Search

Structure imprinted in foreground extragalactic point sources by ionospheric refraction has the potential to contaminate Epoch of Reionization (EoR) power spectra of the 21 cm emission line of neutral hydrogen. The alteration of the spatial and spectral structure of foreground measurements due to total electron content gradients in the ionosphere creates a departure from the expected sky signal. We present a general framework for understanding the signatures of ionospheric behavior in the 2D neutral hydrogen power spectrum measured by a low-frequency radio interferometer. Two primary classes of ionospheric behavior are considered, corresponding to dominant modes observed in Murchison Widefield Array (MWA) EoR data, namely, anisotropic structured wave behavior and isotropic turbulence. Analytic predictions for power spectrum bias due to this contamination are computed and compared with simulations. We then apply the ionospheric metric described in Jordan et al. to study the impact of ionospheric structure on MWA data, by dividing MWA EoR data sets into classes with good and poor ionospheric conditions, using sets of matched 30-minute observations from 2014 September. The results are compared with the analytic and simulated predictions, demonstrating the observed bias in the power spectrum when the ionosphere is active (displays coherent structures or isotropic turbulence). The analysis demonstrates that unless ionospheric activity can be quantified and corrected, active data should not be included in EoR analysis in order to avoid systematic biases in cosmological power spectra. When data are corrected with a model formed from the calibration information, bias reduces below the expected 21 cm signal level. Data are considered “quiet” when the median measured source position offsets are less than 10.″–15.″. [ABSTRACT FROM AUTHOR]

We examine data from the Murchison Widefield Array (MWA) in the frequency range 72–102 MHz for a field of view that serendipitously contained the interstellar object ‘Oumuamua on 2017 November 28. Observations took place with a time resolution of 0.5 s and a frequency resolution of 10 kHz. Based on the interesting but highly unlikely suggestion that ‘Oumuamua is an interstellar spacecraft, due to some unusual orbital and morphological characteristics, we examine our data for signals that might indicate the presence of intelligent life associated with ‘Oumuamua. We searched our radio data for (1) impulsive narrowband signals, (2) persistent narrowband signals, and (3) impulsive broadband signals. We found no such signals with nonterrestrial origins and make estimates of the upper limits on equivalent isotropic radiated power (EIRP) for these three cases of approximately 7 kW, 840 W, and 100 kW, respectively. These transmitter powers are well within the capabilities of human technologies, and are therefore plausible for alien civilizations. While the chances of positive detection in any given search for extraterrestrial intelligence (SETI) experiment are vanishingly small, the characteristics of new generation telescopes such as the MWA (and, in the future, the Square Kilometre Array) make certain classes of SETI experiments easy, or even a trivial by-product of astrophysical observations. This means that the future costs of SETI experiments are very low, allowing large target lists to partially balance the low probability of a positive detection. [ABSTRACT FROM AUTHOR]

We present new radio continuum observations of NGC 253 from the Murchison Widefield Array at frequencies between 76 and 227 MHz. We model the broadband radio spectral energy distribution for the total flux density of NGC 253 between 76 MHz and 11 GHz. The spectrum is best described as a sum of a central starburst and extended emission. The central component, corresponding to the inner 500 pc of the starburst region of the galaxy, is best modeled as an internally free–free absorbed synchrotron plasma, with a turnover frequency around 230 MHz. The extended emission component of the spectrum of NGC 253 is best described as a synchrotron emission flattening at low radio frequencies. We find that 34% of the extended emission (outside the central starburst region) at 1 GHz becomes partially absorbed at low radio frequencies. Most of this flattening occurs in the western region of the southeast halo, and may be indicative of synchrotron self-absorption of shock-reaccelerated electrons or an intrinsic low-energy cutoff of the electron distribution. Furthermore, we detect the large-scale synchrotron radio halo of NGC 253 in our radio images. At 154–231 MHz the halo displays the well known X-shaped/horn-like structure, and extends out to ∼8 kpc in the z-direction (from the major axis). [ABSTRACT FROM AUTHOR]

