bluuebunny/crossref_metadata_2025 huggingface dataset:
In vivo detection of substantia nigra and locus coeruleus volume loss in Parkinson’s disease using neuromelanin-sensitive MRI: Replication in two cohorts
Authors: Hwang Kristy S. , Langley Jason , Tripathi Richa , Hu Xiaoping P. , Huddleston Daniel E.
Published: April 2023

Patients with Parkinson’s disease undergo a loss of melanized neurons in substantia nigra pars compacta and locus coeruleus. Very few studies have assessed substantia nigra pars compacta and locus coeruleus pathology in Parkinson’s disease simultaneously with magnetic resonance imaging (MRI). Neuromelanin-sensitive MRI measures of substantia nigra pars compacta and locus coeruleus volume based on explicit magnetization transfer contrast have been shown to have high scan-rescan reproducibility in controls, but no study has replicated detection of Parkinson’s disease-associated volume loss in substantia nigra pars compacta and locus coeruleus in multiple cohorts with the same methodology. Two separate cohorts of Parkinson’s disease patients and controls were recruited from the Emory Movement Disorders Clinic and scanned on two different MRI scanners. In cohort 1, imaging data from 19 controls and 22 Parkinson’s disease patients were acquired with a Siemens Trio 3 Tesla scanner using a 2D gradient echo sequence with magnetization transfer preparation pulse. Cohort 2 consisted of 33 controls and 39 Parkinson’s disease patients who were scanned on a Siemens Prisma 3 Tesla scanner with a similar imaging protocol. Locus coeruleus and substantia nigra pars compacta volumes were segmented in both cohorts. Substantia nigra pars compacta volume (Cohort 1: p = 0.0148; Cohort 2: p = 0.0011) and locus coeruleus volume (Cohort 1: p = 0.0412; Cohort 2: p = 0.0056) were significantly reduced in the Parkinson’s disease group as compared to controls in both cohorts. This imaging approach robustly detects Parkinson’s disease effects on these structures, indicating that it is a promising marker for neurodegenerative neuromelanin loss.
Evaluation of the role of postoperative radiotherapy in locally invasive thymoma: A propensity-matched study based on the SEER database
Authors: Lin Li-mei , Li Yi-min , Huang Yun-xia , Zhang Zong-kai , Dai Ya-qing , Liu Jun , Lin Qin
Published: April 2023

Objectives

No consensus was reached on the efficacy of postoperative radiotherapy (PORT) in locally invasive thymomas because of the rarity of the thymic epithelial and the variations of study results. Therefore, we aimed to explore the efficacy of PORT in locally invasive thymomas using the Surveillance, Epidemiology, and End Results (SEER) database.

Methods

Patients diagnosed with thymomas from 2004 to 2016 were identified using the SEER database. Prognostic factors of cancer-specific survival (CSS) and overall survival (OS) were identified using univariate and multivariate Cox regression analyses.Propensity score matching (PSM) was performed to balance the baseline characteristics.

Results

A total of 700 eligible patients were identified. After PSM, 262 paired patients were selected from the two groups, those who received or did not receive PORT. Receiving PORT improved CSS and OS before and after PSM. In the matched population, the multivariate analyses showed that tumour invasion into adjacent organs/structures and non-utilisation of PORT were independent poor prognostic factors for CSS, whereas age ≥62 years,tumour invasion into adjacent organs/structures, and non-utilisation of PORT were independently associated with poorer OS. The subgroup analysis revealed that PORT improved CSS and OS in Masaoka-Koga stage III thymoma, but showed no OS benefit in Masaoka-Koga stage IIB thymoma.

Conclusion

Based on the SEER database, we found that PORT provides a significant survival benefit in Masaoka-Koga stage III thymoma with complete or incomplete resection. The role of PORT in thymoma requires further evaluation.
A multispecies corridor in a fragmented landscape: Evaluating effectiveness and identifying high-priority target areas
Authors: DeMatteo Karen E. , Escalante Orlando M. , Ibañez Alegre Daiana M. , Rinas Miguel A. , Sotorres Delfina , Argüelles Carina F.
Published: April 2023

While Misiones, Argentina contains one of the largest remnants of Upper Paraná Atlantic Forest ecoregion, one of the world’s biodiversity hotspots, only ~50% of this native forest is protected. Each protected area is at risk of becoming an island of native forest surrounded by a matrix of altered habitats due to ongoing land conversion. In an effort to maximize long-term connectivity between existing protected areas, DeMatteo [1] used a multifaceted cost analysis to determine the optimal location for the region’s first multispecies corridor using noninvasive data on jaguars (Panthera onca), pumas (Puma concolor), ocelots (Leopardus pardalis), southern tiger cats (Leopardus guttulus), and bush dogs (Speothos venaticus). This work builds on this framework by integrating new field data that broadens the scope of species-specific data across the region’s heterogeneous landscape, which varies in vegetation, disturbance, human proximity, and protective status. In addition, two different land use layers are compared across the distributions of the five carnivores, the overlap in their independent distributions, and their relationship to the multispecies corridor. Interpretation of these land use data to species-specific habitat suitability goes beyond DeMatteo [1], with a subdivision of suitability into marginal and optimal areas. This refined scale allows a reanalysis of key areas in the multispecies corridor, where connectivity was previously defined as at highly-at-risk, allowing for a more directed development of management strategies. These analyses and their interpretation extend beyond northern-central Misiones, as the threats are not unique to this region. The need to develop management strategies that balance human-wildlife needs will continue to grow as humans expand their footprint. The techniques applied in this analysis provide a way to identify key areas that require specific management strategies, either through restoration, protection, or a combination of both.
Predictors of discharge disposition and mortality following hospitalization with SARS-CoV-2 infection
Authors: Ikramuddin Farha , Melnik Tanya , Ingraham Nicholas E. , Nguyen Nguyen , Siegel Lianne , Usher Michael G. , Tignanelli Christopher J. , Morse Leslie
Published: April 2023

Importance

The SARS-CoV-2 pandemic has overwhelmed hospital capacity, prioritizing the need to understand factors associated with type of discharge disposition.

