bluuebunny/crossref_metadata_2025 huggingface dataset:
Quasimetagenomic source tracking of Listeria monocytogenes from naturally contaminated ice cream
Authors: Ottesen Andrea , Ramachandran Padmini , Chen Yi , Brown Eric , Reed Elizabeth , Strain Errol
Published: January 2020

Background The more quickly bacterial pathogens can be linked to a vehicle of transmission or a source, the more illnesses can be prevented. Whole genome sequencing (WGS) based approaches to source tracking have greatly increased the speed and resolution with which public health response can pinpoint the vehicle and source of outbreaks. Traditionally, WGS approaches have focused on the culture of an individual isolate before proceeding to DNA extraction and sequencing. For Listeria monocytogenes (Lm), generation of an individual isolate for sequencing typically takes about 6 days. Here we demonstrate that a hybrid, “quasimetagenomic” approach ie; direct sequencing of microbiological enrichments (first step in pathogen detection and recovery) can provide high resolution source tracking sequence data, five days earlier than response that focuses on culture and sequencing of an individual isolate. This expedited approach could save lives, prevent illnesses and potentially minimize unnecessary destruction of food. Methods Naturally contaminated ice cream (from a 2015 outbreak) was enriched to recover Listeria monocytogenes following protocols outlined in the Bacteriological Analytic Manual (BAM). DNA from enriching microbiota was extracted and sequenced at incremental time-points during the first 48 hours of pre-enrichment using the Illumina MiSeq platform (2 by 250), to evaluate genomic coverage of target pathogen, Listeria monocytogenes . Results Quasimetagenomic sequence data acquired from hour 20 were sufficient to discern whether or not Lm strain/s were part of the ongoing outbreak or not. Genomic data from hours 24, 28, 32, 36, 40, 44, and 48 of pre-enrichments all provided identical phylogenetic source tracking utility to the WGS of individual isolates (which require an additional 5 days to culture). Conclusions The speed of this approach (more than twice as fast as current methods) has the potential to reduce the number of illnesses associated with any given outbreak by as many as 75% percent of total cases and potentially with continued optimization of the entire chain of response, contribute to minimized food waste.
Analysis of the causes of cervical lymphadenopathy using Fine-Needle Aspiration Cytology combining cell block in Chinese Patients with and without HIV infection
Authors: Sun Lei , Zhang Liang , Yang Kun , Chen Xiang-mei , Chen Jia-min , Xiao Jiang , Zhao Hong-xin , Ma Zhi-yuan , Qi Li-ming , Wang Peng
Published: January 2020

Background Cervical lymphadenopathy refers to a frequently observed clinical presentation in numerous pathological conditions. A wide spectrum of diseases can cause cervical lymphadenopathy, irrespective of the fact that the patients are infected with HIV or not. The present study focuses on validating whether the causes of cervical lymphadenopathy differ significantly in HIV and non-HIV patients by using fine-needle aspiration cytology (FNAC) combining cell block.Methods A total of 589 patients with cervical lymphadenopathy were recruited in the FNA clinic. The samples were obtained by an auto-vacuumed syringe that benefited the sampling more materials. The cytological smears were prepared by Hematoxylin and Eosin (HE), Periodic Acid Schiff (PAS), Gomori’s methenamine silver (GMS) and acid-fast staining. Cell blocks were made if required, and immunohistochemistry stain was performed on the cell block section.Results The study found 453 (76.9%) patients with HIV and 136 (23.1%) patients without HIV infection. The average age of HIV-infected patients was 34.8 ±10.2 years, which was significantly lower than that of non-HIV-infected patients (42.9 ±18.1 years) (p<0.01). Of all patients infected with HIV, 390 (86.1%) were males. This proportion was significantly higher than that of non-HIV-infected patients [65/136 (47.8%)] (p<0.01). The major causes of cervical lymphadenopathy in HIV positive patients were mycobacterial infection (38.4%), reactive hyperplasia (28.9%), non-specific inflammation (19.9%), and malignant lesions (4.2%). In contrast, the most common causes in HIV negative patients were reactive hyperplasia (37.5%), malignancy (20.6%), non-specific inflammation (19.1%) and mycobacterial infection (12.5%). Opportunistic infections such as non-tuberculous mycobacteria (4.2%), cryptococcosis (1.5%), Talaromyces marneffei (1.5%) and other fungi (0.4%) were found only in HIV-infected individuals. Non-Hodgkin’s lymphoma (2.4%) was the most common malignant lesion in patients with HIV infection, followed by Kaposi's sarcoma (0.9%) and metastatic squamous cell carcinomas (0.7%). However, the most common malignancy in non-HIV-infected patients was metastatic carcinomas (14%) including small cell carcinomas, adenocarcinomas, squamous cell carcinomas and hepatocellular carcinoma, which were noticeably greater than the HIV patients (p<0.01).Conclusions There were significantly different causes of cervical lymphadenopathy in HIV infected and non-HIV infected patients. FNAC was a useful diagnostic method for differential diagnosis of cervical lymphadenopathy.
Mycoplasma pneumoniae​ pneumonia associated thrombosis at Beijing Children’s Hospital
Authors: Liu Jinrong , He Ruxuan , Wu Runhui , Wang Bei , Xu Hui , Zhang Yue , Li Huimin , Zhao Shunying
Published: January 2020

Background: With the increase of awareness of mycoplasma pneumoniae pneumonia (MPP), we found thrombosis in severe MPP (SMPP) was not rare. The aim of the study was to investigate the clinical characteristics, treatment, and long-term prognosis of MPP-associated thrombosis.