We present a sample of 1483 sources that display spectral peaks between 72 MHz and 1.4 GHz, selected from the GaLactic and Extragalactic All-sky Murchison Widefield Array (GLEAM) survey. The GLEAM survey is the widest fractional bandwidth all-sky survey to date, ideal for identifying peaked-spectrum sources at low radio frequencies. Our peaked-spectrum sources are the low-frequency analogs of gigahertz-peaked spectrum (GPS) and compact-steep spectrum (CSS) sources, which have been hypothesized to be the precursors to massive radio galaxies. Our sample more than doubles the number of known peaked-spectrum candidates, and 95% of our sample have a newly characterized spectral peak. We highlight that some GPS sources peaking above 5 GHz have had multiple epochs of nuclear activity, and we demonstrate the possibility of identifying high-redshift (z > 2) galaxies via steep optically thin spectral indices and low observed peak frequencies. The distribution of the optically thick spectral indices of our sample is consistent with past GPS/CSS samples but with a large dispersion, suggesting that the spectral peak is a product of an inhomogeneous environment that is individualistic. We find no dependence of observed peak frequency with redshift, consistent with the peaked-spectrum sample comprising both local CSS sources and high-redshift GPS sources. The 5 GHz luminosity distribution lacks the brightest GPS and CSS sources of previous samples, implying that a convolution of source evolution and redshift influences the type of peaked-spectrum sources identified below 1 GHz. Finally, we discuss sources with optically thick spectral indices that exceed the synchrotron self-absorption limit. [ABSTRACT FROM AUTHOR]

Detection of the cosmological neutral hydrogen signal from the Epoch of Reionization (EoR) and estimation of its basic physical parameters are principal scientific aims of many current low-frequency radio telescopes. Here we describe the Cosmological H i Power Spectrum Estimator (CHIPS), an algorithm developed and implemented with data from the Murchison Widefield Array, to compute the two-dimensional and spherically-averaged power spectrum of brightness temperature fluctuations. The principal motivations for CHIPS are the application of realistic instrumental and foreground models to form the optimal estimator, thereby maximizing the likelihood of unbiased signal estimation, and allowing a full covariant understanding of the outputs. CHIPS employs an inverse-covariance weighting of the data through the maximum likelihood estimator, thereby allowing use of the full parameter space for signal estimation (“foreground suppression”). We describe the motivation for the algorithm, implementation, application to real and simulated data, and early outputs. Upon application to a set of 3 hr of data, we set a 2σ upper limit on the EoR dimensionless power at Mpc−1 of mK2 in the redshift range z = [6.2–6.6], consistent with previous estimates. [ABSTRACT FROM AUTHOR]

NGS used to diagnose and treat NSCLC patient with initial concern for metaplastic breast cancer.

