Miracle-dz/UniFAR-FTUs huggingface dataset:
The date palm (Phoenix dactylifera L.) in Siwa oasis (Egypt): How ethnographic, morphometric, and genetic analyses together explain the local agrobiodiversity

The agrobiodiversity of the Siwa oasis (in Egypt), located at the crossroads of ancient Trans-Saharan routes, is evaluated in this article focusing on the date palm (Phoenix dactylifera L.), the oasis “ecosystem engineer”. This assessment confronts different ontologies: diversity as expressed and maintained by the folk categorization system of the Siwa inhabitants (through the results of an ethnographical analysis) and diversity described by genetic sciences and a morphometric tool based on the size and geometry of the seeds. This work is also an opportunity to evaluate this tool intended for archaeobotany. Beyond a simple instrumentalization of one discipline by another, this study offers a space of mutual enrichment: on the relative importance of the feral and cultivated date palms, the local relevance of the concept of “cultivar” and the confirmation of the existence of “ethnovarieties”.
Molecular MR Contrast Agents

Abstract Molecular magnetic resonance (MR) imaging utilizes molecular probes to provide added biochemical or cellular information to what can already be achieved with anatomical and functional MR imaging. This review provides an overview of molecular MR and focuses specifically on molecular MR contrast agents that provide contrast by shortening the T1 time. We describe the requirements for a successful molecular MR contrast agent and the challenges for clinical translation. The review highlights work from the last 5 years and places an emphasis on new contrast agents that have been validated in multiple preclinical models. Applications of molecular MR include imaging of inflammation, fibrosis, fibrogenesis, thromboembolic disease, and cancers. Molecular MR is positioned to move beyond detection of disease to the quantitative staging of disease and measurement of treatment response.
The Promotion of Eating Behaviour Change through Digital Interventions

Diet-related chronic disease is a global health epidemic giving rise to a high incidence of morbidity and mortality. With the rise of the digital revolution, there has been increased interest in using digital technology for eating behavioural change as a mean of diet-related chronic disease prevention. However, evidence on digital dietary behaviour change is relatively scarce. To address this problem, this review considers the digital interventions currently being used in dietary behaviour change studies. A literature search was conducted in databases like PubMed, Cochrane Library, CINAHL, Medline, and PsycInfo. Among 119 articles screened, 15 were selected for the study as they met all the inclusion criteria according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) search strategy. Four primary digital intervention methods were noted: use of personal digital assistants, use of the internet as an educational tool, use of video games and use of mobile phone applications. The efficiency of all the interventions increased when coupled with tailored feedback and counselling. It was established that the scalable and sustainable properties of digital interventions have the potential to bring about adequate changes in the eating behaviour of individuals. Further research should concentrate on the appropriate personalisation of the interventions, according to the requirements of the individuals, and proper integration of behaviour change techniques to motivate long-term adherence.
Ultrasound-assisted enzymatic extraction of anthocyanins from grape skins: optimization, identification, and antitumor activity.

Grape skins produced during the grape juice production and processing contain abundant anthocyanins and other active compounds. Consequently, this study optimized the extraction conditions for ultrasound-assisted enzymatic extraction (UAEE) of anthocyanins from grape skins via response surface methodology coupled with genetic algorithm. The optimum extraction parameters to achieve the highest anthocyanins yield (3.01 ± 0.04) mg/g from grape skins by UAEE were obtained under an extraction temperature of 50 °C, ultrasonic power of 400 W, pectinase dosage of 0.16%, and extraction time of 28 min. The AB-8 macroporous resin combined Sephadex LH-20 techniques were further employed to purify the anthocyanins extracts obtained under optimum extraction conditions (AEOEC), and the main anthocyanins were identified using high-performance liquid chromatography tandem mass spectrometry. The purified anthocyanins contained two anthocyanins in terms of delphinidin-3,5-O-diglucoside and cyanidin-3-O-rutinoside with purity of 91.35% and 92.64%, respectively. Ultimately, we further evaluated the antitumor activity of AEOEC and two purified anthocyanins on breast cancer. The results indicated that the antitumor effect of AEOEC on breast cancer MCF-7 cells was better than that of two purified anthocyanins. In addition, AEOEC could memorably increase intracellular reactive oxygen species levels and apoptosis of MCF-7 cells, and arrest MCF-7 cells in the G2/M phases. The findings provide an effective and feasible method for anthocyanins extraction and reduce the environmental burden of this waste.
Fitbit wear-time and patterns of activity in cancer survivors throughout a physical activity intervention and follow-up: Exploratory analysis from a randomised controlled trial

