Miracle-dz/UniFAR-FTUs huggingface dataset:
Informed health choices intervention to teach primary school children in low-income countries to assess claims about treatment effects: process evaluation

Background We developed the informed health choices (IHC) primary school resources to teach children how to assess the trustworthiness of claims about the effects of treatments. We evaluated these resources in a randomised trial in Uganda. This paper describes the process evaluation that we conducted alongside this trial. Objectives To identify factors affecting the implementation, impact and scaling up of the intervention; and potential adverse and beneficial effects of the intervention. Methods All 85 teachers in the 60 schools in the intervention arm of the trial completed a questionnaire after each lesson and at the end of the term. We conducted structured classroom observations at all 60 schools. For interviews and focus groups, we purposively selected six schools. We interviewed district education officers, teachers, head teachers, children and their parents. We used a framework analysis approach to analyse the data. Results Most of the participants liked the IHC resources and felt that the content was important. This motivated the teachers and contributed to positive attitudes. Although some teachers started out lacking confidence, many found that the children’s enthusiasm for the lessons made them more confident. Nearly everyone interviewed thought that the children learnt something important and many thought that it improved their decision-making. The main barrier to scaling up use of the IHC resources that participants identified was the need to incorporate the lessons into the national curriculum. Conclusion The mostly positive findings reflect the trial results, which showed large effects on the children’s and the teachers’ critical appraisal skills. The main limitations of this evaluation are that the investigators were responsible for both developing and evaluating the intervention.
Tracing the production area of citrus fruits using aroma-active compounds and their quality evaluation modles.

BACKGROUND The aroma is one of the most important fruit quality factor and can objectively reflect the characteristic of different fruits. Employing the aroma-active compound to trace the production area of two citrus cultivars (Eureka lemon and Huapi kumquat) and develop an approach to evaluate their aroma quality are of great significance. RESULTS Huapi kumquat peel showed higher content of monoterpene and sesquiterpene compounds, while Eureka lemon peel exhibited higher content of monoterpene and monoterpene aldehyde compounds. Eureka lemon peel (Wanzhou cultivar) had a higher content of nerol acetate and geraniol acetate compounds. Kumquat peel (Suichuan and Rong' cultivars) was a higher content of sesquiterpenes. In addition, 30 and 31 quantified compounds observed as aroma-active compounds in kumquat and lemon according to odor activity value, respectively. Principal component analysis (PCA) and hierarchical clustering analysis (HCA) results indicated a useful classification for production areas based on aroma-active compounds. The selected aroma-active compounds have been checked as aroma quality parameters, which associated with multivariate analysis to establish a model of aroma quality evaluation. Higher aroma quality value of kumquat and lemon were collected from Rong'an and Wanzhou, respectively. CONCLUSION The aroma-active compounds can be used to discriminate production areas by multivariate statistics. An objective method was established to evaluate the aroma quality of citrus fruits. Huapi kumquat and Eureka lemon with highest aroma quality was harvested from Rong'an and Wanzhou production areas. It was the first time to evaluate the aroma quality of citrus fruits objectively by using multivariate analysis. This article is protected by copyright. All rights reserved.
Gut Feeling: A Grounded Theory Study to Identity Clinical Educators' Reasoning Processes in Putting Students on a Learning Contract.

