bluuebunny/crossref_metadata_2025_split huggingface dataset:
Role of age and neuroinflammation in the mechanism of cognitive deficits in sickle cell disease
Authors: Hardy Raven A , Rached Noor Abi , Jones Jayre A , Archer David R , Hyacinth Hyacinth I 
Published: September 2020

This study aims to determine whether sickle cell mice could recapitulate features of cognitive and neurobehavioral impairment observed in sickle cell patients and whether neuroinflammation could be a potential therapeutic target as in other non-sickle cell disease-related cognitive dysfunction. Cognitive (learning and memory) and behavioral (anxiety) deficits in 13- and later 6-month-old male Townes humanized sickle cell (SS) and matched control (AA) mice were evaluated using novel object recognition (NOR) and fear conditioning tests. Immunohistochemistry was performed to quantify peripheral immune cell (CD45+) and activated microglia (Iba1+) as markers of neuroinflammation in the dentate and peri-dentate gyrus areas. We evaluated cell fate by measuring 5'-bromodeoxyuridine and doublecortin fluorescence and phenotyped proliferating cells using either glial fibrillary acid protein (GFAP+), neuronal nuclei (NeuN+), CD45+, and Iba1+. In addition, Golgi-Cox staining was used to assess markers of neuroplasticity (dendritic spine density and morphology and density of dendrite arbors) on cortical and hippocampal pyramidal neurons. Compared to matched AA controls, 13-month-old SS mice showed significant evidence of cognitive and behavioral deficit on NOR and fear conditioning tests. Also, SS mice had significantly higher density of CD45+ and activated microglia cells (i.e. more evidence of neuroinflammation) in the dentate and peri-dentate gyrus area. Additionally, SS mice had significantly lower dendritic spine density, but a higher proportion of immature dendritic spines. Treatment of 13-month-old SS mice with minocycline resulted in improvement of cognitive and behavioral deficit compared to matched vehicle-treated SS mice. Also, treated SS mice had significantly fewer CD45+ and activated microglia cells (i.e. less evidence of neuroinflammation) in the dentate and peri-dentate gyrus, as well as a significant improvement in markers of neuroplasticity. Impact statement This study provides crucial information that could be helpful in the development of new or repurposing of existing therapies for the treatment of cognitive deficit in individuals with sickle cell disease (SCD). Its impact is in demonstrating for the first time that neuroinflammation and along with abnormal neuroplasticity are among the underlying mechanism of cognitive and behavioral deficits in SCD and that drugs such as minocycline which targets these pathophysiological mechanisms could be repurposed for the treatment of this life altering complication of SCD.
Prevalence and correlation of human papillomavirus genotypes with clinical factors in cervical samples from Mexican women
Authors: Hernández-Rosas Fabiola , Orozco-Hernández Erika , Maza-Sánchez Liliana , Salgado-García Pamela Citlalli , Navarro-Vidal Enrique , León-Bautista Mercedes Piedad de 
Published: September 2020

In the last decade, the inclusion of HPV DNA testing in cervical cancer screening has provided one of the best strategies for the prevention and timely detection of HPV. We conducted a high-throughput HPV genotyping study based on MALDI-TOF mass spectrometry to determine the prevalence of 24 HPV genotypes, including oncogenic genotypes, in Mexican women and correlated the results with cytological findings and clinical variables. We likewise identified the risk factors in patients with the HPV infection. Our study included 1000 women from Sonora, Mexico, who participated in cervical cancer screening campaigns and who underwent a Pap smear and HPV DNA test. The results showed that the overall prevalence of HPV was 27.2%, 18.5% with single, and 8.7% multiple infections. The low-risk HPV genotype 6 (8.5%) and oncogenic genotypes 31 (8.1%) and 53 (4.4%) were the most prevalent in the study population. The number of lifetime sexual partners, previous STIs, and age at first intercourse was significantly associated with HPV infection ( P ≤ 0.05). Smoking (OR = 1.5609; 95% IC 1.062–2.292) and more than three lifetime sexual partners (OR = 1.609; 95% IC = 1.124–2.303) represented risk factors for HPV infection. Cytological abnormalities were found in 3.4% of the HPV-positive samples. CIN 1–3 occurred in 0.6% of high-risk HPV cases. In general, the prevalence of the HPV genotypes is high in Mexican women with normal cytological findings. This issue highlights the importance of HPV research in seemingly healthy women and could help guide screening strategies for cervical cancer prevention in Mexico. Impact statement We are submitting data regarding the prevalence and type distribution of the HPV infection and the risk factors associated with it, which may provide a valuable reference to reinforce screening strategies, and to maintain HPV genotype surveillance in Mexico. We discuss the overall prevalence of HPV infection as detected in normal cytological samples stratified by age, different types of infection, and oncogenic capacity. One of the most important findings was that common HPV genotypes detected in healthy women were the genotype numbers: 6, 31, 16, and 56, likewise, smoking and having a history of more than three sexual partners over their lifetime, represented the main risk factors in this study. Furthermore, we found a low frequency of cytological abnormalities and CIN 1–3 in women with HR-HPV.
Jordanian ostomates' health problems and self-care ability to manage their intestinal ostomy: a cross-sectional study
Authors: Elshatarat Rami A , Ebeid Inas A , Elhenawy Khadega A , Saleh Zyad T , Raddaha Ahmad H Abu , Aljohani Mohammed S 
Published: September 2020

