bluuebunny/crossref_metadata_2025_split huggingface dataset:
A versatile and scalable strategy for glycoprofiling bifidobacterial consumption of human milk oligosaccharides
Authors: LoCascio Riccardo G. , Niñonuevo Milady R. , Kronewitter Scott R. , Freeman Samara L. , German J. Bruce , Lebrilla Carlito B. , Mills David A. 
Published: December 2008

SummaryHuman milk contains approximately 200 complex oligosaccharides believed to stimulate the growth and establishment of a protective microbiota in the infant gut. The lack of scalable analytical techniques has hindered the measurement of bacterial metabolism of these and other complex prebiotic oligosaccharides. An in vitro, multi‐strain, assay capable of measuring kinetics of bacterial growth and detailed oligosaccharide consumption analysis by FTICR‐MS was developed and tested simultaneously on 12 bifidobacterial strains. For quantitative consumption, deuterated and reduced human milk oligosaccharide (HMO) standards were used. A custom software suite developed in house called Glycolyzer was used to process the large amounts of oligosaccharide mass spectra automatically with 13C corrections based on de‐isotoping protocols. High growth on HMOs was characteristic of Bifidobacterium longum biovar infantis strains, which consumed nearly all available substrates, while other bifidobacterial strains tested, B. longum bv. longum, B. adolescentis, B. breve and B. bifidum, showed low or only moderate growth ability. Total oligosaccharide consumption ranged from a high of 87% for B. infantis JCM 7009 to only 12% for B. adolescentis ATCC 15703. A detailed analysis of consumption glycoprofiles indicated strain‐specific capabilities towards differential metabolism of milk oligosaccharides. This method overcomes previous limitations in the quantitative, multi‐strain analysis of bacterial metabolism of HMOs and represents a novel approach towards understanding bacterial consumption of complex prebiotic oligosaccharides.
Ethiopian coffee cultivation—Implications for bird conservation and environmental certification
Authors: Gove Aaron D. , Hylander Kristoffer , Nemomisa Sileshi , Shimelis Anteneh 
Published: December 2008

AbstractCoffee cultivation plays a role in biodiversity alteration and conservation in much of the tropics. This is particularly so in Ethiopia, where coffee is an indigenous shrub and a major commodity in national and local trade. In southwestern Ethiopia, coffee (Coffea arabica, “highland coffee”) is harvested from both forests (its natural habitat) and from within farmland where it is grown in small patches under isolated shade trees. We investigated the effects of management practices on bird assemblages in each of these systems. We found that bird assemblages in the forest remnants were distinct from those in the farmland even if many species were regularly found in both habitats. Coffee cultivation in open farmlands promoted bird species diversity through the retention of forest trees, while coffee cultivation in forests reduced bird diversity. Forest coffee management may, however, ensure that forest remnants are not converted to other forms of more open agriculture. Certification standards for “ecologically friendly” coffee in Ethiopia need to take this complexity into account.
BARRIER HEIGHT ENHANCED GaN SCHOTTKY DIODES USING A THIN AlN SURFACE LAYER
Authors: CHUAH L. S. , HASSAN Z. , ABU HASSAN H. , YAM F. K. , CHIN C. W. , THAHAB S. M. 
Published: December 2008

Gallium nitride (GaN) is a highly promising wide band gap semiconductor with applications in high power electronic and optoelectronic devices. Thin films of GaN are most commonly grown in the hexagonal wurtzite structure on sapphire substrates. Growth of GaN onto silicon substrates offers a very attractive opportunity to incorporate GaN devices onto silicon-based integrated circuits. Although direct epitaxial growth of GaN films on Si substrates is a difficult task (mainly due to the 17% lattice mismatch present), substantial progress in the crystal quality can be achieved using a buffer layer. A full characterization of the quality of the material needs to be assessed by a combination of different techniques. In this work, a thin AlN cap layer of 50 nm was incorporated in GaN Schottky diode to enhance the effective Schottky barrier height and reduces the dark current. A barrier height of 0.52 eV for normal GaN Schottky diode was increased to the effective barrier height of 0.63 eV. The resulting Schottky diodes show a dark current of as low as 6.3×10-5 A at 5 V bias, which is about two orders of magnitude lower than that of normal GaN (5.2×10-3 A at 5 V bias) Schottky diode.
Glenohumeral Internal Rotation Deficits in Baseball Players with Ulnar Collateral Ligament Insufficiency
Authors: Dines Joshua S. , Frank Joshua B. , Akerman Meredith , Yocum Lewis A. 
Published: December 2008