Bioenergy sorghum is a low-input, drought-resilient, deep-rooting annual crop that has high biomass yield potential enabling the sustainable production of biofuels, biopower, and bioproducts. Bioenergy sorghum's 4-5 m stems account for ~80% of the harvested biomass. Stems accumulate high levels of sucrose that could be used to synthesize bioethanol and useful biopolymers if information about cell-type gene expression and regulation in stems was available to enable engineering. To obtain this information, laser capture microdissection was used to isolate and collect transcriptome profiles from five major cell types that are present in stems of the sweet sorghum Wray. Transcriptome analysis identified genes with cell-type-specific and cell-preferred expression patterns that reflect the distinct metabolic, transport, and regulatory functions of each cell type. Analysis of cell-type-specific gene regulatory networks (GRNs) revealed that unique transcription factor families contribute to distinct regulatory landscapes, where regulation is organized through various modes and identifiable network motifs. Cell-specific transcriptome data was combined with known secondary cell wall (SCW) networks to identify the GRNs that differentially activate SCW formation in vascular sclerenchyma and epidermal cells. The spatial transcriptomic dataset provides a valuable source of information about the function of different sorghum cell types and GRNs that will enable the engineering of bioenergy sorghum stems, and an interactive web application developed during this project will allow easy access and exploration of the data (https://mc-lab.shinyapps.io/lcm-dataset/)., (© 2024 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Mixed-linkage glucan (MLG) is a component of the cell wall (CW) of grasses and is composed of glucose monomers linked by β-1,3 and β-1,4 bonds. MLG is believed to have several biological functions, such as the mobilizable storage of carbohydrates and structural support of the CW. The extracellular levels of MLG are largely controlled by rates of synthesis mediated by cellulose synthase-like (CSL) enzymes, and turnover by lichenases. Economically important crops like sorghum accumulate MLG to variable levels during development. While in sorghum, like other grasses, there is one major MLG synthase (CSLF6), the identity of lichenases is yet unknown. To fill this gap, we identified three sorghum lichenases (SbLCH1-3) and characterized them in leaves in relation to the expression of SbCSLF6, and the abundance of MLG and starch. We established that SbLCH1-3 are secreted to the apoplast, consistent with a role of degrading MLG extracellularly. Furthermore, while SbCSLF6 expression was associated with cell development, the SbLCH genes exhibited distinct development-, cell-type-specific and diel-regulated expression. Therefore, our study identifies three functional sorghum MLG lichenases and highlights that MLG accumulation in sorghum leaves is likely controlled by the activity of lichenases that tune MLG levels, possibly to suit distinct cell and developmental needs in planta. These findings have important implications for improving the growth, yield, and composition of sorghum as a feedstock., (© 2023 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Objectives: The purpose of this non interventional study was to define changes in anxiety, depression, and sleep quality of medical students in their first two years of medical school while considering potential risk factors of self-reported chronic disease, sleep quantity, year of medical school and exercise habits. Since this study was ongoing during the COVID-19 pandemic, its effect was also evaluated., Participants: /METHODS: A cohort of 197 medical students was evaluated longitudinally using survey methods to quantify changes from pre-medical school and summer break to each semester in medical school throughout years one and two. This study was performed from July 2019 through June 2021. Data was analyzed using Generalized Linear Mixed Models (GLMMs) on the numeric responses of General Anxiety Disorder-7 (GAD-7), Patient Health Questionnaire-9 (PHQ-9), Sleep Quality (SQ-3) and Pittsburg Sleep Quality Index (PSQI). Additional assessments evaluated exercise habits, chronic disease, and impact of COVID-19 Pandemic. The COVID-19 Pandemic was evaluated directly in the model (pre- and post-COVID-19 period variable), and through additional questions on their perceived effect., Results: Depression, anxiety, and sleep habits displayed a cyclical change that was associated with the academic/seasonal cycle. The COVID-19 pandemic was never found significant. Medical students who had a chronic disease diagnosis and fewer hours of sleep had increased severity. Exercise did not play a role., Conclusion: Based on our sample, the main driver for depression, anxiety, and poor sleep quality appears to be the academic/seasonal cycle, while the COVID-19 pandemic did not have an impact on mental health., Competing Interests: Declaration of competing interest The authors have no financial or personal conflicts of interest to declare that are associated with the presented study., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Bioenergy sorghum is a highly productive drought tolerant C 4 grass that accumulates 80% of its harvestable biomass in approximately 4 m length stems. Stem internode growth is regulated by development, shading, and hormones that modulate cell proliferation in intercalary meristems (IMs). In this study, sorghum stem IMs were localized above the pulvinus at the base of elongating internodes using magnetic resonance imaging, microscopy, and transcriptome analysis. A change in cell morphology/organization occurred at the junction between the pulvinus and internode where LATERAL ORGAN BOUNDARIES (SbLOB), a boundary layer gene, was expressed. Inactivation of an AGCVIII kinase in DDYM (dw2) resulted in decreased SbLOB expression, disrupted IM localization, and reduced internode cell proliferation. Transcriptome analysis identified approximately 1000 genes involved in cell proliferation, hormone signaling, and other functions selectively upregulated in the IM compared with a non-meristematic stem tissue. This cohort of genes is expressed in apical dome stem tissues before localization of the IM at the base of elongating internodes. Gene regulatory network analysis identified connections between genes involved in hormone signaling and cell proliferation. The results indicate that gibberellic acid induces accumulation of growth regulatory factors (GRFs) known to interact with ANGUSTIFOLIA (SbAN3), a master regulator of cell proliferation. GRF:AN3 was predicted to induce SbARF3/ETT expression and regulate SbAN3 expression in an auxin-dependent manner. GRFs and ARFs regulate genes involved in cytokinin and brassinosteroid signaling and cell proliferation. The results provide a molecular framework for understanding how hormone signaling regulates the expression of genes involved in cell proliferation in the stem IM., (© 2022 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Stems of bioenergy sorghum (Sorghum bicolor L. Moench.), a drought-tolerant C4 grass, contain up to 50 nodes and internodes of varying length that span 4-5 m and account for approximately 84% of harvested biomass. Stem internode growth impacts plant height and biomass accumulation and is regulated by brassinosteroid signaling, auxin transport, and gibberellin biosynthesis. In addition, an AGCVIII kinase (Dw2) regulates sorghum stem internode growth, but the underlying mechanism and signaling network are unknown. Here we provide evidence that mutation of Dw2 reduces cell proliferation in internode intercalary meristems, inhibits endocytosis, and alters the distribution of heteroxylan and mixed linkage glucan in cell walls. Phosphoproteomic analysis showed that Dw2 signaling influences the phosphorylation of proteins involved in lipid signaling (PLDδ), endomembrane trafficking, hormone, light, and receptor signaling, and photosynthesis. Together, our results show that Dw2 modulates endomembrane function and cell division during sorghum internode growth, providing insight into the regulation of monocot stem development., (© 2020 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

