bluuebunny/crossref_metadata_2025_split huggingface dataset:
Challenges with Scale-up of GeneXpert MTB/RIF® inUganda: a Health Systems Perspective
Authors: Nalugwa Talemwa , Shete Priya B. , Nantale Mariam , Farr Katherine , Ojok Christopher , Ochom Emma , Mugabe Frank , Joloba Moses , Dowdy David W. , Moore David A.J. , Davis J. Lucian , Cattamanchi Adithya , Katamba Achilles 
Published: February 2020

Abstract
Background: Many high burden countries are scaling-up GeneXpert MTB/RIF (Xpert) testing for tuberculosis (TB) using a hub-and-spoke model. However, the effect of scale up on reducing TB has been limited. We sought to characterize variation in implementation of referral-based Xpert TB testing across Uganda, and to identify health system factors that may enhance or prevent high-quality implementation of Xpert testing services. Methods: We conducted a cross-sectional study triangulating quantitative and qualitative data sources at 23 community health centers linked to one of 15 Xpert testing sites between November 2016 and May 2017 to assess health systems infrastructure for hub-and-spoke Xpert testing. Data sources included a standardized site assessment survey, routine TB notification data, and field notes from site visits. Results: Challenges with Xpert implementation occurred at every step of the diagnostic evaluation process, leading to low overall uptake of testing. Of 2,192 patients eligible for TB testing, only 574 (26%) who initiated testing were referred for Xpert testing. Of those, 54 (9.4%)were Xpert confirmed positive just under half initiated treatment within 14 days (n=25, 46%). Gaps in required infrastructure at 23 community health centers to support the hub-and-spoke system included lack of refrigeration (n=14, 61%) for sputum testing and lack of telephone/mobile communication (n=21, 91%). Motorcycle riders responsible for transporting sputum to Xpert sites operated variable with trips once, twice, or three times a week at 10 (43%), nine (39%) and four (17%) health centers, respectively. Staff recorded Xpert results in the TB laboratory register at only one health center and called patients with positive results at only two health centers. Of the 15 Xpert testing sites, five (33%) had at least one non-functioning module. The median number of tests per day was 3.57 (IQR 2.06-4.54), and 10 (67%) sites had error/invalid rates >5%. Conclusions: Although Xpert devices are now widely distributed throughout Uganda, health system factors across the continuum from test referral to results reporting and treatment initiation preclude effective implementation of Xpert testing for patients presenting to peripheral health centers. Support for scale up of innovative technologies should include support for communication, coordination and health systems integration.
Disabled and immigrant, a double minority challenge: A qualitative study about the experiences of immigrant parents of children with disabilities navigating health and rehabilitation services in Norway.
Authors: Arfa Shahrzad , Solvang Per Koren , Berg Berit , Jahnsen Reidun 
Published: February 2020

Abstract
• Background: Immigrants and their Norwegian-born children make up approximately 18% of the total population in Norway. While several studies have been conducted on immigrants’ utilization of healthcare services, immigrant families are systematically underrepresented in international studies of children with disabilities. By focusing on experiences of immigrant parents of children with disabilities navigating health and rehabilitation services in Norway, this study generated knowledge of how accessible and tailored the services were from their point of view.
Methods: This study took a qualitative approach, using semi-structured interviews to explore the experiences of immigrant parents of children with disabilities from non-Western countries. The interviews were transcribed, coded, and analyzed via an inductive thematic analytic approach.

Results: The findings show how the “immigrant experience” influenced the way the parents looked at, experienced, and even praised the services. The parents appreciated the follow-up services provided by the pediatric rehabilitation centers, which they experienced as predictable and well-organized. While navigating the services, they experienced several challenges, including the need for information, support, and timely help. They felt exhausted because of years of struggle in the healthcare system to access the help and services they needed. They expressed how this struggle had affected their own health. The feeling of being treated differently from the majority was another challenge they experienced while navigating the services. The findings also show how parents’ experiences of communication with healthcare providers were influenced not only by their own language and communication skills but also by the healthcare providers’ intercultural communication skills and dominant organizational culture.

