaps and recommendations for future studies. Across Europe, mean density of I. ricinus in urban green space was 6.9 (range; 0.1–28.8) per 100 m2 and mean Borrelia prevalence was 17.3% (range; 3.1%–38.1%). Similar density estimates were obtained for nymphs, which had a Borrelia prevalence of 14.2% (range; 0.5%–86.7%). Few studies provided data on both questing nymph density and Borrelia prevalence, but those that did found an average of 1.7 (range; 0–5.6) Borrelia‐infected nymphs per 100 m2 of urban green space. Although a wide range of genospecies were reported, Borrelia afzelii was the most common in most parts of Europe, except for England where B. garinii was more common. The emerging pathogen Borrelia miyamotoi was also found in several countries, but with a much lower prevalence (1.5%). Our review highlights that I. ricinus and tick‐borne Borrelia pathogens are found in a wide range of urban green space habitats and across several seasons. The impact of human exposure to I. ricinus and subsequent Lyme borreliosis incidence in urban green space has not been quantified. There is also a need to standardize sampling protocols to generate better baseline data for the density of ticks and Borrelia prevalence in urban areas.
Competency Assessment in Physical Medicine and Rehabilitation Resident Education

Objective The aim of this systematic review was to examine the scope and quality of research in physical medicine and rehabilitation resident education as it pertains to the six core competencies defined by the Accreditation Council for Graduate Medical Education. Design All indexed years of Medline, Embase, and ERIC were searched using key words related to physical medicine and rehabilitation and medical education. Data were extracted on core competencies, content categories, teaching interventions, and study quality. Results From a sample of 2544 articles, 62 studies were included in this review. Frequencies of core competencies studied were: patient care 62.9%, medical knowledge 56.5%, systems-based practice 22.6%, practice-based learning and improvement 14.5%, professionalism 25.8%, and interpersonal and communication skills 22.6%. Musculoskeletal and pain medicine was the most frequently studied content category (33.9%). There was no significant difference in quality of studies between the six core competency groups (P = 0.31). Conclusions Available research is highly concentrated in patient care and medical knowledge competencies and in the musculoskeletal and pain medicine content category. This systematic review outlines the current state of education literature and highlights areas for further inquiry. This is an important step toward the translation of research into evidence-based educational practices.
Conceptualizing religious asylum: Security, religiosity, and subjective well-being of Christian asylum-seekers in Hong Kong

This article proposes the concept of religious asylum to examine how Christian asylum-seekers utilize religion to cope with their emotional experiences, induced by a sense of insecurity, during prolonged displacement. Drawing from interviews and ethnographic observations of people seeking asylum in Hong Kong, this research determines that asylum-seekers use religion to redefine their positive sense of self beyond their current situation, which is central to the construct of well-being. While religion supports asylum-seekers going through psychosocial distress and suffering, this discussion on religious asylum shows how asylum-seekers utilize the religiously inflected space to make the experience of prolonged displacement meaningful.
FAST TRANSIENT RESPONSE LOW DROP- OUT VOLTAGE REGULATOR

This paper presents the design of Low Drop-Out (LDO) voltage regulator has fast transient response and which exploits a few current else low quiescent current in the operational amplifier PMOS type. We use band-gap reference for eliminate the temperature dependence. The proposed LDO voltage regulator implemented in 0.18-�m CMOS technology, we use Folded cascode CMOS amplifiers high performance in the stability , provide fast transient response which explains a fast settling, the LDO itself should provide in the output regulator voltages att equal 2ps with transient variation of the voltage less than 170mV. High accuracy in the DC response terms, the simulation results show that the accuracy of the output regulator voltages is 1.54±0.009V, and power consumption of 1.51 mW.
Online Method to Impute Missing Loop Detector Data for Urban Freeway Traffic Control

The dual loop detector provides input data for real-time traffic control. However, the common scenario of missing or invalid loop data samples negatively impacts the performance of the subsequent traffic control or traffic prediction model. This paper describes a method that detects blank data samples when a new data record is listed, then imputes missing data samples to form a complete data record in real time. One three-lane loop detector station on Whitemud Drive in Edmonton, Alberta, Canada, is used as a case study to verify the algorithms. The imputation scope for this study involves diagnosing and filling in the missing data of one lane for at least one whole day at a specific loop station. The diagnosis of missing data for both volume and speed measurements is based on data records from upstream and downstream stations, rather than from single samples. The imputation algorithm for volume and density data models the relationship of one loop detector with all other loop detectors at the same station as linear. The multiple linear regression algorithm is applied to full historic data offline to learn the linear relationship between loops at the same station, and the online data imputation is based on the equations learned. Two other commonly used imputation techniques—pairwise linear regression and the average of the surrounding detectors—are also conducted for comparison. The proposed diagnosis and imputation method enables the loop data input to support control models with high frequency and large data requirements.