bluuebunny/crossref_metadata_2025_split huggingface dataset:
De novo transcriptome analysis provides insights into formation of in vitro adventitious root from leaf explants of Arnebia euchroma
Authors: Devi Jyoti , Kaur Ekjot , Swarnkar Mohit Kumar , Acharya Vishal , Bhushan Shashi 
Published: September 2021

Abstract
Background
Adventitious root formation is considered a major developmental step during the propagation of difficult to root plants, especially in horticultural crops. Recently, adventitious roots induced through plant tissue culture methods have also been used for production of phytochemicals such as flavonoids, anthocyanins and anthraquinones. It is rather well understood which horticultural species will easily form adventitious roots, but the factors affecting this process at molecular level or regulating the induction process in in vitro conditions are far less known. The present study was conducted to identify transcripts involved in in vitro induction and formation of adventitious roots using Arnebia euchroma leaves at different time points (intact leaf (control), 3 h, 12 h, 24 h, 3 d, 7 d, 10 d and 15 d). A. euchroma is an endangered medicinal Himalayan herb whose root contains red naphthoquinone pigments. These phytoconstituents are widely used as an herbal ingredient in Asian traditional medicine as well as natural colouring agent in food and cosmetics.

Results
A total of 137.93 to 293.76 million raw reads were generated and assembled to 54,587 transcripts with average length of 1512.27 bps and N50 of 2193 bps, respectively. In addition, 50,107 differentially expressed genes were identified and found to be involved in plant hormone signal transduction, cell wall modification and wound induced mitogen activated protein kinase signalling. The data exhibited dominance of auxin responsive (AUXIN RESPONSE FACTOR8, IAA13, GRETCHEN HAGEN3.1) and sucrose translocation (BETA-31 FRUCTOFURANOSIDASE and MONOSACCHARIDE-SENSING protein1) genes during induction phase. In the initiation phase, the expression of LATERAL ORGAN BOUNDARIES DOMAIN16, EXPANSIN-B15, ENDOGLUCANASE25 and LEUCINE-rich repeat EXTENSION-like proteins was increased. During the expression phase, the same transcripts, with exception of LATERAL ORGAN BOUNDARIES DOMAIN16 were identified. Overall, the transcriptomic analysis revealed a similar patterns of genes, however, their expression level varied in subsequent phases of in vitro adventitious root formation in A. euchroma.

Conclusion
The results presented here will be helpful in understanding key regulators of in vitro adventitious root development in Arnebia species, which may be deployed in the future for phytochemical production at a commercial scale.
Genome-wide identification and characterization of bZIP transcription factors and their expression profile under abiotic stresses in Chinese pear (Pyrus bretschneideri)
Authors: Manzoor Muhammad Aamir , Manzoor Muhammad Mudassar , Li Guohui , Abdullah Muhammad , Han Wang , Wenlong Han , Shakoor Awais , Riaz Muhammad Waheed , Rehman Shamsur , Cai Yongping 
Published: September 2021

Abstract
Background
In plants, basic leucine zipper transcription factors (TFs) play important roles in multiple biological processes such as anthesis, fruit growth & development and stress responses. However, systematic investigation and characterization of bZIP-TFs remain unclear in Chinese white pear. Chinese white pear is a fruit crop that has important nutritional and medicinal values.

Results
In this study, 62 bZIP genes were comprehensively identified from Chinese Pear, and 54 genes were distributed among 17 chromosomes. Frequent whole-genome duplication (WGD) and dispersed duplication (DSD) were the major driving forces underlying the bZIP gene family in Chinese white pear. bZIP-TFs are classified into 13 subfamilies according to the phylogenetic tree. Subsequently, purifying selection plays an important role in the evolution process of PbbZIPs. Synteny analysis of bZIP genes revealed that 196 orthologous gene pairs were identified between Pyrus bretschneideri, Fragaria vesca, Prunus mume, and Prunus persica. Moreover, cis-elements that respond to various stresses and hormones were found on the promoter regions of PbbZIP, which were induced by stimuli. Gene structure (intron/exon) and different compositions of motifs revealed that functional divergence among subfamilies. Expression pattern of PbbZIP genes differential expressed under hormonal treatment abscisic acid, salicylic acid, and methyl jasmonate in pear fruits by real-time qRT-PCR.