Conclusions: The parents’ experiences show that there is still a gap between the public ideal of equal healthcare services and the reality of the everyday lives of immigrant families of children with disabilities. By exploring immigrant parents’ experiences, this study highlights the importance of mobilization at both the individual and systemic levels to fill the current gap and provide tailored and accessible services to the entire population.
The disease stage-associated imbalance of Th1/Th2 and Th17/Treg in uterine cervical cancer patients and their recovery with the reduction of tumor burden
Authors: Lin Wei , Zhang Hua-ling , Niu Zhao-yuan , Wang Zhen , Kong Yan , Yang Xing-sheng , Yuan Fang 
Published: February 2020

Abstract
Background

Nearly all uterine cervical cancer (UCC) cases result from human papillomavirus (HPV) infection. After high-risk HPV infection, most HPV infections are naturally cleared by humoral and cell-mediated immune responses. Thus, cervical lesions of only few patients progress into cervical cancer via cervical intraepithelial neoplasia (CIN) and lead to persistent oncogenic HPV infection. This suggests that immunoregulation plays an instrumental role in the carcinogenesis. However, there was a few study on the relation between the immunologic dissonance and clinical characteristics of UCC patients.

Method

We examined the related immune cells (Th1, Th2, Th17, and Treg cells) by flow cytometric analysis and analyzed their relations with UCC stages, tumor size, differentiation, histology type, lymph node metastases, and vasoinvasion. Next, we quantified the Th1, Th2, Th17, and Treg cells before and after the operation both in UCC and CIN patients.

Results

When compared with stage I patients, decreased levels of circulating Th1 cells and elevated levels of Th2, Th17, and Treg cells were detected in stage II patients. In addition, the imbalance of Th1/Th2 and Th17/Treg cells was related to the tumor size, lymph node metastases, and vasoinvasion. We found that immunological cell levels normalized after the operations. In general, immunological cell levels in CIN patients normalized sooner than in UCC patients.

Conclusions

Our findings suggested that peripheral immunological cell levels reflect the patient’s condition.
Incidence Trend of Breast Cancer in Women of Eastern Mediterranean Region countries from 1998 to 2019: A Systematic Review and Meta-Analysis
Authors: Zahedi Razieh , Vardanjani Hossein Molavi , Baneshi Mohammad Reza , Haghdoost Ali Akbar , Afshar Reza Malekpour , Sarabi Roghayeh Ershad , Tavakoli Fatemeh , zolala farzaneh 
Published: February 2020

Abstract
Background
This study was conducted to provide evidence on the current status of breast cancer and its incidence trend in Eastern Mediterranean Region during 1998-2019. Also, this study aimed to investigate the association between the incidence of breast cancer and Human Development Index and some factors related to this index, including total fertility rate, and obesity, using a meta-analysis.
Method
Data on incidence of breast cancer were collected from various sources, including PubMed, Embase, Web of Science, and WHO, from 1998 to 2019 using systematic review and meta-analysis. Pooled age standardized rate was calculated based on study duration and quality of data using a subgroup analysis and random effect meta-analysis.
Results
A total of 80 studies (545 data points) were analyzed. Pooled age standardized rate of breast cancer for Eastern Mediterranean Region was 37.1 per 100 000 person-year (95% confidence interval [CI], 34.5, 39.8) during 2011-2019. age standardized rate of breast cancer had an upward trend in Eastern Mediterranean Region from 2005 to 2019. However, the increasing trend was found to be slightly different in various regions based on quality of data. Moreover, pooled age standardized rate had a significant association with Human Development Index [-89.2 (95% CI, -119.8, -58.7)] and obesity [1.2 (95% CI, 0.9, 1.5)].
Conclusion
Pooled age standardized rate of breast cancer in Eastern Mediterranean Region was lower than the global average. Also, the age standardized rate value and its incremental trend have been higher in countries with high-quality data than in other countries of this region in recent years. Data quality or physiological factors, such as increase in obesity rates, could be the reasons for this incremental trend.
Key words
Breast cancer, meta-analysis, Eastern Mediterranean region, Incidence
Setting up a nurse-led model of care for management of Hypertension and Diabetes Mellitus in a high HIV prevalence context in rural Zimbabwe: a descriptive study
Authors: Frieden Marthe Marie , Zamba Blessing , Mukumbi Nisbert , Mafaune Patron Titsha , Makumbe Brian , Irungu Elizabeth , Moneti Virginia , Isaakidis Petros , Garone Daniela , Prasai Madhu Janina 
Published: February 2020

