Miracle-dz/UniFAR-FTUs huggingface dataset:
Enhanced Extraction of Blood and Tissue Time-Activity Curves in Cardiac Mouse FDG PET Imaging by Means of Constrained Nonnegative Matrix Factorization

We propose an enhanced method to accurately retrieve time-activity curves (TACs) of blood and tissue from dynamic 2-deoxy-2-[18F]fluoro-D-glucose ([18F]FDG) positron emission tomography (PET) cardiac images of mice. The method is noninvasive and consists of using a constrained nonnegative matrix factorization algorithm (CNMF) applied to the matrix (A) containing the intensity values of the voxels of the left ventricle (LV) PET image. CNMF factorizes A into nonnegative matrices H and W, respectively, representing the physiological factors (blood and tissue) and their associated weights, by minimizing an extended cost function. We verified our method on 32 C57BL/6 mice, 14 of them with acute myocardial infarction (AMI). With CNMF, we could break down the mouse LV into myocardial and blood pool images. Their corresponding TACs were used in kinetic modeling to readily determine the [18F]FDG influx constant (Ki) required to compute the myocardial metabolic rate of glucose. The calculated Ki values using CNMF for the heart of control mice were in good agreement with those published in the literature. Significant differences in Ki values for the heart of control and AMI mice were found using CNMF. The values of the elements of W agreed well with the LV structural changes induced by ligation of the left coronary artery. CNMF was compared with the recently published method based on robust unmixing of dynamic sequences using regions of interest (RUDUR). A clear improvement of signal separation was observed with CNMF compared to the RUDUR method.
Evaluating surveillance definitions of HIV viral suppression 2015–2019: Which definition best detected barriers to care?

Background: People living with HIV (PLWH) who have not achieved or maintained viral suppression post-diagnosis likely face multiple barriers to HIV care. To identify these barriers a universally accepted definition of viral suppression is needed. The most common definition, the Center for Disease Control and Prevention (CDC) definition, contains simplifying assumptions that may misclassify individuals and attenuate associations. In this study, we evaluated alternative definitions of viral suppression on their ability to identify barriers to care. Design and methods: We used HIV surveillance data to classify participants of the 2015–2019 Washington Medical Monitoring Project (MMP) as virally suppressed or not using the CDC definition and two definitions that assess viral suppression over a longer period (“Enriched” and “Durable”). We identified barriers to suppression from literature (unstable housing, illicit drug use, poor mental health, heavy drinking, recent incarceration, racism, and poverty) and measured them using interview questions from MMP. We compared the rate ratios (RR) of being not virally suppressed using each definition for each barrier. Results: There were 858 PLWH in our study. All viral suppression definitions classified a similar proportion of people as suppressed (85%–89%). The durable viral suppression definition consistently yielded the largest rate ratios (e.g. unstable housing: CDC RR = 1.3, 95% CI 0.9–1.8; Enriched 1.5, 95% CI 1.0–2.2; Durable 2.2, 95% CI 1.6–3.1) and reclassified 10% of the population relative to the CDC definition. Conclusions: Longitudinal definitions for viral suppression may yield less misclassification and serve as superior tools for identifying and curtailing barriers to HIV care.
Predicting hospitalization from real-world measures in patients with chronic kidney disease: A proof-of-principle study

Objective To investigate if in-clinic measures of physical function and real-world measures of physical behavior and mobility effort are associated with one another and to determine if they predict future hospitalization in participants with chronic kidney disease (CKD). Methods In this secondary analysis, novel real-world measures of physical behavior and mobility effort, including the best 6-minute step count (B6SC), were derived from passively collected data from a thigh worn actigraphy sensor and compared to traditional in-clinic measures of physical function (e.g. 6-minute walk test (6MWT). Hospitalization status during 2 years of follow-up was determined from electronic health records. Correlation analyses were used to compare measures and Cox Regression analysis was used to compare measures with hospitalization. Results One hundred and six participants were studied (69 ± 13 years, 43% women). Mean ± SD baseline measures for 6MWT was 386 ± 66 m and B6SC was 524 ± 125 steps. Forty-four hospitalization events over 224 years of total follow-up occurred. Good separation was achieved for tertiles of 6MWT, B6SC and steps/day for hospitalization events. This pattern persisted in models adjusted for demographics (6MWT: HR = 0.63 95% CI 0.43–0.93, B6SC: HR = 0.75, 95% CI 0.56–1.02 and steps/day: HR = 0.75, 95% CI 0.50–1.13) and further adjusted for morbidities (6MWT: HR = 0.54, 95% CI 0.35–0.84, B6SC: HR = 0.70, 95% CI 0.49–1.00 and steps/day: HR = 0.69, 95% CI 0.43–1.09). Conclusion Digital health technologies can be deployed remotely, passively, and continuously to collect real-world measures of physical behavior and mobility effort that differentiate risk of hospitalization in patients with CKD.
Periostin in Osteoporosis and Cardiovascular Disease

