bluuebunny/crossref_metadata_2025_split huggingface dataset:
Exosomes Are Comparable to Source Adipose Stem Cells in Fat Graft Retention with Up-Regulating Early Inflammation and Angiogenesis
Authors: Chen Bin , Cai Junrong , Wei Yating , Jiang Zhaohua , Desjardins Haley E. , Adams Alexandra E. , Li Shengli , Kao Huang-Kai , Guo Lifei 
Published: August 2019

Background:Exosomes derived from mesenchymal stem cells possess functional properties similar to those of their parent cells, suggesting that they could play a pivotal role in tissue repair and regeneration.Methods:Using lipotransfer as a surrogate, exosomes were isolated from mouse adipose-derived stem cell–conditioned medium and characterized. Minced fat tissue mixed with exosomes, source cells (cell-assisted lipotransfer), or saline was implanted subcutaneously in the lower back of C57/BL mice bilaterally (n= 16 each). Transferred fat tissues were harvested and analyzed at 3 and 10 weeks.Results:At 3 and 10 weeks after the transfer, fat grafts in groups of exosomes and cell-assisted lipotransfer showed better fat integrity, fewer oil cysts, and reduced fibrosis. At week 10, graft retention rates in cell-assisted lipotransfer (50.9 ± 2.4 percent;p= 0.03) and exosome groups (56.4 ± 1.6 percent;p< 0.001) were significantly higher than in the saline group (40.7 ± 4.7 percent). Further investigations of macrophage infiltration, inflammatory factors, angiogenic factors, adipogenic factors, and extracellular matrix revealed that those exosomes promoted angiogenesis and up-regulated early inflammation, whereas during mid to late stages of fat grafting, they exerted a proadipogenic effect and also increased collagen synthesis level similarly to their source cells.Conclusions:The adipose-derived stem cell–derived exosomes demonstrated effects comparable to those of their source cells in achieving improved graft retention by up-regulating early inflammation and augmenting angiogenesis. These features may enable exosomes to be an attractive cell-free alternative in therapeutic regenerative medicine.
Stress-Induced Suppression of Food Intake in Overweight and Obese Adolescents
Authors: Nagy Matthew R. , Gill Amaanat , Adams Tessa , Gerras Julia , Mazin Lauren , Leung Cindy , Hasson Rebecca E. 
Published: August 2019

ABSTRACTObjectiveOverweight adolescents exhibit greater cortisol reactivity in response to acute stress and are more likely to eat in response to emotional cues, which suggest an increased susceptibility to stress-induced eating. The purpose of this study was to examine the biological (cortisol and α-amylase reactivity) and behavioral (caloric intake) responses to an acute stressor in overweight adolescents.MethodsFifty-one adolescents ages 14 to 19 years (47% female, 55% white; body mass index, 31.2 ± 0.8 kg/m2) were exposed to the Trier Social Stress Test and a control condition on separate days. Immediately after each condition, participants were provided with snacks to eat at their leisure. Reactivity was assessed via salivary cortisol and α-amylase area under the curve (AUC), and adolescents were categorized as high or low reactors.ResultsCortisol AUC was higher during the stress condition (19.6 ± 0.2 μg/dl · min) compared with the control condition (11.4 ± 0.9 μg/dl · min,p< .001). α-Amylase AUC was not different during the stress condition (9999 ± 987 U/ml · min) compared with the control condition (8762 ± 865 U/ml · min,p= .145). Overall, adolescents consumed fewer calories during the stress condition (488 ± 51 kcal) compared with the control condition (637 ± 42 kcal,p= .007). High cortisol reactors decreased their calorie consumption from the control condition (716 ± 52 kcal) to the stress condition (457 ± 53 kcal,p= .001), whereas low cortisol reactors did not change their consumption (stress: 518 ± 87 kcal versus control: 561 ± 62 kcal,p= .574).ConclusionHigh cortisol reactivity in overweight adolescents resulted in decreased calorie consumption after an acute stressor. Further research is needed to understand the mechanisms underlying stress-induced suppression of food intake in overweight adolescents.
Posttransplant Lymphoproliferative Disorder in Pediatric Patients: Characteristics of Disease in EBV-seropositive Recipients
Authors: L’Huillier Arnaud G. , Dipchand Anne I. , Ng Vicky L. , Hebert Diane , Avitzur Yaron , Solomon Melinda , Ngan Bo-Yee , Yeung Simon , Stephens Derek , Punnett Angela S. , Barton Michelle , Allen Upton D. 
Published: August 2019

