bluuebunny/crossref_metadata_2025_split huggingface dataset:
Heterologous protein-DNA interactions lead to biased allelic expression of circadian clock genes in interspecific hybrids
Authors: Ng Danny W-K. , Chen Helen H. Y. , Chen Z. Jeffrey 
Published: March 2017

AbstractGenomic interactions in allopolyploids create expression variation of homoeologous alleles through protein-protein and protein-DNA interactions. However, the molecular basis for this is largely unknown. Here we investigated the protein-protein and protein-DNA interactions among homoeologous transcription factors in the circadian-clock feedback loop, consisting of CCA1 HIKING EXPEDITION (CHE), CIRCADIAN CLOCK ASSOCIATED1 (CCA1), and TIMING OF CAB EXPRESSION1 (TOC1), plus the interaction with a chromatin factor, HISTONE DEACETYLASE1 (HD1). In the allotetraploids formed between A. thaliana (At) and Arabidopsis arenosa (Aa), AtCCA1 is expressed at lower levels than AaCCA1, which could alter clock output traits. The reduced AtCCA1 expressions in the allotetraploids are consistent with the biochemical data that AaCHE showed preferential binding to the AtCCA1 promoter, in which AaCHE interacts with a higher affinity to AtHD1 than AtCHE. AaCHE also showed a higher affinity to TOC1 than AtCHE, consistent with the effect of TOC1 on repressing CCA1. Thus, stronger AaCHE-TOC1 and AaCHE-AtHD1 interactions reduce AtCC1 allelic expression. Our current data suggest a biochemical basis for protein interactions in trans with a preference to the cis-acting elements in heterologous combinations to reduce AtCCA1 expression, while altered CCA1 expression has been shown to affect metabolic and biomass heterosis in interspecific hybrids or allotetraploids.
Differential roles of caspase-1 and caspase-11 in infection and inflammation
Authors: Man Si Ming , Karki Rajendra , Briard Benoit , Burton Amanda , Gingras Sebastien , Pelletier Stephane , Kanneganti Thirumala-Devi 
Published: March 2017

AbstractCaspase-1, also known as interleukin-1β (IL-1β)-converting enzyme (ICE), regulates antimicrobial host defense, tissue repair, tumorigenesis, metabolism and membrane biogenesis. On activation within an inflammasome complex, caspase-1 induces pyroptosis and converts pro-IL-1β and pro-IL-18 into their biologically active forms. “ICE−/−” or “Casp1−/−” mice generated using 129 embryonic stem cells carry a 129-associated inactivating passenger mutation on thecaspase-11locus, essentially making them deficient in both caspase-1 and caspase-11. The overlapping and unique functions of caspase-1 and caspase-11 are difficult to unravel without additional genetic tools. Here, we generated caspase-1–deficient mouse (Casp1Null) on the C57BL/6 J background that expressed caspase-11.Casp1Nullcells did not release IL-1β and IL-18 in response to NLRC4 activatorsSalmonellaTyphimurium and flagellin, canonical or non-canonical NLRP3 activators LPS and ATP,Escherichia coli, Citrobacter rodentiumand transfection of LPS, AIM2 activatorsFrancisella novicida, mouse cytomegalovirus and DNA, and the infectious agentsListeria monocytogenesandAspergillus fumigatus. We further demonstrated that caspase-1 and caspase-11 differentially contributed to the host defense againstA. fumigatusinfection and to endotoxemia.
Oral chromium picolinate impedes hyperglycemia-induced atherosclerosis and inhibits proatherogenic protein TSP-1 expression in STZ-induced type 1 diabetic ApoE−/− mice
Authors: Ganguly Rituparna , Sahu Soumyadip , Ohanyan Vahagn , Haney Rebecca , Chavez Ronaldo J. , Shah Shivani , Yalamanchili Siri , Raman Priya 
Published: March 2017

