bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transcriptome analysis of the fungal pathogen Rosellinia necatrix during infection of a susceptible avocado rootstock identifies potential mechanisms of pathogenesis
Authors: Zumaquero Adela , Kanematsu Satoko , Nakayashiki Hitoshi , Matas Antonio , Martínez-Ferri Elsa , Barceló-Muñóz Araceli , Alfaro Fernando Pliego , Lopez-Herrera Carlos , Cazorla Francisco , Prieto Clara Pliego 
Published: November 2019

Abstract
Background White root rot disease caused by Rosellinia necatrix is one of the most important threats affecting avocado productivity in tropical and subtropical climates. Control of this disease is complex and nowadays, lies in the use of physical and chemical methods, although none have proven to be fully effective. Detailed understanding of the molecular mechanisms underlying white root rot disease has the potential of aiding future developments in disease resistance and management. In this regard, this study used RNA-Seq technology to compare the transcriptomic profiles of R. necatrix during infection of susceptible avocado `Dusa´ roots with that obtained from the fungus cultured in rich medium. Results The transcriptomes from three biological replicates of R. necatrix colonizing avocado roots (RGA) and R. necatrix growing on potato dextrose agar media (RGPDA) were analyzed using Illumina sequencing. A total of 12,104 transcripts were obtained, among which 1,937 were differentially expressed genes (DEG), 137 exclusively expressed in RGA and 160 in RGPDA. During the root infection process, genes involved in the production of fungal toxins, detoxification and transport of toxic compounds, hormone biosynthesis, gene silencing and plant cell wall degradation were overexpressed. Interestingly, 24 out of the 137 contigs expressed only during R. necatrix growth on avocado roots, were predicted as candidate effector proteins (CEP) with a probability above 60%. The PHI (Pathogen Host Interaction) database revealed that three of the R. necatrix CEP showed homology with previously annotated effectors, already proven experimentally via pathogen-host interaction. Conclusions The analysis of the full-length transcriptome of R. necatrix during the infection process is suggesting that the success of this fungus to infect roots of diverse crops might be attributed to the production of different compounds which, singly or in combination, interfere with defense or signaling mechanisms shared among distinct plant families. The transcriptome analysis of R. necatrix during the infection process provides useful information and facilitates further research to a more in -depth understanding of the biology and virulence of this emergent pathogen. In turn, this will make possible to evolve novel strategies for white root rot management in avocado.
Oral Impact on Daily Performance (OIDP) scale for use in Sri Lankan Adolescents: a cross sectional modification and validation study
Authors: Amilani Uttara , Jayasekara Prasanna , Perera Irosha R , Carter Hannah E , Senanayake Sameera , Kularatna Sanjeewa 
Published: November 2019

Abstract
Background Oral Health Related Quality of Life (OHRQoL) surveys play an important role in understanding subjective patient experiences in oral health care. The Oral Impact on Daily Performance (OIDP) scale is a validated OHRQoL tool that measures the impact and extent to which an individual’s daily activities may be compromised by their oral health. It is commonly used to facilitate oral health service planning. The aim of this study was to modify and validate a Sinhalese version of the OIDP for use in Sri Lankan adolescents. Methods The stage I involved cultural adaptation of the tool through translation and modification. After translation and cultural adaptation, the modified OIDP was tested on 220, 15-19 year secondary school students in the Gampaha district, Sri Lanka. The adolescents completed the modified OIDP scale along with questions on self-reported perceived oral health problems and treatment need which were used to assesses the concurrent validity of the modified OIDP scale. Stage II and III involved the exploring factor structure, validation and a reliability assessment. Factorability was assessed by inspection of correlation matrix and Kaiser-Meyer-Olkin and Bartlett's Test of Sphericity tests as a measure of sampling adequacy. An exploratory factor analysis was carried out using Principal Component Analysis method and factors were rotated using the oblimin method. Results 220 adolescents participated in factor analysis and validation studies. The most prevalent oral health impact related to chewing and enjoying foods, reported by 36.8% of respondents The Kaiser-Meyer-Olkin measure was 0.87 and Bartlett’s test of Sphericity was significant (p<0.001) Cronbach’s alpha was calculated as 0.88, indicating a high level of internal consistency. The principal component analysis produced two factors with Eigen values ranging from 1.12 to 4.40, explaining 70.0% of total variance. Concurrent validity was satisfactory as the OIDP score increased when the adolescents’ perceived oral health decreased.Conclusion This study showed that the modified OIDP scale is applicable for use among adolescents in Sri Lanka. It has promising psychometric properties but further research is required to use this tool in other cohorts.
The Key Candidate Genes in Tubulointerstitial Injury of Chronic Kidney Diseases (CKD) Patients as Determined by Bioinformatic Analysis
Authors: Wang Wanpeng , Shen Jianxiao , Pan Yan , Qi Chaojun , Liang Senlin , Kuai Qiaolin , Zuo Zhi 
Published: November 2019

