bluuebunny/crossref_metadata_2025 huggingface dataset:
A novel insight into nitrogen and auxin signaling in lateral root formation in tea plant [Camellia sinensis (L.) O. Kuntze]
Authors: Author) Shunkai Hu(Former Corresponding , Zhang Mi , Yang Yiqing , Xuan Wei , Zou Zhongwei , Arkorful Emmanuel , Chen Yi , Ma Qingping , Jeyaraj Anburaj , Chen Xuan , Author) Xinghui Li(New Corresponding
Published: January 2020

Background: Tea plant (Camellia sinensis) is one of the most popular non-alcoholic beverage worldwide. Lateral roots (LRs) of tea plant are the main organ used for tea plant to absorb soil moisture and nutrients. Lateral roots formation and development are tightly regulated by the nitrogen and auxin signaling pathway. In order to understand the function of auxin and nitrogen signaling in LRs formation and development, transcriptome analysis was applied to investigate the differentially expressed genes involved in lateral roots of tea plants treated with indole-3-butyric acid (IBA), N-1-naphthylphthalamic acid (NPA), low and high nitrogen concentration. Results: A total of 296 common differentially expressed genes were mainly identified and annotated to four signaling pathways, such as nitrogen metabolism, plant hormone signal transduction, Glutathione metabolism and transcription factors. RNA-sequencing results revealed that majority of differentially expressed genes play important roles in nitrogen metabolism and hormonal signal transduction. Low nitrogen condition induced the biosynthesis of auxin and accumulation of transcripts, thereby regulating lateral roots formation. Furthermore, metabolism of cytokinin and ethylene biosynthesis were also involved in lateral roots development. Transcription factors like MYB genes also contributed to the lateral roots formation of tea plants through secondary cell wall biosynthesis. Reversed phase ultra performance liquid chromatography (RP-UPLC) results showed that the auxin concentration in lateral roots was increased, while the nitrogen level decreased. Thus, tea plant lateral roots formation could be induced by low nitrogen concentration via auxin biosynthesis and accumulation. Conclusion: This study provides new insights into the mechanisms associated with nitrogen and auxin signaling pathways to regulate LRs formation and arises new clues for the efficient utilization of nitrogen in tea plant at the genetic level.
Transcriptome Ortholog Alignment Sequence Tools (TOAST) for Phylogenomic Dataset Assembly
Authors: dornburg alex , Wcisel Dustin J. , Howard J. Thomas , Yoder Jeffrey A.
Published: January 2020

Background: Advances in next-generation sequencing technologies have reduced the cost of whole transcriptome analyses, allowing characterization of non-model species at unprecedented levels. The rapid pace of transcriptomic sequencing has driven the public accumulation of a wealth of data for phylogenomic analyses, however lack of tools aimed towards phylogeneticists to efficiently identify orthologous sequences currently hinders effective harnessing of this resource.Results: We introduce TOAST, an open source R software package that can utilize the ortholog searches based on the software Benchmarking Universal Single-Copy Orthologs (BUSCO) to assemble multiple sequence alignments of orthologous loci from transcriptomes for any group of organisms. By streamlining search, query, and alignment, TOAST automates the generation of locus and concatenated alignments, and also presents a series of outputs from which users can not only explore missing data patterns across their alignments, but also reassemble alignments based on user-defined acceptable missing data levels for a given research question.Conclusions: TOAST provides a comprehensive set of tools for assembly of sequence alignments of orthologs for comparative transcriptomic and phylogenomic studies. This software empowers easy assembly of public and novel sequences for any target database of candidate orthologs, and fills a critically needed niche for tools that enable quantification and testing of the impact of missing data. As open-source software, TOAST is fully customizable for integration into existing or novel custom informatic pipelines for phylogenomic inference. Software, a detailed manual, and example data files are available through github carolinafishes.github.io
Indole -3-acetic acid improves drought tolerance of white clover associated with activating auxin-related genes, abscisic acid and jasmonic acid-induced stress responsive transcription factors, and inhibiting senescence genes
Authors: Zhang Youzhi , Li Yaping , Hassan Muhammad Jawad , Li Zhou , Peng Yan
Published: January 2020

Auxin plays an important role in regulating plant development. To idenfity what effects IAA has in white clover under drought stress and how IAA regulates white clover response to drought. Relative water content, chlorophyll content, six phytohormones content, expression of gene-related to IAA signal perception and synthesis, transcription factor genes related to drought-resistance and senescence genes were investigated in white clover pretreated with 1µM exogenous IAA or 100µM L-AOPP (inhibitor of IAA synthesis) under 15% polyethylene glycol-6000 (PEG-6000). Compared to control, drought stress significantly diminished stem dry weight (g/10 plant), relative water content (RWC, %) and total chlorophyll content (Chl, mg/g). Exogenous IAA significantly increased RWC and Chl, however, L-AOPP decreased stem dry weight, RWC and Chl compared with direct drought treatment. Besides that, compared with direct drought set, exogenous IAA significantly improved ABA content and JA content, up-regulated expression levels of some auxin-responsive genes ( GH3.1 , GH3.9 , IAA8 ) , transcription factor genes ( bZIP11 , DREB2 , MYB14 , MYB48 , WRKY2 , WRKY56 , WRKY108715 ) related to drought-resistance and drought resistance gene ( RD22 ). Meanwhile, exogenous IAA down-regulated expression levels of several auxin-responsive genes ( GH3.3 , GH3.6 , IAA27 ) and leaf senescence genes ( SAG101 and SAG102 ). Contrarily, L-AOPP significantly reduced ABA, GA3 and JA content, down-regulated expression levels of GH3.1 , GH3.9 , IAA8 , bZIP11 , DREB2 , MYB14 , MYB48 , WRKY2 , WRKY56 , WRKY108715 , ERD and RD22 , and up-regulated expression levels of SAG101 and SAG102 . Collectively, these data suggested a positive role of exogenous IAA in alleviating drought damage through many involved physiological processes in white clover.
Influence of pupil dilation on the Barrett Universal II (new generation), Haigis (4th generation), and SRK/T (3rd generation) intraocular lens calculation formulas: a retrospective study
Authors: Teshigawara Takeshi , Meguro Akira , Mizuki Nobuhisa
Published: January 2020

