bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of phylogenetic relationships in Lemnaceae using nuclear ribosomal data
Authors: Tippery N. P. , Les D. H. , Crawford D. J. 
Published: June 2014

AbstractNuclear DNA sequence data are essential for obtaining a complete understanding of plant species relationships, yet these data have been conspicuously absent from phylogenetic analyses of Lemnaceae (duckweeds). Using a modified Sanger sequencing protocol, we obtained DNA sequences of duckweed nuclear ribosomal regions, including 18S and 26S rDNA genes, the external transcribed spacer (ETS) and the frequently used internal transcribed spacer (ITS). After obtaining sequence data for all Lemnaceae species, we ascertained that prior difficulty in sequencing the ITS regions likely resulted from extremely rigid secondary structures, precipitated by a high proportion of G/C nucleotides. In phylogenetic analyses, nuclear ribosomal data largely supported relationships that had been inferred using chloroplast DNA sequence data.
Forced Collapse of the Blastocoel Cavity Improves Developmental Potential in Cryopreserved Bovine Blastocysts by Slow‐Rate Freezing and Vitrification
Authors: Min S‐H , Kim J‐W , Lee Y‐H , Park S‐Y , Jeong P‐S , Yeon J‐Y , Park H , Chang K‐T , Koo D‐B 
Published: June 2014

ContentsThis study was conducted to evaluate the effectiveness of forced collapse of the blastocoel before slow‐rate freezing and vitrification of bovine blastocysts. Cryopreservation of bovine blastocysts has been proposed as a tool to improve the feasibility of cattle production using the embryo transfer technique. However, the low efficiency of frozen–thawed embryos survival and further development is a crucial problem. In this study, bovine in vitro and in vivo blastocysts were slow‐rate frozen and vitrified after forced blastocoele collapse (FBC) of the blastocyst cavity by puncturing the blastocoele with a pulled Pasteur pipet. Differences in the developmental potential of frozen–thawed blastocysts derived from FBC and non‐FBC groups were found in both slow‐rate freezing and vitrification. Furthermore, we found that the total cell number of blastocysts in FBC groups was increased and the index of apoptosis in FBC groups was decreased. Consistent with these results, real‐time RT‐PCR analysis data showed that expression of the anti‐apoptotic Bcl‐XL gene was significantly increased by FBC groups, whereas expression of the pro‐apoptotic Bax gene was significantly decreased by FBC groups. Our results also showed that pregnancy outcomes in both slow‐rate frozen and vitrified bovine in vivo blastocysts could be improved by reducing the fluid content after FBC of the blastocyst cavity. Therefore, we suggest that FBC of the blastocyst cavity with a pulled Pasteur pipet is an effective pre‐treatment technique for both slow‐rate freezing and vitrification of bovine blastocysts.
Roles of small RNAs in soybean defense against Phytophthora sojae infection
Authors: Wong James , Gao Lei , Yang Yang , Zhai Jixian , Arikit Siwaret , Yu Yu , Duan Shuyi , Chan Vicky , Xiong Qin , Yan Jun , Li Shengben , Liu Renyi , Wang Yuanchao , Tang Guiliang , Meyers Blake C. , Chen Xuemei , Ma Wenbo 
Published: June 2014

