bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fused inverse-normal method for integrated differential expression analysis of RNA-seq data
Authors: Prasad Birbal , Li Xinzhong 
Published: August 2022

AbstractBackgroundUse of next-generation sequencing technologies to transcriptomics (RNA-seq) for gene expression profiling has found widespread application in studying different biological conditions including cancers. However, RNA-seq experiments are still small sample size experiments due to the cost. Recently, an increased focus has been on meta-analysis methods for integrated differential expression analysis for exploration of potential biomarkers. In this study, we propose ap-value combination method for meta-analysis of multiple independent but related RNA-seq studies that accounts for sample size of a study and direction of expression of genes in individual studies.ResultsThe proposed method generalizes the inverse-normal method without an increase in statistical or computational complexity and does not pre- or post-hoc filter genes that have conflicting direction of expression in different studies. Thus, the proposed method, as compared to the inverse-normal, has better potential for the discovery of differentially expressed genes (DEGs) with potentially conflicting differential signals from multiple studies related to disease. We demonstrated the use of the proposed method in detection of biologically relevant DEGs in glioblastoma (GBM), the most aggressive brain cancer. Our approach notably enabled the identification of over-expressed tumour suppressor geneRAD51in GBM compared to healthy controls, which has recently been shown to be a target for inhibition to enhance radiosensitivity of GBM cells during treatment. Pathway analysis identified multiple aberrant GBM related pathways as well as novel regulators such asTCF7L2andMAPTas important upstream regulators in GBM.ConclusionsThe proposed meta-analysis method generalizes the existing inverse-normal method by providing a way to establish differential expression status for genes with conflicting direction of expression in individual RNA-seq studies. Hence, leading to further exploration of them as potential biomarkers for the disease.
Phylogenetic lineages of tuberculosis isolates and their association with patient demographics in Tanzania
Authors: Mutayoba Beatrice Kemilembe , Michael Hoelscher  , Heinrich Norbert , Joloba Moses L. , Lyamuya Eligius , Kilale Andrew Martin , Range Nyagosya Segere , Ngowi Bernard James , Ntinginya Nyanda Elias , Mfaume Saidi Mwinjuma , Wilfred Amani , Doulla Basra , Lyimo Johnson , Kisonga Riziki , Kingalu Amri , Kabahita Jupiter Marina , Guido Ocung , Kabugo Joel , Adam Isa , Luutu Moses , Namaganda Maria Magdalene , Namutebi Joanitah , Kasule George William , Nakato Hasfah , Byabajungu Henry , Lutaaya Pius , Musisi Kenneth , Oola Denis , Mboowa Gerald , Pletschette Michel 
Published: August 2022

Abstract
Background
Mycobacterium tuberculosis presents several lineages each with distinct characteristics of evolutionary status, transmissibility, drug resistance, host interaction, latency, and vaccine efficacy. Whole genome sequencing (WGS) has emerged as a new diagnostic tool to reliably inform the occurrence of phylogenetic lineages of Mycobacterium tuberculosis and examine their relationship with patient demographic characteristics and multidrug-resistance development.

Methods
191 Mycobacterium tuberculosis isolates obtained from a 2017/2018 Tanzanian drug resistance survey were sequenced on the Illumina Miseq platform at Supranational Tuberculosis Reference Laboratory in Uganda. Obtained fast-q files were imported into tools for resistance profiling and lineage inference (Kvarq v0.12.2, Mykrobe v0.8.1 and TBprofiler v3.0.5). Additionally for phylogenetic tree construction, RaxML-NG v1.0.3(25) was used to generate a maximum likelihood phylogeny with 800 bootstrap replicates. The resulting trees were plotted, annotated and visualized using ggtree v2.0.4

Results
Most [172(90.0%)] of the isolates were from newly treated Pulmonary TB patients. Coinfection with HIV was observed in 33(17.3%) TB patients. Of the 191 isolates, 22(11.5%) were resistant to one or more commonly used first line anti-TB drugs (FLD), 9(4.7%) isolates were MDR-TB while 3(1.6%) were resistant to all the drugs. Of the 24 isolates with any resistance conferring mutations, 13(54.2%) and 10(41.6%) had mutations in genes associated with resistance to INH and RIF respectively. The findings also show four major lineages i.e. Lineage 3[81 (42.4%)], followed by Lineage 4 [74 (38.7%)], the Lineage 1 [23 (12.0%)] and Lineages 2 [13 (6.8%)] circulaing in Tanzania.