Background: We investigated the effect of pupil dilation on predicted postoperative refraction (PPR) and recommended intraocular lens (IOL) power calculated using three different generations of IOL power calculation formulas: Barrett Universal II (Barrett) (new generation), Haigis (4th generation), and SRK/T (3rd generation).
Methods: This retrospective study included 150 eyes. All variables were measured and calculated using a ZEISS IOL Master 700. The following variables were measured before and after dilation: anterior chamber depth (ACD), lens thickness (LT), white-to-white (WTW). PPR and recommended IOL power were calculated by Barrett, Haigis, and SRK/T IOL calculation formulas. The change in each variable before and after dilation, and correlations between all changes were analyzed using the Wilcoxon signed-rank test and the Spearman’s rank-order correlation test, respectively. The influence of pupil dilation on recommended IOL power calculated by each formula was also analyzed.
Results: The mean absolute change (MAC) in PPR before and after dilation was highest in Barrett, followed by Haigis and SRK/T. Significant differences were found among each MACs (P < 0.0001). Significant changes were observed before and after dilation in ACD and LT (P < 0.0001) but not in WTW. In Barrett and Haigis, there was a significant positive correlation between change in PPR and change in ACD (P < 0.0001) and a negative correlation between change in PPR and change in LT (P < 0.0001). Correlations were strongest in Barret followed by Haigis, especially in LT. Change in PPR in Barrett also demonstrated a significant positive correlation with change in WTW (P = 0.022). The recommended IOL power using Barrett and Haigis changed before and after dilation in 23.3% and 19.3% cases; SRK/T showed no change.
Conclusions: In PPR and recommended IOL power, pupil dilation influenced Barrett most strongly, followed by Haigis and SRK/T. Given the stronger correlation between the change in PPR in Barrett and the change in ACD, LT, and WTW, the change of ACD, LT, and WTW is more important to the influence of dilation on Barrett. The influence of dilation on each formula and variable, including ACD, LT, and WTW, is key to improving IOL calculation.
Fatty acid biosynthesis and transcriptional regulation of Stearoyl-CoA Desaturase 1 (SCD1) in Buffalo milk
Authors: Li Zhipeng , Lu Suyu , Cui Kuiqing , Shafique Laiba , Rehman Saif ur , Luo Chan , Wang Zhiqiang , Ruan Jue , Qian Qian , Liu Qingyou
Published: January 2020

Background: Buffalo milk is considered as a highly nutritious food owing to its higher contents of fatty acids (FA)and rich nutrient profile. Higher fat contents of buffalo milk make it suitable for processing to develop various healthy and nutritious products. Moreover, buffalo milk contains more unsaturated FAs (UFA) such as oleic and linolenic acid, which are important from the human health point of view owing to their desirable physiological effects. However, inadequate information is available about the chemical composition and mechanism of FA synthesis in buffalo milk. In this study, we hypothesized that expression of SCD 1 gene could alter the biosynthesis of FA in epithelial cells of mammary gland and subsequently affect the FA contents in b uffalo milk. We investigated the transcriptional and biological role of Stearoyl-CoA Desaturase 1 ( SCD 1) in the buffalo mammary epithelial cells (BMECs) during FA and triacylglycerol (TAG) synthesis. Results : Results revealed that unsaturated fatty acid contents were much higher in concentration in buffalo milk as compared to Holstein cow. Significant increase in the expression level of FAS , ACACA , SREBP 1, PPARG , GPAT , and AGPAT genes was observed in response to altered expression of SCD 1 in buffalo milk . Moreover, change in SCD1 gene in BMECs also mediated the expression of genes related to FA biosynthesis subsequently leading to alter the FA composition. Overexpression of SCD1 significantly increased the expression of genes associated with FA and TAG synthesis leading to enhance FA and unsaturated FA contents in BMECs. However, down-regulation of SCD1 exhibited opposite consequences. Conclusion: Our study provides mechanistic insights on transcriptional regulation of SCD 1 to alter FA and TAG synthesis through directly or indirectly mediating biosynthesis and metabolic pathways in BMECs. We provide preliminary findings regarding engineering of FA contents in buffalo milk through SCD 1 signaling.
Effects of Lactobacillus plantarum on intestinal integrity and immune responses of egg-laying chickens infected with Clostridium perfringens under the free-range or the specific pathogen free environment
Authors: Xu Tianyue , Chen Yan , Yu Longfei , Wang Jun , Huang Mingxing , Zhu Nianhua
Published: January 2020