Background The kinetic chain of the throwing motion functions to optimize efficiency of proximal segments to decrease force loads seen at smaller, distal segments such as the ulnar collateral ligament. Several studies have shown that shoulder internal rotation forms the physiologic counter to the valgus torque generated during the late cocking phase of throwing. Previous studies have implicated decreased glenohumeral internal rotation as a cause of shoulder internal impingement. To date, an association between pathologic glenohumeral internal rotation deficit and elbow injury has not been exhibited. Hypothesis Throwers with ulnar collateral ligament insufficiency will exhibit significantly increased glenohumeral internal rotation deficit. Study Design Case control study; Level of evidence, 3. Methods Twenty-nine baseball players with ulnar collateral ligament insufficiency were demographically matched with 29 control baseball players who had no history of shoulder, elbow, or cervical spine injury. The investigators measured passive glenohumeral internal and external rotation, elbow flexion and extension, and forearm pronation and supination. The Mann-Whitney test was used to analyze continuous variables. Results There were no significant differences between the groups in terms of demographics. There was a significant difference in dominant arm internal rotation, with injured players having significantly less (P <. 004), and in glenohumeral internal rotation deficit between players with ulnar collateral ligament insufficiency and those who were asymptomatic (28.5° vs 12.7°; P <. 001). Also, total range of motion was significantly decreased in the injured group. There were no significant differences in elbow or forearm range of motion between the groups. Conclusion Our results indicate that pathologic glenohumeral internal rotation deficit may be associated with elbow valgus instability. This has important clinical implications both in terms of preventing ulnar collateral ligament injury and with regard to rehabilitating throwers after ulnar collateral ligament reconstruction.
Interleukin-23 secretion by donor antigen-presenting cells is critical for organ-specific pathology in graft-versus-host disease
Authors: Das Rupali , Chen Xiao , Komorowski Richard , Hessner Martin J. , Drobyski William R. 
Published: December 2008

AbstractDamage to the gastrointestinal tract during graft-versus-host disease (GVHD) from the conditioning regimen in conjunction with alloreactive donor T cells plays a pivotal role in the pathogenesis of this disease. In this study, we have identified secretion of interleukin-23 (IL-23) by donor antigen-presenting cells (APCs) as a critical event in the induction of GVHD of the colon linking conditioning regimen-induced mucosal injury and lipopoly-saccharide (LPS) translocation to subsequent proinflammatory cytokine production and GVHD-associated pathologic damage. In the absence of donor APC-derived IL-23 secretion, there is a selective and profound reduction in pathologic damage as well as a marked reduction in LPS and proinflammatory cytokine production in the colon microenvironment. The downstream proinflammatory effects of IL-23 are dependent upon donor-derived secretion of interferon-γ (IFN-γ), but are independent of donor IL-17 production. These findings define a novel organ-specific role for IL-23 in the pathophysiology of GVHD and demonstrate that IL-23 can direct tissue-specific pathology within the context of a systemic inflammatory disorder. Furthermore, these studies also identify IL-23 as a potential therapeutic target for the prevention of this life-threatening disorder.
In vivo efficacy of anti-MPL agonist antibody in promoting primary human hematopoietic cells
Authors: Kai Masayuki , Hagiwara Tetsuya , Emuta Chie , Chisaka Yukiko , Tsuruhata Kumi , Endo Chisato , Inagaki Yoshimasa , Miyazaki Hiroshi , Kataoka Shiro 
Published: December 2008

AbstractIn a previous study, we generated novel antithrombopoietin receptor agonist antibodies as therapeutic candidates. In this report, we investigated the in vivo effects of one of these antibodies, MA01G4344U, on primary human hematopoietic cells using xenotransplantation. NOD/Shi-scid, IL-2Rγnull (NOG) mice were pretreated by total-body irradiation and received a transplant of human cord blood–derived CD34+ cells. Weekly intraperitoneal injection of MA01G4344U (100 μg/mouse per week) or Peg-rhMGDF (5 μg/mouse per week) or phosphate-buffered saline (PBS) was performed. Human cells in peripheral blood were analyzed by flow cytometry and bone marrow cells were analyzed by flow cytometry and colony assay. MA01G4344U successfully increased the number of human CD41+ platelets and human CD45+ cells in peripheral blood. In the bone marrow, MA01G4344U increased the number of human CD45+/CD34+ cells, which resulted in more multilineage progenitor cells. The efficacy of MA01G4344U in promoting primary human hematopoietic cells in vivo suggests its therapeutic potential for thrombocytopenic and pancytopenic disorders.
Comparison of nonsense-mediated mRNA decay efficiency in various murine tissues
Authors: Zetoune Almoutassem B , Fontanière Sandra , Magnin Delphine , Anczuków Olga , Buisson Monique , Zhang Chang X , Mazoyer Sylvie 
Published: December 2008

