Miracle-dz/UniFAR-FTUs huggingface dataset:
Water‐limited environments affect the association between functional diversity and forest productivity

Abstract The link between biodiversity and ecosystem function can depend on environmental conditions. This contingency can impede our ability to predict how biodiversity‐ecosystem function (BEF) relationships will respond to future environmental change, causing a clear need to explore the processes underlying shifts in BEF relationships across large spatial scales and broad environmental gradients. We compiled a dataset on five functional traits (maximum height, wood density, specific leaf area [SLA], seed size, and xylem vulnerability to embolism [P50]), covering 78%–90% of the tree species in the National Forest Inventory from Italy, to test (i) how a water limitation gradient shapes the functional composition and diversity of forests, (ii) how functional composition and diversity of trees relate to forest annual increment via mass ratio and complementarity effects, and (iii) how the relationship between functional diversity and annual increment varies between Mediterranean and temperate climate regions. Functional composition varied with water limitation; tree communities tended to have more conservative traits in sites with higher levels of water limitation. The response of functional diversity differed among traits and climatic regions but among temperate forest plots, we found a consistent increase of functional diversity with water limitation. Tree diversity was positively associated with annual increment of Italian forests through a combination of mass ratio and niche complementarity effects, but the relative importance of these effects depended on the trait and range of climate considered. Specifically, niche complementarity effects were more strongly associated with annual increment in the Mediterranean compared to temperate forests. Synthesis: Overall, our results suggest that biodiversity mediates forest annual increment under water‐limited conditions by promoting beneficial interactions between species and complementarity in resource use. Our work highlights the importance of conserving functional diversity for future forest management to maintain forest annual increment under the expected increase in intensity and frequency of drought.
Genome-wide analysis highlights genetic admixture in exotic germplasm resources of Eucalyptus and unexpected ancestral genomic composition of interspecific hybrids

Eucalyptus is an economically important genus comprising more than 890 species in different subgenera and sections. Approximately twenty species of subgenus Symphyomyrtus account for 95% of the world’s planted eucalypts. Discrimination of closely related eucalypt taxa is challenging, consistent with their recent phylogenetic divergence and occasional hybridization in nature. Admixture, misclassification or mislabeling of Eucalyptus germplasm resources maintained as exotics have been suggested, although no reports are available. Moreover, hybrids with increased productivity and traits complementarity are planted worldwide, but little is known about their actual genomic ancestry. In this study we examined a set of 440 trees of 16 different Eucalyptus species and 44 interspecific hybrids of multi-species origin conserved in germplasm banks in Brazil. We used genome-wide SNP data to evaluate the agreement between the alleged phylogenetic classification of species and provenances as registered in their historical records, and their observed genetic clustering derived from SNP data. Genetic structure analyses correctly assigned each of the 16 species to a different cluster although the PCA positioning of E. longirostrata was inconsistent with its current taxonomy. Admixture was present for closely related species’ materials derived from local germplasm banks, indicating unintended hybridization following germplasm introduction. Provenances could be discriminated for some species, indicating that SNP-based discrimination was directly proportional to geographical distance, consistent with an isolation-by-distance model. SNP-based genomic ancestry analysis showed that the majority of the hybrids displayed realized genomic composition deviating from the expected ones based on their pedigree records, consistent with admixture in their parents and pervasive genome-wide directional selection toward the fast-growing E. grandis genome. SNP data in support of tree breeding provide precise germplasm identity verification, and allow breeders to objectively recognize the actual ancestral origin of superior hybrids to more realistically guide the program toward the development of the desired genetic combinations.
A SSESSING THE EFFECT OF ANTIBODY RESPONSES ON VIRAL REBOUND DYNAMICS IN POSTNATALLY SHIV-INFECTED INFANT R HESUS MACAQUES

