bluuebunny/crossref_metadata_2025_split huggingface dataset:
Antiretroviral treatment failure and associated factors among HIV patients on first-line antiretroviral treatment in Sekota, northeast Ethiopia
Authors: Nega Jemberu , Taye Solomon , Million Yihenew , Rodrigo Chaturaka , Eshetie Setegn 
Published: July 2020

Abstract
Background
Antiretroviral treatment has played a pivotal role in the reduction of HIV/AIDS-related morbidity and mortality. However, treatment options can be impaired by the development of antiretroviral treatment failure. Regular monitoring of the Human Immunodeficiency Virus treatment outcome via viral load tests is the key approach. There is a scarcity of information about HIV treatment failure and risk factors in the study area. Therefore, the study was aimed to assess antiretroviral treatment failure and associated factors among patients on first-line antiretroviral treatment at Tefera Hailu Memorial Hospital, Sekota, northeast Ethiopia.

Methods
A hospital-based cross-sectional study was conducted on 295 patients on first-line antiretroviral treatment from Nov. 2018 to Apr. 2019. Socio-demographic and clinical variables were collected using a pretested questionnaire, and blood specimen was collected for PCR viral load and CD4 + cell count estimation. Data were entered into Epi-Info and exported to SPSS for analysis. A binary logistic regression model was used to identify associated factors, and P value < 0.05 was considered as statistically significant.

Results
Of the 295 subjects on first-line ART, 49 (16.6%) and 18 (6.1%) experienced virological and immunological failures, respectively. The failure of the former was associated with poor adherence (AOR: 6.367, P < 0.001), CD4 + count < 500 cells/µL (AOR: 4.78, P = 0.031) and shorter (6–24 months) duration on ART (AOR: 0.48, P = 0.048), while poor treatment adherence (AOR: 11.51, P = 0.012) and drug interruption (AOR: 6.374, P = 0.039) were the independent risk factors for latter. Immunological tests to predict virological failures showed as sensitivity, specificity, PPV, and NPV were 20.4%, 96.7%, 55.5%, and 86.0%, respectively.

Conclusions
The rate of ART failure was considerably high. Poor adherence, low CD4 + count, prolonged ART, and drug interruption were found to be the most predictor variables for virological and immunological failures. The discrimination power of the immunological parameter was low in comparison to virological measurements as standard methods. Therefore, the study highlighted the need for more attention and efforts to curb associated factors and maximize virological tests for monitoring treatment failures.
Prevalence and genotype distribution of HPV and cervical pathological results in Sichuan Province, China: a three years surveys prior to mass HPV vaccination
Authors: Luo Qing , Jiang Ni , Wu Qiaoyuan , Wang Jiaqiang , Zhong Jialing 
Published: July 2020

Abstract
Background
HPV persistent infection is a strong carcinogenic factor that can induce cervical cancer. Investigation of HPV epidemiology and genotype distribution is of great meaning for the development of cervical cancer prevention and control strategies.

Methods
By using PCR-based hybridization gene chip assay, HPV genotype was detected from 14,185 women that came from HEC (Health Examination Center) or OGOC (Obstetrics and Gynecology Outpatient Clinics) between 2015 and 2017 in Sichuan area. The epidemiology and genotype distribution as well as the relationship between HPV infection and histology/cytology abnormalities were analyzed.

Results
The positivity rate of HPV was 23.84%. The HPV-positive rate of OGOC group (37.62%) was significantly higher than that of HEC group (15.29%), p < 0.05. The prevalence of HPV reached peak at age 41–50 (5.86%) in HEC group, but at age 21–30 (14.74%) in OGOC group. Of all the HPV positive women, single genotype infection was the most common form in both HEC and OGOC group (62.06% in total screening population, 74.36% in HEC group and 54.01% in OGOC group). Three most prevalent HPV types were HPV-52 (5.02%), 58 (3.61%), and 16 (3.24%) in total screening population. Of all the HPV positive women, the top three types were HPV-52 (20.93%), CP8304 (15.32%), and 58 (14.42%) in HEC group, while were HPV-52 (21.14%), 16 (16.34%), and 58 (15.61%) in OGOC group. HPV 52/16/58 accounted for 41.84% of cytology and 56.52% of histological abnormalities.