Conclusion
The findings in this study show that Lineage 3 is the most prevalent lineage in Tanzania whereas drug resistant mutations were more frequent among isolates that belonged to Lineage 4.
The effectiveness of a mHealth-based integrated hospital-community-home program for people with type 2 diabetes in transitional care: a protocol for a multicenter pragmatic randomized controlled trial
Authors: Zhang Wenhui , Yang Pei , Wang Hongyan , Pan Xinxin , Wang Yanmei 
Published: August 2022

Abstract
Background
Diabetes is a progressive condition requiring long-term medical care and self-management. The ineffective transition from hospital to community or home health care may result in poor glycemic control and increase the risk of serious diabetes-related complications. In China, the most common transitional care model is home visits or telephone interventions led by a single healthcare setting, with a lack of cooperation between specialists and primary care, which leads to inadequate service and discontinuous care. Thus, an integrated hospital-community-home (i-HCH) transitional care program was developed to promote hospital and community cooperation and provide comprehensive and continuous medical care for type 2 diabetes mellitus (T2DM) via mobile health (mHealth) technology.

Methods
This protocol is for a multicenter randomized controlled trial in T2DM patients. Hospitalized patients diagnosed with T2DM who meet the eligibility criteria will be recruited. The patients will be randomly allocated to either the intervention or the control group and receive the i-HCH transitional care or usual transitional care intervention. The change in glycated hemoglobin is the primary outcome. Secondary outcome measures are blood pressure, lipids (total cholesterol, triglycerides, low-density lipoprotein, high-density lipoprotein), body mass index, self-management skills, quality of life, diabetes knowledge, transitional care satisfaction and the rate of readmission. The follow-up period of this study is six months.

Discussion
The study will enhance the cooperation between local hospitals and communities for diabetes transitional care. Research on the effectiveness of diabetes outcomes will have potentially significant implications for chronic disease patients, family members, health caregivers and policymakers.

Trial registration
Chinese Clinical Trial Registry ChiCTR1900023861: June 15, 2019.
Uncommon cause of trigeminal neuritis and central nervous system involvement by herpes labialis: a case report
Authors: Kim Hyunsoo , Kang Kyung Wook , Kim Jae-Myung , Park Man-Seok 
Published: August 2022

Abstract
Background
Trigeminal neuropathy is characterized by numbness in the region innervated by the trigeminal nerves, with or without neuropathic weakness in the muscles of mastication. Trigeminal neuritis is a form of trigeminal neuropathy in which the lesion is caused by an inflammation. Herein, we report a patient with trigeminal neuritis due to central nervous system (CNS) involvement of herpes labialis (HL) infection, which was successfully treated with anti-viral and anti-inflammatory agents.

Case presentation
A young healthy female presented with numbness in the left hemiface for two weeks. She had a preceding typical HL infection on left facial lip one week before the sensory symptom onset. Brain magnetic resonance imaging revealed high signal intensities and asymmetrical thickening with enhancement along the cisternal segment of the left trigeminal nerve. Additionally, brain MR angiography showed multifocal stenoses in the M1 segment of the middle cerebral artery and the cavernous portion of the internal carotid artery. Cerebrospinal fluid (CSF) examination showed mild pleocytosis with normal protein level, glucose ratio, but CSF polymerase chain reaction assay for specific anti-viral antibodies including herpes simplex virus was negative, and CSF culture also did not identify a specific pathogen. The results of serologic testing including tumor markers and autoimmune markers were all unremarkable. A tentative diagnosis of trigeminal neuritis as a complication of HL involving the CNS was made considering the clinical, neuroradiological, and laboratory findings of the patient. Therefore, the patient was treated with intravenous methylprednisolone and acyclovir for 10 days. After the treatments, her sensory disturbance was markedly improved. Brain MRI at the 3-month follow-up also demonstrated improvement of previously identified high signal intensity lesions and multifocal intracerebral artery stenoses.

