bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metagenomic Next-generation Sequencing of Cerebrospinal Fluid for the Diagnosis of Central Nervous System infections in HIV-infected patients
Authors: Zheng Nai qing , Guo Pengle , Chen Xiejie , He Haolan , Li Yueping , Li Linghua , Cai Weiping 
Published: December 2019

Abstract
Background HIV-infected patients have extremely low immunity and various opportunistic infections. Early diagnosis and treatment of these pathogens is critical for patients with HIV infection, especially those with central nervous system (CNS) infections. Metagenomic next generation sequencing (mNGS) has the advantage of identifying a broad range of pathogens and was suggested as a promising tool in the clinical diagnosis for infectious diseases. The clinical application of mNGS in the diagnosis of CNS infections in patients infected with HIV remains inadequately characterized.Methods We retrospectively analyzed data from 22 patients with suspected central nervous system infections who underwent both mNGS and conventional methods including culture, PCR, X-pert/RIF and antigen testing to explored the utility of mNGS in clinical diagnostic microbiology of CNS infections in HIV-infected patients.Results A total of 22 patients participated in the study between June 2018 and May 2019. The consistency of positive percentage of mNGS compared to clinical diagnosis was significantly higher than that of conventional methods (86.36% vs. 45.21%). The proportion of co-infections in mNGS positive samples was significantly higher than that in traditional methods (40.91% vs. 14.39%). Sixteen Extra Pathogens in 14 cases identified by metagenomic NGS only, 6 pathogens affected clinical reasoning and 7 pathogens guided antimicrobial therapy.Conclusions MNGS is a powerful diagnostic method for identifying pathogens in central nervous system infections and provide actionable information in some cases. MNGS technology has positive significance for the diagnosis and clinical treatment of central nervous system infection in HIV-infected patients.
Definitions of poor outcome after total knee arthroplasty: An inventory review
Authors: Molder Malou te , Smolders José M.H. , Heesterbeek Petra J.C. , Ende Cornelia H.M. van den 
Published: December 2019

Abstract
Background: A significant proportion of patients shows poor response (i.e. no or little improvement) after total knee arthroplasty (TKA) because of osteoarthritis. It is difficult to quantify the proportion of patients with poor response to TKA, as different definitions of, and perspectives (clinician’s and patient’s) on poor response are being used. The aim of this study was therefore to review the literature and summarize definitions of poor response to TKA. Methods: A systematic search was performed to identify and review studies that included dichotomous definitions of poor outcome after primary TKA. The type, amount and combination of domains (e.g. functioning), outcome measures, type of responses (absolute/relative, change/cut-off), values and moments of follow-up used in definitions were summarized. Results: A total of 46 different dichotomous definitions of poor response to TKA were extracted from 2163 initially identified studies. 35 definitions incorporated one domain, seven definitions comprised two domains and four definitions comprised three domains. Eight different domains were used in identified definitions: pain, function, physical functioning, quality of life (QoL), patient satisfaction, anxiety, depression and patient global assessment. The absolute cut-off value was the most common type of response, with large variety in value and timing of follow-up. Conclusions: Our inventory review shows that definitions of poor response to TKA are heterogeneous. Our findings stresses the need for an unambiguous definition of poor response to draw conclusions about the prevalence of poor-responders to TKA across hospitals and countries, and to identify patients at risk.
The effect and potential risks of using cement-augmented pedicle screw instrumentation on multiple segment fixation in osteoporotic spine with lumbar degenerative diseases
Authors: Tang Yong-chao , Guo Hui-zhi , Guo Dan-qing , Luo Pei-jie , Li Yong-xian , Mo Guo-ye , Ma Yan-huai , Peng Jian-cheng , Liang De , Zhang Shun-cong 
Published: December 2019

Abstract
Background: Cement-augmented pedicle screw instrumentation (CAPSI) has been found to significantly increase the pedicle screws anchorage in the osteoporotic vertebral body, however, with the increase of augmented level and bone cement dose, the incidence of cement leakage (CL) or side complication of CAPSI also increased. But the effect and potential risks of CAPSI for osteoporotic lumbar degenerative diseases (LDD) have not been investigated in the cases of multiple segment fixation. The purpose of this study was to investigate potential complications of using cement-augmented screws for multilevel fixation (three or four levels) and the effectiveness of this method for treating LDD with low bone quality.
How to improve the safety of bicortical pedicle screw insertion in the thoracolumbar veterbrae with osteoporotic: Analysis base on three-dimensional CT reconstruction of patients in prone position
Authors: Xu Chao , Hou Qingxian , Chu Yanchen , Huang Xiuling , Yang Wenjiu , Ma Jinlong , Wang Zhijie 
Published: December 2019