Methods: We retrospectively reviewed the medical records of 43 children with MPP-associated thrombosis between January 2013 and June 2019 at Beijing Children’s Hospital. The results of blood coagulation studies, autoimmune antibody, thrombophilia screening, contrast-enhanced lung computed tomography, echocardiography, and blood vessel ultrasonography were analyzed, as were treatment outcomes.
Results: Forty-two patients were diagnosed with SMPP. D-dimer was higher than 5.0 mg/L in 58.1% (25/43) of patients. The mean D-dimer level was 11.1 ± 12.4 mg/L. Anticardiolipin-IgM was positive in 60.0% of patients, β2-glycoprotein-IgM in 64.0%, and lupus anticoagulant in 42.1%. Chest imaging revealed pulmonary consolidation with lobe distribution in all patients (2/3–1 lobe in 10 patients, > 1 lobe in 29 patients). In our experience, thrombosis can occur in a vessel of any part of the body, and it can be initially detected as late as 31 days after disease onset. Thrombosis in the brain and abdomen can occur early, at 5 days after disease onset. Pulmonary vessels were the most commonly involved sites in the current study, and accordingly chest pain was the most common symptom (32.6%), followed by neurological symptoms (14.0%) and abdominal pain (9.3%). Thirty-five percent of patients were asymptomatic with regard to thrombosis. All patients underwent anticoagulant therapy, and thrombus absorption took > 3 months in most patients. All patients were followed until October 2019, at which time 41 were asymptomatic and 2 had mild recurrent cough.
Conclusions: SMPP with pulmonary consolidation (> 2/3 lobe) was the most strongly associated risk factor for thrombosis. Thrombosis-associated symptoms may be subtle, even absent. Elevated D-dimer, specifically > 11.1 mg/L (even > 5.0mg/L), would assist in the early diagnosis of thrombosis. The long-term prognosis of thrombosis was good after timely administration of anticoagulant therapy.
Seasonal Variation in the Occurrence of Retinal Vein Occlusion: A 4-Year Cross-sectional Study
Authors: Matsuzawa Moe , Sakanishi Yoshihito , Ebihara Nobuyuki
Published: January 2020

Background: Retinal vein occlusion (RVO) is a common retinal vascular disease that causes a loss of vision. Therefore, we investigated whether there is seasonal variation in the onset of RVO, to examine the possibility of preventing it.
Methods: Patients with RVO who were treated at the Juntendo University Urayasu Hospital between April 2013 and March 2017 were included in this retrospective study. The season in which the RVO occurred was recorded for each case, and the cases were grouped into six 2-month periods based on the month of RVO, and classified by age, sex and hypertension status. The frequency of occurrence of RVO across seasons was compared using a chi-squared test.
Results: A total of 348 patients with RVO presented during the study period, with information regarding the date of RVO onset. The cohort of 348 consisted of 167 males and 181 females who, overall, had a mean age of 64.0 years (range 17–96 years). The highest incidence of RVO onset was during January/February, with the lowest incidence during July/August. Patient age, sex and hypertension status did not influence the results.
Conclusions: The seasonal onset of RVO tended to be higher in January/February and May/June, and lower in July/August. These findings suggest that eyecare professionals should be more vigilant in watching for the occurrence of RVO during winter and the rainy season, regardless of the patient’s sex, age or hypertension status.
Objectively-measured sedentary time and physical activity in a bi-ethnic sample of young children: variation by socio-demographic, temporal and perinatal factors
Authors: Collings Paul , Dogra Sufyan A , Costa Silvia , Bingham Daniel D , Barber Sally E.
Published: January 2020

Background: Evidence suggests that South Asian school-aged children and adults are less active compared to the white British population. It is unknown if this generalises to young children. We aimed to describe variability in levels of physical activity and sedentary time in a bi-ethnic sample of young children from a deprived location. Methods: This observational study included 202 South Asian and 140 white British children aged 1.5 to 5y, who provided 3,181 valid days of triaxial accelerometry (Actigraph GT3X+). Variability in sedentary time and physical activity levels were analysed by linear multilevel modelling. Logistic multilevel regression was used to identify factors associated with physical inactivity (failing to perform ≥180 minutes of total physical activity including ≥60 minutes moderate-to-vigorous physical activity (MVPA) per day). Results: There were no significant ethnic differences in the overall levels of behaviours; South Asian and white British children spent half of daily time sedentary, just over 40% in light physical activity, and the remaining 7.5 to 8% of time in MVPA. Sedentary time was lower and physical activity levels were higher in older children, and levels of MVPA and vector magnitude counts per minute (CPM) were higher on weekends compared to weekdays. In South Asian children, sedentary time was lower on weekends. Sedentary time was lower and physical activity levels were higher in spring compared to winter in white British children, and in all seasons compared to winter in South Asian children. South Asian children born at high birth weight performed more MVPA, and in both ethnicities there was some evidence that children with older mothers were more sedentary and less active. Sedentary time was higher and light physical activity was lower in South Asian children in the highest compared to the lowest income families. South Asian girls performed less MVPA, registered fewer vector magnitude CPM, and were 3.5 times more likely to be physically inactive than South Asian boys. Conclusions: Sedentary time and physical activity levels vary by socio-demographic, temporal and perinatal characteristics in young children from a deprived location. South Asian girls have the most to gain from efforts to increase physical activity levels.
Pilot and feasibility trials in traditional Chinese medicine: a literature survey
Authors: Li Guowei , Wu Darong , Chen Xuejiao , Zeng Jie , Li Ziyi , Thabane Lehana
Published: January 2020

