Miracle-dz/UniFAR-FTUs huggingface dataset:
Modeling Maize Canopy Morphology in Response to Increased Plant Density

Increased plant density markedly affects canopy morphophysiological activities and crop productivity. This study aims to model maize canopy final morphology under increased interplant competition by revising a functional–structural plant model, i.e., ADEL-Maize. A 2-year field experiment was conducted at Mengcheng, Anhui Province, China, in 2016 and 2018. A randomized complete block design of five plant densities (PDs), i.e., 4.5, 6, 7.5, 9, and 15 plants m–2, with three replications was applied using a hybrid, i.e., Zhengdan 958. Canopy morphology at different PDs was measured with destructive samplings when maize canopy was fully expanded. The relationship of changes of organ morphology in relation to increased plant density was analyzed based on 2016 data. The ADEL-Maize was first calibrated for the hybrid at 4.5 plants m–2 and then revised by introducing relationships identified from 2016 data, followed by independent validation with 2018 field data. A heatmap visualization was shown to clearly illustrate the effects of increased plant density on final morphology of laminae, sheaths, and internodes. The logarithmic + linear equations were found to fit changes for the organ size versus increased plant density for phytomers excluding ear position or linear equations for the phytomer at ear position based on 2016 field data. The revision was then further tested independently by having achieved satisfactory agreements between the simulations and observations in canopy size under different PDs with 2018 field data. In conclusion, this study has characterized the relationship between canopy morphology and increased interplant competition for use in the ADEL-Maize and realized the simulations of final size of laminae, sheaths, and internodes, as affected by increased plant density, laying a foundation to test an ideotype for maize withstanding high interplant competition.
Intravital Imaging of Pulmonary Immune Response in Inflammation and Infection

Intravital microscopy (IVM) is a unique imaging method providing insights in cellular functions and interactions in real-time, without the need for tissue extraction from the body. IVM of the lungs has specific challenges such as restricted organ accessibility, respiratory movements, and limited penetration depth. Various surgical approaches and microscopic setups have been adapted in order to overcome these challenges. Among others, these include the development of suction stabilized lung windows and the use of more advanced optical techniques. Consequently, lung IVM has uncovered mechanisms of leukocyte recruitment and function in several models of pulmonary inflammation and infection. This review focuses on bacterial pneumonia, aspiration pneumonia, sepsis-induced acute lung Injury, and cystic fibrosis, as examples of lung inflammation and infection. In addition, critical details of intravital imaging techniques of the lungs are discussed.
Telomere Dysfunction in Chronic Lymphocytic Leukemia

Telomeres are nucleprotein structures that cap the chromosomal ends, conferring genomic stability. Alterations in telomere maintenance and function are associated with tumorigenesis. In chronic lymphocytic leukemia (CLL), telomere length is an independent prognostic factor and short telomeres are associated with adverse outcome. Though telomere length associations have been suggested to be only a passive reflection of the cell’s replication history, here, based on published findings, we suggest a more dynamic role of telomere dysfunction in shaping the disease course. Different members of the shelterin complex, which form the telomere structure have deregulated expression and POT1 is recurrently mutated in about 3.5% of CLL. In addition, cases with short telomeres have higher telomerase (TERT) expression and activity. TERT activation and shelterin deregulation thus may be pivotal in maintaining the minimal telomere length necessary to sustain survival and proliferation of CLL cells. On the other hand, activation of DNA damage response and repair signaling at dysfunctional telomeres coupled with checkpoint deregulation, leads to terminal fusions and genomic complexity. In summary, multiple components of the telomere system are affected and they play an important role in CLL pathogenesis, progression, and clonal evolution. However, processes leading to shelterin deregulation as well as cell intrinsic and microenvironmental factors underlying TERT activation are poorly understood. The present review comprehensively summarizes the complex interplay of telomere dysfunction in CLL and underline the mechanisms that are yet to be deciphered.
Immune Cluster and PPI Network Analyses Identified CXCR3 as a Key Node of Immunoregulation in Head and Neck Cancer

