bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transfer Printing of Perovskite Whispering Gallery Mode Laser Cavities by Thermal Release Tape
Authors: Li Guo-Hui , Zhou Bo-Lin , Hou Zhen , Wei Yan-Fu , Wen Rong , Ji Ting , Wei Yi , Hao Yu-Ying , Cui Yan-Xia 
Published: January 2022

AbstractThe outstanding optoelectrical properties and high-quality factor of whispering gallery mode perovskite nanocavities make it attractive for applications in small lasers. However, efforts to make lasers with better performance have been hampered by the lack of efficient methods for the synthesis and transfer of perovskite nanocavities on desired substrate at quality required for applications. Here, we report transfer printing of perovskite nanocavities grown by chemical vapor deposition from mica substrate onto SiO2 substrate. Transferred perovskite nanocavity has an RMS roughness of ~ 1.2 nm and no thermal degradation in thermal release process. We further use femtosecond laser to excite a transferred perovskite nanocavity and measures its quality factor as high as 2580 and a lasing threshold of 27.89 μJ/cm2 which is almost unchanged as compared with pristine perovskite nanocavities. This method represents a significant step toward the realization of perovskite nanolasers with smaller sizes and better heat management as well as application in optoelectronic devices.
Ultra-High Response Detection of Alcohols Based on CdS/MoS2 Composite
Authors: Liu Lei , Yang Weiye , Zhang Hui , Yan Xueqian , Liu Yingkai 
Published: January 2022

AbstractHybrid CdS/MoS2 with branch and leaf shaped structures are successfully synthesized by hydrothermal method. It is applied to detect volatile organic compounds, a basic source of indoor air pollution with deleterious effects on the human health. The sensor based on CdS/MoS2 displays an outstanding response to alcohols among numerous gases. Their response to 100 ppm ethanol and isopropanol reaches 56 and 94, respectively. Benefiting from the dendrite-like biomimetic structure and synergy effect of CdS and MoS2, the sensor exhibits higher response than traditional gas sensor. For multiple alcohols, the limit of detection reached ppb level. In addition, by comparing the response of ethanol, isopropanol, isoamyl alcohol and their mixtures with acetone and methanal, a strong resistance interference is observed. This work proved that the modified detector holds broad promise in the detection of alcohols.
Uncomplicated Plasmodium vivax malaria: mapping the proteome from circulating platelets
Authors: Fernández Diana , Segura Cesar , Arman Mònica , McGill Suzanne , Burchmore Richard , Lopera-Mesa Tatiana 
Published: January 2022

Abstract
Background
Thrombocytopenia is frequent in Plasmodium vivax malaria but the role of platelets in pathogenesis is unknown. Our study explores the platelet (PLT) proteome from uncomplicated P. vivax patients, to fingerprint molecular pathways related to platelet function. Plasma levels of Platelet factor 4 (PF4/CXCL4) and Von Willebrand factor (VWf), as well as in vitro PLTs—P. vivax infected erythrocytes (Pv-IEs) interactions were also evaluated to explore the PLT response and effect on parasite development.

Methods
A cohort of 48 patients and 25 healthy controls were enrolled. PLTs were purified from 5 patients and 5 healthy controls for Liquid Chromatography–Mass spectrometry (LC–MS/MS) analysis. Plasma levels of PF4/CXCL4 and VWf were measured in all participants. Additionally, P. vivax isolates (n = 10) were co-cultured with PLTs to measure PLT activation by PF4/CXCL4 and Pv-IE schizonts formation by light microscopy.

Results
The proteome from uncomplicated P. vivax patients showed 26 out of 215 proteins significantly decreased. PF4/CXCL4 was significantly decreased followed by other proteins involved in platelet activation, cytoskeletal remodeling, and endothelial adhesion, including glycoprotein V that was significantly decreased in thrombocytopenic patients. In contrast, acute phase proteins, including SERPINs and Amyloid Serum A1 were increased. High levels of VWf in plasma from patients suggested endothelial activation while PF4/CXCL4 plasma levels were similar between patients and controls. Interestingly, high levels of PF4/CXCL4 were released from PLTs—Pv-IEs co-cultures while Pv-IEs schizont formation was inhibited.

