bluuebunny/crossref_metadata_2025_split huggingface dataset:
Identification of miRNAs and their target genes in developing maize ears by combined small RNA and degradome sequencing
Authors: Liu Hongjun , Qin Cheng , Chen Zhe , Zuo Tao , Yang Xuerong , Zhou Huangkai , Xu Meng , Cao Shiliang , Shen Yaou , Lin Haijian , He Xiujing , Zhang Yinchao , Li Lujiang , Ding Haiping , Lübberstedt Thomas , Zhang Zhiming , Pan Guangtang 
Published: January 2014

Abstract

Background
In plants, microRNAs (miRNAs) are endogenous ~22 nt RNAs that play important regulatory roles in many aspects of plant biology, including metabolism, hormone response, epigenetic control of transposable elements, and stress response. Extensive studies of miRNAs have been performed in model plants such as rice and Arabidopsis thaliana. In maize, most miRNAs and their target genes were analyzed and identified by clearly different treatments, such as response to low nitrate, salt and drought stress. However, little is known about miRNAs involved in maize ear development. The objective of this study is to identify conserved and novel miRNAs and their target genes by combined small RNA and degradome sequencing at four inflorescence developmental stages.

Results
We used deep-sequencing, miRNA microarray assays and computational methods to identify, profile, and describe conserved and non-conserved miRNAs at four ear developmental stages, which resulted in identification of 22 conserved and 21-maize-specific miRNA families together with their corresponding miRNA*. Comparison of miRNA expression in these developmental stages revealed 18 differentially expressed miRNA families. Finally, a total of 141 genes (251 transcripts) targeted by 102 small RNAs including 98 miRNAs and 4 ta-siRNAs were identified by genomic-scale high-throughput sequencing of miRNA cleaved mRNAs. Moreover, the differentially expressed miRNAs-mediated pathways that regulate the development of ears were discussed.

Conclusions
This study confirmed 22 conserved miRNA families and discovered 26 novel miRNAs in maize. Moreover, we identified 141 target genes of known and new miRNAs and ta-siRNAs. Of these, 72 genes (117 transcripts) targeted by 62 differentially expressed miRNAs may attribute to the development of maize ears. Identification and characterization of these important classes of regulatory genes in maize may improve our understanding of molecular mechanisms controlling ear development.
Genomic comparison of sporeforming bacilli isolated from milk
Authors: Moreno Switt Andrea I , Andrus Alexis D , Ranieri Matthew L , Orsi Renato H , Ivy Reid , den Bakker Henk C , Martin Nicole H , Wiedmann Martin , Boor Kathryn J 
Published: January 2014

Abstract

Background
Sporeformers in the order Bacillales are important contributors to spoilage of pasteurized milk. While only a few Bacillus and Viridibacillus strains can grow in milk at 6°C, the majority of Paenibacillus isolated from pasteurized fluid milk can grow under these conditions. To gain a better understanding of genomic features of these important spoilage organisms and to identify candidate genomic features that may facilitate cold growth in milk, we performed a comparative genomic analysis of selected dairy associated sporeformers representing isolates that can and cannot grow in milk at 6°C.

Results
The genomes for seven Paenibacillus spp., two Bacillus spp., and one Viridibacillus sp. isolates were sequenced. Across the genomes sequenced, we identified numerous genes encoding antimicrobial resistance mechanisms, bacteriocins, and pathways for synthesis of non-ribosomal peptide antibiotics. Phylogenetic analysis placed genomes representing Bacillus, Paenibacillus and Viridibacillus into three distinct well supported clades and further classified the Paenibacillus strains characterized here into three distinct clades, including (i) clade I, which contains one strain able to grow at 6°C in skim milk broth and one strain not able to grow under these conditions, (ii) clade II, which contains three strains able to grow at 6°C in skim milk broth, and (iii) clade III, which contains two strains unable to grow under these conditions. While all Paenibacillus genomes were found to include multiple copies of genes encoding β-galactosidases, clade II strains showed significantly higher numbers of genes encoding these enzymes as compared to clade III strains. Genome comparison of strains able to grow at 6°C and strains unable to grow at this temperature identified numerous genes encoding features that might facilitate the growth of Paenibacillus in milk at 6°C, including peptidases with cold-adapted features (flexibility and disorder regions in the protein structure) and cold-adaptation related proteins (DEAD-box helicases, chaperone DnaJ).