Conclusion
HL is usually a self-limiting, benign disease without complications, but rarely presents as trigeminal neuritis due to CNS involvement. Therefore, meticulous evaluation may be necessary if trigeminal neuritis or CNS involving symptoms occur after HL.
Differential diagnosis and prognosis of small renal masses: association with collateral vessels detected using contrast-enhanced computed tomography
Authors: Yanagi Masato , Kiriyama Tomonari , Akatsuka Jun , Endo Yuki , Takeda Hayato , Katsu Akifumi , Honda Yuichiro , Suzuki Kyota , Nishikawa Yoshihiro , Ikuma Shunsuke , Mikami Hikaru , Toyama Yuka , Kimura Go , Kondo Yukihiro 
Published: August 2022

Abstract
Background
Active surveillance (AS) is one of the treatment methods for patients with small renal masses (SRMs; < 4 cm), including renal cell carcinomas (RCCs). However, some small RCCs may exhibit aggressive neoplastic behaviors and metastasize. Little is known about imaging biomarkers capable of identifying potentially aggressive small RCCs. Contrast-enhanced computed tomography (CECT) often detects collateral vessels arising from neoplastic angiogenesis in RCCs. Therefore, this study aimed to evaluate the association between SRM differential diagnoses and prognoses, and the detection of collateral vessels using CECT.

Methods
A total of 130 consecutive patients with pathologically confirmed non-metastatic SRMs (fat-poor angiomyolipomas [fpAMLs; n = 7] and RCCs [n = 123]) were retrospectively enrolled. Between 2011 and 2019, SRM diagnoses in these patients were confirmed after biopsy or surgical resection. All RCCs were surgically resected. Regardless of diameter, a collateral vessel (CV) was defined as any blood vessel connecting the tumor from around the kidney using CECT. First, we analyzed the role of CV-detection in differentiating between fpAML and RCC. Then, we evaluated the sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of RCC diagnosis based on CV-detection using CECT. We also assessed the prognostic value of CV-detection using the Fisher exact test, and Kaplan-Meier method and the log-rank test.

Results
The sensitivity, specificity, PPV, NPV, and accuracy of CV-detection for the diagnosis of small RCCs was 48.5, 45.5, 100, 100, and 9.5% respectively. Five of 123 (4.1%) patients with RCC experienced recurrence. CV-detection using CECT was the only significant factor associated with recurrence (p = 0.0177). Recurrence-free survival (RFS) was significantly lower in patients with CV compared with in those without CV (5-year RFS 92.4% versus 100%, respectively; p = 0.005). In addition, critical review of the CT images revealed the CVs to be continuous with the venous vessels around the kidney.

Conclusions
The detection of CVs using CECT is useful for differentiating between small fpAMLs and RCCs. CV-detection may also be applied as a predictive parameter for small RCCs prone to recurrence after surgical resection. Moreover, AS could be suitable for small RCCs without CVs.
Stereotactic irradiation on linear accelerator - ultrasound versus MRI in choroidal melanoma volume calculation
Authors: Furdova Alena , Furda Robert , Sramka Miron , Chorvath Martin , Rybar Jan , Vesely Pavol , Valaskova Jela , Siska Vladimir 
Published: August 2022

Abstract
Background
Stereotactic irradiation is one of the treatment modalities for intraocular uveal melanoma. The study’s purpose was to describe the background of stereotactic one-day session radiosurgery, how the comparison in the difference between the tumor volume measured values from the magnetic resonance imaging (MRI) method and the ultrasound method was related to it, and which method was more precise to be used for tumor regression after irradiation.