Conclusions
Women in Sichuan area were facing the great threat of HPV infection, especially the women aged between 21 ~ 30 or 41–50 years old. The priority HPV types were HPV 52, 58, and 16 in OGOC group, while were HPV 52, CP8304, and 58 in HEC group. HPV 52/16/58 accounted for the majority of cytology and histological abnormalities. Our analysis was found to be valuable for providing a scientific basis for the prevention and control strategies of cervical cancer in Sichuan area.
The impact of scanning data measurements on the Acuros dose calculation algorithm configuration
Authors: Fogliata A. , Esposito E. , Paganini L. , Reggiori G. , Tomatis S. , Scorsetti M. , Cozzi L. 
Published: July 2020

AbstractBackgroundMany dose calculation algorithms for radiotherapy planning need to be configured for each clinical beam using pre-defined measurements. An optimization process adjusts the physical parameters able to estimate the energy released in the medium in any geometrical condition. This work investigates the impact of measured input data quality on the configuration of the type “c” Acuros-XB dose calculation algorithm in the Eclipse (Varian Medical Systems) treatment planning system.MethodsDifferent datasets were acquired with the BeamScan water phantom (PTW) to configure 6 MV beams, for both flattened (6X) and flattening filter free mode (6FFF) for a Varian TrueBeam:(i)a correct dataset measured using a Semiflex-3D ion chamber,(ii)a set in missing lateral scatter conditions (MLS),(iii)a set with incorrect effective point of measurement (EPoM),(iv)sets acquired with PinPoint-3D chamber, DiodeP, microDiamond detectors.The Acuros-XB dose calculation algorithm (version 15.6) was configured using the reference dataset, the sets measured with the different detectors, with intentional errors, and using the representative beam data (RBD) made available by the vendor. The physical parameters obtained from each optimization process (spectrum, mean radial energy, electron contamination), were analyzed and compared. Calculated data were finally compared against the input and reference measurements.ResultsConcerning the physical parameters, the configurations presenting the largest differences were the MLS conditions (mean radial energy) and the incorrect EPoM (electron contamination). The calculation doses relative to the input data present low accuracy, with mean differences > 2% in some conditions. The PinPoint-3D ion chamber presented lower accuracy for the 6FFF beam. Regarding the RBD, calculations compared well with the input data used for the configuration, but not with the reference data.ConclusionThe MLS conditions and the incorrect setting of the EPoM lead to erroneous configurations and should be avoided. The choice of an appropriate detector is important. Whenever the representative beam data is used, a careful check under more clinical geometrical conditions is advised.
Accuracy of real-time respiratory motion tracking and time delay of gating radiotherapy based on optical surface imaging technique
Authors: Chen Li , Bai Sen , Li Guangjun , Li Zhibin , Xiao Qing , Bai Long , Li Changhu , Xian Lixun , Hu Zhenyao , Dai Guyu , Wang Guangyu 
Published: July 2020

Abstract
Background
Surface-guided radiation therapy (SGRT) employs a non-invasive real-time optical surface imaging (OSI) technique for patient surface motion monitoring during radiotherapy. The main purpose of this study is to verify the real-time tracking accuracy of SGRT for respiratory motion and provide a fitting method to detect the time delay of gating.

Methods
A respiratory motion phantom was utilized to simulate respiratory motion using 17 cosine breathing pattern curves with various periods and amplitudes. The motion tracking of the phantom was performed by the Catalyst™ system. The tracking accuracy of the system (with period and amplitude variations) was evaluated by analyzing the adjusted coefficient of determination (A_R2) and root mean square error (RMSE). Furthermore, 13 actual respiratory curves, which were categorized into regular and irregular patterns, were selected and then simulated by the phantom. The Fourier transform was applied to the respiratory curves, and tracking accuracy was compared through the quantitative analyses of curve similarity using the Pearson correlation coefficient (PCC). In addition, the time delay of amplitude-based respiratory-gating radiotherapy based on the OSI system with various beam hold times was tested using film dosimetry for the Elekta Versa-HD and Varian Edge linacs. A dose convolution-fitting method was provided to accurately measure the beam-on and beam-off time delays.