The stems of bioenergy sorghum hybrids at harvest are > 4 m long, contain > 40 internodes and account for ~ 80% of harvested biomass. In this study, bioenergy sorghum hybrids were grown at four planting densities (~ 20,000 to 132,000 plants/ha) under field conditions for 60 days to investigate the impact shading has on stem growth and biomass accumulation. Increased planting density induced a > 2-fold increase in sorghum internode length and a ~ 22% decrease in stem diameter, a typical shade avoidance response. Shade-induced internode elongation was due to an increase in cell length and number of cells spanning the length of internodes. SbGA3ox2 (Sobic.003G045900), a gene encoding the last step in GA biosynthesis, was expressed ~ 20-fold higher in leaf collar tissue of developing phytomers in plants grown at high vs. low density. Application of GA3 to bioenergy sorghum increased plant height, stem internode length, cell length and the number of cells spanning internodes. Prior research showed that sorghum plants lacking phytochrome B, a key photoreceptor involved in shade signaling, accumulated more GA1 and displayed shade avoidance phenotypes. These results are consistent with the hypothesis that increasing planting density induces expression of GA3-oxidase in leaf collar tissue, increasing synthesis of GA that stimulates internode elongation.

Fiber optic sensors have considerable potential for measuring strains in the challenging environment posed by today's civil engineering applications. Their long-term reliability and stability are particularly important attributes for assessing, with confidence, effects such as cracking and response to normal (and abnormal) loads. However, given the fragile nature of the bare fiber, the sensors must be packaged to achieve adequate robustness but the resulting increased cost of installation can frequently limit the number of sensors which can be installed or their use may have to be ruled out altogether due to these financial constraints. There is thus potential for the development of a more affordable type of packaging and this paper describes work undertaken to produce a cost-effective and easy-to-use technique for encapsulating fiber optic sensors in resin, taking advantage of 3D printing techniques which are widely available and at low cost. This approach can be used to produce a robust, inexpensive packaged sensor system which is seen as being suitable to be extended to a wider range of uses including installation in concrete structures prior to casting. To evaluate this approach, several such 3D printed package types and geometries are described and their behavior is assessed from a programme of laboratory trials, the results of which are presented in this paper. This proof-of-concept testing has demonstrated the considerable potential which 3D printed packages have and the scope for further development and consequent use in civil engineering applications. Areas showing promise and potential, which have been identified from the work undertaken, are discussed., Competing Interests: The authors declare no conflicts of interest.

Sorghum bicolor is a drought tolerant C4 grass used for the production of grain, forage, sugar, and lignocellulosic biomass and a genetic model for C4 grasses due to its relatively small genome (approximately 800 Mbp), diploid genetics, diverse germplasm, and colinearity with other C4 grass genomes. In this study, deep sequencing, genetic linkage analysis, and transcriptome data were used to produce and annotate a high-quality reference genome sequence. Reference genome sequence order was improved, 29.6 Mbp of additional sequence was incorporated, the number of genes annotated increased 24% to 34 211, average gene length and N50 increased, and error frequency was reduced 10-fold to 1 per 100 kbp. Subtelomeric repeats with characteristics of Tandem Repeats in Miniature (TRIM) elements were identified at the termini of most chromosomes. Nucleosome occupancy predictions identified nucleosomes positioned immediately downstream of transcription start sites and at different densities across chromosomes. Alignment of more than 50 resequenced genomes from diverse sorghum genotypes to the reference genome identified approximately 7.4 M single nucleotide polymorphisms (SNPs) and 1.9 M indels. Large-scale variant features in euchromatin were identified with periodicities of approximately 25 kbp. A transcriptome atlas of gene expression was constructed from 47 RNA-seq profiles of growing and developed tissues of the major plant organs (roots, leaves, stems, panicles, and seed) collected during the juvenile, vegetative and reproductive phases. Analysis of the transcriptome data indicated that tissue type and protein kinase expression had large influences on transcriptional profile clustering. The updated assembly, annotation, and transcriptome data represent a resource for C4 grass research and crop improvement., (© 2017 The Authors The Plant Journal © 2017 John Wiley & Sons Ltd.)