Abstract
Background: Tubulointerstitial injury (TIL) is common in chronic kidney disease (CKD), which in turn, leads to loss of renal function. The aims of present study were to screen critical genes with tubulointerstitial lesion in CKD by weighted gene correlation network analysis (WGCNA). Methods: GSE104954 gene expression data downloaded from GEO database were used for analysis for differential expression genes(DEGs); Meanwhile, 90 expression data of tubulointerstitial samples in GSE47185 combined with clinic information were applied to WGCNA. According to the enrichment analysis and relationship with estimated glomerular filtration rate (eGFR), the eGFR-associated modules were defined, and the hub gene is selected according to the average intramodular connectivity (Kwithin); Clinical data from Nephroseq were obtained to further validate the relationship between CKD and hub genes. Results: Totally 294 DEGs were screened. Using the WGCNA, we identified 15 co-expressed modules, the blue, brown and yellow modules exhibited strongly association with eGFR, and were significantly enriched in several signaling pathways that have been reported involved in pathogenesis of CKD. Furthermore, it was found that the 4 genes (PLG, ITGB2, CTSS and CCL5) was one of the DEGs which also be identified as hub genes according to Kwithin. Finally, the Nephroseq online tool showed that the tubulointerstitial expression levels of PLG significantly positively correlated with the eGFR, while ITGB2, CTSS and CCL5 connected negatively to the eGFR. Conclusion: WGCNA is an efficient approach to system biology. By this procedure, the present study improved the understanding of the transcriptome status of renal tubulointerstitial injury in CKD.
Virtual Implant Rehabilitation Of The Severely Atrophic Maxilla: A Radiological Study
Authors: Manacorda Michele , Chaurand Bianca Poletti de , Merlone Alberto , Tetè Giulia , Capparè Paolo , Vinci Raffaele 
Published: November 2019

Abstract
Background: Advanced maxillary atrophy is often observed and implant placement could become difficult. Nevertheless, a volumetric evaluation using a proper diagnostic software could facilitate the implant planning. The purpose of the present study is to suggest the potential application of the maxillary retro-canine area as the designated place for virtual tilted implants also in severely atrophic maxillae. Methods: A sample of CBCT images from the Department of Dentistry (IRCCS San Raffaele, Milan) was evaluated. After a 3D anatomical evaluation of the maxilla tilted implants has been virtually positioned in the retro-canine regions. All the implants were inserted with the same procedure at 30° and 45° degrees of tilting. The length, the palatal angulation and the diameter of each implant were identified. Results: 220 tilted implants were placed. An average implant measurement of 13.508 mm of length and 3.42 mm of diameter were calculated. Also, an average buccal-palatal angulation of 6° was identified. After the statistical analysis implant length was found significantly higher at 45° degrees than at 30° degree (<0.0001).Conclusions: A considerable amount of patients show a significant degree of bone atrophy. The implant-supported treatment plan can rely on the three dimensional imaging of the residual bone as a guiding tool to establish the most effective implant position for each specific case. In this study it is founded that an implant could be longer if its mesio-distal angulation is more accentuated. In addition, it is possible to virtually insert tilted implants also in severely atrophic maxilla. This could help clinicians to consider the retro-canine area a viable place to insert longer tilted implant.
Generation of hepato-biliary-pancreatic organoid from human pluripotent stem cells
Authors: Koike Hiroyuki , Iwasawa Kentaro , Takebe Takanori 
Published: November 2019