AbstractIncreasing evidence suggests thrombospondin-1 (TSP-1), a potent proatherogenic matricellular protein, as a putative link between hyperglycemia and atherosclerotic complications in diabetes. We previously reported that the micronutrient chromium picolinate (CrP), with long-standing cardiovascular benefits, inhibits TSP-1 expression in glucose-stimulated human aortic smooth muscle cells in vitro. Here, we investigated the atheroprotective action of orally administered CrP in type 1 diabetic apolipoprotein E-deficient (ApoE−/−) mice and elucidated the role of TSP-1 in this process. CrP decreased lipid burden and neointimal thickness in aortic root lesions of hyperglycemic ApoE−/− mice; also, smooth muscle cell (SMC), macrophage and leukocyte abundance was prevented coupled with reduced cell proliferation. Attenuated lesion progression was accompanied with inhibition of hyperglycemia-induced TSP-1 expression and reduced protein O-glycosylation following CrP treatment; also, PCNA and vimentin (SMC synthetic marker) expression were reduced while SM-MHC (SMC contractile marker) levels were increased. To confirm a direct role of TSP-1 in diabetic atherosclerosis, hyperglycemic TSP-1−/−/ApoE−/− double knockout mice were compared with age-matched hyperglycemic ApoE−/− littermates. Lack of TSP-1 prevented lesion formation in hyperglycemic ApoE−/− mice, mimicking the atheroprotective phenotype of CrP-treated mice. These results suggest that therapeutic TSP-1 inhibition may have important atheroprotective potential in diabetic vascular disease.
Rattusin structure reveals a novel defensin scaffold formed by intermolecular disulfide exchanges
Authors: Min Hye Jung , Yun Hyosuk , Ji Sehyeon , Rajasekaran Ganesan , Kim Jae Il , Kim Jeong-Sun , Shin Song Yub , Lee Chul Won 
Published: March 2017

AbstractDefensin peptides are essential for innate immunity in humans and other living systems, as they provide protection against infectious pathogens and regulate the immune response. Here, we report the solution structure of rattusin (RTSN), an α-defensin-related peptide, which revealed a novel C2-symmetric disulfide-linked dimeric structure. RTSN was synthesized by solid-phase peptide synthesis (SPPS) and refolded by air oxidation in vitro. Dimerization of the refolded RTSN (r-RTSN) resulted from five intermolecular disulfide (SS) bond exchanges formed by ten cysteines within two protomer chains. The SS bond pairings of r-RTSN were determined by mass analysis of peptide fragments cleaved by trypsin digestion. In addition to mass analysis, nuclear magnetic resonance (NMR) experiments for a C15S mutant and r-RTSN confirmed that the intermolecular SS bond structure of r-RTSN showed an I-V’, II-IV’, III-III’, IV-II’, V-I’ arrangement. The overall structure of r-RTSN exhibited a cylindrical array, similar to that of β-sandwich folds, with a highly basic surface. Furthermore, fluorescence spectroscopy results suggest that r-RTSN exerts bactericidal activity by damaging membrane integrity. Collectively, these results provide a novel structural scaffold for designing highly potent peptide-based antibiotics suitable for use under various physiological conditions.
Gut metagenomic analysis reveals prominent roles of Lactobacillus and cecal microbiota in chicken feed efficiency
Authors: Yan Wei , Sun Congjiao , Yuan Jingwei , Yang Ning 
Published: March 2017

AbstractInteractions between the host and gut microbiota can affect gut metabolism. In this study, the individual performances of 252 hens were recorded to evaluate feed efficiency. Hens with contrasting feed efficiencies (14 birds per group) were selected to investigate their duodenal, cecal and fecal microbial composition by sequencing the 16S rRNA gene V4 region. The results showed that the microbial community in the cecum was quite different from those in the duodenum and feces. The highest biodiversity and all differentially abundant taxa between the different efficiency groups were observed in the cecal microbial community with false discovery rate (FDR) <0.05. Of these differentially abundant cecal microbes, Lactobacillus accounted for a greater proportion than the others. The abundances of Lactobacillus and Akkermansia were significantly higher while that of Faecalibacterium was lower (FDR < 0.05) in the better feed efficiency (BFE) group. Phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt) analysis revealed that the functions relating to glycometabolism and amino acid metabolism were enriched in the cecal microbiota of the BFE group. These results indicated the prominent role of cecal microbiota in the feed efficiency of chickens and suggested plausible uses of Lactobacillus to improve the feed efficiency of host.
Prognosis and value of preoperative radiotherapy in locally advanced rectal signet-ring cell carcinoma
Authors: Ling Chun-Run , Wang Rui , Wang Mo-Jin , Ping Jie , Zhuang Wen 
Published: March 2017