Background Ostomates have several physical, psychological and social health problems. These problems negatively impact the ostomates' quality of life. Aims This study aims to identify Jordanian ostomates' health problems and their self-care ability to manage their ostomies. Methods This is a cross-sectional study. A convenience sampling method was used to recruit 168 Jordanian patients with intestinal ostomies. A self-report questionnaire was used to collect the data. Results On average, the participants’ physiological ostomy-related problem scores were 8.76 ± 2.37 (out of 13 problems) and the total score of self-care ability to manage their ostomies was 16.56 ± 2.62 (out of 24). About 22% of the participants had ‘moderately severe’ to ‘severe’ depression (nine-item Patient Health Questionnaire score ≥15) and 33.9% had ‘moderate’ to ‘severe’ anxiety (seven-item General Anxiety Disorder questionnaire score ≥10). About half of the participants had exposure to teaching and/or training about ostomy care. About 85% of participants were willing to attend health education and training programmes about ostomy care. There was a significant correlation between high ostomates’ self-care ability to manage their ostomies and a low number of physiological health problems ( r = −0.67, p = 0.04), a low depression (Patient Health Questionnaire 9) score ( r = −0.54, p = 0.039) and a low anxiety (seven-item General Anxiety Disorder questionnaire) score ( r = −0.71, p < 0.027). Conclusions Health teaching and training about intestinal ostomy management, psychosocial support, follow-up assessment and treatment for ostomy-related problems are recommended for all ostomates.
Physical activity determinants among students based on Pender’s health promotion model constructs: a cross-sectional study using path analysis
Authors: Sabooteh Sahar , Feizi Awat , Shekarchizadeh Parivash , Shahnazi Hossein , Mostafavi Firoozeh 
Published: September 2020

Background: Over recent years, new lifestyles have raised ongoing concerns about the quality of life of students, especially inactivity. The purpose of this study was to determine the factors associated with regular physical activity among students using Pender’s health promotion model. Methods: The present cross-sectional correlational study was conducted on 650 students of Isfahan University of Medical Sciences, Iran, who were selected by stratified sampling with probability proportional to size. Data were collected using a three-part questionnaire, including demographic profile, Pender’s health promotion model constructs and the international physical activity questionnaire. The strongest determinants of physical activity were identified using structural equation modeling by Amos software. Data were analysed by SPSS software (16) using chi-square, one-way analysis of variance and Spearman correlation. Results: The results showed walking activity in 69.1%, moderate activity in 3.8% and vigorous activity in 27.1%. According to path analysis, perceived barriers were the most efficient predictor of physical activity among students, and Pender’s health promotion model constructs explained 84.9% of physical activity changes. Conclusion: The satisfactory predictive value of Pender’s health promotion model constructs for physical activity behaviour focused on effective structures, such as perceived barriers, supports the application of this model to design educational interventions better.
Challenges in the Prenatal Diagnosis of Cloaca
Authors: Shields Lisa B.E. , White Jeffrey T. , Peppas Dennis S. , Rosenberg Eran 
Published: September 2020

Background: Cloaca is a common excretory channel for the genital, urinary, and gastrointestinal tracts. It is considered a severe anorectal malformation caused by failed partitioning of the genital, rectal, and urinary tracts. Methods: We report 5 infants with cloaca at birth who were identified prenatally by one or more of the following on prenatal ultrasound (US): ambiguous genitalia, a cystic pelvic/abdominal mass, hydronephrosis, ascites, a single umbilical artery, and oligohydramnios. Results: A cystic pelvic/abdominal mass and ambiguous genitalia were each observed in 3 cases by prenatal US. Ambiguous genitalia was observed in all 5 neonates at birth. There were 2 twin pregnancies (dichorionic/diamniotic and monochorionic/monoamniotic), with only 1 twin in a set affected with cloaca. Conclusion: Pediatricians should be alert to the prenatal US findings that may raise suspicion of a persistent cloaca to improve both prenatal counseling and family preparation.
Health Literacy and Recall of Postoperative Instructions in Patients Undergoing the Lapidus Procedure
Authors: Garfinkel Jonathan H. , Hummel Amelia , Day Jonathan , Roney Andrew , Jones Mackenzie , Rosenbaum Andrew , Ellis Scott J. 
Published: September 2020