Background The guidelines for pilot and feasibility studies were published in 2016. Little is known about the guideline adherence of TCM (Traditional Chinese Medicine) pilot trials or whether the guidelines can significantly enhance the quality of implementation and reporting of TCM pilot trials. We aimed to investigate the guideline adherence, assess the impact of guidelines on TCM pilot trials, and discuss potentially undetected challenges for TCM pilot trials, by conducting a liteature survey.Methods We systematically searched MEDLINE, EMBASE and CNKI to retreive TCM pilot trials. We randomly chose 50 pilot trials from the eligible studies for analyses. The CONSORT extension to pilot and feasibility studies was used as a framework to assess the methodology and reporting quality of the studies.Results The included stuides had a guideline adherence level ranging from 4% to 96%, where the lowest adherence was found in the item 6c (prespecified criteria used to judge progression to future definitive trial). The guidance published in 2016 seemed to exert minimal effect on guideline adherence in TCM pilot trials. The unidentified issues related to TCM pilot trials from the guidelines included blinding, lack of standard formula of interventions, difficulty in comparison for effect assessment of interventions, and difficulty in bias control.Conclusions The current practice in TCM pilot trials requried substantial improvement in the literature. Further endeavors are needed for training and dissemination of guideline adherence, and development of more detailed methodology in the field of TCM pilot trials.
WITHDRAWN: Changes of the F-wave in the acute phase of permanent spinal cord ischaemic injury predict spinal cord function in animal models of rabbits
Authors: Zhou Yunfei , Liu Xingming , Heng Xueyuan , Zhang Jian , Song Qimin , Chen Chunmei
Published: January 2020

Background ：To explore the changes of the F-wave in the posterior tibial nerve of rabbits after different levels of lumbar spinal cord ischaemic injury and its correlation with motor function and the extent of lumbar spinal cord pathological damage. Methods ： Thirty New Zealand rabbits were randomly divided into 6 groups. The control group (n=5) was used to exclude the influence of anaesthesia and surgery on the F-wave. Different levels of lumbar arteries were ligated in the five experimental groups (n=5). The F-wave was recorded to observe the changes in the acute phase of spinal cord ischaemia.The correlation between the changes of the F-wave in the acute reversible phase and the motor function of the spinal cord was analysed. Results ： The results for the control group indicated that anaesthesia and surgery did not affect the F-wave results.There was no statistically significant difference in the F-wave amplitudes and latency before and after ligation in the 1 and 2 level ligation groups. The F-wave changed immediately after ligation in the 3, 4 and 5 ligation groups. The latency of the F-wave gradually extended, the amplitude of the F-wave gradually reduced.The amplitude variations of the F-wave were positively correlated with the motor function 2 days after ligation, there was a statistically significant difference. Conclusion ：The F-waves in the posterior tibial nerve of rabbits were found to be sensitive to the lumbar spinal cord ischaemic injury and specific to predict motor function.
Intravenous administration of triptonide attenuates CFA-induced pain hypersensitivity through inhibiting AKT signaling pathway in mice
Authors: Ling Yue-Juan , Ding Ting-Yu , Gao Yong-Jing , Jiang Bao-Chun
Published: January 2020

Background: Triptonide (TPN) is a major component of Tripterygium wilfordii Hook.f., and reportedly has anti-inflammatory and neuroprotective effects. Recent studies have demonstrated that the phosphatidylinositol 3-kinase (PI3K)/AKT pathway plays an important role in the pathogenesis of inflammatory pain. Here we investigated the anti-nociceptive effect of systemic treatment with TPN on mouse models of chronic inflammatory pain and explored possible mechanisms. Results: Unilateral hind paw injection of complete Freund’s adjuvant (CFA) induced paw edema and persistent pain hypersensitivity. Intravenous treatment with TPN attenuated CFA-induced paw edema, mechanical allodynia, and thermal hyperalgesia. Western blotting and immunofluorescence results showed that CFA induced AKT activation in the dorsal root ganglion (DRG) neurons, which was inhibited by TPN treatment. Furthermore, TPN treatment inhibited mRNA increase of proinflammatory cytokines [tumor necrosis factor-α (TNF-α), interleukin 1 beta (IL-1β), and Interleukin 6 (IL-6)] induced by CFA. Finally, pretreatment with AKT inhibitor, AKT inhibitor Ⅳ, attenuated CFA-induced mechanical allodynia and thermal hyperalgesia, and decreased the mRNA expression of pro-inflammatory cytokines. Conclusions: These data indicate that TPN attenuates CFA-induced pain potentially via inhibiting AKT-mediated pro-inflammatory cytokines production in DRG. TPN may be used for the treatment of chronic inflammatory pain.
Neuroprotective Effects of Magnesium L-threonate in a Hypoxic Zebrafish Model
Authors: Kim Young Sung , Won Young Ju , Lim Byung Gun , Min Too Jae , Kim Yeon-Hwa , Lee Il-Ok
Published: January 2020

