bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genetic Implication and Dental Consideration in Syndromes with Benign and Malignant Oral Neoplastic Component: A Narrative Review
Authors: Singh Saurabh , Gupta Khushboo , Pendalya Siva Kumar , Kondreddy Kameswari 
Published: November 2019

Background and Objective: The presence of an internal and often occult malignancy may be forewarned by various oral manifestations. Several of these findings are preferentially localized to the head and neck region, including the oral cavity. This places the dental practitioner in a unique position to detect these signs and symptoms of occult neoplastic involvement. Because they may be present before an established syndrome or cancer diagnosis, even representing the initial expression of disease in some cases, early recognition by a dentist may lead to timely diagnosis and management of these syndromes. Thus, the aim of this narrative review was literature search and gathering data of such syndromes. Materials and Methods: A Medline–PubMed search was conducted of the literature using the keywords “syndrome,” “dental management,” “Cowden’s syndrome,” “Peutz–Jeghers syndrome,” “malignant component,” “Gardner’s syndrome,” “Gorlin–Goltz syndrome,” and “McCune–Albright syndrome.” The search strategy was limited to human studies (case reports and case series), full-text English articles published from January 1, 2000, to mid-2019. Irrelevant articles or articles with inadequate information were omitted. Results: A total of 36 pieces of literature were reviewed, of which 13 were literature reviews, 15 case reports, 3 expert committee guides and updates, and 4 original research papers, and 1 was a book. Conclusion: These syndromes pose risk during dental practice, which necessitates extra awareness and caution to prevent potential complications. Although, the multidisciplinary approach in treating these cases is not well documented, any related information may be helpful in understanding the pathogenesis and the nature of these syndromes.
Integrated transcriptomic analysis reveals hub genes involved in diagnosis and prognosis of pancreatic cancer
Authors: Zhou Yang-Yang , Chen Li-Ping , Zhang Yi , Hu Sun-Kuan , Dong Zhao-Jun , Wu Ming , Chen Qiu-Xiang , Zhuang Zhi-Zhi , Du Xiao-Jing 
Published: November 2019

Abstract

Background
The hunt for the molecular markers with specificity and sensitivity has been a hot area for the tumor treatment. Due to the poor diagnosis and prognosis of pancreatic cancer (PC), the excision rate is often low, which makes it more urgent to find the ideal tumor markers.

Methods
Robust Rank Aggreg (RRA) methods was firstly applied to identify the differentially expressed genes (DEGs) between PC tissues and normal tissues from GSE28735, GSE15471, GSE16515, and GSE101448. Among these DEGs, the highly correlated genes were clustered using WGCNA analysis. The co-expression networks and molecular complex detection (MCODE) Cytoscape app were then performed to find the sub-clusters and confirm 35 candidate genes. For these genes, least absolute shrinkage and selection operator (lasso) regression model was applied and validated to build a diagnostic risk score model. Cox proportional hazard regression analysis was used and validated to build a prognostic model.

Results
Based on integrated transcriptomic analysis, we identified a 19 gene module (SYCN, PNLIPRP1, CAP2, GNMT, MAT1A, ABAT, GPT2, ADHFE1, PHGDH, PSAT1, ERP27, PDIA2, MT1H, COMP, COL5A2, FN1, COL1A2, FAP and POSTN) as a specific predictive signature for the diagnosis of PC. Based on the two consideration, accuracy and feasibility, we simplified the diagnostic risk model as a four-gene model: 0.3034*log2(MAT1A)-0.1526*log2(MT1H) + 0.4645*log2(FN1) -0.2244*log2(FAP), log2(gene count). Besides, a four-hub gene module was also identified as prognostic model = − 1.400*log2(CEL) + 1.321*log2(CPA1) + 0.454*log2(POSTN) + 1.011*log2(PM20D1), log2(gene count).

Conclusion
Integrated transcriptomic analysis identifies two four-hub gene modules as specific predictive signatures for the diagnosis and prognosis of PC, which may bring new sight for the clinical practice of PC.
ProtRank: bypassing the imputation of missing values in differential expression analysis of proteomic data
Authors: Medo Matúš , Aebersold Daniel M. , Medová Michaela 
Published: November 2019

Abstract

Background
Data from discovery proteomic and phosphoproteomic experiments typically include missing values that correspond to proteins that have not been identified in the analyzed sample. Replacing the missing values with random numbers, a process known as “imputation”, avoids apparent infinite fold-change values. However, the procedure comes at a cost: Imputing a large number of missing values has the potential to significantly impact the results of the subsequent differential expression analysis.