AIM To develop a substantive theoretical explanation that makes sense of the decision making process that clinical instructors use to place students on a learning contract. BACKGROUND Clinical instructors are challenged with the task of objectively evaluating students using subjective tools such as anecdotal notes, diaries, unstructured observations and verbal feedback from other nurses. Clinical instructors' assessment decisions have a considerable impact on a variety of key stakeholders, not least of all students. DESIGN Grounded theory method and its heuristic tools including the logic of constant comparison, continuous memoing, and theoretical sampling to serve conceptualization were used in the process of data collection and analysis. METHODS Seventeen individual semi-structured interviews with clinical instructors in one university in western Canada were conducted between May 2016 and May 2017. Data were analyzed using open, axial and selective coding consistent with grounded theory methodology. The study was checked for the Standards for Reporting Qualitative Research (SRQR) criteria (See Supplementary File 1). FINDINGS Three subcategories, "brewing trouble," "unpacking thinking" and "benchmarking" led to the study's substantive theoretical explanation. 'Gut feeling' demonstrates how clinical instructors' reason in their decision making process to place a student on a learning contract. CONCLUSION Placing a student on a learning contract is impacted by personal, professional and institutional variables that together shift the process of evaluation towards subjectivity, thus influencing students' competency. A systems level approach, focusing on positive change through implementing innovative assessment strategies, such as using a smart phone application, are needed to provide some degree of consistency and objectivity. RELEVANCE TO CLINICAL PRACTICE Making visible the objective assessments currently being done by clinical instructors has the potential to change organizational standards, which in turn impact patient and clinical outcomes.
Rapid Tuberculosis Diagnosis Using Reporter Enzyme Fluorescence

Tuberculosis is the most frequent cause of death in humans from a single infectious agent. Due to low numbers of bacteria present in sputum during early infection, diagnosis does not usually occur until >3 to 4 months after symptoms develop. We created a new more sensitive diagnostic that can be carried out in 10 min with no processing or technical expertise. ABSTRACT Tuberculosis is the most frequent cause of death in humans from a single infectious agent. Due to low numbers of bacteria present in sputum during early infection, diagnosis does not usually occur until >3 to 4 months after symptoms develop. We created a new more sensitive diagnostic that can be carried out in 10 min with no processing or technical expertise. This assay utilizes the Mycobacterium tuberculosis-specific biomarker BlaC in reporter enzyme fluorescence (REF) that has been optimized for clinical samples, designated REFtb, along with a more specific fluorogenic substrate, CDG-3. We report the first evaluation of clinical specimens with REFtb assays in comparison to the gold standards for tuberculosis diagnosis, culture and smear microscopy. REFtb assays allowed diagnosis of 160 patients from 16 different countries with a sensitivity of 89% for smear-positive, culture-positive samples and 88% for smear-negative, culture-positive samples with a specificity of 82%. The negative predictive value of REFtb for tuberculosis infection is 93%, and the positive predictive value is 79%. Overall, these data point toward the need for larger accuracy studies by third parties using a commercially available REFtb kit to determine whether incorporation of REFtb into the clinical toolbox for suspected tuberculosis patients would improve case identification. If results similar to our own can be obtained by all diagnostic laboratories, REFtb would allow proper treatment of more than 85% of patients that would be missed during their initial visit to a clinic using current diagnostic strategies, reducing the potential for further spread of disease.
Efficacy and Long-term Peripheral Sensory Neuropathy of 3 vs 6 Months of Oxaliplatin-Based Adjuvant Chemotherapy for Colon Cancer

Key Points Question Can a shortened course of adjuvant oxaliplatin-based chemotherapy reduce peripheral sensory neuropathy (PSN) without compromising efficacy in patients with stage III colon cancer? Findings In this phase 3 randomized clinical trial of 1313 patients, 3 months of adjuvant therapy significantly reduced the rate of any grade of PSN at 3 years, compared with 6 months of treatment. The incidence of any grade of PSN lasting for 3 years was significantly lower for the chemotherapy drug capecitabine plus oxaliplatin (CAPOX) than for the drug modified fluorouracil, leucovorin, and oxaliplatin (mFOLFOX6); these treatment outcomes were consistent with those of the International Duration Evaluation of Adjuvant Chemotherapy (IDEA) Collaboration. Meaning A 3-month chemotherapy regimen of CAPOX may be the most appropriate treatment option for colon cancer, particularly in low-risk patients.
Phyllosticta citricarpa and sister species of global importance to Citrus

