Miracle-dz/UniFAR-FTUs huggingface dataset:
Discordant Phylogenomic Placement of Hydnoraceae and Lactoridaceae Within Piperales Using Data From All Three Genomes

Phylogenetic relationships within the magnoliid order Piperales have been studied extensively, yet the relationships of the monotypic family Lactoridaceae and the holoparasitic Hydnoraceae to the remainder of the order remain a matter of debate. Since the first confident molecular phylogenetic placement of Hydnoraceae among Piperales, different studies have recovered various contradictory topologies. Most phylogenetic hypotheses were inferred using only a few loci and have had incomplete taxon sampling at the genus level. Based on these results and an online survey of taxonomic opinion, the Angiosperm Phylogeny Group lumped both Hydnoraceae and Lactoridaceae in Aristolochiaceae; however, the latter family continues to have unclear relationships to the aforementioned taxa. Here we present extensive phylogenomic tree reconstructions based on up to 137 loci from all three subcellular genomes for all genera of Piperales. We infer relationships based on a variety of phylogenetic methods, explore instances of phylogenomic discordance between the subcellular genomes, and test alternative topologies. Consistent with these phylogenomic results and a consideration of the principles of phylogenetic classification, we propose to exclude Hydnoraceae and Lactoridaceae from the broad circumscription of Aristolochiaceae, and instead favor recognition of four monophyletic and morphologically well circumscribed families in the perianth-bearing Piperales: Aristolochiaceae, Asaraceae, Hydnoraceae, and Lactoridaceae, with a total of six families in the order.
Taurine Antagonizes Macrophages M1 Polarization by Mitophagy-Glycolysis Switch Blockage via Dragging SAM-PP2Ac Transmethylation

The excessive M1 polarization of macrophages drives the occurrence and development of inflammatory diseases. The reprogramming of macrophages from M1 to M2 can be achieved by targeting metabolic events. Taurine promotes for the balance of energy metabolism and the repair of inflammatory injury, preventing chronic diseases and complications. However, little is known about the mechanisms underlying the action of taurine modulating the macrophage polarization phenotype. In this study, we constructed a low-dose LPS/IFN-γ-induced M1 polarization model to simulate a low-grade pro-inflammatory process. Our results indicate that the taurine transporter TauT/SlC6A6 is upregulated at the transcriptional level during M1 macrophage polarization. The nutrient uptake signal on the membrane supports the high abundance of taurine in macrophages after taurine supplementation, which weakens the status of methionine metabolism, resulting in insufficient S-adenosylmethionine (SAM). The low availability of SAM is directly sensed by LCMT-1 and PME-1, hindering PP2Ac methylation. PP2Ac methylation was found to be necessary for M1 polarization, including the positive regulation of VDAC1 and PINK1. Furthermore, its activation was found to promote the elimination of mitochondria by macrophages via the mitophagy pathway for metabolic adaptation. Mechanistically, taurine inhibits SAM-dependent PP2Ac methylation to block PINK1-mediated mitophagy flux, thereby maintaining a high mitochondrial density, which ultimately hinders the conversion of energy metabolism to glycolysis required for M1. Our findings reveal a novel mechanism of taurine-coupled M1 macrophage energy metabolism, providing novel insights into the occurrence and prevention of low-grade inflammation, and propose that the sensing of taurine and SAM availability may allow communication to inflammatory response in macrophages.
The Relationship Between Cognition and Cerebrovascular Reactivity: Implications for Task-Based fMRI