Background: Active participation in patients’ own care is essential for success after Lapidus procedure. Poor health literacy, comprehension, and retention of patient instructions may be correlated with patient participation. Currently, there is no objective measure of how well patients internalize and retain instructions before and after a Lapidus procedure. We performed this study to assess how much of the information given to patients preoperatively was able to be recalled at the first postoperative visit. Methods: All patients between ages 18 and 88 years undergoing a Lapidus procedure for hallux valgus by the senior author between June 2016 and July 2018 were considered eligible for inclusion. Patients were excluded if they had a history of previous bunion surgery or if the procedure was part of a flatfoot reconstruction. Patients were given written and verbal instructions at the preoperative visit. Demographic and comprehension surveys were administered at their first visit approximately 2 weeks postoperatively. A total of 50 patients, of which 42 (84%) were female and 43 (86%) had a bachelor’s degree or higher, were enrolled. Results: Mean overall score on the comprehension survey was 6.2/8 (±1.2), mean procedure subscore was 1.8/3 (±0.64), and mean postoperative protocol subscore was 4.4/5 (±0.8). The most frequently missed question asked patients to identify the joint fused in the procedure. Conclusion: Although comprehension and retention of instructions given preoperatively was quite high in our well-educated cohort, our findings highlight the importance of delivering clear instructions preoperatively and reinforcing these instructions often. Level of Evidence: Level II, prospective cohort study.
A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples
Authors: Li Huamei , Sharma Amit , Ming Wenglong , Sun Xiao , Liu Hongde 
Published: September 2020

Abstract
Background
The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of gene expression across multiple conditions. In addition, the knowledge about the identification of gene expression markers across multiple conditions is still paucity.

Results
Herein, we developed a hybrid tool, LinDeconSeq, which consists of 1) identifying marker genes using specificity scoring and mutual linearity strategies across any number of cell types, and 2) predicting cellular fractions of bulk samples using weighted robust linear regression with the marker genes identified in the first stage. On multiple publicly available datasets, the marker genes identified by LinDeconSeq demonstrated better accuracy and reproducibility compared to MGFM and RNentropy. Among deconvolution methods, LinDeconSeq showed low average deviations (≤0.0958) and high average Pearson correlations (≥0.8792) between the predicted and actual fractions on the benchmark datasets. Importantly, the cellular fractions predicted by LinDeconSeq appear to be relevant in the diagnosis of acute myeloid leukemia (AML). The distinct cellular fractions in granulocyte-monocyte progenitor (GMP), lymphoid-primed multipotent progenitor (LMPP) and monocytes (MONO) were found to be closely associated with AML compared to the healthy samples. Moreover, the heterogeneity of cellular fractions in AML patients divided these patients into two subgroups, differing in both prognosis and mutation patterns. GMP fraction was the most pronounced between these two subgroups, particularly, in SubgroupA, which was strongly associated with the better AML prognosis and the younger population. Totally, the identification of marker genes by LinDeconSeq represents the improved feature for deconvolution. The data processing strategy with regard to the cellular fractions used in this study also showed potential for the diagnosis and prognosis of diseases.

Conclusions
Taken together, we developed a freely-available and open-source tool LinDeconSeq (https://github.com/lihuamei/LinDeconSeq), which includes marker identification and deconvolution procedures. LinDeconSeq is comparable to other current methods in terms of accuracy when applied to benchmark datasets and has broad application in clinical outcome and disease-specific molecular mechanisms.
Comparative transcriptome analysis revealed the cooperative regulation of sucrose and IAA on adventitious root formation in lotus (Nelumbo nucifera Gaertn)
Authors: libao Cheng , minrong Zhao , Zhubing Hu , huiying Liu , Shuyan Li 
Published: September 2020

Abstract
Background
In China, lotus is an important cultivated crop with multiple applications in ornaments, food, and environmental purification. Adventitious roots (ARs), a secondary root is necessary for the uptake of nutrition and water as the lotus principle root is underdeveloped. Therefore, AR formation in seedlings is very important for lotus breeding due to its effect on plant early growth. As lotus ARs formation was significantly affected by sucrose treatment, we analyzed the expression of genes and miRNAs upon treatment with differential concentrations of sucrose, and a crosstalk between sucrose and IAA was also identified.