Abstract
Organogenesis is a complex and inter-connected process, orchestrated by multiple boundary tissue interactions. Here, we established the protocol of the continuous patterning of hepatic, biliary and pancreatic structures from a three-dimensional culture of human pluripotent stem cell (PSC). The boundary interactions between anterior and posterior gut spheroids differentiated from human PSCs enables autonomous emergence of hepato-biliary-pancreatic (HBP) organ domains in the absence of extrinsic factor supply. This anterior-poterior gut interaction protocol can be used to model the early human HBP organogenesis process in vitro.
Data quality of drug-resistant tuberculosis and antiretroviral therapy electronic registers in South Africa
Authors: Jamieson Lise , Evans Denise , Berhanu Rebecca , Ismail Nazir , Aucock Samantha , Wallengren Kristina , Long Lawrence 
Published: November 2019

Abstract
Background To assess the quality and completeness of treatment and outcome data in the electronic tuberculosis (TB) and antiretroviral treatment (ART) registers in drug-resistant (DR-) TB patients at three treatment facilities in South Africa. Methods We did a retrospective cohort study using routinely-collected data from DR-TB registers of rifampicin resistant adults (≥18 years old), on ART, initiating DR-TB treatment between January 2012 and December 2013. We linked patient information from the DR-TB register to the ART register using patient identifiers and an algorithm based on string edit distance and date of birth. We describe data gaps and discrepancies found. Results Overall, 2,852 DR-TB patients met our inclusion criteria based on the DR-TB register data, and of these, 1,685 (59%) could be matched to the ART registers. An additional 253 patients from the DR-TB registers were found in the ART registers, having initiated ART, despite the DR-TB register indicating that they were not on ART (or this data was missing). 11% of matched patients did not have TB treatment status recorded in the ART register despite being recorded as being on TB treatment in the DR-TB register, and 78% did not have an ART start date recorded in DR-TB register despite being on ART treatment as per the ART register. 11% of matched patients had a death recorded in one register but not the other, and of those with death recorded in both, 15% of dates differed by >1 month. Conclusions The underreporting of death and the lack of ART or TB status in the electronic DR-TB and ART registers could negatively impact monitoring efforts by downplaying the state of the TB/HIV epidemic. Improved recording of these data sources, and data integration across systems, could improve the accuracy of reporting for the national HIV/ART and TB programs.
Asthma in children treated with paracetamol versus ibuprofen: A systematic review and meta-analysis of randomised controlled trials
Authors: Sherbash Mohamed , Furuya-Kanamori Luis , Nader Joanne Daghfal , Thalib Lukman 
Published: November 2019

Abstract
Background:
Paracetamol and ibuprofen are the most commonly used medications for fever and pain management in children. While the efficacy appears similar with both drugs, there are contradictory findings related to adverse events. In particular, incidence of asthma among children taking paracetamol compared to ibuprofen, remain unsettled.
Methods:
We conducted a meta-analysis of randomized controlled trials (RCTs) that compared asthma in children taking paracetamol versus ibuprofen. A comprehensive search was conducted in five databases. RCTs reporting on cases of asthma in infants or children after the administration of paracetamol or ibuprofen were included. The pooled effect size was estimated using the inverse variance heterogeneity model.
Results:
Five RCTs with 85095 children were included in the analysis. The pooled estimate (RR 1.04; 95%CI 0.84-1.29) revealed no difference in the risk of developing asthma or presenting an exacerbation of asthma in children who received paracetamol compared to ibuprofen. When the analysis was restricted to RCTs that examined the incidence of asthma, the pooled estimate remained similar (RR 1.03; 95%CI 0.64-1.67). Additional bias adjusted quality effect sensitivity model yielded similar results (RR 1.03; 95%CI 0.84-1.28).
Conclusion:
Although, Ibuprofen and paracetamol appear to have similar tolerance and safety profiles in terms of incidence of asthma in children, we suggest high quality trials with clear definition of asthma outcomes after receiving ibuprofen or paracetamol at varying doses with longer follow-up are warranted for any conclusive finding.
A Method to Adjust for Measurement Error in Three Exposures Measured with Correlated Errors in the Absence of Internal Validation Study
Authors: Muoka Alexander K. , Agogo George , Ngesa Oscar , Mwambi Henry 
Published: November 2019