Conclusions
Collectively, a systematic analysis of gene structure, motif composition, subcellular localization, synteny analysis, and calculation of synonymous (Ks) and non-synonymous (Ka) was performed in Chinese white pear. Sixty-two bZIP-TFs in Chinese pear were identified, and their expression profiles were comprehensively analyzed under ABA, SA, and MeJa hormones, which respond to multiple abiotic stresses and fruit growth and development. PbbZIP gene occurred through Whole-genome duplication and dispersed duplication events. These results provide a basic framework for further elucidating the biological function characterizations under multiple developmental stages and abiotic stress responses.
Incidence and survival analyses for occult lung cancer between 2004 and 2015: a population-based study
Authors: Wu Lei-Lei , Li Chong-Wu , Lin Wei-Kang , Qiu Li-Hong , Xie Dong 
Published: September 2021

Abstract
Background
This study aimed to investigate the incidence and long-term survival outcomes of occult lung cancer between 2004 and 2015.

Methods
A total of 2958 patients were diagnosed with occult lung cancer in the 305,054 patients with lung cancer. The entire cohort was used to calculate the crude incidence rate. Eligible 52,472 patients (T1-xN0M0, including 2353 occult lung cancers) were selected from the entire cohort to perform survival analyses after translating T classification according to the 8th TNM staging system. Cancer-specific survival curves for different T classifications were presented.

Results
The crude incidence rate of occult lung cancer was 1.00 per 100 patients, and it was reduced between 2004 and 2015 [1.4 per 100 persons in 2004; 0.6 per 100 persons in 2015; adjusted risk ratio = 0.437, 95% confidence interval (CI) 0.363–0.527]. In the survival analysis, there were 2206 death events in the 2353 occult lung cancers. The results of the multivariable analysis revealed that the prognoses with occult lung cancer were similar to patients with stage T3N0M0 (adjusted hazard ratio = 1.054, 95% CI 0.986–1.127, p = 0.121). Adjusted survival curves presented the same results. In addition, adjusted for other confounders, female, age ≤ 72 years, surgical treatment, radiotherapy, adenocarcinoma, and non-squamous and non-adenocarcinoma non-small cell carcinoma were independent protective prognostic factors (all p < 0.05).

Conclusions
Occult lung cancer was uncommon. However, the cancer-specific survival of occult lung cancer was poor, therefore, we should put the assessment of its prognoses on the agenda. Timely surgical treatment and radiotherapy could improve survival outcomes for those patients. Besides, we still need more research to confirm those findings.
Uev1A promotes breast cancer cell migration by up-regulating CT45A expression via the AKT pathway
Authors: Niu Tong , Wu Zhaojia , Xiao Wei 
Published: September 2021

Abstract
Background
UEV1A encodes a ubiquitin-E2 variant closely associated with tumorigenesis and metastasis, but its underlying mechanism in promoting metastasis remains to be investigated.

Methods
In this study, we experimentally manipulated UEV1A and CT45A gene expression and monitored their effects on cancer-related gene expression, cell migration and the signal transduction cascade.

Results
It was found that UEV1A overexpression induces CT45A family gene expression in breast cancer cells. Indeed, ectopic expression of UEV1A was sufficient to induce CT45A and its downstream genes involved in tumorigenesis, epithelial-mesenchymal transition (EMT), stemness and metastasis, and to promote cell migration and EMT signaling. Consistently, depletion of CT45A abolished the above effects, indicating that CT45A is a critical downstream effector of Uev1A. The Uev1A-induced cell migration and EMT signaling was dependent on AKT but independent of NF-κB, indicating that CT45A acts downstream of the AKT pathway.