Summary Several Phyllosticta species are known as pathogens of Citrus spp. , and are responsible for various disease symptoms including leaf and fruit spots. One of the most important species is P. citricarpa, which causes a foliar and fruit disease called citrus black spot. The Phyllosticta species occurring on citrus can most effectively be distinguished from P. citricarpa by means of multilocus DNA sequence data. Recent studies also demonstrated P. citricarpa to be heterothallic, and reported successful mating in the laboratory. Since the domestication of citrus, different clones of P. citricarpa have escaped Asia to other continents via trade routes, with obvious disease management consequences. This pathogen profile represents a comprehensive literature review of this pathogen and allied taxa associated with citrus, focusing on identification, distribution, genomics, epidemiology and disease management. This review also considers the knowledge emerging from seven genomes of Phyllosticta spp. , demonstrating unknown aspects of these species, including their mating behaviour. Taxonomy Phyllosticta citricarpa (McAlpine) Aa, 1973. Kingdom Fungi, Phylum Ascomycota, Class Dothideomycetes, Order Botryosphaeriales, Family Phyllostictaceae, Genus Phyllosticta, Species citricarpa. Host range Confirmed on more than 12 Citrus species, Phyllosticta citricarpa has only been found on plant species in the Rutaceae. Disease symptoms P. citricarpa causes diverse symptoms such as hard spot, virulent spot, false melanose and freckle spot on fruit, and necrotic lesions on leaves and twigs. Useful websites DOE Joint Genome Institute MycoCosm portals for the Phyllosticta capitalensis (https://genome.jgi.doe.gov/Phycap1), P. citriasiana (https://genome.jgi.doe.gov/Phycit1), P. citribraziliensis (https://genome.jgi.doe.gov/Phcit1), P. citrichinaensis (https://genome.jgi.doe.gov/Phcitr1), P. citricarpa (https://genome.jgi.doe.gov/Phycitr1, https://genome.jgi.doe.gov/Phycpc1), P. paracitricarpa (https://genome.jgi.doe.gov/Phy27169) genomes. All available Phyllosticta genomes on MycoCosm can be viewed at https://genome.jgi. doe.gov/Phyllosticta.
Nursing Practice Related to Intermittent Catheterization

PURPOSE: The purpose of this study was to describe nursing practice and clinical decision-making related to intermittent catheterization (IC). DESIGN: Cross-sectional survey. SUBJECTS AND SETTING: Three hundred forty-three nurses responded to the survey, yielding a margin of error of 5.3%. The majority (70%; n = 240) indicated they were RNs, and 15.6% stated they practiced as advanced practice nurses (nurse practitioners or clinical nurse specialists). Most (75.9%; n = 260) held at least one certification in rehabilitation, WOC, or urologic nursing. Most nurses (70.5%; n = 242) indicated 11 or more years of experience in their specialty practice. METHODS: Data were collected via an electronic questionnaire that comprised 50 items and required 35 to 40 minutes to complete. Ten items queried demographic data and professional background, 13 queried facility policies and practice patterns related to use of IC, and 27 focused on various aspects of decision making regarding IC practice including 8 items related to catheter selection in 4 case scenarios. The questionnaire was completed online after viewing a written explanation of the purpose of the survey. Completion of the questionnaire acted as consent to study participation. RESULTS: All respondents indicated regularly teaching IC within their practice, and 61.2% (n = 210) stated they were confident that 70% or more of patients or caregivers understood the instructions. However, responses varied considerably when asked who they involved in IC education; less than half (48.1%; n = 165) responded that they included a lay caregiver or family member when teaching a patient to perform IC. Responses also varied when asked about who was included in this education; when asked about catheter selection in 4 clinical scenarios, 9.0% to 20.9% selected inappropriate catheters. Similarly, responses varied when they were asked about use of resources to guide IC practice; 25.4% (n = 87) indicated they relied on their own best practice. CONCLUSIONS: Findings from 343 nurses experienced in IC teaching showed considerable variability when asked about sources used to guide IC practice, who should be included in IC education, and catheter selection in 4 case scenarios. Additional research and evidence, and consensus-based resources such as clinical guidelines of a decision-making algorithm, are needed.
Simple Defocused Fiber Optic Volume Probe for Subsurface Raman Spectroscopy in Turbid Media