Objective There has been growing interest in the use of smart wearable technology to promote physical activity (PA) behaviour change. However, little is known concerning PA patterns throughout an intervention or engagement with trackers. The objective of the study was to explore patterns of Fitbit-measured PA and wear-time over 24-weeks and their relationship to changes in Actigraph-derived moderate-to-vigorous PA (MVPA). Methods Twenty-nine intervention participants (88%) from the wearable activity technology and action-planning (WATAAP) trial in colorectal and endometrial cancer survivors accepted a Fitbit friend request from the research team to permit monitoring of Fitbit activity. Daily steps and active minutes were recorded for each participant over the 12-week intervention and throughout the follow-up period to 24-weeks. Accelerometer (GT9X) derived MVPA was assessed at end of intervention (12-weeks) and end of follow-up (24-weeks). Results Fitbit wear-time over the 24-weeks of data was remarkably consistent, with median adherence score of 100% for all weeks. During the intervention, participants recorded a median 8006 steps/day. Daily step count was slightly increased through week-13 to week-24 with a median of 8191 steps/day (p = 0.039). Actigraph and Fitbit derived measures were highly correlated but demonstrated poor agreement overall. Fitbit measured activity was closest to MVPA measured using Freedson cut-points as no bias was observed. Conclusions Step count was maintained throughout the trial displaying promise for the effectiveness of smart-wearable interventions to reduce sedentary behaviour beyond the intervention period. Further worthwhile work should compare more advanced smart-wearable technology with accelerometers in order to improve agreement and explore less resource-intensive methods to assess PA that could be scalable.
Significant genetic differentiation among meroplanktonic barrel jellyfish Rhizostoma pulmo (Cnidaria: Scyphozoa) in the Mediterranean Sea

Molecular data have shown that jellyfishes are more geographically restricted and evolutionarily divergent than previously thought. We examined genetic variation and divergence within the meroplanktonic barrel jellyfish Rhizostoma pulmo in the Mediterranean Sea; specific sampling areas were the northern Adriatic, western Mediterranean and Tunisian coast. A total of 19 sampling sites and 68 sequences of the mtDNA cytochrome c oxidase subunit I (COI) gene were used. Of the 68 COI sequences, 45 were newly collected specimens which originated from nine sampling sites along the Tunisian coast. A total of 24 haplotypes were obtained and the specimens sampled were characterised by relatively high levels of haplotype diversity (h = 0.866) and low levels of nucleotide diversity (π = 0.004). Haplotype network analysis showed the presence of three distinct phylogenetic lineages (populations), with separate geographic ranges in the northern Adriatic, western Mediterranean and Tunisian coast. The observed genetic differentiation between these three lineages was supported by the presence of significant genetic differentiation between the 19 populations (FST = 0.757, p < 0.001). The high level of genetic differentiation detected in the barrel jellyfish investigated could be attributed to either intrinsic and/or extrinsic barriers to genetic exchange between different populations that may have adapted to different environmental conditions.
Stem rot and wilt on Euonymus

In August 2008, stem rot and wilt symptoms of unknown origin were observed on Euonymus japonica. From the symptomatic stem base a fungus belonging to the genus Calonectria (anamorph: Cylindrocladium) was isolated (isolate JKI 2140). The isolate was morphologically very similar to Calonectria colhounii as well as to Ca. fujianensis and Ca. pseudocolhounii, except for the larger conidia. Sequence analysis of genes (ITS, BT, TEF-1α, HIS3) showed high similarity to Ca. colhounii, Ca. eucalypti, Ca. fujianensis and Ca. pseudocolhounii. The taxonomic status of the fungal isolate from E. japonica is not yet clear. It belongs to the complex Ca. colhounii but a definitive allocation to or separation from a known Calonectria species is not possible on the basis of a single isolate. The fungus is provisionally named Calonectria colhounii compl. The pathogenicity of the fungus was tested on E. japonica and E. fortunei. The disease symptoms originally observed on field plants of E. japonica were reproduced and the fungus was re-isolated. Thus the pathogenicity of isolate JKI 2140 on both Euonymus species is proved. Since the first occurrence of this infestation there were no further notifications of stem canker and wilt on Euonymus spp. in Germany. Therefore the importance of this pathogen on Euonymus is considered to be low.
External Validation of a Nomogram Predicting Risk of Bleeding Control Interventions after High-Grade Renal Trauma: The Multi-institutional Genito-Urinary Trauma Study (MiGUTS).

