Miracle-dz/UniFAR-FTUs huggingface dataset:
Predicting Biomass and Yield in a Tomato Phenotyping Experiment Using UAV Imagery and Random Forest

Biomass and yield are key variables for assessing the production and performance of agricultural systems. Modeling and predicting the biomass and yield of individual plants at the farm scale represents a major challenge in precision agriculture, particularly when salinity and other abiotic stresses may play a role. Here, we evaluate a diversity panel of the wild tomato species (Solanum pimpinellifolium) through both field and unmanned aerial vehicle (UAV)-based phenotyping of 600 control and 600 salt-treated plants. The study objective was to predict fresh shoot mass, tomato fruit numbers, and yield mass at harvest based on a range of variables derived from the UAV imagery. UAV-based red–green–blue (RGB) imageries collected 1, 2, 4, 6, 7, and 8 weeks before harvest were also used to determine if prediction accuracies varied between control and salt-treated plants. Multispectral UAV-based imagery was also collected 1 and 2 weeks prior to harvest to further explore predictive insights. In order to estimate the end of season biomass and yield, a random forest machine learning approach was implemented using UAV-imagery-derived predictors as input variables. Shape features derived from the UAV, such as plant area, border length, width, and length, were found to have the highest importance in the predictions, followed by vegetation indices and the entropy texture measure. The multispectral UAV imagery collected 2 weeks prior to harvest produced the highest explained variances for fresh shoot mass (87.95%), fruit numbers (63.88%), and yield mass per plant (66.51%). The RGB UAV imagery produced very similar results to those of the multispectral UAV dataset, with the explained variance reducing as a function of increasing time to harvest. The results showed that predicting the yield of salt-stressed plants produced higher accuracies when the models excluded control plants, whereas predicting the yield of control plants was not affected by the inclusion of salt-stressed plants within the models. This research demonstrates that it is possible to predict the average biomass and yield up to 8 weeks prior to harvest within 4.23% of field-based measurements and up to 4 weeks prior to harvest at the individual plant level. Results from this work may be useful in providing guidance for yield forecasting of healthy and salt-stressed tomato plants, which in turn may inform growing practices, logistical planning, and sales operations.
Not the Root of the Problem—Hair Cortisol and Cortisone Do Not Mediate the Effect of Child Maltreatment on Body Mass Index

Background Experiencing maltreatment during childhood exerts substantial stress on the child and increases the risk for overweight and obesity later in life. The current study tests whether hair cortisol—a measure of chronic stress—and its metabolite cortisone mediate the relation between abuse and neglect on the one hand, and body mass index (BMI) on the other. Method The sample consisted of 249 participants aged 8 to 87 years (M = 36.13, SD = 19.33). We collected data on child abuse and neglect using questionnaires, measured cortisol and cortisone concentrations in hair, and BMI. In a structural model, the effects of abuse and neglect on hair cortisol, hair cortisone, and BMI were tested, as well as the covariance between hair cortisol and BMI, and hair cortisone and BMI. Results Within the sample, 23% were overweight but not obese and 14% were obese. Higher levels of experienced abuse were related to higher cortisone concentrations in hair (β = 0.24, p < .001) and higher BMI (β = 0.17, p =.04). Neglect was not related to hair cortisol, hair cortisone, or BMI. Hair cortisol and cortisone did not mediate the association between maltreatment, and BMI. Sensitivity analyses demonstrate the same pattern of results in a subsample of adult participants currently not living with their parents. However, in younger participants who were still living with their parents, the associations between abuse and cortisone (β = 0.14, p =.35) and abuse and BMI (β = 0.02, p =.92) were no longer significant. Conclusion These findings confirm that experiencing abuse is related to higher BMI but suggest that hair cortisol and cortisone are not the mechanism underlying the association between child maltreatment and BMI. This is the first study to show abuse may be associated to elevated concentrations of hair cortisone—evidence of long-term alterations in chronic stress levels. Future research may benefit from exploring the effects of maltreatment on weight gain in longitudinal designs, including measures of other potential mediators such as eating as a coping mechanism, and more direct indicators of metabolic health.
Noise-Corrected, Exponentially Weighted, Diffusion-Weighted MRI (niceDWI) Improves Image Signal Uniformity in Whole-Body Imaging of Metastatic Prostate Cancer