Abstract
Background: Three-dimensional CT reconstruction of prone position could measure the relative position between the Great vessels and the thoracolumbar vertebrae. The Great vessels positions of the thoracic and lumbar segments were studied to improve the accuracy of pedicle screw insertion, reduce the risk of vascular injury. Methods: Twenty-four adults participated in the present study. Three-dimensional reconstruction of thoracolumbar (T9–L3) CT was performed in the prone and supine positions. The relative distance between the arteriovenous vessels and vertebrae distance (AVD/VVD) was obtained, respectively. The relative position angle of the arteriovenous vessel and the vertebral body was calculated as ∠AOY/∠VOY. Self-controlled experiments were carried out in the prone and supine positions. The data obtained were analyzed using SPSS 22.0 statistical software. Results: With regard to AVD, The AVD of the T12 was the smallest,> 3.2 mm. The difference among the T9, T10, L2 level was statistically significant (P < 0.05). And AVD was greater in the prone position than in the supine position; while the value of ∠AOY is the descending from T9-L3 gradually, there were statistically significant differences in ∠AOY between T9-T12, L2 and L3 in prone and supine position (P < 0.05). The aorta in the prone position was closer to the midline than that of the supine position, varying from 0°to 30°near the Y axis. With regard to VVD, there was no significant difference in contrast between the prone and supine positions (P≥0.05), and the VVD was the smallest in the L3 level> 5.4 mm. Conclusion: The pre-vertebral position of the aorta may change from T9 to L3 due to changes in body position. When the T9-L3 thoracolumbar spine disease was treated with pedicle screw double cortical fixation, the screw was safe and reliable within a range of≤ 3 mm when broken the pre-cortex .The three-dimensional reconstruction of prone position CT could be used to more accurately assess the relative position of the vertebral body and the blood vessel.
The effects of Enhanced Primary Healthcare interventions on primary care providers job satisfaction
Authors: Wong Wen Jun , Norzi Aisyah Mohd , Ang Swee Hung , Chan Chee Lee , Jaafar Faeiz Syezri Adzmin , Sivasampu Sheamini 
Published: December 2019

Abstract
Background In response to address the rising burden of cardiovascular risk factors, Malaysian government has implemented Enhanced Primary Healthcare (EnPHC) interventions in July 2017 at public clinics level. Healthcare providers (HCPs) play crucial roles in healthcare service delivery and health system reform can influence HCPs’ job satisfaction. However, studies evaluating HCPs’ job satisfaction following primary care transformation remain scarce in low- and middle-income countries. This study aims to evaluate the effects of EnPHC interventions on HCPs. Methods This is a quasi-experimental study conducted in 20 intervention and 20 matched control clinics. We surveyed all healthcare providers who were directly involved in patient management. A self-administered questionnaire which included six questions on job satisfaction were distributed at baseline (April and May 2017) and post-intervention (March and April 2019). Difference-in-differences analysis was used in the multivariable linear regression model in which we adjusted for providers and clinics characteristics to detect the changes in job satisfaction following EnPHC interventions. Results A total of 1042 and 1215 HCPs responded at baseline and post-intervention respectively. At post-intervention, the intervention group reported higher level of stress and change in score between two groups was -0.14 (β= -0.139; 95% CI -0.266,-0.012; p =0.032). In subgroup analysis, nurses from intervention group experienced increase in work stress following EnPHC interventions (β= -0.223; 95% CI -0.419,-0.026; p =0.026). Additionally, the same group also responded that they were less likely to perceive their profession as well-respected at post-intervention (β= -0.175; 95% CI -0.331,-0.019; p =0.027). Conversely, allied health professionals from intervention group were more likely to report a good balance between work and effort (β= 0.386; 95% CI 0.033,0.738; p =0.032) after implementing EnPHC interventions. Conclusions Our findings suggest that EnPHC interventions had resulted in some untoward effect on HCPs’ job satisfaction. Job dissatisfaction can have detrimental effects on the organisation and healthcare system. Therefore, provider experience and well-being should be considered before introducing healthcare delivery reforms to avoid overburdening of HCPs.
Custom selected reference genes outperform pre-defined reference genes in transcriptomic analysis
Authors: Santos Karen Cristine Gonçalves Dos , Desgagné-Penix Isabel , Germain Hugo 
Published: December 2019

