Miracle-dz/UniFAR-FTUs huggingface dataset:
Xylem cavitation isolates leaky flowers during water stress in pyrethrum.

Flowers underpin plant evolution, genetic legacy, and global food supply. They are exposed to similar evaporative conditions as leaves, yet floral physiology is a product of different selective forces. We used Tanacetum cinerariifolium, a perennial daisy, to examine the response of flowers to whole-plant water stress, determining if flowers constitute a liability during drought, and how this species has adapted to minimize risk associated with reproduction. We determined the relative transpiration cost of flowers and leaves and confirmed that flowers in this species are xylem-hydrated. The relative water stress tolerance of leaves and flowers was then compared using xylem vulnerability measurements linked with observed tissue damage during an acute drought treatment. Flowers were a major source of water loss during drought but the xylem supplying them was much more vulnerable to cavitation than leaves. This xylem vulnerability segmentation was confirmed by observations that most flowers died while leaves were minimally affected during drought. Early cavitation and hydraulic isolation of flowers during drought benefits the plant by slowing the dehydration of perennial vegetative organs and delaying systemic xylem damage. Our results highlight the need to understand flower xylem vulnerability as a means of predicting plant reproductive failure under future drought.
The function of histone lysine methylation related SET domain group proteins in plants

Histone methylation, which is mediated by the histone lysine (K) methyltransferases (HKMTases), is a mechanism associated with many pathways in eukaryotes. Most HKMTases have a conserved SET (Su(var) 3‐9,E(z),Trithorax) domain, while the HKMTases with SET domains are called the SET domain group (SDG) proteins. In plants, only SDG proteins can work as HKMTases. In this review, we introduced the classification of SDG family proteins in plants and the structural characteristics of each subfamily, surmise the functions of SDG family members in plant growth and development processes, including pollen and female gametophyte development, flowering, plant morphology and the responses to stresses. This review will help researchers better understand the SDG proteins and histone methylation in plants and lay a basic foundation for further studies on SDG proteins.
Integrated Microfluidic Sample-to-Answer System for Direct Nucleic Acid-Based Detection of Group B Streptococcus in Clinical Vaginal/Anal Swab Samples.

Group B Streptococcus (GBS) is a type of pathogen that seriously threatens the health of mothers and infants. Prompt and timely diagnosis is crucial to good patient outcomes. However, traditional bacterial culture and polymerase chain reaction methods are limited by their speed and involve complex operating procedures. Herein, we successfully established an integrated microfluidic sample-to-answer system for nucleic acid-based detection of GBS directly in vaginal/anal swab samples. Meanwhile, we demonstrated a dynamical reaction mechanism of Bst/FEN1-based nucleic acid amplification, which differs from traditional Bst-based isothermal amplification strategies. The system integrates cell lysis and nucleic acid purification, separation, amplification, and detection, enabling rapid (about 45 minutes to the entire analysis) and highly accurate (98% accuracy) analysis in a clinical setting. Experimental results show that the system offers a good detection limit (500 CFU/mL), perfect specificity (no cross-reactivity with 25 other common pathogens), excellent stability (coefficient of variation less than 3%), and good anti-interference performance. This novel system holds great potential as a nucleic acid-based diagnostic tool in clinical applications for detecting not only GBS but also other types of pathogens.
Teachers victimizing students: Contributions of student-to-teacher victimization, peer victimization, school safety, and school climate in Chile.