Conclusions
The PLT proteome analyzed in this study suggests that PLTs actively respond to P. vivax infection. Altogether, our findings suggest important roles of PF4/CXCL4 during uncomplicated P. vivax infection through a possible intracellular localization. Our study shows that platelets are active responders to P. vivax infection, inhibiting intraerythrocytic parasite development. Future studies are needed to further investigate the molecular pathways of interaction between platelet proteins found in this study and host response, which could affect parasite control as well as disease progression.
The impact of polymerase chain reaction (PCR) on diagnosis and management of infectious uveitis at a tertiary care facility
Authors: Fallon Julia , Narayan Swati , Lin Jun , Sassoon Jodi , Llop Stephanie 
Published: January 2022

Abstract
Background
Polymerase Chain Reaction (PCR) is a well-accepted adjunct in the management of infectious uveitis. In turn, few reports in the literature have evaluated how PCR then impacts patient care. This study aims to evaluate the impact of PCR sampling on diagnosis and treatment of infectious uveitidies at a large tertiary care facility.

Main body
This is a retrospective, observational study of patients with aqueous and vitreous PCR samples obtained from 2014 to 2019. The study was undertaken at a single institution. At least one follow up visit following results of PCR testing was required for inclusion. If a patient had multiple PCR samples taken, only the first sample was included. The patients were divided into three categories based on pre-sampling diagnosis. A chi-square test was used to analyze the data. 108 cases were available for analysis. PCR did not change diagnosis or management in any of the cases where pre-sampling diagnosis carried a high clinical suspicion for negative PCR. Overall, the results of PCR testing had a more significant impact on diagnosis in those cases where pre-sampling diagnosis was unknown versus those where it was confirmatory in nature, thus presumed to be related to an infectious entity tested by PCR (74% vs. 29%, p = 0.00006). The rate of treatment change based on PCR was similar between those cases where there was a high clinical suspicion for positive PCR and those where pre-sampling diagnosis was unknown (32% vs. 33%, p = 0.95). Further analyzing specimens separately depending on source of sample, this pattern persisted for aqueous samples, with PCR showing a more significant impact on diagnosis in those cases where the diagnosis was unknown versus those where sampling was confirmatory (86% vs. 31%, p = 0.00004). The rate of change in treatment between the two groups was similar (35% vs. 31%, p = 0.79). Vitreous samples followed a similar pattern with a higher rate of diagnosis change for those cases where pre-sampling diagnosis was unknown and a similar rate in treatment change between the two groups, however this did not reach statistical signifigance (44% vs. 25%, p = 0.28; 27% vs. 33%, p = 0.74).

Conclusion
There is no well-defined algorithm as to when to employ PCR testing in uveitis. As expected, in our experience, it has the largest impact on diagnosis when the diagnosis is unknown, however even when confirmatory in nature, it continues to impact patient management.
DEGnext: classification of differentially expressed genes from RNA-seq data using a convolutional neural network with transfer learning
Authors: Kakati Tulika , Bhattacharyya Dhruba K. , Kalita Jugal K. , Norden-Krichmar Trina M. 
Published: January 2022

