bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cerebrospinal fluid cells immune landscape in multiple sclerosis
Authors: Li Zijian , Liu Yongchao , Jia Aili , Cui Yueran , Feng Juan 
Published: March 2021

Abstract
Background
Multiple Sclerosis (MS) is a potentially devastating autoimmune neurological disorder, which characteristically induces demyelination of white matter in the brain and spinal cord.

Methods
In this study, three characteristics of the central nervous system (CNS) immune microenvironment occurring during MS onset were explored; immune cell proportion alteration, differential gene expression profile, and related pathways. The raw data of two independent datasets were obtained from the ArrayExpress database; E-MTAB-69, which was used as a derivation cohort, and E-MTAB-2374 which was used as a validation cohort. Differentially expressed genes (DEGs) were identified by the false discovery rate (FDR) value of < 0.05 and |log2 (Fold Change)|> 1, for further analysis. Then, functional enrichment analyses were performed to explore the pathways associated with MS onset. The gene expression profiles were analyzed using CIBERSORT to identify the immune type alterations involved in MS disease.

Results
After verification, the proportion of five types of immune cells (plasma cells, monocytes, macrophage M2, neutrophils and eosinophils) in cerebrospinal fluid (CSF) were revealed to be significantly altered in MS cases compared to the control group. Thus, the complement and coagulation cascades and the systemic lupus erythematosus (SLE) pathways may play critical roles in MS. We identified NLRP3, LILRB2, C1QB, CD86, C1QA, CSF1R, IL1B and TLR2 as eight core genes correlated with MS.

Conclusions
Our study identified the change in the CNS immune microenvironment of MS cases by analysis of the in silico data using CIBERSORT. Our data may assist in providing directions for further research as to the molecular mechanisms of MS and provide future potential therapeutic targets in treatment.
The critical intersection of environmental and social justice: a commentary
Authors: Solomonian Leslie , Di Ruggiero Erica 
Published: March 2021

AbstractThe global crises of ecological degradation and social injustice are mutually reinforcing products of the same flawed systems. Dominant human culture is morally obliged to challenge and reconstruct these systems in order to mitigate future planetary harm. In this commentary, we argue that doing so requires a critical examination of the values and narratives which underlie systems of oppression and power. We argue for the moral necessity of a socially just approach to the ecological crisis.
Breastfeeding satisfaction post hospital discharge and associated factors – a longitudinal cohort study of mothers of preterm infants
Authors: Ericson Jenny , Lampa Erik , Flacking Renée 
Published: March 2021

Abstract
Background
Mothers’ satisfaction with breastfeeding is important for breastfeeding duration but rarely investigated in mothers of preterm infants. The aim of this study was to describe breastfeeding satisfaction and associated factors during the first year in mothers of preterm infants (gestational age < 37 weeks).

Methods
This longitudinal cohort study, based on secondary analysis data from a randomized controlled trial, included 493 mothers of 547 preterm infants. Data on breastfeeding duration and satisfaction, parental stress and attachment were collected at 8 weeks post discharge, and at 6 and 12 months after birth. Breastfeeding satisfaction was measured by the Maternal Breastfeeding Evaluation Scale. Descriptive statistics and linear mixed effect models were used when analyzing the data.

Results
During the first 12 months breastfeeding satisfaction increased in the mean summary scores and points in the dimensions “role attainment” and “lifestyle and maternal body image”. In the dimension “infant growth and satisfaction”, there was an increase in mean points from 6 to 12 months after birth, but not between 8 weeks after discharge and 12 months after birth. The findings also showed that partial and no breastfeeding, higher parental stress, and infant gestational age < 32 weeks were associated with decreased breastfeeding satisfaction. Older maternal age and greater maternal attachment were associated with increased maternal breastfeeding satisfaction. There were no associations between maternal breastfeeding satisfaction and maternal educational level, parity, multiple birth, or maternal birth country other than Sweden, during the first 12 months after birth.

Conclusions
Breastfeeding satisfaction was clearly associated with breastfeeding duration during the first year after birth. Breastfeeding satisfaction may be important to take into account when supporting breastfeeding and when designing interventions to support breastfeeding. Furthermore, these findings highlight the complexity of breastfeeding and emphasize the need for early and good support during neonatal care, so that mothers feel trust in themselves and their infant and in exclusive breastfeeding at discharge and in the first months thereafter.