Although most of the school violence literature is focused on peer victimization, interest is growing in teachers being victimized by their students. However, there is far less interest in students being victimized by their teachers, patterns of mutual victimization, and how they are associated with other school factors. Using the conceptual framework of school violence in evolving contexts, the present study examined teacher-to-student victimization in Chile and tested, for the first time, the associations of student-to-teacher victimization, peer victimization, school safety, classroom climate, and school climate at the individual and school levels. The sample consisted of 50,344 students (51.6% female) in Grades 5-8 in 431 schools in Chilean public-funded schools. Findings indicated that verbal types of teacher-student mutual victimization were more prevalent than physical and sexual victimization. Teacher-to-student victimization was higher among male and younger students. Multilevel analyses showed that student-to-teacher victimization, school safety, classroom climate, and school climate were associated with teacher-to-student victimization. We discuss the need for whole-school approaches that enhance social and academic support from teachers to reduce mutual forms of victimization and suggest a public health approach that places the school in the center. (PsycINFO Database Record (c) 2020 APA, all rights reserved).
Identifying Acute Low Back Pain Episodes in Primary Care Practice From Clinical Notes: Observational Study

Background Acute and chronic low back pain (LBP) are different conditions with different treatments. However, they are coded in electronic health records with the same International Classification of Diseases, 10th revision (ICD-10) code (M54.5) and can be differentiated only by retrospective chart reviews. This prevents an efficient definition of data-driven guidelines for billing and therapy recommendations, such as return-to-work options. Objective The objective of this study was to evaluate the feasibility of automatically distinguishing acute LBP episodes by analyzing free-text clinical notes. Methods We used a dataset of 17,409 clinical notes from different primary care practices; of these, 891 documents were manually annotated as acute LBP and 2973 were generally associated with LBP via the recorded ICD-10 code. We compared different supervised and unsupervised strategies for automated identification: keyword search, topic modeling, logistic regression with bag of n-grams and manual features, and deep learning (a convolutional neural network-based architecture [ConvNet]). We trained the supervised models using either manual annotations or ICD-10 codes as positive labels. Results ConvNet trained using manual annotations obtained the best results with an area under the receiver operating characteristic curve of 0.98 and an F score of 0.70. ConvNet’s results were also robust to reduction of the number of manually annotated documents. In the absence of manual annotations, topic models performed better than methods trained using ICD-10 codes, which were unsatisfactory for identifying LBP acuity. Conclusions This study uses clinical notes to delineate a potential path toward systematic learning of therapeutic strategies, billing guidelines, and management options for acute LBP at the point of care.
Age at Diagnosis and Patient Preferences for Treatment Outcomes in AML: A Discrete Choice Experiment to Explore Meaningful Benefits

Background: The recent expansion of treatment options in acute myeloid leukemia (AML) has necessitated a greater understanding of patient preferences for treatment benefits, about which little is known. Methods: We sought to quantify and assess heterogeneity of the preferences of AML patients for treatment outcomes. An AML-specific discrete choice experiment (DCE) was developed involving multiple stakeholders. Attributes included in the DCE were event-free survival (EFS), complete remission (CR), time in the hospital, short-term side effects, and long-term side effects. Continuously coded conditional, stratified, and latent-class logistic regressions were used to model preferences of 294 patients with AML. Results: Most patients were white (89.4%) and in remission (95.0%). A 10% improvement in the chance of CR was the most meaningful offered benefit (P < 0.001). Patients were willing to trade up to 22 months of EFS or endure 8.7 months in the hospital or a two-step increase in long-term side effects to gain a 10% increase in chance of CR. Patients diagnosed at 60 years or older (21.6%) more strongly preferred to avoid short-term side effects (P = 0.03). Latent class analysis showed significant differences of preferences across gender and insurance status. Conclusions: In this national sample of mostly AML survivors, patients preferred treatments that maximized chance at remission; however, significant preference heterogeneity for outcomes was identified. Age and gender may affect patients' preferences. Impact: Survivor preferences for outcomes can inform patient-focused drug development and shared decision-making. Further studies are necessary to investigate the use of DCEs to guide treatment for individual patients.
The effects of predation-risk on prey stoichiometry: a meta-analysis.