Background: Hypoxia inhibits the uptake of glutamate (a major neurotransmitter in the brain closely related to cognitive function) into brain cells, and the initial response of cells to cortical hypoxia depends on glutamate. Previous studies have suggested that magnesium may have protective effects against hypoxic injuries. In particular, magnesium L-threonate (MgT) may increase magnesium ion concentrations in the brain better than MgSO4 and improve cognitive function. Methods: We evaluated cell viability under hypoxic conditions in the MgT- and MgSO4-treated human SH-SY5Y neurons, in vivo behavior using the T-maze test following hypoxia in MgT-treated zebrafish, activity of brain mitochondrial dehydrogenase by 2,3,5-triphenyltetrazolium chloride (TTC) staining, and protein expression of the excitatory amino acid transporter (EAAT) 4 glutamate transporter by western blotting. Results: Among the groups treated with hypoxia, cell viability significantly increased when pre-treated with 1 or 10 mM MgT (p = 0.009 and 0.026, respectively) Despite hypoxic insult, MgT-treated zebrafish showed preferences for the red compartment (p= 0.025 for distance and p= 0.007 for frequency of entries), suggesting memory preservation. TTC staining showed reduced cerebral infarction and preserved absorbance in the MgT-treated zebrafish brain after hypoxia (p=0.010 compared to the hypoxia group). In addition, western blot showed upregulation of EAAT4 protein in the MgT treated group. Conclusions: Pre-treatment with MgT attenuated cell death and cerebral infarction due to hypoxia and protected cognitive function in zebrafish. In addition, MgT appeared to modulate expression of the glutamate transporter, EAAT4.
Factors associated with tuberculosis treatment completion by Gender during 2014 - 2016 in Kampala, Uganda: A retrospective descriptive study
Authors: Alfred Etwom , Sekadde Moorine Penninah , Burua Aldomoro , Mugabe Frank , Kawooya Ismael , Tweya Hannock
Published: January 2020

BackgroundTo date, limited number of studies have explored the effect of gender in treatment outcomes in Uganda. No data on disaggregated treatment outcomes and influential factors by gender has been comprehensive compiled by the existing studies.Objective To determine the gender differences in TB patients treatment outcomes between 2014 and 2016 in Kampala in order to inform national policy and provide targeted interventions.Methods A retrospective cohort study using routine data of all eligible individuals who were initiated on first-line TB therapy between 2014 and 2016. De-identified data was obtained from all the Kampala divisions electronic TB registers, cleaned and analysed using STATA version 13.Results Of the 18,855 patients started on treatment during the study period, only 17,461 were included in the final analysis. Males were more likely to be 35 years or older, received DOT at facility yet females were more likely to be new patients. In addition, males were more likely to be pulmonary bacteriologically confirmed than females (OR 1.08 95% CI 1.00 - 1.17). Successful treatment completion and ART uptake were similar by gender. Of all outcomes, 83% were treatment successfully, 11% died, 1% treatment failed treatment and 5% got lost to follow-up. Compared to females, males were more likely to be lost from TB care and die compared to females.Conclusion Among TB patients in Kampala from 2014 to 2016, we found evidence that successful treatment completion is not influenced by gender. However other factors that may be associated with successful TB treatment completion include age, disease classification, HIV status and type of patient.
Drosophila Hox genes induce melanised pseudo-tumours when misexpressed in hemocytes
Authors: Ponratnam Titus , Saini Ravina , Mishra Rakesh
Published: January 2020

Background: Hox genes are key early determinants of cell identity along the anterior-posterior body axis across bilaterians. Recently, several late non-homeotic functions of Hox genes have emerged in a variety of processes involved in organogenesis in several organisms, including mammals. Being crucial factors in determining cell identity and organogenesis, the misregulation of Hox genes is likely to be associated with defects in these processes. Several studies have reported the misexpression of Hox genes in a variety of malignancies including acute myeloid leukaemia. Methods: The Hox genes Dfd, Ubx, abd-A and Abd-B were overexpressed via the UAS-Gal4 system using Cg-Gal4, Lsp2-Gal4, He-Gal4 and HmlD3-Gal4 as specific drivers. Genetic interaction was tested by bringing overexpression lines in heterozygous mutant backgrounds of Polycomb and trithorax group factors. Larvae were visually scored for melanised bodies. Hemocytes were quantified by dissecting larvae for lymph in 4mm wells and staining nuclei with DAPI and tested for differentiation by staining them with anti-myospheroid and for proliferation with anti-PH3. Pupal lethality was carried out by letting pupae eclose and scoring those that failed after the time point. Results: Expression of Dfd, Ubx and abd-A, but not Abd-B in the hematopoietic compartment of Drosophila led to the appearance of circulating melanised bodies, and increase in cell numbers, cell-autonomous proliferation and differentiation of hemocytes. Pupal lethality and the melanised pseudo-tumor phenotype were suppressed by the mutations in Psc1 and esc2 background while polycomb group member mutations Pc1 and Su(z)123 and trithorax group member mutation TrlR85 increased the phenotype.Conclusions: Dfd, Ubx and abd-A are leukemogenic. Mutations in Polycomb and trithorax group members, which are responsible for maintaining the expression state of the Hox genes, lead to repression in the leukemogenic phenotype. Drosophila, widely used as a model for myeloid leukemias, can serve as a testbed for Hox expression induced leukemias.
Whole genome analysis and characterization of Salmonella enterica subsp. enterica serovar Typhimurium strain UPM 260 for mediated genetic manipulation
Authors: Roslan Najwa Syahirah , Isa Nurulfiza Mat , Omar Abdul Rahman , Bejo Mohd. Hair , Ideris Aini
Published: January 2020