Results
We propose a method that identifies differentially expressed proteins by ranking their observed changes with respect to the changes observed for other proteins. Missing values are taken into account by this method directly, without the need to impute them. We illustrate the performance of the new method on two distinct datasets and show that it is robust to missing values and, at the same time, provides results that are otherwise similar to those obtained with edgeR which is a state-of-art differential expression analysis method.

Conclusions
The new method for the differential expression analysis of proteomic data is available as an easy to use Python package.
Complete chloroplast genomes of all six Hosta species occurring in Korea: molecular structures, comparative, and phylogenetic analyses
Authors: Lee Soo-Rang , Kim Kyeonghee , Lee Byoung-Yoon , Lim Chae Eun 
Published: November 2019

Abstract

Background
The genus Hosta is a group of economically appreciated perennial herbs consisting of approximately 25 species that is endemic to eastern Asia. Due to considerable morphological variability, the genus has been well recognized as a group with taxonomic problems. Chloroplast is a cytoplasmic organelle with its own genome, which is the most commonly used for phylogenetic and genetic diversity analyses for land plants. To understand the genomic architecture of Hosta chloroplasts and examine the level of nucleotide and size variation, we newly sequenced four (H. clausa, H. jonesii, H. minor, and H. venusta) and analyzed six Hosta species (including the four, H. capitata and H. yingeri) distributed throughout South Korea.

Results
The average size of complete chloroplast genomes for the Hosta taxa was 156,642 bp with a maximum size difference of ~ 300 bp. The overall gene content and organization across the six Hosta were nearly identical with a few exceptions. There was a single tRNA gene deletion in H. jonesii and four genes were pseudogenized in three taxa (H. capitata, H. minor, and H. jonesii). We did not find major structural variation, but there were a minor expansion and contractions in IR region for three species (H. capitata, H. minor, and H. venusta). Sequence variations were higher in non-coding regions than in coding regions. Four genic and intergenic regions including two coding genes (psbA and ndhD) exhibited the largest sequence divergence showing potential as phylogenetic markers. We found compositional codon usage bias toward A/T at the third position. The Hosta plastomes had a comparable number of dispersed and tandem repeats (simple sequence repeats) to the ones identified in other angiosperm taxa. The phylogeny of 20 Agavoideae (Asparagaceae) taxa including the six Hosta species inferred from complete plastome data showed well resolved monophyletic clades for closely related taxa with high node supports.

Conclusions
Our study provides detailed information on the chloroplast genome of the Hosta taxa. We identified nucleotide diversity hotspots and characterized types of repeats, which can be used for developing molecular markers applicable in various research area.
Low pre-transplant levels of mannose-binding lectin are associated with viral infections and mortality after haematopoietic allogeneic stem cell transplantation
Authors:   on behalf of SCT team, Puente M. , Fariñas-Alvarez C. , Moreto A. , Sánchez-Velasco P. , Ocejo-Vinyals J. G. , Fariñas M. C. 
Published: November 2019

Abstract

Background
Mannose-binding lectin (MBL) is a key component of innate immunity. Low serum MBL levels, related to promoter polymorphism and structural variants, have been associated with an increased risk of infection. The aim of this work was to analyse the incidence and severity of infections and mortality in relation to the MBL2 genotype and MBL levels in patients underwent allogeneic haematopoietic stem cell transplantation (Allo-HSCT).

Results
This was a prospective cohort study of 72 consecutive patients underwent Allo-HSCT between January 2007 and June 2009 in a tertiary referral centre. Three periods were considered in the patients’ follow-up: the early period (0–30 days after Allo-HSCT), the intermediate period (30–100 days after Allo-HSCT) and the late period (> 100 days after Allo-HSCT). A commercial line probe assay for MBL2 genotyping and an ELISA Kit were used to measure MBL levels. A total of 220 episodes of infection were collected in the 72 patients. No association between donor or recipient MBL2 genotype and infection was found. The first episode of infection presented earlier in patients with pre-transplant MBL levels of < 1000 ng/ml (median 6d vs 8d, p = 0.036). MBL levels < 1000 ng/ml in the pre-transplant period (risk ratio (RR) 2.48, 95% CI 1.00–6.13), neutropenic period (0–30 days, RR 3.28, 95% CI 1.53–7.06) and intermediate period (30–100 days, RR 2.37, 95% CI 1.15–4.90) were associated with increased risk of virus infection. No association with bacterial or fungal disease was found. Mortality was associated with pre-transplant MBL levels < 1000 ng/ml (hazard ratio 5.55, 95% CI 1.17–26.30, p = 0.03) but not with MBL2 genotype.