A decade ago, the General Stress Paradigm (GSP) aimed to develop a predictive framework linking predator effects to ecosystem function. The GSP was based on the notion that animals, across taxa, exhibit similar physiological responses to predation risk that divert resources from growth and reproduction [which require N-rich biomolecules (i.e., protein)] to emergency functions [which require C-rich biomolecules (e.g., carbohydrates)]. The GSP predicts that stressed prey should have a greater dietary demand for C-rich resources, a higher body C:N ratio, and elevated N excretion. Now, ten years later, we aim to revisit the GSP- using quantitative meta-analysis to test the original predictions of the GSP and how 1) predator hunting mode, 2) multiple stressors, and 3) prey dietary shifts affect prey stoichiometric responses to predation-risk. Our dataset was consistent with previous work showing that predation-risk increases prey glucocorticoid levels and metabolic rates and decreases prey growth rates. We found that predation-risk tended to decrease the fat, carbohydrate, and protein content of prey bodies; increased the C:P and N:P of prey bodies; but had no effect on the C, N, P or C:N content of prey bodies. Additionally, we found no effect of predation risk on the N content of prey excretions. Prey responses to predation risk were unaffected by multiple stressors or the prey's ability to shift their diet, but predator hunting mode did affect the nature of prey stoichiometric responses. Specifically, ambush predators decreased prey macronutrient content and suppressed prey growth, while active predators had no effect on prey macronutrient content and a smaller effect on prey growth than ambush predators. The significant effects of predation risk were supported by robust fail-safe numbers, despite the high between comparison heterogeneity that was found in all analyses. Our findings highlight the need to 1) test the underlying mechanisms and emerging patterns of the GSP in diverse taxa, 2) explore the mismatch between prey macronutrient content and elemental stoichiometry, and 3) expand the conceptual framework to include more inducible defenses (e.g., behavioral and morphological) and predator traits.
Development of a Sensitive and Rapid Recombinase Polymerase Amplification Assay for Detection of Anaplasma phagocytophilum

Human granulocytic anaplasmosis (HGA) is a tick-borne disease caused by the obligate intracellular Gram-negative bacterium Anaplasma phagocytophilum. The disease often presents with nonspecific symptoms with negative serology during the acute phase. Direct pathogen detection is the best approach for early confirmatory diagnosis. Over the years, PCR-based molecular detection methods have been developed, but optimal sensitivity is not achieved by conventional PCR while real-time PCR requires expensive and sophisticated instruments. ABSTRACT Human granulocytic anaplasmosis (HGA) is a tick-borne disease caused by the obligate intracellular Gram-negative bacterium Anaplasma phagocytophilum. The disease often presents with nonspecific symptoms with negative serology during the acute phase. Direct pathogen detection is the best approach for early confirmatory diagnosis. Over the years, PCR-based molecular detection methods have been developed, but optimal sensitivity is not achieved by conventional PCR while real-time PCR requires expensive and sophisticated instruments. To improve the sensitivity and also develop an assay that can be used in resource-limited areas, an isothermal DNA amplification assay based on recombinase polymerase amplification (RPA) was developed. To do this, we identified a 171-bp DNA sequence within multiple paralogous copies of msp2 within the genome of A. phagocytophilum. Our novel RPA assay targeting this sequence has an analytical limit of detection of one genome equivalent copy of A. phagocytophilum and can reliably detect 125 bacteria/ml in human blood. A high level of specificity was demonstrated by the absence of nonspecific amplification using genomic DNA from human or DNA from other closely-related pathogenic bacteria, such as Anaplasma platys, Ehrlichia chaffeensis, Orientia tsutsugamushi, and Rickettsia rickettsii, etc. When applied to patient DNA extracted from whole blood, this new RPA assay was able to detect 100% of previously diagnosed A. phagocytophilum cases. The sensitivity and rapidness of this assay represents a major improvement for early diagnosis of A. phagocytophilum in human patients and suggest a role for better surveillance in its reservoirs or vectors, especially in remote regions where resources are limited.
In Vitro, In Silico, and In Vivo Assessments of Pharmacokinetic Properties of ZM241385