The tumor microenvironment (TME) is significantly associated with clinical outcomes and therapeutic efficacy. However, the landscape of the head and neck cancer (HNC) microenvironment is not fully understood. Therefore, we divided HNCs into three classes according to differences in the TME to determine effective personalized treatments. We explored the immune landscape of head and neck cancer by analysing the gene expression profile of 501 cases from the Cancer Genome Atlas (TCGA) data portal and validated our findings in 270 cases from the Gene Expression Omnibus (GEO) database. The levels of immune components in the tumor microenvironment were evaluated via single-sample gene set enrichment (ssGSEA) analysis. The HNCs were clustered into an Immunity-H group, Immunity-M group and Immunity-L group according to 40 immune components in the tumor microenvironment. DNA damage and HLA genes play an important role in immune regulation. The patients in the Immunity-H group had a favourable survival compared with patients in the Immunity-M group and the Immunity-L group. The patients in the Immunity-H group and Immunity-M group could benefit from radiotherapy. In addition, the Immunity-L group showed the lowest immunophenoscore and had poor response to anti-PD-1 treatment. CXCR3 was demonstrated to be downregulated in the Immunity-L group, which was related to shorter OS in the TCGA and GEO databases, suggesting CXCR3 as a potential therapeutic target. Taken together, our findings proposed three new microenvironment-related phenotypes of HNCs and suggested that CXCR3 played a major role in immune regulation and could be a novel therapeutic target, providing a reference for clinical decisions and research directions in the future.
Social Cognition and Friendships in Adolescents With Autistic-Like Experiences and Psychotic-Like Experiences

Autism spectrum conditions (ASC) and schizophrenia spectrum conditions (SSC) are both characterized by changes in social-cognitive functioning. Less is known about the overlap and the differences in social-cognitive functioning when comparing individuals with subclinical levels of ASC and SSC, while studies in non-clinical samples have the benefit of avoiding confounds that are present in clinical groups. Therefore, we first examined how autistic-like experiences, positive psychotic-like experiences and the co-occurrence of both correlated with the performance on an extensive battery of social cognition tasks in young adolescents. Second, we examined the effect of autistic-like experiences, psychotic-like experiences and their co-occurrence on friendships in daily life. A total of 305 adolescents (Mage = 12.6, sd = 0.4, 147 boys) participated in the current study. A battery of social cognition tasks, comprising the Reading the Mind in the Eyes task, Dot perspective task and trust game were individually administered in a classroom setting, along with a friendship peer nomination questionnaire. Results indicated no evidence for a relationship between the performance on the social cognition battery and subclinical experiences of autism and/or psychosis. However, results did show that the amount of autistic-like experiences of adolescents were associated with being less often selected as a friend by their peers. By contrast, no relationship between self-reported friendships and autistic-like experiences was found. Neither a relationship between friendships and psychotic-like experiences was reported. This study provides initial evidence that information provided by peers may shed light on (altered) social behavior associated with autistic-like experiences that is not apparent on performance measures, as well as elucidate possible differences between autistic- and psychotic-like experiences.
Robot-Assisted Laparoscopic Living Donor Nephrectomy: The University of Florence Technique

