bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of label-free quantification and missing value imputation for proteomics in non-human primates
Authors: Hamid Zeeshan , Zimmerman Kip D. , Guillen-Ahlers Hector , Li Cun , Nathanielsz Peter , Cox Laura A. , Olivier Michael 
Published: July 2022

Abstract
Background
Reliable and effective label-free quantification (LFQ) analyses are dependent not only on the method of data acquisition in the mass spectrometer, but also on the downstream data processing, including software tools, query database, data normalization and imputation. In non-human primates (NHP), LFQ is challenging because the query databases for NHP are limited since the genomes of these species are not comprehensively annotated. This invariably results in limited discovery of proteins and associated Post Translational Modifications (PTMs) and a higher fraction of missing data points. While identification of fewer proteins and PTMs due to database limitations can negatively impact uncovering important and meaningful biological information, missing data also limits downstream analyses (e.g., multivariate analyses), decreases statistical power, biases statistical inference, and makes biological interpretation of the data more challenging. In this study we attempted to address both issues: first, we used the MetaMorphues proteomics search engine to counter the limits of NHP query databases and maximize the discovery of proteins and associated PTMs, and second, we evaluated different imputation methods for accurate data inference. We used a generic approach for missing data imputation analysis without distinguising the potential source of missing data (either non-assigned m/z or missing values across runs).

Results
Using the MetaMorpheus proteomics search engine we obtained quantitative data for 1622 proteins and 10,634 peptides including 58 different PTMs (biological, metal and artifacts) across a diverse age range of NHP brain frontal cortex. However, among the 1622 proteins identified, only 293 proteins were quantified across all samples with no missing values, emphasizing the importance of implementing an accurate and statiscaly valid imputation method to fill in missing data. In our imputation analysis we demonstrate that Single Imputation methods that borrow information from correlated proteins such as Generalized Ridge Regression (GRR), Random Forest (RF), local least squares (LLS), and a Bayesian Principal Component Analysis methods (BPCA), are able to estimate missing protein abundance values with great accuracy.

Conclusions
Overall, this study offers a detailed comparative analysis of LFQ data generated in NHP and proposes strategies for improved LFQ in NHP proteomics data.
In vitro assessment of 17 antimicrobial agents against clinical Mycobacterium avium complex isolates
Authors: Lin Siran , Hua Wenya , Wang Shiyong , Zhang Yu , Chen Xinchang , Liu Hong , Shao Lingyun , Chen Jiazhen , Zhang Wenhong 
Published: July 2022

Abstract
Background
Recently, Mycobacterium avium complex (MAC) infections have been increasing, especially in immunocompromised and older adults. The rapid increase has triggered a global health concern due to limited therapeutic strategies and adverse effects caused by long-term medication. To provide more evidence for the treatment of MAC, we studied the in vitro inhibitory activities of 17 antimicrobial agents against clinical MAC isolates.

Results
A total of 111 clinical MAC isolates were enrolled in the study and they were identified as M. intracellulare, M. avium, M. marseillense, M. colombiense, M. yongonense, and two isolates could not be identified at the species level. MAC strains had relatively low (0–21.6%) resistance to clarithromycin, amikacin, bedaquiline, rifabutin, streptomycin, and clofazimine, and the resistant rates to isoniazid, rifampin, linezolid, doxycycline, and ethionamide were very high (72.1–100%). In addition, M. avium had a significantly higher resistance rate than that of M. intracellulare for ethambutol (92.3% vs 40.7%, P < 0.001), amikacin (15.4% vs 1.2%, P = 0.049), and cycloserine (69.2% vs 25.9%, P = 0.004).

Conclusions
Our results supported the current usage of macrolides, rifabutin, and aminoglycosides in the regimens for MAC infection, and also demonstrated the low resistance rate against new drugs, such as clofazimine, tedizolid, and bedaquiline, suggesting the possible implementation of these drugs in MAC treatment.
Floral morphology and phenology of Sassafras tzumu (Lauraceae)
Authors: Yang Zhi , Tan Chao , Wei Yi-Min , Rohwer Jens G , Liu Bing , Yang Yong 
Published: July 2022