Results
Notably, 20 mg/L sucrose promoted the ARs development, whereas 60 mg/L sucrose inhibited the formation of ARs. To investigate the regulatory pathway during ARs formation, the expression of genes and miRNAs was evaluated by high-throughput tag-sequencing. We observed that the expression of 5438, 5184, and 5345 genes was enhanced in the GL20/CK0, GL60/CK0, and CK1/CK0 libraries, respectively. Further, the expression of 73, 78, and 71 miRNAs was upregulated in the ZT20/MCK0, ZT60/MCK0, and MCK1/MCK0 libraries, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that most of the differentially expressed genes and miRNAs in the GL20/GL60 and ZT20/ZT60 libraries were involved in signal transduction. A large number of these genes (29) and miRNAs (53) were associated with plant hormone metabolism. We observed an association between five miRNAs (miR160, miR156a-5p, miR397-5p_1, miR396a and miR167d) and nine genes (auxin response factor, protein brassinosteroid insensitive 1, laccase, and peroxidase 27) in the ZT20/ ZT60 libraries during ARs formation. Quantitative polymerase chain reaction (qRT-PCR) was used to validate the high-throughput tag-sequencing data.

Conclusions
We found that the expression of many critical genes involved in IAA synthesis and IAA transport was changed after treatment with various concentration of sucrose. Based on the change of these genes expression, IAA and sucrose content, we concluded that sucrose and IAA cooperatively regulated ARs formation. Sucrose affected ARs formation by improving IAA content at induction stage, and increased sucrose content might be also required for ARs development according to the changes tendency after application of exogenous IAA.
B chromosomes of multiple species have intense evolutionary dynamics and accumulated genes related to important biological processes
Authors: Ahmad Syed F. , Jehangir Maryam , Cardoso Adauto L. , Wolf Ivan R. , Margarido Vladimir P. , Cabral-de-Mello Diogo C. , O’Neill Rachel , Valente Guilherme T. , Martins Cesar 
Published: September 2020

Abstract
Background
One of the biggest challenges in chromosome biology is to understand the occurrence and complex genetics of the extra, non-essential karyotype elements, commonly known as supernumerary or B chromosomes (Bs). The non-Mendelian inheritance and non-pairing abilities of B chromosomes make them an interesting model for genomics studies, thus bringing to bear different questions about their genetic composition, evolutionary survival, maintenance and functional role inside the cell. This study uncovers these phenomena in multiple species that we considered as representative organisms of both vertebrate and invertebrate models for B chromosome analysis.

Results
We sequenced the genomes of three animal species including two fishes Astyanax mexicanus and Astyanax correntinus, and a grasshopper Abracris flavolineata, each with and without Bs, and identified their B-localized genes and repeat contents. We detected unique sequences occurring exclusively on Bs and discovered various evolutionary patterns of genomic rearrangements associated to Bs. In situ hybridization and quantitative polymerase chain reactions further validated our genomic approach confirming detection of sequences on Bs. The functional annotation of B sequences showed that the B chromosome comprises regions of gene fragments, novel genes, and intact genes, which encode a diverse set of functions related to important biological processes such as metabolism, morphogenesis, reproduction, transposition, recombination, cell cycle and chromosomes functions which might be important for their evolutionary success.

Conclusions
This study reveals the genomic structure, composition and function of Bs, which provide new insights for theories of B chromosome evolution. The selfish behavior of Bs seems to be favored by gained genes/sequences.
Autoreceptor control of serotonin dynamics
Authors: Best Janet , Duncan William , Sadre-Marandi Farrah , Hashemi Parastoo , Nijhout H. Frederik , Reed Michael 
Published: September 2020

Abstract
Background
Serotonin is a neurotransmitter that has been linked to a wide variety of behaviors including feeding and body-weight regulation, social hierarchies, aggression and suicidality, obsessive compulsive disorder, alcoholism, anxiety, and affective disorders. Full understanding involves genomics, neurochemistry, electrophysiology, and behavior. The scientific issues are daunting but important for human health because of the use of selective serotonin reuptake inhibitors and other pharmacological agents to treat disorders. This paper presents a new deterministic model of serotonin metabolism and a new systems population model that takes into account the large variation in enzyme and transporter expression levels, tryptophan input, and autoreceptor function.

Results
We discuss the steady state of the model and the steady state distribution of extracellular serotonin under different hypotheses on the autoreceptors and we show the effect of tryptophan input on the steady state and the effect of meals. We use the deterministic model to interpret experimental data on the responses in the hippocampus of male and female mice, and to illustrate the short-time dynamics of the autoreceptors. We show there are likely two reuptake mechanisms for serotonin and that the autoreceptors have long-lasting influence and compare our results to measurements of serotonin dynamics in the substantia nigra pars reticulata. We also show how histamine affects serotonin dynamics. We examine experimental data that show very variable response curves in populations of mice and ask how much variation in parameters in the model is necessary to produce the observed variation in the data. Finally, we show how the systems population model can potentially be used to investigate specific biological and clinical questions.

Conclusions
We have shown that our new models can be used to investigate the effects of tryptophan input and meals and the behavior of experimental response curves in different brain nuclei. The systems population model incorporates individual variation and can be used to investigate clinical questions and the variation in drug efficacy. The codes for both the deterministic model and the systems population model are available from the authors and can be used by other researchers to investigate the serotonergic system.