Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes.

Plant disease resistance genes (R genes) encode proteins that function to monitor signals indicating pathogenic infection, thus playing a critical role in the plant's defense system. Although many studies have been performed to explore the functional details of these important genes, their origin and evolutionary history remain unclear. In this study, focusing on the largest group of R genes, the nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes, we conducted an extensive genome-wide survey of 38 representative model organisms and obtained insights into the evolutionary stage and timing of NBS-LRR genes.

A comparison of surgical intervention and stereotactic body radiation therapy for stage I lung cancer in high-risk patients: a decision analysis.

Objective: We sought to compare the relative cost-effectiveness of surgical intervention and stereotactic body radiation therapy in high risk patients with clinical stage I lung cancer (non-small cell lung cancer).

Methods: We compared patients chosen for surgical intervention or SBRT for clinical stage I non-small cell lung cancer. Propensity score matching was used to adjust estimated treatment hazard ratios for the confounding effects of age, comorbidity index, and clinical stage.

Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage.

Small RNAs have a variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify previously unknown rice (Oryza sativa) microRNAs (miRNAs) and those regulated by environmental stress, 62 small RNA libraries were constructed from rice plants and used for deep sequencing with Illumina technology.

MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs.

Legumes and many nonleguminous plants enter symbiotic interactions with microbes, and it is poorly understood how host plants respond to promote beneficial, symbiotic microbial interactions while suppressing those that are deleterious or pathogenic. Trans-acting siRNAs (tasiRNAs) negatively regulate target transcripts and are characterized by siRNAs spaced in 21-nucleotide (nt) "phased" intervals, a pattern formed by DICER-LIKE 4 (DCL4) processing. A search for phased siRNAs (phasiRNAs) found at least 114 Medicago loci, the majority of which were defense-related NB-LRR-encoding genes.

A shift in the collagen V antigenic epitope leads to T helper phenotype switch and immune response to self-antigen leading to chronic lung allograft rejection.

Immune responses to human leucocyte antigen (HLA) and self-antigen collagen V (Col-V) have been proposed in the pathogenesis of chronic rejection (bronchiolitis obliterans syndrome, BOS) following human lung transplantation (LTx). In this study, we defined the role for the shift in immunodominant epitopes of Col-V in inducing T helper phenotype switch leading to immunity to Col-V and BOS. Sera and lavage from BOS(+) LTx recipients with antibodies to Col-V were analysed.

Video-assisted thoracoscopic lobectomy is less costly and morbid than open lobectomy: a retrospective multiinstitutional database analysis.

Background: The Premier Perspective Database (Premier Inc, Charlotte, NC) was used to compare hospital costs and perioperative outcomes for video-assisted thoracoscopic surgery (VATS) and open lobectomy procedures in the United States.

Methods: Eligible patients underwent a lobectomy for cancer by a thoracic surgeon, by VATS or open thoracotomy and were captured in the database between third quarter of 2007 and through 2008. Multivariable logistic regression analyses were performed for binary outcomes.

RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildew.

Lima bean is an important vegetable processing crop to the mid-Atlantic USA and is highly susceptible to the oomycete pathogen Phytophthora phaseoli, which causes downy mildew. Genetic resistance and fungicides are used to manage P. phaseoli and often fail.

Impact of video-assisted thoracoscopic surgery on benign resections for solitary pulmonary nodules.

Background: Differentiating benign from malignant pulmonary lesions is an important part of surgical decision making. We reviewed our experience of resecting suspicious pulmonary nodules to test the hypothesis that the increased use of video-assisted thoracic surgery (VATS) has increased the resection rate of benign lesions.

Methods: A retrospective analysis was carried out on 3,217 patients who underwent resection for focal pulmonary lesions between 1995 and 2009.

AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana.

RNA-directed DNA methylation (RdDM) is a small interfering RNA (siRNA)-mediated epigenetic modification that contributes to transposon silencing in plants. RdDM requires a complex transcriptional machinery that includes specialized RNA polymerases, named Pol IV and Pol V, as well as chromatin remodelling proteins, transcription factors, RNA binding proteins, and other plant-specific proteins whose functions are not yet clarified. In Arabidopsis thaliana, DICER-LIKE3 and members of the ARGONAUTE4 group of ARGONAUTE (AGO) proteins are involved, respectively, in generating and using 24-nt siRNAs that trigger methylation and transcriptional gene silencing of homologous promoter sequences.

Efficacy and safety of acute injection laryngoplasty for vocal cord paralysis following thoracic surgery.

Objectives/hypothesis: The primary objective of this study was to evaluate the effectiveness and safety of injection laryngoplasty using a temporary injectable agent in the acute setting for patients with unilateral vocal cord paralysis following thoracic surgical procedures.

Study Design: Retrospective consecutive case series in an academic institution.

Methods: Inclusion criteria included patients acutely treated with injection laryngoplasty from January 1, 2006, to March 31, 2010, for a unilateral vocal cord paralysis that occurred after a thoracic surgical procedure (N = 20).

Demographic, clinical, and functional factors associated with antidepressant use in the home healthcare elderly.

Objectives: Determine rates and demographic, clinical, and functional correlates of antidepressants (ADs) in home healthcare patients.

Methods: Year 2007 cross-sectional National Home Health and Hospice Care Survey (N = 3,226) of patients 65 years or older (mean 80.11, confidence interval [CI] = 79.

Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing.

Background: Common bean (Phaseolus vulgaris) is the most important food legume in the world. Although this crop is very important to both the developed and developing world as a means of dietary protein supply, resources available in common bean are limited. Global transcriptome analysis is important to better understand gene expression, genetic variation, and gene structure annotation in addition to other important features.