Trial registration
The randomized controlled trial was registered NCT01806480 with www.clinicaltrials.gov on 2013-03-07.
A conceptual framework for contemporary professional foot care practice: ‘’The value based digital foot care framework’’
Authors: Deschamps Kevin , Brabants Antoine , Nester Chris , Gijon‐Nogueron Gabriel , Simşek Engin , Newton Veronica 
Published: March 2021

AbstractBackgroundA small minority of countries around the globe have podiatry as a recognized profession, hence, there are considerable differences among these countries when it comes to the curricula, the duration of training and legislation regulating the profession. The growth in research led evidence based practice, and the emerging digital landscape of health care practice, occur alongside trends in disease and health behaviours that strongly impact on foot health. As such, the changing complex role of the podiatrist requires critical reflection on current frameworks of practice and whether they are fit for purpose. This commentary presents a conceptual framework which sets the scene for further development of concepts in a podiatry context, reflecting contemporary health care beliefs and the changing expectations of health care and society.The proposed conceptual framework for podiatry practice utilizes the metaphor of an electronic circuit to reflect the vast and complex interconnections between factors that affect practice and professional behaviours. The framework helps in portraying and defining drivers of practice, actual practice as well potential barriers for current and future practice.The circuit emphasis the interconnectedness/interaction of three clusters: 1) internal factors, 2) interaction factors, 3) external factors.ConclusionWhatever promise this new framework holds, it will only be realised through conscious development of community consensus, respectful dialogue, constructive critical appraisal, and maintaining passion and focus on improving the health of people with foot related problems.
High IRF8 expression correlates with CD8 T cell infiltration and is a predictive biomarker of therapy response in ER-negative breast cancer
Authors: Gatti Gerardo , Betts Courtney , Rocha Darío , Nicola Maribel , Grupe Verónica , Ditada Cecilia , Nuñez Nicolas G. , Roselli Emiliano , Araya Paula , Dutto Jeremías , Boffelli Lucia , Fernández Elmer , Coussens Lisa M. , Maccioni Mariana 
Published: March 2021

Abstract
Background
Characterization of breast cancer (BC) through the determination of conventional markers such as ER, PR, HER2, and Ki67 has been useful as a predictive and therapeutic tool. Also, assessment of tumor-infiltrating lymphocytes has been proposed as an important prognostic aspect to be considered in certain BC subtypes. However, there is still a need to identify additional biomarkers that could add precision in distinguishing therapeutic response of individual patients. To this end, we focused in the expression of interferon regulatory factor 8 (IRF8) in BC cells. IRF8 is a transcription factor which plays a well-determined role in myeloid cells and that seems to have multiple antitumoral roles: it has tumor suppressor functions; it acts downstream IFN/STAT1, required for the success of some therapeutic regimes, and its expression in neoplastic cells seems to depend on a cross talk between the immune contexture and the tumor cells.
The goal of the present study was to examine the relationship between IRF8 with the therapeutic response and the immune contexture in BC, since its clinical significance in this type of cancer has not been thoroughly addressed.

Methods
We identified the relationship between IRF8 expression and the clinical outcome of BC patients and validated IRF8 as predictive biomarker by using public databases and then performed in silico analysis. To correlate the expression of IRF8 with the immune infiltrate in BC samples, we performed quantitative multiplex immunohistochemistry.

Results
IRF8 expression can precisely predict the complete pathological response to monoclonal antibody therapy or to select combinations of chemotherapy such as FAC (fluorouracil, adriamycin, and cytoxan) in ER-negative BC subtypes. Analysis of immune cell infiltration indicates there is a strong correlation between activated and effector CD8+ T cell infiltration and tumoral IRF8 expression.

Conclusions
We propose IRF8 expression as a potent biomarker not only for prognosis, but also for predicting therapy response in ER-negative BC phenotypes. Its expression in neoplastic cells also correlates with CD8+ T cell activation and infiltration. Therefore, our results justify new efforts towards understanding mechanisms regulating IRF8 expression and how they can be therapeutically manipulated.
The Cupola: an additional layer of protection for providers working in the oropharyngeal region
Authors: Villa Alessandro , Grenon Marlene 
Published: March 2021

Abstract
Objectives
To reduce the spread of the infection, especially during aerosol generating procedures, we invented “The Cupola”, a shield that creates a mechanical barrier around the patient’s head and body. With this pilot study we aimed to assess the effectiveness of an additional layer of protection (The Cupola) developed for providers working in the oropharyngeal region.