Abstract
Difficulty in obtaining the correct measurement for an individual's long-term exposure is a major challenge in epidemiological studies that investigate the association between exposures and health outcomes. Measurement error in an exposure biases the association between the exposure and a disease outcome. Usually an internal validation study is required to adjust for exposure measurement error; it is challenging if such a study is not available. We proposed a method (trivariate method) that adjusts for measurement error in three correlated exposures in the absence of internal validation study and illustrated the method using real data. We compared the results from the proposed method with those obtained using a method that ignores measurement error and a method that ignores correlations between the errors and true exposures (the univariate method). It was found that ignoring measurement error leads to bias and underestimates the standard error. It was also found that the magnitude of adjustment in the trivariate method is sensitive to the magnitude of measurement error, sign and correlation between the errors. We conclude that the proposed method can be used to adjust for bias in the outcome-exposure association in a case where three exposures are measured with correlated errors in the absence of an internal validation study. The method is useful in conducting a sensitivity analysis on the magnitude of measurement error and the sign of the error correlation.
Synchronization of surface electromyography and 3D electromagnetic articulography applied to study the biomechanics of the mandible: proof of concept.
Authors: Lezcano Florencia , Dias Fernando Jose , Farfán Constanza , Céspedes María Cristina Manzanares , Fuentes Ramon 
Published: November 2019

Abstract
Background. The aim of this study was to propose and establish the proof of concept of an approach to synchronize 3D Electromagnetic Articulography (3D-EMA) with Surface Electromyography (SEMG) systems based on the standard components of these equipment. Methods. Initially it was planned and obtained the required equipment with the appropriate characteristics required, and them it was created the proper conditions to register the synchronized signals provided by both systems. Thus, we selected a SEMG with a switch module incorporated to be able to achieve synchronization of signals. After the system setup was stablished, chewing tasks were recorded on a healthy volunteer, collecting a proof-of-concept database. The variability among recordings of the database were analyzed in order to detect possible interferences. Results. The analysis of the chewing task recordings obtained with the synchronized 3D EMA and SEMG signals in the present study did not reveal significant distortions, all values were within the informed by the manufacturers of both systems. The method presented the advantage of using only components that are already included with the equipment employed.Conclusion. The method of analysis described in this paper is an effective tool that facilitates the investigation of mandibular movements synchronized in two domains: articulatory movements and electromyographic activity. Thus, it is promising to be applied in different clinical situations to improve the analysis of the complexity of masticatory activity, in addition being able to generate new insights on this topic.
Peripheral administration of a cell-penetrating MOTS-c analogue enhances memory and attenuates Aβ1-42 or LPS induced memory impairment through inhibiting neuroinflammation
Authors: Jiang JinHong , Chang Xin , Nie YaoYan , Shen YuXuan , Liang XueYa , Xu KangTai , Peng YaLi , Chang Min 
Published: November 2019

