bluuebunny/crossref_metadata_2025_split huggingface dataset:
Drosophila Hox genes induce melanised pseudo-tumours when misexpressed in hemocytes
Authors: Ponratnam Titus , Saini Ravina , Mishra Rakesh 
Published: January 2020

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
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

Abstract
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

Abstract
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: &lt;1 year (−52%), 1–3 years (−44%), and &gt;3 years (−38%).
A Framework for Auditing and Strategizing to Ensure Cloud Privacy
Authors: Coss David L. , Dhillon Gurpreet 
Published: December 2019

ABSTRACT
In this study we present a framework for auditing and strategizing to ensure cloud privacy. Management of cloud privacy is a problem since it continues to remain an elusive concept due to the evolving relationship between the pervasiveness of technology and its use by individuals. The Cloud Privacy Framework presented in this paper can be utilized to develop privacy audits, establish privacy practices, and help in defining privacy strategies that are in alignment with individual value systems. The paper extends the privacy objectives presented in Coss and Dhillon (2019) to define a design science-based Cloud Privacy Framework. The framework is externally evaluated, validated, and assessed by a group of information system auditors.
TRADISI TURUN MANDI DI DUSUN PENGHIJAUAN DESA PASAR BARU KECAMATAN PANGEAN KABUPATEN KUANTAN SINGINGI RIAU
Authors: Isla Ika Mar , Fatimah Siti 
Published: January 2020

AbstrakTradisi bacungak atau turun mandi ini adalah sebuah tradisi yang dilakukan oleh masyarakat pangean untuk meresmikan seorang bayi yang baru lahir agar bisa mandi kesungai dan keluar rumah dengan “bebas”. Tujuan dari penelitian ini adalah untuk pertama-tama mengetahui tradisi mandi di desa penghijauan. Tujuan kedua adalah untuk mengetahui apa saja peralatan dan prosedur untuk melaksanakan tradisi mandi di desa penghijauan. Tujuan ketiga adalah untuk mengetahui kearifan lokal dari dusun Penghijauan. Penelitian ini menggunakan pendekatan kualitatif dengan metode deskriptif. Pengumpulan data dilakukan dengan observasi, wawancara, dokumentasi dan studi literatur. Berdasarkan temuan penelitian, terlihat bahwa orang-orang di dusun penghijauan masih mengangkat dan menjalankan tradisi turun mandi meskipun ada perubahan yang terjadi, yaitu tempat prosesi pelaksanaan di mana tradisi turun mandi dulu dilakukan di sungai tetapi sekarang sungai telah tercemar dan tidak lagi cocok digunakan untuk melaksanakan tradisi mandi. Karena itu, orang sekarang menjalankan tradisi mandi di rumah mereka dan tradisi bacungak ini salah satu kearifan lokal dari masyarakat dusun penghijauan. Kata Kunci: tradisi turun mandi, kuantan singingi.AbstractThis tradition of bacungak or bathing is a tradition carried out by the Pangean society to inaugurate a newborn baby in order to take a bath in the river and leave the house "freely". The purpose of this study is to first find out the tradition of bathing in the Penghijauan village. The second objective is to find out what equipment and procedures to carry out the tradition of bathing in the Penghijauan village. The third objective is to find out the local wisdom of the Penghijauan Village. This research uses a qualitative approach with descriptive methods. Data collection is done by observation, interviews, documentation and literature studies. Based on the research findings, it appears that people in the greening village still adopt and carry out the tradition of bathing despite changes that occur, namely the place of the procession where the tradition of bathing was done in the river but now the river has been polluted and is no longer suitable to carry out bathing traditions. Because of this, people now carry out the tradition of bathing in their homes and this tradition is one of the local wisdoms of the people in greening villages. . Keywords: tradition of bathing, kuantan singingi.