Parkinson’s disease is one of the most common neurodegenerative diseases. Adenosine regulates the response to other neurotransmitters in the brain regions related to motor function. In the several subtypes of adenosine receptors, especially, adenosine 2A receptors (A2ARs) are involved in neurodegenerative conditions. ZM241385 is one of the selective non-xanthine A2AR antagonists with high affinity in the nanomolar range. This study describes the in vitro and in vivo pharmacokinetic properties of ZM241385 in rats. A liquid chromatography-quadrupole time-of-flight mass spectrometric (LC-qToF MS) method was developed for the determination of ZM241385 in rat plasma. In vivo IV administration studies showed that ZM241385 was rapidly eliminated in rats. However, the result of in vitro metabolic stability studies showed that ZM241385 had moderate clearance, suggesting that there is an extra clearance pathway in addition to hepatic clearance. In addition, in vivo PO administration studies demonstrated that ZM241385 had low exposure in rats. The results of semi-mass balance studies and the in silico PBPK modeling studies suggested that the low bioavailability of ZM241385 after oral administration in rats was due to the metabolism and by liver, kidney, and gut.
Investigating the impact of disease and health record duration on the eMERGE algorithm for rheumatoid arthritis

OBJECTIVE The study sought to determine the dependence of the Electronic Medical Records and Genomics (eMERGE) rheumatoid arthritis (RA) algorithm on both RA and electronic health record (EHR) duration. MATERIALS AND METHODS Using a population-based cohort from the Mayo Clinic Biobank, we identified 497 patients with at least 1 RA diagnosis code. RA case status was manually determined using validated criteria for RA. RA duration was defined as time from first RA code to the index date of biobank enrollment. To simulate EHR duration, various years of EHR lookback were applied, starting at the index date and going backward. Model performance was determined by sensitivity, specificity, positive predictive value, negative predictive value, and area under the curve (AUC). RESULTS The eMERGE algorithm performed well in this cohort, with overall sensitivity 53%, specificity 99%, positive predictive value 97%, negative predictive value 74%, and AUC 76%. Among patients with RA duration <2 years, sensitivity and AUC were only 9% and 54%, respectively, but increased to 71% and 85% among patients with RA duration >10 years. Longer EHR lookback also improved model performance up to a threshold of 10 years, in which sensitivity reached 52% and AUC 75%. However, optimal EHR lookback varied by RA duration; an EHR lookback of 3 years was best able to identify recently diagnosed RA cases. CONCLUSIONS eMERGE algorithm performance improves with longer RA duration as well as EHR duration up to 10 years, though shorter EHR lookback can improve identification of recently diagnosed RA cases.
Multiple Drug Resistance Patterns in Various Phylogenetic Groups of Hospital-Acquired Uropathogenic E. coli Isolated from Cancer Patients

Cancer patients are more susceptible to several bacterial infections, particularly urinary tract infections caused by uropathogenic E. coli (UPEC). The objective of this work was detection and the phylogenetic characterization of hospital-acquired isolates of uropathogenic E. coli in cancer patients and the determination of its relation with antibiotic resistance. A total of 110 uropathogenic E. coli responsible for hospital-acquired urinary tract infections in cancer patients were included in this study. A triplex PCR was employed to segregate different isolates into four different phylogenetic groups (A, B1, B2 and D). Drug resistance was evaluated by the disc diffusion method. All of the isolates were multiple drug-resistant (MDR) and 38.18% of all UPEC isolates were extended-spectrum beta-lactamase (ESBL) producers from which 52% were positive for the blaCTX-M gene, 40% for the blaTEM gene, and 17% for the blaSHVgene. Among 42 ESBL-producing uropathogenic E. coli isolates, the majority belonged to phylogenetic group B2 (43%), followed by group D (36%), group A (19%) and group B1 (2%). Our results have shown the emergence of MDR isolates among uropathogenic E. coli with the dominance of phylogenetic group B2. Groups A and B1 were relatively less common. The most effective drug in all phylogenetic groups was imipenem.
Relationship between Changes in Myocardial F-18 Fluorodeoxyglucose Uptake and Radiation Dose after Adjuvant Three-Dimensional Conformal Radiotherapy in Patients with Breast Cancer