INTRODUCTION Renal trauma grading has a limited ability to distinguish patients who will need intervention after high-grade renal trauma (HGRT). A nomogram incorporating both clinical and radiologic factors has been previously developed to predict bleeding control interventions after HGRT. We aimed to externally validate this nomogram using multi-center data from level-1 trauma centers. METHODS We gathered data from 7 Level-1 trauma centers. Patients with available initial CT scans were included. Each CT scan was reviewed by two radiologists blinded to the intervention data. Nomogram variables included trauma mechanism, hypotension/shock, concomitant injuries, vascular contrast extravasation (VCE), pararenal hematoma extension, and hematoma rim distance (HRD). Mixed-effect logistic regression was used to assess the associations between predictors and bleeding intervention. The prediction accuracy of the nomogram was assessed using the area under the receiver operating characteristic curve (AUC) and its 95% confidence interval (CI). RESULTS Overall, 569 HGRT patients were included for external validation. Injury mechanism was blunt in 89%. Using initial CT scans, 14% had VCE and median HRD was 1.7 (0.9-2.6) cm. Overall, 12% underwent bleeding control interventions including 34 angioembolizations and 24 nephrectomies. In the multivariable analysis, presence of VCE was associated with a 3-fold increase in the odds of bleeding interventions (OR: 3.06, 95% CI: 1.44-6.50). Every centimeter increase in HRD was associated with 66% increase in odds of bleeding interventions. External validation of the model provided excellent discrimination in predicting bleeding interventions with an AUC of 0.88 (95% CI: 0.84-0.92). CONCLUSIONS Our results reinforce the importance of radiologic findings such as VCE and hematoma characteristics in predicting bleeding control interventions after renal trauma. The prediction accuracy of the proposed nomogram remains high using external data. These variables can help to better risk stratify high-grade renal injuries. LEVEL OF EVIDENCE Prognostic and Epidemiological Study, Level III.
Analysis of Economic Efficiency in Some Irish Farms Using the DEA Approach

Irish farms are predominately and highly specialized in crops as cereals, protein crops and in dairy productions. The aim of this research was to estimate the economic efficiency in Irish farms part of the Farm Accountancy Data Network (FADN) dataset stratified in function of their own typology of productive specialization since 2004 to 2015 by a quantitative approach such as the Data Envelopment Analysis (DEA). Positive has been the role of inputs as financial subsidies allocated by the Common Agricultural Policy, the first and second pillar, in increasing the economic efficiency of Irish farms. Field crops farms have not had the best results in terms of the economic efficiency even if over the time, in particular during the economic crises 2008-2009, findings have not been stable with significant fluctuations and a sharply decrease of efficiency as a consequence of economic turbulences. Focusing the attention on the research outcomes in all years of investigation comparing also the different typology of farming, mixed farms and farms with animals, such as specialist cattle, sheep, goats and other grazing livestock, have had the highest levels of economic efficiency equal to 100%; by contrast Irish dairy farms have had the modest levels of economic efficiency close to 77%.
One step forward: Successful end-of-treatment outcomes of drug-resistant TB patients who received concomitant bedaquiline and delamanid in Mumbai, India.