Background Salmonella enterica serovar Typhimurium persists as one of the most frequent food-borne zoonoses, causing a major public health concern worldwide. Furthermore, Salmonella infection has a large economic impact. Globally, the main sources of infection for humans include the consumption of contaminated poultry meat and eggs. In animals however, Salmonella transmission usually occurs horizontally from infected birds and contaminated environments. Hence, to delve further on how the impact of this disease can be lessened, an epidemiological study needs to be performed. It is vital to determine the genomic sequences of microorganisms to understand their biology and functional characterization. Thus, we determined the whole-genome sequence and virulence profile of S. enterica serovar Typhimurium strain UPM 260 isolated from Perak, Malaysia. Whole genome sequencing (WGS) using paired-end sequencing generated 107 contigs with a total genome size of 4.9 Mbp and 52% G+C content. The contigs were annotated for phylogenetic and functional analysis. Results Through the analysis, it is revealed that the genome were resistant to a number of antimicrobial drug classes including aminoglycoside, fluoroquinolone, tetracycline and phenicol. Also found in UPM 260 genome were three intact prophages (Fels-1, Gifsy-2 and one unique prophage, mEp390). The genome housed four types of restriction-modification systems (RMS) and Type I-E subtype of CRISPR-Cas system. Two metal resistance operons (mer and cop) and six pathogenicity islands (SPIs) were also discovered in UPM 260 genome. The SPIs contributed mostly to the bacterial virulence properties since 1054 CDS were reported to be homologous to the virulence factors in the database VFDB. Conclusion This study benefits us specifically in the field of genome engineering where gene-based genetic manipulations can be applied in reducing the prevalence and pathogenicity in Salmonella.
Comparative transcriptome analysis of root, stem, and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis
Authors: Liao Weifang , Miao Lihong , Liu Pulin , Gao Ruijie , Mei Zhinan
Published: January 2020

Background Entada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness and remarkable anti-inflammatory activities. Triterpenoid saponins are the major bioactive compounds of Entada phaseoloides. However, genomic or transcriptomic technologies have not been used to study the triterpenoid saponin biosynthetic pathway in this plant.Results We performed comparative transcriptome analysis of the root, stem, and leaf tissues of Entada phaseoloides with three independent biological replicates and obtained a total of 53.26 Gb clean data and 116,910 unigenes, with an average N50 length of 1218 bp. Putative functions could be annotated to 42,191 unigenes (36.1%) based on BLASTx searches against the Non-redundant, Uniprot, KEGG, Pfam, GO, KEGG and COG databases. Most of the unigenes related to triterpenoid saponin backbone biosynthesis were specifically upregulated in the stem. A total of 26 cytochrome P450 and 17 uridine diphosphate glycosyltransferase candidate genes related to triterpenoid saponin biosynthesis were identified. The differential expressions of selected genes were further verified by qPT-PCR.Conclusions The dataset reported here will facilitate the research about the functional genomics of triterpenoid saponin biosynthesis and genetic engineering of Entada phaseoloides .
Transcriptome analysis reveals rapid defence responses in wheat induced by phytotoxic aphid Schizaphis graminum feeding
Authors: Zhang Yong , Fu Yu , Wang Qian , Liu Xiaobei , Li Qian , Chen Julian
Published: January 2020

Background Schizaphis graminum is one of the most important and devastating cereal aphids worldwide, and its feeding can cause chlorosis and necrosis in wheat. However, little information is available on the wheat defence responses triggered by S. graminum feeding at the molecular level.Results Here, we collected and analysed transcriptome sequencing data from leaf tissues of wheat infested with S. graminum at 2, 6, 12, 24 and 48 hpi (hours post infestation). A total of 125,289 genes were either up- or downregulated and differed significantly in response to aphid feeding. The expression levels of a number of genes (9,761 genes) were significantly altered within 2 hpi and continued to change during the entire 48 h experiment. Gene Ontology analysis showed that the downregulated DEGs were mainly enriched in photosynthesis and light harvesting, and the total chlorophyll content in wheat leaves was also significantly reduced after S. graminum infestation at 24 and 48 hpi. However, a number of related genes of the salicylic acid (SA)-mediated defence signalling pathway and MAPK-WRKY pathway were significantly upregulated at early feeding time points (2 and 6 hpi). In addition, the gene expression and activity of antioxidant enzymes, such as peroxidase and superoxide dismutase, were rapidly increased at 2, 6 and 12 hpi. DAB staining results showed that S. graminum feeding induced hydrogen peroxide (H 2 O 2 ) accumulation at the feeding sites at 2 hpi, and increased H 2 O 2 production was detected with the increases in aphid feeding time. Pretreatment with diphenylene iodonium, an NADPH oxidase inhibitor, repressed the H 2 O 2 accumulation and expression levels of SA-associated defence genes in wheat.Conclusions Our transcriptomic analysis revealed that defence-related pathways and oxidative stress in wheat were rapidly induced within hours after the initiation of aphid feeding. Additionally, NADPH oxidase plays an important role in aphid-induced defence responses and H 2 O 2 accumulation in wheat. These results provide valuable insight into the dynamic transcriptomic responses of wheat leaves to phytotoxic aphid feeding and the molecular mechanisms of aphid-plant interactions.
Validity, reliability and feasibility of assessment of cilinical reasoning of medical students by observation versus post encounter assessment in a clinical practice setting.
Authors: Haring Catharina Maria , Klaarwater Claudia , Bouwmans Geert , Cools Bernadette , Gurp Petra van , Meer Jos van der , Postma Cornelis
Published: January 2020