Background Necrotic enteritis, which is caused by Clostridium perfringens, has resulted in more than $2 billion losses in the poultry industry every year. Due to the ban of antibiotics in feed industry, alternatives like environment improvement and probiotics have been found to be effective as well. In our study, we aim to explore the protective effect of Lactobacillus plantarum supplementation on CP infected chickens in two environments. Results The results showed that the Clostridium perfringens administration led to visible and histomorphological gut lesions. In the specific pathogen free or free-range system environment, dietary supplementation with LP obvious increased the ratio of intestinal villus height to crypt depth and the expression of MUC2 mRNA in ileum mucosa, then reduced the mRNA expression level of TNF-α gene in the ileum mucosa. LP treatment significantly reduced the contents of total protein, total superoxide dismutase and glutamic oxaloacetic transaminase in serum of the chickens. Conclusions The specific pathogen free environment contributed to the recovery of pre-inflammation of the chickens, and free-range system environment contributed to the repair of damage in the later stages of chicken inflammation. Supplementation of LP in FRS environment was more conducive to the recovery of CP infected in chickens.
Complete genome sequencing and comparative genomic analyses of Bacillus sp. S3, a novel hyper Sb(III)-oxidizing bacterium
Authors: Li Jiaokun , Gu Tianyuan , Zeng Weimin , Yu Runlan , Liu Yuandong , Wu Xueling , Shen Li , Qiu Guanzhou , Li Liang Zhi
Published: January 2020

Background: Antimonite [Sb(III)]-oxidizing bacterium has great potential in the environmental bioremediation of Sb-polluted sites. Bacillus sp. S3 that was previously isolated from antimony-contaminated soil displayed high Sb(III) resistance and Sb(III) oxidation efficiency. However, the genomic information and evolutionary feature of Bacillus sp. S3 are very scarce. Results: Here, we identified a 5,579,638 bp chromosome with 40.30% GC content and a 241,339 bp plasmid with 36.74% GC content in the complete genome of Bacillus sp. S3. Genomic annotation showed that Bacillus sp. S3 contained a key aioB gene potentially encoding As(III)/Sb(III) oxidase, which was not shared with other Bacillus strains. Further, a series of genes associated with Sb(III) and other heavy metal(loid)s were also ascertained in Bacillus sp. S3, reflecting its adaptive advantage for growth in the harsh eco-environment. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), we found that Bacillus sp. S3 was a novel species within the Bacillus genus. The majority of mobile genetic elements (MGEs) mainly distributed on chromosomes within the Bacillus genus. Pan-genome analysis showed that the 45 genomes contained 554 core genes and many unique genes were dissected in analyzed genomes. Whole genomic alignment showed that Bacillus genus underwent frequently large-scale evolutionary events. In addition, the origin and evolution analysis of Sb(III)-resistance genes revealed that evolutionary relationships and horizontal gene transfer (HGT) events among the Bacillus genus. The assessment of functionality of heavy metal(loid)s resistance genes emphasized its indispensable roles in the harsh eco-environment of Bacillus genus. The real-time Quantitative PCR (RT-qPCR) results of Sb(III)-related genes indicated that the Sb(III) resistance was constantly increased under the Sb(III) stress. Conclusions: The results in this study shed light on the molecular mechanisms of Bacillus sp. S3 coping with Sb(III), extended our understanding on the evolutionary relationship between Bacillus sp. S3 and other closely related species, and further enriched the Sb(III) resistance genetic data sources.
Classification of Andrographis paniculata extracts by solvent extraction using HPLC fingerprint and chemometric analysis
Authors: Rafi Mohamad , Devi Anggun Fenika , Syafitri Utami Dyah , Heryanto Rudi , Suparto Irma Herawati , Amran Muhammad Bachri , Rohman Abdul , Prajogo Bambang , Lim Lee Wah
Published: January 2020

Objective: Andrographis paniculata, widely used as an antidiabetic in Indonesian traditional medicines (jamu), contains chemical compounds whose concentration is related to its therapeutic effects. The concentration of solvents used for extraction will also affect the number of compounds extracted. Therefore, a quality control method is needed to ensure consistency in quantifying these compounds in A. paniculata to improve its therapeutic application. High-performance liquid chromatography fingerprint analysis combined with chemometrics was used to evaluate extracts from different solvent extraction treatments. The content of andrographolide, the main bioactive compound in A. paniculata, and the level of α-glucosidase inhibition activity, an indicator of its antidiabetic activity, were also determined.
Results: Fingerprint chromatograms of A. paniculata extracts from different treatments exhibited a similar pattern with several peaks in common, only differing in area and intensity value. The A. paniculata extracts were classified using HPLC fingerprint and principal component analysis to allow grouping according to their respective solvent extraction treatments. The highest andrographolide content and α-glucosidase inhibition activity occurred in the 50% ethanol extract and the lowest in the water extract. HPLC fingerprint analysis could be used for identifying A. paniculata extracts based on solvent extraction, thus improving quality control for their therapeutic application.
Deep learning improves the ability of sgRNA off-target propensity prediction
Authors: Liu Qiaoyue , Cheng Xiang , Liu Gan , Li Bohao , Liu Xiuqin
Published: January 2020