Purpose: To characterize the voxel-wise uncertainties of Apparent Diffusion Coefficient (ADC) estimation from whole-body diffusion-weighted imaging (WBDWI). This enables the calculation of a new parametric map based on estimates of ADC and ADC uncertainty to improve WBDWI imaging standardization and interpretation: NoIse-Corrected Exponentially-weighted diffusion-weighted MRI (niceDWI). Methods: Three approaches to the joint modeling of voxel-wise ADC and ADC uncertainty (σADC) are evaluated: (i) direct weighted least squares (DWLS), (ii) iterative linear-weighted least-squares (IWLS), and (iii) smoothed IWLS (SIWLS). The statistical properties of these approaches in terms of ADC/σADC accuracy and precision is compared using Monte Carlo simulations. Our proposed post-processing methodology (niceDWI) is evaluated using an ice-water phantom, by comparing the contrast-to-noise ratio (CNR) with conventional exponentially-weighted DWI. We present the clinical feasibility of niceDWI in a pilot cohort of 16 patients with metastatic prostate cancer. Results: The statistical properties of ADC and σADC conformed closely to the theoretical predictions for DWLS, IWLS, and SIWLS fitting routines (a minor bias in parameter estimation is observed with DWLS). Ice-water phantom experiments demonstrated that a range of CNR could be generated using the niceDWI approach, and could improve CNR compared to conventional methods. We successfully implemented the niceDWI technique in our patient cohort, which visually improved the in-plane bias field compared with conventional WBDWI. Conclusions: Measurement of the statistical uncertainty in ADC estimation provides a practical way to standardize WBDWI across different scanners, by providing quantitative image signals that improve its reliability. Our proposed method can overcome inter-scanner and intra-scanner WBDWI signal variations that can confound image interpretation.
Tep1 Regulates Yki Activity in Neural Stem Cells in Drosophila Glioma Model

Glioblastoma Multiforme (GBM) is the most common form of malignant brain tumor with poor prognosis. Amplification of Epidermal Growth Factor Receptor (EGFR), and mutations leading to activation of Phosphatidyl-Inositol-3 Kinase (PI3K) pathway are commonly associated with GBM. Using a previously published Drosophila glioma model generated by coactivation of PI3K and EGFR pathways [by downregulation of Pten and overexpression of oncogenic Ras] in glial cells, we showed that the Drosophila Tep1 gene (ortholog of human CD109) regulates Yki (the Drosophila ortholog of human YAP/TAZ) via an evolutionarily conserved mechanism. Oncogenic signaling by the YAP/TAZ pathway occurs in cells that acquire CD109 expression in response to the inflammatory environment induced by radiation in clinically relevant models. Further, downregulation of Tep1 caused a reduction in Yki activity and reduced glioma growth. A key function of Yki in larval CNS is stem cell renewal and formation of neuroblasts. Other reports suggest different upstream regulators of Yki activity in the optic lobe versus the central brain regions of the larval CNS. We hypothesized that Tep1 interacts with the Hippo pathway effector Yki to regulate neuroblast numbers. We tested if Tep1 acts through Yki to affect glioma growth, and if in normal cells Tep1 affects neuroblast number and proliferation. Our data suggests that Tep1 affects Yki mediated stem cell renewal in glioma, as reduction of Tep significantly decreases the number of neuroblasts in glioma. Thus, we identify Tep1-Yki interaction in the larval CNS that plays a key role in glioma growth and progression.
Improvement of a Three-Layered in vitro Skin Model for Topical Application of Irritating Substances

In the field of skin tissue engineering, the development of physiologically relevant in vitro skin models comprising all skin layers, namely epidermis, dermis, and subcutis, is a great challenge. Increasing regulatory requirements and the ban on animal experiments for substance testing demand the development of reliable and in vivo-like test systems, which enable high-throughput screening of substances. However, the reproducibility and applicability of in vitro testing has so far been insufficient due to fibroblast-mediated contraction. To overcome this pitfall, an advanced 3-layered skin model was developed. While the epidermis of standard skin models showed an 80% contraction, the initial epidermal area of our advanced skin models was maintained. The improved barrier function of the advanced models was quantified by an indirect barrier function test and a permeability assay. Histochemical and immunofluorescence staining of the advanced model showed well-defined epidermal layers, a dermal part with distributed human dermal fibroblasts and a subcutis with round-shaped adipocytes. The successful response of these advanced 3-layered models for skin irritation testing demonstrated the suitability as an in vitro model for these clinical tests: only the advanced model classified irritative and non-irritative substances correctly. These results indicate that the advanced set up of the 3-layered in vitro skin model maintains skin barrier function and therefore makes them more suitable for irritation testing.
Personality Traits in Marathon Runners and Sedentary Controls With MMPI-2-RF