Background The assessment of clinical reasoning by medical students in clinical practice is very difficult. Partly this is because the fundamental mechanisms of clinical reasoning are difficult to uncover and when known, hard to observe and interpret. We developed an observation tool to assess the clinical reasoning ability of medical students during clinical practice. The observation tool consists of an 11-item observation rating form. The validity, reliability and feasibility of this tool were verified among medical students during the internal medicine clerkship and compared to a post-encounter rating tool. Results Six raters assessed each the same 15 student patient encounters. The internal consistency (Cronbach’s alfa) for the observation rating tool (ORT) was 0.87 (0.71-0.84) and the 5-item post encounter rating tool (PERT) was 0.81 (0.71-0.87). The intraclass-correlation coefficient for single measurements was poor for both the ORT; 0.32 (p<0.001) as well as the PERT; 0.36 (p<0.001). The G and D-study showed that 6 raters are required to achieve a G-coefficient of > 0.7 for the ORT and 7 raters for the PERT. The largest sources of variance are the interaction between raters and students. There was a correlation between the ORT and PERT of 0.53 (p=0.04) Conclusions The ORT and PERT are both feasible, valid and reliable instruments to assess students’ clinical reasoning skills in clinical practice.
How video cases in preparatory teaching influence students’ approaches to patients in psychiatric clerkship. A qualitative study.
Authors: Pedersen Kamilla , Morcke Anne Mette , Paltved Charlotte , Mors Ole , Ringsted Charlotte
Published: January 2020

Background This study explored how a preparatory teaching format using patient cases portrayed in videos influenced medical students’ clinical learning and practice experiences in their psychiatric clerkship.Methods The study applied a qualitative explorative design. We asked the students to draw their experience with a patient encounter in real clinical setting. Subsequently we interviewed the students unfold the students’ perspectives on how they navigated learning from the preparatory teaching in their clerkship. Data was transcribed verbatim and coded by an inductive thematic analysis.ResultsThe results demonstrated that students’ use of learning from the video cases varied according to their roles in patient encounter situations in their clerkship. Students having active roles in the diagnostic interview adopted a patient-centred focus demonstrated by empathic engagement with the patient and self-reflexivity related to the video cases. Students with passive roles, observing a doctor, described a self-centred focus on how to adopt an appropriate appearance and copied the surface behaviour of the simulated doctors in the video cases.Conclusion Our study findings contribute to broadening the understanding of how video cases in preparatory teaching formats affect students’ approach to patient encounters and their clinical learning experience. The results also reflect the importance of active engagement of students in the clinical learning context if preparatory teaching should have an effect.
Education is as an important factor in palliative care knowledge: results from a survey of physicians attitudes and knowledge in Palliative Medicine
Authors: Ioshimoto Thais , Shitara Danielle Ioshimoto , Prado Gilmar Fernandes do , Pizzoni Raymon , Sassi Rafael Hennemann , de Gois Aécio Flávio Teixeira
Published: January 2020

Background: According to the Latin America Association for palliative care, Brazil offers only 0.48
palliative care services per 1 million inhabitants. In 2012, no accredited physicians were working in
palliative care, while only 1.1% of medical schools included palliative care education in their
undergraduate curricula.
Aim: The aim of the study is to assess medical knowledge in end-of-life care, in order to identify key
factors that could be useful in improving palliative care in Brazilian medical schools and residency.
Design: Cross sectional study, conducted in São Paulo, Brazil. Students were invited to voluntarily participate in an
anonymous and self-administered questionnaire survey. The latter included demographic
information, attitudes, prior training in palliative care, prior palliative care experience and the 20-item
Palliative Care Knowledge Test (PCKT).
Participants: Physicians applying for the medical residency of the Federal University of
São Paulo.
Results: Of the 3086 subjects, 2349 (76%) answered the survey, 2225 were
eligible for analysis while 124 were excluded due to incomplete data. Although the vast majority
(99,2%) thought it was important to have palliative care education in the medical curriculum, less
than half (46,2%) reported having received any education on palliative care. The overall
performance in the PCKT was poor, with a mean score of 10,79 (± 3). While philosophical questions
were correctly answered (81,8%), most participants lacked knowledge in
symptom control (50,7% for pain, 57,3% for dyspnea, 52,2% for psychiatric and 43,4% for
gastrointestinal problems).
The high performance group (> 50% of correct answers) had received more training, showed more interest in learning,
had a better sense of preparedness,
as well as a higher percentage of experience in caring for terminal patients (p<0,001).
Conclusions: Our study showed that Brazilian’s physicians lack not only knowledge, but also
training in palliative medicine. Important factors to better knowledge in end-of-life care were prior
training, previous contact with dying patients and prior medical residency. Corroborating the
literature, training showed to be a key factor in overall knowledge. Therefore,
medical schools and residency programs should focus on improving palliative training,
especially those involving contact with dying patients.
Korean medicine students' entrance factors and satisfaction with their college experience: a quantitative nationwide study
Authors: Kim Hyun-Seok , Lee Joohyun , Kim Hwimun , Yang Unho , Kim Hyunho
Published: January 2020