SummaryThe genus Phytophthora consists of many notorious pathogens of crops and forestry trees. At present, battling Phytophthora diseases is challenging due to a lack of understanding of their pathogenesis. We investigated the role of small RNAs in regulating soybean defense in response to infection by Phytophthora sojae, the second most destructive pathogen of soybean. Small RNAs, including microRNAs (miRNAs) and small interfering RNAs (siRNAs), are universal regulators that repress target gene expression in eukaryotes. We identified known and novel small RNAs that differentially accumulated during P. sojae infection in soybean roots. Among them, miR393 and miR166 were induced by heat‐inactivated P. sojae hyphae, indicating that they may be involved in soybean basal defense. Indeed, knocking down the level of mature miR393 led to enhanced susceptibility of soybean to P. sojae; furthermore, the expression of isoflavonoid biosynthetic genes was drastically reduced in miR393 knockdown roots. These data suggest that miR393 promotes soybean defense against P. sojae. In addition to miRNAs, P. sojae infection also resulted in increased accumulation of phased siRNAs (phasiRNAs) that are predominantly generated from canonical resistance genes encoding nucleotide binding‐leucine rich repeat proteins and genes encoding pentatricopeptide repeat‐containing proteins. This work identifies specific miRNAs and phasiRNAs that regulate defense‐associated genes in soybean during Phytophthora infection.
The powdery mildew resistance gene Pm8 derived from rye is suppressed by its wheat ortholog Pm3
Authors: Hurni Severine , Brunner Susanne , Stirnweis Daniel , Herren Gerhard , Peditto David , McIntosh Robert A. , Keller Beat 
Published: June 2014

SummaryThe powdery mildew resistance gene Pm8 derived from rye is located on a 1BL.1RS chromosome translocation in wheat. However, some wheat lines with this translocation do not show resistance to isolates of the wheat powdery mildew pathogen avirulent to Pm8 due to an unknown genetically dominant suppression mechanism. Here we show that lines with suppressed Pm8 activity contain an intact and expressed Pm8 gene. Therefore, the absence of Pm8 function in certain 1BL.1RS‐containing wheat lines is not the result of gene loss or mutation but is based on suppression. The wheat gene Pm3, an ortholog of rye Pm8, suppressed Pm8‐mediated powdery mildew resistance in lines containing Pm8 in a transient single‐cell expression assay. This result was further confirmed in transgenic lines with combined Pm8 and Pm3 transgenes. Expression analysis revealed that suppression is not the result of gene silencing, either in wheat 1BL.1RS translocation lines carrying Pm8 or in transgenic genotypes with both Pm8 and Pm3 alleles. In addition, a similar abundance of the PM8 and PM3 proteins in single or double homozygous transgenic lines suggested that a post‐translational mechanism is involved in suppression of Pm8. Co‐expression of Pm8 and Pm3 genes in Nicotiana benthamiana leaves followed by co‐immunoprecipitation analysis showed that the two proteins interact. Therefore, the formation of a heteromeric protein complex might result in inefficient or absent signal transmission for the defense reaction. These data provide a molecular explanation for the suppression of resistance genes in certain genetic backgrounds and suggest ways to circumvent it in future plant breeding.
Red blood cell storage increases hypoxia‐induced nitric oxide bioavailability and methemoglobin formation in vitro and in vivo
Authors: Almac Emre , Bezemer Rick , Hilarius‐Stokman Petra M. , Goedhart Peter , de Korte Dirk , Verhoeven Arthur J. , Ince Can 
Published: June 2014

BackgroundIn this study we investigated whether storage of red blood cells (RBCs) leads to alterations in nitrite reductase activity, hence in altered hypoxia‐induced nitric oxide (NO) bioavailability and methemoglobin formation.Study Design and MethodsHypoxia‐induced NO bioavailability and methemoglobin formation were measured in vitro after nitrite administration to fresh (<1 week of storage) and aged (5‐6 weeks of storage) human RBC units and in blood samples of hemodiluted rats subjected to hypoxic ventilation after transfusion with fresh or aged human RBCs.ResultsIn vitro, NO and methemoglobin levels 10 minutes after nitrite administration were lower in the fresh RBC samples compared to the aged RBC samples (p = 0.026 and p = 0.022, respectively). In vivo, NO bioavailability was also significantly lower in the rats receiving fresh RBCs compared to the group receiving aged RBCs (p = 0.003). In line with NO bioavailability, methemoglobin levels were higher, albeit not significantly, in the group receiving aged RBCs compared to in the group receiving fresh RBCs (p = 0.154). The difference in methemoglobin formation after nitrite administration between fresh and aged RBCs was only present under deoxygenated conditions and not under oxygenated conditions. There were no differences in methemoglobin reductase activity between fresh and aged RBCs.ConclusionsStorage of RBCs leads to an increased rate of hypoxia‐induced nitrite reduction to NO and this is associated with increased methemoglobin formation. The increased methemoglobin formation and consequent decrease in oxygen delivery capacity might contribute to the storage‐related impairment of aged RBCs to oxygenate the microcirculation.
How do we manage cardiopulmonary bypass coagulopathy?
Authors: Welsh Kerry J. , Nedelcu Elena , Bai Yu , Wahed Amer , Klein Kimberly , Tint Hlaing , Gregoric Igor , Patel Manish , Kar Biswajit , Loyalka Pranav , Nathan Sriram , Loubser Paul , Weeks Phillip A. , Radovancevic Rajko , Nguyen Andy N.D. 
Published: June 2014