Abstract
Background

In the light of the increasing burden of non-communicable diseases on health systems in low- and middle-income countries, particularly in Sub-Saharan Africa, context-adapted, cost-effective service delivery models are required urgently. Multiple models have been trialled across Africa with varying degrees of success. Zimbabwe is a low-income country with unique socio-economic challenges and a dual disease burden of infectious chronic diseases such as HIV and non-communicable diseases. We describe the experience of setting up and organising a nurse-led Diabetes Mellitus (DM) and Hypertension (HTN) model of care in rural Zimbabwe from July 2016 to June 2019.

Programme design and implementation

We used a conceptual framework successfully applied in the roll-out of antiretroviral therapy in Zimbabwe. Mirroring the HIV experience, we describe key enablers in the design and implementation of the model: decentralization of services, integration of care, simplification of guidelines, mentoring and task-sharing, provision of affordable medicines, quality assured laboratory support, patient empowerment, a dedicated monitoring and evaluation system, and a robust referral system. DM and HTN services were set up in 9 primary health care (PHC) facilities and two hospitals in Chipinge district, and integrated into the general out-patient department or pre-existing HIV clinics. In one hospital, an integrated chronic care clinic (ICCC) emerged. We provided mentoring for staff using simplified protocols, and patient education. Free medication and monitoring with point of care (POC) glycosylated haemoglobin (HbA1c) were provided. Nurses in 7 PHC facilities and one hospital developed sufficient knowledge and skills to diagnose and manage DM and HTN patients, and 3094 patients were registered. Major lessons learned include: the value of POC devices in the management of diabetes; the pressure on services due to added caseload, exacerbated by the availability of free medications; and the importance of leadership in successful programme implementation.

Conclusion

Our experience demonstrates a model for nurse-led decentralized integrated DM and HTN care in a high HIV prevalence rural, low-income context. Developing a context-adapted model of care is a dynamic process. We present our lessons learned with the intention of sharing experience which may be of value to other public health programme managers.
Exploring and analysing single cell multi-omics data with VDJView
Authors: Samir Jerome , Rizzetto Simone , Gupta Money , Luciani Fabio 
Published: February 2020