Methods
The group of 147 patients with choroidal melanoma was treated by stereotactic irradiation on the linear accelerator with a single dose of 35.0 Gy. During the standard treatment process the uveal melanoma volumes, needed for dose calculation, were obtained using MRI from the individual stereotactic planning scheme and by ultrasound from the ultrasound device. All volumes were statistically compared using the paired t-test, and for the visualization purpose, the Bland-Altman plot was used.

Results
In the group of patients, it was 70 (47.6%) males and 77 (52.4%) females. The tumor volume median was from MRI equal to 0.44 cm3 and from ultrasound equal to 0.53 cm3. The difference between the ultrasound and the MRI volume measured values was statistically significant. However, the Bland-Altman plot clearly documents that the two methods are in agreement and can be used interchangeably. In most of the cases, the measured values of the ultrasound-calculated volume achieved slightly higher measured values.

Conclusions
The calculation of the intraocular uveal tumor volume is a crucial part of the stereotactic irradiation treatment. The ultrasound volume measured values were in most of the cases higher than the measured values from the MRI. Although the methods are comparable and can be used interchangeably, we are recommending using the more precise MRI method not only during the treatment but also on later regular medical checks of tumor regression or progression.
Protocol and programme factors associated with referral and loss to follow-up from newborn hearing screening: a systematic review
Authors: Mackey Allison R. , Bussé Andrea M. L. , Del Vecchio Valeria , Mäki-Torkko Elina , Uhlén Inger M. 
Published: August 2022

AbstractBackgroundAn effective newborn hearing screening programme has low referral rate and low loss to follow-up (LTFU) rate after referral from initial screening. This systematic review identified studies evaluating the effect of protocol and programme factors on these two outcomes, including the screening method used and the infant group.MethodsFive databases were searched (latest: April 2021). Included studies reported original data from newborn hearing screening and described the target outcomes against a protocol or programme level factor. Studies were excluded if results were only available for one risk condition, for each ear, or for < 100 infants, or if methodological bias was observed. Included studies were evaluated for quality across three domains: sample, screening and outcome, using modified criteria from the Ottawa-Newcastle and QUADAS-2 scales. Findings from the included studies were synthesised in tables, figures and text.ResultsFifty-eight studies reported on referral rate, 8 on LTFU rate, and 35 on both. Only 15 studies defined LTFU. Substantial diversity in referral and LTFU rate was observed across studies. Twelve of fourteen studies that evaluated screening method showed lower referral rates with aABR compared to TEOAE for well babies (WB). Rescreening before hospital discharge and screening after 3 days of age reduced referral rates. Studies investigating LTFU reported lower rates for programmes that had audiologist involvement, did not require fees for step 2, were embedded in a larger regional or national programme, and scheduled follow-up in a location accessible to the families. In programmes with low overall LTFU, higher LTFU was observed for infants from the NICU compared to WB.ConclusionAlthough poor reporting and exclusion of non-English articles may limit the generalisability from this review, key influential factors for referral and LTFU rates were identified. Including aABR in WB screening can effectively reduce referral rates, but it is not the only solution. The reported referral and LTFU rates vary largely across studies, implying the contribution of several parameters identified in this review and the context in which the programme is performed. Extra attention should be paid to infants with higher risk for hearing impairment to ensure their return to follow-up.
Soil-transmitted helminthes and Schistosoma mansoni infections among primary school children at Ambasame primary school, North-West Ethiopia: a cross-sectional study
Authors: Feleke Daniel Getacher , Ali Abdurahaman , Bisetegn Habtye , Debash Habtu , Birara Workineh , Andualem Alehegn 
Published: August 2022

Abstract
Background
Schistosomiasis and soil-transmitted helminthiasis (STHs) are the major public health problem in the world especially in school age children. Therefore, this study aimed to determine the burden of soil transmitted helminths and Schistosoma mansoni among Ambesame primary school children, North-West Ethiopia.