Conclusions
Patients who underwent Allo-HSCT with low pre-transplant MBL levels presented the first episode of infection earlier and had an increased risk of viral infections and mortality in the first 6 months post-transplant. Thus, pre-transplant MBL levels would be important in predicting susceptibility to viral infections and mortality and might be considered a biomarker to be included in the pre-transplantation risk assessment.
Antibiotics resistance and toxin profiles of Bacillus cereus-group isolates from fresh vegetables from German retail markets
Authors: Fiedler Gregor , Schneider Carmen , Igbinosa Etinosa O. , Kabisch Jan , Brinks Erik , Becker Biserka , Stoll Dominic A. , Cho Gyu-Sung , Huch Melanie , Franz Charles M. A. P. 
Published: November 2019

Abstract

Background
This study aimed to evaluate the safety of raw vegetable products present on the German market regarding toxin-producing Bacillus cereus sensu lato (s.l.) group bacteria.

Results
A total of 147 B. cereus s.l. group strains isolated from cucumbers, carrots, herbs, salad leaves and ready-to-eat mixed salad leaves were analyzed. Their toxinogenic potential was assessed by multiplex PCR targeting the hemolysin BL (hbl) component D (hblD), non-hemolytic enterotoxin (nhe) component A (nheA), cytotoxin K-2 (cytK-2) and the cereulide (ces) toxin genes. In addition, a serological test was used to detect Hbl and Nhe toxins. On the basis of PCR and serological results, none of the strains were positive for the cereulide protein/genes, while 91.2, 83.0 and 37.4% were positive for the Hbl, Nhe and CytK toxins or their genes, respectively. Numerous strains produced multiple toxins. Generally, strains showed resistance against the β-lactam antibiotics such as penicillin G and cefotaxim (100%), as well as amoxicillin/clavulanic acid combination and ampicillin (99.3%). Most strains were susceptible to ciprofloxacin (99.3%), chloramphenicol (98.6%), amikacin (98.0%), imipenem (93.9%), erythromycin (91.8%), gentamicin (88.4%), tetracycline (76.2%) and trimethoprim/sulfamethoxazole combination (52.4%). The genomes of eight selected strains were sequenced. The toxin gene profiles detected by PCR and serological test mostly agreed with those from whole-genome sequence data.

Conclusions
Our study showed that B. cereus s.l. strains encoding toxin genes occur in products sold on the German market and that these may pose a health risk to the consumer if present at elevated levels. Furthermore, a small percentage of these strains harbor antibiotic resistance genes. The presence of these bacteria in fresh produce should, therefore, be monitored to guarantee their safety.
Molecular cloning and metabolomic characterization of the 5-enolpyruvylshikimate-3-phosphate synthase gene from Baphicacanthus cusia
Authors: Yu Jian , Zhang Yihan , Ning Shuju , Ye Qi , Tan Hexin , Chen Ruibing , Bu Qitao , Zhang Rui , Gong Peimin , Ma Xiaoli , Zhang Lei , Wei Daozhi 
Published: November 2019

Abstract

Background
Indigo alkaloids, such as indigo, indirubin and its derivatives, have been identified as effective antiviral compounds in Baphicacanthus cusia. Evidence suggests that the biosynthesis of indigo alkaloids in plants occurs via the shikimate pathway. The enzyme 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) is involved in plant metabolism; however, its underlying putative mechanism of regulating the production of indigo alkaloids is currently unknown.

Results
One gene encoding EPSPS was isolated from B. cusia. Quantitative real-time PCR analysis revealed that BcEPSPS was expressed at the highest level in the stem and upregulated by methyl jasmonate (MeJA), salicylic acid (SA) and abscisic acid (ABA) treatment. The results of subcellular localization indicated that BcEPSPS is mainly expressed in both the plastids and cytosol, which has not been previously reported. An enzyme assay revealed that the heterogeneously expressed BcEPSPS protein catalysed the generation of 5-enolpyruvyl shikimate-3-phosphate. The overexpression of BcEPSPS in Isatis indigotica hairy roots resulted in the high accumulation of indigo alkaloids, such as indigo, secologanin, indole and isorhamnetin.