AbstractBackgroundA limitation of traditional differential expression analysis on small datasets involves the possibility of false positives and false negatives due to sample variation. Considering the recent advances in deep learning (DL) based models, we wanted to expand the state-of-the-art in disease biomarker prediction from RNA-seq data using DL. However, application of DL to RNA-seq data is challenging due to absence of appropriate labels and smaller sample size as compared to number of genes. Deep learning coupled with transfer learning can improve prediction performance on novel data by incorporating patterns learned from other related data. With the emergence of new disease datasets, biomarker prediction would be facilitated by having a generalized model that can transfer the knowledge of trained feature maps to the new dataset. To the best of our knowledge, there is no Convolutional Neural Network (CNN)-based model coupled with transfer learning to predict the significant upregulating (UR) and downregulating (DR) genes from both trained and untrained datasets.ResultsWe implemented a CNN model, DEGnext, to predict UR and DR genes from gene expression data obtained from The Cancer Genome Atlas database. DEGnext uses biologically validated data along with logarithmic fold change values to classify differentially expressed genes (DEGs) as UR and DR genes. We applied transfer learning to our model to leverage the knowledge of trained feature maps to untrained cancer datasets. DEGnext’s results were competitive (ROC scores between 88 and 99$$\%$$%) with those of five traditional machine learning methods: Decision Tree, K-Nearest Neighbors, Random Forest, Support Vector Machine, and XGBoost. DEGnext was robust and effective in terms of transferring learned feature maps to facilitate classification of unseen datasets. Additionally, we validated that the predicted DEGs from DEGnext were mapped to significant Gene Ontology terms and pathways related to cancer.ConclusionsDEGnext can classify DEGs into UR and DR genes from RNA-seq cancer datasets with high performance. This type of analysis, using biologically relevant fine-tuning data, may aid in the exploration of potential biomarkers and can be adapted for other disease datasets.
ImmunoDataAnalyzer: a bioinformatics pipeline for processing barcoded and UMI tagged immunological NGS data
Authors: Vetter Julia , Schaller Susanne , Heinzel Andreas , Aschauer Constantin , Reindl-Schwaighofer Roman , Jelencsics Kira , Hu Karin , Oberbauer Rainer , Winkler Stephan M. 
Published: January 2022

Abstract
Background
Next-generation sequencing (NGS) is nowadays the most used high-throughput technology for DNA sequencing. Among others NGS enables the in-depth analysis of immune repertoires. Research in the field of T cell receptor (TCR) and immunoglobulin (IG) repertoires aids in understanding immunological diseases. A main objective is the analysis of the V(D)J recombination defining the structure and specificity of the immune repertoire. Accurate processing, evaluation and visualization of immune repertoire NGS data is important for better understanding immune responses and immunological behavior.

Results
ImmunoDataAnalyzer (IMDA) is a pipeline we have developed for automatizing the analysis of immunological NGS data. IMDA unites the functionality from carefully selected immune repertoire analysis software tools and covers the whole spectrum from initial quality control up to the comparison of multiple immune repertoires. It provides methods for automated pre-processing of barcoded and UMI tagged immune repertoire NGS data, facilitates the assembly of clonotypes and calculates key figures for describing the immune repertoire. These include commonly used clonality and diversity measures, as well as indicators for V(D)J gene segment usage and between sample similarity. IMDA reports all relevant information in a compact summary containing visualizations, calculations, and sample details, all of which serve for a more detailed overview. IMDA further generates an output file including key figures for all samples, designed to serve as input for machine learning frameworks to find models for differentiating between specific traits of samples.

Conclusions
IMDA constructs TCR and IG repertoire data from raw NGS reads and facilitates descriptive data analysis and comparison of immune repertoires. The IMDA workflow focus on quality control and ease of use for non-computer scientists. The provided output directly facilitates the interpretation of input data and includes information about clonality, diversity, clonotype overlap as well as similarity, and V(D)J gene segment usage. IMDA further supports the detection of sample swaps and cross-sample contamination that potentially occurred during sample preparation. In summary, IMDA reduces the effort usually required for immune repertoire data analysis by providing an automated workflow for processing raw NGS data into immune repertoires and subsequent analysis. The implementation is open-source and available on https://bioinformatics.fh-hagenberg.at/immunoanalyzer/.
Complete chloroplast genomes of Rubus species (Rosaceae) and comparative analysis within the genus
Authors: Yu Jiaojun , Fu Jun , Fang Yuanping , Xiang Jun , Dong Hongjin 
Published: January 2022

Abstract
Background
Rubus is the largest genus of the family Rosaceae and is valued as medicinal, edible, and ornamental plants. Here, we sequenced and assembled eight chloroplast (cp) genomes of Rubus from the Dabie Mountains in Central China. Fifty-one Rubus species were comparatively analyzed for the cp genomes including the eight newly discovered genomes and forty-three previously reported in GenBank database (NCBI).