BackgroundPatients who undergo cardiopulmonary bypass (CPB) are at risk for coagulopathy. Suboptimal turnaround time (TAT) of laboratory coagulation testing results in empiric administration of blood products to treat massive bleeding. We describe our initiative in establishing the coagulation‐based hemotherapy (CBH) service, a clinical pathology consultation service that uses rapid TAT coagulation testing and provides comprehensive assessment of bleeding in patients undergoing CPB. A transfusion algorithm that treats the underlying cause of coagulopathy was developed.Study Design and MethodsThe coagulation testing menu includes all aspects of coagulopathy with close proximity of the laboratory to the operating room to allow for rapid test results. The hemotherapy pathologist monitors laboratory results at several stages in surgery and uses a comprehensive algorithm to monitor a patient's hemostasis. The optimal number and type of blood products are selected when the patient is taken off CPB.ResultsThe CBH service was consulted for 44 ventricular assist device implants, 30 heart transplants, and 31 other cardiovascular surgeries from May 2012 through November 2013. The TAT for laboratory tests was 15 minutes for complete blood count, antithrombin, and coagulation panel and 30 minutes for VerifyNow and thromboelastography, in comparison to 45 to 60 minutes in normal settings. The transfusion algorithms were used with optimal administration of blood components with preliminary data suggestive of reduced blood product usage and better patient outcomes.ConclusionWe described the successful introduction of a novel pathology consultation service that uses a rapid TAT coagulation testing menu with transfusion algorithms for improved management of CPB patients.
Risk‐adjusted clinical outcomes in patients enrolled in a bloodless program
Authors: Frank Steven M. , Wick Elizabeth C. , Dezern Amy E. , Ness Paul M. , Wasey Jack O. , Pippa Andrew C. , Dackiw Elizabeth , Resar Linda M.S. 
Published: June 2014

BackgroundAlthough clinical outcomes have been reported for patients who do not accept allogeneic blood transfusion (ABT), many previous studies lack a control group, fail to use risk adjustment, and focus exclusively on cardiac surgery.Study Design and MethodsWe report a risk‐adjusted, propensity score–matched, retrospective case‐control study of clinical outcomes for inpatients who did not accept ABT (bloodless, n = 294) and those who did accept ABT (control, n = 1157). Multidisciplinary specialized care was rendered to the bloodless patients to conserve blood and optimize clinical outcomes. Differences in hemoglobin (Hb), mortality, five morbid outcomes, and hospital charges and costs were compared. Subgroups of medical and surgical patients were analyzed, and independent predictors of outcome were determined by multivariate analysis.ResultsOverall, mortality was lower in the bloodless group (0.7%) than in the control group (2.7%; p = 0.046), primarily attributed to the surgical subgroup. After risk adjustment, bloodless care was not an independent predictor of the composite adverse outcome (death or any morbid event; p = 0.91; odds ratio, 1.02; 95% confidence interval, 0.68‐1.53). Discharge Hb concentrations were similar in the bloodless (10.8 ± 2.7 g/dL) and control (10.9 ± 2.3 g/dL) groups (p = 0.42). Total and direct hospital costs were 12% (p = 0.02) and 18% (p = 0.02) less, respectively, in the bloodless patients, a difference attributed to the surgical subgroup.ConclusionsUsing appropriate blood conservation measures for patients who do not accept ABT results in similar or better outcomes and is associated with equivalent or lower costs. This specialized care may be beneficial even for those patients who accept ABT.
Termination of pregnancy for maternal indications at the limits of fetal viability: a retrospective cohort study in the Dutch tertiary care centres
Authors: van Eerden L , Zeeman G G , Page-Christiaens G C M , Vandenbussche F , Oei S G , Scheepers H C J , van Eyck J , Middeldorp J M , Pajkrt E , Duvekot J J , de Groot C J M , Bolte A C 
Published: June 2014