Objective: To provide a step-by-step overview of the University of Florence technique for robotic living donor nephrectomy (LDN), focusing on its technical nuances and perioperative outcomes. Methods: A dedicated robotic LDN program at our Institution was codified in 2012. Data from patients undergoing robotic LDN from 2012 to 2019 were prospectively collected. All robotic LDNs were performed by a highly experienced surgeon, using the da Vinci Si robotic platform in a three-arm configuration. In this report we provide a detailed overview of our surgical technique for robotic LDN. The main objective of the study was to evaluate the technical feasibility and safety of the technique, including perioperative surgical complications rate and mid-term functional outcomes. Results: Overall, 36 patients undergoing robotic LDNs were included in the study. Of these, 28 (78%) were left LDNs. Median (IQR) donor pre-operative eGFR was 88 (75.6–90) ml/min/1.73 m2. In all cases, robotic LDN was completed without need of conversion. The median (IQR) overall operative time was 230 (195–258) min, while the median console time was 133 (IQR 117-166) min. The median (IQR) warm ischemia time was 175 (140–255) s. No intraoperative adverse events or 90-d major surgical complications were recorded. At a median (IQR) follow-up of 24 months (IQR 11-46), median (IQR) eGFR patients undergoing in living donor nephrectomy was 57.4 (47.9; 63.9) ml/min/1.73 m2. Conclusions: In our experience, robotic LDN is technically feasible and safe. The use of robotic surgery for LDN may provide distinct advantages for surgeons while ensuring optimal donors' perioperative and functional outcomes.
Prediction of Solubility of Cholesterol in Supercritical Solvents

In this study the solubility of cholesterol was calculated in two supercritical pure solvents (carbon dioxide and ethane) as binary systems, and four supercritical solvent/co-solvent systems as ternary systems (cholesterol/carbon dioxide/methanol, cholesterol/ethane/acetone, cholesterol/ethane/hexane, cholesterol/ethane/propane) in various temperatures by SRK, PR, and SAFT equations of state. Pure molecular parameters of SAFT equation of state were obtained by fitting vapor pressure and liquid density data. Also the molecular parameters of cholesterol were obtained by fitting the solubility data of binary systems in one temperature, then they were used for the same system in other temperatures and for ternary systems with the same solvent. Results show that the SAFT equation of state can predict the trend and amount solubility of cholesterol in supercritical solvents much better than the other equations of state.
Parentage Atlas of Italian Grapevine Varieties as Inferred From SNP Genotyping

The Italian grape germplasm is characterized by a high level of richness in terms of varieties number, with nearly 600 wine grape varieties listed in the Italian National Register of Grapevine Varieties and with a plethora of autochthonous grapes. In the present study an extended SNP genotyping has been carried out on Italian germplasm of cultivated Vitis vinifera subsp. sativa and Vitis hybrids. Several hundred Italian varieties maintained in the repositories of scientific Institutions and about one thousand additional varieties derived from previous studies on European, Southern Italy, Magna Graecia and Georgian germplasm were considered. The large genotyping data obtained were used to check the presence of homonyms and synonyms, determine parental relationships, and identify the main ancestors of traditional Italian cultivars and closely-related accessions. The parentage among a set of 1,232 unique varieties has been assessed. A total of 92 new parent-offspring (PO) pairs and 14 new PO trios were identified. The resulted parentage network suggested that the traditional Italian grapevine germplasm originates largely from a few central varieties geographically distributed into several areas of genetic influence: “Strinto porcino” and its offspring “Sangiovese”, “Mantonico bianco” and “Aglianico” mainly as founder varieties of South-Western Italy (IT-SW); Italian Adriatic Coast (IT-AC); and Central Italy with most varieties being offsprings of “Visparola”, “Garganega” and “Bombino bianco”; “Termarina (Sciaccarello)” “Orsolina” and “Uva Tosca” as the main varieties of North-Western Italy (IT-NW) and Central Italy. The pedigree reconstruction by full-sib and second-degree relationships highlighted the key role of some cultivars, and, in particular, the centrality of “Visparola” in the origin of Italian germplasm appeared clear. An hypothetical migration of this variety within the Italian Peninsula from South to North along the eastern side, as well as of “Sangiovese” from South to Central Italy along the Western side might be supposed. Moreover, it was also highlighted that, among the main founders of muscat varieties, “Moscato bianco” and “Zibibbo (Muscat of Alexandria)” have spread over the whole Italy, with a high contribution by the former to germplasm of the North-Western of the peninsula.
Origins, Development, and Compartmentation of the Granule Cells of the Cerebellum

