bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structured-light surface scanning system to evaluate breast morphology in standing and supine positions
Authors: Tong Olivia L. H. , Chamson-Reig Astrid , Yip Lawrence C. M. , Brackstone Muriel , Diop Mamadou , Carson Jeffrey J. L. 
Published: August 2020

AbstractBreast shapes are affected by gravitational loads and deformities. Measurements obtained in the standing position may not correlate well with measurements in the supine position, which is more representative of patient position during breast surgery. A dual color 3D surface imaging system capable of scanning patients in both supine and standing positions was developed to evaluate the effect of changes in body posture on breast morphology. The system was evaluated with breast phantoms to assess accuracy, then tested on ten subjects in three body postures to assess its effectiveness as a clinical tool. The accuracy of the system was within 0.4 mm on average across the model. For the human study, there was no effect of body posture on breast volumes (p value > 0.05), but we observed an effect of completeness of breast scans on body posture (p value  < 0.05). Post-hoc tests showed that the supine position and the standing position with hands at the waist differed significantly (p value  < 0.05). This study shows that the system can quantitatively evaluate the effect of subject postures, and thereby has the potential to be used to investigate peri-operative changes in breast morphology.
Programmed death ligand-1 (PD-L1) expression in meningioma; prognostic significance and its association with hypoxia and NFKB2 expression
Authors: Karimi Shirin , Mansouri Sheila , Mamatjan Yasin , Liu Jeff , Nassiri Farshad , Suppiah Suganth , Singh Olivia , Aldape Kenneth , Zadeh Gelareh 
Published: August 2020

AbstractManagement of clinically aggressive meningiomas is a considerable challenge. PD-L1 induced immune suppression has increasingly gained attention in clinical management of cancer; however, to date, the clinical significance and regulatory mechanisms of PD-L1 in meningioma is not yet fully characterized. We sought to characterize PD-L1 expression in meningioma and elucidate its regulatory mechanisms. Immunohistochemical staining of PD-L1 expression in meningiomas showed 43% positivity in both tumor and immune cells and we observed intra and inter tumoral heterogeneity. Univariate and multivariate analyses confirmed that PD-L1 protein expression is an independent prognostic marker for worse recurrence free survival in meningioma. Furthermore, our transcriptomic analysis revealed a strong association between PD-L1 expression and that of NFKB2 and carbonic anhydrase 9 (CA9). We also demonstrated that both of these markers, when co-expressed with PD-L1, predict tumor progression. Our studies on several meningioma cell lines cultured in hypoxic conditions validated the association of CA9 and PD-L1 expression. Here we show the clinical significance of PD-L1 in meningioma as a marker that can predict tumor recurrence. We also show an association PD-L1 expression with NFKB2 expression and its induction under hypoxic conditions. These findings may open new avenues of molecular investigation in pathogenesis of meningioma.
A biphasic nanohydroxyapatite/calcium sulphate carrier containing Rifampicin and Isoniazid for local delivery gives sustained and effective antibiotic release and prevents biofilm formation
Authors: Qayoom Irfan , Verma Rahul , Murugan Prem Anand , Raina Deepak Bushan , Teotia Arun Kumar , Matheshwaran Saravanan , Nair Nisanth N. , Tägil Magnus , Lidgren Lars , Kumar Ashok 
Published: August 2020

AbstractLong term multiple systemic antibiotics form the cornerstone in the treatment of bone and joint tuberculosis, often combined with local surgical eradication. Implanted carriers for local drug delivery have recently been introduced to overcome some of the limitations associated with conventional treatment strategies. In this study, we used a calcium sulphate hemihydrate (CSH)/nanohydroxyapatite (nHAP) based nanocement (NC) biomaterial as a void filler as well as a local delivery carrier of two standard of care tuberculosis drugs, Rifampicin (RFP) and Isoniazid (INH). We observed that the antibiotics showed different release patterns where INH showed a burst release of 67% and 100% release alone and in combination within one week, respectively whereas RFP showed sustained release of 42% and 49% release alone and in combination over a period of 12 weeks, respectively indicating different possible interactions of antibiotics with nHAP. The interactions were studied using computational methodology, which showed that the binding energy of nHAP with RFP was 148 kcal/mol and INH was 11 kcal/mol, thus varying substantially resulting in RFP being retained in the nHAP matrix. Our findings suggest that a biphasic ceramic based drug delivery system could be a promising treatment alternative to bone and joint TB.
Signatures of local adaptation in the spatial genetic structure of the ascidian Pyura chilensis along the southeast Pacific coast
Authors: Segovia Nicolás I. , González-Wevar Claudio A. , Haye Pilar A. 
Published: August 2020

