Takshan/R1 huggingface dataset:
A 3-D functional-structural grapevine model that couples the dynamics of water transport with leaf gas exchange.

Background and Aims: Predicting both plant water status and leaf gas exchange under various environmental conditions is essential for anticipating the effects of climate change on plant growth and productivity. This study developed a functional-structural grapevine model which combines a mechanistic understanding of stomatal function and photosynthesis at the leaf level (i.e. extended Farqhuhar-von Caemmerer-Berry model) and the dynamics of water transport from soil to individual leaves (i.e. Tardieu-Davies model). Methods: The model included novel features that account for the effects of xylem embolism (fPLC) on leaf hydraulic conductance and residual stomatal conductance (g0), variable root and leaf hydraulic conductance, and the microclimate of individual organs. The model was calibrated with detailed datasets of leaf photosynthesis, leaf water potential, xylem sap abscisic acid (ABA) concentration and hourly whole-plant transpiration observed within a soil drying period, and validated with independent datasets of whole-plant transpiration under both well-watered and water-stressed conditions. Key Results: The model well captured the effects of radiation, temperature, CO2 and vapour pressure deficit on leaf photosynthesis, transpiration, stomatal conductance and leaf water potential, and correctly reproduced the diurnal pattern and decline of water flux within the soil drying period. In silico analyses revealed that decreases in g0 with increasing fPLC were essential to avoid unrealistic drops in leaf water potential under severe water stress. Additionally, by varying the hydraulic conductance along the pathway (e.g. root and leaves) and changing the sensitivity of stomatal conductance to ABA and leaf water potential, the model can produce different water use behaviours (i.e. iso- and anisohydric). Conclusions: The robust performance of this model allows for modelling climate effects from individual plants to fields, and for modelling plants with complex, non-homogenous canopies. In addition, the model provides a basis for future modelling efforts aimed at describing the physiology and growth of individual organs in relation to water status.
[Rhabdomyolysis associated with respiratory infection in chronic psychiatric patients during neuroleptic treatment].

Rabdomiolisi associata a infezione polmonare in pazienti schizofrenici in trattamento con neurolettici. Rhabdomyolysis is a disorder characterized by skeletal muscle injury and fatal complications at times. The causes of rhabdomyolysis are usually traumatic and non-traumatic, such as neuroleptic malignant syndrome and rhabdomyolysis associated to septicemia. The cases of 2 schizophrenic patients with rhabdomyolisis during pneumonia infection and neuroleptic therapy are reported. At admission, both patients had important respiratory distress and hyperthermia; the clinical conditions required endotracheal intubation. Blood and urine cultures were always negative, while the bronchial sputum culture was positive. The diagnosis of rhabdomyolysis was confirmed by myoglobinemia dosage and ortholuidine test. Pneumonia infection was treated with antibiotic specific therapy whereas renal failure was treated with adequate hydratation and strained diuresis. The absence of muscle rigidity, the improvement of X-r images and the reduction of corporeal temperature, during antibiotic treatment, excluded neuroleptic malignant syndrome. The impro-vement allowed extubation and discharge of the patients from intensive care unit. In both cases neuroleptic malignant syndrome was excluded, therefore rhabdomyolysis was the consequence of pneumonia infection or of a combination of factors capable to cause an important damage of skeletal muscles.
The Role of Quinine-Responsive Taste Receptor Family 2 in Airway Immune Defense and Chronic Rhinosinusitis.