Conclusions
Through a comparative genomics approach we identified a number of genomic features that may relate to the ability of selected Paenibacillus strains to cause spoilage of refrigerated fluid milk. With additional experimental evidence, these data will facilitate identification of targets to detect and control Gram positive spore formers in fluid milk.
Wireless home automation networks for indoor surveillance: technologies and experiments
Authors: Spadacini Milo , Savazzi Stefano , Nicoli Monica 
Published: January 2014

Abstract
The use of wireless technologies for critical surveillance and home automation introduces a number of opportunities as well as technological challenges. New emerging technologies give the opportunity to exploit the full potential of the internet of things paradigm by augmenting existing wired installations with smart wireless architectures. This work gives an overview of requirements, characteristics, and challenges of wireless home automation networks with special focus on intrusion detection systems. The proposed wireless network is based on several sensors that are deployed over a monitored area for detecting possible risky situations and triggering appropriate actions in response. The network needs to support critical traffic patterns with different characteristics and quality constraints. Namely, it should provide a periodic low-power monitoring service and, in case of intrusion detection, a real-time alarm propagation mechanism over inherently unreliable wireless links subject to fluctuations of the signal power. Following the guidelines introduced by recent standardization, this paper proposes the design of a wireless network prototype at 868 MHz which is able to satisfy the specifications of typical intrusion detection applications. A proprietary medium access control is developed based on the low-power SimpliciTI radio stack (Texas Instruments Incorporated, San Diego, CA, USA). Network performance is assessed by experimental measurements using a test-bed in an indoor office environment with severe multipath and nonline-of-sight propagation conditions. The measurement campaigns highlight the potential of the sub-GHz technology for cable replacing.
Effects of a novel curcumin derivative on insulin synthesis and secretion in streptozotocin-treated rat pancreatic islets in vitro
Authors: Aziz MohammedTalaat Abdel , El-Asmar Mohammed Farid , Rezq Ameen Mahmoud , Wassef MohammedAbdel Aziz , Fouad Hanan , Roshdy Nagwa Kamal , Ahmed Hanan Hosni , Rashed Laila Ahmed , Sabry Dina , Taha Fatma Mohammed , Hassouna Amira 
Published: January 2014

Abstract

Background
Hyperglycemia induces activation of the c-Jun N-terminal kinase (JNK) pathway, which suppresses insulin gene expression and reduces DNA binding of pancreatic and duodenal homeobox factor (PDX)-1. This study aims to investigate the effects of a novel curcumin derivative (NCD) on JNK signaling pathway on insulin synthesis and secretion in streptozotocin (STZ)-treated rat pancreatic islets in vitro.

Methods
Isolated rat pancreatic islets were divided into five groups: untreated control group; group treated with NCD (10 μM); group exposed to STZ (5 mM); group treated with NCD (10 μM) and then exposed to STZ (5 mM); and group exposed to STZ (5 mM) and then treated with NCD (10 μM). The pancreatic islets from all groups were used for DNA fragmentation assays and quantitative assessments of the JNK, Pdx1, glucose transporter-2 (GLUT2), heme oxygenase (HO)-1, transcription factor 7-like 2 (TCF7L2), and glucagon-like peptide (GLP)-1 gene expression levels. The intracellular calcium, zinc, and the phosphorylated and total JNK protein levels were assessed. The insulin (secreted/total) and C-peptide levels were examined in islet culture medium.

Results
NCD protected pancreatic islets against STZ-induced DNA damage, improved total insulin (P = 0.001), secreted insulin (P = 0.001), and C-peptide levels (P = 0.001), normalized mRNA expressions of insulin, Pdx1, and GLUT2 (P = 0.0001), and significantly elevated calcium and zinc levels (P = 0.0001). All effects were significant when islets were treated with NCD before STZ (P = 0.05). JNK gene overexpression and JNK protein levels induced by STZ were significantly inhibited after NCD treatment of islets ( P = 0.0001). NCD-treated islets showed significantly elevated gene expressions of HO-1, TCF7L2, and GLP-1 (P = 0.0001), and these upregulated gene expressions were more significantly elevated with NCD treatment before STZ than after STZ (P = 0.05).