Background Korean medicine (KM) has equal legal rights with conventional Western medicine in South Korea and is taught at KM colleges. To date, no research has been conducted on the entrance factors and satisfaction of KM college students. Thus, this study attempts to fill this gap in the literature. Methods Content validity tests and face validity tests were conducted during the development of the questionnaires used in this study. The scores of each item and the correlation between items and sub-items were analyzed and factors were correlated with students’ satisfaction and willingness to re-enter KM colleges.Results A total of 420 students responded to the survey. The mean of the item considering stable incumbency and examination scores was the highest. The highest correlation between an item and sub-item concerned interaction with people. The questionnaire items or sub-questionnaire items that showed moderate high correlation with the questionnaire items asked whether participants were willing to re-enter the KM college and were both about independent choices. Conclusions Identifying college entrance factors can contribute to increasing current students’ academic satisfaction and decreasing drop-out rates. College entrance factors that are closely related to students’ motivation to become KM doctors may increase the current academic satisfaction of KM students and decrease drop-out rates. This study highlights factors that can be applied in college curriculum or subject teaching, such as interest in research on KM.
Vibrotactile frequency discrimination on the wrist of visually impaired people
Authors: Czopek Dorota , Wiciak Jerzy
Published: December 2019

Development of devices for the visually impaired people equipped with a vibrating interface was the motivation of the research presented in the paper. Knowledge about discriminative ability of touch is crucial when designing devices which use tactile interfaces. The paper presents results of psychophysical studies on determining the vibrotactile frequency discrimination threshold on the wrist of blind and partially sighted people. The transformed adaptive method 1 up/2 down was used in the presented research. Thresholds were obtained on the ventral wrist at 5 frequencies: 25, 31.5, 63, 125 and 250 Hz. Results were examined to find factors which could influence the threshold value. Additionally, the guidelines for devices with vibrating interfaces supporting spatial orientation of the blind and partially sighted people was developed based on results and analysis
Quantifying the impact of human activities on water quality based on spatialization of social data: a case study of the Pingzhai Reservoir Basin
Authors: Zhang Yongrong , Zhou Zhongfa , Zhang Haotian , Dan Yusheng
Published: January 2020

In water pollution source research, it is difficult to quantify the impact of human activities on water quality. Based on pollution load theory and the concept of spatialization of social data, this study integrates land-use type, slope gradient, and spatial position, and uses the contribution of human activities to quantify the impact of farmland fertilizers, livestock and poultry wastes, and human domestic pollution on water quality in the study area. The results show that livestock manure is the largest source of total phosphorus (TP) and total nitrogen (TN) discharges in the research area, and domestic pollution is the largest source of chemical oxygen demand (COD) discharges. The total equal standard pollution load (as well as the load of each pollution source and its pollutant amount) is the highest in the Nayong River Basin and the lowest in the Baishui River Basin. The contributions of human activities to TP and TN have similar spatial distributions. The impact of human activities on COD discharge is minimal. The quantitative results of this model are basically consistent with the actual conditions in the Pingzhai Reservoir Basin, which suggests that the model reasonably reflects the impact of human activities on the water environment of the basin.
The effect of nitrogen mitigation measures evaluated by monitoring of nitrogen concentrations and loadings in Danish mini-catchments – 1990–2015
Authors: Blicher-Mathiesen G. , Windolf J. , Larsen S. E. , Rolighed J. , Carstensen M. V. , Højberg A. L. , Tornbjerg H. , Kronvang B.
Published: January 2020

Monitoring of agricultural mini-catchments (AMC) has been part of the Danish national monitoring programme (National Monitoring Programme for Water and Nature) since 1989. Thus, nitrogen (N) concentrations and loads have been monitored in soil water, tile drains, and streams within five AMC. Moreover, extensive monitoring of N concentrations and loads in streams draining 46 mini-catchments has been conducted every year since 1989. This has resulted in two national datasets on trends in flow-weighted N concentrations relative to factors such as groundwater age and management history. We analyzed these datasets and found that the intensively monitored micro-catchments generally showed a strong signal with significant downward trends in flow-weighted N concentrations in monitored soil water (−22% to −68%), tile drains (−38% to −59%), and streams (−19% to −53%). The 46 micro-catchments monitored for N in streams also exhibited downward trends in flow-weighted N concentrations, which can mainly be ascribed to the introduction of mandatory national regulation of N in agriculture in Denmark in the mid-1980s. However, classification of the mini-catchments according to the age of the oxidized groundwater revealed significant differences in N trends between the groups of mini-catchments. Thus, the strongest downward trend in flow-weighted N concentrations was as follows: <1 year (−52%), 1–3 years (−44%), and >3 years (−38%).
Inhalation Delivery of Host Defense Peptides (HDP) using Nano- Formulation Strategies: A Pragmatic Approach for Therapy of Pulmonary Ailments
Authors: Adlakha Suneera , Sharma Ankur , Vaghasiya Kalpesh , Ray Eupa , Verma Rahul Kumar
Published: December 2019