Background: Bioenergy sorghum accumulates 75% of shoot biomass in stem internodes. Grass stem internodes are formed during vegetative growth and elongate in response to developmental and environmental signals. To identify genes and molecular mechanisms that modulate the extent of internode growth, we conducted microscopic and transcriptomic analyses of four successive sub-apical vegetative internodes representing different stages of internode development of the bioenergy sorghum genotype R.07020., Results: Stem internodes of sorghum genotype R.07020 are formed during the vegetative phase and their length is enhanced by environmental signals such as shade and floral induction in short days. During vegetative growth, the first visible and youngest sub-apical internode was ~0.7 cm in length, whereas the fourth fully expanded internode was ~5 cm in length. Microscopic analyses revealed that all internode tissue types including pith parenchyma and vascular bundles are present in the four successive internodes. Growth in the first two sub-apical internodes occurred primarily through an increase in cell number consistent with expression of genes involved in the cell cycle and DNA replication. Growth of the 3rd internode was associated with an increase in cell length and growth cessation in the 4th internode was associated with up-regulation of genes involved in secondary cell wall deposition. The expression of genes involved in hormone metabolism and signaling indicates that GA, BR, and CK activity decreased while ethylene, ABA, and JA increased in the 3rd/4th internodes. While the level of auxin appears to be increasing as indicated by the up-regulation of ARFs, down-regulation of TIR during development indicates that auxin signaling is also modified. The expression patterns of transcription factors are closely associated with their role during the development of the vegetative internodes., Conclusions: Microscopic and transcriptome analyses of four successive sub-apical internodes characterized the developmental progression of vegetative stem internodes from initiation through full elongation in the sorghum genotype R.07020. Transcriptome profiling indicates that dynamic variation in the levels and action of GA, CK, IAA, BR, ethylene, ABA, and JA modulate gene expression and growth during internode growth and development. This study provides detailed microscopic and transcriptomic data useful for identifying genes and molecular pathways regulating internode elongation in response to various developmental and environmental signals.

Biomass accumulated preferentially in leaves of the sweet sorghum Della until floral initiation, then stems until anthesis, followed by panicles until grain maturity, and apical tillers. Sorghum stem RNA-seq transcriptome profiles and composition data were collected for approximately 100 days of development beginning at floral initiation. The analysis identified >200 differentially expressed genes involved in stem growth, cell wall biology, and sucrose accumulation. Genes encoding expansins and xyloglucan endotransglucosylase/hydrolases were differentially expressed in growing stem internodes. Genes encoding enzymes involved in the synthesis of cellulose, lignin, and glucuronoarabinoxylan were expressed at elevated levels in stems until approximately 7 days before anthesis and then down-regulated. CESA genes involved in primary and secondary cell wall synthesis showed different temporal patterns of expression. Following floral initiation, the level of sucrose and other non-structural carbohydrates increased to approximately 50% of the stem's dry weight. Stem sucrose accumulation was inversely correlated with >100-fold down-regulation of SbVIN1, a gene encoding a vacuolar invertase. Accumulation of stem sucrose was also correlated with cessation of leaf and stem growth at anthesis, decreased expression of genes involved in stem cell wall synthesis, and approximately 10-fold lower expression of SbSUS4, a gene encoding sucrose synthase that generates UDP-glucose from sucrose for cell wall biosynthesis. Genes for mixed linkage glucan synthesis (CSLF) and turnover were expressed at high levels in stems throughout development. Overall, the stem transcription profile resource and the genes and regulatory dynamics identified in this study will be useful for engineering sorghum stem composition for improved conversion to biofuels and bio-products., (© 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.)

Keele medical students spend 113 days in general practices over our five-year programme. We collect practice data thought to indicate good quality teaching. We explored the relationships between these data and two outcomes for students; Objective Structured Clinical Examination (OSCE) scores and feedback regarding the placements. Though both are surrogate markers of good teaching, they are widely used. We collated practice and outcome data for one academic year. Two separate statistical analyses were carried out: (1) to determine how much of the variation seen in the OSCE scores was due to the effect of the practice and how much to the individual student. (2) to identify practice characteristics with a relationship to student feedback scores. (1) OSCE performance: 268 students in 90 practices: six quality indicators independently influenced the OSCE score, though without linear relationships and not to statistical significance. (2) Student satisfaction: 144 students in 69 practices: student feedback scores are not influenced by practice characteristics. The relationships between the quality indicators we collect for practices and outcomes for students are not clear. It may be that neither the quality indicators nor the outcome measures are reliable enough to inform decisions about practices' suitability for teaching.