Background Endurance exercise in general and marathon running in particular have become increasingly popular over the past decades. Recent investigations about personality structures in this cohort and comparisons to non-active cohorts are lacking. Methods In the ReCaP study (Running effects on Cognition and Plasticity), a total of 100 marathon runners and 46 sedentary controls were recruited. After elimination of Minnesota Multiphasic Personality Inventory 2 Restructured Form (MMPI-2-RF) profiles with insufficient validity, 79 marathon runners (MA) and 27 sedentary controls (SC) remained for final analyses. Depressive symptoms were evaluated with Beck Depression Inventory (BDI) and Hamilton Depression Scale (HAMD). Results Marathon runners had lower scores in scales measuring somatic and cognitive complaints, stress, demoralization, hopelessness and distrust. Within the marathon group, committed runners exhibited hypomanic traits compared to regular runners. Discussion and Conclusion Personality differences could be summarized as (sub-)depressive personality traits in SC compared to MA rather than typical (sub-) depressive symptoms in the meaning of depressive disorders. Future studies should further evaluate cause and consequence of endurance training and hypomanic or euthymic symptoms, as a two-way interaction exists. Trial Registration http://apps.who. int/trialsearch/Trial2.aspx? TrialID=DRKS00012496.
Genes and Proteomes Associated With Increased Mutation Frequency and Multidrug Resistance of Naturally Occurring Mismatch Repair-Deficient Salmonella Hypermutators

The emergence of antibiotic-resistant Salmonella through mutations led to mismatch repair (MMR) deficiency that represents a potential hazard to public health. Here, four representative MMR-deficient Salmonella hypermutator strains and Salmonella Typhimurium LT2 were used to comprehensively reveal the influence of MMR deficiency on antibiotic resistance among Salmonella. Our results indicated that the mutation frequency ranged from 3.39 × 10–4 to 5.46 × 10–2 in the hypermutator. Mutation sites in MutS, MutL, MutT, and UvrD of the four hypermutators were all located in the essential and core functional regions. Mutation frequency of the hypermutator was most highly correlated with the extent of mutation in MutS. Mutations in MMR genes (mutS, mutT, mutL, and uvrD) were correlated with increased mutation in antibiotic resistance genes, and the extent of antibiotic resistance was significantly correlated with the number of mutation sites in MutL and in ParC. The number of mutation sites in MMR genes and antibiotic resistance genes exhibited a significant positive correlation with the number of antibiotics resisted and with expression levels of mutS, mutT, and mutL. Compared to Salmonella Typhimurium LT2, a total of 137 differentially expressed and 110 specifically expressed proteins were identified in the four hypermutators. Functional enrichment analysis indicated that the proteins significantly overexpressed in the hypermutators primarily associated with translation and stress response. Interaction network analysis revealed that the ribosome pathway might be a critical factor for high mutation frequency and multidrug resistance in MMR-deficient Salmonella hypermutators. These results help elucidate the mutational dynamics that lead to hypermutation, antibiotic resistance, and activation of stress response pathways in Salmonella.
Peer Support in Coordination of Physical Health and Mental Health Services for People With Lived Experience of a Serious Mental Illness

Background Engaging peer support to augment and enhance traditional mental health services presents novel opportunities to improve service engagement and delivery. However, there has not been an in-depth analysis of the processes and methods behind the coordination of physical health and mental health care by peer support specialists. Study aim To explore the potential of peer support specialists in community mental health centers and as a means to improve coordination of physical health and mental health services for people with a serious mental illness. Methods We conducted 28 semi-structured qualitative interviews with peer support specialists and mental healthcare professionals in community mental health centers in two states (blinded for review) in the United States. Data were triangulated to explore peer support specialists and mental health professionals’ perspectives. Results We found five themes characterizing the role of peer support services in the coordination of physical health and mental health services for individuals with serious mental illness: (1) Advocacy in interprofessional meetings, clinical teams, and advisory councils; (2) Sharing lived experiences and connecting with available resources and services; (3) Preparing for mental health and physical health care visits; (4) Mutuality; and (5) Affiliations, funding, and sustainability of peer support services. Conclusion This study suggests that peer support specialists can uniquely contribute to the coordination of physical health and mental health services for individuals with serious mental illness.
Expression and Functional Studies of INS-5, an Insulinase-Like Protein in Cryptosporidium parvum

The small Cryptosporidium genome (∼9 Mb) has over 20 copies of genes encoding insulinase-like proteases (INS), suggesting that these enzymes may have important biological functions in the pathogen and could be developmentally regulated. In this study, INS-5, a unique member of the INS family in Cryptosporidium parvum, was cloned and expressed in Escherichia coli BL21 (DE3). In addition to the predicted INS-5 of ∼78 kDa, smaller fragments of ∼70, ∼55, and ∼30 kDa were simultaneously generated. After purification through a nickel-nitrilotriacetic acid affinity column, the full recombinant protein obtained was used to prepare polyclonal antibodies. Antibodies raised against INS-5 recognized the recombinant protein and native protein in sporozoite extracts. Further characterization of INS-5 included qRT-PCR assessment of gene expression; immunofluorescence localization of the protein expression in sporozoites, merozoites, and other developmental stages; and neutralization of invasion of C. parvum in vitro. The results obtained indicated that although INS-5 was expressed in sporozoites and merozoites, the high gene expression was from 36 to 48 h of the in vitro culture after invasion. Anti-INS-5 antibodies partially neutralized the invasion (inhibition rate = 38.5%). Results of this study suggest that INS-5 plays some role in the invasion and growth of C. parvum.
Characterization of Calcium-Dependent Protein Kinases 3, a Protein Involved in Growth of Cryptosporidium parvum

