bluuebunny/crossref_metadata_2025_split huggingface dataset:
NanoSIMS observations of mouse retinal cells reveal strict metabolic controls on nitrogen turnover
Authors: Bonnin Elisa A. , Fornasiero Eugenio F. , Lange Felix , Turck Christoph W. , Rizzoli Silvio O. 
Published: January 2021

Abstract
Background
Most of the cells of the mammalian retina are terminally differentiated, and do not regenerate once fully developed. This implies that these cells have strict controls over their metabolic processes, including protein turnover. We report the use of metabolic labelling procedures and secondary ion mass spectrometry imaging to examine nitrogen turnover in retinal cells, with a focus on the outer nuclear layer, inner nuclear layer, and outer plexiform layer.

Results
We find that turnover can be observed in all cells imaged using NanoSIMS. However, the rate of turnover is not constant, but varies between different cellular types and cell regions. In the inner and outer nuclear layers, turnover rate is higher in the cytosol than in the nucleus of each cell. Turnover rates are also higher in the outer plexiform layer. An examination of retinal cells from mice that were isotopically labeled very early in embryonic development shows that proteins produced during this period can be found in all cells and cell regions up to 2 months after birth, even in regions of high turnover.

Conclusions
Our results indicate that turnover in retinal cells is a highly regulated process, with strict metabolic controls. We also observe that turnover is several-fold higher in the synaptic layer than in cell layers. Nevertheless, embryonic proteins can still be found in this layer 2 months after birth, suggesting that stable structures persist within the synapses, which remain to be determined.
Complementary transcriptomic and proteomic analyses reveal the cellular and molecular processes that drive growth and development of Fasciola hepatica in the host liver
Authors: Cwiklinski Krystyna , Robinson Mark W. , Donnelly Sheila , Dalton John P. 
Published: January 2021

AbstractBackgroundThe major pathogenesis associated withFasciola hepaticainfection results from the extensive tissue damage caused by the tunnelling and feeding activity of immature flukes during their migration, growth and development in the liver. This is compounded by the pathology caused by host innate and adaptive immune responses that struggle to simultaneously counter infection and repair tissue damage.ResultsComplementary transcriptomic and proteomic approaches defined theF. hepaticafactors associated with their migration in the liver, and the resulting immune-pathogenesis. Immature liver-stage flukes express ~ 8000 transcripts that are enriched for transcription and translation processes reflective of intensive protein production and signal transduction pathways. Key pathways that regulate neoblast/pluripotent cells, including the PI3K-Akt signalling pathway, are particularly dominant and emphasise the importance of neoblast-like cells for the parasite’s rapid development. The liver-stage parasites display different secretome profiles, reflecting their distinct niche within the host, and supports the view that cathepsin peptidases, cathepsin peptidase inhibitors, saposins and leucine aminopeptidases play a central role in the parasite’s destructive migration, and digestion of host tissue and blood. Immature flukes are also primed for countering immune attack by secreting immunomodulating fatty acid binding proteins (FABP) and helminth defence molecules (FhHDM). Combined with published host microarray data, our results suggest that considerable immune cell infiltration and subsequent fibrosis of the liver tissue exacerbates oxidative stress within parenchyma that compels the expression of a range of antioxidant molecules within both host and parasite.ConclusionsThe migration of immatureF. hepaticaparasites within the liver is associated with an increase in protein production, expression of signalling pathways and neoblast proliferation that drive their rapid growth and development. The secretion of a defined set of molecules, particularly cathepsin L peptidases, peptidase-inhibitors, saponins, immune-regulators and antioxidants allow the parasite to negotiate the liver micro-environment, immune attack and increasing levels of oxidative stress. This data contributes to the growingF. hepatica-omics information that can be exploited to understand parasite development more fully and for the design of novel control strategies to prevent host liver tissue destruction and pathology.
Genome-wide identification of the histone acetyltransferase gene family in Triticum aestivum
Authors: Gao Shiqi , Li Linzhi , Han Xiaolei , Liu Tingting , Jin Peng , Cai Linna , Xu Miaoze , Zhang Tianye , Zhang Fan , Chen Jianping , Yang Jian , Zhong Kaili 
Published: January 2021

Abstract
Background
Histone acetylation is a ubiquitous and reversible post-translational modification in eukaryotes and prokaryotes that is co-regulated by histone acetyltransferase (HAT) and histone deacetylase (HDAC). HAT activity is important for the modification of chromatin structure in eukaryotic cells, affecting gene transcription and thereby playing a crucial regulatory role in plant development. Comprehensive analyses of HAT genes have been performed in Arabidopsis thaliana, Oryza sativa, barley, grapes, tomato, litchi and Zea mays, but comparable identification and analyses have not been conducted in wheat (Triticum aestivum).