initiation is likely to affect the size of the latent viral reservoir established, as well as the development of adaptive immune responses, such as the generation of neutralizing antibody responses against the virus. How these parameters impact the ability of infants to control viremia and the time to viral rebound after ART interruption is unclear. To gain insight into the dynamics, we utilized mathematical models to investigate the effect of time of ART initiation via latent reservoir size and autologous virus neutralizing antibody responses in delaying viral rebound when treatment is interrupted. We used an infant nonhuman primate Simian/Human Immunodeficiency Virus (SHIV) infection model that mimics breast milk HIV transmission in human infants. Infant Rhesus macaques (RMs) were orally challenged with SHIV.C. CH505 375H dCT and either given ART at 4-7 days post-infection (early ART condition), at 2 weeks post-infection (intermediate ART condition), or at 8 weeks post-infection (late ART condition). These infants were then monitored for up to 60 months post-infection with serial viral load and immune measurements. We develop a stochastic mathematical model to investigate the joint effect of latent reservoir size, the autologous neutralizing antibody potency, and CD4+ T cell levels on the time to viral rebound and control of post-rebound viral loads. We find that the latent reservoir size is an important determinant in explaining time to viral rebound by affecting the growth rate of the virus. The presence of neutralizing antibodies also can delay rebound, but we find this effect for high potency antibody responses only.
Are live lectures a discontinued model? A survey on the influence of synchronous online lecturing on the perception of teaching and assessment outcome

Objectives: In the early phase of their studies, students are confronted with a number of teaching and learning methods they are usually not familiar with. Beyond, learning in a university environment requires a high degree of self-organization. Thus, the transition from learning in a school environment to university can be challenging for students and associated with adjustment difficulties. We hypothesized that synchronous online lecturing might be able to serve as a thematic superstructure and a curricular guide that can positively influence course perception, motivation and exam outcome. Methods: We investigated this hypothesis in a retrospective approach by comparing results from histology exams (2020 n=411, 2021 n= 423) and questionnaires for course evaluation received from medical and dentistry second semester students of the RWTH Aachen University, Germany, in 2020 (n=113 questionnaire participants) and 2021 (n=106 questionnaire participants). While in 2020, due to the Corona Pandemic, no synchronous online lectures were held, these were reintroduced in 2021. Results: Our results show several differences in between the two study cohorts. Most important findings include a significantly (p<0.001) lower number of students that failed to pass or withdrew from the exam in 2021, an increased motivation to deal with the learning content (p<0.001) and a higher perceived quality of the study materials (p<0.001) in 2021. Conclusion: Our study indicates that synchronous online lectures can be an important tool to help students to accustom to new learning environments and to structure private study. Further studies will now have to show whether live (online) lectures can have the same significance during clinical training.
Papillary carcinoma on thyroglossal tract cyst: our attitude toward a rare pathology whose management is often controversial

Abstract Malignant degeneration on remnants of the thyroglossal tract is a very rare phenomenon. In our practice setting, we report the management of papillary carcinoma on a thyroglossal tract cyst. This was a 44-year-old female patient with a postoperative diagnosis of papillary carcinoma of the thyroglossal tract with an atypical clinical and ultrasound presentation. She subsequently underwent total thyroidectomy and bilateral recurrent lymph node dissection, with resection of fibrous scar tissue in the previously operated hyoid region. We have discussed our therapeutic attitude to this rare pathology, the management of which is the subject of controversy.
Learning surgical knot tying and suturing technique – effects of different forms of training in a controlled randomized trial with dental students

