Miracle-dz/UniFAR-FTUs huggingface dataset:
How light and biomass density influence the reproduction of delayed Saccharina latissima gametophytes (Phaeophyceae)

Kelp life‐cycle transitions are complex and susceptible to various (a)biotic controls. Understanding the microscopic part of the kelp's lifecycle is of key importance, as gametophytes form a critical phase influencing, among others, the distributional limits of the species. Many environmental controls have been identified that affect kelp gametogenesis, whose interactive effects can be subtle and counterintuitive. Here we performed a fully factorial experiment on the (interactive) influences of light intensity, light quality, and the Initial Gametophyte Density (IGD) on Saccharina latissima reproduction and vegetative growth of delayed gametophytes. A total of 144 cultures were followed over a period of 21 d. The IGD was a key determinant for reproductive success, with increased IGDs (≥0.04 mg DW · mL−1) practically halting reproduction. Interestingly, the effects of IGDs were not affected by nutrient availability, suggesting a resource‐independent effect of density on reproduction. The Photosynthetically Usable Radiation (PUR), overarching the quantitative contribution of both light intensity and light quality, correlated with both reproduction and vegetative growth. The PUR furthermore specifies that the contribution of light quality, as a lifecycle control, is a matter of absorbed photon flux instead of color signaling. We hypothesize that (i) the number of photons absorbed, independent of their specific wavelength, and (ii) IGD interactions, independent of nutrient availability, are major determinants of reproduction in S. latissima gametophytes. These insights help understand kelp gametophyte development and dispersal under natural conditions, while also aiding the control of in vitro gametophyte cultures.
Muscle Hypertrophy Response Is Affected by Previous Resistance Training Volume in Trained Individuals

Abstract Scarpelli, MC, Nóbrega, SR, Santanielo, N, Alvarez, IF, Otoboni, GB, Ugrinowitsch, C, and Libardi, CA. Muscle hypertrophy response is affected by previous resistance training volume in trained individuals. J Strength Cond Res 36(4): 1153–1157, 2022—The purpose of this study was to compare gains in muscle mass of trained individuals after a resistance training (RT) protocol with standardized (i.e., nonindividualized) volume (N-IND), with an RT protocol using individualized volume (IND). In a within-subject approach, 16 subjects had one leg randomly assigned to N-IND (22 sets·wk−1, based on the number of weekly sets prescribed in studies) and IND (1.2 × sets·wk−1 recorded in training logs) protocols. Muscle cross-sectional area (CSA) was assessed by ultrasound imaging at baseline (Pre) and after 8 weeks (Post) of RT, and the significance level was set at p < 0.05. Changes in the vastus lateralis CSA (difference from Pre to Post) were significantly higher for the IND protocol (p = 0.042; mean difference: 1.08 cm2; confidence interval [CI]: 0.04–2.11). The inferential analysis was confirmed by the CI of the effect size (0.75; CI: 0.03–1.47). Also, the IND protocol had a higher proportion of individuals with greater muscle hypertrophy than the typical error of the measurement (chi-square, p = 0.0035; estimated difference = 0.5, CI: 0.212–0.787). In conclusion, individualizing the weekly training volume of research protocols provides greater gains in muscle CSA than prescribing a group standard RT volume.
Sex-Based Differences in Melanoma Survival in a Contemporary Patient Cohort.