Background: Bitter (T2R) and sweet (T1R) taste receptors in the airway are important in innate immune defense, and variations in taste receptor functionality in one T2R (T2R38) correlate with disease status and disease severity in chronic rhinosinusitis (CRS). Quinine is a bitter compound that is an agonist for several T2Rs also expressed on sinonasal cells, but not for T2R38. Because of this property, quinine may stimulate innate immune defense mechanisms in the airway, and functional differences in quinine perception may be reflective of disease status in CRS. Methods: Demographic and taste intensity data were collected prospectively from CRS patients and non-CRS control subjects. Sinonasal tissue from patients undergoing rhinologic surgery was also collected and grown at an air-liquid interface (ALI). Nitric oxide (NO) production and dynamic regulation of ciliary beat frequency in response to quinine stimulation were assessed in vitro. Results: Quinine reliably increased ciliary beat frequency and NO production in ALI cultures in a manner consistent with T2R activation (p < 0.01). Quinine taste intensity rating was performed in 328 CRS patients and 287 control subjects demonstrating that CRS with nasal polyps (CRSwNP) patients rated quinine as significantly less intense than did control subjects. Conclusion: Quinine stimulates airway innate immune defenses by increasing ciliary beat frequency and stimulating NO production in a manner fitting with T2R activation. Patient variability in quinine sensitivity is observed in taste intensity ratings, and gustatory quinine "insensitivity" is associated with CRSwNP status. Thus, taste tests for quinine may be a biomarker for CRSwNP, and topical quinine has therapeutic potential as a stimulant of innate defenses.
Developing indicators for measuring low-value care: mapping Choosing Wisely recommendations to hospital data.

OBJECTIVE: Low-value health care refers to interventions where the risk of harm or costs exceeds the likely benefit for a patient. We aimed to develop indicators of low-value care, based on selected Choosing Wisely (CW) recommendations, applicable to routinely collected, hospital claims data. RESULTS: We assessed 824 recommendations from the United States, Canada, Australia and the United Kingdom CW lists regarding their capacity to be measured in administrative hospital admissions datasets. We selected recommendations if they met the following criteria: the service occurred in the hospital setting (observable in setting); a claim recorded the use of the service (record of service); the appropriate/inappropriate use of the service could be mapped to information within the hospital claim (indication); and the service is consistently recorded in the claims (consistent documentation). We identified 17 recommendations (15 services) as measurable. We then developed low-value care indicators for two hospital datasets based on the selected recommendations, previously published indicators, and clinical input.
Capturing patient-reported area of knee pain: a concurrent validity study using digital technology in patients with patellofemoral pain.

Background: Patellofemoral pain (PFP) is often reported as a diffuse pain at the front of the knee during knee-loading activities. A patient's description of pain location and distribution is commonly drawn on paper by clinicians, which is difficult to quantify, report and compare within and between patients. One way of overcoming these potential limitations is to have the patient draw their pain regions using digital platforms, such as personal computer tablets. Objective: To assess the validity of using computer tablets to acquire a patient's knee pain drawings as compared to paper-based records in patients with PFP. Methods: Patients (N = 35) completed knee pain drawings on identical images (size and colour) of the knee as displayed on paper and a computer tablet. Pain area expressed as pixel density, was calculated as a percentage of the total drawable area for paper and digital records. Bland-Altman plots, intraclass correlation coefficient (ICC), Pearson's correlation coefficients and one-sample tests were used in data analysis. Results: No significant difference in pain area was found between the paper and digital records of mapping pain area (p = 0.98), with the mean difference = 0.002% (95% CI [-0.159-0.157%]). A very high agreement in pain area between paper and digital pain drawings (ICC = 0.966 (95% CI [0.93-0.98], F = 28.834, df = 31, p < 0.001). A strong linear correlation (R2 = 0.870) was found for pain area and the limits of agreement show less than ±1% difference between paper and digital drawings. Conclusion: Pain drawings as acquired using paper and computer tablet are equivalent in terms of total area of reported knee pain. The advantages of digital recording platforms, such as quantification and reporting of pain area, could be realized in both research and clinical settings.
An ethnobotanical study in Midyat (Turkey), a city on the silk road where cultures meet.