Objective: The acquisition of surgical skills requires motor learning. A special form of this is intermanual transfer by transferring motor skills from the nondominant hand (NDH) to the dominant hand (DH). The purpose of this study was to determine the learning gains that can be achieved for the DH by training with the DH, the NDH, and by non-surgical alternative training (AT). Methods: 124 preclinical (n=62) and clinical (n=62) dental students completed surgical knot tying and suturing technique training with the DH, with the NDH, and an AT in a controlled randomized trial. Results: A statistically significant learning gain in knot tying and suture technique with the DH was evident only after training with the DH when compared to training with the NDH (p<0.001 and p=0.004, respectively) and an AT (p=0.001 and p=0.010, respectively). Of those students who achieved a learning gain ≥4 OSATS points, 46.4% (n=32) benefited in their knot tying technique with the DH from training with the DH, 29.0% (n=20) from training with the NDH, and 24.6% (n=17) from an AT while 45.7% (n=32) benefited in their suturing technique with the DH from training with the DH, 31.4% (n=22) from training with the NDH, and 22, 9% (n=16) from an AT. Conclusions: Training with the DH enabled significantly better learning gains in the surgical knot tying and suturing techniques with the DH.
Nonadherence to anti-tuberculosis treatment, reasons and associated factors among pulmonary tuberculosis patients in the communities in Indonesia

Background Tuberculosis (TB) is the world’s major public health problem. We assessed the proportion, reasons, and associated factors for anti-TB treatment nonadherence in the communities in Indonesia. Methods This national coverage cross-sectional survey was conducted from 2013 to 2014 with stratified multi-stage cluster sampling. Based on the region and rural-urban location. The 156 clusters were distributed in 136 districts/cities throughout 33 provinces, divided into three areas. An eligible population of age ≥15 was interviewed to find TB symptoms and screened with a thorax x-ray. Those whose filtered result detected positive followed an assessment of Sputum microscopy, LJ culture, and Xpert MTB/RIF. Census officers asked all participants about their history of TB and their treatment—defined Nonadherence as discontinuation of anti-tuberculosis treatment for <6 months. Data were analyzed using STATA 14.0 (College Station, TX, USA). Results Nonadherence to anti-TB treatment proportion was 27.24%. Multivariate analysis identified behavioral factors significantly associated with anti-TB treatment nonadherence, such as smoking (OR = 1.78, 95% CI (1.47–2.16)); place of first treatment received: government hospital (OR = 1.45, 95% CI:1.06–1.99); private hospital (OR = 1.93, 95% CI: 1.38–2.72); private practitioner (OR = 2.24, 95% CI: 1.56–3.23); socio-demographic and TB status included region: Sumatera (OR = 1.44, 95% CI: 1.05–1.98); other areas (OR = 1.84, 95% CI: 1.30–2.61); low level of education (OR = 1.60, 95% CI: 1.27–2.03); and current TB positive status (OR = 2.17, 95% CI: 1.26–3.73). Conclusions Nonadherence to anti-TB drugs was highly related to the personal perception of the respondents, despite smoking, current TB status, a place for the first treatment, education, and region. The position of the first TB treatment at the private practitioner was significantly associated with the risk of Nonadherence to treatment.
Gluconeogenesis in the Yolk Sac Membrane: Enzyme Activity, Gene Expression, and Metabolites During Layer Chicken Development

ABSTRACT Yolk sac membranes of layer eggs were collected daily (n = 7–9) from day three of incubation to day three post-hatch, and mRNA expression and activities were quantified for key gluconeogenesis enzymes (glucose-6-phosphatase, fructose-1,6-bisphosphatase, cytosolic and mitochondrial phosphoenolpyruvate carboxykinases, and pyruvate carboxylase). Lactate, triglycerides, non-esterified fatty acids, glycogen, and glucose in the yolk sac membrane, and blood glucose levels were also measured. The mRNA expression and activity were detected for all enzymes. Differences in expression levels and enzyme activities seemed to reflect the embryo’s developmental environment and physiological demands at different developmental stages. During the first week to the mid-second week of incubation, the expression and activity of gluconeogenic enzymes and lactate concentrations were high, suggesting an active period of gluconeogenesis from lactate, reflecting possible hypoxia in the embryo before completed formation of the chorioallantoic capillaries. From the mid-second week to mid-third week, when embryos were in an aerobic state, the triglyceride and non-esterified fatty acid contents increased in the yolk sac. Triglycerides from yolk lipids are typically hydrolyzed to produce non-esterified fatty acids as an energy source, whereas the glycerol skeleton is used for gluconeogenesis. In the late third week, when embryos were considered to re-enter an anaerobic state, the mRNA expression and enzyme activity of only glucose-6-phosphatase were high and the amount of glycogen in the yolk sac was reduced. Therefore, it is suggested that gluconeogenesis activity is low during this period, and the carbohydrates stored in the yolk sac membrane are secreted into the blood as energy for hatching. This study confirmed the role of the yolk sac membrane as a vital gluconeogenic organ during chicken egg incubation.
Rheology of a gypsum suspension in the presence of different superplasticizers