AbstractBackgroundSassafrashas been considered to belong to trib. Laureae of Lauraceae and has been assumed to have unisexual flowers. However, recent molecular phylogenetic studies have consistently suggested thatSassafrasdoes not belong to the trib. Laureae but to Cinnamomeae and that it is nested withinCinnamomum. A recent morphological study revealed that one of the Asian species,S. randaiense, possesses bisexual flowers that are plesiomorphic in the family Lauraceae. As reports on the flower structure of the second Asian species,S. tzumu, have been contradictory, we wanted to ascertain if it has bisexual flowers or not. If the flowers were bisexual, could earlier reports that they were unisexual have been based on dichogamous flowering?ResultsIn this study, we investigated two populations ofS. tzumu. We found that this species has determinate botryoid racemes, and possesses bisexual flowers. Among the three extant species,S. tzumuis more similar to its sister speciesS. randaiensebut markedly different from the AmericanS. albidum: the two Asian species possess bisexual flowers while the American species has unisexual flowers. The bisexual flower ofS. tzumuis protogynous, and shows two phenological phases typical of Lauraceae: 1) in a flower, the pistil functions first, the stigma is fresh and white, stamens of the outer two whorls are spreading, anthers do not open, and the staminodes secrete nectar at this stage; 2) in the second phase, the stigma becomes brown, staminodes are withered, stamens of the third whorl stand up and surround the pistil, glands of the third whorl of stamens secrete nectar, and the anthers open and release pollen.ConclusionsThe similarity of racemose inflorescences betweenSassafrasand some members of Laureae were caused by parallel evolution; the racemose inflorescence of ancestralSassafrasoriginated from the thyrsoid-cymose inflorescence inCinnamomum. The Asian speciesS. tzumuandS. randaiensepossess bisexual flowers with two phenological phases, the AmericanS. albidumevolved unisexual flowers independently from other clades with unisexual flowers in the Lauraceae, i.e., the Laureae,Alseodaphnopsisin the Perseeae and the unisexual clade in theOcoteacomplex of the Cinnamomeae.
Transporter NRT1.5/NPF7.3 suppresses primary root growth under low K+ stress by regulating the degradation of PIN-FORMED2
Authors: Wang Youyou , Wang Ran , Zhao Shuang , Lu Changmei , Zhu Ziqiang , Li Hong 
Published: July 2022

Abstract
Background
The availability of potassium is one of the main environmental factors for modifying the plasticity of root architecture. Many potassium channels and transporters are involved in regulating primary root growth in response to low potassium stress. NRT1.5/NPF7.3 transporter is a NO3−/H+ and K+/H+ cotransporter, and participates in NO3− and K+ translocation from the roots to the shoots. However, the underlying mechanism of NRT1.5-regulated primary root growth under low potassium stress is unclear.

Results
We show that NRT1.5/NPF7.3 inhibited primary root growth under low potassium conditions by regulating the accumulation of PIN2 protein and auxin levels. Under low potassium conditions, the mutants nrt1.5 and lks2 exhibited longer primary roots, longer meristem regions and elongation zones of primary roots, and more cell activity in the meristem region compared to WT plants, revealing the involvement of NRT1.5 in LK (low potassium)-inhibition primary root growth. In addition, exogenous auxin (IAA), auxin analogue (NAA, 2.4-D) or auxin precursor (IBA) promoted the primary root growth of WT and the complementation line NRT1.5 COM plants. In addition, the application of NPA inhibited the primary root growth of the nrt1.5 and lks2 mutants. Auxin accumulation was higher in the root tip of nrt1.5 plants than in WT plants, indicating that NRT1.5 regulates root growth inhibition by regulating auxin distribution. Furthermore, PIN2 was degraded more quickly in nrt1.5 plants under LK stress.

Conclusions
Our findings reveal that NRT1.5 inhibits primary root growth by modulating the auxin level in the root tip via the degradation of PIN2.
Defining the ethical considerations surrounding kidney transplantation for frail and cognitively impaired patients: a Delphi study of geriatric transplant experts
Authors: Shrestha Prakriti , Van Pilsum Rasmussen Sarah E. , King Elizabeth A. , Gordon Elisa J. , Faden Ruth R. , Segev Dorry L. , Humbyrd Casey Jo , McAdams-DeMarco Mara 
Published: July 2022

Abstract
Background
Among adult kidney transplant (KT) candidates, 21% are frail and 55% have cognitive impairment, increasing the risk of pre- and post-KT mortality. Centers often assess frailty status and cognitive function during transplant evaluation to help identify appropriate candidate. Yet, there are no ethical guidelines regarding the use of frailty and cognitive function during this evaluation. We seek to develop a clinical consensus on balancing utility and justice in access to KT for frail and cognitively impaired patients.

