bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional polysaccharides of carob fruit: a review
Authors: Zhu Bao-Jie , Zayed Mohamed Zaky , Zhu Hua-Xu , Zhao Jing , Li Shao-Ping 
Published: September 2019

Abstract
Polysaccharides in carob fruit, including carob bean gum (also known as carob gum, locust bean gum) and carob fiber, are widely used in industries such as food, pharmaceuticals, paper, textile, oil well drilling and cosmetics. Carob bean gum is a galactomannan obtained from the seed endosperm of carob tree and the fiber is obtained by removing most of soluble carbohydrates in carob pulp by water extraction. Both the gum and fiber are beneficial to health for many diseases such as diabetes, bowel movements, heart disease and colon cancer. This article reviewed the composition, properties, food applications and health benefits of polysaccharides from carob fruit.
Specific DNA identification of Pheretima in the Naoxintong capsule
Authors: Zhu Xiaoxiao , Wu Hoi-Yan , Shaw Pang-Chui , Peng Wei , Su Weiwei 
Published: September 2019

Abstract

Background
Pheretima is a minister drug in Naoxintong capsule (NXTC), a well-known traditional Chinese medicine (TCM) formula for the treatment of cardiovascular and cerebrovascular diseases. Owing to the loss of morphological and microscopic characteristics and the lack of recognized chemical marker, it is difficult to identify Pheretima in NXTC. This study aims to evaluate the feasibility of using DNA techniques to authenticate Pheretima, especially when it is processed into NXTC.

Methods
DNA was extracted from crude drugs of the genuine and adulterant species, as well as nine batches of NXTCs. Based on mitochondrial cytochrome c oxidase subunit I (COI) gene, specific primers were designed for two genera of genuine species, Metaphire and Amynthas, respectively. PCR amplification was performed with the designed primers on crude drugs of Pheretima and NXTCs. The purified PCR products were sequenced and the obtained sequences were identified to species level with top hit of similarity with BLAST against GenBank nucleotide database.

Results
Primers MF2R2 and AF3R1 could amplify specific DNA fragments with sizes around 230–250 bp, both in crude drugs and NXTC. With sequencing and the BLAST search, identities of the tested samples were found.

Conclusion
This study indicated that the molecular approach is effective for identifying Pheretima in NXTC. Therefore, DNA identification may contribute to the quality control and assurance of NXTC.
Discovery and implementation of a novel pathway for n-butanol production via 2-oxoglutarate
Authors: Ferreira Sofia , Pereira Rui , Liu Filipe , Vilaça Paulo , Rocha Isabel 
Published: September 2019

Abstract

Background
One of the European Union directives indicates that 10% of all fuels must be bio-synthesized by 2020. In this regard, biobutanol—natively produced by clostridial strains—poses as a promising alternative biofuel. One possible approach to overcome the difficulties of the industrial exploration of the native producers is the expression of more suitable pathways in robust microorganisms such as Escherichia coli. The enumeration of novel pathways is a powerful tool, allowing to identify non-obvious combinations of enzymes to produce a target compound.

Results
This work describes the in silico driven design of E. coli strains able to produce butanol via 2-oxoglutarate by a novel pathway. This butanol pathway was generated by a hypergraph algorithm and selected from an initial set of 105,954 different routes by successively applying different filters, such as stoichiometric feasibility, size and novelty. The implementation of this pathway involved seven catalytic steps and required the insertion of nine heterologous genes from various sources in E. coli distributed in three plasmids. Expressing butanol genes in E. coli K12 and cultivation in High-Density Medium formulation seem to favor butanol accumulation via the 2-oxoglutarate pathway. The maximum butanol titer obtained was 85 ± 1 mg L−1 by cultivating the cells in bioreactors.

Conclusions
In this work, we were able to successfully translate the computational analysis into in vivo applications, designing novel strains of E. coli able to produce n-butanol via an innovative pathway. Our results demonstrate that enumeration algorithms can broad the spectrum of butanol producing pathways. This validation encourages further research to other target compounds.
Identifying Crohn’s disease signal from variome analysis
Authors: Wang Yanran , Miller Maximilian , Astrakhan Yuri , Petersen Britt-Sabina , Schreiber Stefan , Franke Andre , Bromberg Yana 
Published: September 2019

Abstract

Background
After years of concentrated research efforts, the exact cause of Crohn’s disease (CD) remains unknown. Its accurate diagnosis, however, helps in management and preventing the onset of disease. Genome-wide association studies have identified 241 CD loci, but these carry small log odds ratios and are thus diagnostically uninformative.