AbstractBackground Single cell RNA sequencing provides unprecedented opportunity to simultaneously explore the transcriptomic and immune receptor diversity of T and B cells. However, there are limited tools available that simultaneously analyse large multi-omics datasets integrated with metadata such as patient and clinical information.Results We developed VDJView, which permits the simultaneous or independent analysis and visualisation of gene expression, immune receptors, and clinical metadata of both T and B cells. This tool is implemented as an easy-to-use R shiny web-application, which integrates numerous gene expression and TCR analysis tools, and accepts data from plate-based sorted or high-throughput single cell platforms. We utilised VDJView to analyse several 10X scRNA-seq datasets, including a recent dataset of 150,000 CD8+ T cells with available gene expression, TCR sequences, quantification of 15 surface proteins, and 44 antigen specificities (across viruses, cancer, and self-antigens). We performed quality control, filtering of tetramer non-specific cells, clustering, random sampling and hypothesis testing to discover antigen specific gene signatures which were associated with immune cell differentiation states and clonal expansion across the pathogen specific T cells. We also analysed 563 single cells (plate-based sorted) obtained from 11 subjects, revealing clonally expanded T and B cells across primary cancer tissues and metastatic lymph-node. These immune cells clustered with distinct gene signatures according to the breast cancer molecular subtype. VDJView has been tested in lab meetings and peer-to-peer discussions, showing effective data generation and discussion without the need to consult bioinformaticians.Conclusions VDJView enables researchers without profound bioinformatics skills to analyse immune scRNA-seq data, integrating and visualising this with clonality and metadata profiles, thus accelerating the process of hypothesis testing, data interpretation and discovery of cellular heterogeneity. VDJView is freely available at https://bitbucket.org/kirbyvisp/vdjview .
Positive deviance for dual-method promotion among women in Uganda: Study protocol for a cluster randomized controlled trial
Authors: Kosugi Hodaka , Shibanuma Akira , Kiriya Junko , Ong Ken Ing Cherng , Mucunguzi Stephen , Muzoora Conrad , Jimba Masamine 
Published: February 2020

Abstract
Background Dual-method use is known as the most reliable protection against unintended pregnancies and sexually transmitted infections, including HIV. However, it is not commonly used in sub-Sharan Africa, especially among women using highly effective contraceptives. This article describes a protocol to evaluate the effect of an intervention formulated under the positive deviance approach for promoting dual-method use in Uganda. Methods One hundred women will be interviewed using a structured questionnaire to find those practicing dual-method use. Then, in-depth interviews will be conducted with all women using dual-method and ten women using only highly effective contraceptives to identify their unique practice. Then, a cluster randomized controlled trial will be conducted to examine the effect of an intervention formulated under the positive deviance approach on dual-method uptake and adherence. Twenty health facilities will be randomized to an intervention or control arm, and 480 women will be enrolled in each group. The participants will be followed up for eight months. Discussion This trial focuses on women who already adapted dual-method use and identifies their unique solutions to promote dual-method use. This trial could tackle barriers for dual-method use, which expert outsiders may fail to recognize, by analyzing and promulgating their unique behaviors. This study could provide evidence that the positive deviance approach can address unintended pregnancies and sexually transmitted infections as well as other health problems which usual approaches have failed to address.
Lapatinib in combination with capecitabine versus continued use of trastuzumab in breast cancer patients with trastuzumab-resistance: a retrospective study of a Chinese population.
Authors: Yang fan , Huang Xiang , Sun Chunxiao , Li Jianbin , Wang Biyun , Yan Min , Jin Feng , Wang Haibo , Zhang Jin , Fu Peifen , Zeng Tianyu , Wang Jian , Li Wei , Li Yongfei , Yang Mengzhu , Li Jun , Wu Hao , Fu Ziyi , Yin Yongmei , jiang zefei 
Published: February 2020

Abstract
Background: The efficacy and safety of lapatinib plus capecitabine (LC or LX) versus trastuzumab plus chemotherapy in patients with HER-positive metastatic breast cancer who are resistant to trastuzumab is unknown.
Methods: We retrospectively analyzed data from breast cancer patients who began treatment with regimens of lapatinib plus capecitabine (LC or LX) or trastuzumab beyond progression (TBP) at eight hospitals between May 2010 and October 2017.
Results: Among 554 patients who had developed resistance to trastuzumab, the median PFS (progression free survival) was 6.77 months in the LX group compared with 5.6 months in the TBP group (hazard ratio 0.804; 95% CI, 0.67 to 0.96; P=0.019). The central nervous system progression rate during treatment was 5.9% in the LX group and 12.5% in the TBP group (P=0.018).
Conclusion: The combination of lapatinib and capecitabine showed a prolonged PFS relative to TBP in patients who had progressed on trastuzumab.
The construction of a conceptual framework explaining the relation between barriers to change of management of neuropsychiatric symptoms in nursing homes: a qualitative study using focus groups
Authors: Teunenbroek Charlotte Frederike van , Verhagen Kim , Smalbrugge Martin , Persoon Anke , Zuidema Sytse U. , Gerritsen Debby L. 
Published: February 2020