Granule cells (GCs) are the most numerous cell type in the cerebellum and indeed, in the brain: at least 99% of all cerebellar neurons are granule cells. In this review article, we first consider the formation of the upper rhombic lip, from which all granule cell precursors arise, and the way by which the upper rhombic lip generates the external granular layer, a secondary germinal epithelium that serves to amplify the upper rhombic lip precursors. Next, we review the mechanisms by which postmitotic granule cells are generated in the external granular layer and migrate radially to settle in the granular layer. In addition, we review the evidence that far from being a homogeneous population, granule cells come in multiple phenotypes with distinct topographical distributions and consider ways in which the heterogeneity of granule cells might arise during development.
Experimental Constraints on Homogenization of Plagioclase-Hosted Melt Inclusions From Plagioclase Ultraphyric Basalts

Study of melt inclusions (MIs) is a commonly applied method for defining the composition of magmas present at depth prior to mixing, fractionation, and degassing. Our ability to use data from MIs is complicated by post-entrapment processes (PEP) that can modify their composition during transport and eruption. Many of the PEP can be reversed by heating the MIs to temperatures near those at which the MI and its host were formed. However, the process of reversing PEP by homogenization may introduce changes in MI compositions, making interpretation difficult. We present a series of low and high pressure homogenization experiments on plagioclase-hosted MIs from Plagioclase Ultraphyric Basalts (PUBs) designed to develop a methodology for recovering the composition at the time of entrapment of plagioclase-hosted MIs. These experiments included low pressure (1 bar) homogenization experiments conducted as a time series for 30 min, 4 h, 1 day, 4 days, and 8 days), and at 7.5 kbar for 2 and 4 days. The 7.5 kbar pressure used for the high pressure experiments was based on the CO2-based entrapment pressures determined from MI from this sample. Experiments run at low pressure and run times of 4 and 8 days exhibited compositional drift, most notably in the form of increasing MgO in MIs. This drift was not observed at 7.5 kbars or for the shorter run time 1 atm experiments. These results are consistent with a model where drift in composition with time is caused by crystal relaxation driven by the high internal pressure within the MI (the pressure at which the MI formed), together with the lower confining pressure during homogenization (1 bar). Therefore, MI homogenization will produce the least amount of drift if runs are made for short time periods (∼30 min) or at the pressure of entrapment.
Texture Analysis of 18F-FDG PET/CT for Differential Diagnosis Spinal Metastases

Purpose: To evaluate the value of texture analysis for the differential diagnosis of spinal metastases and to improve the diagnostic performance of 2-deoxy-2-[fluorine-18]fluoro-D-glucose positron emission tomography/computed tomography (18F-FDG PET/CT) for spinal metastases. Methods: This retrospective analysis of patients who underwent PET/CT between December 2015 and January 2020 at Shanghai Tenth People's Hospital due to high FDG uptake lesions in the spine included 45 cases of spinal metastases and 44 cases of benign high FDG uptake lesions in the spine. The patients were randomly divided into a training group of 65 and a test group of 24. Seventy-two PET texture features were extracted from each lesion, and the Mann-Whitney U-test was used to screen the training set for texture parameters that differed between the two groups in the presence or absence of spinal metastases. Then, the diagnostic performance of the texture parameters was screened out by receiver operating characteristic (ROC) curve analysis. Texture parameters with higher area under the curve (AUC) values than maximum standardized uptake values (SUVmax) were selected to construct classification models using logistic regression, support vector machines, and decision trees. The probability output of the model with high classification accuracy in the training set was used to compare the diagnostic performance of the classification model and SUVmax using the ROC curve. For all patients with spinal metastases, survival analysis was performed using the Kaplan-Meier method and Cox regression. Results: There were 51 texture parameters that differed meaningfully between benign and malignant lesions, of which four had higher AUC than SUVmax. The texture parameters were input to build a classification model using logistic regression, support vector machine, and decision tree. The accuracy of classification was 87.5, 83.34, and 75%, respectively. The accuracy of the manual diagnosis was 84.27%. Single-factor survival analysis using the Kaplan-Meier method showed that intensity was correlated with patient survival. Conclusion: Partial texture features showed higher diagnostic value for spinal metastases than SUVmax. The machine learning part of the model combined with the texture parameters was more accurate than manual diagnosis. Therefore, texture analysis may be useful to assist in the diagnosis of spinal metastases.
Rehabilitation and Biomarkers of Stroke Recovery: Study Protocol for a Randomized Controlled Trial