Conclusions
The function of BcEPSPS in catalysing the production of EPSP and regulating indigo alkaloid biosynthesis was revealed, which provided a distinct view of plant metabolic engineering. Our findings have practical implications for understanding the effect of BcEPSPS on active compound biosynthesis in B. cusia.
A prospective observational study testing liquid crystal phase change type thermometer placed on skin against oesophageal/pharyngeal placed thermometers in participants undergoing general anesthesia
Authors: Simpson G. , Rodseth R. N. 
Published: November 2019

AbstractsBackgroundPatient outcomes are influenced by intraoperative temperature management. Oesophageal/pharyngeal temperature monitoring is the standard of care at our institute but is not well tolerated in awake patients. Many non-invasive temperature monitors have been studied. Only the TraxIt® Wearable Children’s Underarm Thermometer which contains liquid crystals that undergo phase changes according to temperature is available at our institution. We tested these non-invasive monitors against our standard of care which is the oesophageal/pharyngeal temperature monitor.MethodsWe conducted a prospective observational study of 100 patients receiving general anaesthesia for elective surgery. Patients were eligible for inclusion if they were ≥ 18 years old, were planned to have a general anaesthetic > 60 min during which no body cavity (chest or abdomen) would be opened. Patient temperature was measured with an oesophageal/pharyngeal thermistor probe and skin surface temperature monitors placed over the forehead, in the axilla, over the sternum, and behind the ear (over major vessels to the brain). Temperatures were recorded and then analysed using Altman-Bland plots. Pre-determined clinically relevant limits of agreement were set at −/+ 0.5 °C.ResultsFrom the 100 patients we collected 500 data points for each monitor with an average monitoring time of 102 min (30–300 min) across a range of surgical procedures. None of the skin surface temperature monitors achieved the pre-determined limits of agreement and results were impacted by the use of a forced air warmer.ConclusionThe TraxIt® Wearable Children’s Underarm Thermometers are not suitable for temperature monitoring during general anaesthesia.
Does the implementation of a care pathway for patients with hip or knee osteoarthritis lead to fewer diagnostic imaging and referrals by general practitioners? A pre-post-implementation study of claims data
Authors: van den Bogaart Esther H. A. , Kroese Mariëlle E. A. L. , Spreeuwenberg Marieke D. , Ottenheijm Ramon P. G. , Deckers Patrick , Ruwaard Dirk 
Published: November 2019

Abstract

Background
The Dutch care for hip and knee osteoarthritis (OA) is of good quality, but there is room for improvement regarding the efficient use of diagnostic imaging and conservative treatment. Therefore a stepped-care approach, in the shape of the care pathway ‘Better exercise in osteoarthritis’, was implemented to reduce the number of diagnostic imaging requested by GPs and referrals of GPs to orthopaedic care.

Methods
In 2015, the pathway is implemented with the use of educational meetings, distributing guidelines and incorporating reminders in the GPs’ referral application. To evaluate the effect of the pathway on the diagnostic and referral behaviour of GPs, hip and knee related health insurance claims are used together with claims of other joints and of a control region for comparison. The average number of claims and the percentage change in the post-implementation period are described. Binary logistic regression analysis is used to examine the interaction between region (intervention and control) and period (pre- and post-implementation). Using random sampling of patient records, information about the practical application of the pathway and the number of hip or knee arthroplasties is added.

Results
In both regions, the number of diagnostic imaging decreased and the number of initial orthopaedic consultations increased during the post-implementation period. Significant interaction effects were found in knee-related diagnostics (p ≤ 0.001) and diagnostics of other joints (p = 0.039). No significant interaction effects were found in hip-related diagnostics (p = 0.060) and in initial orthopaedic consultation claims of hip (p = 0.979), knee (p = 0.281), and other joints (p = 0.464). Being referred according to the pathway had no significant effect on the probability of undergoing arthroplasty.