Objective

Characterization of disposition associated factors following SARS-CoV-2.

Design

Retrospective study of SARS-CoV-2 positive patients from March 7th, 2020, to May 4th, 2022, requiring hospitalization.

Setting

Midwest academic health-system.

Participants

Patients above the age 18 years admitted with PCR + SARS-CoV-2.

Intervention

None.

Main outcomes

Discharge to home versus PAC (inpatient rehabilitation facility (IRF), skilled-nursing facility (SNF), long-term acute care (LTACH)), or died/hospice while hospitalized (DH).

Results

We identified 62,279 SARS-CoV-2 PCR+ patients; 6,248 required hospitalizations, of whom 4611(73.8%) were discharged home, 985 (15.8%) to PAC and 652 (10.4%) died in hospital (DH).

Patients discharged to PAC had a higher median age (75.7 years, IQR: 65.6–85.1) compared to those discharged home (57.0 years, IQR: 38.2–69.9), and had longer mean length of stay (LOS) 14.7 days, SD: 14.0) compared to discharge home (5.8 days, SD: 5.9).

Older age (RRR:1.04, 95% CI:1.041–1.055), and higher Elixhauser comorbidity index [EI] (RRR:1.19, 95% CI:1.168–1.218) were associated with higher rate of discharge to PAC versus home. Older age (RRR:1.069, 95% CI:1.060–1.077) and higher EI (RRR:1.09, 95% CI:1.071–1.126) were associated with more frequent DH versus home. Blacks, Asians, and Hispanics were less likely to be discharged to PAC (RRR, 0.64 CI 0.47–0.88), (RRR 0.48 CI 0.34–0.67) and (RRR 0.586 CI 0.352–0.975). Having alpha variant was associated with less frequent PAC discharge versus home (RRR 0.589 CI 0.444–780).

The relative risks for DH were lower with a higher platelet count 0.998 (CI 0.99–0.99) and albumin levels 0.342 (CI 0.26–0.45), and higher with increased CRP (RRR 1.006 CI 1.004–1.007) and D-Dimer (RRR 1.070 CI 1.039–1.101). Increased albumin had lower risk to PAC discharge (RRR 0.630 CI 0.497–0.798. An increase in D-Dimer (RRR1.033 CI 1.002–1.064) and CRP (RRR1.002 CI1.001–1.004) was associated with higher risk of PAC discharge. A breakthrough (BT) infection was associated with lower likelihood of DH and PAC.

Conclusion

Older age, higher EI, CRP and D-Dimer are associated with PAC and DH discharges following hospitalization with COVID-19 infection. BT infection reduces the likelihood of being discharged to PAC and DH.
Cultural landscape perception of the Chinese traditional settlement: Based on tourists’ online comments
Authors: Zhou Jingjing , Wu Shanshan , Wu Xiaojing , Xia Xiumin
Published: April 2023

The cultural landscape in traditional settlements is an important historical and cultural resource created by human beings in the process of historical evolution, and is an important resource for the development of traditional settlement tourism. This paper selected 21 representative traditional settlements for research using online comments from tourists as data and content analytical methods including high-frequency vocabulary, semantic networks and emotional attitudes to explore the public perspective on the connotations of cultural landscape features in traditional settlements. There are four major findings, showing first that the cultural landscape of traditional settlements contains three core elements. Second, the semantic network relationships of the core elements show a significant central–edge tendency; and third, the emotional perception of cultural landscapes in traditional settlements is generally positive, and there is no significant difference emotionally between each core element. Last, the public’s perception of the cultural connotations of the landscape is seriously insufficient. Based on the research results, planning suggestions and countermeasures for the conservation and utilization of cultural landscapes in traditional settlements are proposed.
Income-related inequalities in diagnosed diabetes prevalence among US adults, 2001−2018
Authors: Chen Yu , Zhou Xilin , Bullard Kai McKeever , Zhang Ping , Imperatore Giuseppina , Rolka Deborah B.
Published: April 2023

Aims

The overall prevalence of diabetes has increased over the past two decades in the United States, disproportionately affecting low-income populations. We aimed to examine the trends in income-related inequalities in diabetes prevalence and to identify the contributions of determining factors.

Methods

We estimated income-related inequalities in diagnosed diabetes during 2001−2018 among US adults aged 18 years or older using data from the National Health Interview Survey (NHIS). The concentration index was used to measure income-related inequalities in diabetes and was decomposed into contributing factors. We then examined temporal changes in diabetes inequality and contributors to those changes over time.