Abstract

Background
The Nonsense-Mediated mRNA Decay (NMD) pathway detects and degrades mRNAs containing premature termination codons, thereby preventing the accumulation of potentially detrimental truncated proteins. Intertissue variation in the efficiency of this mechanism has been suggested, which could have important implications for the understanding of genotype-phenotype correlations in various genetic disorders. However, compelling evidence in favour of this hypothesis is lacking. Here, we have explored this question by measuring the ratio of mutant versus wild-type Men1 transcripts in thirteen tissues from mice carrying a heterozygous truncating mutation in the ubiquitously expressed Men1 gene.

Results
Significant differences were found between two groups of tissues. The first group, which includes testis, ovary, brain and heart, displays a strong decrease of the nonsense transcript (average ratio of 18% of mutant versus wild-type Men1 transcripts, identical to the value measured in murine embryonic fibroblasts). The second group, comprising lung, intestine and thymus, shows much less pronounced NMD (average ratio of 35%). Importantly, the extent of degradation by NMD does not correlate with the expression level of eleven genes encoding proteins involved in NMD or with the expression level of the Men1 gene.

Conclusion
Mouse models are an attractive option to evaluate the efficiency of NMD in multiple mammalian tissues and organs, given that it is much easier to obtain these from a mouse than from a single individual carrying a germline truncating mutation. In this study, we have uncovered in the thirteen different murine tissues that we examined up to a two-fold difference in NMD efficiency.
A cross-species transcriptomics approach to identify genes involved in leaf development
Authors: Street Nathaniel Robert , Sjödin Andreas , Bylesjö Max , Gustafsson Petter , Trygg Johan , Jansson Stefan 
Published: December 2008

AbstractBackgroundWe have made use of publicly available gene expression data to identify transcription factors and transcriptional modules (regulons) associated with leaf development inPopulus. Different tissue types were compared to identify genes informative in the discrimination of leaf and non-leaf tissues. Transcriptional modules within this set of genes were identified in a much wider set of microarray data collected from leaves in a number of developmental, biotic, abiotic and transgenic experiments.ResultsTranscription factors that were over represented in leaf EST libraries and that were useful for discriminating leaves from other tissues were identified, revealing that the C2C2-YABBY, CCAAT-HAP3 and 5, MYB, and ZF-HD families are particularly important in leaves. The expression of transcriptional modules and transcription factors was examined across a number of experiments to select those that were particularly active during the early stages of leaf development. Two transcription factors were found to collocate to previously published Quantitative Trait Loci (QTL) for leaf length. We also found that miRNA family 396 may be important in the control of leaf development, with three members of the family collocating with clusters of leaf development QTL.ConclusionThis work provides a set of candidate genes involved in the control and processes of leaf development. This resource can be used for a wide variety of purposes such as informing the selection of candidate genes for association mapping or for the selection of targets for reverse genetics studies to further understanding of the genetic control of leaf size and shape.
Possible contribution of endogenous carbon monoxide to the development of allergic rhinitis in guinea pigs
Authors: Shaoqing Yu , Ruxin Zhang , Yinjian Chen , Jianqiu Chen , Chunsheng Zhu , Jiangfeng Tang , Genhong Li 
Published: December 2008