ObjectiveMaternal morbidity, either pregnancy related or pre-existent, can become life threatening and of such severity as to warrant termination of pregnancy (TOP). In this situation, chances of fetal survival are usually poor, either because of low gestational age and/or because of the fetal effects of the maternal condition. Examples include severe growth restriction in pre-eclampsia and intrauterine infection due to the very early preterm prelabour rupture of membranes. There are very few reports on the prevalence of TOP for maternal indication at the limits of fetal viability. We investigated the prevalence of and indications for TOP on maternal indication in the 10 tertiary care centres in the Netherlands during the past decade.Study designWe conducted a retrospective review of the medical records of all women who underwent TOP for maternal indications between 22 and 27 completed weeks of gestation in all 10 tertiary care centres from 2000 to 2009.ResultsDuring the study period, there were 1 929 470 deliveries; 163 052 (8.4%) of these took place in one of the 10 tertiary care centres and 177 pregnancies were terminated for severe maternal disease, 131 for hypertensive disorders, 29 for intrauterine infection and 17 for other reasons. The mean gestational age at TOP was 171 days (243/7)±10 days. No maternal deaths were recorded. The overall perinatal mortality was 99.4%.ConclusionsOver a 10-year period, TOP for maternal indications was performed in 1 in 1000 deliveries in the 10 Dutch tertiary care centres. Hypertensive disorders comprised three-quarters of the cases.
Heart rate variability analysis during head-up tilt test predicts nitroglycerine-induced syncope
Authors: Efremov Kristian , Brisinda Donatella , Venuti Angela , Iantorno Emilia , Cataldi Claudia , Fioravanti Francesco , Fenici Riccardo 
Published: June 2014

ObjectiveThe aim of this study was to determine whether or not heart rate variability (HRV) analysis during the first 20 min of head-up tilt testing could predict whether patients will develop syncope after nitroglycerine administration.Design64 patients with previous loss of consciousness underwent head-up tilt testing with the Italian protocol, which involves the administration of nitroglycerine after 20 min of tilt. HRV parameters were analysed from 5 min intervals selected during pretest supine rest (phase 1), the first 5 min (phase 2) and the last 5 min (phase 3) of passive 20 min of tilting, prior to the administration of nitroglycerine. Differences in power (ms2) of the spectral components between the various phases of tilting were calculated for each patient and expressed as Δ.Results20 patients (group 1, 9 women, mean age 43.2±24.5 years) had a syncope during tilt testing after nitroglycerine, while the other 44 (group 2, 24 women, mean age 41±20.5 years) did not. In group 1, the HRV spectral parameters high frequency (HF) and total power (TP) had a significant decrement from phases 2 to 3 (p=0.012 and 0.027, respectively), while in group 2 the average HF and TP values did not change. The Δ of spectral parameters between phases 2 and 3 were able to differentiate between the two groups and to predict syncope after nitroglycerine administration (p<0.05).ConclusionsHRV analysis within the first 20 min of passive tilting demonstrated that patients with nitroglycerine-induced syncope are characterised by a progressive decrement of parasympathetic activity, which does not occur in patients with a negative response to nitroglycerine. If confirmed on a wider population, HRV analysis could replace nitroglycerine administration and shorten the duration of the tilt test.
Increased Dietary Vitamin D Suppresses MAPK Signaling, Colitis, and Colon Cancer
Authors: Meeker Stacey , Seamons Audrey , Paik Jisun , Treuting Piper M. , Brabb Thea , Grady William M. , Maggio-Price Lillian 
Published: June 2014