AbstractThe highly heterogeneous Humboldt Current System (HCS) and the 30°S transition zone on the southeast Pacific coast, represent an ideal scenario to test the influence of the environment on the spatial genomic structure in marine near-shore benthic organisms. In this study, we used seascape genomic tools to evaluate the genetic structure of the commercially important ascidian Pyura chilensis, a species that exhibits a low larval transport potential but high anthropogenic dispersal. A recent study in this species recorded significant genetic differentiation across a transition zone around 30°S in putatively adaptive SNPs, but not in neutral ones, suggesting an important role of environmental heterogeneity in driving genetic structure. Here, we aim to understand genomic-oceanographic associations in P. chilensis along the Southeastern Pacific coast using two combined seascape genomic approaches. Using 149 individuals from five locations along the HCS, a total of 2,902 SNPs were obtained by Genotyping-By-Sequencing, of which 29–585 were putatively adaptive loci, depending on the method used for detection. In adaptive loci, spatial genetic structure was better correlated with environmental differences along the study area (mainly to Sea Surface Temperature, upwelling-associated variables and productivity) than to the geographic distance between sites. Additionally, results consistently showed the presence of two groups, located north and south of 30°S, which suggest that local adaptation processes seem to allow the maintenance of genomic differentiation and the spatial genomic structure of the species across the 30°S biogeographic transition zone of the Humboldt Current System, overriding the homogenizing effects of gene flow.
C24:0 and C24:1 sphingolipids in cholesterol-containing, five- and six-component lipid membranes
Authors: González-Ramírez Emilio J. , García-Arribas Aritz B. , Sot Jesús , Goñi Félix M. , Alonso Alicia 
Published: August 2020

AbstractThe biophysical properties of sphingolipids containing lignoceric (C24:0) or nervonic (C24:1) fatty acyl residues have been studied in multicomponent lipid bilayers containing cholesterol (Chol), by means of confocal microscopy, differential scanning calorimetry and atomic force microscopy. Lipid membranes composed of dioleoyl phosphatidylcholine and cholesterol were prepared, with the addition of different combinations of ceramides (C24:0 and/or C24:1) and sphingomyelins (C24:0 and/or C24:1). Results point to C24:0 sphingolipids, namely lignoceroyl sphingomyelin (lSM) and lignoceroyl ceramide (lCer), having higher membrane rigidifying properties than their C24:1 homologues (nervonoyl SM, nSM, or nervonoyl Cer, nCer), although with a similar strong capacity to induce segregated gel phases. In the case of the lSM-lCer multicomponent system, the segregated phases have a peculiar fibrillar or fern-like morphology. Moreover, the combination of C24:0 and C24:1 sphingolipids generates interesting events, such as a generalized bilayer dynamism/instability of supported planar bilayers. In some cases, these sphingolipids give rise to exothermic curves in thermograms. These peculiar features were not present in previous studies of C24:1 combined with C16:0 sphingolipids. Conclusions of our study point to nSM as a key factor governing the relative distribution of ceramides when both lCer and nCer are present. The data indicate that lCer could be easier to accommodate in multicomponent bilayers than its C16:0 counterpart. These results are relevant for events of membrane platform formation, in the context of sphingolipid-based signaling cascades.
Public institutions’ capacities regarding climate change adaptation and risk management support in agriculture: the case of Punjab Province, Pakistan
Authors: Khan Nasir Abbas , Gao Qijie , Abid Muhammad 
Published: August 2020