Results
A_R2 and RMSE for the cosine curves were 0.9990–0.9996 and 0.110–0.241 mm for periods ranging from 1 s to 10 s and 0.9990–0.9994 and 0.059–0.175 mm for amplitudes ranging from 3 mm to 15 mm. The PCC for the actual respiratory curves ranged from 0.9955 to 0.9994, which was not significantly affected by breathing patterns. For gating radiotherapy, the average beam-on and beam-off time delays were 1664 ± 72 and 25 ± 30 ms for Versa-HD and 303 ± 45 and 34 ± 25 ms for Edge, respectively. The time delay was relatively stable as the beam hold time increased.

Conclusions
The OSI technique provides high accuracy for respiratory motion tracking. The proposed dose convolution-fitting method can accurately measure the time delay of respiratory-gating radiotherapy. When the OSI technique is used for respiratory-gating radiotherapy, the time delay for the beam-on is considerably longer than the beam-off.
The application and value of continuous nursing in patients after coronary artery bypass grafting
Authors: Zhou Sheng-Huo , Huang Shu-Ting , Xu Ning , Chen Qiang , Chen Liang-Wang , Kuo Yur-Ren 
Published: July 2020

Abstract
Objective
To investigate the application and value of continuous nursing after coronary artery bypass grafting.

Methods
The clinical data of 62 patients after coronary artery bypass grafting from January 2016 to January 2018 were analyzed retrospectively. According to the nursing mode, the patients were divided into two groups: the continuous nursing group (n = 30) and the conventional nursing group (n = 32). All patients completed Self-Rating Depression Scale (SDS) and Self-Rating Anxiety Scale (SAS) at admission and 1 year after operation. All patients completed Seattle Angina Pectoris Questionnaire (SAQ) at discharge and 1 year after operation.

Results
All patients were followed up for more than one year. One year after operation, SAQ score in five items in continuous nursing group was significantly better than that in conventional nursing group.(P < 0.05) The continuous nursing group exhibited significantly decreased SAS and SDS scores 1 year after surgery compared to the preoperative SAS and SDS scores.(P < 0.05) The SAS and SDS scores of the continuous nursing group were significantly better than those of the conventional nursing group 1 year after surgery.(P < 0.05) Then incidence rate of chest tightness or chest pain and coronary restenosis in continuous nursing group were significantly less than that in conventional nursing group.(P < 0.05).

Conclusion
Continuous nursing improved patient compliance with treatment and reduces the occurrence of complications. The patient also receives proper psychological evaluations, which relieve patient anxiety and depression and improve the quality of life.
“We can’t carry the weight of the whole world”: illness experiences among Peruvian older adults with symptoms of depression and anxiety
Authors: Flores-Flores Oscar , Zevallos-Morales Alejandro , Carrión Ivonne , Pawer Dalia , Rey Lorena , Checkley W. , Hurst J. R. , Siddharthan T. , Parodi Jose F. , Gallo Joseph J. , Pollard Suzanne L. 
Published: July 2020

Abstract
Background
Despite the high levels of depression and anxiety symptoms in old age, the use of mental health services in this population is low. Help-seeking behaviors are shaped by how an individual perceives and experiences their illness. The objective of this study was to characterize the illness experiences of Peruvian older adults with depression and anxiety symptoms in order to lay the foundation for tailored community-based mental health interventions.

Methods
In this qualitative study, we conducted in-depth interviews with a purposively selected sample of older adults (≥ 60 years) from peri-urban areas of Lima, Peru. We included individuals with only depressive symptoms (Patient Health Questionnaire-9 ≥ 10), only anxiety symptoms (Beck Anxiety Inventory ≥ 16), with depressive and anxiety symptoms, and older adults who mentioned they had received mental health treatment/care. The interview guide included the following topics: perceptions and experiences about depression and anxiety; perceptions about the relationship between physical chronic diseases and mental health; experiences with mental health professionals and treatments, and coping mechanisms. Data collection was conducted between October 2018 and February 2019.

Results
We interviewed 38 participants (23 women, 15 men) with a mean age of 67.9 years. Participants’ ideas and perceptions of depression and anxiety showed considerable overlap. Participants attributed depression and anxiety mainly to familial and financial problems, loneliness, loss of independence and past traumatic experiences. Coping strategies used by older adults included ‘self-reflection and adaptation’ to circumstances, ‘do your part’, and seeking ‘emotional support’ mainly from non-professionals (relatives, friends, acquaintances, and religion).