Methods
Here, we describe a machine learning method—AVA,Dx (Analysis of Variation for Association with Disease)—that uses exonic variants from whole exome or genome sequencing data to extract CD signal and predict CD status. Using the person-specific coding variation in genes from a panel of only 111 individuals, we built disease-prediction models informative of previously undiscovered disease genes. By additionally accounting for batch effects, we were able to accurately predict CD status for thousands of previously unseen individuals from other panels.

Results
AVA,Dx highlighted known CD genes including NOD2 and new potential CD genes. AVA,Dx identified 16% (at strict cutoff) of CD patients at 99% precision and 58% of the patients (at default cutoff) with 82% precision in over 3000 individuals from separately sequenced panels.

Conclusions
Larger training panels and additional features, including other types of genetic variants and environmental factors, e.g., human-associated microbiota, may improve model performance. However, the results presented here already position AVA,Dx as both an effective method for revealing pathogenesis pathways and as a CD risk analysis tool, which can improve clinical diagnostic time and accuracy. Links to the AVA,Dx Docker image and the BitBucket source code are at https://bromberglab.org/project/avadx/.
microRNA-92a regulates the expression of aphid bacteriocyte-specific secreted protein 1
Authors: Feng Honglin , Park Joun S. , Zhai R. Grace , Wilson Alexandra C. C. 
Published: September 2019

Abstract

Objective
Aphids harbor a nutritional obligate endosymbiont in specialized cells called bacteriocytes, which aggregate to form an organ known as the bacteriome. Aphid bacteriomes display distinct gene expression profiles that facilitate the symbiotic relationship. Currently, the mechanisms that regulate these patterns of gene expression are unknown. Recently using computational pipelines, we identified miRNAs that are conserved in expression in the bacteriomes of two aphid species and proposed that they function as important regulators of bacteriocyte gene expression. Here using a dual luciferase assay in mouse NIH/3T3 cell culture, we aimed to experimentally validate the computationally predicted interaction between Myzus persicae miR-92a and the predicted target region of M. persicae bacteriocyte-specific secreted protein 1 (SP1) mRNA.

Results
In the dual luciferase assay, miR-92a interacted with the SP1 target region resulting in a significant downregulation of the luciferase signal. Our results demonstrate that miR-92a interacts with SP1 to alter expression in a heterologous expression system, thereby supporting our earlier assertion that miRNAs are regulators of the aphid/Buchnera symbiotic interaction.
Malignant mesothelioma in construction workers: the Apulia regional mesothelioma register, Southern Italy
Authors: Vimercati L. , Cavone D. , Caputi A. , Delfino M. C. , De Maria L. , Ferri G. M. , Serio G. 
Published: September 2019

Abstract

Objective
Asbestos was widely used in construction in both a friable and a compact form until the 1990s, before its use was banned. Today, many of these materials are still in situ and represent a source of risk for construction workers. The objective of the study was to analyse the cases of mesothelioma arising among construction workers registered in the Apulia regional register of mesothelioma.

Results
For the period 1993–2018, there were 178 male cases, and 10.2% of the cases were present in the regional register. The average age at diagnosis was 64.7 years. The site was pleural in 96.06% of cases, with a diagnosis of certainty in 86.5% of the total cases and 61.8% of cases with epithelial histology. The average latency is 43.9 years. In 75.2% of cases, the exposure began between 1941 and 1970, with an average duration of 24.3 years. The age at the start of exposure in 68.5% of cases is between 8 and 20 years. The ORs were 2.5 (C.I. 95% 1.01–6.17) for the epithelioid histotype and the high duration of exposure. The data underline the need for prevention and information on all activities involving construction workers in which asbestos-containing materials are still used.
Breast self-examination practice and associated factors among female healthcare workers in West Shoa Zone, Western Ethiopia 2019: a cross-sectional study
Authors: Shallo Seifadin Ahmed , Boru Jibril Dori 
Published: September 2019