Abstract Context Osteoporosis (OP) and cardiovascular disease (CVD), prevalent disorders worldwide, often coexist and share common risk factors. The identification of common biomarkers could significantly improve patients’ preventive care. Objectives The objectives are 1, to review periostin (Postn) involvement in osteoporosis and in CVD, and 2, identify if Postn could be a common biomarker. Design This is a scoping review on Postn in OP and CVD. Methods Databases were searched, in vitro and in vivo, for publications in English on Postn, bone, and the cardiovascular system, with no limit regarding publication date. Results Postn appears as a key factor in OP and CVD. Its role as a potential biomarker in both pathologies is described in recent studies, but a number of limitations have been identified. Conclusions Current evidence provides fragmented views on Postn in OP and CVD and does not encapsulate Postn as a common pivotal thread linking these comorbidities. A number of gaps impede highlighting Postn as a common biomarker. There is room for future basic and clinical research with Postn as a marker and a target to provide new therapeutic options for aging patients with concomitant OP and CVD.
The role of microRNAs in responses to drought and heat stress in peanut (Arachis hypogaea)

MicroRNAs (miRNAs) are 21–24 nt small RNAs (sRNAs) that negatively regulate protein‐coding genes and/or trigger phased small‐interfering RNA (phasiRNA) production. Two thousand nine hundred miRNA families, of which ∼40 are deeply conserved, have been identified in ∼80 different plant species genomes. miRNA functions in response to abiotic stresses is less understood than their roles in development. Only seven peanut MIRNA families are documented in miRBase, yet a reference genome assembly is now published and over 480 plant‐like MIRNA loci were predicted in the diploid peanut progenitor Arachis duranensis genome. We explored by computational analysis of a leaf sRNA library and publicly available sRNA, degradome, and transcriptome datasets the miRNA and phasiRNA space associated with drought and heat stresses in peanut. We characterized 33 novel candidate and 33 ancient conserved families of MIRNAs and present degradome evidence for their cleavage activities on mRNA targets, including several noncanonical targets and novel phasiRNA‐producing noncoding and mRNA loci with validated novel targets such as miR1509 targeting serine/threonine‐protein phosphatase7 and miRc20 and ahy‐miR3514 targeting penta‐tricopeptide repeats (PPRs), in contradistinction to other claims of miR1509/173/7122 superfamily miRNAs indirectly targeting PPRs via TAS‐like noncoding RNA loci. We characterized the inverse correlations of significantly differentially expressed drought‐ and heat‐regulated miRNAs, assayed by sRNA blots or transcriptome datasets, with target mRNA expressions in the same datasets. Meta‐analysis of an expression atlas and over representation of miRNA target genes in co‐expression networks suggest that miRNAs have functions in unique aspects of peanut gynophore development. Genome‐wide MIRNA annotation of the published allopolyploid peanut genome can facilitate molecular breeding of value‐added traits.
Precision Measurement of Delbrück Scattering via Laser Compton Scattered γ-rays

Precision measurements such as the muon anomalous magnetic moment have indicated deviations from the standard model and have in turn prompted higher precision theoretical calculations. Delbrück scattering is the scattering of photons off the Coulomb field of nuclei via virtual electron-positron pairs and has been measured using γ-rays from radioactivities and following neutron capture reactions. However, because low flux γ-rays from nuclear transitions have been used in the low photon energy regime fairly large uncertainty exists in the data. In addition, due to the complexity and time consuming nature of the theoretical calculation the scattering cross sections are obtained from tables with interpolation between the tabular values. In recent years high flux γ-ray sources via laser Compton scattering (LCS) using energy-recovery linacs have been proposed. These sources allow measuring the Delbrück scattering with high precision. We will present our own independent calculations for the scattering cross section and show what precision can be obtained using the new LCS γ-ray sources in the low photon energy regime.
Teleconsultation Perceptions of Medical and Radiation Oncologists in the COVID-19 and Post–COVID-19 Era: A National Survey in the Philippines