Background CRISPR/Cas9 system, as the third-generation genome editing technology, has been widely applied in target gene repair and gene expression regulation. Selection of appropriate sgRNA can improve the on-target knockout efficacy of CRISPR/Cas9 system with high sensitivity and specificity. However, when CRISPR/Cas9 system is operating, unexpected cleavage may occur at some sites, known as off-target. Presently, a number of prediction methods have been developed to predict the off-target propensity of sgRNA at specific DNA fragment. Most of them use artificial feature extraction operations and machine learning techniques to obtain off-target scores. With the rapid expansion of off-target data and the rapid development of deep learning theory, the existing prediction methods can no longer satisfy the prediction accuracy at the clinical level. Results Here, we propose a prediction method named CnnCrispr to predict the off-target propensity of sgRNA at specific DNA fragments. CnnCrispr automatically trains the sequence features of sgRNA-DNA pairs with GloVe model, and embeds the trained word vector matrix into the deep learning model including biLSTM and CNN with five hidden layers. We conducted performance verification on the data set provided by DeepCrispr, and found that the auROC and auPRC in the "leave-one-sgRNA-out" cross validation could reach 0.957 and 0.429 respectively (the pearson value and spearman value could reach 0.495 and 0.151 respectively under the same settings). Conclusion Our results show that CnnCrispr has better classification and regression performance than the existing states-of-art models. The code of CnnCrispr can be freely downloaded from https://github.com/LQYoLH/CnnCrispr.
Development and outcomes of a comprehensive multidisciplinary incidental lung nodule and lung cancer screening program
Authors: LeMense Gregory , Waller Ernest A. , Campbell Cheryl , Bowen Tyler
Published: January 2020

Background: Appropriate management of lung nodules detected incidentally or through lung cancer screening can increase the rate of early-stage diagnoses and potentially improve treatment outcomes. However, the implementation and management of comprehensive lung nodule programs is challenging. Methods: This single-center, retrospective report describes the development and outcomes of a comprehensive lung nodule program at a community practice in Tennessee. Computed tomography (CT) scans potentially revealing incidental lung nodules were identified by a computerized search. Incidental or screening-identified lung nodules that were enlarging or not seen in prior scans were entered into a nodule database and guideline-based review determined whether to conduct a diagnostic intervention or radiologic follow-up. Referral rates, diagnosis methods, stage distribution, treatment modalities, and days to treatment are reported. Results: The number of patients with lung nodules referred to the program increased over 2 years, from 665 patients in Year 1 to 745 patients in Year 2. Most nodules were incidental (62%-65%). Nodules identified with symptoms (15.2% in Year 1) or through screening (12.6% in Year 1) were less common. In Year 1, 27% (182/665) of nodules required a diagnostic intervention and 18% (121/665) were malignant. Most diagnostic interventions were image-guided bronchoscopy (88%) or percutaneous biopsy (9%). The proportion of Stage I-II cancer diagnoses increased from 23% prior to program implementation to 36% in Year 1 and 38% in Year 2. In screening cases, 71% of patients completed follow-up scans within 18 months. Only 2% of Year 1 patients under watchful waiting required a diagnostic intervention, of which 1% received a cancer diagnosis. Conclusions: The current study reports outcomes over the first two years of a lung cancer screening and incidental nodule program. The results show that the program was successful, given the appropriate level of data management and oversight. Comprehensive lung nodule programs have the potential to benefit the patient, physician, and hospital system.
Maternal pre-pregnancy body mass index, gestational weight gain and breastfeeding outcomes
Authors: Martin Hayley , Thevenet-Morrison Kelly , Dozier Ann
Published: January 2020

Background: It is well established that mothers with above-normal pre-pregnancy BMI are at increased risk of breastfeeding cessation; however, the impact of pregnancy weight-gain (PWG) is less well-defined. Excess PWG may alter the hormonal preparation of breast tissue for lactation, increase the risk of complications that negatively impact breastfeeding (e.g. Cesarean-section, gestational diabetes), and may make effective latch more difficult to achieve. Methods: Our objective was to determine the impact of PWG and pre-pregnancy BMI on the risk of breastfeeding cessation utilizing the Institute of Medicine’s 2009 recommendations. Cox proportional hazards models were utilized to estimate the risk of cessation of exclusive breastfeeding, and cessation of any breastfeeding among women who initiated exclusive and any breastfeeding, respectively, in a cross sectional sample of survey respondents from a New York county (N=1207). PWG category was interacted with pre-pregnancy BMI (3 levels of pre-pregnancy BMI, 3 levels of PWG). Confounders of the relationship of interest were evaluated using directed acyclic graphs and bivariate analyses; variables not on the proposed causal pathway and associated with the exposure and outcome were included in multivariate models. Results: After adjustment, women of normal and obese pre-pregnancy BMI with greater-than-recommended PWG had 1.39 (1.03-1.86) and 1.48 (1.06-2.07) times the risk of any breastfeeding cessation within the first 3 months postpartum compared to women with normal pre-pregnancy BMI who gained within PWG recommendations. Overweight women with greater-than-recommended PWG were at increased risk of cessation, although not significantly (aHR[95% CI]: 1.29 [0.95 – 1.75]). No significant relationship was observed for exclusive breastfeeding cessation. Conclusions: Pre-pregnancy BMI and PWG may be modifiable risk factors for early breastfeeding cessation. Understanding the mechanism behind this risk should be ascertained by additional studies aimed at understanding the physiological, social, logistical (positioning) and other issues that may lead to early breastfeeding cessation.
Metaphase spread of mouse oocytes
Authors: SANKAR ADITYA
Published: January 2020

this protocol briefly described the procedure of performing metaphase spreads on single mouse MII (metaphase-II) oocytes. This will allow the user to count the chromosomes as well as perform additional immunofluorescence based stains for protein localization on fixed samples. the assay is however prone to false positive whole chromosome aneuploidies due to the nature of dropping the oocytes onto the etched glass slides. Hence, some skill development by repetition is required to ensure consistent outcomes. The whole procedure from obtaining oocytes to imaging happens over two days.
Effects of Ultrasound-Guided Paravertebral Block on MMP-9 and Postoperative Pain in Patients Undergoing VATS Lobectomy: A Randomized, Controlled Clinical Trial
Authors: Chu Haichen , Dong He , Wang Yongjie , Niu Zejun
Published: January 2020