Results

Results showed that income-related inequalities in diabetes, unfavorable to low-income groups, persisted throughout the study period. The income-related inequalities in diabetes decreased during 2001−2011 and then increased during 2011−2018. Decomposition analysis revealed that income, obesity, physical activity levels, and race/ethnicity were important contributors to inequalities in diabetes at almost all time points. Moreover, changes regarding age and income were identified as the main factors explaining changes in diabetes inequalities over time.

Conclusions

Diabetes was more prevalent in low-income populations. Our study contributes to understanding income-related diabetes inequalities and could help facilitate program development to prevent type 2 diabetes and address modifiable factors to reduce diabetes inequalities.
Mapping CircRNA–miRNA–mRNA regulatory axis identifies hsa_circ_0080942 and hsa_circ_0080135 as a potential theranostic agents for SARS-CoV-2 infection
Authors: Ayaz Hassan , Aslam Nouman , Awan Faryal Mehwish , Basri Rabea , Rauff Bisma , Alzahrani Badr , Arif Muhammad , Ikram Aqsa , Obaid Ayesha , Naz Anam , Khan Sadiq Noor , Yang Burton B. , Nazir Azhar
Published: April 2023

Non-coding RNAs (ncRNAs) can control the flux of genetic information; affect RNA stability and play crucial roles in mediating epigenetic modifications. A number of studies have highlighted the potential roles of both virus-encoded and host-encoded ncRNAs in viral infections, transmission and therapeutics. However, the role of an emerging type of non-coding transcript, circular RNA (circRNA) in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection has not been fully elucidated so far. Moreover, the potential pathogenic role of circRNA-miRNA-mRNA regulatory axis has not been fully explored as yet. The current study aimed to holistically map the regulatory networks driven by SARS-CoV-2 related circRNAs, miRNAs and mRNAs to uncover plausible interactions and interplay amongst them in order to explore possible therapeutic options in SARS-CoV-2 infection. Patient datasets were analyzed systematically in a unified approach to explore circRNA, miRNA, and mRNA expression profiles. CircRNA-miRNA-mRNA network was constructed based on cytokine storm related circRNAs forming a total of 165 circRNA-miRNA-mRNA pairs. This study implies the potential regulatory role of the obtained circRNA-miRNA-mRNA network and proposes that two differentially expressed circRNAs hsa_circ_0080942 and hsa_circ_0080135 might serve as a potential theranostic agents for SARS-CoV-2 infection. Collectively, the results shed light on the functional role of circRNAs as ceRNAs to sponge miRNA and regulate mRNA expression during SARS-CoV-2 infection.
Validated assessment tools for screen media use: A systematic review
Authors: Perez Oriana , Garza Tatyana , Hindera Olivia , Beltran Alicia , Musaad Salma M. , Dibbs Tracey , Singh Anu , Chug Shria , Sisson Amy , Kumar Vadathya Anil , Baranowski Tom , O’Connor Teresia M.
Published: April 2023

Objective

Accurate measurement of adult and child screen media use are needed to robustly assess its impact on health outcomes. Our objective was to systematically review screen media use measurement tools that have been validated against an objective “gold standard” tool.

Methods

The search strategy was initially conducted in Medline Ovid and translated to Embase, Web of Science, PsychInfo and Cochrane. A modified natural language search was conducted in Google Scholar and IEEE. The initial search was conducted in March 2021, and an updated search was conducted in June 2022. Additional studies were included from the references. Studies had to describe the validation of a tool to measure screen media use on participants of any age against a ‘gold standard’ or comparable objective measure. The COnsensus-based Standards for the selection of health Measurement INstruments (COSMIN) was used to assess the criterion validity. Four authors reviewed the titles in two rounds and extracted data.

Results

Twenty-nine articles were included in the review. Studies measured TV, computer, mobile device and social media site screen media use through: self or parent report, direct or video observation, computer and mobile device use tracking programs, and through other novel devices such as wearable devices and cameras. Correlations of self or parent report of screen media with the gold standard were lower than correlations of technology-based measures, and video observation with the gold standard. The COSMIN criterion validity ratings ranged from poor to excellent; most of the studies received a global score of fair or poor.

Conclusions

Technology based validated tools that more directly measure screen use are emerging that have been validated against a gold standard for measuring screen use. However, practical, objective measures of diverse types of screen media use that have been tested on diverse populations are needed to better understand the impact of screen media use on the development and physical and mental health of children and adults.
Cardiac autonomic modulation in response to postural transition during a virtual reality task in individuals with spinal cord injury: A cross-sectional study
Authors: Papa Denise Cardoso Ribeiro , Menezes Lilian Del Ciello de , Moraes Íbis Ariana Peña de , Silveira Ana Clara , Padula Natalia , Silva Suellen de Oliveira Veronez , Gaspar Roberta Caveiro , Dias Eduardo Dati , Ferreira Celso , Araújo Luciano Vieira de , Astorino Todd A. , Dawes Helen , Monteiro Carlos Bandeira de Mello , Silva Talita Dias da
Published: April 2023

Purpose

The postural transition from sitting to standing is a moment of dysautonomic occurrence in individuals with Spinal Cord Injury (SCI). Different tools can be used to minimize this event, such as virtual reality. Thus, we aimed to analyze cardiac autonomic modulation in individuals with SCI during postural transition from the sitting to orthostatism position using a cognitive virtual reality (VR) task.

