bluuebunny/crossref_metadata_2025_split huggingface dataset:
Biochemical markers of bone turnover following high-dose chemotherapy and autografting in multiple myeloma
Authors: Clark Richard E. , Flory Angela J. , Ion Edwina M. , Woodcock Barry E. , Durham Brian H. , Fraser William D. 
Published: October 2019

AbstractThe effect of high-dose chemotherapy and autografting on bone turnover in myeloma is not known. A study of 32 myeloma patients undergoing blood or marrow transplant (BMT), conditioned with high-dose melphalan, was done. Bone resorption was assessed by urinary free pyridinoline (fPyr) and deoxypyridinoline (fDPyr), expressed as a ratio of the urinary creatinine concentration. Bone formation was assessed by serum concentration of procollagen 1 extension peptide (P1CP) and bone-specific alkaline phosphatase (BSAP). Eighteen cases had normal fPyr and fDPyr at transplant, and in all but one of these cases the level remained normal throughout subsequent follow-up. In contrast, in 14 cases urinary fPyr and fDPyr levels were increased at transplant. In these cases, both fPyr and fDPyr fell to normal levels over the next few months (P = .0009 and .0019, respectively). fPyr and fDPyr levels at transplant and their trends post-BMT were unrelated to the use of pre-BMT or post-BMT bisphosphonate or post-BMT interferon. Nine cases had elevated P1CP or BSAP at transplant, which rapidly normalized. In most patients there was an increase in P1CP and/or BSAP several months post-transplant. In conclusion, increased osteoclast activity may be present even in apparent plateau phase of myeloma. High-dose chemotherapy with autografting may normalize abnormal bone resorption, although the effect may take several weeks to emerge and may be paralleled by increased osteoblast activity. The findings provide biochemical evidence that autografting may help normalize the abnormal bone turnover characteristic of myeloma.
Analysis of engraftment, graft-versus-host disease, and immune recovery following unrelated donor cord blood transplantation
Authors: Thomson Blythe G. , Robertson Kent A. , Gowan Darla , Heilman Doug , Broxmeyer Hal E. , Emanuel David , Kotylo Patricia , Brahmi Zacharie , Smith Franklin O. 
Published: October 2019

Abstract
Unrelated cord blood (UCB) is being used as a source of alternative hematopoietic stem cells for transplantation with increasing frequency. From November 1994 to February 1999, 30 UCB transplant procedures were performed for both malignant and nonmalignant diseases in 27 children, aged 0.4 to 17.1 years. Patients received either HLA-matched (n = 3) or 1- or 2-antigen–mismatched (n = 27) UCB following 1 of 2 standardized preparative and graft-versus-host disease regimens (hyperfractionated total body irradiation, cyclophosphamide, and antithymocyte globulin [ATG] with cyclosporine A and methotrexate; or busulfan, melphalan, and ATG with cyclosporine A and prednisone). The median time to neutrophil and platelet engraftment was 27 days (12-60 days) and 75 days (33-158 days) posttransplantation, respectively. No correlation was noted between neutrophil and platelet engraftment and nucleated cells per kilogram, CD34+ cells per kilogram infused, or cytomegalovirus status of recipient. The cumulative probability of acute grade 2 or greater graft-versus-host disease (GVHD) was 37.2%, and of grade 3 or greater GVHD was 8.8%. No patients developed chronic GVHD. CD4, CD19, and natural killer cell recovery was achieved at a median of 12, 6, and 2 months, respectively. CD8 recovery was delayed at a median of 9 months. Normal mitogen response was achieved at 6 to 9 months. The probability of survival, disease-free survival, and event-free survival at 1 year was 52.3% (34.1%-70.5%), 54.7% (34.5%-74.9%) and 49.6% (29.9%-69.4%), respectively. This series of 30 UCB transplants suggests that although CD8 cell recovery is delayed, the pattern of immune reconstitution with UCB is similar to that reported for other stem cell sources.
CFU-S11 activity does not localize solely with the aorta in the aorta-gonad-mesonephros region
Authors: de Bruijn Marella F. T. R. , Peeters Marian C. E. , Luteijn Tanya , Visser Pim , Speck Nancy A. , Dzierzak Elaine 
Published: October 2019