AbstractAs well known, signet-ring cell carcinoma (SRCC) is a rare histological subtype of colorectal adenocarcinoma, which has been associated with poor prognosis and resistant to non-surgery therapy compared with common adenocarcinoma. In this study, we assessed the effect of preoperative radiotherapy (PRT) for locally advanced rectal SRCC in a large patient group from the Surveillance, Epidemiology, and End Results program (SEER, 1988–2011) database. SRCC was found in 0.9% (n = 622) rectal cancer (RC) patients in our study. In the PRT setting, SRCC had significantly worse cancer-specific survival than mucinous adenocarcinoma and nonmucinous adenocarcinoma patients (log-rank, P < 0.001). In terms of SRCC, stage III RC patients benefited from PRT (log-rank, P < 0.001) while stage II did not (P = 0.095). The multivariate Cox proportional hazard model showed that PRT was an independent benefit factor in stage III rectal SRCC patients (HR, 0.611; 95% CI, 0.407–0.919; P = 0.018). In conclusion, SRCC was an independent predictor of poor prognosis in stage III RC patients, but not in stage II. In the PRT setting of locally advanced RC, SRCC patients had significantly worse prognosis. PRT was an independent prognostic factor associated with improved survival in stage III rectal SRCC.
III-nitride core–shell nanorod array on quartz substrates
Authors: Bae Si-Young , Min Jung-Wook , Hwang Hyeong-Yong , Lekhal Kaddour , Lee Ho-Jun , Jho Young-Dahl , Lee Dong-Seon , Lee Yong-Tak , Ikarashi Nobuyuki , Honda Yoshio , Amano Hiroshi 
Published: March 2017

AbstractWe report the fabrication of near-vertically elongated GaN nanorods on quartz substrates. To control the preferred orientation and length of individual GaN nanorods, we combined molecular beam epitaxy (MBE) with pulsed-mode metal–organic chemical vapor deposition (MOCVD). The MBE-grown buffer layer was composed of GaN nanograins exhibiting an ordered surface and preferred orientation along the surface normal direction. Position-controlled growth of the GaN nanorods was achieved by selective-area growth using MOCVD. Simultaneously, the GaN nanorods were elongated by the pulsed-mode growth. The microstructural and optical properties of both GaN nanorods and InGaN/GaN core–shell nanorods were then investigated. The nanorods were highly crystalline and the core–shell structures exhibited optical emission properties, indicating the feasibility of fabricating III-nitride nano-optoelectronic devices on amorphous substrates.
Thermal Resistance Variations of Fly Ash Geopolymers: Foaming Responses
Authors: Cheng-Yong Heah , Yun-Ming Liew , Abdullah Mohd Mustafa Al Bakri , Hussin Kamarudin 
Published: March 2017

AbstractThis paper presents a comparative study of the characteristic of unfoamed and foamed geopolymers after exposure to elevated temperatures (200–800 °C). Unfoamed geopolymers were produced with Class F fly ash and sodium hydroxide and liquid sodium silicate. Porous geopolymers were prepared by foaming with hydrogen peroxide. Unfoamed geopolymers possessed excellent strength of 44.2 MPa and degraded 34% to 15 MPa in foamed geopolymers. The strength of unfoamed geopolymers decreased to 5 MPa with increasing temperature up to 800 °C. Foamed geopolymers behaved differently whereby they deteriorated to 3 MPa at 400 °C and increased up to 11 MPa at 800 °C. Even so, the geopolymers could withstand high temperature without any disintegration and spalling up to 800 °C. The formation of crystalline phases at higher temperature was observed deteriorating the strength of unfoamed geopolymers but enhance the strength of foamed geopolymers. In comparison, foamed geopolymer had better thermal resistance than unfoamed geopolymers as pores provide rooms to counteract the internal damage.
Sexual epigenetics: gender-specific methylation of a gene in the sex determining region of Populus balsamifera
Authors: Bräutigam Katharina , Soolanayakanahally Raju , Champigny Marc , Mansfield Shawn , Douglas Carl , Campbell Malcolm M. , Cronk Quentin 
Published: March 2017

AbstractMethylation has frequently been implicated in gender determination in plants. The recent discovery of the sex determining region (SDR) of balsam poplar, Populus balsamifera, pinpointed 13 genes with differentiated X and Y copies. We tested these genes for differential methylation using whole methylome sequencing of xylem tissue of multiple individuals grown under field conditions in two common gardens. The only SDR gene to show a marked pattern of gender-specific methylation is PbRR9, a member of the two component response regulator (type-A) gene family, involved in cytokinin signalling. It is an ortholog of Arabidopsis genes ARR16 and ARR17. The strongest patterns of differential methylation (mostly male-biased) are found in the putative promoter and the first intron. The 4th intron is strongly methylated in both sexes and the 5th intron is unmethylated in both sexes. Using a statistical learning algorithm we find that it is possible accurately to assign trees to gender using genome-wide methylation patterns alone. The strongest predictor is the region coincident with PbRR9, showing that this gene stands out against all genes in the genome in having the strongest sex-specific methylation pattern. We propose the hypothesis that PbRR9 has a direct, epigenetically mediated, role in poplar sex determination.
PJA2 ubiquitinates the HIV-1 Tat protein with atypical chain linkages to activate viral transcription
Authors: Faust Tyler B. , Li Yang , Jang Gwendolyn M. , Johnson Jeffrey R. , Yang Shumin , Weiss Amit , Krogan Nevan J. , Frankel Alan D. 
Published: March 2017