Background.
Patients at greatest risk of posttransplant lymphoproliferative disorder (PTLD) are those who acquire primary Epstein-Barr virus (EBV) infection after solid organ transplantation. The incidence of PTLD among patients who are EBV-seropositive before transplant is lower, and little is known about the differences in presentation and outcome of this population. We describe the characteristics of EBV-seropositive transplant recipients (R+) who developed PTLD and compare survival outcomes with EBV-seronegative recipients (R−).

Methods.
A hospital-based registry was used to identify all patients with biopsy-proven PTLD for the period 2000–2014. Characteristics and outcomes were compared between R+ and R− patients with PTLD.

Results.
Sixty-nine patients were included, among which 20 (29.0%) were R+ and 49 (71.0%) were R−. Multiorgan transplant patients accounted for 25% of PTLD cases in R+ patients, while accounting for only 2.1% of all transplants during the study period. There was no difference in PTLD site between R+ and R− patients. PTLD among R+ individuals occurred during the second year after transplant (median: 1.92; range: 0.35–3.09 y) compared with during the first year for R− individuals (median: 0.95; range: 0.48–2.92 y; P = 0.380). There was a trend for a higher overall mortality among R+ individuals (log rank: 0.09). PTLD-related mortality did not differ between R+ and R− individuals (log rank: 0.17).

Conclusions.
PTLD among R+ individuals was more likely to occur among multiorgan recipients, and there was a tendency for poorer outcomes at 1 and 5 years after the diagnosis of PTLD.
Dissociative recombination of H3+and D5+
Authors: Larsson Mats 
Published: August 2019

Compared with earlier years, the dissociative recombination ofH3+has not been very actively studied in recent years. New results from afterglow experiments are quoted and compared with results from ion storage rings and theory. New results forD5+are discussed. This article also contains some historical remarks on hydrogen and its importance for the advancement of physics and chemistry.This article is part of a discussion meeting issue ‘Advances in hydrogen molecular ions: H3+, H5+and beyond’.
An 11-bit High Dynamic Range (HDR) Luminance Display and Its Use to Discover Contextual Mechanisms of Real-World Luminance Normalization for Visual Acuity and Target Discrimination
Authors: Hung Chou P , Callahan-Flintoft Chloe , Fedele Paul D , Fluitt Kim F , Odoemene Onyekachi , Vaughan Barry D , Walker Anthony J , Jaswa Matthew M , Wei Min , Harrison Andre V 
Published: August 2019

ABSTRACTLuminance can vary widely when scanning across a scene, by up to 10^9 to 1, requiring multiple normalizing mechanisms spanning from the retina to cortex to support visual acuity and recognition. Vision models based on standard dynamic range luminance contrast ratios below 100 to 1 have limited ability to generalize to real-world scenes with contrast ratios over 10,000 to 1 (high dynamic range [HDR]). Understanding and modeling brain mechanisms of HDR luminance normalization is thus important for military applications, including automatic target recognition, display tone mapping, and camouflage. Yet, computer display of HDR stimuli was until recently unavailable or impractical for research. Here we describe procedures for setup, calibration, and precision check of an HDR display system with over 100,000 to 1 luminance dynamic range (650–0.0065 cd/m^2), pseudo 11-bit grayscale precision, and 3-ms temporal precision in the MATLAB/Psychtoolbox software environment. The setup is synchronized with electroencephalography and IR eye-tracking measurements. We report measures of HDR visual acuity and the discovery of a novel phenomenon—that abrupt darkening (from 400 to 4 cd/m^2) engages contextual facilitation, distorting the perceived orientation of a high-contrast central target. Surprisingly, the facilitation effect depended on luminance similarity, contradicting both classic divisive and subtractive models of contextual normalization.
Physiological and Biochemical Analyses of Sorghum Varieties Reveal Differential Responses to Salinity Stress
Authors: Mbinda W , Kimtai M 
Published: August 2019