Calcium-dependent protein kinases (CDPKs) are considered promising targets for pharmaceutical intervention of cryptosporidiosis. Whole-genome sequencing has revealed the presence of several CDPKs (CpCDPKs) in Cryptosporidium parvum. In this study, we expressed recombinant CpCDPK3 encoded by the cgd5_820 gene in Escherichia coli. The biologic characteristics and functions of CpCDPK3 were examined using qRT-PCR, immunofluorescence microscopy, and in vitro neutralization assay. The expression of the cgd5_820 gene peaked in merozoites during in vitro culture while the CpCDPK3 protein was expressed in both sporozoites and merozoites. Polyclonal antibodies against CpCDPK3 showed no significant inhibitory effects on host invasion by the parasites. We assessed the inhibitory effects of 46 candidate compounds from molecular docking of CpCDPK3 on both C. parvum development and CpCDPK3 enzyme activities. One compound was identified to be effective. Results of these analyses suggest that CpCDPK3 might play an important role in the growth of C. parvum.
The importomer is a peroxisomal membrane protein translocase

Three sites of membrane protein biogenesis (the endoplasmic reticulum, mitochondria and chloroplasts) receive unfolded substrates from organelle-specific protein targeting factors, then integrate them using separate translocation channels. Peroxisomes also receive membrane proteins from known targeting factors, but whether a separate translocase is needed for integration remains unknown. Here, using a novel genetic screening strategy, we reveal that the importomer–known for matrix protein import–integrates the peroxisomal membrane protein Pex14. In importomer mutants, Pex14 is arrested in a pre-integrated state on the peroxisome surface. To undergo integration, a Pex14 translocation signal binds the importomer’s substrate receptor Pex5 at a distinct site from matrix proteins. En bloc translocation of an engineered protein complex with Pex14’s luminal region argues that integration occurs without substrate unfolding. Our work shows that the handling of membrane protein targeting and integration by discrete machineries is a fundamental principle shared by diverse membrane protein biogenesis pathways.
Homology-directed repair involves multiple strand invasion cycles in fission yeast

Homology-directed repair of DNA double-strand breaks (DSBs) can be a highly faithful pathway. Non-crossover repair dominates in mitotically growing cells, likely through a preference for synthesis-dependent strand annealing (SDSA). While genetic studies highlight a key role for the RecQ helicase BLM/Rqh1 (in human and S. pombe cells, respectively) in promoting noncrossover repair, how homology-directed repair mechanism choice is orchestrated in time and space is not well understood. Here, we develop a microscopy-based assay in living fission yeast to determine the dynamics and kinetics of an engineered, site-specific interhomologue repair event. We observe highly efficient homology search and homology-directed repair in this system. Surprisingly, we find that the initial distance between the DSB and the donor sequence does not correlate with the duration of repair. Instead, we observe that repair is likely to involve multiple site-specific and Rad51-dependent co-localization events between the DSB and donor sequence, suggesting that efficient interhomologue repair in fission yeast often involves multiple strand invasion events. By contrast, we find that loss of Rqh1 leads to successful repair through a single strand invasion event, suggesting that multiple strand invasion cycles reflect ongoing SDSA. However, failure to repair is also more likely in rqh1Δ cells, which could reflect increased strand invasion at non-homologous sites. This work has implications for the molecular etiology of Bloom syndrome, caused by mutations in BLM and characterized by aberrant sister chromatid crossovers and inefficient repair.
Infanticide by females is a leading source of juvenile mortality in a large social carnivore

Social animals benefit from their group-mates, so why do they sometimes kill each other’s offspring? A major barrier to understanding the evolution of infanticide is a lack of data from natural populations. Especially when perpetrated by females, infanticide remains poorly understood, because the increased mating opportunities that explain infanticide by males do not apply in females. Using 30 years of data from several spotted hyena groups, we show that infanticide is a leading source of juvenile mortality, and we describe the circumstances under which it occurs. In all observed cases, killers were adult females, but victims could be of both sexes. Killers only sometimes consumed the victims. Mothers sometimes cared for their deceased offspring, and sometimes consumed the body. Killers tended to be higher-ranking than the mothers of victims, and killers were sometimes aided by kin. Our results are consistent with theory that infanticide by females reflects competition among matrilines.