AbstractThe aorta-gonad-mesonephros (AGM) region is a potent hematopoietic site in the midgestation mouse conceptus and first contains colony-forming units–spleen day 11 (CFU-S11) at embryonic day 10 (E10). Because CFU-S11 activity is present in the AGM region before the onset of hematopoietic stem cell (HSC) activity, CFU-S11 activity in the complex developing vascular and urogenital regions of the AGM was localized. From E10 onward, CFU-S11 activity is associated with the aortic vasculature, and is found also in the urogenital ridges (UGRs). Together with data obtained from organ explant cultures, in which up to a 16-fold increase in CFU-S11 activity was observed, it was determined that CFU-S11 can be increased autonomously both in vascular sites and in UGRs. Furthermore, CFU-S11 activity is present in vitelline and umbilical vessels. This, together with the presence of CFU-S11 in the UGRs 2 days before HSC activity, suggests both temporally and spatially distinct emergent sources of CFU-S11.
Characterization of the protein Z–dependent protease inhibitor
Authors: Han Xin , Fiehler Ryan , Broze George J. 
Published: October 2019

AbstractProtein Z-dependent protease inhibitor (ZPI) is a 72-kd member of the serpin superfamily of proteinase inhibitors that produces rapid inhibition of factor Xa in the presence of protein Z (PZ), procoagulant phospholipids, and Ca++ (t1/2 less than 10 seconds). The rate of factor Xa inhibition by ZPI is reduced more than 1000-fold in the absence of PZ. The factor Xa–ZPI complex is not stable to sodium dodecyl sulfate–polyacrylamide gel electrophoresis, but is detectable by alkaline–polyacrylamide gel electrophoresis. The combination of PZ and ZPI dramatically delays the initiation and reduces the ultimate rate of thrombin generation in mixtures containing prothrombin, factor V, phospholipids, and Ca++. In similar mixtures containing factor Va, however, PZ and ZPI do not inhibit thrombin generation. Thus, the major effect of PZ and ZPI is to dampen the coagulation response prior to the formation of the prothrombinase complex. Besides factor Xa, ZPI also inhibits factor XIa in the absence of PZ, phospholipids, and Ca++. Heparin (0.2 U/mL) enhances the rate (t1/2 = 25 seconds vs 50 seconds) and the extent (99% vs 93% at 30 minutes) of factor XIa inhibition by ZPI. During its inhibitory interaction with factor Xa and factor XIa, ZPI is proteolytically cleaved with the release of a 4.2-kd peptide. The N-terminal amino acid sequence of this peptide (SMPPVIKVDRPF) establishes Y387 as the P1 residue at the reactive center of ZPI. ZPI activity is consumed during the in vitro coagulation of plasma through a proteolytic process that involves the actions of factor Xa with PZ and factor XIa.
Interferon γ and interleukin 6 modulate the susceptibility of macrophages to human immunodeficiency virus type 1 infection
Authors: Zaitseva Marina , Lee Shirley , Lapham Cheryl , Taffs Rolf , King Lisa , Romantseva Tatiana , Manischewitz Jody , Golding Hana 
Published: October 2019

AbstractThe effect of interferon γ (IFN-γ) and interleukin 6 (IL-6) on infection of macrophages with human immunodeficiency virus type 1 (HIV-1) was investigated. By using a polymerase chain reaction–based viral entry assay and viral infectivity assay, it was demonstrated that IL-6 and IFN-γ augmented susceptibility of monocyte-derived macrophages (MDMs) to infection with T-cell tropic CXCR4-utilizing (X4) HIV-1 strains. Consistent with this finding, IFN-γ and IL-6 augmented fusion of MDMs with T-tropic envelope-expressing cells. The enhanced fusion of cytokine-treated MDMs with T-tropic envelopes was inhibited by the CXCR4 ligand, SDF-1, and by T22 peptide. IFN-γ and IL-6 did not affect expression of surface CXCR4 or SDF-1–induced Ca++ flux in MDMs. In contrast to the effect of IFN-γ on the infection of MDMs with X4 strains, IFN-γ inhibited viral entry and productive infection of MDMs with macrophage-tropic (M-tropic) HIV-1. Consistent with this finding, IFN-γ induced a decrease in fusion with M-tropic envelopes that correlated with a modest reduction in surface CCR5 and CD4 on MDMs. It was further demonstrated that macrophage inflammatory protein (MIP)-1α and MIP-β secreted by cytokine-treated MDMs augmented their fusion with T-tropic–expressing cells and inhibited their fusion with M-tropic envelope-expressing cells. These data indicate that proinflammatory cytokines, which are produced during opportunistic infections or sexually transmitted diseases, may predispose macrophages to infection with X4 strains that, in turn, could accelerate disease progression.
Nonopsonic monocyte/macrophage phagocytosis of Plasmodium falciparum–parasitized erythrocytes: a role for CD36 in malarial clearance
Authors: McGilvray Ian D. , Serghides Lena , Kapus Andras , Rotstein Ori D. , Kain Kevin C. 
Published: October 2019