Method
A cross sectional study was carried out at Ambasame primary school children from March to May, 2019. Study participants were selected using systematic random sampling technique. Socio-demographic characteristics and other factors were collected using structured questionnaire. Moreover, stool samples were examined microscopically using wet mount and formol ether concentration techniques. Data were entered and analyzed using SPSS version 20. Logistic regression analysis was done to investigate the association between dependent and independent variables. P-value less than 0.05 was considered as statistically significant.

Result
The overall prevalence of intestinal parasites was 117(31.2%). The prevalence of soil-transmitted helminthes and S.mansoni was 110 (29.3%) using formol ether concentration technique. The most predominant parasite was S. mansoni (10.7%), followed by hookworm (5.6%). Multivariate logistic regression analysis revealed that, helminthic infection was associated with children less than 7 years of age (P-value = 0.019, AOR = 3.29, 95% CI (1.21–8.91)); fathers who are able to read and write (P-value< 0.001, AOR = 5.4, 95% CI (2.37–12.33)); absence of latrine (P-value = 0.016, AOR = 12.96, 95% CI (1.60–104.87)) and untrimmed nail (P-value = 0.043, AOR = 2.09, 95% CI (1.02–4.27)).

Conclusion
This study revealed that the prevalence of intestinal helminthes among Ambasame primary school children was relatively high. The lower educational status of father, absence of latrine and untrimmed finger nail showed statistically significant association with intestinal helminthic infection. This indicates the school community, health offices and other stakeholders should plan a strategy to tackle problems associated with sanitary condition. Furthermore, Health policy makers, healthcare workers and health extension workers should enhance their effort of awareness creation for school children, parents, school community about personal hygiene, environmental sanitation, intestinal parasites transmission, prevention and control. Moreover, mass deworming of school children and periodic screening for parasitic infection should be done.
Associations of physical activity with academic achievement and academic burden in Chinese children and adolescents: do gender and school grade matter?
Authors: Zhang Danqing , Hong Jintao , Chen Sitong , Liu Yang 
Published: August 2022

Abstract
Background
Physical activity (PA) was significantly associated with cognition and mental health in children and adolescent. However, there were few studies examining the associations of PA with academic achievement (AA) and academic burden (AB) by gender and school grade. Hence, this study aimed to 1) investigate the associations of moderate-to-vigorous PA (MVPA) with AA and AB in Chinese children and adolescents, and 2) assess whether these associations vary by gender and school grade.

Methods
Using a multi-stage stratified cluster sampling design (at four different regions in Southern east China), 2653 children and adolescents (8–19 years old, 51.2% girls) were included. A self-reported questionnaire was used to collect data on study participants’ gender, school grade, family social economic status (SES), parental education level, MVPA, AA and AB. Binary logistic regression was applied to examine the associations of MVPA with AA (groups: above-average AA, average and below-average AA) and AB (groups: reporting AB, reporting no AB) with odds ratios (ORs) and 95% confidence intervals (CIs). After testing gender*grade interaction, those associations were explored by gender and school grade separately.

Results
In the overall sample, compared with children and adolescents who did not meet the PA guidelines (at least 60 min MVPA daily), children and adolescents who met the PA guidelines were more likely to have above-average (OR = 1.61, 95% CI: 1.21–2.11) AA, and report no AB (OR = 1.61, 95% CI: 1.13–2.30). In both genders, meeting the PA guidelines was positively associated with above-average AA (OR = 1.43, 95% CI: 1.01–2.03 for boys; OR = 2.22, 95% CI: 1.43–3.44 for girls). However, the significant relationship between meeting the PA guidelines and AB was observed only in girls (OR = 1.99, 95% CI: 1.17–3.39). Meeting the PA guidelines was positively associated with above-average AA (OR = 1.68, 95% CI: 1.18–2.40), and reporting no AB (OR = 1.77, 95% CI: 1.08–2.91) only in middle school students.

Conclusions
This study suggested that sufficient PA may be a contributary factor of improved AA and lower level of AB in Chinese children and adolescents. However, associations of PA with AA and AB may be different across gender or school grade. Promoting PA among girls or middle school students may be a good approach to improve AA and reduce AB.