Results
The mean number of 0.3 μm particles with no Cupola was 3777 (SD: ± 556), with The Cupola was 2068 (SD: ± 1468) and with the Cupola and Drape was 2031 (SD: ± 1108) (p < 0.015). The mean number of 0.5 μm airborne particles with no Cupola was 65 (SD: ± 7), with The Cupola was 29 (SD: ± 28) and with the Cupola and Drape was 28 (SD: ± 23) (p < 0.05). Results showed a significant reduction of aerosols generated during simulated dental procedures when the Cupola was used. The Cupola offers an extra layer of protection in addition to the recommended personal protective equipment.
Transcriptome of Aquilaria malaccensis containing agarwood formed naturally and induced artificially
Authors: Abdul Kadir Farah Adibah , Azizan Kamalrul Azlan , Othman Roohaida 
Published: March 2021

Abstract
Objectives
Agarwood is the aromatic heartwood formed upon wounding of Aquilaria trees either naturally formed due to physical wound sustained from natural phenomena followed by microbial infection, or artificially induced using different inoculation methods. Different induction methods produce agarwoods with different aromas which have impacts on their commercial values. In lieu of elucidating the molecular mechanisms of agarwood formation under different treatment conditions, the transcriptome profiles of trunk tissues from healthy A. malaccensis tree, and naturally and artificially induced trees were obtained.

Data description
The transcriptome of trunk tissues from healthy A. malaccensis, and naturally and artificially induced trees were sequenced using Illumina HiSeq™ 4000 platform which resulted in a total of 38.4 Gb clean reads with Q30 rate of at least 91%. The transcriptome consists of 85,986 unigenes containing 1305 bases on average which were annotated against several databases. From this, 44,654 unigenes were mapped to 290 metabolic pathways in the Kyoto Encyclopedia of Genes and Genomes database. These transcriptome data represent considerable contribution towards Aquilaria transcriptome data and enhance current knowledge in comprehending the molecular mechanisms underlying agarwood formation in Aquilaria spp.
Pre-adolescence DNA methylation is associated with BMI status change from pre- to post-adolescence
Authors: Wang Jiajing , Zhang Hongmei , Rezwan Faisal I. , Relton Caroline , Arshad S. Hasan , Holloway John W. 
Published: March 2021

Abstract
Background
Previous studies have shown that DNA methylation (DNAm) is associated with body mass index (BMI). However, it is unknown whether DNAm at pre-adolescence is associated with BMI status transition from pre- to post-adolescence. In the Isle of Wight (IoW) birth cohort, genome-wide DNA methylation in whole blood was measured using Illumina Infinium Human450 and EPIC BeadChip arrays in n = 325 subjects, and pre- to post-adolescence BMI transition was classified into four groups: (1) normal to normal, (2) normal to overweight or obese, (3) overweight or obese to normal, and (4) persistent overweight or obese. We used recursive random forest to screen genome-wide Cytosine-phosphate-Guanine (CpG) sites with DNAm potentially associated with BMI transition for each gender, and the association of BMI status transition with DNAm at an earlier age was assessed via logistic regressions. To evaluate gender specificity, interactions between DNAm and gender were included in the model. Findings in the IoW cohort were further tested in an independent cohort, the Avon Longitudinal Study of Parents and Children (ALSPAC).

Results
In total, 174 candidate CpGs were selected including CpGs from screening and CpGs previously associated correctionally with BMI in children and adults. Of these 174 CpGs, pre-adolescent DNAm of 38 CpGs in the IoW cohort was associated with BMI status transition, including 30 CpGs showing gender-specific associations. Thirteen CpGs showed consistent associations between the IoW cohort and the ALSPAC cohort (11 of which were gender-specific).