Background: Periampullary adenocarcinoma (PA) includes: pancreatic, duodenal and ampullary adenocarcinoma; and cholangiocarcinoma. Pancreaticoduodenectomy (PD) is required for cure of PA. Previous studies demonstrated the likelihood of cure increases when a microscopically negative (R0) margin is achieved. Clearance of the superior mesenteric artery (SMA) margin has been identified as the most critical margin in PD. Some authors have emphasized the importance of certain techniques to clear the SMA margin. Neither the degree to which these techniques have been incorporated nor their impact on margin status and survival has been described. We hypothesized that use of techniques focusing on clearing the SMA margin would result in higher R0 resection rates and improved survival after PD in patients with PA., Methods: A retrospective study was performed on patients from 1/1/1985 until 7/31/2007. Data on patient demographics, clinical presentation, preoperative treatment, operative technique, margins, and postoperative outcomes were collected. Ninety-three patients were identified for inclusion in the study. Three approximately equal groups were created for analysis., Results: The overall survival (OS) for the entire cohort was 19 months and was not different among the groups studied. Margins were microscopically negative in 81% of cases. The percentage of node-positive cases increased during the time period, as did the number of lymph nodes (LNs) examined (P=0.017). The use of pylorus-preserving PD decreased (P=0.001) while resection of the superior mesenteric/portal vein (SMV/PV) increased during the study period. We observed an increase in descriptions of the clearance of the anterior aspect of the aorta and inferior vena cava (IVC), dissection to the right side of the SMA, dissection to the origin of the SMA and intra-operative identification of the SMA margin. Dissecting to the SMA did not change the likelihood of achieving an R0 margin. OS was improved after R0 resections (R0: 21 months vs. R1/2: 10 months) but this difference was not statistically significant (P=0.099). There was no association between margin status and OS. Changes in the pathology reporting of margins were observed, with statistically significant increases in the percentage of cases in which the SMA, common bile duct and pancreatic neck margins were separately reported. However, the SMA margin was separately reported in only 26% of pathology reports., Conclusions: The operative techniques used in PD at this institution have changed over time. The increasing frequency of dissection to the SMA and identification of the SMA margin by both surgeon and pathologist suggest an increased attention to the SMA margin. This shift did not result in significant improvements in survival or margin status, but it is consistent with the recognition of the importance of the SMA margin. Our analysis has also identified areas of potential improvement in the ways in which operative and pathology reports for PD are generated.

Many surgeons prefer to perform endoscopic retrograde cholangiopancreatography (ERCP) before cholecystectomy, specifically in patients at significant risk of having biliary pathology. However, a preoperative diagnostic ERCP, without the use of an endoscopic ultrasound or magnetic retrograde cholangiopancreatoscopy, remains controversial. This is the result of the risk of either performing an unnecessary procedure and/or the development of post-ERCP pancreatitis (PEP). We performed a retrospective review of all surgeon-performed ERCPs at our institution between July 2011 and May 2013. This was done to examine patients who had pericholecystectomy ERCP. We had 550 ERCPs performed at our institution during this time period, 169 of which were pericholecystectomy procedures. We divided the 169 patients who had a diagnostic procedure (Diagnostic group) from those who had known biliary pathology before intervention (Therapeutic group). As a result, 34 patients (20.1%) were placed in the Diagnostic group and 135 patients (79.9%) in the Therapeutic group. Of the 34 Diagnostic patients, four (11.8%) developed PEP. Fifteen (44.1%) had unnecessary procedures, two of which had PEP (2.9%). Of the 135 ERCPs in the Therapeutic group, 18 patients (13.4%) developed PEP. Five of the 11 who had unnecessary procedures developed PEP. Based on the low incidence of complications, diagnostic ERCP has an acceptable rate of pancreatitis and/or unnecessary procedures when performed in highly selected patients and before cholecystectomy when compared with patients undergoing therapeutic ERCP. However, more aggressive use of diagnostic imaging before ERCP should be adopted given the number of unnecessary procedures performed.