We investigated the ability to perform deep subsurface Raman spectroscopy in turbid media using a simple fiber optic volume probe. Being able to collect Raman signals from regions deep within a biological sample provides the ability to noninvasively study underlying living tissue and tissue engineered constructs with high chemical specificity. Spatially offset Raman spectroscopy has shown great potential for obtaining subsurface Raman signals in biological samples. The applicability of the method for in vivo studies depends on the system complexity and small size probes are often desirable. Most real-time studies on human patients utilizing Raman spectroscopy have been performed with easy-to-handle miniaturized probes. Here we show both experimentally and theoretically that the sampling depth from a simple volume probe can be controlled by changing the probe to sample distance effectively suppressing Raman and fluorescence contributions from shallow sample layers while favoring the collection of signals from deeper layers. Relative spectral intensities as function of probe to sample distance were investigated for layered phantoms of poly(methyl methacrylate) and trans-stilbene and compared with theory. The volume probe was then utilized for the collection of spectra from phantoms mimicking in vivo transcutaneous measurement configurations of bone and engineered scaffold as well as from an ex vivo sample of bone and soft tissue. Together the results show that Raman fiber optic volume probes can be utilized for subsurface Raman spectroscopy in turbid media, providing a simple alternative to spatially offset Raman systems for, e.g., noninvasive monitoring and studying mineralized tissue and implanted scaffolds in vivo.
Novel phosphorylation‐dependent regulation in an unstructured protein

This work explores how phosphorylation of an unstructured protein region in inhibitor‐2 (I2) regulates protein phosphatase‐1 (PP1) enzyme activity using molecular dynamics (MD). Free I2 is largely unstructured; however, when bound to PP1, three segments adopt a stable structure. In particular, an I2 helix (i‐helix) blocks the PP1 active site and inhibits phosphatase activity. I2 phosphorylation in the PP1‐I2 complex activates phosphatase activity without I2 dissociation. The I2 Thr74 regulatory phosphorylation site is in an unstructured domain in PP1‐I2. PP1‐I2 MD demonstrated that I2 phosphorylation promotes early steps of PP1‐I2 activation in explicit solvent models. Moreover, phosphorylation‐dependent activation occurred in PP1‐I2 complexes derived from I2 orthologs with diverse sequences from human, yeast, worm, and protozoa. This system allowed exploration of features of the 73‐residue unstructured human I2 domain critical for phosphorylation‐dependent activation. These studies revealed that components of I2 unstructured domain are strategically positioned for phosphorylation responsiveness including a transient α‐helix. There was no evidence that electrostatic interactions of I2 phosphothreonine74 influenced PP1‐I2 activation. Instead, phosphorylation altered the conformation of residues around Thr74. Phosphorylation uncurled the distance between I2 residues Glu71 to Tyr76 to promote PP1‐I2 activation, whereas reduced distances reduced activation. This I2 residue Glu71 to Tyr76 distance distribution, independently from Thr74 phosphorylation, controls I2 i‐helix displacement from the PP1 active site leading to PP1‐I2 activation.
The use of urinary fluoride excretion to facilitate monitoring fluoride intake: A systematic scoping review