AbstractPlasmodium falciparum is the most lethal form of malaria and is increasing both in incidence and in its resistance to antimalarial agents. An improved understanding of the mechanisms of malarial clearance may facilitate the development of new therapeutic interventions. We postulated that the scavenger receptor CD36, an important factor in cytoadherence of P falciparum–parasitized erythrocytes (PEs), might also play a role in monocyte- and macrophage-mediated malarial clearance. Exposure of nonopsonized PEs to Fc receptor–blocked monocytes resulted in significant PE phagocytosis, accompanied by intense clustering of CD36 around the PEs. Phagocytosis was blocked 60% to 70% by monocyte pretreatment with monoclonal anti-CD36 antibodies but not by antibodies to αvβ3, thrombospondin, intercellular adhesion molecule-1, or platelet/endothelial cell adhesion molecule-1. Antibody-induced CD36 cross-linking did result in the early increase of surface CD11b expression, but there was no increase in, or priming for, tumor necrosis factor (TNF)-α secretion following either CD36 cross-linking or PE phagocytosis. CD36 clustering does support intracellular signaling: Antibody-induced cross-linking initiated intracellular tyrosine phosphorylation as well as extracellular signal-regulated kinase (ERK) and p38 mitogen-activated protein kinase (MAPK) phosphorylation. Both broad-spectrum tyrosine kinase inhibition (genistein) and selective ERK and p38 MAPK inhibition (PD98059 and SB203580, respectively) reduced PE uptake to almost the same extent as CD36 blockade. Thus, CD36-dependent binding and signaling appears to be crucial for the nonopsonic clearance of PEs and does not appear to contribute to the increase in TNF-α that is prognostic of poor outcome in clinical malaria.
Sequence properties of certain GC rich avian genes, their origins and absence from genome assemblies: case studies
Authors: Beauclair Linda , Ramé Christelle , Arensburger Peter , Piégu Benoît , Guillou Florian , Dupont Joëlle , Bigot Yves 
Published: October 2019

Abstract

Background
More and more eukaryotic genomes are sequenced and assembled, most of them presented as a complete model in which missing chromosomal regions are filled by Ns and where a few chromosomes may be lacking. Avian genomes often contain sequences with high GC content, which has been hypothesized to be at the origin of many missing sequences in these genomes. We investigated features of these missing sequences to discover why some may not have been integrated into genomic libraries and/or sequenced.

Results
The sequences of five red jungle fowl cDNA models with high GC content were used as queries to search publicly available datasets of Illumina and Pacbio sequencing reads. These were used to reconstruct the leptin, TNFα, MRPL52, PCP2 and PET100 genes, all of which are absent from the red jungle fowl genome model. These gene sequences displayed elevated GC contents, had intron sizes that were sometimes larger than non-avian orthologues, and had non-coding regions that contained numerous tandem and inverted repeat sequences with motifs able to assemble into stable G-quadruplexes and intrastrand dyadic structures. Our results suggest that Illumina technology was unable to sequence the non-coding regions of these genes. On the other hand, PacBio technology was able to sequence these regions, but with dramatically lower efficiency than would typically be expected.

Conclusions
High GC content was not the principal reason why numerous GC-rich regions of avian genomes are missing from genome assembly models. Instead, it is the presence of tandem repeats containing motifs capable of assembling into very stable secondary structures that is likely responsible.
Parsing the synonymous mutations in the maize genome: isoaccepting mutations are more advantageous in regions with codon co-occurrence bias
Authors: Chu Duan , Wei Lai 
Published: October 2019