Background: A female survival advantage in cutaneous melanoma has been long recognized. However, whether this extends across all age groups, with risk stratification using the latest prognostic staging system or in the current era of efficacious systemic therapies is unknown. Therefore, we evaluated whether sex-based differences in melanoma survival persisted within a recent population-based patient cohort with consideration of these factors. Materials and Methods: We identified stage II-IV cutaneous melanoma patients from 2010 to 2014 Surveillance, Epidemiology, and End Results cancer registries data. We recalculated stage per American Joint Committee on Cancer 8th edition guidelines. Cancer-specific survival (CSS) was estimated by using the Kaplan-Meier method and multivariable Cox proportional hazards regression. Results: Of 16,807 patients (39.8% female), 8,990 were stage II, 4,826 stage III, and 2,991 stage IV at diagnosis. Unadjusted 3-/5-year CSS estimates for females versus males were 64.2% versus 59.7%, and 53.5% versus 49.9%, respectively, p ≤ 0.0001. Five-year CSS varied within each stage and across age strata of <45, 45 - 59, and ≥60 years. Within each stage, females <45 had better CSS than all other sex/age groups (p < 0.0001). In multivariable analysis of stage II/III patients, female sex, younger age, and lower mitotic index retained favorable CSS prognostic significance (p < 0.001). Conclusions: Sex-based differences in melanoma survival persist in a contemporary patient cohort staged with the latest prognostic system. These data may guide decision marking regarding adjuvant therapy, highlight the importance of including sex as a pre-specified clinical trial variable, and suggest that investigation of underlying biologic mechanisms may drive discovery of biomarkers and therapeutic targets to improve patient care.
Physician understanding, explainability, and trust in a hypothetical machine learning risk calculator

OBJECTIVE Implementation of machine learning (ML) may be limited by patients' right to "meaningful information about the logic involved" when ML influences healthcare decisions. Given the complexity of healthcare decisions, it is likely that ML outputs will need to be understood and trusted by physicians, and then explained to patients. We therefore investigated the association between physician understanding of ML outputs, their ability to explain these to patients, and their willingness to trust the ML outputs, using various ML explainability methods. MATERIALS AND METHODS We designed a survey for physicians with a diagnostic dilemma that could be resolved by an ML risk calculator. Physicians were asked to rate their understanding, explainability, and trust in response to 3 different ML outputs. One ML output had no explanation of its logic (the control) and 2 ML outputs used different model-agnostic explainability methods. The relationships among understanding, explainability, and trust were assessed using Cochran-Mantel-Haenszel tests of association. RESULTS The survey was sent to 1315 physicians, and 170 (13%) provided completed surveys. There were significant associations between physician understanding and explainability (P < .001), between physician understanding and trust (P < .001), and between explainability and trust (P < .001). ML outputs that used model-agnostic explainability methods were preferred by 88% of physicians when compared with the control condition; however, no particular ML explainability method had a greater influence on intended physician behavior. CONCLUSIONS Physician understanding, explainability, and trust in ML risk calculators are related. Physicians preferred ML outputs accompanied by model-agnostic explanations but the explainability method did not alter intended physician behavior.
Study on the Mechanism of Nano-SiO2 for Improving the Properties of Cement-Based Soil Stabilizer

A new nano-soil stabilizer (N-MBER, Nanometer Material Becoming Earth into Rock) material was developed in this research by using the high activity and ultrafine properties of nano-SiO2 (NS), which were able to improve the properties of cement-based soil stabilizer and had broad application prospects. The results showed that (1) the strength of N-MBER obeyed a compound function relation with curing period and additive amount of NS. The relationship between strength and curing period obeyed an exponential function when the additive amount was constant. The strength and additive amount were a power function when the curing period was fixed. The compressive strength of N-MBER increased by more than 15% compared with MBER at day 28 of the curing period, and 50% compared with grade 32.5 cement. (2) The pozzolanic catalytic activity of NS significantly increased the amount of calcium silicate hydrate gel (C–S–H) in the N-MBER colloid. NS was also able to make the distribution of the network structure of colloidal space more uniform and improved the fractal dimension of particles by 0.05. The above results provide theoretical data for exploring the mechanism of soil stabilizer strength growth and for promoting the application of solid waste utilization.
Pervasive Discrimination and Allostatic Load in African American and White Adults