BACKGROUND Médecins Sans Frontières clinic in Mumbai, India has been providing concomitant Bedaquiline (BDQ) and Delamanid (DLM) in treatment regimen for patients with drug-resistant tuberculosis (DR-TB) and limited therapeutic options, referred from other healthcare institutions, since 2016. The study documents the end-of-treatment outcomes, culture-conversion rates, and serious adverse events (SAEs) during treatment. METHODS This was a retrospective cohort study based on routinely collected programme data. In clinic, treatment regimens are designed based on culture-drug sensitivity test patterns, previous drug-exposures and are provided for 20-22 months. The BDQ and DLM are extended beyond 24 weeks as off-label use. Patients who initiated DR-TB treatment including BDQ and DLM (concomitantly for at least 4 weeks) during February2016-February2018 were included. RESULT Of the 70 patients included, the median (IQR) age was 25(22-32) years and 56% were females. All except one were fluoroquinolone resistant. The median(IQR) duration of exposure to BDQ and DLM was 77(43-96) weeks. Thirty-nine episodes of serious-adverse-events(SAEs) were reported among 30(43%) patients, including five instances of QTc prolongation-assessed as possibly related to BDQ and/or DLM. Majority(69%) had culture conversion before 24 weeks of treatment. In 61(87%), use of BDQ and DLM was extended beyond 24 weeks. Successful end-of-treatment outcomes were reported in 49(70%) patients. CONCLUSION The successful treatment outcomes of this cohort show that regimens including concomitant bedaquiline and delamanid for longer than 24 weeks are effective and can be safely administered on ambulatory basis. National TB programmes globally should scale up access to life saving DR-TB regimens with new drugs.
Natural Language Processing in Surgery

Supplemental Digital Content is available in the text Objective: The aim of this study was to systematically assess the application and potential benefits of natural language processing (NLP) in surgical outcomes research. Summary Background Data: Widespread implementation of electronic health records (EHRs) has generated a massive patient data source. Traditional methods of data capture, such as billing codes and/or manual review of free-text narratives in EHRs, are highly labor-intensive, costly, subjective, and potentially prone to bias. Methods: A literature search of PubMed, MEDLINE, Web of Science, and Embase identified all articles published starting in 2000 that used NLP models to assess perioperative surgical outcomes. Evaluation metrics of NLP systems were assessed by means of pooled analysis and meta-analysis. Qualitative synthesis was carried out to assess the results and risk of bias on outcomes. Results: The present study included 29 articles, with over half (n = 15) published after 2018. The most common outcome identified using NLP was postoperative complications (n = 14). Compared to traditional non-NLP models, NLP models identified postoperative complications with higher sensitivity [0.92 (0.87–0.95) vs 0.58 (0.33–0.79), P < 0.001]. The specificities were comparable at 0.99 (0.96–1.00) and 0.98 (0.95–0.99), respectively. Using summary of likelihood ratio matrices, traditional non-NLP models have clinical utility for confirming documentation of outcomes/diagnoses, whereas NLP models may be reliably utilized for both confirming and ruling out documentation of outcomes/diagnoses. Conclusions: NLP usage to extract a range of surgical outcomes, particularly postoperative complications, is accelerating across disciplines and areas of clinical outcomes research. NLP and traditional non-NLP approaches demonstrate similar performance measures, but NLP is superior in ruling out documentation of surgical outcomes.
The Transcription Factors of Tall Fescue in Response to Temperature Stresses.

Tall fescue (Festuca arundinacea) is an important grass species worldwide, and the temperature stresses severely affect its distribution and yield. Transcription factors (TFs) as the master switches in sophisticated regulatory networks play essential roles in plant growth development and abiotic stress responses. In this study, we identified 877 TF genes belonging to 35 families in tall fescue under heat stress (40 ℃), cold stress (-10 ℃) and control (22 ℃) conditions. Of them, 784 differentially expressed genes were screened and classified to 33 families, such as bHLH, AP2/ERF, MYB, WRKY, NAC, bZIP, GTF, HD-ZIP, HSF etc. Among them, the expressions of bZIP and GTF family members were up-regulated mainly exposed to both heat and cold, but conversely the most members of WRKY and NAC families were reduced. Upon heat, HSF, GTE families and DREB2Bs were mainly up-regulated. Otherwise, bHLH, MYB, HD-ZIP and ERF families holistically were elevated under cold stress. Function richment analysis indicated that the TFs were involved in the pathways of "Plant hormone signal transduction", "Plant-pathogen interaction", "Circadian rhythm", etc. It showed these pathways were relevant to responding temperature stress. In the main, the temperature threats up-regulated the expressions of the stress tolerance-related genes, whereas down-regulated those genes associated with growth and disease resistance. The results exhibited that the expressions of a slew of TF genes were significantly altered by heat and cold stresses, and different TF families have commonalities and differences in response to the threats, indicating that TFs exert the crucial roles in plant adaption to adverse environment. This study profiled the response pattern of TFs to heat and cold conditions, partially explained the adaptation mechanism of cold-season forages to temperature stress, and screened plenty of candidate stress-tolerant TF genes.
New wings on the interaction between conventional subsoiler and paraplow tines with the soil: effects on the draft and the properties of soil