AbstractBackgroundSynonymous mutations do not change amino acids but do sometimes change the tRNAs (anticodons) that decode a particular codon. An isoaccepting codon is a synonymous codon that shares the same tRNA. If a mutated codon could base pair with the same anticodon as the original, the mutation is termed an isoaccepting mutation. An interesting but less-studied type of codon bias is codon co-occurrence bias. There is a trend to cluster the isoaccepting codons in the genome. The proposed advantage of codon co-occurrence bias is that the tRNA released from the ribosome E site could be quickly recharged and subsequently decode the following isoaccepting codons. This advantage would enhance translation efficiency. In plant species, whether there are signals of positive selection on isoaccepting mutations in the codon co-occurred regions has not been studied.ResultsWe termed polymorphic mutations in coding regions using publicly available RNA-seq data in maize (Zea mays). Next, we classified all synonymous mutations into three categories according to the context, i.e., the relationship between the focal codon and the previous codon, as follows: isoaccepting, nonisoaccepting and nonsynonymous. We observed higher fractions of isoaccepting mutations in the isoaccepting context. If we looked at the minor allele frequency (MAF) spectrum, the isoaccepting mutations have a higher MAF in the isoaccepting context than that in other regions, and accordingly, the nonisoaccepting mutations have a higher MAF in the nonisoaccepting context.ConclusionOur results indicate that in regions with codon co-occurrence bias, natural selection maintains this pattern by suppressing the nonisoaccepting mutations. However, if the consecutive codons are nonisoaccepting, mutations tend to switch these codons to become isoaccepting. Our study demonstrates that the codon co-occurrence bias in the maize genome is selectively maintained by natural selection and that the advantage of this trend could potentially be the rapid recharging and reuse of tRNAs to increase translation efficiency.
Effects of computer-assisted navigation versus the conventional technique for total knee arthroplasty on levels of plasma thrombotic markers: a prospective study
Authors: Siu Ka-Kit , Wu Kwan-Ting , Ko Jih-Yang , Wang Feng-Sheng , Chou Wen-Yi , Wang Ching-Jen , Kuo Shu-Jui 
Published: October 2019

Abstract

Background
Venous thromboembolism (VTE) is a major sequela after total knee arthroplasty (TKA). We prospectively compared the differences in the perioperative plasma d-dimer and fibrinogen levels between the individuals undergoing TKA via computer-assisted navigation and via a conventional method as the surrogate comparison for VTE. There were 174 patients fulfilling the inclusion criteria and providing valid informed consent between September 2011 and November 2013. There were 69 females and 20 males in the navigation-assisted group (median age: 71.00 years), while the conventional group was composed of 59 females and 26 males (median age: 69.00 years). Blood samples were obtained prior to and at 24 and 72 h after surgery for measurement of the levels of plasma d-dimer and fibrinogen.

Results
A significantly lower plasma d-dimer level 24 h after TKA (p = 0.001) and a milder postoperative surge 24 h after TKA (p = 0.002) were observed in patients undergoing navigation-assisted TKA. The proportions of subjects exceeding the plasma d-dimer cut-off values of 7.5, 8.6 and 10 mg/L 24 h after TKA were all significantly higher in the conventional group than in the navigation-assisted group (p = 0.024, 0.004, and 0.004, respectively).

Conclusions
A lower plasma d-dimer level and a milder surge in the plasma d-dimer level were observed in patients undergoing navigation-assisted TKA in comparison with patients undergoing conventional TKA 24 h after surgery. These findings may supplement the known advantages of navigation-assisted TKA.
Is there any association between gut microbiota and type 1 diabetes? A systematic review
Authors: Jamshidi Parnian , Hasanzadeh Saba , Tahvildari Azin , Farsi Yeganeh , Arbabi Mahta , Mota João Felipe , Sechi Leonardo A. , Nasiri Mohammad Javad 
Published: October 2019

AbstractIntroductionType 1 diabetes (T1D) is the second most common autoimmune disease among children. There is evidence suggesting that dysbiosis of some gut colonizing bacteria are associated with the pathogenesis of T1D. However, these studies are still controversial and a systematic review was conducted to evaluate the association between gut microbiota and T1D.MethodsA systematic search was carried out in Medline (Via Pubmed) and Embase from January 2000 to January 2019 for all original cross-sectional, cohort, case–control or nested case–control studies investigating the association between gut microbiota and T1D.ResultsOf 568 articles identified, 26 studies met the inclusion criteria. The total population study of these articles consists of 2600 children (under 18 years old) and 189 adults. Among the included studies, 24 articles confirmed the association between gut microbiota dysbiosis and T1D. The most common bacterial alterations in T1D patients includedBacteroidesspp.,Streptococcusspp.,Clostridiumspp.,Bifidobacteriumspp.,Prevotellaspp.,Staphylococcusspp.,Blautiaspp.,Faecalibacteriumspp.,Roseburiaspp., andLactobacillusspp.ConclusionOur study showed a significant association between alterations in intestinal microbial composition and T1D; however, in some articles, it is not clear which one happens first. Investigation of altered gut microbiota can help in the early detection of T1D before seropositivity. Targeted microbiome modulation can be a novel potential therapeutic strategy.
Impact of solar radiation and environmental temperature on Art Nouveau glass windows
Authors: Palomar Teresa , Silva Miguel , Vilarigues Marcia , Pombo Cardoso Isabel , Giovannacci David 
Published: October 2019