Elucidating the brain regions and networks associated with cognitive processes has been the mainstay of task-based fMRI, under the assumption that BOLD signals are uncompromised by vascular function. This is despite the plethora of research highlighting BOLD modulations due to vascular changes induced by disease, drugs, and aging. On the other hand, BOLD fMRI-based assessment of cerebrovascular reactivity (CVR) is often used as an indicator of the brain's vascular health and has been shown to be strongly associated with cognitive function. This review paper considers the relationship between BOLD-based assessments of CVR, cognition and task-based fMRI. How the BOLD response reflects both CVR and neural activity, and how findings of altered CVR in disease and in normal physiology are associated with cognition and BOLD signal changes are discussed. These are pertinent considerations for fMRI applications aiming to understand the biological basis of cognition. Therefore, a discussion of how the acquisition of BOLD-based CVR can enhance our ability to map human brain function, with limitations and potential future directions, is presented.
The Individual Inclination to an Occupation and its Neuronal Correlate

Many young people decide their professional direction during adolescence. This often coincides with vulnerable phases of puberty-related maturation that is usually accompanied by difficulties in assessing one’s personal inclinations and competences. Several psychological tests have been established among teachers and career advisers serving as a tool for professional coaching the teenagers’ competences and preferences. Many tools are based on the “Theory of Vocational Personalities in Work Environment” developed by John L. Holland since the 1950s, comprising the “RIASEC” model. Today, this theory provides the basis for tests which are used and refined all over the world. Professor Stangl’s online assessable “Situational Interest Test” (SIT) is based on Holland’s theory. By means of 30 short assessments the SIT questionnaire assesses the participant’s personality traits: Realistic (“Doers”), Investigative (“Thinkers”), Artistic (“Creators”), Social (“Helpers”), Enterprising (“Persuaders”), and Conventional (“Organizers”). Modern Magnetic Resonance Imaging (MRI) is able to discriminate between the brain’s compartments as Gray and White Matter using Voxel-Based Morphometry (VBM). This tool allows to reshape and to normalize human brains’ structure to statistically examining individual brains. Up to now findings from 20 years of functional MRI gave detailed insights in correlations between brain structures and mental functions. Hence, knowledge on structural base of cognitive or behavioral patterns is available as a brain’s map for assigning anatomical regions to their functions. The present study demonstrates that there are statistically relevant correlations between all dimensions of Holland’s RIASEC theory by assessing individual professional inclinations and the neuronal structures of the brain. Results show correspondence between the personality traits assigned by the RIASEC test and the functions of significant structural alterations in distinct brain areas well-known from literature.
A Clinical Perspective on the Role of Electronic Devices in Monitoring and Promoting Adherence in Airways Disease

Poor adherence to treatment is a common reason why patients with chronic disease have worse outcomes than might be expected. Poor treatment adherence is of particular concern among people with airways disease because, apart from not taking treatment as prescribed, inhaled medication can also be administered incorrectly. Recently, a number of technological advances that accurately document when an inhaled treatment has been used and, in certain instances, how it was used have been developed. There is good evidence from a number of research groups that these devices, either by patient reminders or physician feedback, promote adherence to inhaled treatments. What is less certain is how, in a real-world setting, these devices change outcomes. In this perspective article, the role of electronic devices in quantifying treatment use and addressing poor treatment adherence and their potential role in clinical practice outside of clinical validation trials are described.
Fear of Cancer Recurrence, Health Anxiety, Worry, and Uncertainty: A Scoping Review About Their Conceptualization and Measurement Within Breast Cancer Survivorship Research