Abstract
Epidemiologic studies associate low serum vitamin D levels with an increased risk of colon cancer and inflammatory diseases such as inflammatory bowel disease (IBD). 129-Smad3tm1Par/J (Smad3−/−) mice are a model of bacteria-driven colitis and colon cancer when infected with Helicobacter bilis (H. bilis). Thus, we used this mouse model to determine whether increased dietary vitamin D would reduce inflammation and colon cancer. Smad3−/− mice were fed purified diet with either maintenance (1 IU vitamin D/g diet; maintenance) or increased concentrations of vitamin D (5 IU vitamin D/g diet; high vitamin D). One week after diet initiation, mice were inoculated with broth or H. bilis and were necropsied at several time points postinoculation to assess inflammation, dysplasia, and neoplasia incidence. At 16 weeks postinfection, 11% of mice fed high vitamin D diet had cancer compared with 41% of mice fed maintenance diet (P = 0.0121). Evaluation at an early time point (1 week postinfection) showed that animals fed high vitamin D had decreased MAPK (p-P38 and p-JNK) activation in lamina propria leukocytes as well as decreased NFκB activation in colonic epithelial cells. Reduction in MAPK and NFκB activation correlated with decreased IBD scores (2.7 vs. 15.5; P &lt; 0.0001) as well as decreased inflammatory cell infiltrates and reduced expression of proinflammatory cytokines in cecal tissue. These findings suggest that increased dietary vitamin D is beneficial in preventing inflammation-associated colon cancer through suppression of inflammatory responses during initiation of neoplasia or early-stage carcinogenesis. Cancer Res; 74(16); 4398–408. ©2014 AACR.
Cigarette Smoking and Pulmonary Function in Adult Survivors of Childhood Cancer Exposed to Pulmonary-Toxic Therapy: Results from the St. Jude Lifetime Cohort Study
Authors: Oancea S. Cristina , Gurney James G. , Ness Kirsten K. , Ojha Rohit P. , Tyc Vida L. , Klosky James L. , Srivastava DeoKumar , Stokes Dennis C. , Robison Leslie L. , Hudson Melissa M. , Green Daniel M. 
Published: June 2014

Abstract
Treatments for childhood cancer can impair pulmonary function. We assessed the potential impact of cigarette smoking on pulmonary function in 433 adult childhood cancer survivors (CCS) who received pulmonary-toxic therapy, using single breath diffusion capacity for carbon monoxide corrected for hemoglobin (DLCOcorr), forced expiratory volume in 1 second (FEV1), forced vital capacity (FVC), and total lung capacity (TLC). FEV1/FVC median values among current [1.00; interquartile range (IQR): 0.94–1.04] and former smokers (0.98; IQR: 0.93–1.04) were lower than those who had never smoked (1.02; IQR: 0.96–1.06; P = 0.003). Median FEV1/FVC values were lower among those who smoked ≥ 6 pack-years (0.99; IQR: 0.92–1.03) and those who smoked &lt;6 pack-years (1.00; IQR: 0.94–1.04), than among those who had never smoked (P = 0.005). Our findings suggest that CCSs have an increased risk for future obstructive and restrictive lung disease. Follow-up is needed to determine whether smoking imparts more than additive risk. Smoking prevention and cessation need to be a priority in this population. Cancer Epidemiol Biomarkers Prev; 23(9); 1938–43. ©2014 AACR.
PreoperativeGNASandKRASTesting in the Diagnosis of Pancreatic Mucinous Cysts
Authors: Singhi Aatur D. , Nikiforova Marina N. , Fasanella Kenneth E. , McGrath Kevin M. , Pai Reetesh K. , Ohori N. Paul , Bartholow Tanner L. , Brand Randall E. , Chennat Jennifer S. , Lu Xuong , Papachristou Georgios I. , Slivka Adam , Zeh Herbert J. , Zureikat Amer H. , Lee Kenneth K. , Tsung Allan , Mantha Geeta S. , Khalid Asif 
Published: June 2014