Abstract

Objective
Breast cancer is the leading cause of death among reproductive-age women worldwide and the second leading cause of death among women in Ethiopia. Regular breast self-examination is the most cost-effective methods for early detection of breast cancer. Despite this fact, breast self-examination was low among women in the general population and it was not well documented among health care workers. Therefore, this study intended to assess the magnitude of breast self-examination practice and associated factors among female healthcare workers in public health facility in West Shoa Zone, Ethiopia. Institutional based cross-sectional study was conducted among 379 female healthcare workers. The study participants were recruited by lottery method. Data were collected from March to April 2019. Data were entered into Epi data version 4.5 and analyzed using SPSS version 25. Bivariate and multiple logistic regressions analysis were done. With 95% CI, the level of significance was decided at P-value ≤ 0.05.

Results
The magnitude of regular breast self-examination practice was 32.6%. Educational levels, breast cancer awareness, knowledge towards breast self-examination were predictors of breast self-examination. Regular awareness creation forum on breast self-examination technique, risk factors, and related matters should be facilitated so that all female health care workers will be reminded.
Morpho-functional evaluation of lung aeration as a marker of sickle-cell acute chest syndrome severity in the ICU: a prospective cohort study
Authors: Garnier Marc , Hafiani El Mahdi , Arbelot Charlotte , Blayau Clarisse , Labbe Vincent , Stankovic-Stojanovic Katia , Lionnet François , Bonnet Francis , Fulgencio Jean-Pierre , Fartoukh Muriel , Quesnel Christophe 
Published: September 2019

Abstract

Background
Acute chest syndrome (ACS) is the main cause of morbi-mortality in patients with sickle-cell disease in the intensive care unit (ICU). ACS definition encompasses many types of lung damage, making early detection of the most severe forms challenging. We aimed to describe ACS-related lung ultrasound (LU) patterns and determine LU performance to assess ACS outcome.

Results
We performed a prospective cohort study including 56 ICU patients hospitalized for ACS in a tertiary university hospital (Paris, France). LU and bedside spirometry were performed at admission (D0) and after 48 h (D2). Complicated outcome was defined by the need for transfusion of ≥ 3 red blood cell units, mechanical ventilation, ICU length-of-stay > 5 days, or death. A severe loss of lung aeration was observed in all patients, predominantly in inferior lobes, and was associated with decreased vital capacity (22 [15–33]% of predicted). The LU Score was 24 [20–28] on D0 and 20 [15–24] on D2. Twenty-five percent of patients (14/56) had a complicated outcome. Neither oxygen supply, pain score, haemoglobin, LDH and bilirubin values at D0; nor their change at D2, differed regarding patient outcome. Conversely, LU re-aeration score and spirometry change at D2 improved significantly more in patients with a favourable outcome. A negative LU re-aeration score at D2 was an independent marker of severity of ACS in ICU.

Conclusions
ACS is associated with severe loss of lung aeration, whose resolution is associated with favourable outcome. Serial bedside LU may accurately and early identify ACS patients at risk of complicated outcome.
Early prediction of noninvasive ventilation failure in COPD patients: derivation, internal validation, and external validation of a simple risk score
Authors: Duan Jun , Wang Shengyu , Liu Ping , Han Xiaoli , Tian Yao , Gao Fan , Zhou Jing , Mou Junhuan , Qin Qian , Yu Jingrong , Bai Linfu , Zhou Lintong , Zhang Rui 
Published: September 2019

AbstractBackgroundEarly identification of noninvasive ventilation (NIV) failure is a promising strategy for reducing mortality in chronic obstructive pulmonary disease (COPD) patients. However, a risk-scoring system is lacking.MethodsTo develop a scale to predict NIV failure, 500 COPD patients were enrolled in a derivation cohort. Heart rate, acidosis (assessed by pH), consciousness (assessed by Glasgow coma score), oxygenation, and respiratory rate (HACOR) were entered into the scoring system. Another two groups of 323 and 395 patients were enrolled to internally and externally validate the scale, respectively. NIV failure was defined as intubation or death during NIV.ResultsUsing HACOR score collected at 1–2 h of NIV to predict NIV failure, the area under the receiver operating characteristic curves (AUC) was 0.90, 0.89, and 0.71 for the derivation, internal-validation, and external-validation cohorts, respectively. For the prediction of early NIV failure in these three cohorts, the AUC was 0.91, 0.96, and 0.83, respectively. In all patients with HACOR score > 5, the NIV failure rate was 50.2%. In these patients, early intubation (< 48 h) was associated with decreased hospital mortality (unadjusted odds ratio = 0.15, 95% confidence interval 0.05–0.39,p < 0.01).ConclusionsHACOR scores exhibited good predictive power for NIV failure in COPD patients, particularly for the prediction of early NIV failure (< 48 h). In high-risk patients, early intubation was associated with decreased hospital mortality.
A New 3D Empirical Plastic and Damage Model for Simulating the Failure of Concrete Structure
Authors: Jiao Yan-tao , Wang Bo , Shen Zhen-zhong 
Published: September 2019