Conclusions
Illness experiences of depression and anxiety set the pathway for tailored community-based mental health interventions for older adults. Overlapping narratives and perceptions of depression and anxiety suggest that these conditions should be addressed together. Mental health interventions should incorporate addressing areas related to depression and anxiety such as prevention of loss of independence, trauma, and loneliness. Good acceptability of receiving emotional support for non-professionals might offer an opportunity to incorporate them when delivering mental health care to older adults.
DISC: a highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning
Authors: He Yao , Yuan Hao , Wu Cheng , Xie Zhi 
Published: July 2020

AbstractDropouts distort gene expression and misclassify cell types in single-cell transcriptome. Although imputation may improve gene expression and downstream analysis to some degree, it also inevitably introduces false signals. We develop DISC, a novel deep learning network with semi-supervised learning to infer gene structure and expression obscured by dropouts. Compared with seven state-of-the-art imputation approaches on ten real-world datasets, we show that DISC consistently outperforms the other approaches. Its applicability, scalability, and reliability make DISC a promising approach to recover gene expression, enhance gene and cell structures, and improve cell type identification for sparse scRNA-seq data.
Association between rare variants in specific functional pathways and human neural tube defects multiple subphenotypes
Authors: Zou Jizhen , Wang Fang , Yang Xueyan , Wang Hongyan , Niswander Lee , Zhang Ting , Li Huili 
Published: July 2020

Abstract
Background
Neural tube defects (NTDs) are failure of neural tube closure, which includes multiple central nervous system phenotypes. More than 300 mouse mutant strains exhibits NTDs phenotypes and give us some clues to establish association between biological functions and subphenotypes. However, the knowledge about association in human remains still very poor.

Methods
High throughput targeted genome DNA sequencing were performed on 280 neural tube closure-related genes in 355 NTDs cases and 225 ethnicity matched controls,

Results
We explored that potential damaging rare variants in genes functioning in chromatin modification, apoptosis, retinoid metabolism and lipid metabolism are associated with human NTDs. Importantly, our data indicate that except for planar cell polarity pathway, craniorachischisis is also genetically related with chromatin modification and retinoid metabolism. Furthermore, single phenotype in cranial or spinal regions displays significant association with specific biological function, such as anencephaly is associated with potentially damaging rare variants in genes functioning in chromatin modification, encephalocele is associated with apoptosis, retinoid metabolism and one carbon metabolism, spina bifida aperta and spina bifida cystica are associated with apoptosis; lumbar sacral spina bifida aperta and spina bifida occulta are associated with lipid metabolism. By contrast, complex phenotypes in both cranial and spinal regions display association with various biological functions given the different phenotypes.

Conclusions
Our study links genetic variant to subphenotypes of human NTDs and provides a preliminary but direct clue to investigate pathogenic mechanism for human NTDs.
Candidate genes for monitoring hydrogen peroxide resistance in the salmon louse, Lepeophtheirus salmonis
Authors: Agusti-Ridaura Celia , Bakke Marit Jørgensen , Helgesen Kari Olli , Sundaram Arvind Y. M. , Bakke Sigrid Jørgensen , Kaur Kiranpreet , Horsberg Tor Einar 
Published: July 2020

Abstract
Background
Hydrogen peroxide (H2O2) is one of the delousing agents used to control sea lice infestations in salmonid aquaculture. However, some Lepeophtheirus salmonis populations have developed resistance towards H2O2. An increased gene expression and activity of catalase, an enzyme that breaks down H2O2, have been detected in resistant lice, being therefore introduced as a resistance marker in the salmon industry. In the present study the aim was to validate the use of catalase expression as a marker and to identify new candidate genes as additional markers to catalase, related to H2O2 resistance in L. salmonis.

Methods
A sensitive and an H2O2 resistant laboratory strain (P0 generation, not exposed to H2O2 for several years) were batch crossed to generate a cohort with a wide range of H2O2 sensitivities (F2 generation). F2 adult females were then exposed to H2O2 to separate sensitive and resistant individuals. Those F2 lice, the P0 lice and field-collected resistant lice (exposed to H2O2 in the field) were used in an RNA sequencing study.