Background: Local anesthesia can reduce the response to surgical stress and decrease the consumption of opioids, which may reduce immunosuppression and potentially delay postoperative tumor recurrence. We compared paravertebral block(PVB) combined with general anesthesia(GA) and general anesthesia regarding their effects on matrix metalloproteinase-9 (MMP-9) and postoperative pain after video-assisted thoracoscopic surgery(VATS) lobectomy.
Methods: 54 patients undergoing elective VATS lobectomy at a single tertiary care, teaching hospital located in Qingdao between May 2 2018 and Sep 28 2018 were randomised by computer to either paravertebral block combined with general anesthesia or general anesthesia. The primary outcome was pain scores during postoperative 48h. The secondary outcome were plasma concentrations of MMP-9, complications, and duration of postoperative hospital stay.
Results: 75 were enrolled to the study, of whom 21 were excluded before surgery. We analyzed lobectomy patients undergoing paravertebral block combined with general anesthesia (n=25) or general anesthesia (n=24). Both groups were similar regarding baseline characteristics. Pain scores were lower at 4h and 24h in PVB/GA group, compared with GA group (2.53±0.83 vs 3.4±0.91; 2.2±0.94 vs 3.0±0.93, respectively, P <0.05). There were no difference at 1h and 48h between groups. Patients in the PVB/GA group showed a greater decrease in plasma MMP-9 level at T1 and T2 after VATS lobectomy ( P <0.05). Postoperative complications and length of stay did not differ by anesthetic technique.
Conclusions: The paravertebral block/general anesthesia can provide statistically better pain relief and attenuate MMP-9 response to surgery and after VATS lobectomy. This technique may be beneficial for patients to recover rapidly after lung surgery and reduce postoperative tumor recurrence.
Antibiotic treatment regimens for bone infection after debridement: a study of 902 cases
Authors: Author) Xiaohua Wang(Former Corresponding , Fang Li , Chen Yueqi , Wang Shulin , Ma Huan , Zhao Hongwen , Author) Zhao Xie(New Corresponding
Published: January 2020

Purpose: Our aim was to investigate the clinical efficacy and complications of antibiotics treatment duration for the patients of bone infection. Methods: We retrospectively analyzed the patients with bone infection admitted to our hospital between March 2013 and October 2018. The surgical debridement was performed and the patients were divided into three groups: IV group (Intravenous antibiotics for 2 weeks); Oral group (Intravenous antibiotics for 2 weeks followed by oral antibiotics for 4 weeks); Rifampicin group (Intravenous antibiotics for 2 weeks followed by oral antibiotics plus rifampicin for 4 weeks). The infection control rate and complications were compared. Results ： A total of 902 patients were enrolled, the infection sites included 509 tibias, 228 femurs, 32 humeri, 23 radii and ulnae, 40 calcanei, 23 multiple-site infections and the other sites 47 cases. After at least 6 months of follow-up, 148 (16.4%) patients had recurrence of infection. The recurrence rate of IV group was 17.9%, which was no significant higher than that of Oral group (10.1%) or Rifampicin group (10.5%). The abnormal rate of Glutamic-pyruvic transaminase(ALT) in IV group was 15.1%, which was lower than that of Oral group (18.0%) and Rifampicin group (27.4%), P=0.026. The positive rates of proteinuria in the three groups were 3.2%, 4.5%, and 9.3%, respectively, P=0.020. Conclusion: After debridement of bone infection, the additional oral antibiotic treatment may increase the damage of liver and kidney, and can not significantly reduce the infection recurrence rate. Therefore, it is recommended to adopt short-term systemic antibiotic treatment after debridement.
Exposure to Baby-Friendly Hospital Practices and Mothers’ Achievement of their Planned Duration of Breastfeeding.
Authors: Lok Kris Y.W. , Chow Charlotte L.Y. , Fan Heidi S.L. , Chan Vincci H.S. , Tarrant Marie
Published: January 2020

Background: Both breastfeeding intentions and exposure to baby-friendly hospital practices have been associated with a longer duration of breastfeeding. This study aims to examine the effect of exposure to baby-friendly hospital practices on mothers’ achievement of their planned duration of breastfeeding.
Methods: A total of 1011 mother-newborn pairs from the postnatal units of four public hospitals in Hong Kong were recruited. Sociodemographic data and breastfeeding intention data were collected via self-report questionnaires during the postnatal hospitalization and exposure to Baby-Friendly hospital practices were assessed through hospital records and maternal self-report. Breastfeeding status after hospital discharge was assessed through telephone follow-up for up to 12 months postnatal, or until participants were no longer breastfeeding.
Results: Only 55% (n=552) of study participants achieved their intended duration of breastfeeding. Participants with higher socioeconomic status, previous breastfeeding experience, and those who had lived in Hong Kong for less than 5 years, were more likely to achieve their planned duration of breastfeeding. Among baby-friendly hospital practices, feeding only breast milk during the hospitalization and providing information about breastfeeding support on discharge were associated with participants’ achieving their individual breastfeeding intentions. After adjustment, when compared with women who experienced one baby-friendly practice, participants who experienced six baby-friendly hospital practices were significantly more likely to achieve their planned duration of breastfeeding (adjusted odds ratio=8.45, 95% confidence interval 3.03 – 23.6).
Conclusions : Nearly half of participants did not achieve their planned breastfeeding duration. Exposure to baby-friendly hospital practices, especially in-hospital exclusive breastfeeding and providing breastfeeding support information upon hospital discharge may help more mothers to achieve their individual breastfeeding goals.
Immunofluorescence of mouse zygotes and preimplantation embryos
Authors: SANKAR ADITYA
Published: January 2020