Host defense peptides (HDP) are small cationic molecules released by the immune systems
of the body, having multidimensional properties including anti-inflammatory, anticancer, antimicrobial
and immune-modulatory activity. These molecules gained importance due to their broad-spectrum
pharmacological activities, and hence being actively investigated. Presently, respiratory infections
represent a major global health problem, and HDP has an enormous potential to be used as an alternative
therapeutics against respiratory infections and related inflammatory ailments. Because of their
short half-life, protease sensitivity, poor pharmacokinetics, and first-pass metabolism, it is challenging
to deliver HDP as such inside the physiological system in a controlled way by conventional delivery
systems. Many HDPs are efficacious only at practically high molar-concentrations, which is not convincing
for the development of drug regimen due to their intrinsic detrimental effects. To avail the
efficacy of HDP in pulmonary diseases, it is essential to deliver an appropriate payload into the targeted
site of lungs. Inhalable HDP can be a potentially suitable alternative for various lung disorders
including tuberculosis, Cystic fibrosis, Pneumonia, Lung cancer, and others as they are active against
resistant microbes and cells and exhibit improved targeting with reduced adverse effects. In this review,
we give an overview of the pharmacological efficacy of HDP and deliberate strategies for designing
inhalable formulations for enhanced activity and issues related to their clinical implications.
Combining Antimicrobial Peptides with Nanotechnology: An Emerging Field in Theranostics
Authors: Mohid Sk Abdul , Bhunia Anirban
Published: December 2019

The emergence of multidrug-resistant pathogens and their rapid adaptation against new antibiotics is a major challenge for scientists and medical professionals. Different approaches have been taken to combat this problem, which includes rationally designed potent antimicrobial peptides (AMPs) and several nanoparticles and quantum dots. AMPs are considered as a new generation of super antibiotics that hold enormous potential to fight against bacterial resistance by the rapidly killing planktonic as well as their biofilm form while keeping low toxicity profile against eukaryotic cells. Various nanoparticles and quantum dots have proved their effectiveness against a vast array of infections and diseases. Conjugation and functionalization of nanoparticles with potentially active antimicrobial peptides have added advantages that widen their applications in the field of drug discovery as well as delivery system including imaging and diagnostics. This article reviews the current progress and implementation of different nanoparticles and quantum dots conjugated antimicrobial peptides in terms of bio-stability, drug delivery, and therapeutic applications.
Beta-Blockers and Cardiovascular Outcomes in Acute Heart Failure with a History of Coronary Artery Disease and an Ejection Fraction ≥ 40%
Authors: Abi Khalil Charbel , Sulaiman Kadhim , Asaad Nidal , AlHabib Khalid F. , Alsheikh-Ali Alawi , Jameesh Mohammed , Al-Jarallah Mohammed , Bulbanat Bassam , AlMahmeed Wael , Ridha Mustafa , Bazargani Nooshin , Amin Haitham , Al-Motarreb Ahmed , AlFaleh Husam , Panduranga Prashanth , Mahfoud Ziyad , Al Suwaidi Jassim
Published: December 2019

The prognostic impact of beta-blockers (BB) in coronary artery disease (CAD) is controversial,
especially in the post-reperfusion era. We studied in-hospital cardiovascular events in patients hospitalized
for acute HF, a previous history of CAD and a left ventricular ejection fraction (LVEF) ≥40%,
in relation to BB on admission; and 1-year outcome in relation to BB on discharge, in the GULF aCute
heArt failuRe (GULF-CARE) registry. From a total of 5005 patients included in the GULF-CARE registry,
303 patients with a previous history of CAD and a LVEF ≥40% on BB were propensity-matched
to 303 patients without BB on admission. In-hospital mortality (OR= 0.82; 95% CI [0.35-1.94]), stroke
and cardiogenic shock were not reduced by BB. On discharge, 306 patients on BB, including the ones
newly diagnosed with myocardial infarction as a precipitating cause of HF, were propensity-scored
matched with 306 patients without BB. Mortality (OR= 0.86; 95%CI [0.51-1.45], hospitalization for HF
or PCI/CABG at 1 year were also not reduced by BB at discharge. In summary, our data show that BB
have a neutral effect on in-hospital and 1-year outcomes in acute heart failure patients with a previous
history of CAD and a LVEF ≥40%.
Biomarkers in Pediatric Lung Diseases Including Cystic Fibrosis
Authors: Parisi Giuseppe Fabio , Papale Maria , Tardino Lucia , Nenna Raffaella , Midulla Fabio , Leonardi Salvatore
Published: January 2020

In recent decades, scientific studies of chemical processes involving metabolites have been steadily increasing, indicating that we are well into the metabolomics era. This has resulted in numerous studies that explore the field of biomarkers. One of the medical areas most concerned with these innovations is certainly that of childhood respiratory disorders, including asthma and cystic fibrosis. This current study is a review of the literature about biomarkers used or studied in the field of pediatric pulmonology, including asthma and cystic fibrosis.