Methods

Individuals with and without SCI were positioned on the Easy Stand® device, sitting at rest, at 0° considering the angle between the seat and the floor, elevation at 45°, and orthostatism at 90°, for 5 minutes in each position. Heart rate variability (HRV) measures of sympathovagal balance were collected (heart rate receiver: Polar V800). The groups were subdivided into two groups, one that performed VR as an intervention during the postural angle changes and another group that did not perform VR.

Results

We evaluated 76 individuals, 40 with a medical diagnosis of SCI and 36 who composed the able-bodied control group without SCI, matched by age and sex. The HRV results showed that the SCI group who performed the task in VR demonstrated no significant difference in parasympathetic activation and global variability between the sitting versus 90° positions. There was better sympathovagal balance in SCI and able-bodied control groups who performed the VR task between the sitting versus 90° positions.

Conclusion

The use of a VR task seems to contribute to better sympathovagal balance, with the potential to reduce dysautonomia during postural changes.
Coliphages of the human urinary microbiota
Authors: Crum Elias , Merchant Zubia , Ene Adriana , Miller-Ensminger Taylor , Johnson Genevieve , Wolfe Alan J. , Putonti Catherine
Published: April 2023

Due to its frequent association with urinary tract infections (UTIs), Escherichia coli is the best characterized constituent of the urinary microbiota (urobiome). However, uropathogenic E. coli is just one member of the urobiome. In addition to bacterial constituents, the urobiome of both healthy and symptomatic individuals is home to a diverse population of bacterial viruses (bacteriophages). A prior investigation found that most bacterial species in the urobiome are lysogens, harboring one or more phages integrated into their genome (prophages). Many of these prophages are temperate phages, capable of entering the lytic cycle and thus lysing their bacterial host. This transition from the lysogenic to lytic life cycle can impact the bacterial diversity of the urobiome. While many phages that infect E. coli (coliphages) have been studied for decades in the laboratory setting, the coliphages within the urobiome have yet to be cataloged. Here, we investigated the diversity of urinary coliphages by first identifying prophages in all publicly available urinary E. coli genomes. We detected 3,038 intact prophage sequences, representative of 1,542 unique phages. These phages include both novel species as well as species also found within the gut microbiota. Ten temperate phages were isolated from urinary E. coli strains included in our analysis, and we assessed their ability to infect and lyse urinary E. coli strains. We also included in these host range assays other urinary coliphages and laboratory coliphages. The temperate phages and other urinary coliphages were successful in lysing urinary E. coli strains. We also observed that coliphages from non-urinary sources were most efficient in killing urinary E. coli strains. The two phages, T2 and N4, were capable of lysing 83.5% (n = 86) of strains isolated from females with UTI symptoms. In conclusion, our study finds a diverse community of coliphages in the urobiome, many of which are predicted to be temperate phages, ten of which were confirmed here. Their ability to infect and lyse urinary E. coli strains suggests that urinary coliphages may play a role in modulating the E. coli strain diversity of the urobiome.
Matrix factorization-based multi-objective ranking–What makes a good university?
Authors: Abonyi János , Ipkovich Ádám , Dörgő Gyula , Héberger Károly
Published: April 2023

Non-negative matrix factorization (NMF) efficiently reduces high dimensionality for many-objective ranking problems. In multi-objective optimization, as long as only three or four conflicting viewpoints are present, an optimal solution can be determined by finding the Pareto front. When the number of the objectives increases, the multi-objective problem evolves into a many-objective optimization task, where the Pareto front becomes oversaturated. The key idea is that NMF aggregates the objectives so that the Pareto front can be applied, while the Sum of Ranking Differences (SRD) method selects the objectives that have a detrimental effect on the aggregation, and validates the findings. The applicability of the method is illustrated by the ranking of 1176 universities based on 46 variables of the CWTS Leiden Ranking 2020 database. The performance of NMF is compared to principal component analysis (PCA) and sparse non-negative matrix factorization-based solutions. The results illustrate that PCA incorporates negatively correlated objectives into the same principal component. On the contrary, NMF only allows non-negative correlations, which enable the proper use of the Pareto front. With the combination of NMF and SRD, a non-biased ranking of the universities based on 46 criteria is established, where Harvard, Rockefeller and Stanford Universities are determined as the first three. To evaluate the ranking capabilities of the methods, measures based on Relative Entropy (RE) and Hypervolume (HV) are proposed. The results confirm that the sparse NMF method provides the most informative ranking. The results highlight that academic excellence can be improved by decreasing the proportion of unknown open-access publications and short distance collaborations. The proportion of gender indicators barely correlate with scientific impact. More authors, long-distance collaborations, publications that have more scientific impact and citations on average highly influence the university ranking in a positive direction.
What condition leads to an unreasonable pharmaceutical price? Impact research on the effect of medical service provision on pharmaceutical price regulation based on fuss-set QCA
Authors: Fang Lingzhi Brian , Wang Xinmeng , Tang Liu
Published: April 2023