AbstractBackgroundThe mechanisms responsible for the development of allergic rhinitis(AR) are not fully understood. The present study was designed to explore the possible roles of carbon monoxide(CO) on the pathogenesis of AR.MethodsAR guinea pig model was established by nasal ovalbumin sensitization. Twenty-four AR guinea pigs were divided into four groups, 6 in each: Saline control group, AR sensitized group, Hemin treated group, and Zinc protoporphyrin (ZnPP) treated group. The frequency of sneezing and nose rubbing was recorded. Leukocyte infiltration in nasal lavage fluid, serum IgE level and plasma CO were measured. Expression of heme oxygenase-1 (HO-1) mRNA in nasal mucosa was determined by real time RT-PCR, and expression of HO-1 protein was detected by immunohistochemistry.ResultsThe frequency of sneezing and nose rubbing, leukocyte infiltration, serum IgE, plasma CO, and HO-1 mRNA levels in sensitized guinea pigs were higher than those of control (P < 0.05). Except for serum IgE level, all above parameters were even higher (P < 0.05) when treated with Hemin, a heme oxygenase-1 inducer; but significantly decreased (P < 0.05) when treated with ZnPP, a heme oxygenase inhibitor. Immunohistochemical results showed that positive staining of HO-1 was present in the lamina of mucosa of sensitized guinea pigs, and there was an increase of HO-1 immunoreactivity with Hemin administration (P < 0.05) and a decrease with ZnPP treatment.ConclusionThe endogenous CO may take part in the inflammation process of AR and is positively correlated with expression of HO-1 in nasal mucosa. Endogenous CO plays a significant role in the pathogenesis of AR.
First isolation of two colistin-resistant emerging pathogens, Brevundimonas diminuta and Ochrobactrum anthropi, in a woman with cystic fibrosis: a case report
Authors: Menuet Magalie , Bittar Fadi , Stremler Nathalie , Dubus Jean-Christophe , Sarles Jacques , Raoult Didier , Rolain Jean-Marc 
Published: December 2008

Abstract

Introduction
Cystic fibrosis afflicted lungs support the growth of many bacteria rarely implicated in other cases of human infections.

Case presentation
We report the isolation and identification, by 16S rRNA amplification and sequencing, of two emerging pathogens resistant to colistin, Brevundimonas diminuta and Ochrobactrum anthropi, in a 17-year-old woman with cystic fibrosis and pneumonia. The patient eventually responded well to a 2-week regime of imipenem and tobramycin.

Conclusion
Our results clearly re-emphasize the emergence of new colistin-resistant pathogens in patients with cystic fibrosis.
Facile Carbolithiation of Bent Alkyne without Catalyst. Tandem Route to Dibenzo[b,f]pentalenes from Dibenzocyclooctadiyne
Authors: Babu Govindarajulu , Orita Akihiro , Otera Junzo 
Published: December 2008

Abstract
Nucleophilic addition of RLi to a triple bond of dibenzocycloocta[a,e]diyne provides dibenzo[b,f]pentalene motif through trans-annulation of the resulting vinyllithium. Dibenzopentalene anion thus formed reacts with various electrophiles such as aldehydes, alkyl halides, acid halide, and Me3SiCl to give the corresponding products.
Catalytic Enantioselective Reformatsky Reaction of Alkyl Iodoacetate with Aldehydes Catalyzed by Chiral Schiff Base
Authors: Tanaka Takanori , Hayashi Masahiko 
Published: December 2008

Abstract
The catalytic enantioselective Reformatsky reaction with aldehydes catalyzed by chiral Schiff base 1 in the presence of Me2Zn under Ar–O2 atmosphere was achieved (up to 72% ee). This process provides a potential method for the synthesis of chiral β-hydroxy esters in high enantiomeric excess.
Convenient Synthesis of Linear-extended Bipyridines Involving a Central Phenyl Linking Group
Authors: Gan Zhibin , Okui Ayaka , Kawashita Yuka , Hayashi Masahiko 
Published: December 2008

Abstract
Linear-extended bipyridines were synthesized via the Hantzsch dihydropyridine synthesis, subsequent oxidative aromatization with molecular oxygen in the presence of activated carbon, and decarboxylation. 4,4″-p-Terphenyldicarboxaldehyde was prepared by the Suzuki–Miyaura cross-coupling reaction.
Successful Low-Risk Hematopoietic Cell Therapy in a Mouse Model of Type 1 Gaucher Disease
Authors: Enquist Ida Berglin , Nilsson Eva , Månsson Jan-Eric , Ehinger Mats , Richter Johan , Karlsson Stefan 
Published: December 2008