Results
Catalase was upregulated in resistant lice exposed to H2O2 compared to sensitive lice. This was, however, not the case for unexposed resistant P0 lice. Several other genes were found differentially expressed between sensitive and resistant lice, but most of them seemed to be related to H2O2 exposure. However, five genes were consistently up- or downregulated in the resistant lice independent of exposure history. The upregulated genes were: one gene in the DNA polymerase family, one gene encoding a Nesprin-like protein and an unannotated gene encoding a small protein. The downregulated genes encoded endoplasmic reticulum resident protein 29 and an aquaporin (Glp1_v2).

Conclusions
Catalase expression seems to be induced by H2O2 exposure, since it was not upregulated in unexposed resistant lice. This may pose a challenge for its use as a resistance marker. The five new genes associated with resistance are put forward as complementary candidate genes. The most promising was Glp1_v2, an aquaglyceroporin that may serve as a passing channel for H2O2. Lower channel number can reduce the influx or distribution of H2O2 in the salmon louse, being directly involved in the resistance mechanism.
Evaluation of multiplex ARMS-PCR for detection of Helicobacter pylori mutations conferring resistance to clarithromycin and levofloxacin
Authors: Li Yangxia , Lv Tangshan , He Chaochao , Wang Hongyan , Cram David S. , Zhou Linfu , Zhang Jun , Jiang Weiqin 
Published: July 2020

Abstract
Background
Helicobacter pylori bacterium is a major cause of gastritis. With increasing use of antibiotics to treat infections, mutation resistant strains have emerged in most human populations. To effectively treat patients to help resolve infections, the clinician needs information on the antibiotic susceptibility profile of the infection. Therefore, a rapid and accurate test is required to provide this information. To address this issue, we designed and validated a real time multiplex ARMS-PCR assay for rapid detection of highly prevalent H. pylori clarithromycin and levofloxacin resistance mutations. The aim of the study was to evaluate the analytical and diagnostic sensitivity and specificity of ARMS-PCR, using direct Sanger sequencing of the known resistance mutations as the gold standard.

Results
In preliminary studies using a defined number of plasmids with clarithromycin and levofloxacin resistance mutations, the analytical sensitivity of our ARMS-PCR assay was 50 plasmid copies, equating to around 50 bacterium in a gastric biopsy sample. In terms of specificity, the assay was highly specific for the targeted resistance mutations. The assay was also able to reliably and efficiently detect heteroresistance of clarithromycin and levofloxacin mutations, even at a disproportional ratio of 1:1000. From the analysis of 192 samples with suspected H. pylori infections, the diagnostic sensitivity and specificity of the assay was very high for detection of clarithromycin resistance (100% and 100%), levofloxacin resistance (98.04% and 95.04%) and clarithromycin and levofloxacin double resistance (100% and 96.91%). Amongst the 74 patients diagnosed antibiotic resistance bacteria, 23 (31.1%) had clarithromycin resistance, 21 (28.4%) had levofloxacin resistance and 30 (40.5%) had double resistance. From sample receipt to results, our single tube assay could be routinely completed in under 2 h.

Conclusions
Our assay demonstrated high diagnostic sensitivity and specificity for detection of clarithromycin and levofloxacin resistant H. pylori. Based on proven accuracy, together with high efficiency, scalability and low cost, our assay has useful clinical utility for rapid diagnosis of clarithromycin and levofloxacin resistant H. pylori infections. Our assay results will provide patients with a clear diagnosis, enabling the treating clinician to administer the most effective antibiotic regimen to help the clear the infection.
Solving a nonlinear fractional Schrödinger equation using cubic B-splines
Authors: Erfanian M. , Zeidabadi H. , Rashki M. , Borzouei H. 
Published: July 2020

AbstractWe study the inhomogeneous nonlinear time-fractional Schrödinger equation for linear potential, where the order of fractional time derivative parameter α varies between $0 < \alpha < 1$
0
<
α
<
1
. First, we begin from the original Schrödinger equation, and then by the Caputo fractional derivative method in natural units, we introduce the fractional time-derivative Schrödinger equation. Moreover, by applying a finite-difference formula to time discretization and cubic B-splines for the spatial variable, we approximate the inhomogeneous nonlinear time-fractional Schrödinger equation; the simplicity of implementation and less computational cost can be mentioned as the main advantages of this method. In addition, we prove the convergence of the method and compute the order of the mentioned equations by getting an upper bound and using some theorems. Finally, having solved some examples by using the cubic B-splines for the spatial variable, we show the plots of approximate and exact solutions with the noisy data in figures.