Results
The eight newly obtained cp genomes had the same quadripartite structure as the other cp genomes in Rubus. The length of the eight plastomes ranged from 155,546 bp to 156,321 bp with similar GC content (37.0 to 37.3%). The results indicated 133–134 genes were annotated for the Rubus plastomes, which contained 88 or 89 protein coding genes (PCGs), 37 transfer RNA genes (tRNAs), and eight ribosomal RNA genes (rRNAs). Among them, 16 (or 18) of the genes were duplicated in the IR region. Structural comparative analysis results showed that the gene content and order were relatively preserved. Nucleotide variability analysis identified nine hotspot regions for genomic divergence and multiple simple sequences repeats (SSRs), which may be used as markers for genetic diversity and phylogenetic analysis. Phylogenetic relationships were highly supported within the family Rosaceae, as evidenced by sub-clade taxa cp genome sequences.

Conclusion
Thus, the whole plastome may be used as a super-marker in phylogenetic studies of this genus.
High prevalence and low awareness of hyperuricemia in hypertensive patients among adults aged 50–79 years in Southwest China
Authors: Zhang Yang , Nie Feng-Qin , Huang Xiao-Bo , Tang Weiwei , Hu Rong , Zhang Wen-Qiang , Liu Jian-Xiong , Xu Rong-Hua , Liu Ya , Wei Dong , Wang Tzung-Dau , Fan Xu 
Published: January 2022

Abstract
Introduction
This study was aimed to assess the prevalence of hyperuricemia and its associated risk factors among hypertensive patients in Southwest China.

Methods
From September 2013 to March 2014, a multistage, stratified sampling was conducted on 3505 hypertensive people aged 50–79 years who lived in urban communities within Chengdu and Chongqing, using a questionnaire and performing physical and biochemical measurements.

Results
In the study population, approximately 18.2% of all hypertensive participants had hyperuricemia (638/3505), with a prevalence rate of 21.5% in men and 16.2% in women (p < 0.05). Multivariate logistic regression analysis showed that aging, without spouse, current drinking, preferring hotpot, hypertriglyceridemia, BMI ≥ 25 kg/ m2, and central obesity were all positively correlated with hyperuricemia, whereas female gender was negatively correlated with hyperuricemia. The prevalence of hyperuricemia among hypertensive patients in urban adults aged 50–79 years in southwestern China was high, while levels of awareness were extremely low.

Discussion
Improved hyperuricemia health knowledge should be delivered to improve public awareness of the disease and it may need aggressive strategies aiming at the prevention and treatment of hyperuricemia. It is may necessary to encourage people to check blood uric acid levels when they first time to be diagnosed with hypertension, especially in the elderly.
The impact of lookback windows on the prevalence and incidence of chronic diseases among people living with HIV: an exploration in administrative health data in Canada
Authors: Nanditha Ni Gusti Ayu , Dong Xinzhe , McLinden Taylor , Sereda Paul , Kopec Jacek , Hogg Robert S. , Montaner Julio S. G. , Lima Viviane D. 
Published: January 2022

AbstractBackgroundWe described the impact of different lengths of lookback window (LW), a retrospective time period to observe diagnoses in administrative data, on the prevalence and incidence of eight chronic diseases.MethodsOur study populations included people living with HIV (N = 5151) and 1:5 age-sex-matched HIV-negative individuals (N = 25,755) in British Columbia, Canada, with complete follow-up between 1996 and 2012. We measured period prevalence and incidence of diseases in 2012 using LWs ranging from 1 to 16 years. Cases were deemed prevalent if identified in 2012 or within a defined LW, and incident if newly identified in 2012 with no previous cases detected within a defined LW. Chronic disease cases were ascertained using published case-finding algorithms applied to population-based provincial administrative health datasets.ResultsOverall, using cases identified by the full 16-year LW as the reference, LWs ≥8 years and ≥ 4 years reduced the proportion of misclassified prevalent and incidence cases of most diseases to < 20%, respectively. The impact of LWs varied across diseases and populations.ConclusionsThis study underscored the importance of carefully choosing LWs and demonstrated data-driven approaches that may inform these choices. To improve comparability of prevalence and incidence estimates across different settings, we recommend transparent reporting of the rationale and limitations of chosen LWs.
Associations of social isolation, social participation, and loneliness with frailty in older adults in Singapore: a panel data analysis
Authors: Ge Lixia , Yap Chun Wei , Heng Bee Hoon 
Published: January 2022

Abstract
Background
There is a shortage of research evidence about how social isolation, social participation, and loneliness were longitudinally associated with frailty. This study was to 1) examine the associations of social isolation, social participation, and loneliness with level of frailty among community-dwelling older adults using panel data, and 2) explore the moderating effect of gender on the association of social isolation, social participation and loneliness with frailty.