This protocol is based on previously published work and described the procedure of immunofluorescence of mouse zygotes and preimplantation embryos. The procedure takes 2 days from recovery of gametes/embryos from the mouse to imaging of samples in a confocal microscope. The procedure uses bent capillaries and a mouth pipette with a filter, allowing for movement of the samples between solutions following necessary incubation times. This simple procedure works quite efficiently and is an easy skill to master with the availability of the necessary tools.
Simulation-based low-dose, high-frequency plus mobile mentoring versus traditional group-based trainings among health workers in Ebonyi and Kogi States, Nigeria; a cluster randomized controlled trial
Authors: UGWA EMMANUEL , Kabue Mark , Otolorin Emmanuel , Yenokyan Gayane , Oniyire Adetiloye , Orji Bright , Okoli Ugo , Enne Joseph , Alobo Gabriel , Olisaekee Gladys , Oluwatobi Adebayo , Oduenyi Chioma , Aledare Adekunle , Onwe Boniface , Ishola Gbenga
Published: January 2020

Background: There are few studies from low- and middle-income countries on learning outcomes among health workers trained on day of birth care using onsite, simulation-based, low-dose, high frequency (LDHF) training plus mobile (m) mentoring. The aim of this study was to compare their knowledge and skills competencies with those of health workers trained using the traditional offsite, group-based training (TRAD) approach in Kogi and Ebonyi states, Nigeria, over a 12-month period.

Methods: We conducted a prospective cluster randomized controlled trial, enrolling 299 health workers in 60 health facilities in Kogi and Ebonyi states, randomized to either LDHF/m-mentoring (intervention, n=30 facilities) or traditional group-based training (TRAD, n=30 facilities) control arm. Health workers in both arms received basic emergency obstetric and newborn care training with simulated practice using anatomic models and role-plays. The control arm participants were trained offsite while the intervention arm were trained onsite where they work. Mentorship was done through telephone calls and reminder text messages. The multiple choice questions and objective structured clinical examinations mean scores were compared; p-value <0.05 was considered statistically significant. Qualitative data were collected and analyzed along themes of interest.

Results: The mean knowledge scores between the two arms at months 3 and 12 post-training were equally high; no statistically significant differences. Both arms showed improvements in composite scores for assessed BEmONC clinical skills from around 30% at baseline to 75% and above at endline (p <0.05). Overall, the observed improvement and retention of skills was higher in intervention arm compared to the control arm at 12 months post-training, (p<0.05). Some LDHF/m-mentoring approach trainees reported that mentors’ support improved their acquisition and maintenance of knowledge and skills, which may have led to reductions in maternal and newborn deaths in their facilities.

Conclusion: The LDHF/m-mentoring intervention is more effective than TRAD approach in improving health workers’ skills acquisition and retention. Health care managers should have the option to select the LDHF/m-mentoring learning approach, depending on their country’s priorities or context, as it ensures health workers remain in their place of work during training events thus less disruption to service delivery.
IgG anti-hinge antibody against IgG4 F(ab’)2 generated by not matrix metalloproteinase-3 but pepsin is a useful diagnostic marker for rheumatoid arthritis, even seronegative rheumatoid arthritis.
Authors: Ota Toshiyuki , Ota Shun-ichiro , Uchino Ayumi , Nagano Shuji
Published: January 2020

Background The pepsin agglutinator, discovered over 50 years ago, has recently referred to be an anti-hinge antibody (AHA) because of main reacting with the IgG hinge epitope. AHA shows different reactivity for each hinge epitope generated by each protease that cleaves the hinge region at different sites. Moreover, AHA shows different reactivity against different hinge epitopes derived from each IgG subclass even when the same protease is used. Since production of matrix metalloproteinase-3 (MMP-3) is enhanced in rheumatoid arthritis (RA), the specific AHA might be increasingly produced. The purpose of this study is to determine whether AHA against IgG hinge epitopes produced by MMP-3 is specifically elevated in RA. Methods Serum IgG or IgA class of AHA against the IgG1- or IgG4 F(ab’) 2 generated by either matrix metalloproteinase 3 (MMP-3) or pepsin was measured by ELISA in 81 healthy controls (HC) and 111 patients with RA. Receiver operating characteristic (ROC) analysis was used for obtaining optimal cutoff values and cutoff values indicating high specificity (>95%) of the AHA. Targeted epitope of the AHA was investigated by inhibition ELISA. Results Seven AHAs were statistically higher in RA than HC, except IgG AHA against IgG1 F(ab’) 2 generated by proteolytic cleavage of MMP-3. The areas under the curve of ROC curve were 0.66-0.80, although the sensitivities at high specificity were low (5.4-24.3%). The cumulative number of positive AHA in each individual was statistically higher in RA than HC, suggesting the extreme extent of AHA repertoires in RA. Inhibition studies revealed that IgG AHA against IgG4 F(ab’) 2 generated by pepsin cross-reacted with IgG1 F(ab’) 2 generated by pepsin. Although development of IgA AHAs in RA seems to be remarkable and specific, multivariate logistic regression analysis identified IgG AHA against IgG4 F(ab’) 2 generated by pepsin as an independent variable for RA diagnosis, even in RA patients who were negative for both RF and ACPA [odds ratio 1.18 (95% confidence interval 1.06-1.32); P =0.003]. Conclusion In RA, we observed diversification and amplification of AHA repertoires and diagnostic utility of the specific AHA against IgG4 F(ab’) 2 generated by pepsin, but not MMP-3.
Bioinformatics approach for potential genes associated with osteoarthritis
Authors: Chai Yi , Mai Cong-Ying , Zhang Ming-Yue , Xu Dao-Ming , Tan Feng , Li Xing , Fan Qiaoling
Published: January 2020