AbstractPublic institutions could play an important role in building agricultural resilience to climate change by providing information and technology support to farmers. This study takes the case of Pakistan to investigate the perspective and capacities of public institutions as well as to identify gaps in current institutional arrangements in dealing and managing climate change in the agriculture sector. For this purpose, 53 office bearers from thirteen public institutions in Punjab province of Pakistan were interviewed using a semi-structured questionnaire to collect data on climate knowledge, training, coordination, and resource availability. The study uses an index-based approach to calculate Institutional Capacity Indices (ICI) based on selected seven indicators. The results of the index analysis show that institutions have the least financial capacity, followed by lacking physical and human resources. Whereas results show high index value for perception and knowledge, indicating a good understanding of climate change at the institutional level. The overall ICI index value indicates a medium level capacity of institutions in dealing with climate change. Moreover, the study shows that gaps in management, non-availability of financial and physical resources, and lack of training are the key bottlenecks for limited adaptation support from public institutions. This study highlights the importance of reducing gaps so that institutions could play their role in building the resilience of the agriculture sector to climate change.
Effects of conical intersections on hyperfine quenching of hydroxyl OH in collision with an ultracold Sr atom
Authors: Li Ming , Kłos Jacek , Petrov Alexander , Li Hui , Kotochigova Svetlana 
Published: August 2020

AbstractThe effect of conical intersections (CIs) on electronic relaxation, transitions from excited states to ground states, is well studied, but their influence on hyperfine quenching in a reactant molecule is not known. Here, we report on ultracold collision dynamics of the hydroxyl free-radical OH with Sr atoms leading to quenching of OH hyperfine states. Our quantum-mechanical calculations of this process reveal that quenching is efficient due to anomalous molecular dynamics in the vicinity of the conical intersection at collinear geometry. We observe wide scattering resonance features in both elastic and inelastic rate coefficients at collision energies below$$k_{\text {B}}\times 10 \, \hbox {mK}$$kB×10mK. They are identified as eitherp- ord-wave shape resonances. We also describe the electronic potentials relevant for these non-reactive collisions, their diabatization procedure, as well as the non-adiabatic coupling between the diabatic potentials near the CIs.
Ischemia reperfusion injury provokes adverse left ventricular remodeling in dysferlin-deficient hearts through a pathway that involves TIRAP dependent signaling
Authors: Evans Sarah , Weinheimer Carla J. , Kovacs Attila , Williams Jesse W. , Randolph Gwendalyn J. , Jiang Wenlong , Barger Philip M. , Mann Douglas L. 
Published: August 2020

AbstractCardiac myocytes have multiple cell autonomous mechanisms that facilitate stabilization and repair of damaged sarcolemmal membranes following myocardial injury. Dysferlin is a protein which facilitates membrane repair by promoting membrane resealing. Although prior studies have shown that dysferlin-deficient (Dysf−/−) mouse hearts have an impaired recovery from acute ischemia/reperfusion (I/R) injury ex vivo, the role of dysferlin in mediating the recovery from myocardial injury in vivo is unknown. Here we show that Dysf−/− mice develop adverse LV remodeling following I/R injury secondary to the collateral damage from sustained myocardial inflammation within the infarct zone. Backcrossing Dysf−/− mice with mice lacking signaling through the Toll-Interleukin 1 Receptor Domain-Containing Adaptor Protein (Tirap−/−), attenuated inflammation and abrogated adverse LV remodeling following I/R injury. Subsequent studies using Poloxamer 188 (P188), a membrane resealing reagent, demonstrated that P188 did not attenuate inflammation nor prevent adverse LV remodeling in Dysf−/− mice following I/R injury. Viewed together these studies reveal a previously unappreciated role for the importance of membrane sealing and the resolution of inflammation following myocardial injury.
Comparative analysis of racial differences in breast tumor microbiome
Authors: Thyagarajan Srikantha , Zhang Yan , Thapa Santosh , Allen Michael S. , Phillips Nicole , Chaudhary Pankaj , Kashyap Meghana V. , Vishwanatha Jamboor K. 
Published: August 2020