Objective: Fear of Cancer Recurrence (FCR), Health Anxiety (HA), worry, and uncertainty in illness are psychological concerns commonly faced by cancer patients. In survivorship research, these similar, yet different constructs are frequently used interchangeably and multiple instruments are used in to measure them. The lack of clear and consistent conceptualization and measurement can lead to diverse or contradictory interpretations. The purpose of this scoping review was to review, compare, and analyze the current conceptualization and measurements used for FCR, HA, worry, and uncertainty in the breast cancer survivorship literature to improve research and practice. Inclusion Criteria: We considered quantitative, qualitative, and mixed methods studies of breast cancer survivors that examined FCR, HA, worry, or uncertainty in illness as a main topic and included a definition or assessment of the constructs. Methods and Analysis: The six-staged framework was used to guide the scoping review process. Searches of PubMed, CINAHL, and PsycINFO databases were conducted. The principle-based qualitative analysis and simultaneous content analysis procedures were employed to synthesize and map the findings. Findings: After duplicate removal, the search revealed 3,299 articles, of which 82 studies met the inclusion criteria. Several critical attributes overlapped the four constructs, for example, all were triggered by internal somatic and external cues. However, several unique attributes were found (e.g., a sense of loss of security in the body is observed only among survivors experiencing FCR). Overall, findings showed that FCR and uncertainty in illness are more likely to be triggered by cancer-specific factors, while worry and HA have more trait-like in terms of characteristics, theoretical features, and correlates. We found that the measures used to assess each construct were on par with their intended constructs. Eighteen approaches were used to measure FCR, 15 for HA, 8 for worry, and 4 for uncertainty. Conclusion: While consensus on the conceptualization and measurement of the four constructs has not yet been reached, this scoping review identifies key similarities and differences to aid in their selection and measurement. Considering the observed overlap between the four studied constructs, further research delineating the unique attributes for each construct is warranted.
In Ovo and Oral Administration of Probiotic Lactobacilli Modulate Cell- and Antibody-Mediated Immune Responses in Newly Hatched Chicks

There is some evidence that lactobacilli can strengthen the immune system of chickens. This study evaluated the effects of in ovo and oral administration of a lactobacilli cocktail on cytokine gene expression, antibody-mediated immune responses, and spleen cellularity in chickens. Lactobacilli were administered either in ovo at embryonic day 18, orally at days 1, 7, 14, 21, and 28 post-hatches, or a combination of both in ovo and post-hatch inoculation. On day 5 and 10 post-hatch, spleen and bursa of Fabricius were collected for gene expression and cell composition analysis. On days 14 and 21 post-hatch, birds were immunized with sheep red blood cells (SRBC) and keyhole limpet hemocyanin (KLH), and sera were collected on days 7, 14, and 21 post-primary immunization. Birds that received lactobacilli (107 CFU) via in ovo followed by weekly oral administration showed a greater immune response by enhancing antibody responses, increasing the percentage of CD4+ and CD4+CD25+ T cells in the spleen and upregulating the expression of interferon (IFN)-α, IFN-β, interleukin (IL)-8, IL-13, and IL-18 in the spleen and expression of IFN-γ, IL-2, IL-6, IL-8, IL-12, and IL-18 in the bursa. These findings suggest that pre-and post-hatch administration of lactobacilli can modulate the immune response in newly hatched chickens.
Quantifying the Resilience of the U.S. Domestic Aviation Network During the COVID-19 Pandemic

This paper analyzes the impacts of COVID-19 pandemic on the United States air transportation network between March and August 2020. Despite dramatic reductions in flight and passenger volumes, the network remained robust and resilient against perturbation. Although 24% of airports closed, the reduction in network efficiency was only 5.1%, which means airlines continued to serve most destinations. A deeper analysis of airport closures reveals that 1) small peripheral airports were the most likely to be closed; 2) socio-economic and epidemiological factors characterizing the airport’s region such as income, income inequality, political leaning, and the number of observed COVID cases were not predictive of airport closure. Finally, we show that high network robustness has a downside: although emissions from United States air traffic in 2020 fell by 37.4% compared to 2019, mostly due to the drop in the number of flights, emissions per passenger doubled in the period April to August 2020 and increased eightfold in the week of April 5–11. This rise indicates inefficient use of resources by airlines.
Lack of Cell Cycle Inhibitor p21 and Low CD4+ T Cell Suppression in Newborns After Exposure to IFN-β