Abstract
Background. Several efforts have been made to change management of neuropsychiatric symptoms (NPS) in nursing homes, however only few were successful. Numerous barriers to change in healthcare were identified, yet only one conceptual model is known to study their interrelationships . Unfortunately, this model does not discuss specific barriers encountered in nursing home practice. The aim of this study is to explore perceived barriers to change in the management of NPS in nursing homes and to construct a conceptual framework providing insight into the relative importance and interrelationships of these barriers when improving quality of care.
Methods. Four focus groups were conducted in different dementia special care units of one Dutch nursing home. Participants were either nursing staff, treatment staff or relatives of residents. Qualitative thematic analysis was conducted according to the five phases defined by Braun & Clarke. Finally, a conceptual framework showing the interrelations of barrier-themes was constructed using text fragments of the focus groups.
Results. We constructed a conceptual framework consisting of eight themes of barriers explaining the extent to which change in NPS-management can be achieved: 'organizational barriers', 'personal barriers', 'deficiency of staff knowledge', 'suboptimal communication', 'inadequate (multidisciplinary) collaboration', 'disorganization of processes', 'reactive coping' and 'differences in perception'. Addressing 'organizational barriers' and 'deficiency of staff knowledge' is a precondition for change. 'Suboptimal communication' and 'inadequate (multidisciplinary) collaboration' play a key role in the extent of change achieved via the themes 'differences in perception' and 'disorganization of processes'. Furthermore, 'personal barriers' influence all themes - except 'organizational barriers' - and may cause 'reactive coping', which in turn may lead to 'difficulties to structure processes'.
Conclusions. A conceptual framework was created explaining the relationships between barriers towards achieving change focused on improving management of NPS in nursing homes. After this framework has been confirmed and refined in additional research, it can be used to study the interrelatedness of barriers to change, and to determine the importance of addressing them for achieving change in the provided care.
Oral rinses in growth inhibition and treatment of Helicobacter pylori infection
Authors: Kashyap Dharmendra , Baral Budhadev , Verma Tarun Prakash , Sonkar Charu , Chatterji Debi , Jain Ajay Kumar , Jha Hem Chandra 
Published: February 2020

AbstractBackground Helicobacter pylori ( H. pylori ) is well-known for its role in chronic gastritis and gastric cancer. Eradication of these carcinogenic bacteria from the gut is one of the challenges for clinicians. The complexity of treatment mainly owes to antibiotic resistance and relapse due to an additional reservoir in the oral cavity. Our study emphases the isolation of H. pylori from distinct habitats of the gut microenvironment (gastric biopsy and gastric juice) and its subsequent characterization. We have also evaluated the effect of various oral rinses on isolated H. pylori from different anatomical locations of included subjects. Results The possible strains isolated from two different habitats of the same subject shows a striking difference in their growth pattern. Promisingly, some of the included oral rinses are efficient in growth inhibition as per recommended 30 sec treatment. The subsequent evaluation shows that oral rinse B (among A-E) is most effective and down-regulates the expression of one of the potent H. pylori gene, CagA, in the infected gastric adenocarcinoma (AGS) cells. Conclusion Our study, for the first time, revealed that H. pylori, isolated from the different habitat of the same subject, show a different growth pattern. The expression of H. pylori pathogenic gene (CagA) was down-regulated by the use of oral rinses. Hence, oral rinses will reduce the H. pylori in the oral cavity and help to control its migration from oral to the gastric compartment and may be used as an adjuvant treatment option for its re-infection.