Sorghum is emerging as an excellent genetic model for the design of C4 grass bioenergy crops. Annual energy Sorghum hybrids also serve as a source of biomass for bioenergy production. Elucidation of Sorghum's flowering time gene regulatory network, and identification of complementary alleles for photoperiod sensitivity, enabled large-scale generation of energy Sorghum hybrids for testing and commercial use. Energy Sorghum hybrids with long vegetative growth phases were found to accumulate more than twice as much biomass as grain Sorghum, owing to extended growing seasons, greater light interception, and higher radiation use efficiency. High biomass yield, efficient nitrogen recycling, and preferential accumulation of stem biomass with low nitrogen content contributed to energy Sorghum's elevated nitrogen use efficiency. Sorghum's integrated genetics-genomics-breeding platform, diverse germplasm, and the opportunity for annual testing of new genetic designs in controlled environments and in multiple field locations is aiding fundamental discovery, and accelerating the improvement of biomass yield and optimization of composition for biofuels production. Recent advances in wide hybridization between Sorghum and other C4 grasses could allow the deployment of improved genetic designs of annual energy Sorghums in the form of wide-hybrid perennial crops. The current trajectory of energy Sorghum genetic improvement indicates that it will be possible to sustainably produce biofuels from C4 grass bioenergy crops that are cost competitive with petroleum-based transportation fuels., (© The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Background: We recently proffered that a new syndrome persistent inflammation, immunosuppression, and catabolism syndrome (PICS) has replaced late multiple-organ failure as a predominant phenotype of chronic critical illness. Our goal was to validate this by determining whether severely injured trauma patients with complicated outcomes have evidence of PICS at the genomic level., Methods: We performed a secondary analysis of the Inflammation and Host Response to Injury database of adults with severe blunt trauma. Patients were classified into complicated, intermediate, and uncomplicated clinical trajectories. Existing genomic microarray data were compared between cohorts using Ingenuity Pathways Analysis. Epidemiologic data and outcomes were also analyzed between cohorts on admission, Day 7, and Day 14., Results: Complicated patients were older, were sicker, and required increased ventilator days compared with the intermediate/uncomplicated patients. They also had persistent leukocytosis as well as low lymphocyte and albumin levels compared with uncomplicated patients. Total white blood cell leukocyte analysis in complicated patients showed that overall genome-wide expression patterns and those patterns on Days 7 and 14 were more aberrant from control subjects than were patterns from uncomplicated patients. Complicated patients also had significant down-regulation of adaptive immunity and up-regulation of inflammatory genes on Days 7 and 14 (vs. magnitude in fold change compared with control and in magnitude compared with uncomplicated patients). On Day 7, complicated patients had significant changes in functional pathways involved in the suppression of myeloid cell differentiation, increased inflammation, decreased chemotaxis, and defective innate immunity compared with uncomplicated patients and controls. Subset analysis of monocyte, neutrophil, and T-cells supported these findings., Conclusion: Genomic analysis of patients with complicated clinical outcomes exhibit persistent genomic expression changes consistent with defects in the adaptive immune response and increased inflammation. Clinical data showed persistent inflammation, immunosuppression, and protein depletion. Overall, the data support the hypothesis that patients with complicated clinical outcomes are exhibiting PICS., Level of Evidence: Epidemiologic study, level III.

Background: Recent publications have identified positive associations between numbers of lymph nodes pathologically examined and five-year overall survival (5-yr OS) in colon cancer. However, focused examinations of relationships between survival of rectal cancer and lymph node counts are less common. We conducted a single institution, retrospective review of rectal cancer resections to determine whether lymph node counts correlated with 5-yr OS and to explore the relationship between lymph node counts and various clinical and pathologic factors., Methods: A retrospective review of our institutional tumor registry identified 159 patients with AJCC Stage 1, 2, or 3 rectal cancers that underwent surgical resection at our institution over eleven years. Univariate analysis was used to explore the relationship between lymph node counts and age, AJCC Stage, time period of diagnosis, preoperative radiotherapy, and performance of TME. Survival analysis was performed by the Kaplan-Meier method and the Cox proportional hazards model., Results: In univariate analysis, there was an association between increased lymph node counts and age <70, higher stage, and diagnosis during the later portion of the study period [all P-values <0.05]. Lymph node counts were not associated with survival in Kaplan-Meier analysis or in multivariate Cox proportional hazards analysis., Conclusions: Increasing lymph node counts improve survival and the accuracy of colorectal cancer staging. The body of literature recommends identical minimum lymph node counts in both colon and rectal cancer. In our study, which exclusively examined rectal cancer, we could not demonstrate that increased lymph node counts were associated with improved survival.

For the past thirty years, since IL-1β and TNFα were first cloned, there have been efforts to measure plasma cytokine concentrations in patients with severe sepsis and trauma, and to use these measurements to predict clinical outcome and response to therapies. The numbers of cytokines and chemokines that have been measured in the plasma have literally exploded with the development of multiplex immune approaches. Dozens of relatively small cohort studies have shown plasma cytokine concentrations correlating with outcome in sepsis and trauma. Despite what appears to be a consensus that plasma cytokine concentrations should be useful in the clinical setting, only two cytokines, IL-6 and procalcitonin, have approached routine clinical use. IL-6 has been used as a research tool for entry into sepsis-intervention trials, while procalcitonin is being used clinically at a large number of institutions to distinguish sepsis from other inflammatory processes. For most cytokines, the relative lack of sensitivity and specificity of individual or multiplex cytokine measurements has hindered their utility to predict clinical trajectory in individual patients. The problem rests with a general misunderstanding of cytokine biology, failing to appreciate the general paracrine nature of these mediators, the presence of binding proteins, chaperones and inhibitors in the plasma, and the rapid clearance of these proteins by binding to cell receptors and clearance predominantly by the kidney. The future of using plasma cytokine measurements as an indicator of sepsis/trauma severity or predicting outcome is generally behind us, although there is optimism that procalcitonin measurements may ultimately prove to have utility in the diagnosis of severe sepsis., (Copyright © 2013 Elsevier Inc. All rights reserved.)