Supplemental digital content is available in the text. ABSTRACT Objective This study aimed to examine associations among race, the accumulation of multiple forms of discriminatory experiences (i.e., “pervasive discrimination”), and allostatic load (AL) in African Americans and whites in midlife. Methods Using data collected in 2004 to 2006 from 226 African American and 978 white adults (57% female; mean [SD] age = 54.7 [0.11] years) in the Midlife in the United States II Biomarker Project, a pervasive discrimination score was created by combining three discrimination scales, and an AL score was created based on 24 biomarkers representing seven physiological systems. Linear regression models were conducted to examine the association between pervasive discrimination and AL, adjusting for demographics and medical, behavioral, and personality covariates. A race by pervasive discrimination interaction was also examined to determine whether associations varied by race. Results African Americans had higher pervasive discrimination and AL scores than did whites. In models adjusted for demographics, socioeconomic status, medications, health behaviors, neuroticism, and negative affect, a pervasive discrimination score of 2 versus 0 was associated with a greater AL score (b = 0.30, SE = 0.07, p < .001). Although associations seemed to be stronger among African Americans as compared with whites, associations did not statistically differ by race. Conclusions More pervasive discrimination was related to greater multisystemic physiological dysregulation in a cohort of African American and white adults. Measuring discrimination by combining multiple forms of discriminatory experiences may be important for studying the health effects of discrimination.
Effects of Seedling Age on Colonization Patterns of Citrus limon Plants by Endophytic Beauveria bassiana and Metarhizium anisopliae and Their Influence on Seedlings Growth

The inoculation methods, the fungal strains, and several other factors are known to influent the success of fungal entomopathogens colonization in plants. The physiological status of the plant could also be another determinant. In the present study, the ability of three strains of Beauveria bassiana and one strain of Metarhizium anisopliae to successfully colonize Citrus limon plants and the influence of seedling age on endophytic colonization success was examined. Three, 4, and 6 months old seedlings were inoculated with 10 mL of 1 × 108 conidial·mL−1 suspensions of each of the four fungal strains via foliar spraying. All fungal strains successfully colonized citrus seedlings and were sustained up to 2 months in colonized plants irrespective of the seedling age, with differences in the mean percentage colonization recorded at various post-inoculation periods among the fungal strains. The highest percent endophytic fungi recovery rate was recorded in the 3 months old seedlings, where fungal mycelia of inoculated fungi were successfully re-isolated from 65.6% of the untreated newly developed leaf and stem tissues. One strain of B. bassiana, BB Fafu-12, significantly improved seedling height and leaf number. The study demonstrates the influence of seedling age on B. bassiana and M. anisopliae successful colonization in the citrus plant.
Maternal Glucocorticoid Metabolism Across Pregnancy: A Potential Mechanism Underlying Fetal Glucocorticoid Exposure.

CONTEXT Across pregnancy, maternal serum cortisol levels increase up to 3-fold. It is not known whether maternal peripheral cortisol metabolism and clearance change across pregnancy or influence fetal cortisol exposure and development. OBJECTIVES The primary study objective was to compare maternal urinary glucocorticoid metabolites, as markers of cortisol metabolism and clearance, between the second and third trimester of pregnancy. Secondary objectives were to test associations of total maternal urinary glucocorticoid excretion, with maternal serum cortisol levels and offspring birth weight z score. DESIGN, PARTICIPANTS, AND SETTING A total of 151 women with singleton pregnancies, recruited from prenatal clinic at the Pittsburgh site of the Measurement of Maternal Stress (MOMS) study, had 24-hour urine collections during both the second and third trimesters. RESULTS Between the second and third trimester, total urinary glucocorticoid excretion increased (ratio of geometric means [RGM] 1.37, 95% CI 1.22-1.52, P < .001), and there was an increase in calculated 5β-reductase compared to 5α-reductase activity (RGM 3.41, 95% CI 3.04-3.83, P < .001). During the third trimester total urinary glucocorticoid excretion and serum cortisol were negatively correlated (r = -0.179, P = .029). Mean total urinary glucocorticoid excretion across both trimesters and offspring birth weight z score were positively associated (β = 0.314, P = .001). CONCLUSIONS The estimated activity of maternal enzymes responsible for cortisol metabolism change between the second and third trimester of pregnancy. Additionally, maternal peripheral metabolism and clearance of cortisol may serve as a novel mechanism affecting fetal cortisol exposure and growth.
Ab Initio Construction and Evolutionary Analysis of Protein-Coding Gene Families with Partially Homologous Relationships: Closely Related Drosophila Genomes as a Case Study