Conclusions
Based on previous reports and observations in this study, we propose that the Ubc13-Uev1A complex activates AKT through K63-linked polyubiquitination, which leads to enhanced CT45A expression, stimulated cell migration and EMT signaling in breast cells. Since similar effects were also observed in a colorectal cancer cell line, the Ubc13/Uev1A-AKT-CT45A axis may also promote tumorigenesis and metastasis in other tissues.
Application of CD54 in diagnosing bone marrow involvement by using flow cytometry in patients with diffuse large B-cell lymphoma
Authors: Wang Wei , Li Yan , Rivera Rivera Xavier , Zhao Linjun , Mei Di , Hu Wenqing , Jiang Bin 
Published: September 2021

AbstractBackgroundFlow cytometry plays a key role in detecting bone marrow (BM) involvement in patients with diffuse large B-cell lymphoma (DLBCL). To improve its detection sensitivity, we need to explore novel markers. In this study, we detected the expression CD54 on lymphoma cells in BM specimens from DLBCL patients and clarified its diagnostic significance in BM involvement by DLBCL.MethodsWe collected BM specimens from 76 patients with DLBCL (germinal center B-cell (GCB) = 25, non-GCB = 51) and 10 control patients without lymphoma. We detected and compared the expression of CD54 on lymphoma cells and normal mature B cells by using 10-color panels.ResultsNormal plasma cells expressed a higher level of CD54 as compared with hematogones (p < 0.05) and normal mature B cells (p < 0.05). Among 76 patients, 23 of them (GCB = 12, non-GCB = 11) had BM involvement. Lymphoma B cells from 12 cases (GBC = 4, non-GCB = 8) expressed a higher level of CD54 compared to normal mature B cells (p < 0.05). Additionally, lymphoma cells of the non-GCB subtype frequently expressed a higher level of CD54 in comparison to the GCB subtype (p < 0.05). And the high expression of CD54 was not related to plasmacytoid differentiation.ConclusionAberrant expression of CD54 on lymphoma cells is frequently seen in patients’ BM specimens involved by DLBCL, especially in the non-GCB subtype. CD54 could be used as a new marker to gate on lymphoma cells and improve the detection sensitivity of BM involvement in patients with DLBCL.
The diagnostic trajectory in autism and intellectual disability in Quebec: pathways and parents’ perspective
Authors: Rivard Mélina , Patrick Coulombe , Mello Catherine , Morin Diane , Morin Marjorie 
Published: September 2021

Abstract
Background
This paper aimed to describe the diagnostic service trajectory of families of children with autism or intellectual disability in the province of Québec and identify predictors of parents’ perceptions of its quality.

Methods
The Evaluation of the services Trajectory in Autism by Parents instrument was completed by 259 parents at an assessment clinic. Children’s clinical records were also examined.

Results
On average 26 months elapsed between their first concerns and their child’s diagnosis, a period during which few (25%) received support. Parents’ evaluations were generally positive but were lower for the accessibility of the pre-assessment phase and the flexibility of the assessment process. Longer delays and a greater number of professionals consulted were associated with lower quality ratings. Some language-, immigration status-, and income-related differences in families’ appraisals were noted.

Conclusion
The diagnostic trajectory for neurodevelopmental disorders within public services in Québec presents some efficiency and accessibility challenges. Possible improvements are proposed to facilitate screening and to support families throughout this phase of their trajectory.
Pharmacies in informal settlements: a retrospective, cross-sectional household and health facility survey in four countries
Authors:   Improving Health in Slums Collaborative, Bakibinga Pauline , Kabaria Caroline , Kasiira Ziraba , Kibe Peter , Kyobutungi Catherine , Mbaya Nelson , Mberu Blessing , Mohammed Shukri , Njeri Anne , Azam Iqbal , Iqbal Romaina , Nazish Ahsana , Rizvi Narijis , Shifat Ahmed Syed A. K. , Choudhury Nazratun , Alam Ornob , Khan Afreen Zaman , Rahman Omar , Yusuf Rita , Odubanjo Doyin , Ayobola Motunrayo , Fayehun Olufunke , Omigbodun Akinyinka , Osuh Mary , Owoaje Eme , Taiwo Olalekan , Lilford Richard J. , Sartori Jo , Watson Samuel I. , Diggle Peter J. , Aujla Navneet , Chen Yen-Fu , Gill Paramjit , Griffiths Frances , Harris Bronwyn , Madan Jason , Muir Helen , Oyebode Oyinlola , Pitidis Vangelis , de Albuquerque João Porto , Smith Simon , Taylor Celia , Ulbrich Philip , Uthman Olalekan A. , Wilson Ria , Yeboah Godwin , Watson Sam 
Published: September 2021