ABSTRACTSalinity is among the most severe and widespread environmental constrains to global crop production, especially in arid and semi-arid climates and negatively affecting productivity of salt sensitive crop species. Breeding and selection of salt tolerant crop varieties is therefore necessary for sustainable plant productivity. Given that germination and seeding phases are the most critical phase in the plant life cycle, this study aimed to evaluate seed germination potential and associated traits under salt stress conditions as a simple approach to identify salt tolerant Sorghum varieties. There Sorghum varieties whose adaptation to various agroclimatic conditions is not well elucidated. Salinity stress was applied by addition of NaCl at three different levels of stress (100, 200 and 300 mM NaCl), while plants irrigated with water were used as controls. Evaluation of tolerance was performed on the basis of germination percentage, shoot and seed water absorbance, shoot and root length, leave water content, seedling total chlorophyll content and morphologic abnormality. Our results showed that salinity stress significantly impacts all features associated with germination and early development of seedlings. Our results indicated that that salinity stress substantially affects all traits associated with germination and early seedling growth, with the effect of salinity being dependent on the variety used and level of salinity stress applied. Among the tested Sorghum varieties, Gadam was established to the most salt tolerant variety, suggesting its potential use for cultivation under salinity stress conditions as well as its suitability for use as germplasm material in future Sorghum breeding programmes. For a greater insight into comprehensive mechanisms of salinity tolerance in Sorghum, we suggest further research on genomic and molecular analysis.
Peppy: A Virtual Reality Environment for Exploring the Principles of Polypeptide Structure
Authors: Doak David G , Denyer Gareth S , Gerrard Juliet A , Mackay Joel P , Allison Jane R 
Published: August 2019

ABSTRACTA key learning outcome for undergraduate biochemistry classes is a thorough understanding of the principles of protein structure. Traditional approaches to teaching this material, which include two-dimensional (2D) images on paper, physical molecular modelling kits, and projections of 3D structures into 2D, are unable to fully capture the dynamic, 3D nature of proteins. We have built a virtual reality application, Peppy, aimed at facilitating teaching of the principles of protein secondary structure. Rather than attempt to model molecules with the same fidelity to the underlying physical chemistry as existing, research-oriented molecular modelling approaches, we took the more straightforward approach of harnessing the Unity video game physics engine. Indeed, the simplicity and limitations of our model are a strength in a teaching context, provoking questions and thus deeper understanding. Peppy allows exploration of the relative effects of hydrogen bonding (and electrostatic interactions more generally), backbone ϕ/ψ angles, basic chemical structure and steric effects on polypeptide structure in an accessible format that is novel, dynamic and fun to use. As well as describing the implementation and use of Peppy, we discuss the outcomes of deploying Peppy in undergraduate biochemistry courses.STATEMENTProtein structure is inherently dynamic and three-dimensional, but traditional teaching tools are static and/or two-dimensional. We have developed a virtual reality teaching tool, Peppy, that facilitates undergraduate teaching of the principles of protein structure. We outline how Peppy works in terms of how it is used and what goes on ‘under the hood’. We then illustrate its use in undergraduate teaching, where its playful nature stimulated exploration and, thus, deeper understanding.
Immunohistochemistry-based taxonomical classification of bladder cancer predicts response to neoadjuvant chemotherapy
Authors: Font A. , Domènech M. , Benítez R. , Rava M. , Marqués M. , Ramírez J. L. , Pineda S. , Domínguez S. , Gago J. L. , Badal J. , Carrato C. , López H. , Quer A. , Castellano D. , Malats N. , Real F.X 
Published: August 2019