BACKGROUND: Studies of ethnobotanical usages in south-eastern Turkey are rare. To widen this field of knowledge, we conducted an ethnobotanical study in Midyat (Mardin Province), Turkey. METHODS: The field study was completed during three years (2007-2010). Our aim was to document the ethnobotanical uses of local plants and to make an ethnobotanical inventory of uncommon plants using qualitative interviews. RESULTS: During field studies, 368 voucher specimens were collected in the investigated area. Ninety-two traditionally used plant species were reported from Midyat and surrounding vicinities in Turkey. Among the 92 taxa (129 usages), 35% were used for medical purposes, 22% for food, 13% for animal fodder, 7% as ornamental plants and dyes, 6% as brooms, 4% for latex and as fragrance, 4% for herbal tea, molasses and wine preparation, 3% for agricultural purposes, and 6% for other purposes. Comparative assessment showed that Teucrium polium (0.51), Matricaria aurea (0.26), Alcea setosa (0.21), and Malva neglecta (0.21) have the highest recorded UVs, and the following taxa had UVs between 0.10-0.20: Anthemis cotula (0.12), Allium cepa (0.13), Alcea striata subsp. striata (0.14), Crupina crupinastrum (0.12), Papaver rhoeas (0.13), Salvia multicaulis (0.14), Thymbra spicata (0.11), and Vicia pannonica subsp. striata (0.15). We reported the ethnobotanical usages of 21 taxa for the first time, in addition to indicating usages previously recorded in the literature. We also recorded four endemic plant usages in the area: Alkanna trichophila var. mardinensis, Centaurea kurdica, Centaurea stapfiana, and Sideritis libanotica subsp. linearis. They have variable leaf and flower morphology that are used traditionally. They are present as well-developed populations and thus their conservation status is not compromised. Additionally, Thymbra sintenisii is a recorded species that is classified as a rare and extensively used species in the region. CONCLUSIONS: These results contribute to the fundamental knowledge of ethnobotanical usages in Midyat. To date, ethnobotanical studies have not been carried out in this region. This investigation uncovered usages of endemic medicinal plant species and traditional knowledge of Midyat communities living in a mixed culture. The people of Midyat, Batman, and Şırnak are Turkish citizens from various ethnic backgrounds, such as Kurdish, Arabic, and Syriac. We compared our data with results from other studies conducted in Turkey, particularly in south-eastern and eastern regions, as well as with studies from bordering countries, Iraq, Jordan, Syria, and Iran. Nonetheless, more work needs to be conducted to extend the present knowledge for locals to contribute to and evaluate economic potential in the region.
Modulation of mitochondrial activity in HaCaT keratinocytes by the cell penetrating peptide Z-Gly-RGD(DPhe)-mitoparan.

OBJECTIVE: Biologically active cell penetrating peptides (CPPs) are an emerging class of therapeutic agent. The wasp venom peptide mastoparan is an established CPP that modulates mitochondrial activity and triggers caspase-dependent apoptosis in cancer cells, as does the mastoparan analogue mitoparan (mitP). Mitochondrial depolarisation and activation of the caspase cascade also underpins the action of dithranol, a topical agent for treatment of psoriasis. The effects of a potent mitP analogue on mitochondrial activity were therefore examined to assess its potential as a novel approach for targeting mitochondria for the treatment of psoriasis. RESULTS: In HaCaT keratinocytes treated with the mitP analogue Z-Gly-RGD(DPhe)-mitP for 24 h, a dose-dependent loss of mitochondrial activity was observed using the methyl-thiazolyl-tetrazolium (MTT) assay. At 10 μmol L-1, MTT activity was less than 30% that observed in untreated cells. Staining with the cationic dye JC-1 suggested that Z-Gly-RGD(DPhe)-mitP also dissipated the mitochondrial membrane potential, with a threefold increase in mitochondrial depolarisation levels. However, caspase activity appeared to be reduced by 24 h exposure to Z-Gly-RGD(DPhe)-mitP treatment. Furthermore, Z-Gly-RGD(DPhe)-mitP treatment had little effect on overall cell viability. Our findings suggest Z-Gly-RGD(DPhe)-mitP promotes the loss of mitochondrial activity but does not appear to evoke apoptosis in HaCaT keratinocytes.
Taxonomy-based content analysis of sedentary behavior questionnaires: A systematic review.