Background: Stroke is a leading cause of disability. Nonetheless, the care pathway for stroke rehabilitation takes partially into account the needs of chronic patients. This is due in part to the lack of evidence about the mechanisms of recovery after stroke, together with the poor knowledge of related and influencing factors. Here we report on the study protocol “Rehabilitation and Biomarkers of Stroke Recovery,” which consists of 7 work-packages and mainly aim to investigate the effects of long-term neurorehabilitation on stroke patients and to define a related profile of (clinical-biological, imaging, neurophysiological, and genetic-molecular) biomarkers of long-term recovery after stroke. The work-package 1 will represent the main part of this protocol and aims to compare the long-term effects of intensive self-rehabilitation vs. usual (rehabilitation) care for stroke. Methods: We planned to include a total of 134 adult subacute stroke patients (no more than 3 months since onset) suffering from multidomain disability as a consequence of first-ever unilateral ischemic stroke. Eligible participants will be randomly assigned to one of the following groups: intensive self-rehabilitation (based on the principles of “Guided Self-Rehabilitation Contract”) vs. usual care (routine practice). Treatment will last 1 year, and patients will be evaluated every 3 months according to their clinical presentation. The following outcomes will be considered in the main work-package: Fugl-Meyer assessment, Cognitive Oxford Screen Barthel Index, structural and functional neuroimaging, cortical excitability, and motor and somatosensory evoked potentials. Discussion: This trial will deal with the effects of an intensive self-management rehabilitation protocol and a related set of biomarkers. It will also investigate the role of training intensity on long-term recovery after stroke. In addition, it will define a set of biomarkers related to post-stroke recovery and neurorehabilitation outcome in order to detect patients with greater potential and define long-term individualized rehabilitation programs. Clinical Trial Registration: www.ClinicalTrials. gov, identifier: NCT04323501.
Increased Amygdala-Paracentral Lobule/Precuneus Functional Connectivity Associated With Patients With Mood Disorder and Suicidal Behavior

Mood disorder patients have greater suicide risk than members of the general population, but how suicidal behavior relates to brain functions has not been fully elucidated. This study investigated how functional connectivity (FC) values between the right/left amygdala and the whole brain relate to suicidal behavior in patients with mood disorder. The participants in this study were 100 mood disorder patients with suicidal behavior (SB group), 120 mood disorder patients with non-suicidal behavior (NSB group), and 138 age- and gender-matched healthy controls (HC group). Whole-brain FC values among the three groups were compared using an analysis of covariance (ANCOVA). Compared to the NSB and HC groups, increased FC values in the right amygdala-bilateral paracentral lobule/precuneus circuit were observed in the SB group (Bonferroni-corrected, p < 0.017). The FC values in the NSB group did not differ significantly from those in the HC group (Bonferroni-corrected, p > 0.017). Moreover, there were no significant differences in FC values between mood disorder patients with suicide attempt (SA group) and mood disorder patients with suicidal ideation (SI group), while the FC values between the right amygdala and bilateral paracentral lobule/precuneus in the SA group were higher than the mean in the SI group. These findings suggest that right amygdala-paracentral lobule/precuneus dysfunction has an important role in patients with mood disorder and suicidal behavior.