ABSTRACTPlatinum-based neoadjuvant chemotherapy (NAC) increases the survival of patients with organ-confined urothelial bladder cancer (UBC). Because not all patients benefit from treatment, NAC has not been widely applied in the clinical setting. There is strong evidence, based on retrospective studies, that patients with Basal/Squamous (BASQ)-like tumours present with more advanced disease and have worse prognosis; global transcriptomics can identify tumour subtypes associated with response to NAC. We aimed to investigate whether tumour immunohistochemical (IHC) subtyping predicts NAC response. Patients with muscle-invasive UBC having received platinum-based NAC were identified in two hospitals in Spain. Tissue microarrays were constructed; RNA and DNA were extracted from full sections. Nanostring analysis and immunohistochemistry to identify BASQ-like tumours and mutational analysis of UBC oncogenes. We used hierarchical clustering to classify 126 tumours and adjusted logistic regression to assess association with treatment response. Outcomes were progression-free survival and disease-specific survival; univariable and multivariate Cox regression models were applied. We found very high concordance between mRNA and protein for the 4 markers analyzed. We identified three main subgroups: BASQ-like (FOXA1/GATA3 low; KRT5/6/14 high), Luminal-like (FOXA1/GATA3 high; KRT5/6/14 low), and mixed-cluster (FOXA1/GATA3 high; KRT5/6 high; KRT14 low). Patients with BASQ-like tumours were more likely to achieve a pathological response to NAC, displaying a disease-specific survival similar to that of the remaining patients. In conclusion, patients with BASQ-like tumours - identified through simple and robust immunohistochemistry - have a higher likelihood of undergoing a pathological complete response to NAC. Prospective validation in independent series is required.Novelty and impactNeoadjuvant chemotherapy is an important component of the management of patietns with muscle-invasive bladder cancer but improved stratification is necessary. This retrospective study shows that patients with BASQ-like tumors can be identified using immunohistochemistry on paraffin-embedded tissue and are 4-fold more likely to achieve a pathological complete response to platinum-based NAC. The disease-specific survival of patients with BASQ-like tumours treated with NAC was not different from that of other tumour subtypes.
GUN1 influences the accumulation of NEP-dependent transcripts and chloroplast protein import in Arabidopsis cotyledons upon perturbation of chloroplast protein homeostasis
Authors: Tadini Luca , Peracchio Carlotta , Trotta Andrea , Colombo Monica , Mancini Ilaria , Jeran Nicolaj , Costa Alex , Faoro Franco , Marsoni Milena , Vannini Candida , Aro Eva-Mari , Pesaresi Paolo 
Published: August 2019

AbstractCorrect chloroplast development and function require coordinated expression of chloroplast and nuclear genes. This is achieved through chloroplast signals that modulate nuclear gene expression in accordance with the chloroplast’s needs. Genetic evidence indicates that GUN1, a chloroplast-localized pentatricopeptide-repeat (PPR) protein with a C-terminal Small MutS-Related (SMR) domain, is involved in integrating multiple developmental and stress-related signals in both young seedlings and adult leaves. Recently, GUN1 was found to interact physically with factors involved in chloroplast protein homeostasis, and with enzymes of tetrapyrrole biosynthesis in adult leaves that function in various retrograde signaling pathways. Here we show that, following perturbation of chloroplast protein homeostasis i) by growth in lincomycin-containing medium, or ii) in mutants defective in either the FtsH protease complex (ftsh), plastid ribosome activity (prps21-1andprpl11-1) or plastid protein import and folding (cphsp70-1), GUN1 influences NEP-dependent transcript accumulation during cotyledon greening and also intervenes in chloroplast protein import.
Cell-of-Origin Analysis of Metastatic Gastric Cancer Uncovers the Origin of Inherent Intratumor Heterogeneity and a Fundamental Prognostic Signature
Authors: Wang Ruiping , Song Shumei , Harada Kazuto , Han Guangchun , Pizzi Melissa Pool , Zhao Meina , Tatlonghari Ghia , Zhang Shaojun , Wang Yuanxin , Zhao Shuangtao , Badgwell Brian D. , Murphy Mariela Blum , Shanbhag Namita , Estrella Jeannelyn S. , Roy-Chowdhuri Sinchita , Abdelhakeem Ahmed Adel Fouad , Peng Guang , Calin George A. , Hanash Samir , Lazar Alexander J. , Futreal Andrew , Ajani Jaffer A. , Wang Linghua 
Published: August 2019