Abstract
Hematopoietic stem cell-based gene therapy offers the possibility of permanent correction for genetic disorders of the hematopoietic system. However, optimization of present protocols is required before gene therapy can be safely applied as general treatment of genetic diseases. In this study we have used a mouse model of type 1 Gaucher disease (GD) to demonstrate the feasibility of a low-risk conditioning regimen instead of standard radiation, which is associated with severe adverse effects. We first wanted to establish what level of engraftment and glucosylceramidase (GCase) activity is required to correct the pathology of the type 1 GD mouse. Our results demonstrate that a median wild-type (WT) cell engraftment of 7%, corresponding to GCase activity levels above 10 nmoles/hour and mg protein, was sufficient to reverse pathology in bone marrow and spleen in the GD mouse. Moreover, we applied nonmyeloablative doses of busulfan as a pretransplant conditioning regimen and show that even WT cell engraftment in the range of 1%–10% can confer a beneficial therapeutical outcome in this disease model. Taken together, our data provide encouraging evidence for the possibility of developing safe and efficient conditioning protocols for diseases that require only a low level of normal or gene-corrected cells for a permanent and beneficial therapeutic outcome.
High Concordance of KRAS Status Between Primary Colorectal Tumors and Related Metastatic Sites: Implications for Clinical Practice
Authors: Santini Daniele , Loupakis Fotios , Vincenzi Bruno , Floriani Irene , Stasi Irene , Canestrari Emanuele , Rulli Eliana , Maltese Paolo Enrico , Andreoni Francesca , Masi Gianluca , Graziano Francesco , Baldi Giacomo Giulio , Salvatore Lisa , Russo Antonio , Perrone Giuseppe , Tommasino Maria Rosa , Magnani Mauro , Falcone Alfredo , Tonini Giuseppe , Ruzzo Annamaria 
Published: December 2008

Abstract

Purpose.
Several studies have suggested that KRAS somatic mutations may predict resistance to cetuximab- and panitumumab-based treatments in metastatic colorectal cancer (CRC) patients. Nevertheless, most experiences were conducted on samples from primaries. The aim of this study was to evaluate the grade of concordance in terms of KRAS status between primaries and related metastases.

Patients and Methods.
We analyzed KRAS codon 12 and 13 mutations from formalin-fixed sections of 107 CRC primaries and related metastases. Eight pairs were excluded from the analysis because of the low amount of tumor tissue in the available samples. The main characteristics were: 50 men, 49 women; median age at diagnosis, 71 years (range, 41–84). The metastatic sites analyzed were the liver in 80 patients (80.8%), lung in seven patients (7.1%), and other sites in 12 patients (12.1%).

Results.
A KRAS mutation was found in 38 (38.4%) primary tumors and in 36 (36.4%) related metastases. The rate of concordance was 96.0% (95% confidence interval, 90.0%–98.9%). Discordance was observed in only four (4%) patients.

Conclusions.
Our results indicate that the detection of KRAS mutations in either primary or metastatic tumors from patients with CRC is concordant and this assessment could be used to predict response to targeted therapies such as cetuximab and panitumumab.

Learning Objectives
After completing this course, the reader should be able to: Describe the importance of KRAS mutations in CRC patients.Explain the relevance to cancer treatment of concordance of KRAS status between primary tumors and metastases in CRC patients.Discuss the impact of KRAS mutations as a predictive/prognostic factor in CRC patients.
CME This article is available for continuing medical education credit at http://CME.TheOncologist.com
Neighborhood Context and Infant Birthweight Among Recent Immigrant Mothers: A Multilevel Analysis
Authors: Urquia Marcelo L. , Frank John W. , Glazier Richard H. , Moineddin Rahim , Matheson Flora I. , Gagnon Anita J. 
Published: December 2008

Objectives. We compared the influence of the residential environment and maternal country of origin on birthweight and low birthweight of infants born to recent immigrants to urban Ontario. Methods. We linked delivery records (1993–2000) to an immigration database (1993–1995) and small-area census data (1996). The data were analyzed with cross-classified random-effects models and standard multilevel methods. Higher-level predictors included 4 independent measures of neighborhood context constructed by factor analysis and maternal world regions of origin. Results. Births (N = 22 189) were distributed across 1396 census tracts and 155 countries of origin. The associations between neighborhood indices and birthweight disappeared after we controlled for the maternal country of origin in a cross-classified multilevel model. Significant associations between world regions and birthweight and low birthweight persisted after we controlled for neighborhood context and individual characteristics. Conclusions. The residential environment has little, if any, influence on birthweight among recent immigrants to Ontario. Country of origin appears to be a much more important factor in low birthweight among children of recent immigrants than current neighborhood. Findings of neighborhood influences among recent immigrants should be interpreted with caution.