AbstractStudies have demonstrated that environmental, host genetic, and socioeconomic factors influence the breast cancer prevalence landscape with a far-reaching influence on racial disparity to subtypes of breast cancer. To understand whether breast tissue harbors race-specific microbiota, we performed 16S rRNA gene-based sequencing of retrospective tumor and matched normal tissue adjacent to tumor (NAT) samples collected from Black non-Hispanic (BNH) and White non-Hispanic (WNH) women. Analysis of Triple Negative Breast cancer (TNBC) and Triple Positive Breast Cancer (TPBC) tissues for microbiota composition revealed significant differences in relative abundance of specific taxa at both phylum and genus levels between WNH and BNH women cohorts. Our main findings are that microbial diversity as measured by Shannon index was significantly lower in BNH TNBC tumor tissue as compared to matched NAT zone. In contrast, the WNH cohort had an inverse pattern for the Shannon index, when TNBC tumor tissue was compared to the matched NAT. Unweighted Principle Coordinates Analysis (PCoA) revealed a distinct clustering of tumor and NAT microbiota in both BNH and WNH cohorts.
Improvement of sleep quality after treatment in patients with lumbar spinal stenosis: a prospective comparative study between conservative versus surgical treatment
Authors: Kim Jihye , Lee Seung Hun , Kim Tae-Hwan 
Published: August 2020

AbstractDespite the importance of sleep and the evidence on its relationship with various chronic diseases, quality of sleep is not considered in patients with lumbar spinal stenosis (LSS). This prospective comparative study aimed to investigate the changes in sleep disturbance after treatment in patients with LSS. Patients with LSS and sleep disturbance (n = 201; 147 conservatively treated and 54 patients with surgical treatment) were included. The Pittsburgh sleep quality index (PSQI) was used to evaluate sleep quality. Propensity score matching was used to attenuate the potential bias. Clinical outcome of surgery, as determined by the Oswestry disability index, and the PSQI was compared between the two groups at 6 weeks, 3 months, and 6 months after enrollment. Multivariate logistic analysis was performed to adjust for possible confounders within the matched cohorts. Among the 201 patients, 96 (47.7%) patients were finally matched (48 patients in each group). Sleep quality was initially improved after treatment, regardless of the treatment method. Sleep quality in the surgical group was improved by 6 weeks after surgery and consistently improved during the 6-month follow-up period, despite less use of pain killer. Conversely, the improvement in sleep quality at 6-weeks following conservative treatment was not maintained during the follow-up, although the treatment outcome for LSS measured by ODI was continuously improved. After multivariate logistic regression analysis within propensity score matched cohorts, surgical treatment had a significantly greater chance to improve sleep quality compared to conservative treatment. The failure of sleep improvement in conservative group was significantly associated with depression presented by worse score in Hamilton depression rating scale, and more severe degree of foraminal-type stenosis, which should be carefully considered for conservative treatment of LSS patients with sleep disturbance.
Development and validation of a nomogram to predict the prognosis of patients with gastric cardia cancer
Authors: Shi Xiuquan , Xu Lijun , Ma Bingwei , Wang Siben 
Published: August 2020

AbstractOur goal was to develop a prognostic nomogram to predict overall survival (OS) and cancer-specific survival (CSS) in patients with gastric cardia cancer (GCC). Patients diagnosed with GCC from 2004 to 2015 were screened from the surveillance, epidemiology, and end results (SEER) database. A nomogram was developed based on the variables associated with OS and CSS using multivariate Cox analysis regression models, which predicted 3- and 5-year OS and CSS. The predictive performance of the nomogram was evaluated using the consistency index (C-index), calibration curve and decision curve analysis (DCA), and the nomogram was calibrated for 3- and 5-year OS and CSS. A total of 7,332 GCC patients were identified and randomized into a training cohort (5,231, 70%) and a validation cohort (2,200, 30%). Multivariate Cox regression analysis showed that marital status, race, SEER stage, grade, T stage, N stage, M stage, tumor size, and surgery were independent risk factors for OS and CSS in GCC patients. Based on the multivariate Cox regression results, we constructed prognostic nomograms of OS and CSS. In the training cohort, the C-index for the OS nomogram was 0.714 (95% CI = 0.705–0.723), and the C-index for the CSS nomogram was 0.759 (95% CI = 0.746–0.772). In the validation cohort, the C-index for the OS nomogram was 0.734 (95% CI = 0.721–0.747), while the C-index for the CSS nomogram was 0.780 (95% CI = 0.759–0.801). Our nomogram has better prediction than the nomogram based on TNM stage. In addition, in the training and external validation cohorts, the calibration curves of the nomogram showed good consistency between the predicted and actual 3- and 5-year OS and CSS rates. The nomogram can effectively predict OS and CSS in GCC patients, which may help clinicians personalize prognostic assessments and clinical decisions.
Integrative genomics analysis identifies five promising genes implicated in insomnia risk based on multiple omics datasets
Authors: Sun Haozhen , Zhang Jianhua , Ma Yunlong , Liu Jingjing 
Published: August 2020