AbstractTranscription complexes that assemble at the HIV-1 promoter efficiently initiate transcription but generate paused RNA polymerase II downstream from the start site. The virally encoded Tat protein hijacks positive transcription elongation factor b (P-TEFb) to phosphorylate and activate this paused polymerase. In addition, Tat undergoes a series of reversible post-translational modifications that regulate distinct steps of the transcription cycle. To identify additional functionally important Tat cofactors, we performed RNAi knockdowns of sixteen previously identified Tat interactors and found that a novel E3 ligase, PJA2, ubiquitinates Tat in a non-degradative manner and specifically regulates the step of HIV transcription elongation. Interestingly, several different lysine residues in Tat can function as ubiquitin acceptor sites, and variable combinations of these lysines support both full transcriptional activity and viral replication. Further, the polyubiquitin chain conjugated to Tat by PJA2 can itself be assembled through variable ubiquitin lysine linkages. Importantly, proper ubiquitin chain assembly by PJA2 requires that Tat first binds its P-TEFb cofactor. These results highlight that both the Tat substrate and ubiquitin modification have plastic site usage, and this plasticity is likely another way in which the virus exploits the host molecular machinery to expand its limited genetic repertoire.
Time- and dose dependent actions of cardiotonic steroids on transcriptome and intracellular content of Na+ and K+: a comparative analysis
Authors: Klimanova Elizaveta A. , Tverskoi Artem M. , Koltsova Svetlana V. , Sidorenko Svetlana V. , Lopina Olga D. , Tremblay Johanne , Hamet Pavel , Kapilevich Leonid V. , Orlov Sergei N. 
Published: March 2017

AbstractRecent studies demonstrated that in addition to Na+,K+-ATPase inhibition cardiotonic steroids (CTSs) affect diverse intracellular signaling pathways. This study examines the relative impact of [Na+]i/[K+]i-mediated and -independent signaling in transcriptomic changes triggered by the endogenous CTSs ouabain and marinobufagenin (MBG) in human umbilical vein endothelial cells (HUVEC). We noted that prolongation of incubation increased the apparent affinity for ouabain estimated by the loss of [K+]i and gain of [Na+]i. Six hour exposure of HUVEC to 100 and 3,000 nM ouabain resulted in elevation of the [Na+]i/[K+]i ratio by ~15 and 80-fold and differential expression of 258 and 2185 transcripts, respectively. Neither [Na+]i/[K+]i ratio nor transcriptome were affected by 6-h incubation with 30 nM ouabain. The 96-h incubation with 3 nM ouabain or 30 nM MBG elevated the [Na+]i/[K+]i ratio by ~14 and 3-fold and led to differential expression of 880 and 484 transcripts, respectively. These parameters were not changed after 96-h incubation with 1 nM ouabain or 10 nM MBG. Thus, our results demonstrate that elevation of the [Na+]i/[K+]i ratio is an obligatory step for transcriptomic changes evoked by CTS in HUVEC. The molecular origin of upstream [Na+]i/[K+]i sensors involved in transcription regulation should be identified in forthcoming studies.
Association of high normal HbA1c and TSH levels with the risk of CHD: a 10-year cohort study and SVM analysis
Authors: Li Hui , Cui Ying , Zhu Yanan , Yan Haiying , Xu Wenge 
Published: March 2017

AbstractThis study aimed to determine the association between the clinical reference range of serum glycated hemoglobin A1c (HbA1c) and thyrotropin (TSH) and the risk of coronary heart disease (CHD) in non-diabetic and euthyroid patients. We examined baseline HbA1c and TSH in 538 healthy participants, and then analyzed the associations and potential value of these indicators for predicting CHD using Cox proportional hazard and support vector machine analyses. During the median follow-up of 120 months, 39 participants later developed CHD. The baseline HbA1c and TSH within the reference range were positively associated with CHD risk. No correlation and interaction were found between the baseline HbA1c and TSH for the development of CHD. Disease event-free survival varied among participants with different baseline HbA1c quintiles, whereas disease event-free survival was similar for different TSH tertiles. The combination of these baselines showed sensitivity of 87.2%, specificity of 92.7%, and accuracy of 92.3% for identifying the participants who will later develop CHD. Relatively high but clinically normal HbA1c and TSH levels may increase the risk of CHD. Therefore, the combination of these indicators can serve as a biomarker for identifying healthy individuals from those who would later develop CHD.
Immune involvement in the pathogenesis of schizophrenia: a meta-analysis on postmortem brain studies
Authors: van Kesteren C F M G , Gremmels H , de Witte L D , Hol E M , Van Gool A R , Falkai P G , Kahn R S , Sommer I E C 
Published: March 2017