Methods
Twenty-seven experts caring for ESRD patients completed a two-round Delphi panel designed to facilitate consensus (> 80% agreement).

Results
Experts believed that denying patients transplantation based solely on expected patient survival was inequitable to frail or cognitively impaired candidates; 100% agreed that frailty and cognitive impairment are important factors to consider during KT evaluation. There was consensus that health related quality of life and social support are important to consider before waitlisting frail or cognitively impaired patients. Experts identified important factors to consider before waitlisting frail (likely to benefit from KT, frailty reversibility, age, and medical contraindications) and cognitively impaired (degree of impairment and medication adherence) patients.

Conclusions
Clinical experts believed it was ethically unacceptable to allocate organs solely based on patients’ expected survival; frailty and cognitive impairment should be measured at evaluation when weighed against other clinical factors. Ethical guidelines regarding the use of frailty and cognitive function during KT evaluation ought to be developed.
Remote care and triage of obstetric patients with COVID-19 in the community: operational considerations
Authors: Bircher Charles , Wilkes Matt , Zahradka Nicole , Wells Emily , Prosser-Snelling Ed 
Published: July 2022

Abstract
Background
During the SARS-CoV-2 (COVID-19) pandemic, routine antenatal care was disrupted, and pregnant women positive for COVID-19 were at increased risk of caesarean section, intensive care admission or neonatal unit admission for their baby. Virtual care and telehealth can reduce barriers to care and improve maternity outcomes, and adoption has been encouraged by health authorities in the United Kingdom.

Methods
Norfolk and Norwich University Hospitals Trust deployed a flexible maternity virtual ward (MVW) service using the Current Health platform to care for pregnant women during the pandemic. Patients were monitored either intermittently with finger pulse oximetry or continuously with a wearable device. We outline the MVW technology, intervention and staffing model, triage criteria and patient feedback, as an example of an operational model for other institutions.

Results
Between October 2021 and February 2022, 429 patients were referred, of which 228 were admitted to the MVW. Total bed-days was 1,182, mean length of stay was 6 days (SD 2.3, range 1–14 days). Fifteen (6.6%) required hospital admission and one (0.4%) critical care. There were no deaths. Feedback alluded to feelings of increased safety, comfort, and ease with the technology.

Conclusions
The MVW offered a safety net to pregnant women positive for COVID-19. It provided reassurance for staff, while relieving pressures on infrastructure. When setting up similar services in future, attention should be given to identifying clinical champions, triage criteria, technology and alarm selection, and establishing flexible escalation pathways that can adapt to changing patterns of disease.
Determinants of place birth: a multinomial logistic regression and spatial analysis of the Ethiopian mini demographic and health survey data, 2019
Authors: Gudayu Temesgen Worku 
Published: July 2022

Abstract
Background
Maternal and neonatal health significantly improves when birth is attended at health institutions where there are quality services and skilled attendants. In contrary, home birth results in high rates of maternal and neonatal mortality. Thus, this study aimed to determine the spatial distribution of home birth and to identify determinants of place of birth in Ethiopia based on the recent national survey.

Methods
Ethiopian mini-DHS-2019 data was used in this analysis. A weighted sample of 5423 mothers were included. While health facility was a reference, home and health post were used as comparison categories to identify determinants of place of birth in a survey multinomial logistic regression model. An adjusted relative risk ratio, marginal effect, and a corresponding 95% confidence interval and a p-value of < 0.05 were used to declare statistical significance. The Global Moran’s I analysis was done by using ArcMap 10.8 to evaluate the clustering of home birth. The prevalence of home birth was predicted by ordinary kriging interpolation. Then, scanning was done by SaTScan V.9.6 software to detect scanning windows with low or high rates of home birth.