AbstractA new plastic–damage constitutive model based on the combination of damage mechanics and classical plastic theory was developed to simulate the failure of concrete. In order to explain different material behaviors of concrete under tensile and compressive loadings, the plastic yield criterion, the different kinematic hardening rule for tension and compressive and the isotropic flow rule were established in the effective stress space. Meanwhile, two different empirical damage evolution equations were adopted: one for compression and the other for tension. A multi-axial damage influence factor was also introduced to fully describe the anisotropic damage of concrete. Finally, the model response was compared with a wide range of experiment results. The results showed that the model could well describe the nonlinear behavior of concrete in a complex stress state.
Micro-invasive glaucoma surgery – an interventional glaucoma revolution
Authors: Shah Manjool 
Published: September 2019

Abstract
The glaucoma surgical landscape has changed dramatically over the last decade with the introduction and integration of micro-invasive glaucoma surgery (MIGS) techniques. These modalities target physiologic outflow pathways or optimize previously utilized glaucoma surgical methods in order to deliver safety, efficacy, and individualized care to the patient. MIGS techniques can be classified based on anatomical location as well as method of intraocular pressure (IOP) reduction. This review will focus on MIGS optimizing the conventional outflow pathway via intervention at Schlemm’s canal, MIGS optimizing the uveoscleral outflow pathway via suprachoroidal shunting, and MIGS optimizing the transscleral or subconjunctival outflow pathway which has long been utilized by glaucoma surgeons performing traditional filtration procedures. The wide array of currently available MIGS modalities can be staggering to the glaucoma care provider, but an understanding of the landscape and the large classes of interventional strategies can allow for clinical decision making based on the specifics of the patient’s needs and the pathophysiology of their disease.
Draft genome sequence of fastidious pathogen Ceratobasidium theobromae, which causes vascular-streak dieback in Theobroma cacao
Authors: Ali Shahin S. , Asman Asman , Shao Jonathan , Firmansyah Amanda P. , Susilo Agung W. , Rosmana Ade , McMahon Peter , Junaid Muhammad , Guest David , Kheng Tee Yei , Meinhardt Lyndel W. , Bailey Bryan A. 
Published: September 2019

Abstract

Background
Ceratobasidium theobromae, a member of the Ceratobasidiaceae family, is the causal agent of vascular-streak dieback (VSD) of cacao, a major threat to the chocolate industry in the South-East Asia. The fastidious pathogen is very hard to isolate and maintain in pure culture, which is a major bottleneck in the study of its genetic diversity and genome.

Result
This study describes for the first time, a 33.90 Mbp de novo assembled genome of a putative C. theobromae isolate from cacao. Ab initio gene prediction identified 9264 protein-coding genes, of which 800 are unique to C. theobromae when compared to Rhizoctonia spp., a closely related group. Transcriptome analysis using RNA isolated from 4 independent VSD symptomatic cacao stems identified 3550 transcriptionally active genes when compared to the assembled C. theobromae genome while transcripts for only 4 C. theobromae genes were detected in 2 asymptomatic stems. De novo assembly of the non-cacao associated reads from the VSD symptomatic stems uniformly produced genes with high identity to predicted genes in the C. theobromae genome as compared to Rhizoctonia spp. or genes found in Genbank. Further analysis of the predicted C. theobromae transcriptome was carried out identifying CAZy gene classes, KEGG-pathway associated genes, and 138 putative effector proteins.