PURPOSE The study reports on the current perception of medical and radiation oncologists regarding teleconsultation in the Philippines. Before the COVID-19 pandemic, the adoption of telemedicine was not widespread. With movement restrictions imposed during the pandemic, physicians were compelled to use telemedicine. It is uncertain whether physicians will still adopt its use in practice in the post–COVID-19 era. This study gives insight into the possible adaptation of this mode of consultation in the future, especially in areas with limited health care resources. MATERIALS AND METHODS We conducted a national survey among medical oncologists and radiation oncologists in the Philippines. A 43-item online survey was developed, validated, and administered to the oncologists. The demographics and data from categorical questions were reported as frequencies and percentages. RESULTS A total of 142 responses were gathered from 82 medical oncologists and 60 radiation oncologists. There was agreement among participants that, during the pandemic, teleconsultation could be used for the first visit, diagnostic workup request, treatment explanation, follow-up care, and chronic disease management. There was disagreement whether cancer diagnosis disclosure and cancer prognosis revelation could be performed via teleconsultation, and there was agreement that emergency consultation and physical examination would warrant a face-to-face consultation. After the COVID-19 pandemic, 78.7% intend to continue using teleconsultation except for emergency consultations, first visits, physical examination, diagnosis disclosure, and cancer prognosis revelation. CONCLUSION Teleconsultation was perceived by oncologists as an acceptable method of providing cancer care during and after the COVID-19 pandemic. Oncologists also intend to use teleconsultation in the post–COVID-19 era in certain aspects of patient care.
Reply to Ward et al.

including metabolically active microbiota, may be physiological and homeostatic, with disruption in lung disease (7, 8). In bronchiectasis, gastroesophageal reflux disease, a potential precursor to aspiration, ranges from 34% to 74%, and asymptomatic reflux is documented in 42–73% of patients (5). Three large prospective studies associate gastroesophageal reflux disease with increased bronchiectasis symptoms, exacerbations, and hospitalizations. Increased mortality has been described in a single-center, 212-patient study and a multicenter study of 986 patients (5, 6). We postulate that increased microaspiration of gastric content may be consistent with airway and lung injury. In patients with hypochlorhydria who were treated for symptoms of reflux with acid-suppressing medications (4–7), gastric content can include metabolically active, viable microbiota (7). Our proposed interactions of the gastric and lung compartment potentially fit ecology-model explanations of microbial species present in the respiratory system, with diverse immigration and extinction factors at play, including direct microaspiration (8, 9). Narayana and colleagues (1) discussed that the “low percentage of bacterial versus fungal overlap between the gut and lung does suggest that direct microbial interaction between sites is less likely” (p. 915). We wonder whether one potential explanation of our varied interpretations is that gut microbiome analyses are commonly predicated on the use of stool samples, influenced by the large intestine, whereas few data exist from gastric samples? Fecal samples are valuable and accessible, and they have informed studies of the microbiome.We have also found that paired, contemporaneous gastric secretion and lung samples provide insights. Gastric secretions are routinely discarded during endoscopy and ethics review boards, and patients are broadly supportive of interdisciplinary translational research.We suggest that future research could benefit from a discussion of a recommended panel of biological samples that could inform future studies of gut-lung interaction in chronic lung disease, including bronchiectasis.
Exploring communication by public health leaders and organizations during the pandemic: a content analysis of COVID-related tweets

Health communication is an essential competency in public health practice. The increasing use of social media and the connectivity between the general public and public health leaders present a unique opportunity to explore how digital communications tools were leveraged in the COVID-19 pandemic. This study explores Twitter-based communications from public health leaders and organizations across Canada and compares them with those from the World Health Organization (WHO). This research aimed to understand Twitter communications strategies to address the COVID-19 pandemic, other public health emergencies, and non-emergency public health issues. A content analysis of COVID-related Twitter content during the first wave of the pandemic (January 1–August 31, 2020) was performed. The Canadian Institute for Health Information (CIHI) Policy Intervention Scan was used as a framework to analyze messaging from public health leaders and the WHO. Findings demonstrate that most tweets from public health leaders and organizations in Canada and the WHO focused on case management and public information. Gaps and areas of weakness identified include the lack of Twitter participation by some public health leaders and a narrow range of policy intervention topics, limiting the breadth and depth of public health messages. Strengthening communications can serve to improve information sharing in future pandemics or public health crises. Further research should assess how public health leaders and organizations applied communication best practices on all social media platforms and across different policy interventions.
Convex Coordinates, Probabilities, and the Superposition of States

J. N. Boyd received his BA. from Hampden-Sydney College in 1958. Thereafter, he earned master's degrees in physics (1960) and mathematics (1972) at the University of Virginia. In 1977, he received his M.S. in applied mathematics from Virginia Commonwealth University, where he continues to pursue research with Professor Raychowdhury. He is chair? man of the Mathematics and Science departments at St. Christopher's School.
Altered Dynamic Resting State Functional Connectivity Associated With Somatosensory Impairments in the Upper Limb in the Early Sub-Acute Phase Post-Stroke