Background: Osteoarthritis is the main cause of disability and pain. Due to limited understanding of the disease mechanism, it is generally difficult to diagnose early and eliminate sequelae. The aim of this study was to identify novel biomarkers for osteoarthritis (OA) using a bioinformatics approach.

Method: The gene expression dataset GSE82107 were obtained from the Gene Expression Omnibus (GEO) database. Matrix quality assessment was performed using corrplot packages and principal component analysis. The differentially expressed genes (DEGs) picked out using GEO2R tool. Enrichment analyses were performed using The Database for Annotation, Visualization and Integrated Discovery and Gene Set Enrichment Analysis (GSEA). Weighted correlation network analysis (WGCNA) was used to find gene modules highly associated with OA. Cytoscape with Molecular Complex Detection (MCODE) plug-in was utilized to analyze protein-protein interaction of these DEGs. Receiver operator characteristic curve analysis was used to evaluate the diagnostic effectiveness of genes.

Results: Samples with different conditions (HC and OA) are obviously distinguished, and the distance between biological replicates is relatively close. In total, 1676 DEGs were identified. Enrichment analysis showed that there were some gene sets related to OA pathology, such as chondrocyte development. The results of WGCNA analysis showed that 298 genes were most positive associated with OA. 10 common genes obtained were selected as candidate core genes. ROC results showed that 5 of these genes had the greatest diagnostic value.

Conclusion: This is the first study to identify biomarkers related to OA by combining multiple algorithms such as GSEA, WGCNA, MCODE and ROC. We suggest that GLG1, PAPSS2, CTSK, TIMP1 and SDC1 could serve as valuable biomarkers. Further studies are needed to examine the precise role and mechanism of these genes in OA.
The outcome for surgical fixation of distal radial fractures in patients with Idiopathic Parkinson’s Disease: a cohort study
Authors: Chou Te-Feng , Chang Chun Yao , Huang Chun-Ching , Chang Ming-Chau , Chen Wei-Ming , Huang Tung-Fu
Published: January 2020

Introduction Idiopathic Parkinson’s Disease (PD) is a progressive neurologic disorder causing postural instability and unsteady gait. These patients are at increased risk for fractures and have inferior outcomes after treatment. Several studies have evaluated the incidence and outcome of PD patients after hip fractures. However, there are limited studies assessing the outcome of upper extremity fractures in these patients. In this study, we evaluated the outcome of PD patients that received surgical intervention for distal radial fractures (DRF). We hypothesize that these patients have an inferior outcome after surgery in comparison with non-PD patients. Methods Between May 2005 through May 2017, we retrospectively reviewed all of the patients with DRF and subsequently underwent open reduction and internal fixation (ORIF) at a level 1 trauma center. All of the surgeries were performed by fellowship trained orthopedic surgeons. The inclusion criteria include patients with a definitive diagnosis of PD, non-pathological DRF and a minimum follow-up of 1 year. Each PD patient was matched for age and gender to 3 non-PD patients. The primary objective was to determine the failure rate after surgical fixation for DRF. The secondary outcomes include time to treatment failure, reoperation rate, readmission rate, length of hospital stay, and postoperative complications. Results A total of 88 patients were included in this study (23 PD, 65 non-PD patients). All underwent ORIF and received standard postoperative follow-ups. The overall treatment failure rate in PD was 39.1% vs. 4.6% in the non-PD group (p<0.001). The time to treatment failure were 9.11 ± 3.86 weeks and 14.67 ± 5.8 weeks for PD and non-PD, respectively (p=0.028). The length of hospital stay for PD was 5.3 ± 4.69 days compared with 3.78 ± 0.96 days for non-PD (p=0.007). There were 3 PD patients readmitted within 30 days after surgery, and 1 patient had pneumonia after the surgery. Conclusion This study revealed that patients with PD have a high treatment failure rate despite surgical intervention for DRF. PD patients had a longer hospital stay and had a shorter time to treatment failure. In treating PD patients complicated with DRF, the surgeon must take into consideration the complex disease course of PD and the associated comorbidities such as osteoporosis, frail status, unintentional tremor and frequent falls. Rehabilitation and disposition plans should be discussed in advance and longer hospital stays should be expected.
Evaluation of personal protection afforded by repellent-treated sandals against mosquito bites in south-eastern Tanzania.
Authors: Sangoro Peter Onyango , Gavana Tegemeo , Finda Marceline , Mponzi Winfrida , Hape Emmanuel , Limwagu Alex , Govella Nicodem J. , Chaki Prosper , Okumu Fredros O.
Published: January 2020