This study aimed to assess the relationship between radiation dose and changes in the irradiated myocardial F-18 fluorodeoxyglucose (FDG) uptake after radiotherapy (RT) in breast cancer patients. The data of 55 patients with left and 48 patients with right breast cancer who underwent curative surgical resection and adjuvant three-dimensional conformal RT and staging (PET1), post-adjuvant chemotherapy (PET2), post-RT (PET3), and surveillance (PET4) FDG positron emission tomography/computed tomography (PET/CT) were retrospectively reviewed. The median interval between PET1 and curative surgical resection, between the end of adjuvant chemotherapy and PET2, between the end of RT and PET3, and between the end of RT and PET4 were five days, 13 days, 132 days, and 353 days, respectively. The myocardial-to-blood pool uptake ratio was measured in all patients. For patients with left breast cancer, the 30 Gy- (30 Gy) and 47.5 Gy-irradiated myocardium-to-low-irradiated myocardium (47.5 Gy) FDG uptake ratios were additionally measured. There were no differences in the myocardial-to-blood pool uptake ratios between left and right breast cancer on all PET scans. For left breast cancer, higher 30 Gy and 47.5 Gy uptake ratios were observed on PET3 than on PET1 and PET2. Both uptake ratios decreased on PET4 compared to PET3, but, were still higher compared to PET1. On PET3 and PET4, the 47.5 Gy were higher than the 30 Gy uptake ratios, while there were no differences between them on PET1 and PET2. Although the whole myocardium FDG uptake showed no significant change, the irradiated myocardium FDG uptake significantly increased after RT and was related to radiation dose to the myocardium in breast cancer patients. These results might be an imaging evidence that supports the increased risk of heart disease after RT in patients with left breast cancer.
The Course Of IGF-1 Levels and Nutrient Intake in Extremely and Very Preterm Infants During Hospitalisation

Background: Insulin-like growth factor 1 (IGF-1) plays an important role in the complex association between nutrition, growth, and maturation in extremely and very preterm infants. Nevertheless, in this population, research on associations between IGF-1 and nutrition is limited. Therefore this study aimed to evaluate the possible associations between the course of IGF-1 levels and nutrient intake between preterm birth and 36 weeks postmenstrual age (PMA). Methods: 87 infants born between 24 and 32 weeks gestational age were followed up to 36 weeks PMA. Actual daily macronutrient intake was calculated, and growth was assessed weekly. IGF-1 was sampled from umbilical cord blood at birth and every other week thereafter. Results: There was an inverse relationship between the amount of parenteral nutrition in the second week of life and IGF-1. Total protein, fat, and carbohydrate intake, as well as total energy intake, primarily showed a positive association with IGF-1 levels, particularly between 30 and 33 weeks PMA. Gestational age, bronchopulmonary dysplasia (BPD), and weight were significant confounders in the association between nutrient intake and IGF-1 levels. Conclusion: Parenteral nutrition was found to be a negative predictor of IGF-1 levels, and there could potentially be a time frame in which macronutrient intake is unable to impact IGF-1 levels. Future research should aim to narrow down this time frame and to gain more insight into factors enhancing or decreasing the response of IGF-1 to nutrition, e.g., age and inflammatory state, to align nutritional interventions accordingly.
Asymmetron lucayanum: How many species are valid?

The cephalochordates amphioxus or lancelets are benthic marine animals representing the earliest divergent evolutionary lineage within chordates. Although amphioxus are present in most of the world’s tropical and temperate oceans, only about thirty different species grouped into three different genera, Branchiostoma, Epigonichthys and Asymmetron have been described. In the genus Asymmetron, only two species have been characterized, although for one of them, A. lucayanum, several cryptic lineages exist. In this work we have sequenced and analyzed the mitogenome of an A. lucayanum population previously described in the Red Sea. The phylogenetic study using this complete mitogenome as well as the analysis of COI gene sequences of several individuals of this Red Sea population show that the Red Sea population is a new cryptic species. We propose to call this new species Asymmetron rubrum.