Type I IFNs, such as interferon alpha and interferon beta, are key regulators of the adaptive immune response during infectious diseases. Type I IFNs are induced upon infection, bind interferon α/β receptors on T-cells and activate intracellular pathways. The activating and inhibitory consequences of type I IFN-signaling are determined by cell type and cellular environment. The neonatal immune system is associated with increased vulnerability to infectious diseases which could partly be explained by an immature CD4+ T-cell compartment. Here, we show low IFN-β-mediated inhibition of CD4+ T-cell proliferation, phosphorylation of retinoblastoma protein and cytokine production in human newborns compared to adults. In addition, both naïve and total newborn CD4+ T-cells are unable to induce the cell-cycle inhibitor p21 upon exposure to IFN-β in contrast to adults. The distinct IFN-β-signaling in newborns provides novel insights into T cell functionality and regulation of T cell-dependent inflammation during early life immune responses.
The Development of the College Students' Experience of Family Harmony Questionnaire (CSEFHQ)

The experience of family harmony, as an individual's subjective evaluation of harmonious family relations, has an important influence on the development of their physical and mental health. This study aimed to develop the College Students' Experience of Family Harmony Questionnaire that is fit for college students in China. On the basis of literature analysis and survey with questionnaires, five pairs of opposite assessment indexes were constructed in this paper, namely, Atmosphere of family (getting along vs. conflict), Responsibility to housework (undertaking housework vs. refusing housework), Time-sharing (sharing vs. self-isolatedness), Seeking help (help-seeking vs. avoidance), and Supporting family members (support-providing vs. indifference). Items of this questionnaire were collected from investigation, relevant scales, and discussion with experts. Here, 562 college students were selected for the pre-test and 696 for the formal test. The results showed that, except for the dimension of refusing housework, which has been deleted, other dimensions remain unchanged, and the final nine dimensions accounted for 66.03% of variance variation. Furthermore, the result of confirmatory factor analysis indicates that the model fit well with the data in construct validity [χ2/df = 2.71, Incremental Fit Index (IFI) = 0.90, Tucker–Lewis Index (TLI) = 0.89, Comparative Fit Index (CFI) = 0.90, root mean square error of approximation (RMSEA) = 0.05, standardized root mean square residual (SRMR) = 0.05]. The Cronbach's alpha (α) coefficient of this questionnaire was 0.97. The split-half reliability was 0.92, and the test–retest reliability was 0.75 for the total questionnaire. The total score of the questionnaire was significantly positively correlated with the total score of family function, family cohesion, family adaptability, and well-being (r = 0.73, 0.71, 0.75, 0.51, respectively, all p < 0.01), and it had a significant negative correlation with loneliness (r = −0.56, p < 0.01). The results showed that the final structure was reasonable, and reliability and validity conformed to the requirements of psychometrics. Therefore, the questionnaire developed in this study can be used as a valid instrument for assessing the experience of family harmony among college students in China.
Grasping of Real-World Objects Is Not Biased by Ensemble Perception

The visual system is known to extract summary representations of visually similar objects which bias the perception of individual objects toward the ensemble average. Although vision plays a large role in guiding action, less is known about whether ensemble representation is informative for action. Motor behavior is tuned to the veridical dimensions of objects and generally considered resistant to perceptual biases. However, when the relevant grasp dimension is not available or is unconstrained, ensemble perception may be informative to behavior by providing gist information about surrounding objects. In the present study, we examined if summary representations of a surrounding ensemble display influenced grip aperture and orientation when participants reached-to-grasp a central circular target which had an explicit size but importantly no explicit orientation that the visuomotor system could selectively attend to. Maximum grip aperture and grip orientation were not biased by ensemble statistics during grasping, although participants were able to perceive and provide manual estimations of the average size and orientation of the ensemble display. Support vector machine classification of ensemble statistics achieved above-chance classification accuracy when trained on kinematic and electromyography data of the perceptual but not grasping conditions, supporting our univariate findings. These results suggest that even along unconstrained grasping dimensions, visually-guided behaviors toward real-world objects are not biased by ensemble processing.
Number of Social Determinants of Health and Fatal and Nonfatal Incident Coronary Heart Disease in the Reasons for Geographic and Racial Differences in Stroke (REGARDS) Study.