BACKGROUND: Health effects of sedentary behaviors (SB) may vary depending on their characteristics such as type, purpose, duration, and intensity of the behavior. While a growing number of questionnaires assess sedentary behaviors, it is unclear which characteristics of SB are measured. The aim of this review was to examine the content of self-report SB questionnaires. METHODS: Three databases were searched for sedentary behavior questionnaires published before January 1st, 2016. Based on the inclusion criteria, 82 articles out of 1369 were retrieved for a total of 60 questionnaires. For each questionnaire, the sedentary behavior characteristics identified were reported and analyzed. RESULTS: Most of the questionnaires assessed the time (n = 60), posture (n = 54), purpose (n = 46) and the types (n = 45) of SB performed. Fewer questionnaires assessed the environment (n = 20) social context (n = 11), status (n = 2), and associated behaviors (n = 2) related to sedentary behaviors. All the questionnaires except two assessed time spent in SB with 17 assessing frequency and 6 assessing breaks in SB. The most frequent characteristics identified in the questionnaires were the categories of sitting (90%), a day (95%), watching television (65%) and using a computer (55%). Many characteristics of SB were not measured. CONCLUSIONS: By knowing the breadth of SB included in questionnaires, this review provides support to shape the design of new questionnaires designed to reduce the gaps in measuring sedentary behaviors.
Rational combination of a MEK inhibitor, selumetinib, and the Wnt/calcium pathway modulator, cyclosporin A, in preclinical models of colorectal cancer.

PURPOSE: The mitogen-activated protein kinase (MAPK) pathway is a crucial regulator of cell proliferation, survival, and resistance to apoptosis. MEK inhibitors are being explored as a treatment option for patients with KRAS-mutant colorectal cancer who are not candidates for EGFR-directed therapies. Initial clinical results of MEK inhibitors have yielded limited single-agent activity in colorectal cancer, indicating that rational combination strategies are needed. EXPERIMENTAL DESIGN: In this study, we conducted unbiased gene set enrichment analysis and synthetic lethality screens with selumetinib, which identified the noncanonical Wnt/Ca++ signaling pathway as a potential mediator of resistance to the MEK1/2 inhibitor selumetinib. To test this, we used shRNA constructs against relevant WNT receptors and ligands resulting in increased responsiveness to selumetinib in colorectal cancer cell lines. Further, we evaluated the rational combination of selumetinib and WNT pathway modulators and showed synergistic antiproliferative effects in in vitro and in vivo models of colorectal cancer. RESULTS: Importantly, this combination not only showed tumor growth inhibition but also tumor regression in the more clinically relevant patient-derived tumor explant (PDTX) models of colorectal cancer. In mechanistic studies, we observed a trend toward increased markers of apoptosis in response to the combination of MEK and WntCa(++) inhibitors, which may explain the observed synergistic antitumor effects. CONCLUSIONS: These results strengthen the hypothesis that targeting both the MEK and Wnt pathways may be a clinically effective rational combination strategy for patients with metastatic colorectal cancer.
Runners with patellofemoral pain demonstrate sub-groups of pelvic acceleration profiles using hierarchical cluster analysis: an exploratory cross-sectional study.

BACKGROUND: Previous studies have suggested that distinct and homogenous sub-groups of gait patterns exist among runners with patellofemoral pain (PFP), based on gait analysis. However, acquisition of 3D kinematic data using optical systems is time consuming and prone to marker placement errors. In contrast, axial segment acceleration data can represent an overall running pattern, being easy to acquire and not influenced by marker placement error. Therefore, the purpose of this study was to determine if pelvic acceleration patterns during running could be used to classify PFP patients into homogeneous sub-groups. A secondary purpose was to analyze lower limb kinematic data to investigate the practical implications of clustering these subjects based on 3D pelvic acceleration data. METHODS: A hierarchical cluster analysis was used to determine sub-groups of similar running profiles among 110 PFP subjects, separately for males (n = 44) and females (n = 66), using pelvic acceleration data (reduced with principal component analysis) during treadmill running acquired with optical motion capture system. In a secondary analysis, peak joint angles were compared between clusters (α = 0.05) to provide clinical context and deeper understanding of variables that separated clusters. RESULTS: The results reveal two distinct running gait sub-groups (C1 and C2) for female subjects and no sub-groups were identified for males. Two pelvic acceleration components were different between clusters (PC1 and PC5; p < 0.001). While females in C1 presented similar acceleration patterns to males, C2 presented greater vertical and anterior peak accelerations. All females presented higher and delayed mediolateral acceleration peaks than males. Males presented greater ankle eversion (p < 0.001), lower knee abduction (p = 0.007) and hip adduction (p = 0.002) than all females, and lower hip internal rotation than C1 (p = 0.007). CONCLUSIONS: Two distinct and homogeneous kinematic PFP sub-groups were identified for female subjects, but not for males. The results suggest that differences in running gait patterns between clusters occur mainly due to sex-related factors, but there are subtle differences among female subjects. This study shows the potential use of pelvic acceleration patterns, which can be acquired with accessible wearable technology (i.e. accelerometers).
Outbreak of Invasive Wound Mucormycosis in a Burn Unit Due to Multiple Strains of Mucor circinelloides f. circinelloides Resolved by Whole-Genome Sequencing.