Abstract
In recent decades, many genome-wide association studies on insomnia have reported numerous genes harboring multiple risk variants. Nevertheless, the molecular functions of these risk variants conveying risk to insomnia are still ill-studied. In the present study, we integrated GWAS summary statistics (N=386,533) with two independent brain expression quantitative trait loci (eQTL) datasets (N=329) to determine whether expression-associated SNPs convey risk to insomnia. Furthermore, we applied numerous bioinformatics analyses to highlight promising genes associated with insomnia risk. By using Sherlock integrative analysis, we detected 449 significant insomnia-associated genes in the discovery stage. These identified genes were significantly overrepresented in six biological pathways including Huntington’s disease (P=5.58 × 10−5), Alzheimer’s disease (P=5.58 × 10−5), Parkinson’s disease (P=6.34 × 10−5), spliceosome (P=1.17 × 10−4), oxidative phosphorylation (P=1.09 × 10−4), and wnt signaling pathways (P=2.07 × 10−4). Further, five of these identified genes were replicated in an independent brain eQTL dataset. Through a PPI network analysis, we found that there existed highly functional interactions among these five identified genes. Three genes of LDHA (P=0.044), DALRD3 (P=5.0 × 10−5), and HEBP2 (P=0.032) showed significantly lower expression level in brain tissues of insomnic patients than that in controls. In addition, the expression levels of these five genes showed prominently dynamic changes across different time points between behavioral states of sleep and sleep deprivation in mice brain cortex. Together, the evidence of the present study strongly suggested that these five identified genes may represent candidate genes and contributed risk to the etiology of insomnia.
Bioinformatics analysis of prognostic value of PITX1 gene in breast cancer
Authors: Wang Qiaoyun , Zhao Shuai , Gan Lei , Zhuang Zhixiang 
Published: August 2020

Abstract
Background: Paired-like homeodomain transcription factor 1 (PITX1) participates in miscellaneous biological processes including cell growth, development, progression and invasion in various malignant tumors. However, the analysis of the association between PITX1 expression and the survival in breast cancer remains unclear. Methods: Clinical prognostic parameters and survival data related to PITX1 in breast cancer patients were performed using the bioinformatic analysis including Oncomine, Bc-GenExMiner v4.3, PrognoScan and UCSC Xena. Results: We found that PITX1 gene expression was significantly higher in different histological classification of breast cancer. The Scarff–Bloom–Richardson (SBR) grade, Nottingham prognostic index (NPI), estrogen receptor (ER) negative, epidermal growth factor receptor-2 (HER2) positive, lymph node positive, triple-negative status and basal-like status were positively correlated with PITX1 level, except for patients’ age and the progesterone receptor (PR) status. We have found that the increased PITX1 expression correlated with worse relapse-free survival, disease specific survival and overall survival. PITX1 was positively correlated with metastatic relapse-free survival and distant metastasis-free survival. We also confirmed positive correlation between PITX1 and the nucleotide-binding oligomerization domain 2 (NOD2). Conclusion: The lower expression of PITX1 was associated with better clinical prognostic parameters and clinical survival in breast cancer according to the bioinformatic analysis.
Metabolism
Authors: Judge Ayesha , Dodd Michael S. 
Published: August 2020

Abstract
Metabolism consists of a series of reactions that occur within cells of living organisms to sustain life. The process of metabolism involves many interconnected cellular pathways to ultimately provide cells with the energy required to carry out their function. The importance and the evolutionary advantage of these pathways can be seen as many remain unchanged by animals, plants, fungi, and bacteria. In eukaryotes, the metabolic pathways occur within the cytosol and mitochondria of cells with the utilisation of glucose or fatty acids providing the majority of cellular energy in animals. Metabolism is organised into distinct metabolic pathways to either maximise the capture of energy or minimise its use. Metabolism can be split into a series of chemical reactions that comprise both the synthesis and degradation of complex macromolecules known as anabolism or catabolism, respectively. The basic principles of energy consumption and production are discussed, alongside the biochemical pathways that make up fundamental metabolic processes for life.