ABSTRACT Equipping tines with the wings increases draft and soil loosening. Wing angles affect tine performance, soil aggregation and remained residue. In this research, conventional wing with no bent plus backward and forward bent wings with bend angles of 10 and 20° were attached to both a subsoiler and paraplow tine. The rake angle of all wings was 15°. The effects of tine and wing on draft, soil disturbance area, specific draft, remained residue, and mean weight diameter (MWD) were investigated in a clay loam soil at depth of 40 cm and speed of 1.6 km h−1. The effect of tine and wing plus interaction of them on all parameters was significant (p < 0.01) with the exception of remained residue. The bent-winged tines required higher draft and caused higher disturbance area, lower specific draft, and lower MWD than the conventional tines and those without wing. The highest draft, disturbed area and remained residue plus the lowest specific draft and MWD were obtained when applying the 10° forward bent-winged tines. In present work, the paraplow equipped with forward bent wings with a bend angle of 10° was suggested as a suitable tool for deep soil loosening under a conservation tillage system.
More than a Feeling: Microscopy Approaches to Understanding Surface-Sensing Mechanisms

The mechanisms by which bacteria sense and respond to surface attachment have long been a mystery. Our understanding of the structure and dynamics of bacterial appendages, notably type IV pili (T4P), provided new insights into the potential ways that bacteria sense surfaces. T4P are ubiquitous, retractable hair-like adhesins that until recently, due to their nanoscale size, were difficult to image in the absence of fixation. This review focuses on recent microscopy innovations used to visualize T4P in live cells to reveal the dynamics of their retraction and extension. ABSTRACT The mechanisms by which bacteria sense and respond to surface attachment have long been a mystery. Our understanding of the structure and dynamics of bacterial appendages, notably type IV pili (T4P), provided new insights into the potential ways that bacteria sense surfaces. T4P are ubiquitous, retractable hair-like adhesins that until recently, due to their nanoscale size, were difficult to image in the absence of fixation. This review focuses on recent microscopy innovations used to visualize T4P in live cells to reveal the dynamics of their retraction and extension. We discuss recently proposed mechanisms by which T4P facilitate bacterial surface sensing, including the role of surface-exposed PilY1, two-component signal transduction pathways, force-induced structural modifications of the major pilin, and altered dynamics of the T4P motor complex.
Response to the comment on "Number and Station of Lymph Node Metastasis After Curative-intent Resection of Intrahepatic Cholangiocarcinoma Impact Prognosis".

Reply: We appreciate the comments by Yoh et al on our recent publication examining the impact of number and station of lymph node metastasis (LNM) on outcomes of patients who underwent curative-intent resection for intrahepatic cholangiocarcinoma (ICC). In our study, 186 patients had detailed information on LNM station. Patients who had regional LNM beyond station number 12 (n1⁄4 33) has a worse outcome compared with patients who had LNM within station 12 (n1⁄4 153) (median overall survival, 15.0 vs 20.0 months, respectively; P 1⁄4 0.005). Of note, the clinicopathologic characteristics, postoperative complications, and use of adjuvant therapies among patients who had LNM within versus beyond station 12 were comparable. Among 153 patients who had LNM within station 12, 129 (84.3%) had lymph nodes examined only at station 12. Among the 57 patients who had lymph nodes evaluated beyond station 12, the 24 patients who had LNM only within station 12 had a more favorable overall survival compared with the 33 patients who had LNM beyond station 12 (median overall survival, 49.0 vs 15.0 months, P 1⁄4 0.015). In turn, the data strongly suggested that LNM beyond station