Abstract
Background : RNA sequencing allows the measuring of gene expression at a resolution unmet by expression arrays or RT-qPCR. It is however necessary to normalize sequencing data by library size, transcript size and composition, among other factors, before comparing expression levels. The use of internal control genes or spike-ins is advocated in the literature for scaling read counts, but the methods for choosing reference genes are mostly targeted at RT-qPCR studies and require a set of pre-selected candidate controls or pre-selected target genes.
Results : Here, we report an R-based pipeline to select internal control genes based solely on read counts and gene sizes. This novel method first normalizes the read counts to Transcripts per Million (TPM) and then excludes weakly expressed genes using the DAFS script to calculate the cut-off. It then selects as references the genes with lowest TPM covariance. We used this method to pick custom reference genes for the differential expression analysis of three transcriptome sets from transgenic Arabidopsis plants expressing heterologous fungal effector proteins tagged with GFP (using GFP alone as the control). The custom reference genes showed lower covariance and fold change as well as a broader range of expression levels than commonly used reference genes. When analyzed with NormFinder, both typical and custom reference genes were considered suitable internal controls, but the expression of custom selected genes was more stable. geNorm produced a similar result in which most custom selected genes ranked higher ( i.e. expression more stable) than commonly used reference genes.
Conclusions : The proposed method is innovative, rapid and simple. Since it does not depend on genome annotation, it can be used with any organism, and does not require pre-selected reference candidates or target genes that are not always available.
THE PERCEPTION OF MEDICAL AND PHARMACY UNDERGRADUATE STUDENTS IN YOGYAKARTA ON INTERPROFESSIONAL COLLABORATION CLASS
Authors: Hapsari Saverina Nungky Dian , Triastuti Ida Ayu 
Published: December 2019

Introduction: Improving the quality of health services requires collaborative work skills in managing health problems from health workers. An understanding about interdisciplinary collaboration needs to be given since students take theoretical education. Learning about interprofessional education (IPE) needs to be evaluated whether it provides benefits to students in achieving learning objectives. The purpose of this study was to determine student perceptions after participating in IPE collaborative learning.
Method: This research is a descriptive cross-sectional quantitative study. Samples from this study were students of the UKDW Medical Faculty and the USD Pharmacy Faculty who participated in the IPE Communication Clinical Skills. A total of 269 students were given the Google Questionnaire IPE questionnaire, which was adapted from the Student Perceptions of Physician-Pharmacist Interprofessional Clinical Education (SPICE). The reliability of the questionnaire measured by Cronbachâ€™s Alpha was 0.72.
Results: The number of students who filled out the questionnaire was 176 people (response rate of 65.43%), consisting of 99 undergraduate students of the UKWD Faculty of Medicine and 170 students of the Faculty of Pharmacy. Students tend to choose to agree or strongly agree from all four research scales.
Discussion: The instrument contains 10 questions and contains 3 factors that emphasize collaborative teamwork, roles and responsibilities of each profession, and patient outcomes. The total mean value of all questions shows that according to students' perceptions, interprofessional education sessions are beneficial for students in understanding these factors. The results of the study generally describe students having a positive perception about IPE learning.
Conclusion: Students consider that the management of health by the interprofessional team can improve the health and satisfaction of patients, the importance of working with other professions, and understanding roles and responsibilities in collaborative practice.
Relationship verification between CO2 and pollutant emissions: policy evaluation based on the pollutant discharge fee in China
Authors: Ji Siping , Chen Haiyun , Chuan Yongming , Gao Libin , Liu Chenhui , Liu Hongqin , Lv Wendai 
Published: December 2019