Given that the pharmaceutical market has experienced severe market failures, it is necessary that we regulate pharmaceutical prices for many countries. Toward ensuring that pharmaceutical price regulation is efficient, this study investigated the antecedents that lead to an unreasonable pharmaceutical price. Based on 33 case-study countries, this study utilized QCA to analyze the conditional configuration of unreasonable pharmaceutical prices from the perspective of medical service provision. The results showed that the causes of unreasonable pharmaceutical prices are configured by medical service provision, especially cost compensation systems and payment mechanism. This study’s conclusions contribute to the research on pharmaceutical price regulation and the institution of medical service provision.
Comparison of survival times of advanced cancer patients with palliative care at home and in hospital
Authors: Hamano Jun , Takeuchi Ayano , Mori Masanori , Saitou Yasuhiro , Yamaguchi Takahide , Miyata Nobuyuki , Shimizu Masakatsu , Yamamoto Ryo , Kimura Yousuke , Kamiyama Yoshiyuki , Arai Yasuyuki , Matsuo Hiroshi , Shishido Hideki , Nakano Kazushi , Nishi Tomohiro , Nagaoka Hiroka , Yokomichi Naosuke , Maeda Isseki , Yamaguchi Takashi , Morita Tatsuya , Shinjo Takuya
Published: April 2023

Objectives

One primary concern about receiving care at home is that survival might be shortened because the quality and quantity of treatment provided at home will be inferior to that given in the hospital. Although our previous study demonstrated a longer survival of those with home-based palliative care (PC), it lacked adjustment for some potential confounders including symptoms and treatments during the stay. We aimed to compare the survival times among advanced cancer patients receiving home-based and hospital-based PC with adjusting for symptoms and treatments.

Method

We compared survival time of participants who enrolled two multicenter, prospective cohort studies of advanced cancer patients at 45-home-based PC services between July 2017 and December 2017, and at 23-hospital-based PC services between January 2017 and December 2017. We analyzed with stratification by the estimated survival of Days, Weeks, and Months, which were defined by modified Prognosis in Palliative care Study predictor models-A. We conducted a Cox regression analysis with adjusting for potential confounders including symptoms and treatments during the stay.

Results

A total of 2,998 patients were enrolled in both studies and 2,878 patients were analyzed; 988 patients receiving home-based PC and 1,890 receiving hospital-based PC. The survival time of patients receiving home-based PC was significantly longer than that of patients receiving hospital-based PC for the Days Prognosis (estimated median survival time: 10 days [95% CI 8.1–11.8] vs. 9 days [95% CI 8.3–10.4], p = 0.157), the Weeks prognosis (32 days [95% CI 28.9–35.4] vs. 22 days [95% CI 20.3–22.9], p < 0.001), and the Months Prognosis, (65 days [95% CI 58.2–73.2] vs. 32 days [95% CI 28.9–35.4], p < 0.001).

Conclusion

In this cohort of advanced cancer patients with a Weeks or Months prognosis, those receiving home-based PC survived longer than those receiving hospital-based PC after adjusting for symptoms and treatments.
Extracting relevant predictive variables for COVID-19 severity prognosis: An exhaustive comparison of feature selection techniques
Authors: Hayet-Otero Miren , García-García Fernando , Lee Dae-Jin , Martínez-Minaya Joaquín , España Yandiola Pedro Pablo , Urrutia Landa Isabel , Nieves Ermecheo Mónica , Quintana José María , Menéndez Rosario , Torres Antoni , Zalacain Jorge Rafael , Arostegui Inmaculada ,   with the COVID-19 & Air Pollution Working Group
Published: April 2023

With the COVID-19 pandemic having caused unprecedented numbers of infections and deaths, large research efforts have been undertaken to increase our understanding of the disease and the factors which determine diverse clinical evolutions. Here we focused on a fully data-driven exploration regarding which factors (clinical or otherwise) were most informative for SARS-CoV-2 pneumonia severity prediction via machine learning (ML). In particular, feature selection techniques (FS), designed to reduce the dimensionality of data, allowed us to characterize which of our variables were the most useful for ML prognosis. We conducted a multi-centre clinical study, enrollingn= 1548 patients hospitalized due to SARS-CoV-2 pneumonia: where 792, 238, and 598 patients experienced low, medium and high-severity evolutions, respectively. Up to 106 patient-specific clinical variables were collected at admission, although 14 of them had to be discarded for containing ⩾60% missing values. Alongside 7 socioeconomic attributes and 32 exposures to air pollution (chronic and acute), these becamed= 148 features after variable encoding. We addressed this ordinal classification problem both as a ML classification and regression task. Two imputation techniques for missing data were explored, along with a total of 166 unique FS algorithm configurations: 46 filters, 100 wrappers and 20 embeddeds. Of these, 21 setups achieved satisfactory bootstrap stability (⩾0.70) with reasonable computation times: 16 filters, 2 wrappers, and 3 embeddeds. The subsets of features selected by each technique showed modest Jaccard similarities across them. However, they consistently pointed out the importance of certain explanatory variables. Namely: patient’s C-reactive protein (CRP), pneumonia severity index (PSI), respiratory rate (RR) and oxygen levels –saturation Sp O2, quotients Sp O2/RR and arterial Sat O2/Fi O2–, the neutrophil-to-lymphocyte ratio (NLR) –to certain extent, also neutrophil and lymphocyte counts separately–, lactate dehydrogenase (LDH), and procalcitonin (PCT) levels in blood. A remarkable agreement has been founda posterioribetween our strategy and independent clinical research works investigating risk factors for COVID-19 severity. Hence, these findings stress the suitability of this type of fully data-driven approaches for knowledge extraction, as a complementary to clinical perspectives.
Leaf functional traits and pathogens: Linking coffee leaf rust with intraspecific trait variation in diversified agroecosystems
Authors: Gagliardi Stephanie , Avelino Jacques , Martin Adam R. , Cadotte Marc , Virginio Filho Elias de Melo , Isaac Marney E.
Published: April 2023