Conclusions
NCD improved insulin synthesis and secretion in vitro in isolated pancreatic islets treated with STZ through inhibition of the JNK pathway, up-regulation of the gene expressions of HO-1, TCF7L2, and GLP-1 and enhancing effects on calcium and zinc levels.
Design and implementation of integrated solid wastes management pattern in industrial zones, case study of Shahroud, Iran
Authors: Saeid Nazemi , Roudbari Aliakbar , Yaghmaeian Kamyar 
Published: January 2014

Abstract

Background
The aim of the study was to design and implementation of integrated solid wastes management pattern in Shahroud industrial zone, evaluates the results and determine possible performance problems. This cross - sectional study was carried out for 4 years in Shahroud industrial zone and the implementation process included:1- Qualitative and quantitative analysis of all solid waste generated in the city, 2- determine the current state of solid waste management in the zone and to identify programs conducted, 3- Design and implementation of integrated solid wastes management pattern including design and implementation of training programs, laws, penalties and incentives and explain and implement programs for all factories and 4- The monitoring of the implementation process and determine the results.

Results
Annually, 1,728 tons of solid wastes generated in the town including 1603 tons of industrial wastes and 125 tons of municipal wastes. By implementing this pattern, the two separated systems of collection and recycling of domestic and industrial wastes was launched in this zone. Also consistent with the goals, the amount of solid wastes generated and disposed in 2009 was 51.5 and 28.6 kg per 100 million Rials production, respectively.

Conclusion
Results showed that implementation of pattern of separated collection, training programs, capacity building, providing technical services, completing chain of industries and strengthening the cooperation between industrial estate management and industrial units could greatly reduce the waste management problems.
Real-time in silico experiments on gene regulatory networks and surgery simulation on handheld devices
Authors: Alfaro Icíar , González David , Bordeu Felipe , Leygue Adrien , Ammar Amine , Cueto Elías , Chinesta Francisco 
Published: January 2014

Abstract

Abstract
Simulation of all phenomena taking place in a surgical procedure is a formidable task that involves, when possible, the use of supercomputing facilities over long time periods. However, decision taking in the operating room needs for fast methods that provide an accurate response in real time. To this end, Model Order Reduction (MOR) techniques have emerged recently in the field of Computational Surgery to help alleviate this burden. In this paper, we review the basics of classical MOR and explain how a technique recently developed by the authors and coined as Proper Generalized Decomposition could make real-time feedback available with the use of simple devices like smartphones or tablets. Examples are given on the performance of the technique for problems at different scales of the surgical procedure, form gene regulatory networks to macroscopic soft tissue deformation and cutting.
The gray zone of the qualitative assessment of respiratory changes in inferior vena cava diameter in ICU patients
Authors: Duwat Antoine , Zogheib Elie , Guinot Pierre Grégoire , Levy Franck , Trojette Faouzi , Diouf Momar , Slama Michel , Dupont Hervé 
Published: January 2014

Abstract
Introduction
Transthoracic echocardiography (TTE) is a useful tool for minimally invasive hemodynamic monitoring in the ICU. Dynamic indices (such as the inferior vena cava distensibility index (dIVC)) can be used to predict fluid responsiveness in mechanically ventilated patients. Although quantitative use of the dIVC has been validated, the routinely used qualitative (visual) approach had not been assessed before the present study.

Methods
Qualitative and quantitative assessments of the dIVC were compared in a prospective, observational study. After operators with differing levels in critical care echocardiography had derived a qualitative dIVC, the last (expert) operator performed a standard, numeric measurement of the dIVC (referred to as the quantitative dIVC). Two groups of patients were separated into two groups: group (dIVC < 18%) and group (dIVC ≥ 18%).