Background: Social determinants of health (SDH) are individually associated with incident coronary heart disease (CHD) events. Indices reflecting social deprivation have been developed for population management, but are difficult to operationalize during clinical care. We examined whether a simple count of SDH is associated with fatal incident CHD and nonfatal myocardial infarction (MI). Methods: We used data from the prospective longitudinal REasons for Geographic And Racial Differences in Stroke cohort study, a national population-based sample of community-dwelling Black and white adults age ≥45 years recruited from 2003-7. Seven SDH from the five Healthy People 2020 domains included social context (Black race, social isolation); education (educational attainment); economic stability (annual household income); neighborhood (living in a zip code with high poverty); and healthcare (lacking health insurance, living in one of the 9 US states with the least public health infrastructure). Outcomes were expert adjudicated fatal incident CHD and nonfatal MI. Results: Of 22,152 participants free of CHD at baseline, 58.8% were women, 42.0% were Blacks, 20.6% had no SDH, 30.6% had 1, 23.0% had 2, and 25.8% had ≥3. There were 463 fatal incident CHD events and 932 nonfatal MIs over median 10.7 years [IQR 6.6-12.7]. Fewer SDH were associated with nonfatal MI than with fatal incident CHD. The age-adjusted incidence per 1000 person-years increased with the number of SDH for both fatal incident CHD (0 SDH 1.30, 1 SDH 1.44, 2 SDH 2.05, ≥3 SDH 2.86) and nonfatal MI (0 SDH 3.91, 1 SDH 4.33, ≥2 SDH 5.44). Compared to those without SDH, crude and fully adjusted hazard ratios (HR) for fatal incident CHD among those with ≥3 SDH were 3.00 (95% CI 2.17, 4.15) and 1.67 (95% CI 1.18, 2.37), respectively; and that for nonfatal MI among those with ≥2 SDH were 1.57 (95% CI 1.30, 1.90) and 1.14 (0.93, 1.41), respectively. Conclusions: A greater burden of SDH was associated with a graded increase in risk of incident CHD, with greater magnitude and independent associations for fatal incident CHD. Counting the number of SDH may be a promising approach that could be incorporated into clinical care to identify individuals at high risk of CHD.
Silhouette Body Measurement Benchmarks

Anthropometric body measurements are important for industrial design, garment fitting, medical diagnosis and ergonomics. A number of methods have been proposed to estimate the body measurements from images, but progress has been slow due to the lack of realistic and publicly available datasets. The existing works train and test on silhouettes of 3D body meshes obtained by fitting a human body model to the commercial CAESAR scans. In this work, we introduce the BODY-fit dataset that contains fitted meshes of 2,675 female and 1,474 male 3D body scans. We unify evaluation on the CAESAR-fit and BODY-fit datasets by computing body measurements from geodesic surface paths as the ground truth and by generating two-view silhouette images. We also introduce BODY-rgb - a realistic dataset of 86 male and 108 female subjects captured with an RGB camera and manually tape measured ground truth. We propose a simple yet effective deep CNN architecture as a baseline method which obtains competitive accuracy on the three datasets.
Analyzing the Feasibility of Generating Data Visualizations from Hand-drawn Sketches Using Deep Learning

—Data visualization has become a vital tool to help people understand the driving forces behind real-world phenomena. Although the learning curves of visualization tools have been reduced signiﬁcantly, domain experts still may require training to use them. This paper investigates the feasibility of using deep learning techniques and tools to generate the source code for multi-platform data visualizations automatically from hand-drawn sketches provided by a domain expert. The idea is similar to how an expert might sketch on a cocktail napkin and ask a software engineer to implement the sketched visualization. We explore key challenges in generating visualization code from hand-drawn sketches, particularly model training challenges, since acquiring a large dataset of sketches paired with visualization source code is expensive. We present solutions for these problems and conduct experiments that demonstrate the feasibility of generating visualizations from hand-drawn sketches. The best models tested reach an structural accuracy of 95% in generating correct data visualization source code from hand-drawn sketches of visualizations.