Background. Altered dynamic functional connectivity has been associated with motor impairments in the acute phase post-stroke. Its association with somatosensory impairments in the early sub-acute phase remains unexplored. Objective. To investigate altered dynamic functional connectivity associated with somatosensory impairments in the early sub-acute phase post-stroke. Methods. We collected resting state magnetic resonance imaging and clinical somatosensory function of the upper limb of 20 subacute stroke patients and 16 healthy controls (HC). A sliding-window approach was used to identify 3 connectivity states based on the estimated dynamic functional connectivity of sensorimotor related networks. Network components were subdivided into 3 domains: cortical and subcortical sensorimotor, as well as cognitive control network. Between-group differences were investigated using independent t-tests and Mann–Whitney-U tests. Analyzes were performed with correction for age, head motion and time post-stroke and corrected for multiple comparisons. Results. Stroke patients spent significantly less time in a weakly connected network state (state 3; dwell time: pstate3 = 0.003, meanstroke = 53.02, SDstroke = 53.13; meanHC = 118.92, SDHC = 72.84), and stayed shorter but more time intervals in a highly connected intra-domain network state (state 1; fraction time: pstate 1 < 0.001, meanstroke = 0.46, SDstroke = 0.26; meanHC = 0.26, SDHC = 0.21) compared to HC. After 8 weeks of therapy, improvements in wrist proprioception were moderately associated with decreases in dwell and fraction times toward a more normalized pattern. Conclusion. Changes in temporal properties of large-scale network interactions are present in the early rehabilitation phase post-stroke and could indicate enhanced neural plasticity. These findings could augment the understanding of cerebral reorganization after loss of neural tissue specialized in somatosensory functions.
Spatial structure favors microbial coexistence except when slower mediator diffusion weakens interactions

Microbes often exist in spatially structured environments and many of their interactions are mediated through diffusible metabolites. How does such a context affect microbial coexistence? To address this question, we use a model in which the spatial distributions of species and diffusible interaction mediators are explicitly included. We simulate the enrichment process, examining how microbial species spatially reorganize and how eventually a subset of them coexist. In our model, we find that slower motility of cells promotes coexistence by allowing species to co-localize with their facilitators and avoid their inhibitors. We additionally find that a spatially structured environment is more influential when species mostly facilitate each other, rather than when they are mostly competing. More coexistence is observed when species produce many mediators and consume some (not many or few) mediators, and when overall consumption and production rates are balanced. Interestingly, coexistence appears to be disfavored when mediators are diffusing slowly because that leads to weaker interaction strengths. Overall, our results offer new insights into how production, consumption, motility, and diffusion intersect to determine microbial coexistence in a spatially structured environment.
Ultimate fate, transformation, and toxicological consequences of herbicide pretilachlor to biotic components and associated environment: An overview

Herbicides are applied for effective weed management in order to increase the crop yield. In recent decades, the overuse of these chemicals has posed adverse effects on different biotic components of the environment. Pretilachlor has been widely used during last few decades for weed management in paddy crop. Its excessive use may prove fatal for environment, various organisms, and nontarget plants. Thus, it is pertinent to know the extent to which herbicide residues remain in environment. The potential mobility and the release rate of herbicide in the soil are important factors governing ecotoxicological impact and degradation rate. Therefore, several techniques are being investigated for its effective removal from the contaminated sites. Furthermore, efforts have also been made to study the degradation of pretilachlor by various physicochemical processes, resulting into the formation of different types of metabolites. This review summarizes the available information on environmental fate, various degradation processes, microbial biotransformation, metabolites formed, ecotoxicological effects, techniques for detection in environmental samples, effect of safener, and various control release formulations for sustained release of pretilachlor in applied fields. The information so obtained will be very advantageous in deciding the future policies for safe and judicious use of the herbicide by maintaining health and environmental sustainability.
ESTIMATION-ADJUSTED VAR

Standard risk measures, such as the value-at-risk (VaR), or the expected shortfall, have to be estimated, and their estimated counterparts are subject to estimation uncertainty. Replacing, in the theoretical formulas, the true parameter value by an estimator based on n observations of the profit and loss variable induces an asymptotic bias of order 1/n in the coverage probabilities. This paper shows how to correct for this bias by introducing a new estimator of the VaR, called estimation-adjusted VaR (EVaR). This adjustment allows for a joint treatment of theoretical and estimation risks, taking into account their possible dependence. The estimator is derived for a general parametric dynamic model and is particularized to stochastic drift and volatility models. The finite sample properties of the EVaR estimator are studied by simulation and an empirical study of the S&P index is proposed.
Root-N Consistent Estimation of a Panel Data Binary Response Model With Unknown Correlated Random Effects

In this article, we consider the estimation of a panel data binary response model with a weak restriction imposed on the individual specific effects. Our estimator is -consistent and asymptotically normal under reasonable regularity conditions. Furthermore, we allow the error terms to be heteroscedastic over time. The proposed estimator has a closed form expression and thus is very easy to compute. Simulations and the empirical illustration demonstrate the usefulness of our proposed estimator.