Results
In total, 114 patients were assessed for inclusion, and 97 (63 men and 34 women) were included. The mean sensitivity and specificity values for qualitative assessment of the dIVC by an intensivist were 80.7% and 93.7%, respectively. A qualitative evaluation detected all quantitative dIVCs >40%. Most of the errors concerned quantitative dIVCs of between 15% and 30%. In the dIVC <18% group, two qualitative evaluation errors were noted for quantitative dIVCs of between 0 and 10%. The average of positive predictive values and negative predictive values for qualitative assessment of the dIVC by residents, intensivists and cardiologists were 83%, 83%, and 90%; and 92%, 94%, and 90%, respectively. The Fleiss kappa for all operators was estimated to be 0.68, corresponding to substantial agreement.

Conclusion
The qualitative dIVC is a rather easy and reliable assessment for extreme numeric values. It has a gray zone between 15% and 30%. The highest and lowest limitations of the gray area are rather tedious to define.
Despite reliability of the qualitative assessment when it comes to extreme to numerical values, the quantitative dIVC measurement must always be done within a hemodynamic assessment for intensive care patients. The qualitative approach can be easily integrated into a fast hemodynamic evaluation by using portable ultrasound scanner for out-of-hospital patients.
The ethical dimension in published animal research in critical care: the public face of science
Authors: Bara Meredith , Joffe Ari R 
Published: January 2014

Abstract
Introduction
The ethical quality of animal research is important for many reasons, including for maintaining public support. We aimed to determine the reported attention to the ethical dimensions of the 3Rs (Refinement, Reduction, and Replacement) in critical care animal research published in 2012.

Methods
A data-collection form and instruction manual were created based on published recommendations, and completed for all consecutive critical care animal research (using mammals) publications from January to June 2012 in three critical care journals. Predefined subgroups were by journal, sepsis model, and animal age, compared by using the χ2 statistic, with statistical significance accepted at P < 0.05.

Results
In total, 77 consecutive animal research publications were reviewed. Most studies did not report monitoring the level of anesthesia during invasive procedures, even when muscle paralytics were used, nor monitoring or treatment of expected pain. When euthanasia was used, the method was often not stated, and when stated, most methods were not appropriate for the species. A sample-size calculation was rarely used, and animal numbers were often poorly described. No studies performed a systematic review to ensure that the animal research would be useful and not simple repetition. Seventeen (22%) publications met the composite outcome of, if indicated, using anesthesia and pain control, and stating the method of euthanasia. Most studies were funded with public funds (foundation or government funding). Sepsis models less often met the composite outcome of, if indicated, using anesthesia and pain control, and stating the method of euthanasia (2 (7%) of 27 versus 15 (30%) of 50; P = 0.023). No other statistically significant differences were found in reporting of any criterion by animal age, sepsis model, or journal.

Conclusions
Reported (although not necessarily actual) ethical quality of animal research in three high-impact critical care journals during 6 months of 2012 was poor. This has important implications for the practice of critical care animal research.
Difference in mobilization of progenitor cells after myocardial infarction in smoking versus non-smoking patients: insights from the BONAMI trial
Authors: Lamirault Guillaume , Susen Sophie , Forest Virginie , Hemont Caroline , Parini Angelo , Corvoisier Philippe Le , Piot Christophe , Richard Marie-Jeanne , Delasalle Béatrice , Rouard Hélène , Sportouch Catherine , Persoons Virginie , Van Belle Eric , Roncalli Jérôme , Lemarchand Patricia 
Published: January 2014

Abstract
Introduction
Although autologous bone marrow cell (BMC) therapy has emerged as a promising treatment for acute myocardial infarction (AMI), trials reported mixed results. In the BONAMI trial, active smoking reduced cardiac function recovery after reperfused AMI. Therefore, we hypothesized that variability in the functionality of BMCs retrieved from patients with cardiovascular risk factors may partly explain these mixed results. We investigated the characteristics of progenitor cells in active smokers and non-smokers with AMI and their potential impact on BMC therapy efficacy.

Methods
Bone marrow and blood samples from 54 smoking and 47 non-smoking patients enrolled in the BONAMI cell therapy trial were analyzed.