AbstractAlthough the precise pathogenesis of schizophrenia is unknown, genetic, biomarker and imaging studies suggest involvement of the immune system. In this study, we performed a systematic review and meta-analysis of studies investigating factors related to the immune system in postmortem brains of schizophrenia patients and healthy controls. Forty-one studies were included, reporting on 783 patients and 762 controls. We divided these studies into those investigating histological alterations of cellular composition and those assessing molecular parameters; meta-analyses were performed on both categories. Our pooled estimate on cellular level showed a significant increase in the density of microglia (P=0.0028) in the brains of schizophrenia patients compared with controls, albeit with substantial heterogeneity between studies. Meta-regression on brain regions demonstrated this increase was most consistently observed in the temporal cortex. Densities of macroglia (astrocytes and oligodendrocytes) did not differ significantly between schizophrenia patients and healthy controls. The results of postmortem histology are paralleled on the molecular level, where we observed an overall increase in expression of proinflammatory genes on transcript and protein level (P=0.0052) in patients, while anti-inflammatory gene expression levels were not different between schizophrenia and controls. The results of this meta-analysis strengthen the hypothesis that components of the immune system are involved in the pathogenesis of schizophrenia.
Dynamic Assessment of Narratives: Efficient, Accurate Identification of Language Impairment in Bilingual Students
Authors: Petersen Douglas B. , Chanthongthip Helen , Ukrainetz Teresa A. , Spencer Trina D. , Steeve Roger W. 
Published: March 2017

Purpose
This study investigated the classification accuracy of a concentrated English narrative dynamic assessment (DA) for identifying language impairment (LI).

Method
Forty-two Spanish–English bilingual kindergarten to third-grade children (10 LI and 32 with no LI) were administered two 25-min DA test–teach–test sessions. Pre- and posttest narrative retells were scored in real time. Using a structured intervention approach, examiners taught children missing story grammar elements and subordination. A posttest was administered using a parallel story.

Results
Four classification predictors were analyzed: posttest scores, gain scores, modifiability ratings, and teaching duration. Discriminant function analysis indicated that an overall modifiability rating was the best classifier, with 100% sensitivity and 88% specificity after 1 DA session and 100% sensitivity and specificity after 2 sessions. Any 2 combinations of posttest scores, modifiability ratings, and teaching duration for just 1 session resulted in sensitivity and specificity rates over 90%. Receiver operating characteristic analyses were used to identify clinically usable cutoff points. Post hoc exploration indicated that similar results could be obtained after only one 5–10-min teaching cycle, potentially further abbreviating the DA process.

Conclusion
Concentrated English narrative DA results in high classification accuracy for bilingual children with and without LI. This efficient version of DA is amenable to clinical use.
Impact of Successful Choanal Atresia Repair on the Nasal Mucosa: A Preliminary Study
Authors: Elsheikh Ezzeddin , El-Anwar Mohammad , Abdel-aziz Hesham 
Published: March 2017

Introduction The main histological features of the nasal mucosa in choanal atresia are distorted cilia, marked increase of mucous submucosal glands associated with marked reduction of goblet cell density, and lymphocytic cellular infiltration.
Objective To study the nasal mucosal changes in cases of choanal atresia after successful repair compared with pre-repair mucosal histological features.
Methods Tissue samples were taken from the inferior turbinate of 3 patients (1 bilateral and 2 unilateral) who were successfully operated. Then, the biopsies were subjected to histopathological, histochemical and immunohistochemical studies. After that, the results were compared with pre-repair findings in the choanal atresia side and in the normal side.
Results Four biopsies (4 repaired choanal atresia sides) of the mucosa of the inferior turbinate revealed that 1 patient (who had a bilateral choanal atresia repaired), after achieving a patent choana for 8 months, had not completely recovered a normal nasal mucosa. The other 2 patients, after 18 and 23 months of achieving a patent choana, showed normal nasal cavities.
Conclusion The main histological features of the nasal mucosa in choanal atresia could be reversed by surgery, making the patients regain their choanal patency, with their mucosae changing back to normal gradually with time.