Background: The Indonesian government has put malaria as a priority disease that needs to be addressed. Lampung is one of the provinces with a high malaria incidence with Annual Paracite Incidence at 4.44 per 1000 population. The most cases occurred in Pesawaran Regency. There were 1.915 malaria cases in 2016. The highest positive case of malaria occurred in the Hanura Health Center with 1.738 cases, with the most cases being vivax malaria. The high case of malaria in the region is due to the favorable natural conditions as mosquito breeding places such as forests, lagoons and abandoned ponds. One of the biggest challenges in the treatment of malaria is the decline in the efficacy of even anti-malaria drug resistance due to low adherence in taking the drug. So this research is important to know the level of adherence to take medication in patients with vivax malaria in the work area of ​​the Hanura Health Center.Methods: This research was a descriptive analytic study with survey methods. Morisky Medication Adherence Scale (MMAS-8) questionnaire was used as the instrument. Eligible patients’who had undergone treatment with Artemisinin-based Combination Therapy and primaquine for 14 days were The subject of study. They were numbered 68 people in the working area of ​​Hanura Health Center.Results: The level of adherence to take medication in patients with vivax malaria in the working area of ​​Hanura Health Center is classified as low, namely a high compliance rate of 44.1% and a low compliance rate of 55.9%. The highest proportion of respondents with low levels of adherence were aged 25-45 years (55.3%), low education level (81.6%), working (57.9%), and having a history of malaria more than once (94, 7%).Conclusions: The level of adherence to take treatment in patients with vivax malaria in the working area of ​​Hanura Health Center is relatively low, with the highest proportion of adults, low education, work and have a history of malaria more than once.
International tuberculosis contact-tracing notifications in Germany: Analysis of national data from 2010-2018 and implications for efficiency
Authors: Glasauer Saskia , Kröger Stefan , Haas Walter , Perumal Nita
Published: January 2020

Background International contact-tracing (CT) following exposure during long-distance air travel is resource-intensive, whereas evidence for risk of tuberculosis (TB) transmission during international travel is weak. In this study, we systematically analyzed the information from international requests for CT received at the national level in Germany in order to evaluate the continued utility of the current approach and to identify areas for improvement. Methods An anonymized archive of international CT notifications received by the Robert Koch Institute between 2010 and 2018 was searched for key parameters for data collection. A total of 31 parameters, such as characteristics of TB patients and their identified contacts, were extracted from each CT notification and collated into a dataset. Descriptive data analysis and trend analyses were performed to identify key characteristics of CT notifications, patients, and contacts over the years. Results 192 CT notifications, each corresponding to a single TB index case were included in the study, increasing from 12 in 2010 to 41 in 2018. The majority of notifications (N=130, 67.7%) concerned international air travel, followed by private contact (N=39, 20.3%) and work exposure (N=16, 8.3%). 159 (82.8%) patients had sputum smear results available, of which 147 (92.5%) were positive. Of 119 (62.0%) patients with drug susceptibility testing results, most (N=92, 77.3%) had pan-sensitive TB, followed by 15 (12.6%) with multi-drug resistant TB. 115 (59.9%) patients had information on infectiousness, of whom 99 (86.1%) were considered infectious during the exposure period. 7 (5.3%) patients travelled on long-distance flights despite a prior diagnosis of active TB. Of the 771 contact persons, 34 (4.4%) could not be reached for CT measures due to lack of contact information. Conclusion The high variability in completeness of information contained within the international CT requests emphasizes the need for international standards for reporting of CT information. With the large proportion of TB patients reported to have travelled while being infectious in our study, we feel that raising awareness among patients and health professionals to detect TB early and prevent international long-distance travel during the infectious disease phase should be a cornerstone strategy to safeguard against possible transmission during international travel.
EEG alpha reactivity and cholinergic system integrity in Lewy body dementia and Alzheimer’s disease
Authors: Schumacher Julia , Thomas Alan J. , Peraza Luis R. , Firbank Michael , Cromarty Ruth , Hamilton Calum A. , Donaghy Paul C. , O’Brien John T. , Taylor John-Paul
Published: January 2020

Background Lewy body dementia (LBD), which includes dementia with Lewy bodies (DLB) and Parkinson’s disease dementia (PDD), is characterized by marked deficits within the cholinergic system which are more severe than in Alzheimer’s disease (AD) and are mainly caused by degeneration of the nucleus basalis of Meynert (NBM) whose widespread cholinergic projections provide the main source of cortical cholinergic innervation. EEG alpha reactivity, which refers to the reduction in alpha power over occipital electrodes upon opening the eyes, has been suggested as a potential marker of cholinergic system integrity. Methods Eyes-open and eyes-closed resting state EEG data were recorded from 41 LBD patients, 21 patients with AD, and 41 age-matched healthy controls. Alpha reactivity was calculated as the relative reduction in alpha power over occipital electrodes when opening the eyes. Structural MRI data were used to assess volumetric changes within the NBM using a probabilistic anatomical map. Results Alpha reactivity was reduced in AD and LBD patients compared to controls with a significantly greater reduction in LBD compared to AD. Reduced alpha reactivity was associated with smaller volumes of the NBM across all groups (ρ=0.42, p FDR =0.0001) and in the PDD group specifically (ρ=0.66, p FDR =0.01). Conclusions We demonstrate that LBD patients show an impairment in alpha reactivity upon opening the eyes which distinguishes this form of dementia from AD. Furthermore, our results suggest that reduced alpha reactivity might be related to a loss of cholinergic drive from the NBM, specifically in PDD.