AbstractPurpose: Management guidelines for pancreatic intraductal papillary mucinous neoplasms (IPMN) and mucinous cystic neoplasms (MCN) are based on the assumption that mucinous cysts can be accurately distinguished from other pancreatic cystic lesions. Previous studies using surgical material have identified recurrent mutations in GNAS and KRAS in pancreatic mucinous neoplasms. Yet, the diagnostic utility of testing for both genes in pancreatic cyst fluid obtained by endoscopic ultrasound–fine-needle aspiration (EUS–FNA) remains unclear.Experimental Design: GNAS and KRAS testing was performed on EUS–FNA pancreatic cyst fluid from 91 pancreatic cysts: 41 IPMNs, 9 IPMNs with adenocarcinoma, 16 MCNs, 10 cystic pancreatic neuroendocrine tumors (PanNET), 9 serous cystadenomas (SCA), 3 retention cysts, 2 pseudocysts, and 1 lymphoepithelial cyst.Results: Mutations in GNAS were detected in 16 (39%) IPMNs and 2 (22%) IPMNs with adenocarcinoma. KRAS mutations were identified in 28 (68%) IPMNs, 7 (78%) IPMNs with adenocarcinoma, and 1 (6%) MCN. Mutations in either gene were present in 34 (83%) IPMNs, 8 (89%) IPMNs with adenocarcinoma, and 1 (6%) MCN. No mutations were found in cystic PanNETs, SCAs, retention cysts, pseudocysts, and a lymphoepithelial cyst. GNAS and KRAS mutations had 100% specificity [95% confidence interval (CI), 0.83–1.00] but 65% sensitivity (95% CI, 0.52–0.76) for mucinous differentiation. Among IPMNs, mutations in either gene had 98% specificity (95% CI, 0.86–1.00) and 84% sensitivity (95% CI, 0.70–0.92).Conclusions: The combination of GNAS and KRAS testing was highly specific and sensitive for IPMNs; however, the lack of sensitivity for MCNs highlights the need for additional markers to improve the detection of pancreatic mucinous neoplasms. Clin Cancer Res; 20(16); 4381–9. ©2014 AACR.
Oncogenic Ras/ERK Signaling Activates CDCP1 to Promote Tumor Invasion and Metastasis
Authors: Uekita Takamasa , Fujii Satoko , Miyazawa Yuri , Iwakawa Reika , Narisawa-Saito Mako , Nakashima Katsuhiko , Tsuta Koji , Tsuda Hitoshi , Kiyono Tohru , Yokota Jun , Sakai Ryuichi 
Published: June 2014

Abstract
Involvement of Ras in cancer initiation is known, but recent evidence indicates a role in cancer progression, including metastasis and invasion; however, the mechanism is still unknown. In this study, it was determined that human lung cancer cells with Ras mutations, among other popular mutations, showed significantly higher expression of CUB domain–containing protein 1 (CDCP1) than those without. Furthermore, activated Ras clearly induced CDCP1, whereas CDCP1 knockdown or inhibition of CDCP1 phosphorylation by Src-directed therapy abrogated anoikis resistance, migration, and invasion induced by activated-Ras. Activation of MMP2 and secretion of MMP9, in a model of Ras-induced invasion, was found to be regulated through induction of phosphorylated CDCP1. Thus, CDCP1 is required for the functional link between Ras and Src signaling during the multistage development of human malignant tumors, highlighting CDCP1 as a potent target for treatment in the broad spectrum of human cancers associated with these oncogenes.
Implications: CDCP1 protein induced by oncogenic Ras/Erk signaling is essential for Ras-mediated metastatic potential of cancer cells. Mol Cancer Res; 12(10); 1449–59. ©2014 AACR.