Abstract
This work presents the results of the evaluation of two Art Nouveau glass windows from the Casa-Museu Dr. Anastácio Gonçalves (Lisbon, Portugal) with IR-thermography during the summer solstice. According to the measurements, the surface temperature of glass depended on the outdoor environmental temperature and, mainly, on the direct solar radiation. Colored glasses presented a higher surface temperature due to the absorption of their chromophores at near-IR wavelengths. Enamels and grisailles showed higher surface temperatures than their support glasses due to both their chemical composition and color. The protective glazing, with small slits in one of the window panels, induced a hot-air pocket in its upper part due to the insufficient ventilation.
A novel customized ceramic bracket for esthetic orthodontics: in vitro study
Authors: Yang Liu , Yin Guangfu , Liao Xiaoming , Yin Xing , Ye Niansong 
Published: October 2019

Abstract

Background
This study aims to develop a novel process to establish a standardized manufacturing technique of customized esthetic ceramic bracket system (CCB) which could be endowed with individual color and shape to satisfy patients’ individual demands. Material characteristics and mechanical parameters of CCB were evaluated.

Subjects and methods
CCB virtual models were designed individually according to patient’s teeth morphology and clinical demands. 3D printing technology, lost-wax technology, and selected glass-ceramic ingots were employed to fabricate CCB. Scanning electron microscopy (SEM) analyses were performed to characterize the surface morphology of CCB and commercially available brackets (Clarity Advanced; Crystalline VII; Inspire ICE; Damon Q). Static and kinetic frictional resistance (FR), shear bond strength (SBS) and adhesive remnant index (ARI) scores were recorded. One-way analyses of variance (ANOVA) and post-hoc Tukey’s HSD multiple tests were used for statistical analyses.

Results
Multi-color and multi-transparency raw materials facilitated CCB with a wide range of color options and controllable optical properties to satisfy different esthetic demands of individual orthodontic patients. CCB presented same level of FR as commercially available ceramic brackets did. No significant differences (P ≥ 0.05) of SBS were observed among CCB-ES (treated silane), Clarity Advanced and Crystalline VII groups, and CCB-E (no silane) attained the highest ARI mean score 3. In the preliminary clinical trial, CCB presented excellent color-matching and shape-matching appearances similar to natural teeth, which made it highly invisible from social intercourse distance.

Conclusions
CCB were demonstrated to be an applicable labial orthodontic bracket system with optimized esthetics and biomechanics. We envision that it would be an ideal alternative for patients who pursue esthetic orthodontic treatment but were not likely to take lingual appliances or clear aligners.
Exotic parrots breeding in urban tree cavities: nesting requirements, geographic distribution, and potential impacts on cavity nesting birds in southeast Florida
Authors: Diamond Joshua M. , Ross Michael S. 
Published: October 2019

AbstractBackgroundExotic parrots have established breeding populations in southeast Florida, including several species that nest in tree cavities. We aimed to determine the species identity, nest site requirements, relative nest abundance, geographic distribution, and interactions of parrots with native cavity-nesting bird species.MethodsWe searched Miami-Dade County, Florida, and nearby areas for natural cavities and holes excavated by woodpeckers, recording attributes of potential nest trees. We inspected all cavities with an elevated video inspection system to determine occupancy by parrots or other birds. We mapped nearly 4000 citizen science observations of parrots in our study area corresponding to our study period, and used these to construct range maps, comparing them to our nesting observations.ResultsNot all parrots reported or observed in our study area were actively breeding. Some parrots were observed at tree cavities, which previous studies have suggested is evidence of reproduction, but our inspections with an elevated video inspection system suggest they never initiated nesting attempts. Several parrot species did successfully nest in tree cavities, Red-masked Parakeets (Psittacara erythrogenys) and Orange-winged Parrots (Amazona amazonica) being the most common (n = 7 and 6 nests, respectively). These two parrots had similar nesting requirements, but Orange-winged Parrots use nests with larger entrance holes, which they often enlarge. Geographic analysis of nests combined with citizen science data indicate that parrots are limited to developed areas. The most common parrots were less abundant cavity nesters than the native birds which persist in Miami’s urban areas, and far less abundant than the invasive European Starling (Sturnus vulgaris).ConclusionsExotic parrots breeding elsewhere in the world have harmed native cavity-nesting birds through interference competition, but competitive interference in southeast Florida is minimized by the urban affinities of parrots in this region. The relative abundance and geographic distribution suggest that these parrots are unlikely to invade adjacent wilderness areas.