Abstract
Serious environmental problems are exacerbated with economic growth. Pollution control and emission reduction are now challenged, and we have to pay real attention. Pollutant discharge fee (PDF), one of the enforced levy regulations on pollutant discharge in China, was introduced in a new perspective as a direct economic representation of multi-pollutant emission. The DPSIR framework and regression model were constructed to analyze the co-control process of pollutant emission based on the provincial data from 2000 to 2012. The results showed that PDF had a significant and positive relationship with CO2 emission in China during 2000–2012. A special contradiction was found that CO2 emission and PDF increased greatly, verified with empirical analysis, while the pollutant emission reduction target in the 11th and 12th Five-Year Plan (FYP) was achieved for the corresponding periods, which indicated that emission co-control is still unrealized in China. Conversely, the single indicator control of pollutant emission generated by opportunistic behavior of the Chinese government failed to bring real environmental improvement. In addition, PDF can be seen as a mirror for the Environment Tax (ET) to achieve authentic emission reduction and pollution control, even for sustainable development in China.
Hydrological classification and performance of Himalayan springs in climate change scenario – a case study
Authors: Rathi Vinay Kumar , Ram Shobha , Kumar Rohitashw , Agarwal Avinash , Nema R. K. 
Published: December 2019

AbstractThe present study was conducted to evaluate 33 springs' hydrology (discharge and yield estimation) of Chandrabhaga and Danda watersheds of Uttarakhand, India. The springs were classified using Meinzer method and evaluated the relative performance for rejuvenation strategy. It was found that most of springs fall in sixth and seventh class order with flow rate 6.5 to 65.5 and 0.8 to 6.5 m3·day−1, respectively. The relative performance of springs were analyzed based on four methods: (i) spring flow variability, (ii) normalized spring flow (short and long duration), (iii) rainfall spring flow lag and (iv) spring flow gradient. The relative results of springs were analyzed on a scale of 0–5. The Chandrabhaga springs 01, 03, 4B, 05, 06 and 13 were found to be relatively good on a scale value of 4 out of 5 as compared to springs 4A, 07, and 10A with a scale value of 1. For the Danda watershed, the relative performance of springs 4A and 28 found on scale value of 5 and springs 4B, 11 and 20 with a scale value of 4 are relatively good compared to springs 02, 06, 07, 15 and 17. The cumulative flow of spring showed a linear response with cumulative rainfall for the period of June to September (monsoon period). The spring-shed was delineated and evaluated for optimization for the maximum efficiency, spring flow, ratio of area and relief versus maximum spring flow yield. The results revealed that the quantification of water fluxes for water balances, storage of groundwater and development of mathematical models can be used for sustainable water resources development and to revive the mountain springs which helped the adverse impacts of climate change.
Recognition of Invasive Prostate Cancer Using a GHRL Polypeptide Probe Targeting GHSR in a Mouse Model In Vivo
Authors: Ye Huamao , Yang Yue , Chen Rui , Shi Xiaolei , Fang Yu , Yang Jun , Dong Yuanzhen , Chen Lili , Xia Jianghua , Wang Chao , Yang Chenghua , Feng Jun , Wang Yang , Feng Xiang , Lü Chen 
Published: December 2019

Background:
Ghrelin (GHRL) is a polypeptide that can specifically bind to the growth hormone secretagogue
receptor (GHSR). The expression of GHSR is significantly different in normal and prostate cancer
(PC) tissues in humans. It is important to find an effective diagnostic method for the diagnosis and prognosis of
invasive PC/neuroendocrine prostate cancer (NEPC).

Methods:
GHRL and GHSR mRNA levels were determined by a quantitative real-time polymerase chain reaction
in PC tissues. The expression of GHRL and GHSR proteins was assessed by Western blot assay and immunohistochemistry.
A GHRL polypeptide probe was synthesized by standard solid-phase polypeptide synthesis, and
labeled with Alexa Fluor 660. Confocal microscopy was used to capture fluorescence images. Living imaging
analysis showed tumor areas of different invasiveness in mice models.

Results:
GHRL and GHSR mRNA levels were determined by a quantitative real-time polymerase chain reaction
in PC tissues. The expression of GHRL and GHSR proteins was assessed by Western blot assay and immunohistochemistry.
A GHRL polypeptide probe was synthesized by standard solid-phase polypeptide synthesis, and
labeled with Alexa Fluor 660. Confocal microscopy was used to capture fluorescence images. Living imaging
analysis showed tumor areas of different invasiveness in mice models.