Abstract How have genes evolved within a well-known genome phylogeny? Many protein-coding genes should have evolved as a whole at the gene level, and some should have evolved partly through fragments at the subgene level. To comprehensively explore such complex homologous relationships and better understand gene family evolution, here, with de novo-identified modules, the subgene units which could consecutively cover proteins within a set of closely related species, we applied a new phylogeny-based approach that considers evolutionary models with partial homology to classify all protein-coding genes in nine Drosophila genomes. Compared with two other popular methods for gene family construction, our approach improved practical gene family classifications with a more reasonable view of homology and provided a much more complete landscape of gene family evolution at the gene and subgene levels. In the case study, we found that most expanded gene families might have evolved mainly through module rearrangements rather than gene duplications and mainly generated single-module genes through partial gene duplication, suggesting that there might be pervasive subgene rearrangement in the evolution of protein-coding gene families. The use of a phylogeny-based approach with partial homology to classify and analyze protein-coding gene families may provide us with a more comprehensive landscape depicting how genes evolve within a well-known genome phylogeny.
Influence of Activators on Mechanical Properties of Modified Fly Ash Based Geopolymer Mortars

The aim of this work was to study the influence of the type of activator on the formulation of modified fly ash based geopolymer mortars. Geopolymer and alkali-activated materials (AAM) were made from fly ashes derived from coal and biomass combustion in thermal power plants. Basic activators (NaOH, CaO, and Na2SiO3) were mixed with fly ashes in order to develop binding properties other than those resulting from the use of Portland cement. The results showed that the mortars with 5 mol/dm3 of NaOH and 100 g of Na2SiO3 (N5-S22) gave a greater compressive strength than other mixes. The compressive strengths of analyzed fly ash mortars with activators N5-S22 and N5-C10 (5 mol/dm3 NaOH and 10% CaO) varied from 14.3 MPa to 5.9 MPa. The better properties of alkali-activated mortars with regular fly ash were influenced by a larger amount of amorphous silica and alumina phases. Scanning electron microscopy and calorimetry analysis provided a better understanding of the observed mechanisms.
Endosialin (TEM1) as a Diagnostic, Progression, and Prognostic Serum Marker for Patients With Colorectal Cancer—A Preliminary Study

Colorectal cancer (CRC) is one of the most common cancers worldwide usually diagnosed in the advanced stage. In this study, the serum concentration of tumor endothelial marker 1 (TEM1) was measured and correlated with clinicopathological features to evaluate whether TEM1 might serve as a biomarker for early CRC diagnosis, progression, and prognosis. The concentration of TEM1 was measured in the serum samples of 45 patients with CRC and 35 healthy individuals using enzyme-linked immunosorbent assay test. The mean serum concentration of TEM1 was significantly higher in the patients with CRC compared to the healthy individuals (1.31 ± 0.16 vs 0.92 ± 0.90 ng/mL; P < .001). The mean concentration of TEM1 significantly increased in the patients having CRC with early stage (stage I + II) compared to noncancer control individuals (stage I + II vs control 1.21 ± 0.13 ng/mL: 0.92 ± 0.90 ng/mL; P < .001). The TEM1 concentration in blood serum also showed a significant association with the development of T stages (P < .001), N stages (P < .001), and M stages (P = .006). The TEM1 sensitivity and specificity in CRC detection are higher than routinely used blood markers (carcinoembryonic antigen [CEA] and carbohydrate antigen [Ca 19-9]). Patients with high TEM1 concentration (≥1.055 ng/mL) had a worse overall survival rate compared to the patients having CRC with low TEM1 concentration (<1.055 ng/mL). In conclusion, TEM1 can act as a potential diagnostic, progression, and prognostic serum biomarker for patients with CRC; TEM1 might be a good supplement for commonly used markers CEA and Ca 19-9.
Can Cities Activate Sleeper Species and Predict Future Forest Pests? A Case Study of Scale Insects