Research has demonstrated that intraspecific functional trait variation underpins plant responses to environmental variability. However, few studies have evaluated how trait variation shifts in response to plant pathogens, even though pathogens are a major driver of plant demography and diversity, and despite evidence of plants expressing distinct strategies in response to pathogen pressures. Understanding trait-pathogen relationships can provide a more realistic understanding of global patterns of functional trait variation. We examined leaf intraspecific trait variability (ITV) in response to foliar disease severity, using Coffea arabica cv. Caturra as a model species. We quantified coffee leaf rust (CLR) severity—a fungal disease prominent in coffee systems—and measured key coffee leaf functional traits under contrasting, but widespread, management conditions in an agroforestry system. We found that coffee plants express significant ITV, which is largely related to shade tree treatment and leaf position within coffee canopy strata. Yet within a single plant canopy stratum, CLR severity increased with increasing resource conserving trait values. However, coffee leaves with visible signs of disease expressed overall greater resource acquiring trait values, as compared to plants without visible signs of disease. We provide among the first evidence that leaf traits are correlated with foliar disease severity in coffee, and that functional trait relationships and syndromes shift in response to increased disease prevalence in this plant-pathogen system. In doing so, we address a vital gap in our understanding of global patterns of functional trait variation and highlight the need to further explore the potential role of pathogens within established global trait relationships and spectra.
The influence of the age-period-cohort effects on male suicide in Brazil from 1980 to 2019
Authors: Rodrigues Weverton Thiago da Silva , Simões Taynãna César , Magnago Carinne , Dantas Eder Samuel Oliveira , Guimarães Raphael Mendonça , Jesus Jordana Cristina de , de Andrade Fernandes Sandra Michelle Bessa , Meira Karina Cardoso
Published: April 2023

Suicide is a complex and multi-determined phenomenon. Higher rates are observed in men and are related to multiple risk factors, including mental disorders, financial crises, unemployment, and easy access to highly lethal means of perpetration, such as firearms. We studied the effects of age, period, and cohort (APC) on total and firearm-related suicides in men in Brazil and its major regions from 1980 to 2019. Death records were extracted from the Brazilian Ministry of Health’s Mortality Information System. Estimable functions were used to estimate APC models, through the Epi library of the R statistical program, version 4.2.1. During the study period, Brazil had an average rate of 10.22 deaths per 100,000 men. Among regions, rates ranged from 8.62 (Northeast) to 16.93 (South). The same profile was observed in suicides by firearms. After estimating the APC models, we observed a temporal trend of increasing total suicides for Brazil and regions, except for the South region, where the trend was stationary. The trend was downward for firearm suicides for all locations. A positive gradient was observed in the mortality rate with advancing age for total suicides; and peak incidence between 20–29 years, with subsequent stabilization, for suicides perpetrated by firearms. There was a reduction in the risk of death for suicides perpetrated by firearms in relation to the reference period (1995–1999) for all locations, except in the North region, where the effect was not significant. The younger generations from the 1960s onwards had a higher risk of death from total suicide and a lower risk for those perpetrated by firearms in relation to the reference cohort (1950–1954). We observed a reduction in the mortality trend for suicides perpetrated by firearms, a reduction in the risk of death in the 2000s and for men born after 1960. Our results suggest reducing the risk of death from suicide by firearms in Brazil and regions. However, there is an upward trend in mortality from total suicides in the study period (1980–2019) and for younger cohorts.
Diagnosis and prognosis of serum Fut8 for epilepsy and refractory epilepsy in children
Authors: Huang Yunxiu , Zhang Zhou , Chen Linmu
Published: April 2023

With adequate serum concentration of antiepileptic drugs, the epilepsy symptoms in many patients still cannot be controlled well. The alteration of glycosyltransferase has obvious influence on the pathogenesis of epilepsy. In this study, we focus on the diagnostic and prognostic value of fucosyltransferase 8 (Fut8) on epilepsy and refractory epilepsy. Serum samples of 199 patients with epilepsy, 59 patients with refractory epilepsy and 22 healthy controls who were diagnosed in Shenzhen Children’s hospital from August 2018 to August 2019 were collected. The level of lectins was further analyzed by lectin chip and enzyme linked immunosorbent assay (ELISA). The diagnostic value of serum Fut8 for epilepsy and refractory epilepsy was evaluated by receiver operating characteristic curve. Finally, the difference in the recurrence rate of convulsion in patients with epilepsy or refractory epilepsy within 2 years were observed in different Fut8 expression patients. The concentration of valproic acid (VPA) were significant different between epilepsy and refractory epilepsy group. The expression of α1, 6-fucosylation and Fut8 was significantly increased in the refractory epilepsy group compared with healthy controls. The area under the curve of Fut8 as a biomarker for predicting epilepsy or refractory epilepsy was 0.620 and 0.856, respectively. There was a significant difference in the recurrence rate of convulsion within 2 years in the children with refractory epilepsy (p = 0.0493) not epilepsy (p = 0.1865) between the high and low Fut8 expression groups. Fut8 was one of the effective indicators for the diagnosis and prognosis of refractory epilepsy.
Data sharing upon request and statistical consistency errors in psychology: A replication of Wicherts, Bakker and Molenaar (2011)
Authors: Claesen Aline , Vanpaemel Wolf , Maerten Anne-Sofie , Verliefde Thomas , Tuerlinckx Francis , Heyman Tom
Published: April 2023