Results
In this study, 31 TaHATs were identified and divided into six groups with conserved gene structures and motif compositions. Phylogenetic analysis was performed to predict functional similarities between Arabidopsis thaliana, Oryza sativa and Triticum aestivum HAT genes. The TaHATs appeared to be regulated by cis-acting elements such as LTR and TC-rich repeats. The qRT–PCR analysis showed that the TaHATs were differentially expressed in multiple tissues. The TaHATs in expression also responded to temperature changes, and were all significantly upregulated after being infected by barley streak mosaic virus (BSMV), Chinese wheat mosaic virus (CWMV) and wheat yellow mosaic virus (WYMV).

Conclusions
These results suggest that TaHATs may have specific roles in the response to viral infection and provide a basis for further study of TaHAT functions in T. aestivum plant immunity.
Berberine alters gut microbial function through modulation of bile acids
Authors: Wolf Patricia G. , Devendran Saravanan , Doden Heidi L. , Ly Lindsey K. , Moore Tyler , Takei Hajime , Nittono Hiroshi , Murai Tsuyoshi , Kurosawa Takao , Chlipala George E. , Green Stefan J. , Kakiyama Genta , Kashyap Purna , McCracken Vance J. , Gaskins H. Rex , Gillevet Patrick M. , Ridlon Jason M. 
Published: January 2021

Abstract
Background
Berberine (BBR) is a plant-based nutraceutical that has been used for millennia to treat diarrheal infections and in contemporary medicine to improve patient lipid profiles. Reduction in lipids, particularly cholesterol, is achieved partly through up-regulation of bile acid synthesis and excretion into the gastrointestinal tract (GI). The efficacy of BBR is also thought to be dependent on structural and functional alterations of the gut microbiome. However, knowledge of the effects of BBR on gut microbiome communities is currently lacking. Distinguishing indirect effects of BBR on bacteria through altered bile acid profiles is particularly important in understanding how dietary nutraceuticals alter the microbiome.

Results
Germfree mice were colonized with a defined minimal gut bacterial consortium capable of functional bile acid metabolism (Bacteroides vulgatus, Bacteroides uniformis, Parabacteroides distasonis, Bilophila wadsworthia, Clostridium hylemonae, Clostridium hiranonis, Blautia producta; B4PC2). Multi-omics (bile acid metabolomics, 16S rDNA sequencing, cecal metatranscriptomics) were performed in order to provide a simple in vivo model from which to identify network-based correlations between bile acids and bacterial transcripts in the presence and absence of dietary BBR. Significant alterations in network topology and connectivity in function were observed, despite similarity in gut microbial alpha diversity (P = 0.30) and beta-diversity (P = 0.123) between control and BBR treatment. BBR increased cecal bile acid concentrations, (P < 0.05), most notably deoxycholic acid (DCA) (P < 0.001). Overall, analysis of transcriptomes and correlation networks indicates both bacterial species-specific responses to BBR, as well as functional commonalities among species, such as up-regulation of Na+/H+ antiporter, cell wall synthesis/repair, carbohydrate metabolism and amino acid metabolism. Bile acid concentrations in the GI tract increased significantly during BBR treatment and developed extensive correlation networks with expressed genes in the B4PC2 community.

Conclusions
This work has important implications for interpreting the effects of BBR on structure and function of the complex gut microbiome, which may lead to targeted pharmaceutical interventions aimed to achieve the positive physiological effects previously observed with BBR supplementation.
Relaxing the assumption of constant transition rates in a multi-state model in hospital epidemiology
Authors: Hill Micki , Lambert Paul C. , Crowther Michael J. 
Published: January 2021

Abstract
Background
Multi-state models are being increasingly used to capture complex disease pathways. The convenient formula of the exponential multi-state model can facilitate a quick and accessible understanding of the data. However, assuming time constant transition rates is not always plausible. On the other hand, obtaining predictions from a fitted model with time-dependent transitions can be challenging. One proposed solution is to utilise a general simulation algorithm to calculate predictions from a fitted multi-state model.