Result
Prevalence of home birth in Ethiopia was 52.19% (95% CI: 46.49 – 57.83). Whereas, only 2.99% (95% CI: 1.68 – 5.25) of mothers gave birth in the health posts. Bigger family size, family wealth, multiparity, none and fewer antenatal visits, and low coverage of cluster level 4 + antenatal visits were predictors of home birth. Also, home birth was clustered across enumeration areas and it was over 40% in most parts of the country with > 75% in the Somali region. SaTScan analysis detected most likely primary clusters in the Somali region and secondary clusters in the rest five regions of the country.

Conclusion
Home birth is a common practice in Ethiopia. Among public health facilities, health posts are the least utilized institutions for labor and delivery care. Nationally, implementing the 2016 WHO’s recommendations on antenatal care for a positive pregnancy experience and providing quality antenatal and delivery care in public facilities by qualified providers and back-up systems in place could be supportive.
Women’s view on shared decision making and autonomy in childbirth: cohort study of Belgian women
Authors: Deherder Elke , Delbaere Ilse , Macedo Adriana , Nieuwenhuijze Marianne J. , Van Laere Sven , Beeckman Katrien 
Published: July 2022

Abstract
Background
Health care providers have an important role to share evidence based information and empower patients to make informed choices. Previous studies indicate that shared decision making in pregnancy and childbirth may have an important impact on a woman’s birth experience. In Flemish social media, a large number of women expressed their concern about their birth experience, where they felt loss of control and limited possibilities to make their own choices. The aim of this study is to explore autonomy and shared decision making in the Flemish population.

Methods
This is a cross-sectional, non-interventional study to explore the birth experience of Flemish women. A self-assembled questionnaire was used to collect data, including the Pregnancy and Childbirth Questionnaire (PCQ), the Labor Agentry Scale (LAS), the Mothers Autonomy Decision Making Scale (MADM), the 9-item Shared Decision Making Questionnaire (SDM–Q9) and four questions on preparation for childbirth. Women who gave birth two to 12 months ago were recruited by means of social media in the Flemish area (Northern part of Belgium).
Linear mixed-effect modelling with backwards variable selection was applied to examine relations with autonomy in decision making.

Results
In total, 1029 mothers participated in this study of which 617 filled out the survey completely. In general, mothers experienced moderate autonomy in decision-making, both with an obstetrician and with a midwife with an average on the MADM score of respectively 18.5 (± 7.2) and 29.4 (±10.4) out of 42. The linear mixed-effects model showed a relationship between autonomy in decision-making (MADM) for the type of healthcare provider (p < 0.001), the level of self-control during labour and birth (LAS) (p = 0.003), the level of perceived quality of care (PCQ) (p < 0.001), having epidural analgesia during childbirth (p = 0.026) and feeling to have received sufficient information about the normal course of childbirth (p < 0.001).

Conclusions
Childbearing women in Flanders experience moderate levels of autonomy in decision- making with their health care providers, where lower autonomy was observed for obstetricians compared to midwives. Future research should focus more on why differences occur between obstetrics and midwives in terms of autonomy and shared decision-making as perceived by the mother.
Evaluation of active inflammation, chronic structural damage, and response to treatment of sacroiliitis in axial spondyloarthritis using the Spondyloarthritis research consortium of Canada scoring system
Authors: Zhang Yimeng , Guo Zikang , Zhan Ying , Qu Jin , Lei Xinwei 
Published: July 2022

Abstract
Background
Axial spondyloarthritis (axSpA) is a chronic inflammatory rheumatic disease affecting the spine and sacroiliac joints. To investigate whether there are differences in inflammatory and chronic structural damages, as assessed by a semiquantitative MRI scoring method, between non-radiographic axial spondyloarthritis (nr-axSpA) and ankylosing spondylitis (AS) patients with active inflammation at baseline, and to evaluate the treatment response in these patients after 3 months of tumor necrosis factor-alpha (TNF-α) inhibitor treatment.

Methods
Fifty-eight axSpA patients with active inflammation were included in the study. The patients were divided into nr-axSpA group and AS group. MRI examinations of the sacroiliac joints were performed before and after treatment. Inflammatory and structural damages in these patients were assessed using the established Spondyloarthritis Research Consortium of Canada (SPARCC) inflammation and sacroiliac joint structural (SSS) scoring methods, which are two MRI-based scoring methods. The SPARCC score, SSS score, erythrocyte sedimentation rate (ESR), and C-reactive protein (CRP) level were compared between the two groups.