Conclusion
Pre-adolescence DNAm is associated with the change in BMI status from pre- to post-adolescence and such associations are likely to be gender-specific.
Plasma neurofilament light and phosphorylated tau 181 as biomarkers of Alzheimer’s disease pathology and clinical disease progression
Authors: Clark Christopher , Lewczuk Piotr , Kornhuber Johannes , Richiardi Jonas , Maréchal Bénédicte , Karikari Thomas K. , Blennow Kaj , Zetterberg Henrik , Popp Julius 
Published: March 2021

Abstract
Background
To assess the performance of plasma neurofilament light (NfL) and phosphorylated tau 181 (p-tau181) to inform about cerebral Alzheimer’s disease (AD) pathology and predict clinical progression in a memory clinic setting.

Methods
Plasma NfL and p-tau181, along with established cerebrospinal fluid (CSF) biomarkers of AD pathology, were measured in participants with normal cognition (CN) and memory clinic patients with cognitive impairment (mild cognitive impairment and dementia, CI). Clinical and neuropsychological assessments were performed at inclusion and follow-up visits at 18 and 36 months. Multivariate analysis assessed associations of plasma NfL and p-tau181 levels with AD, single CSF biomarkers, hippocampal volume, and clinical measures of disease progression.

Results
Plasma NfL levels were higher in CN participants with an AD CSF profile (defined by a CSF p-tau181/Aβ1–42 > 0.0779) as compared with CN non-AD, while p-tau181 plasma levels were higher in CI patients with AD. Plasma NfL levels correlated with CSF tau and p-tau181 in CN, and with CSF tau in CI patients. Plasma p-tau181 correlated with CSF p-tau181 in CN and with CSF tau, p-tau181, Aβ1–42, and Aβ1–42/Aβ1–40 in CI participants. Compared with a reference model, adding plasma p-tau181 improved the prediction of AD in CI patients while adding NfL did not. Adding p-tau181, but not NfL levels, to a reference model improved prediction of cognitive decline in CI participants.

Conclusion
Plasma NfL indicates neurodegeneration while plasma p-tau181 levels can serve as a biomarker of cerebral AD pathology and cognitive decline. Their predictive performance depends on the presence of cognitive impairment.
Distinct tooth regeneration systems deploy a conserved battery of genes
Authors: Square Tyler A. , Sundaram Shivani , Mackey Emma J. , Miller Craig T. 
Published: March 2021

AbstractBackgroundVertebrate teeth exhibit a wide range of regenerative systems. Many species, including most mammals, reptiles, and amphibians, form replacement teeth at a histologically distinct location called the successional dental lamina, while other species do not employ such a system. Notably, a ‘lamina-less’ tooth replacement condition is found in a paraphyletic array of ray-finned fishes, such as stickleback, trout, cod, medaka, and bichir. Furthermore, the position, renewal potential, and latency times appear to vary drastically across different vertebrate tooth regeneration systems. The progenitor cells underlying tooth regeneration thus present highly divergent arrangements and potentials. Given the spectrum of regeneration systems present in vertebrates, it is unclear if morphologically divergent tooth regeneration systems deploy an overlapping battery of genes in their naïve dental tissues.ResultsIn the present work, we aimed to determine whether or not tooth progenitor epithelia could be composed of a conserved cell type between vertebrate dentitions with divergent regeneration systems. To address this question, we compared the pharyngeal tooth regeneration processes in two ray-finned fishes: zebrafish (Danio rerio) and threespine stickleback (Gasterosteus aculeatus). These two teleost species diverged approximately 250 million years ago and demonstrate some stark differences in dental morphology and regeneration. Here, we find that the naïve successional dental lamina in zebrafish expresses a battery of nine genes (bmpr1aa, bmp6, cd34, gli1, igfbp5a, lgr4, lgr6, nfatc1,andpitx2), while active Wnt signaling andLef1expression occur during early morphogenesis stages of tooth development. We also find that, despite the absence of a histologically distinct successional dental lamina in stickleback tooth fields, the same battery of nine genes (Bmpr1a,Bmp6,CD34,Gli1,Igfbp5a,Lgr4,Lgr6,Nfatc1, andPitx2) are expressed in the basalmost endodermal cell layer, which is the region most closely associated with replacement tooth germs. Like zebrafish, stickleback replacement tooth germs additionally expressLef1and exhibit active Wnt signaling. Thus, two fish systems that either have an organized successional dental lamina (zebrafish) or lack a morphologically distinct successional dental lamina (sticklebacks) deploy similar genetic programs during tooth regeneration.ConclusionsWe propose that the expression domains described here delineate a highly conserved “successional dental epithelium” (SDE). Furthermore, a set of orthologous genes is known to mark hair follicle epithelial stem cells in mice, suggesting that regenerative systems in other epithelial appendages may utilize a related epithelial progenitor cell type, despite the highly derived nature of the resulting functional organs.
Spontaneous primary pneumomediastinum: is it always benign?
Authors: Alemu Berhanu N. , Yeheyis Ephraim T. , Tiruneh Abraham G. 
Published: March 2021