Results
The white BMC and CD45dimCD34+ cell numbers were higher in active smokers (P = 0.001, P = 0.03, respectively). In marked contrast, either bone marrow or blood endothelial progenitor CD45dimCD34 + KDR + cells (EPCs) were decreased in active smokers (P = 0.005, P = 0.04, respectively). Importantly, a multivariate analysis including cardiovascular risk factors confirmed the association between active smoking and lower EPC number in bone marrow (P = 0.04) and blood (P = 0.04). Furthermore, baseline circulating EPC count predicted infarct size decrease at three months post-AMI in non-smokers (P = 0.01) but not in active smokers. Interestingly, baseline circulating EPCs were no longer predictive of cardiac function improvement in the BMC therapy group.

Conclusions
These data suggest that circulating EPCs play an important role in cardiac repair post-AMI only in non-smokers and that active smoking-associated EPC alterations may participate in the impairment of cardiac function recovery observed in smokers after AMI, an effect that was overridden by BMC therapy.
International Myeloma Working Group Consensus Statement for the Management, Treatment, and Supportive Care of Patients With Myeloma Not Eligible for Standard Autologous Stem-Cell Transplantation
Authors: Palumbo Antonio , Rajkumar S. Vincent , San Miguel Jesus F. , Larocca Alessandra , Niesvizky Ruben , Morgan Gareth , Landgren Ola , Hajek Roman , Einsele Hermann , Anderson Kenneth C. , Dimopoulos Meletios A. , Richardson Paul G. , Cavo Michele , Spencer Andrew , Stewart A. Keith , Shimizu Kazuyuki , Lonial Sagar , Sonneveld Pieter , Durie Brian G.M. , Moreau Philippe , Orlowski Robert Z. 
Published: January 2014

Purpose To provide an update on recent advances in the management of patients with multiple myeloma who are not eligible for autologous stem-cell transplantation. Methods A comprehensive review of the literature on diagnostic criteria is provided, and treatment options and management of adverse events are summarized. Results Patients with symptomatic disease and organ damage (ie, hypercalcemia, renal failure, anemia, or bone lesions) require immediate treatment. The International Staging System and chromosomal abnormalities identify high- and standard-risk patients. Proteasome inhibitors, immunomodulatory drugs, corticosteroids, and alkylating agents are the most active agents. The presence of concomitant diseases, frailty, or disability should be assessed and, if present, treated with reduced-dose approaches. Bone disease, renal damage, hematologic toxicities, infections, thromboembolism, and peripheral neuropathy are the most frequent disabling events requiring prompt and active supportive care. Conclusion These recommendations will help clinicians ensure the most appropriate care for patients with myeloma in everyday clinical practice.
Nomogram to Predict Cycle-One Serious Drug-Related Toxicity in Phase I Oncology Trials
Authors: Hyman David M. , Eaton Anne A. , Gounder Mrinal M. , Smith Gary L. , Pamer Erika G. , Hensley Martee L. , Spriggs David R. , Ivy Percy , Iasonos Alexia 
Published: January 2014

Purpose All patients in phase I trials do not have equivalent susceptibility to serious drug-related toxicity (SDRT). Our goal was to develop a nomogram to predict the risk of cycle-one SDRT to better select appropriate patients for phase I trials. Patients and Methods The prospectively maintained database of patients with solid tumor enrolled onto Cancer Therapeutics Evaluation Program–sponsored phase I trials activated between 2000 and 2010 was used. SDRT was defined as a grade ≥ 4 hematologic or grade ≥ 3 nonhematologic toxicity attributed, at least possibly, to study drug(s). Logistic regression was used to test the association of candidate factors to cycle-one SDRT. A final model, or nomogram, was chosen based on both clinical and statistical significance and validated internally using a bootstrapping technique and externally in an independent data set. Results Data from 3,104 patients enrolled onto 127 trials were analyzed to build the nomogram. In a model with multiple covariates, Eastern Cooperative Oncology Group performance status, WBC count, creatinine clearance, albumin, AST, number of study drugs, biologic study drug (yes v no), and dose (relative to maximum administered) were significant predictors of cycle-one SDRT. All significant factors except dose were included in the final nomogram. The model was validated both internally (bootstrap-adjusted concordance index, 0.60) and externally (concordance index, 0.64). Conclusion This nomogram can be used to accurately predict a patient's risk for SDRT at the time of enrollment. Excluding patients at high risk for SDRT should improve the safety and efficiency of phase I trials.