AbstractBackgroundSlums or informal settlements characterize most large cities in LMIC. Previous evidence suggests pharmacies may be the most frequently used source of primary care in LMICs but that pharmacy services are of variable quality. However, evidence on pharmacy use and availability is very limited for slum populations.MethodsWe conducted household, individual, and healthcare provider surveys and qualitative observations on pharmacies and pharmacy use in seven slum sites in four countries (Nigeria, Kenya, Pakistan, and Bangladesh). All pharmacies and up to 1200 households in each site were sampled. Adults and children were surveyed about their use of healthcare services and pharmacies were observed and their services, equipment, and stock documented.ResultsWe completed 7692 household and 7451 individual adults, 2633 individual child surveys, and 157 surveys of pharmacies located within the seven sites. Visit rates to pharmacies and drug sellers varied from 0.1 (Nigeria) to 3.0 (Bangladesh) visits per person-year, almost all of which were for new conditions. We found highly variable conditions in what constituted a “pharmacy” across the sites and most pharmacies did not employ a qualified pharmacist. Analgesics and antibiotics were widely available but other categories of medications, particularly those for chronic illness were often not available anywhere. The majority of pharmacies lacked basic equipment such as a thermometer and weighing scales.ConclusionsPharmacies are locally and widely available to residents of slums. However, the conditions of the facilities and availability of medicines were poor and prices relatively high. Pharmacies may represent a large untapped resource to improving access to primary care for the urban poor.
Geospatial analysis and impact of targeted development of breast cancer care in The Gambia: a cross-sectional study
Authors: Sanyang Ousman , Lopez-Verdugo Fidel , Mali Meghan , Moustafa Moustafa , Nellermoe Jonathan , Sorensen Justin , Bittaye Mustapha , Njie Ramou , Singhateh Yankuba , Sambou Ngally Aboubacarr , Goldsmith Alison , Mohammed Nuredin I. , Brownson Kirstyn E. , Price Raymond R. , Sutherland Edward 
Published: September 2021

Abstract
Background
The Gambia has one of the lowest survival rates for breast cancer in Africa. Contributing factors are late presentation, delays within the healthcare system, and decreased availability of resources. We aimed to characterize the capacity and geographic location of healthcare facilities in the country and calculate the proportion of the population with access to breast cancer care.

Methods
A facility-based assessment tool was administered to secondary and tertiary healthcare facilities and private medical centers and clinics in The Gambia. GPS coordinates were obtained, and proximity of service availability and population analysis were performed. Distance thresholds of 10, 20, and 45 km were chosen to determine access to screening, pathologic diagnosis, and surgical management. An additional population analysis was performed to observe the potential impact of targeted development of resources for breast cancer care.

Results
All 102 secondary and tertiary healthcare facilities and private medical centers and clinics in The Gambia were included. Breast cancer screening is mainly performed through clinical breast examination and is available in 52 facilities. Seven facilities provide pathologic diagnosis and surgical management of breast cancer. The proportion of the Gambian population with access to screening, pathologic diagnosis, and surgical management is 72, 53, and 62%, respectively. A hypothetical targeted expansion of resources would increase the covered population to 95, 62, and 84%.