Methods
Predictions obtained from an exponential multi-state model were compared to those obtained from two different parametric models and to non-parametric Aalen-Johansen estimates. The first comparative approach fitted a multi-state model with transition-specific distributions, chosen separately based on the Akaike Information Criterion. The second approach was a Royston-Parmar multi-state model with 4 degrees of freedom, which was chosen as a reference model flexible enough to capture complex hazard shapes. All quantities were obtained analytically for the exponential and Aalen-Johansen approaches. The transition rates for the two comparative approaches were also obtained analytically, while all other quantities were obtained from the fitted models via a general simulation algorithm. Metrics investigated were: transition probabilities, attributable mortality (AM), population attributable fraction (PAF) and expected length of stay. This work was performed on previously analysed hospital acquired infection (HAI) data. By definition, a HAI takes three days to develop and therefore selected metrics were also predicted from time 3 (delayed entry).

Results
Despite clear deviations from the constant transition rates assumption, the empirical estimates of the transition probabilities were approximated reasonably well by the exponential model. However, functions of the transition probabilities, e.g. AM and PAF, were not well approximated and the comparative models offered considerable improvements for these metrics. They also provided consistent predictions with the empirical estimates in the case of delayed entry time, unlike the exponential model.

Conclusion
We conclude that methods and software are readily available for obtaining predictions from multi-state models that do not assume constant transition rates. The package in facilitates a range of predictions with confidence intervals, which can provide a more comprehensive understanding of the data. User-friendly code is provided.
Flexible modelling of risk factors on the incidence of pneumonia in young children in South Africa using piece-wise exponential additive mixed modelling
Authors: Ramjith Jordache , Roes Kit C.B. , Zar Heather J. , Jonker Marianne A. 
Published: January 2021

AbstractIntroductionRecurrent episodes of pneumonia are frequently modeled using extensions of the Cox proportional hazards model with the underlying assumption of time-constant relative risks measured by the hazard ratio. We aim to relax this assumption in a study on the effect of factors on the evolution of pneumonia incidence over time based on data from a South African birth cohort study, the Drakenstein child health study.MethodsWe describe and apply two models: a time-constant and a time-varying relative effects model in a piece-wise exponential additive mixed model’s framework for recurrent events. A more complex model that fits in the same framework is applied to study the continuously measured seasonal effects.ResultsWe find that several risk factors (male sex, preterm birth, low birthweight, lower socioeconomic status, lower maternal education and maternal cigarette smoking) have strong relative effects that are persistent across time. When time-varying effects are allowed in the model, HIV exposure status (HIV exposed & uninfected versus HIV unexposed) shows a strong relative effect for younger children, but this effect weakens as children grow older, with a null effect reached from about 15 months. Weight-for-length at birth shows a time increasing relative effect. We also find that children born in the summer have a much higher risk of pneumonia in the 3-to-8-month age period compared with children born in winter.ConclusionThis work highlights the usefulness of flexible modelling tools in recurrent events models. It avoids stringent assumptions and allows estimation and visualization of absolute and relative risks over time of key factors associated with incidence of pneumonia in young children, providing new perspectives on the role of risk factors such HIV exposure.
General practitioner trainees’ career perspectives after COVID-19: a qualitative study in China
Authors: Yin Yue , Chu Xiaotian , Han Xinxin , Cao Yu , Di Hong , Zhang Yun , Zeng Xuejun 
Published: January 2021