Results
At baseline, SPARCC scores for patients in the nr-axSpA and AS groups did not differ significantly (P > 0.05); however, SSS scores for fat metaplasia, erosion, and backfill for patients in the AS group were significantly higher (P < 0.001). Compared with baseline, SPARCC scores were significantly decreased in both groups after treatment (P < 0.001); however, after treatment, no statistically significant difference was found regarding SPARCC scores between the AS and nr-axSpA groups. Compared with baseline, a significant increase in the SSS scores for fat metaplasia and backfill (P < 0.001) and a significant decrease in the SSS scores for erosion (P < 0.001) were observed in all axSpA patients. Changes in the SPARCC score was inversely correlated with the changes in the SSS score for fat metaplasia (r = − 0.634, P < 0.001). Changes in the SSS score for backfill were positively correlated with the changes in the SSS score for fat metaplasia (r = 0.277, P < 0.05) and inversely correlated with those for erosion (r = − 0.443, P < 0.001).

Conclusion
The SPARCC and SSS scoring systems can be used to assess inflammatory and chronic structural damages as well as treatment responses in patients with axSpA. More severe structural damages were seen in AS patients. TNF-α inhibitor treatment for 3 months could effectively reduce inflammation in axSpA patients.
Tumor-induced osteomalacia characterized by “painful knee joint with difficulty in moving”: a case report
Authors: Jiang Lan , Tan Qing-Qing , Gao Chen-Lin , Xu Ling , Zhu Jian-Hua , Yan Pi-Jun , Miao Ying , Wan Qin , Xu Yong 
Published: July 2022

Abstract
Background
Tumor-related osteomalacia (TIO) is a rare paraneoplastic syndrome characterized by severe hypophosphatemia and osteomalacia. The diagnosis of TIO can be very difficult because of its nonspecific nature of clinical manifestations. Here we reported a case of young TIO patient with “painful knee joint with difficulty in moving” to improve the clinical diagnosis and treatment levels.

Case presentation
The patient’s clinical features were consistent with TIO. A tumor was successfully located in left tibial by 68Ga-DOTATATE PET/CT, and then was surgically resected. Upon pathologic assessment, the tumor was diagnosed as phosphaturia stromal tumor (PMT) with positive Vim staining. After the surgery, serum phosphate level rapidly recovered and symptoms significantly improved.

Conclusion
TIO should be considered in patients with chronically hypophosphorus osteomalacia in the setting of no family history. Early removal of the responsible tumors is clinically essential for the treatment, and imaging examination is of great significance for tumor localization.
Analysis of risk factors for the development of type 2 diabetes mellitus complicated with Hashimoto’s thyroiditis
Authors: Han Meng , Wu Haoneng , Yang Weiming , Chen Juanjuan 
Published: July 2022

Abstract
Aims
The purpose of this study is to elucidate the correlation between thyroid hormone, glycosylated hemoglobin (HbA1c), vitamin D and type 2 diabetes mellitus (T2DM) with Hashimoto’s thyroiditis (HT), and to seek the independent predictors affecting disease development.

Methods
The study included 44 T2DM with HT, 94 T2DM, and 112 healthy subjects. We investigated some laboratory factors like thyroid hormone and compared the levels. Independent predictors determination by logistic univariate regression analysis were analyzed. The diagnostic value of thyroid-stimulating hormone (TSH) and threshold concentration were determined by ROC curve.

Results
In T2DM with HT group, levels of PTH, HbA1c were lower and levels of TSH were significantly higher, when compared with T2DM group. But there was no significant difference in vitamin D between these two groups. In both logistic univariate regression analysis and multiple logistic regression analysis, TSH, HbA1c were independent predictors for T2DM with HT. Based on the ROC curve, the best cut-off value of the TSH was 4 mIU/L (sensitivity 72.7%, specificity 94.6%, AUC = 0.832) for predicting T2DM with HT in T2DM patients.

Conclusions
TSH has increased risk for T2DM evolving into T2DM complicated with HT, so it is important to monitor the concentrations of TSH in patients with T2DM. Although vitamin D was not the independent predictor in T2DM with HT development, effect of vitamin D deficiency on the progress of diabetes and its complications should be taken into consideration.