Abstract
Background: MOTS-c is a 16-amino acid mitochondrial derivative peptide reported to be involved in regulating insulin resistance and obesity, osteoporosis and inflammatory responses. Accumulating evidences suggest that inhibiting neuroinflammation is a potential target in therapeutic or preventive strategies for Alzheimer’s disease (AD). Due to the widespread distribution of MOTS in the CNS and its role in metabolism and immune system, previous reports also pointed out that MOTS-c may be effective as a therapeutic option toward the prevention of the aging processes. Therefore, it is important to understand the roles of MOTS-c in neuroinflammation. Methods: The mouse memory function was evaluated using novel object recognition (NOR) and object location recognition (OLR) tasks. Brain hippocampus tissue samples were analyzed by quantitative PCR, western blotting, ELISA and immunostaining. Near-infrared fluorescent and confocal microscopy experiments were used to detect the brain uptake and distribution of intranasal or intravenous MOTS-c or MP (MOTS-c conjugated with cell penetrating peptides). Peptides drugs were synthesized by a standard Fmoc-based solid-phase synthetic method. Results: Central MOTS-c enhances object and location recognition memory formation and consolidation, and ameliorates the memory deficit induced by Aβ1-42 or LPS in NOR and OLR tasks, whereas dorsomorphin (AMPK inhibitor, i.p.) significantly blocked the memory-ameliorating effects of MOTS-c. Western blotting experiments showed that MOTS-c provided neuroprotection against LPS or Aβ1-42-induced neuroinflammation, which was related with phosphorylation of AMPK, but not MAPK including ERK, JNK and p38. The underlying mechanism of MOTS-c neuroprotection may be involved of inhibiting the activation of astrocytes and microglia and production of proinflammatory cytokines including TNF-α, IL-6, IL-1β, COX-2 and iNOS. In order to improve the brain intake of MOTS-c, we screen out (PRR)5, a cell penetrating peptides, as a carrier for MOTS-c into the brain. Then in NOR task, intranasal or intravenous MP, but not MOTS-c, showed good memory performance on memory formation, memory consolidation and memory impairment. Finally, compared with control and Rho-MOTS-c groups, significant fluorescence signals of Rho-MP were detected in the brain by NIR fluorescence imaging. Conclusion: MOTS-c might be a new potential target for treatment of cognitive decline in AD and this way of administration MP will be the potential strategy for non-invasive therapeutic intervention.
The Characteristics and Social Functioning of Pathological Social Withdrawal, “Hikikomori,” in a Secondary Care Setting: A One-Year Cohort Study
Authors: Imai Hissei , Takamatsu Toko , Mitsuya Hideaki , Yoshizawa Hajime , Mitsuya Hidehiko , Furukawa Toshi A 
Published: November 2019

Abstract
Background: Pathological social withdrawal, named “Hikikomori,” is a Japanese culture-bound syndrome and a serious social problem in Japan. The number of Hikikomori cases in Japan was estimated at about 563,000 in 2016 according to governmental surveys. However, no studies have reported how many Hikikomori have access to community-based psychiatry clinics, and how different they are from non-Hikikomori patients regarding their baseline characteristics and outcomes.　The aim of the present study is to evaluate the baseline characteristics, clinical attendance, and social functioning of community psychiatric clinic patients treated for social withdrawal at one-year follow-ups.

Method : Participants (n = 304) were all patients (aged under 65) of a psychiatric clinic in a one-year period. Baseline patient characteristics were compared among “current” Hikikomori patients, “past” Hikikomori,” and “other” patients. Logistic regression analysis of “clinic attendance status” and “social functioning” at one-year follow-ups was used to assess patient outcomes. Independent variables were age, gender, Hikikomori status, and support from clinical staff.

Results : Numbers of “current”, “past” Hikikomori, and “other” patients were 60 (19.7%), 81 (26.6%), and 163 (53.6%), respectively. The percentage of “current” Hikikomori who attended in person (56.7%) was significantly smaller than for “past” (92.6%) and “other” (92.6) (p < .001). The age distribution of “current” Hikikomori patients was bimodal, peaking at 20 and 40–45 years. The “current” state predicted significantly fewer regular visits (OR = 0.43; 95% CI = 0.22–0.83; p = .012); support from psychiatric social workers increased visits (OR = 2.35; 95% CI = 1.14–4.86; p = .021). Among the “current” Hikikomori patients, first visit attendance in-person predicted regular attendance; no factor consistently predicted working/schooling status.

Conclusion : A sizable percentage of community clinic patients experienced Hikikomori. The “current” Hikikomori state corresponded with low clinic attendance and social function; “support from clinical staff” may increase visit regularity; no factors consistently improved social functioning. Further multi-site study is warranted to examine the generalizability of the findings from the current single-center study.