In this work, the rheological properties of suspensions of micron-sized gypsum particles dispersed in water were studied in the presence of different fluidizer molecules. The yield stress and the shear moduli were measured versus the volume fraction in the presence of these molecules. Using the same polyelectrolyte with different molecular weights, the dependence of yield stress versus the gyration radius of the polymer was investigated; also different sizes of the gypsum particles allowed to check the size dependence of the yield stress. A particular attention was brought to the change of the thickness of the polymer layer with the volume fraction. From a model, which relates the steric interaction between the two polymer layers to the yield stress and shear modulus, an important compression of the polymer layer with the volume fraction was found. At higher volume fractions a dynamic jamming transition was observed at a critical volume fraction of 0.485 which does not depend on the presence of the fluidi.
Prevalence and factors associated with excess weight in adolescents in a low-income neighborhood - Northeast, Brazil

Abstract Objectives: to study the prevalence of excess weight and associated factors among adolescents from a low-income neighborhood located in the city of Recife, Pernambuco. Methods: cross-sectional study, in which behavioral, socioeconomic and demographic information was collected from June to December 2014. Excess weight was calculated based on body mass index for age and the cut-off points, by the World Health Organization (2007). To analyze associations between predictor variables and the outcome, multivariate data analysis was performed following the Poisson Regression (Prevalence Ratio - PR) with their respective 95% confidence intervals (95%CI). Results: twenty-five adolescents participated in the study, with a prevalence of 36.4% of excess weight: 20.4% overweight (95%CI=15.1-25.7) and 16.0% obesity (95%CI= 11.2-20.8), predominantly in female gender (42.5%; p=0.031). The outcome was associated with internet access (PR=1.20; 95%CI=1.01-1.43), the number of people in the family (PR= 1.12; 95%CI=1.01-1.28) and screen time (PR=1.13; 95%CI=1.01-1.27), but only in male gender. Conclusions: the prevalence found was higher than that of other national researches, especially for the female gender. In the male gender, not having internet access, a lesser number of family members and a longer screen time proved to be factors associated with being excess weight.
Adaptive Control and Data Assimilation for Nonlinear Systems.

This dissertation draws a connection between the problem of adaptive command following and data assimilation with driver estimation. For these two different problems, two different approaches are adapted retrospective cost adaptive control (RCAC) and ensemble adjustment Kalman filter (EAKF). Both methods are first applied to linear minimum phase examples to demonstrate the modeling requirements and operating principles. Next, RCAC robustness to the accuracy of nonminimum phase (NMP) zero is investigated for plants of varying order and relative degree and is then improved through a convex constraint on the controller poles. It is demonstrated that the convex constraint significantly improves the transient and steady state command following and disturbance rejection performance. RCAC is then shown to successfully solve the command following problem for a nonlinear system (planar multilink arm) in a particular range of command amplitudes. This nonlinear example serves as a nice introduction to the data assimilation problem for a particular space weather model, which can be thought of as a generalization of the command following problem. The command in this case comes from real satellite data and the goal is to make a space weather model track the conditions observed by the satellites. The particular model used in this project is the global ionosphere-thermosphere model (GITM). GITM’s states (densities, temperatures and velocities for multiple species over a threedimensional grid) and inputs (solar flux index F10.7) are estimated using the
Operational system for automatic coastal upwelling detection in the Baltic Sea based on the 3D CEMBS model