Sharing research data allows the scientific community to verify and build upon published work. However, data sharing is not common practice yet. The reasons for not sharing data are myriad: Some are practical, others are more fear-related. One particular fear is that a reanalysis may expose errors. For this explanation, it would be interesting to know whether authors that do not share data genuinely made more errors than authors who do share data. (Wicherts, Bakker and Molenaar 2011) examined errors that can be discovered based on the published manuscript only, because it is impossible to reanalyze unavailable data. They found a higher prevalence of such errors in papers for which the data were not shared. However, (Nuijten et al. 2017) did not find support for this finding in three large studies. To shed more light on this relation, we conducted a replication of the study by (Wicherts et al. 2011). Our study consisted of two parts. In the first part, we reproduced the analyses from (Wicherts et al. 2011) to verify the results, and we carried out several alternative analytical approaches to evaluate the robustness of the results against other analytical decisions. In the second part, we used a unique and larger data set that originated from (Vanpaemel et al. 2015) on data sharing upon request for reanalysis, to replicate the findings in (Wicherts et al. 2011). We applied statcheck for the detection of consistency errors in all included papers and manually corrected false positives. Finally, we again assessed the robustness of the replication results against other analytical decisions. Everything taken together, we found no robust empirical evidence for the claim that not sharing research data for reanalysis is associated with consistency errors.
The (dis)engagement of mangrove forests and mangrove rice in academic and non-academic literature on Guinea-Bissau–a systematic review protocol
Authors: Sousa Joana , Campos Rita , Mendes Orlando , Duarte Lopes Paula , Matias Madalena , Rosa Ana Paula , Mendes Fernandes Raul , Cruz Cristina , Indjai Bucar , Infande Adilson , da Costa Maira , Salvaterra Gonçalo , Lourenço Juelson , Tavares Dionísio , Camala Djone , Ainslie Andrew , Catarino Luís
Published: April 2023

Background

Coastal areas in Guinea-Bissau and elsewhere in West Africa are bordered by mangrove forests. In several of these places, swaths of mangrove forest have been removed and the landscape has been technologically adapted for the production of mangrove rice–a regionally important staple. However, the effects of global warming, in particular sea-level rise, pose challenges to these socioecological environments. In this context, knowledge appears as an important resource and knowing what knowledge has been produced and which perspectives have guided that production may inform future responses to climate change. We have developed a systematic literature review protocol focusing on the main question: “How have mangrove forest and mangrove rice spaces been represented in the literature on Guinea-Bissau?” The main hypothesis is that although they occupy contiguous, interrelated and interactant spaces in coastal environments, mangrove forests and mangrove rice have been studied and analyzed independently in the literature.

Methods

This is a protocol for conducting a systematic review that will include academic and non-academic literature in Portuguese, English and French. The academic literature will be retrieved from both Web of Science and Scopus using Boolean expressions. The non-academic literature will be accessed from relevant institutions, specialized libraries, and reference lists of previously selected items. Data extraction will follow a standard procedure based on an information sheet. Our analysis will be both qualitative (inductive and deductive coding, content analysis) and quantitative (word clouds, descriptive statistics and statistical testing).

Discussion

This systematic review will provide information about the conceptual framework that has been produced through research, policymaking, and conservation and development programs in the management of coastal areas. This study will identify the limitations of previous approaches and contribute to both future research and strategies for planning adaptation to climate change. Finally, the outputs will add to broader debates about people-nature coexistence and climate change adaptation and mitigation.
Mice lacking nucleotide sugar transporter SLC35A3 exhibit lethal chondrodysplasia with vertebral anomalies and impaired glycosaminoglycan biosynthesis
Authors: Saito Soichiro , Mizumoto Shuji , Yonekura Tsukasa , Yamashita Rina , Nakano Kenta , Okubo Tadashi , Yamada Shuhei , Okamura Tadashi , Furuichi Tatsuya
Published: April 2023