Conclusion:
GHSR and GHRL might be used in molecular imaging diagnosis for invasive PC/NEPC in the future.
Neuraminidase from Influenza A and B Viruses is Susceptible to the Compound 4-(4-Phenyl-1H-1,2,3-Triazol-1-yl)-2,2,6,6-Tetramethylpiperidine-1- Oxyl
Authors: Sacramento Carolina Q. , Jordão Alessandro Kappel , Abrantes Juliana L. , Alves Cristiane M. , Marttorelli Andressa , Fintelman-Rodrigues Natalia , de Freitas Caroline S. , de Melo Gabrielle R. , Cunha Anna Claudia , Ferreira Vitor F. , Souza Thiago Moreno L. 
Published: December 2019

Background:
Since the influenza virus is the main cause of acute seasonal respiratory infections
and pandemic outbreaks, antiviral drugs are critical to mitigate infections and impair chain of
transmission. Neuraminidase inhibitors (NAIs) are the main class of anti-influenza drugs in clinical use.
Nevertheless, resistance to oseltamivir (OST), the most used NAI, has been detected in circulating
strains of the influenza virus. Therefore, novel compounds with anti-influenza activity are necessary.

Objective:
To verify whether the NA from influenza A and B virus is susceptible to the compound 4-(4-
phenyl-1H-1,2,3-triazol-1-yl)-2,2,6,6-tetramethylpiperidine-1-oxyl (Tritempo).

Methods:
Cell-free neuraminidase inhibition assays were performed with Tritempo, using wild-type
(WT) and OST-resistant influenza strains. Cell-based assays in MDCKs were performed to confirm
Tritempo`s antiviral activity and cytotoxicity. Multiple passages of the influenza virus in increasing concentrations
of our compound, followed by the sequencing of NA gene and molecular docking, were used
to identify our Tritempo’s target.

Results/Discussion:
Indeed, Tritempo inhibited the neuraminidase activity of WT and OSTresistant
strains of influenza A and B, at the nanomolar range. Tritempo bound to WT and OST-resistant
influenza NA isoforms at the sialic acid binding site with low free binding energies. Cell-free assays
were confirmed using a prototypic influenza A infection assay in MDCK cells, in which we found an
EC50 of 0.38 µM, along with very low cytotoxicity, CC50 > 2,000 µM. When we passaged the influenza
A virus in the presence of Tritempo, a mutant virus with the G248P change in the NA was detected. This
mutant was resistant to Tritempo but remained sensitive to OST, indicating no cross-resistance between
the studied and reference drugs.

Conclusion:
Our results suggest that Tritempo’s chemical structure is a promising one for the development
of novel antivirals against influenza.
ABC-Gly: Identifying Protein Lysine Glycation Sites with Artificial Bee Colony Algorithm
Authors: Yao Yanqiu , Zhao Xiaosa , Ning Qiao , Zhou Junping 
Published: December 2019

Background:
Glycation is a nonenzymatic post-translational modification process by attaching
a sugar molecule to a protein or lipid molecule. It may impair the function and change the characteristic
of the proteins which may lead to some metabolic diseases. In order to understand the underlying molecular
mechanisms of glycation, computational prediction methods have been developed because of their
convenience and high speed. However, a more effective computational tool is still a challenging task in
computational biology.

Methods:
In this study, we showed an accurate identification tool named ABC-Gly for predicting lysine
glycation sites. At first, we utilized three informative features, including position-specific amino
acid propensity, secondary structure and the composition of k-spaced amino acid pairs to encode the
peptides. Moreover, to sufficiently exploit discriminative features thus can improve the prediction and
generalization ability of the model, we developed a two-step feature selection, which combined the
Fisher score and an improved binary artificial bee colony algorithm based on the support vector machine.
Finally, based on the optimal feature subset, we constructed an effective model by using the
Support Vector Machine on the training dataset.

Results:
The performance of the proposed predictor ABC-Gly was measured with the sensitivity of
76.43%, the specificity of 91.10%, the balanced accuracy of 83.76%, the Area Under the receiveroperating
characteristic Curve (AUC) of 0.9313, a Matthew’s Correlation Coefficient (MCC) of
0.6861 by 10-fold cross-validation on training dataset, and a balanced accuracy of 59.05% on independent
dataset. Compared to the state-of-the-art predictors on the training dataset, the proposed predictor
achieved significant improvement in the AUC of 0.156 and MCC of 0.336.

Conclusion:
The detailed analysis results indicated that our predictor may serve as a powerful complementary
tool to other existing methods for predicting protein lysine glycation. The source code and
datasets of the ABC-Gly were provided in the Supplementary File 1.