AbstractIntra-tumoral heterogeneity (ITH) is the fundamental property of cancer, however, the origin of ITH remains poorly understood. Here we performed single-cell RNA sequencing of peritoneal carcinomatosis (PC) from 20 patients with advanced gastric adenocarcinoma (GAC), constructed a transcriptome map of 45,048 PC cells, determined the cell-of-origin of each tumor cell, and incisively explored ITH of PC tumor cells at single-cell resolution. The links between cell-of-origin and ITH was illustrated at transcriptomic, genotypic, molecular, and phenotypic levels. This study characterized the origins of PC tumor cells that populate and thrive in the peritoneal cavity, uncovered the diversity in tumor cell-of-origins and defined it as a key determinant of ITH. Furthermore, cell-of-origin-based analysis classified PC into two cellular subtypes that were prognostic independent of clinical variables, and a 12-gene prognostic signature was then derived and validated in multiple large-scale GAC cohorts. The prognostic signature appears fundamental to GAC carcinogenesis/progression and could be practical for patient stratification.
CODC: A copula based model to identify differential coexpression
Authors: Ray Sumanta , Lall Snehalika , Bandyopadhyay Sanghamitra 
Published: August 2019

ABSTRACTDifferential coexpression has recently emerged as a new way to establish a fundamental difference in expression pattern among a group of genes between two populations. Earlier methods used some scoring techniques to detect changes in correlation patterns of a gene pair in two conditions. However, modeling differential coexpression by mean of finding differences in the dependence structure of the gene pair has hitherto not been carried out.We exploit a copula-based framework to model differential coexpression between gene pair in two different conditions. The Copula is used to model the dependency between expression profiles of a gene pair. For a gene pair, the distance between two joint distributions produced by copula is served as differential coexpression. We used five pan-cancer TCGA RNA-Seq data to evaluate the model which outperforms the existing state-of-the-art. Moreover, the proposed model can detect a mild change in the coexpression pattern across two conditions. For noisy expression data, the proposed method performs well because of the popular scale-invariant property of copula. Additionally, we have identified differentially coexpressed modules by applying hierarchical clustering on the distance matrix. The identified modules are analyzed through Gene Ontology terms and KEGG pathway enrichment analysis.
A threefold superstructure of the anti-epileptic drug phenytoin sodium as a mixed methanol solvate hydrate
Authors: Shah Harsh S. , Chaturvedi Kaushalendra , Zeller Matthias , Bates Simon , Morris Kenneth 
Published: August 2019

Phenytoin sodium, a salt of 5,5-diphenylimidazolidine-2,4-dione, or phenytoin, is commercially available in various dosage forms for its anti-epileptic properties to treat and prevent seizures. The title compound, poly[aquatris(μ3-4,4-diphenyl-2,5-dioxoimidazolidin-1-ido)trimethanoltrisodium(I)], [Na3(C15H11N2O2)3(CH4O)3(H2O)1.08]
n
, a methanol solvate and hydrate of phenytoin sodium, forms a modulated crystal structure that consists of a supercell made up of three close-to-identical repeat units. Each of the basic fragments consists of one phenytoin anion, a sodium cation, and either a methanol, or a methanol and a water molecule coordinated to the sodium ion, yielding a formula unit of Na(C15H11N2O2)(CH3OH)
x
(H2O)
y
for each of the three segments (x, y = 0 or 1; x + y = 1 or 2). Modulation along the b axis is introduced due to the presence or absence of water or methanol molecules at sodium and by the alternating torsion angles of one of the two phenytoin phenyl rings. Individual segments within the asymmetric unit are linked by covalent Na—O and Na—N bonds, with each sodium ion coordinated to one anionic amide N atom and three keto O atoms. The Na—N and one of the Na—O bonds connect (C15H11N2O2)·Na units along the modulation direction, creating an infinite [(C15H11N2O2)·Na]_{\infty} chain that is further stabilized by intramolecular N—H...O hydrogen bonding parallel to [010]. The second Na—O bond connects this chain with a symmetry-equivalent copy of itself created by a screw-axis operation, yielding double strands of [(C15H11N2O2)·Na]_{\infty} chains. Two of these double strands, propagating in opposite directions, constitute the content of the unit cell. Neighboring double strands are connected with each other to form layers perpendicular to the a axis, tethered together via O—H...O hydrogen bonds involving the water and methanol molecules. In addition to modulation, each of the repeat units also exhibits disorder of the modulated segments. Phenyl rings of each repeat unit are rotationally disordered, and sodium-coordinated methanol and water molecules are also positionally disordered and/or partially occupied. The solvated structure reported here, while not matching the patterns reported for any of the known forms of phenytoin sodium, does provide a first insight into the complications and complexities involved in resolving the structure of anhydrous phenytoin sodium.