AbstractBackgroundThe coronavirus disease 2019 (COVID-19) has been a worldwide public health emergency that has put great pressure on medical workers and the medical system. General Practitioners (GPs) played an important role in controlling the epidemic, and GP trainees also took an active part in this approach. This study was to explore Chinese GP trainees’ career perspectives after COVID-19.MethodsWe conducted a qualitative research study which included 12 GP trainees from three teaching hospitals in China. Semi-structured telephone interviews were conducted. Grounded theory and thematic analysis were used to code the data and identify categories and factors.ResultsEleven participants chose to continue a GP career after COVID-19, and nearly half of the participants strengthened their determination to dedicate themselves to this career. Only one participant decided to change the career choice because of interest in another specialty. Four main themes influencing GP trainees’ perceptions of career development after COVID-19 emerged from the interviews: changes of GPs’ work content in COVID-19, challenges of being a GP, psychological changes of the career, how to provide better primary care. Although some negative psychological changes existed, most of participants were inspired by role models and medical colleagues. They had more in-depth understanding of GPs’ role and responsibility during COVID-19, and exhibited intensions for self-improvement in career development, especially in public health education and self-protection in preventing infectious diseases. In addition, the wide use of telemedicine provided a new work way for GP trainees. However, challenges, such as increased workloads, low income, lack of resources in primary medical institutions, and distrust of GPs are faced by trainees during the outbreak.ConclusionsOverall, no substantial changes were seen in the career choice of GP trainees after COVID-19 outbreak. However, they were inspired and had an in-depth understanding about the GP’s work and responsibility during an epidemic. Owing to the challenges faced by the GPs, measures are needed to improve the GP education and work environment in the training phase.
JAK-inhibitor and type I interferon ability to produce favorable clinical outcomes in COVID-19 patients: a systematic review and meta-analysis
Authors: Walz Lucas , Cohen Avi J. , Rebaza Andre P. , Vanchieri James , Slade Martin D. , Dela Cruz Charles S. , Sharma Lokesh 
Published: January 2021

Abstract
Background
The spread of a highly pathogenic, novel coronavirus (SARS-CoV-2) has emerged as a once-in-a-century pandemic, having already infected over 63 million people worldwide. Novel therapies are urgently needed. Janus kinase-inhibitors and Type I interferons have emerged as potential antiviral candidates for COVID-19 patients due to their proven efficacy against diseases with excessive cytokine release and their direct antiviral ability against viruses including coronaviruses, respectively.

Methods
A search of MEDLINE and MedRxiv was conducted by three investigators from inception until July 30th 2020 and included any study type that compared treatment outcomes of humans treated with Janus kinase-inhibitor or Type I interferon against controls. Inclusion necessitated data with clearly indicated risk estimates or those that permitted their back-calculation. Outcomes were synthesized using RevMan.

Results
Of 733 searched studies, we included four randomized and eleven non-randomized trials. Five of the studies were unpublished. Those who received Janus kinase-inhibitor had significantly reduced odds of mortality (OR, 0.12; 95% CI, 0.03–0.39, p< 0.001) and ICU admission (OR, 0.05; 95% CI, 0.01–0.26, p< 0.001), and had significantly increased odds of hospital discharge (OR, 22.76; 95% CI, 10.68–48.54, p< 0.00001) when compared to standard treatment group. Type I interferon recipients had significantly reduced odds of mortality (OR, 0.19; 95% CI, 0.04–0.85, p< 0.05), and increased odds of discharge bordering significance (OR, 1.89; 95% CI, 1.00–3.59, p=0.05).

Conclusions
Janus kinase-inhibitor treatment is significantly associated with positive clinical outcomes in terms of mortality, ICU admission, and discharge. Type I interferon treatment is associated with positive clinical outcomes in regard to mortality and discharge. While these data show promise, additional well-conducted RCTs are needed to further elucidate the relationship between clinical outcomes and Janus kinase-inhibitors and Type I interferons in COVID-19 patients.
HIV infection and multidrug resistant tuberculosis: a systematic review and meta-analysis
Authors: Sultana Zeeba Zahra , Hoque Farhana Ul , Beyene Joseph , Akhlak-Ul-Islam Md. , Khan Md Hasinur Rahman , Ahmed Shakil , Hawlader Delwer Hossain , Hossain Ahmed 
Published: January 2021

Abstract
Background
Multidrug-resistant tuberculosis (MDR-TB) in HIV infected individuals is a serious threat to global efforts to combat tuberculosis. Inconsistent findings on the association between HIV infection and MDR-TB were present in many studies. We aimed to review existing data on the relationship between HIV infection and MDR-TB systematically to assess the contribution of HIV on MDR-TB worldwide. We also investigated the patterns of MDR-TB by age, country-wise income, study designs, and global regions.