Abstract
Background
Spontaneous Pneumomediastinum is a rare disease. It could be a simple and self-limited condition or be a life-threatening complication of underlying diseases. The therapeutic options also differ by the cause. This systematic review was done to provide, as far as we know, the first attempt to broadly assess the clinical feature, predisposing factors, possible management, and outcome of spontaneous primary pneumomediastinum.

Methods
In addition to the two patients treated at our hospital, a Pub Med Search for literature on case reports of spontaneous pneumomediastinum published in English up to November 2018 was done. We extracted data on patients' demographic characteristics, symptoms, timing, diagnosis, management, and outcome of the treatment were analyzed based on the preferred Reporting Items for Systematic reviews and Meta-analysis (PRISMA)

Result
A total of 339 cases were reviewed. 71.7% of them were male. The Mean age affected was 22.4 ± 11.3 years. Chest pain, 196 (57.8%), is the most common presenting symptom, followed by dyspnea, 156 (46%), cough 95 (28%), neck swelling 92 (27.13%), cervical pain 88 (25.9%), dysphagia 39 (11.5%), odynophagia 37 (10.9%), and Dysphonia 14 (4.1%). Fifty-seven patients (16.8%) had a prior history of Asthma, 19 (5.6%) had Connective Tissue Disorders, and 12 (3.5%) had associated malignancy as an identified risk factor. In 35 (10.3%) patients, spontaneous pneumomediastinum was found incidentally. The mean number of days before the clinical resolution of spontaneous pneumomediastinum was 6.65 ± 11.8 days and the average hospital stay was 4.15 ± 1.93 days. Nineteen (5.6%) patients have died as a result of the underlying disease not related to SPM.

Conclusion
Spontaneous pneumomediastinum is uncommon, usually benign, a self-limited disorder that commonly occurs in a young adult without any apparent precipitating factor or disease. Spontaneous pneumomediastinum usually responds very well to conservative treatment without recurrence. However, secondary causes should be ruled out to minimize the unfavorable outcome.
SMPLIP-Score: predicting ligand binding affinity from simple and interpretable on-the-fly interaction fingerprint pattern descriptors
Authors: Kumar Surendra , Kim Mi-hyun 
Published: March 2021

AbstractIn drug discovery, rapid and accurate prediction of protein–ligand binding affinities is a pivotal task for lead optimization with acceptable on-target potency as well as pharmacological efficacy. Furthermore, researchers hope for a high correlation between docking score and pose with key interactive residues, although scoring functions as free energy surrogates of protein–ligand complexes have failed to provide collinearity. Recently, various machine learning or deep learning methods have been proposed to overcome the drawbacks of scoring functions. Despite being highly accurate, their featurization process is complex and the meaning of the embedded features cannot directly be interpreted by human recognition without an additional feature analysis. Here, we propose SMPLIP-Score (Substructural Molecular and Protein–Ligand Interaction Pattern Score), a direct interpretable predictor of absolute binding affinity. Our simple featurization embeds the interaction fingerprint pattern on the ligand-binding site environment and molecular fragments of ligands into an input vectorized matrix for learning layers (random forest or deep neural network). Despite their less complex features than other state-of-the-art models, SMPLIP-Score achieved comparable performance, a Pearson’s correlation coefficient up to 0.80, and a root mean square error up to 1.18 in pKunits with several benchmark datasets (PDBbind v.2015, Astex Diverse Set, CSAR NRC HiQ, FEP, PDBbind NMR, and CASF-2016). For this model, generality, predictive power, ranking power, and robustness were examined using direct interpretation of feature matrices for specific targets.