Sleeper species are innocuous native or naturalized species that exhibit invasive characteristics and become pests in response to environmental change. Climate warming is expected to increase arthropod damage in forests, in part, by transforming innocuous herbivores into severe pests: awakening sleeper species. Urban areas are warmer than natural areas due to the urban heat island effect and so the trees and pests in cities already experience temperatures predicted to occur in 50–100 years. We posit that arthropod species that become pests of urban trees are those that benefit from warming and thus should be monitored as potential sleeper species in forests. We illustrate this with two case studies of scale insects that are important pests of urban trees in parts of the US. Melanaspis tenebricosa and Parthenolecanium quercifex are geographically native to the US but take on invasive characteristics such as higher survival and reproduction and become disconnected from natural enemies on urban trees due to the urban heat island effect. This allows them to reach high densities and damage their host trees. Parthenolecanium quercifex density increases up to 12 times on urban willow oaks with just 2 °C of warming due to higher survival and adaptation to warmer temperatures. The urban heat island effect also creates a phenological mismatch between P. quercifex and its parasitoid complex, and so egg production is higher. Melanaspis tenebricosa density can increase 300 times on urban red maples with 2.5 °C of warming. This too is due to direct effects of warmer temperatures on survival and fecundity but M. tenebricosa also benefits from the drought stress incurred by warmer urban trees. These effects combine to increase M. tenebricosa density in forests as well as on urban trees at latitudes higher than its native range. We illustrate how cities provide a unique opportunity to study the complex effects of warming on insect herbivores. Studying pestilent urban species could be a pragmatic approach for identifying and preparing for sleeper species.
Self-organized emergence of folded protein-like network structures from geometric constraints

The intricate three-dimensional geometries of protein tertiary structures underlie protein function and emerge through a folding process from one-dimensional chains of amino acids. The exact spatial sequence and configuration of amino acids, the biochemical environment and the temporal sequence of distinct interactions yield a complex folding process that cannot yet be easily tracked for all proteins. To gain qualitative insights into the fundamental mechanisms behind the folding dynamics and generic features of the folded structure, we propose a simple model of structure formation that takes into account only fundamental geometric constraints and otherwise assumes randomly paired connections. We find that despite its simplicity, the model results in a network ensemble consistent with key overall features of the ensemble of Protein Residue Networks we obtained from more than 1000 biological protein geometries as available through the Protein Data Base. Specifically, the distribution of the number of interaction neighbors a unit (amino acid) has, the scaling of the structure’s spatial extent with chain length, the eigenvalue spectrum and the scaling of the smallest relaxation time with chain length are all consistent between model and real proteins. These results indicate that geometric constraints alone may already account for a number of generic features of protein tertiary structures.
Injury characteristics of the Pulse Nightclub shooting: Lessons for mass casualty incident preparation.

BACKGROUND On the morning of June 12, 2016, an armed assailant entered the Pulse Nightclub in Orlando, Florida, and initiated an assault that killed 49 people and injured 53. The regional Level I trauma center and two community hospitals responded to this mass casualty incident. A detailed analysis was performed to guide hospitals who strive to prepare for future similar events. METHODS A retrospective review of all victim charts and/or autopsy reports was performed to identify victim presentation patterns, injuries sustained, and surgical resources required. Patients were stratified into three groups: survivors who received care at the regional Level I trauma center, survivors who received care at one of two local community hospitals, and decedents. RESULTS Of the 102 victims, 40 died at the scene and 9 died upon arrival to the Level I trauma center. The remaining 53 victims received definitive medical care and survived. Twenty-nine victims were admitted to the trauma center and five victims to a community hospital. The remaining 19 victims were treated and discharged that day. Decedents sustained significantly more bullet impacts than survivors (4 ± 3 vs. 2 ± 1; p = 0.008) and body regions injured (3 ± 1 vs. 2 ± 1; p = 0.0002). Gunshots to the head, chest, and abdominal body regions were significantly more common among decedents than survivors (p < 0.0001). Eighty-two percent of admitted patients required surgery in the first 24 hours. Essential resources in the first 24 hours included trauma surgeons, emergency room physicians, orthopedic/hand surgeons, anesthesiologists, vascular surgeons, interventional radiologists, intensivists, and hospitalists. CONCLUSION Mass shooting events are associated with high mortality. Survivors commonly sustain multiple, life-threatening ballistic injuries requiring emergent surgery and extensive hospital resources. Given the increasing frequency of mass shootings, all hospitals must have a coordinated plan to respond to a mass casualty event. LEVEL OF EVIDENCE Epidemiological Study, level V.