Methods
We utilized PubMed, Google Scholar, and ScienceDirect databases to select eligible studies for meta-analysis that were published between January 1, 2010, and July 30, 2020. The random-effects model was used to obtain the pooled odds ratio of the crude association between HIV and MDR-TB with a 95% confidence interval. We investigated the potential publication-bias by checking funnel plot asymmetry and using the Egger’s test. Moreover, we assessed the heterogeneity using the I2 statistic. Sensitivity analysis was performed based on sample size and adjustment factors. The protocol was registered with PROSPERO-CRD42019132752.

Results
We identified 1603 studies through a database search, and after subsequent eliminations we selected 54 studies including 430,534 TB patients. The pooled odds of MDR-TB was 1.42 times higher in HIV-positive patients than HIV-negative patients (OR=1.42,CI=1.17–1.71, I2=75.8%). Subgroup analysis revealed that the estimated pooled odds for South-East Asian countries was 1.86, which is the highest in WHO regions (OR=1.86,CI=1.30–2.67, I2=0.00%), followed by Europe and Africa. The effect estimate was found to be higher for primary MDR-TB (OR=2.76,CI=1.70–4.46, I2=0.00%). There was also a trend towards increased odds of MDR-TB for HIV patients older than 40 years (OR=1.56,CI=1.17–2.06). The association was found to be significant in high-burden TB countries (OR=1.75, CI=1.39–2.19) and in high-income countries (OR=1.55, CI=1.06–2.27).

Conclusion
Such findings indicate that HIV infection raises the risk of MDR-TB, and after contrasting it with the results of the earlier pooled study, it appeared to be an upward risk trend. Moreover, we found that the risk is the highest in the South-East Asian region. A balanced allocation of resources is needed to halt both primary and secondary MDR-TB, particularly in HIV infected people with 40 years of age and older.
Balanced steady-state free precession MRCP is a robust alternative to respiration-navigated 3D turbo-spin-echo MRCP
Authors: Hasse Felix Christian , Selmi Buket , Albusaidi Hamed , Mokry Theresa , Mayer Philipp , Rupp Christian , Kauczor Hans-Ulrich , Weber Tim Frederik 
Published: January 2021

Abstract
Background
Despite synchronization to respiration, respiration-navigated (RN) 3D turbo-spin-echo MRCP is limited by susceptibility to motion artifacts. The aim of this study was to assess the quality of pancreaticobiliary duct visualization of a non-RN MRCP alternative based on balanced steady-state free precession imaging (BSSFP) with overlapping slices compared with RN-MRCP.

Methods
This is a retrospective study on 50 patients without pancreaticobiliary duct disease receiving MRCP at 1.5 T. We performed an intraindividual comparison of coronal RN-MRCP with combined coronal and transverse BSSFP-MRCP. Image quality was scored by 3 readers for 6 pancreaticobiliary duct segments (3 pancreatic, 3 biliary) using a 6-point scale. A segment score of 3 or lower as assessed by at least 2 of 3 readers was defined as insufficient segment visualization. Nonparametric tests and interrater reliability testing were used for statistical analysis.

Results
Overall duct visualization averaged over all readers was scored with 4.5 ± 1.1 for RN-MRCP (pancreatic, 4.1 ± 0.5; biliary, 5.0 ± 0.4) and 4.9 ± 0.9 for combined coronal and transverse BSSFP-MRCP (pancreatic, 4.6 ± 0.6; biliary, 5.1 ± 0.6), respectively (p < 0.001). The number of segments visualized insufficiently was 81/300 for RN-MRCP and 43/300 for BSSFP-MRCP (p < 0.001). Segments visualized insufficiently only in RN-MRCP had a mean score of 4.4 ± 0.8 in BSSFP-MRCP. Overall interrater agreement on superiority of BSSFP-MRCP segment scores over corresponding RN-MRCP was 0.70. Mean acquisition time was 98% longer for RN-MRCP (198.0 ± 98.7 s) than for combined coronal and transverse BSSFP-MRCP (100.2 ± 0.4 s).

Conclusions
Non-RN BSSFP-MRCP with overlapping slices is a fast alternative to RN-MRCP, frequently providing sufficient duct visualization when RN-MRCP fails.