Methods
The study included 606 participants aged 60 years and above from the longitudinal Population Health Index Survey conducted in Singapore. At each timepoint, level of frailty was determined using the Clinical Frailty Scale. Social isolation was assessed by the Lubben Social Network Scale-6, and loneliness was assessed using the three-item UCLA Loneliness Scale. Fixed-effects ordinal logistic regressions were conducted with level of frailty as the dependent variable and social isolation and loneliness as the independent variables, adjusting for time-varying socio-demographic, lifestyle, and health-related factors.

Results
Increase in social participation was associated with lower level of frailty (odds ratio: 0.96, 95% confidence interval: 0.93–0.99) and feeling lonely was associated with higher level of frailty (odds ratio: 2.90, 95% confidence interval: 1.44–5.84). Social isolation was not associated with frailty. Gender did not have moderating effect on these associations.

Conclusions
This study observed that social isolation and loneliness had differential longitudinal association with level of frailty among community-dwelling older adults and suggested that loneliness and frailty should be measured and addressed concurrently among community-dwelling older adults.
Causes of death and associated factors over a decade of follow-up in a cohort of people living with HIV in rural Tanzania
Authors: Mollel Getrud Joseph , Moshi Lilian , Hazem Hoda , Eichenberger Anna , Kitau Olivia , Mapesi Herry , Glass Tracy R. , Paris Daniel Henry , Weisser Maja , Vanobberghen Fiona 
Published: January 2022

Abstract
Background
Nearly half of HIV-related deaths occur in East and Southern Africa, yet data on causes of death (COD) are scarce. We determined COD and associated factors among people living with HIV (PLHIV) in rural Tanzania.

Methods
PLHIV attending the Chronic Diseases Clinic of Ifakara, Morogoro are invited to enrol in the Kilombero and Ulanga Antiretroviral Cohort (KIULARCO). Among adults (≥ 15 years) enrolled in 2005–2018, with follow-up through April 2019, we classified COD in comprehensive classes and as HIV- or non-HIV-related. In the subset of participants enrolled in 2013–2018 (when data were more complete), we assessed cause-specific mortality using cumulative incidences, and associated factors using proportional hazards models.

Results
Among 9871 adults (65% female, 26% CD4 count < 100 cells/mm3), 926 (9%) died, among whom COD were available for 474 (51%), with missing COD mainly in earlier years. The most common COD were tuberculosis (N = 127, 27%), non-AIDS-related infections (N = 72, 15%), and other AIDS-related infections (N = 59, 12%). Cardiovascular and renal deaths emerged as important COD in later calendar years, with 27% of deaths in 2018 attributable to cardiovascular causes. Most deaths (51%) occurred within the first six months following enrolment. Among 3956 participants enrolled in 2013–2018 (N = 203 deaths, 200 with COD ascertained), tuberculosis persisted as the most common COD (25%), but substantial proportions of deaths from six months after enrolment onwards were attributable to renal (14%), non-AIDS-related infections (13%), other AIDS-related infections (10%) and cardiovascular (10%) causes. Factors associated with higher HIV-related mortality were sex, younger age, living in Ifakara town, HIV status disclosure, hospitalisation, not being underweight, lower CD4 count, advanced WHO stage, and gaps in care. Factors associated with higher non-HIV-related mortality included not having an HIV-positive partner, lower CD4 count, advanced WHO stage, and gaps in care.

Conclusion
Incidence of HIV-related mortality was higher than that of non-HIV-related mortality, even in more recent years, likely due to late presentation. Tuberculosis was the leading specific COD identified, particularly soon after enrolment, while in later calendar years cardiovascular and renal causes emerged as important, emphasising the need for improved screening and management.