Conclusion
The implementation of the pathway had a positive effect on GPs diagnostic behaviour related to the knee, but not to the hip. The referral behaviour of GPs to orthopaedic care needs attention for future interventions and research, since an increase (instead of a desired decrease) in the number of initial orthopaedic consultations was found. Focusing on the entire width of care for hip and knee OA could be helpful.
Indirect costs associated with ulcerative colitis: a systematic literature review of real-world data
Authors: Constantin Joelle , Atanasov Petar , Wirth Daniel , Borsi Andras 
Published: November 2019

Abstract

Background
The economic burden of ulcerative colitis (UC), specifically related to indirect costs, is not extensively documented. Understanding and quantifying it is required by health care decision makers.

Aim
To assess the impact of indirect costs of UC in observation studies.

Method
A systematic literature search was conducted in MEDLINE®, Embase® and Cochrane Library to capture all relevant publications reporting outcomes on absenteeism, presenteeism and productivity losses in moderate to severe UC. Eligibility criteria for inclusion into the review were established using a predefined PICOS scheme. All costs were adjusted to 2017 currency values (USD dollars, $).

Results
In total, 18 studies reporting data on indirect costs were included in the analysis. Absenteeism costs were classified into three categories: sick leave, short-term and long-term disability. Most of the studies captured absenteeism costs related specifically to sick leave, which was experienced on average by 10 to 24% patients with UC. Only three studies captured presenteeism costs, as these are difficult to measure, however costs ranged from 1602 $ to 2947 $ per patient year. The proportion of indirect costs accounted for 35% of total UC costs (Total UC costs were defined as the sum of healthcare costs, productivity costs and out-of-pocket costs).

Discussion
A limited number of studies were identified describing the indirect costs in patients with moderate to severe UC. Insufficient data on different components of costs allowed a limited analysis on the impact of indirect costs in patients with UC. Further studies are needed to gain an understanding of the influence of UC on patients’ functional abilities.
Mumps: MMR vaccination and genetic diversity of mumps virus, 2007–2011 in Catalonia, Spain
Authors:   the Working Group for the Study for Mumps in Catalonia, Barrabeig Irene , Antón Andrés , Torner Núria , Pumarola Tomàs , Costa Josep , Domínguez Àngela 
Published: November 2019

Abstract

Background
Mumps is a vaccine-preventable disease but outbreaks have been reported in persons vaccinated with two doses of MMR vaccine.
The objective was to describe the demographic features, vaccination effectiveness and genetic mumps virus diversity among laboratory-confirmed cases between 2007 and 2011 in Catalonia.

Methods
Cases and outbreaks of mumps notified to the notifiable diseases system of Catalonia between 2007 and 2011 retrospectively registered were included. Public health care centres provided written immunization records to regional public health staff to determine the vaccination history.
Saliva and serum specimens were collected from suspected cases for laboratory-confirmation using real-time reverse-transcriptase PCR (rtRT-PCR) or serological testing.
Phylogenetic analysis of the complete SH gene (316 nucleotides) and complete coding HN protein (1749 nucleotides) sequences was made.
Categorical variables were compared using the Chi-square or Fisher’s tests and continuous variables using the Student test. Vaccination effectiveness by number of MMR doses was estimated using the screening method.

Results
During the study period, 581 confirmed cases of mumps were notified (incidence rate 1.6 cases/100,000 persons-year), of which 60% were male. Three hundred sixty-four laboratory-confirmed cases were reported, of which 44% were confirmed by rtRT-PCR. Of the 289 laboratory-confirmed cases belonging to vaccination cohorts, 33.5% (97) had received one dose of MMR vaccine and 50% (145) two doses.
Based on phylogenetic analyses of 316-nucleotide and 174-nucleotide SH sequences, the viruses belonging to viral genotypes were: genotype G (126), genotype D (23), genotype H (2), genotype F (2), genotype J (1), while one remained uncharacterized.
Amino acid differences were detected between circulating strains and the Jeryl Lynn vaccine strains, although the majority of amino acid substitutions were genotype-specific.
Fifty-one outbreaks were notified that included 324 confirmed mumps cases. Genotype G was the most frequent genotype detected. The family (35%), secondary schools (25%) and community outbreaks (18%) were the most frequent settings.

Conclusions
Our study shows that genotype G viruses are the most prevalent in Catalonia. Most cases occurred in people who had received two doses of MMR, suggesting inadequate effectiveness of the Jeryl Lynn vaccine strain. The possible factors related are discussed.