Conclusion
These findings put forth, for the first time, a predicted genome for the fastidious basidiomycete C. theobromae causing VSD on cacao providing a model for testing and comparison in the future. The C. theobromae genome predicts a pathogenesis model involving secreted effector proteins to suppress plant defense mechanisms and plant cell wall degrading enzymes.
Patients’ appreciation of pre-implant augmentation of the severely resorbed maxilla with calvarial or anterior iliac crest bone:a randomized controlled trial
Authors: Wortmann Dagmar E. , Boven Carina G. , Schortinghuis Jurjen , Vissink Arjan , Raghoebar Gerry M. 
Published: September 2019

Abstract

Background
Little is known about the impact of bone graft harvesting for pre-implant augmentation of the maxilla from a patient’s perspective. To assess patient-reported outcome measures (PROMs) related to augmentation of the extremely resorbed edentulous maxilla with calvarial or anterior iliac crest bone.

Materials and methods
For this randomised controlled trial, 20 consecutive edentulous patients needing extensive pre-implant surgery of the maxilla were randomly assigned to either calvarial (n = 10) or anterior iliac crest (n = 10) bone harvesting. Patient reports on procedure-related satisfaction, questionnaires on oral functionality (denture satisfaction, chewing ability) and oral health-related quality of life (OHIP-49NL) and subjective donor site-related outcomes (e.g. of post-operative pain, scar formation, physical mobility) were assessed.

Results
Irrespective of the harvesting site, patients were generally satisfied (median VAS score 93 (86–99) mm, p = 0.400) with the procedure and its final results. Post-operative pain was mild (median 40 (20–40) mm) and decreased to no pain (4 (0–16) mm) within 14 days. Early post-operative pain was significantly higher following anterior iliac crest harvesting (p < 0.00). Impact on physical mobility, daily functioning and satisfaction with the scar formation were similar in both groups.

Conclusions
The assessed PROMs confirmed that bone graft harvesting from the calvarium or anterior iliac crest is an appropriate procedure, reflected by high levels of satisfaction, minor long-term sequela and improvement of perceived oral health. For clinical decision-making, decisions can be based on individual features and preferences.

Trial registration
NTR, NTR3968, registered 1 July 2013.
Prevalence of focal incidental breast uptake on FDG-PET/CT and risk of malignancy: a systematic review and meta-analysis
Authors: Aarstad Else Marie , Nordhaug Petter , Naghavi-Behzad Mohammad , Larsen Lisbet Brønsro , Gerke Oke , Hildebrandt Malene Grubbe 
Published: September 2019

AbstractBackgroundFDG-PET/CT is increasingly used for oncologic and inflammatory diseases. Focal incidental FDG uptake occurs rarely in breast tissue but has often significant consequences. This study aimed to systematically review literature regarding focal incidental breast uptake (FIBU) on FDG-PET/CT in order to yield an update on the prevalence and risk of malignancy for FIBU.MethodsA systematic search for relevant articles published between 2012 and 2018 was performed through MEDLINE, Embase, and Cochrane databases. Studies addressing the detection of FIBU in patients without a previous history of breast malignancy were included. The QUADAS-2 was used for quality assessment, and eligible data were pooled using a fixed-effects model.I2was calculated for the heterogeneity between studies.ResultsEight studies containing 180,002 scans were included in the systematic review. The median prevalence of FIBU for both genders was 0.52% (range 0.18–22.5%). Prevalence for women was mentioned separately in five studies and varied from 0.51 to 23.5%. One study reporting a high prevalence was based on patients being staged for known malignancy, and the word “breast” was used in the search, which may have caused selection bias. Data from four studies were eligible for meta-analysis. A high degree of heterogeneity was observed for prevalence data (I2of 97.5%), while moderate heterogeneity was observed for data on malignancy risk assessment (I2of 62.8%). The pooled prevalence of FIBU in women was 0.61% (range 0.56–0.66%), and the pooled prevalence of malignancy of FIBUs was 38.7% (range 34.4–43.0%). The most commonly detected malignancy was invasive ductal carcinoma.ConclusionFIBU occurs rarely on FDG-PET/CT for female patients but yields a high risk of malignancy according to the results of published papers. Therefore, it should be considered relevant to further elucidate patients with incidentally detected FDG uptake in breast in clinical practice.