Roles of DCL4 and DCL3b in rice phased small RNA biogenesis.

Higher plants have evolved multiple proteins in the RNase III family to produce and regulate different classes of small RNAs with specialized molecular functions. In rice (Oryza sativa), numerous genomic clusters are targeted by one of two microRNAs (miRNAs), miR2118 and miR2275, to produce secondary small interfering RNAs (siRNAs) of either 21 or 24 nucleotides in a phased manner. The biogenesis requirements or the functions of the phased small RNAs are completely unknown.

Sociodemographic and clinical factors associated with antidepressant type in a national sample of the home health care elderly.

Objective: The study examined in home health care (HHC) the demographic, functional and clinical factors by antidepressant (AD) type including selective serotonin reuptake inhibitors (SSRIs), serotonin-norepinephrine reuptake inhibitors (SNRIs), tricyclic antidepressants (TCAs) and "Other" ADs such as bupropion and mirtazapine.

Method: Cross-sectional sample (N=909) was analyzed from the 2007 National Home Health and Hospice Care Survey that included patients 65 years and older [mean=78.79 years, confidence interval (CI)=77.

A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice.

DNA 5-methylcytosine (5-meC) is an important epigenetic mark for transcriptional gene silencing in many eukaryotes. In Arabidopsis, 5-meC DNA glycosylase/lyases actively remove 5-meC to counteract transcriptional gene silencing in a locus-specific manner, and have been suggested to maintain the expression of transposons. However, it is unclear whether plant DNA demethylases can promote the transposition of transposons.

Depression Care for Patients at Home (Depression CAREPATH): home care depression care management protocol, part 2.

High levels of depressive symptoms are common and contribute to poorer clinical outcomes even in geriatric patients who are already taking antidepressant medication. The Depression CARE for PATients at Home (Depression CAREPATH) intervention was designed to meet the needs of medical and surgical patients who suffer from depression. The intervention's clinical protocols are designed to guide clinicians in managing depression as part of routine home care.

Thirty- and ninety-day outcomes after sublobar resection with and without brachytherapy for non-small cell lung cancer: results from a multicenter phase III study.

Objective: Sublobar resection (SR) is commonly used for patients considered high risk for lobectomy. Nonoperative therapies are increasingly being reported for patients with similar risk because of perceived lower morbidity. We report 30- and 90-day adverse events (AEs) from American College of Surgeons Oncology Group Z4032, a multicenter phase III study for high-risk patients with stage I non-small cell lung cancer.

Validation of an automated latex particle-enhanced immunoturbidimetric von Willebrand factor activity assay.

Background: Laboratory diagnosis of von Willebrand disease (VWD) requires accurate measurement of plasma von Willebrand factor (VWF) activity.

Objectives: To evaluate laboratory characteristics, diagnostic accuracy and testing utilities of an automated latex particle-enhanced immunoturbidimetric VWF assay (VWF:Lx) based on a monoclonal antibody recognizing the VWF-platelet glycoprotein (GP) Ib binding domain.

Methods: Laboratory characteristics including lower detection limit, linearity, precision, sample stability, and method comparison between VWF:Lx and VWF ristocetin cofactor activity by platelet aggregometry (VWF:RCo) were examined.

Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing.

Polyadenylation sites mark the ends of mRNA transcripts. Alternative polyadenylation (APA) may alter sequence elements and/or the coding capacity of transcripts, a mechanism that has been demonstrated to regulate gene expression and transcriptome diversity. To study the role of APA in transcriptome dynamics, we analyzed a large-scale data set of RNA "tags" that signify poly(A) sites and expression levels of mRNA.

In-hospital clinical and economic consequences of pulmonary wedge resections for cancer using video-assisted thoracoscopic techniques vs traditional open resections: a retrospective database analysis.

Objective: The objective of this study was to compare the safety, use, and cost profiles of open thoracotomy vs video-assisted thoracoscopic surgery (VATS) for wedge resection in lung cancer performed by thoracic surgeons in the United States.

Methods: The Premier database, which contains complete patient billing, hospital cost, and coding histories from > 25 million inpatient discharges and > 175 million hospital outpatient visits, was used for this analysis. Eligible patients were those who underwent wedge resection by a thoracic surgeon for cancer diagnosis or treatment through open thoracotomy or VATS in 2007 or 2008.

Single-lung transplantation in the setting of aborted bilateral lung transplantation.

Background. The outcome of patients undergoing a single-lung transplant in the setting of an aborted bilateral lung transplant is unclear. Methods.

The impact of adjuvant brachytherapy with sublobar resection on pulmonary function and dyspnea in high-risk patients with operable disease: preliminary results from the American College of Surgeons Oncology Group Z4032 trial.

Background: Z4032 was a randomized study conducted by the American College of Surgeons Oncology Group comparing sublobar resection alone versus sublobar resection with brachytherapy for high-risk operable patients with non-small cell lung cancer (NSCLC). This evaluates early impact of adjuvant brachytherapy on pulmonary function tests, dyspnea, and perioperative (30-day) respiratory complications in this impaired patient population.

Methods: Eligible patients with stage I NSCLC tumors 3 cm or smaller were randomly allocated to undergo sublobar resection with (SRB group) or without (SR group) brachytherapy.

Impact of anastomotic techniques on airway complications after lung transplant.

Background: Airway complications are a source of morbidity and expense after lung transplant. Posttransplant stenosis can occur when the donor bronchus is rendered ischemic and is dependent upon collateral flow from the pulmonary capillary system. By shortening the donor bronchus, the tissue at risk for ischemia is reduced.