Conclusions
Almost half of the Gambian population does not have access to pathologic diagnosis and surgical management of breast cancer within the distance threshold utilized in the study. Mapping and population analysis can identify areas for targeted development of resources to increase access to breast cancer care.
Pathologic tau conformer ensembles induce dynamic, liquid-liquid phase separation events at the nuclear envelope
Authors: Kang Sang-Gyun , Han Zhuang Zhuang , Daude Nathalie , McNamara Emily , Wohlgemuth Serene , Molina-Porcel Laura , Safar Jiri G. , Mok Sue-Ann , Westaway David 
Published: September 2021

Abstract
Background
The microtubule-associated protein tau forms aggregates in different neurodegenerative diseases called tauopathies. Prior work has shown that a single P301L mutation in tau gene, MAPT, can promote alternative tau folding pathways that correlate with divergent clinical diagnoses. Using progressive chemical denaturation, some tau preparations from the brain featured complex transitions starting at low concentrations of guanidine hydrochloride (GdnHCl) denaturant, indicating an ensemble of differently folded tau species called conformers. On the other hand, brain samples with abundant, tangle-like pathology had simple GdnHCl unfolding profile resembling the profile of fibrillized recombinant tau and suggesting a unitary conformer composition. In studies here we sought to understand tau conformer progression and potential relationships with condensed liquid states, as well as associated perturbations in cell biological processes.

Results
As starting material, we used brain samples from P301L transgenic mice containing tau conformer ensembles that unfolded at low GdnHCl concentrations and with signatures resembling brain material from P301L subjects presenting with language or memory problems. We seeded reporter cells expressing a soluble form of 4 microtubule-binding repeat tau fused to GFP or YFP reporter moieties, resulting in redistribution of dispersed fluorescence signals into focal assemblies that could fuse together and move within processes between adjacent cells. Nuclear envelope fluorescent tau signals and small fluorescent inclusions behaved as a demixed liquid phase, indicative of liquid-liquid phase separation (LLPS); these droplets exhibited spherical morphology, fusion events and could recover from photobleaching. Moreover, juxtanuclear tau assemblies were associated with disrupted nuclear transport and reduced cell viability in a stable cell line. Staining for thioflavin S (ThS) became more prevalent as tau-derived inclusions attained cross-sectional area greater than 3 μm2, indicating (i) a bipartite composition, (ii) in vivo progression of tau conformers, and (iii) that a mass threshold applying to demixed condensates may drive liquid-solid transitions.

Conclusions
Tau conformer ensembles characterized by denaturation at low GdnHCl concentration templated the production of condensed droplets in living cells. These species exhibit dynamic changes and develop in vivo, and the larger ThS-positive assemblies may represent a waystation to arrive at intracellular fibrillar tau inclusions seen in end-stage genetic tauopathies.
Tuberculosis related disability: a systematic review and meta-analysis
Authors: Alene Kefyalew Addis , Wangdi Kinley , Colquhoun Samantha , Chani Kudakwashe , Islam Tauhid , Rahevar Kalpeshsinh , Morishita Fukushi , Byrne Anthony , Clark Justin , Viney Kerri 
Published: September 2021

AbstractBackgroundThe sustainable development goals aim to improve health for all by 2030. They incorporate ambitious goals regarding tuberculosis (TB), which may be a significant cause of disability, yet to be quantified. Therefore, we aimed to quantify the prevalence and types of TB-related disabilities.MethodsWe performed a systematic review of TB-related disabilities. The pooled prevalence of disabilities was calculated using the inverse variance heterogeneity model. The maps of the proportions of common types of disabilities by country income level were created.ResultsWe included a total of 131 studies (217,475 patients) that were conducted in 49 countries. The most common type of disabilities were mental health disorders (23.1%), respiratory impairment (20.7%), musculoskeletal impairment (17.1%), hearing impairment (14.5%), visual impairment (9.8%), renal impairment (5.7%), and neurological impairment (1.6%). The prevalence of respiratory impairment (61.2%) and mental health disorders (42.0%) was highest in low-income countries while neurological impairment was highest in lower middle-income countries (25.6%). Drug-resistant TB was associated with respiratory (58.7%), neurological (37.2%), and hearing impairments (25.0%) and mental health disorders (26.0%), respectively.ConclusionsTB-related disabilities were frequently reported. More uniform reporting tools for TB-related disability and further research to better quantify and mitigate it are urgently needed.Prospero registration numberCRD42019147488