ABSTRACT The upwelling in the Baltic Sea region is very common phenomenon. According to different studies, in some places it can exist almost one-third of the year leading to vertical mixing and transporting fresh, rich in nutrients water from deeper layers to the surface. The upwelling phenomenon has been analysed for years 2010–2016, during thermally stratified period, i.e. between May and September. Surface layer temperature from coupled ecosystem model of the Baltic Sea – 3D CEMBS was analysed together with NOAA/AVHRR satellite SST observations. Wind data from weather forecasting model – UM from ICM UW were also analysed to describe favourable conditions for the upwelling occurrences. The research includes statistical analysis of entire Baltic Sea region as well as particular examples from selected areas. Areas of upwelling occurrences were found along almost entire coastline of the Baltic Sea. Main areas were located along Swedish coast in Baltic Proper, Oland and along Finnish coast in the Gulf of Finland, where the event can last up to 30% of the time. Other areas, with frequencies over 20%, include Polish coast, Gotland and Bay of Bothnia. It was determined that collected results were in good agreement with earlier studies, with satellite data giving slightly higher frequencies closer to the shore. Based on these results, an automated coastal upwelling detection system was designed and launched in operational mode together with the 3D CEMBS model.
Machine learning-based identification of a novel prognosis-related long noncoding RNA signature for gastric cancer

Gastric cancer (GC) is one of the most common malignancies with a poor prognosis. Immunotherapy has attracted much attention as a treatment for a wide range of cancers, including GC. However, not all patients respond to immunotherapy. New models are urgently needed to accurately predict the prognosis and the efficacy of immunotherapy in patients with GC. Long noncoding RNAs (lncRNAs) play crucial roles in the occurrence and progression of cancers. Recent studies have identified a variety of prognosis-related lncRNA signatures in multiple cancers. However, these studies have some limitations. In the present study, we developed an integrative analysis to screen risk prediction models using various feature selection methods, such as univariate and multivariate Cox regression, least absolute shrinkage and selection operator (LASSO), stepwise selection techniques, subset selection, and a combination of the aforementioned methods. We constructed a 9-lncRNA signature for predicting the prognosis of GC patients in The Cancer Genome Atlas (TCGA) cohort using a machine learning algorithm. After obtaining a risk model from the training cohort, we further validated the model for predicting the prognosis in the test cohort, the entire dataset and two external GEO datasets. Then we explored the roles of the risk model in predicting immune cell infiltration, immunotherapeutic responses and genomic mutations. The results revealed that this risk model held promise for predicting the prognostic outcomes and immunotherapeutic responses of GC patients. Our findings provide ideas for integrating multiple screening methods for risk modeling through machine learning algorithms.
Heart and brain: Change in cardiac entropy is related to lateralised visual inspection in horses

Cerebral lateralisation is the tendency for an individual to preferentially use one side of their brain and is apparent in the biased use of paired sensory organs. Horses vary in eye use when viewing a novel stimulus which may be due to different physiological reactions. To understand the interplay between physiology and lateralisation, we presented a novel object (an inflated balloon) to 20 horses while electrocardiogram traces were collected. We measured the amount of time each horse looked at the balloon with each eye. We calculated ‘sample entropy’ as a measure of non-linear heart rate variability both prior to and during the stimulus presentation. A smaller drop in sample entropy values between the habituation phase and the sample presentation indicates the maintenance of a more complex signal associated with a relaxed physiological state. Horses that spent longer viewing the balloon with their left eye had a greater reduction in sample entropy, while time spend looking with the right eye was unrelated to the change in sample entropy. Therefore, the horses that exhibited a greater reduction in sample entropy tended to use their right hemisphere more, which may take precedence in emotional reactions. These results may help to explain the variation in lateralisation observed among horses.