Mucorales are ubiquitous environmental molds responsible for mucormycosis in diabetic, immunocompromised, and severely burned patients. Small outbreaks of invasive wound mucormycosis (IWM) have already been reported in burn units without extensive microbiological investigations. We faced an outbreak of IWM in our center and investigated the clinical isolates with whole-genome sequencing (WGS) analysis. We analyzed M. circinelloides isolates from patients in our burn unit (BU1, Hôpital Saint-Louis, Paris, France) together with nonoutbreak isolates from Burn Unit 2 (BU2, Paris area) and from France over a 2-year period (2013 to 2015). A total of 21 isolates, including 14 isolates from six BU1 patients, were analyzed by whole-genome sequencing (WGS). Phylogenetic classification based on de novo assembly and assembly free approaches showed that the clinical isolates clustered in four highly divergent clades. Clade 1 contained at least one of the strains from the six epidemiologically linked BU1 patients. The clinical isolates were specific to each patient. Two patients were infected with more than two strains from different clades, suggesting that an environmental reservoir of clonally unrelated isolates was the source of contamination. Only two patients from BU1 shared one strain, which could correspond to direct transmission or contamination with the same environmental source. In conclusion, WGS of several isolates per patients coupled with precise epidemiological data revealed a complex situation combining potential cross-transmission between patients and multiple contaminations with a heterogeneous pool of strains from a cryptic environmental reservoir. IMPORTANCE Invasive wound mucormycosis (IWM) is a severe infection due to environmental molds belonging to the order Mucorales. Severely burned patients are particularly at risk for IWM. Here, we used whole-genome sequencing (WGS) analysis to resolve an outbreak of IWM due to Mucor circinelloides that occurred in our hospital (BU1). We sequenced 21 clinical isolates, including 14 from BU1 and 7 unrelated isolates, and compared them to the reference genome (1006PhL). This analysis revealed that the outbreak was mainly due to multiple strains that seemed patient specific, suggesting that the patients were more likely infected from a pool of diverse strains from the environment rather than from direct transmission among them. This study revealed the complexity of a Mucorales outbreak in the settings of IWM in burn patients, which has been highlighted based on WGS combined with careful sampling.
Distributional patterns of item responses and total scores on the PHQ-9 in the general population: data from the National Health and Nutrition Examination Survey.

BACKGROUND: Recently, item responses and total scores on depression screening scales have been reported to have characteristic distributions in the general population. The distributional pattern of responses to the Patient Health Questionnaire-9 (PHQ-9) in the general population has not been well studied. Thus, we carried out a pattern analysis of the PHQ-9 item responses and total scores in US adults. METHODS: Data (5372 individuals) were drawn from the 2013-2014 National Health and Nutrition Examination Survey in the United States. The item responses and total score distributions of the PHQ-9 data were investigated with graphical analysis and exponential regression model. RESULTS: Lines of item responses showed the same pattern among the nine items, characterized by crossing at a single point between "not at all" and "several days" and a parallel pattern from "several days" to "nearly every day" on a log-normal scale. The total score distribution of the PHQ-9 exhibited an exponential pattern, except for at the lower end of the distribution. CONCLUSIONS: The present results support that the item responses and total scores on the PHQ-9 in the general population show the same characteristic patterns, consistent with the previous studies using the Center for Epidemiologic Studies Depression Scale (CES-D) and Kessler Screening Scale for Psychological Distress (K6).