Background As a recognised effective and economical agent for dental caries prevention, fluoride has been used in many different fluoridation schemes implemented across the world. Considering the narrow ‘dose-gap’ between the benefit of caries reduction and the risk of dental fluorosis, it is recommended that fluoride intake is monitored by measuring urinary fluoride excretion. The aim of this scoping review is to map the current literature/evidence on fluoride intake and excretion studies in relation to the study population, settings, type of study design, methodology, and analytical approach. Methods Embase/Ovid, MEDLINE/Ovid, CINAHL/EBSCO, Scopus/Elsevier were searched for relevant articles until April 2018. Studies were included if they reported intake and excretion of fluoride in healthy humans of all age groups. Findings were explored using a narrative synthesis to summarise studies characteristics and outcome measures. Results Removal of duplicates from the originally 2295 identified records yielded 1093 studies of which 206 articles were included. Only 21.6% of the studies were conducted in children (<8-year-olds). Most studies (38.8%) used drinking water concentration as a proxy for fluoride intake, whereas only 11.7% measured fluoride intake from all sources. Of the 72 studies that measured dietary fluoride intake, only 10 reported the validity of the employed dietary assessment method. Only 14 studies validated the urine sample collection methods. No information on the validity of the employed analytical method was reported by the majority (64.6%) of studies. Only a small proportion (8.7%) of the included studies investigated the association between fluoride intake and excretion. Conclusion The findings reveal much variability in terms of conducting the studies and reporting the findings, illustrating a high heterogeneity in data collection across settings and populations. Future studies should provide more detail on sampling technique, measurement protocols (including validation), and on clearly defining the relationship between intake and urinary excretion of fluoride.
Aging in Fabry Disease: Role of Telomere Length, Telomerase Activity, and Kidney Disease

Introduction: The lifespan of patients with Fabry disease (FD) is shorter than that seen in the general population. Leukocyte telomere length (LTL) and telomerase activity (TA) are potential markers of biologic aging. The aim of the current study was to determine the LTL and TA in FD patients and to assess the correlation between LTL and TA and renal involvement. Methods: We included 33 FD patients and 66 healthy matched controls. LTL and TA were measured using a quantitative PCR assay and gene expression assay. FD patients were stratified by renal function (estimated glomerular filtration rate [eGFR] higher or lower than 60 mL/min/1.73 m2) and proteinuria (urine protein creatinine ratio higher or lower than 0.5 g/g). Results: LTL was significantly shorter (0.69 vs. 0.73, p = 0.015) and TA significantly higher (1.55 vs. 1.19, p = 0.047) in FD patients compared to controls. Males with FD had significantly shorter LTL (p = 0.020) and lower, but non-significant, TA compared to male controls (p = 0.333). Female FD patients had similar LTL (p = 0.285) but significantly higher TA compared to female controls (p = 0.005). LTL was not influenced by eGFR, but TA was significantly lower in the low eGFR group (p = 0.003). Conclusions: FD patients have significantly shorter LTL, but significantly higher TA compared to healthy controls. Increased TA activity in FD patients could be the compensation mechanism to prevent LTL decrease (and accelerated ageing), which seems to be exhausted at the advanced stage of renal disease.
Evaluation of Undergraduate Students’ Responsiveness to a 4-Week University-Based Animal-Assisted Stress Prevention Program

An increase in the prevalence of stress among college students is compromising their mental health and academic success. One approach to stress prevention that has seen a surge in implementation is the use of university-based Animal Visitation Programs (AVPs). Despite their popularity and promising causal findings, program evaluations on students’ responsiveness (e.g., enjoyment, attendance, perceptions on usefulness and behavioral change) have yet to be conducted. Using a mixed methods approach, this study reports results of a program evaluation embedded in a randomized controlled trial examining the efficacy of incorporating various levels (0%, 50% or 100%) of Human Animal Interaction (HAI) into a four-week long university-based stress prevention program resulting in three conditions: (1) Evidence-based Academic Stress Management content only (0% HAI), (2) Human Animal Interaction with therapy dogs only (100% HAI) and (3) equal combinations of Academic Stress Management and HAI (50% HAI). Responsiveness (e.g., enjoyment, usefulness, recommendation and behavioral change) was assessed quantitatively and qualitatively using self-reported survey data collected immediately following the program and again six weeks later. The results suggest that combining evidence-based content presentations with HAI was associated with higher levels of enjoyment, perceived usefulness, and likelihood of recommendation compared to presenting content presentation or HAI alone, although doing so did not result in differences in perceived behavioral change by condition. Themes of students’ perceptions on the role of HAI in shaping program enjoyment, usefulness, recommendations and behavioral change were described.