SLC35A3 is considered an uridine diphosphate N-acetylglucosamine (UDP-GlcNAc) transporter in mammals and regulates the branching of N-glycans. A missense mutation in SLC35A3 causes complex vertebral malformation (CVM) in cattle. However, the biological functions of SLC35A3 have not been fully clarified. To address these issues, we have established Slc35a3–/–mice using CRISPR/Cas9 genome editing system. The generated mutant mice were perinatal lethal and exhibited chondrodysplasia recapitulating CVM-like vertebral anomalies. During embryogenesis, Slc35a3 mRNA was expressed in the presomitic mesoderm of wild-type mice, suggesting that SLC35A3 transports UDP-GlcNAc used for the sugar modification that is essential for somite formation. In the growth plate cartilage of Slc35a3–/–embryos, extracellular space was drastically reduced, and many flat proliferative chondrocytes were reshaped. Proliferation, apoptosis and differentiation were not affected in the chondrocytes of Slc35a3–/–mice, suggesting that the chondrodysplasia phenotypes were mainly caused by the abnormal extracellular matrix quality. Because these histological abnormalities were similar to those observed in several mutant mice accompanying the impaired glycosaminoglycan (GAG) biosynthesis, GAG levels were measured in the spine and limbs of Slc35a3–/–mice using disaccharide composition analysis. Compared with control mice, the amounts of heparan sulfate, keratan sulfate, and chondroitin sulfate/dermatan sulfate, were significantly decreased in Slc35a3–/–mice. These findings suggest that SLC35A3 regulates GAG biosynthesis and the chondrodysplasia phenotypes were partially caused by the decreased GAG synthesis. Hence, Slc35a3−/− mice would be a useful model for investigating the in vivo roles of SLC35A3 and the pathological mechanisms of SLC35A3-associated diseases.
Condyloma acuminata: An evaluation of the immune response at cellular and molecular levels
Authors: Stuqui Bruna , Provazzi Paola Jocelan Scarin , Lima Maria Leticia Duarte , Cabral Ágata Silva , Leonel Ellen Cristina Rivas , Candido Natalia Maria , Taboga Sebastião Roberto , da Silva Márcia Guimarães , Lima Flávio de Oliveira , Melli Patrícia Pereira dos Santos , Quintana Silvana Maria , Calmon Marilia de Freitas , Rahal Paula
Published: April 2023

Condyloma acuminata (CA) is a benign proliferative disease mainly affecting in non-keratinized epithelia. Most cases of CA are caused by low-risk human papillomavirus (HPV), mainly HPV 6 and 11. The aim of the current study was to highlight the candidate genes and pathways associated with immune alterations in individuals who did not spontaneously eliminate the virus and, thus, develop genital warts. Paraffin-embedded condyloma samples (n = 56) were analyzed by immunohistochemistry using antibodies against CD1a, FOXP3, CD3, CD4, CD8, and IFN-γ. The immunomarkers were chosen based on the evaluation of the innate and adaptive immune pathways using qPCR analysis of 92 immune-related genes, applying a TaqMan Array Immune Response assay in HPV 6 or HPV 11 positive samples (n = 27). Gene expression analysis revealed 31 differentially expressed genes in CA lesions. Gene expression validation revealed upregulation ofGZMB,IFNG,IL12B, andIL8and downregulation ofNFATC4andIL7in CA samples. Immunohistochemical analysis showed increased FOXP3, IFN-γ, CD1a, and CD4 expression in CA than in the control tissue samples. In contrast, CD3 and CD8 expression was decreased in CA lesion samples. Increased levels of pro-inflammatory cytokines in HPV-positive patients compared with HPV-negative patients seem to reflect the elevated immunogenicity of HPV-positive CA lesions. Host defense against HPV begins during the early stages of the innate immune response and is followed by activation of T lymphocytes, which are mainly represented by CD4+ and regulatory T cells. The low CD8+ T cell count in CA may contribute to this recurrent behavior. Additional studies are needed to elucidate the mechanism of host defense against HPV infection in CA.
Nutritional status of under-five aged children of ready-made garment workers in Bangladesh: A cross-sectional study
Authors: Haque Sadika , Al Rafi Dewan Abdullah , Zaman Nafisa , Salman Md. , Al Noman Md. Abdullah , Hoque Md. Nazmul , Bhattacharjee Lalita , Farquhar Samantha , Yasmin Sabina , Hasan Md. Mehedi , Hira Fatema Tuj Zohora , Prithi Aunjuman Ara , Shammi Shamim Ara , Banu Bilkish , Hossain Akbar
Published: April 2023

Background

The ready-made garment (RMG) sector is a significant contributor to the economic growth of Bangladesh, accounting for 10% of the country’s GDP and more than 80% of its foreign exchange earnings. The workforce in this sector is predominantly made up of women, with 2.5 million women working in the industry. However, these women face numerous challenges in carrying out their culturally-expected household responsibilities, including childcare, due to severe resource constraints. As a result, the children of these working women have a higher incidence of malnutrition, particularly stunted growth. This study aims to identify the factors that contribute to stunting in children under the age of five whose mothers work in the RMG sector in Bangladesh.

Methods

The study collected data from 267 female RMG workers in the Gazipur district of Bangladesh using a simple random sampling technique. Chi-square tests were used to determine the associations between the factors influencing child stunting, and Multinomial Logit Models were used to estimate the prevalence of these factors.

Results

The study found that the prevalence of moderate and severe stunting among the children of RMG workers living in the Gazipur RMG hub was 19% and 20%, respectively. The study identified several significant predictors of child stunting, including the mother’s education level, nutritional knowledge, control over resources, receipt of antenatal care, household size, sanitation facilities, and childbirth weight. The study found that improving the mother’s education level, increasing household size, and receiving antenatal care during pregnancy were important factors in reducing the likelihood of child stunting. For example, if a mother’s education level increased from no education to primary or secondary level, the child would be 0.211 (0.071–0.627) and 0.384 (0.138–1.065) times more likely to have a normal weight and height, respectively, than to be moderately stunted.

Conclusion

The study highlights the challenges faced by working women in the RMG sector, who often receive minimal wages and have limited access to antenatal care services. To address these challenges, the study recommends policies that support antenatal care for working-class mothers, provide daycare facilities for their children, and implement a comprehensive social safety net program that targets child nutrition. Improving the socioeconomic status of mothers is also critical to reducing child malnutrition in this population.