Background: The management of surgical sepsis is challenging because of the complexity of interventions. The authors therefore created a computerized clinical decision support program to facilitate this process, with the goal of improving abdominal sepsis mortality., Methods: The authors evaluated a prospective database for all patients requiring surgery for abdominal sepsis. Patient demographics, Acute Physiology and Chronic Health Evaluation II score, sepsis source, and hospital mortality data were obtained. Observed mortality was compared with predicted mortality using Fisher's exact test., Results: Eighty-seven patients met the inclusion criteria. The average age was 59 ± 17.0 years, and 39% were men. The most common source of infection was the colon (45%). The average Acute Physiology and Chronic Health Evaluation II score was 27.6 ± 9.72. The overall actual mortality rate for the cohort was 24% compared with a predicted Acute Physiology and Chronic Health Evaluation II mortality of 62.5% (P < .0001)., Conclusion: The use of computerized clinical decision support results in significantly improved survival in patients with intra-abdominal surgical sepsis., (Copyright © 2010 Elsevier Inc. All rights reserved.)

Although ductal carcinoma in situ (DCIS) does not require axillary evaluation, controversy exists regarding the use of sentinel lymph node biopsy (SLNB) in patients with DCIS diagnosed by core needle biopsy (CNB). Advocates of concomitant SLNB and lumpectomy cite the low morbidity of SLNB, the high rate of invasive ductal carcinoma in resected specimens, and the positive nodes found in 1 to 2 per cent of patients with resected DCIS despite finding no invasive component. Opponents of this practice cite the complication risk and the improbability of clinically significant axillary recurrence. We therefore proposed to determine our rate of invasive cancer in DCIS diagnosed by CNB and to determine whether SLNB at first operation would decrease return to the operating room. We retrospectively reviewed patients diagnosed with DCIS by CNB from 2003 to 2008. Standard clinicopathological data were collected and analyzed. In 110 patients, the prevalence of invasive cancer on final resection pathology was 13.6 per cent (15 of 110). Of those patients with invasive cancer, 93 per cent (14 of 15) had high-grade DCIS (P = 0.077) by CNB. Seventeen per cent (14 of 82) of patients with high-grade DCIS had invasive cancer. Of 34 patients with SLNB, three (9%) had positive nodes. Fifteen patients required re-excision to obtain negative margins, including 13 patients with invasive cancer. Five patients (4.5%) were spared additional operative intervention by initially performing SLNB. We suggest using concomitant SLNB when a high clinical suspicion of invasive cancer exists, in the presence of a palpable mass, or when mastectomy precludes future SLNB. Intraoperative margin assessment is needed to avoid return to the operating room.

Background: Sepsis is the leading cause of mortality in noncoronary intensive care units. Recent evidence based guidelines outline strategies for the management of sepsis and studies have shown that early implementation of these guidelines improves survival. We developed an extensive logic-based sepsis management protocol; however, we found that early recognition of sepsis was a major obstacle to protocol implementation. To improve this, we developed a three-step sepsis screening tool with escalating levels of decision making. We hypothesized that aggressive screening for sepsis would improve early recognition of sepsis and decrease sepsis-related mortality by insuring early appropriate interventions., Methods: Patients admitted to the surgical intensive care unit were screened twice daily by our nursing staff. The initial screen assesses the systemic inflammatory response syndrome parameters (heart rate, temperature, white blood cell count, and respiratory rate) and assigns a numeric score (0-4) for each. Patients with a score of > or = 4 screened positive proceed to the second step of the tool in which a midlevel provider attempts to identify the source of infection. If the patients screens positive for both systemic inflammatory response syndrome and an infection, the intensivist was notified to determine whether to implement our sepsis protocol., Results: Over 5 months, 4,991 screens were completed on 920 patients. The prevalence of sepsis was 12.2%. The screening tool yielded a sensitivity of 96.5%, specificity of 96.7%, a positive predictive value of 80.2%, and a negative predictive value of 99.5%. In addition, sepsis-related mortality decreased from 35.1% to 23.3%., Conclusions: The three step sepsis screening tool is a valid tool for the early identification of sepsis. Implementation of this tool and our logic-based sepsis protocol has decreased sepsis-related mortality in our SICU by one third.

Background: The pathogenesis of multiple organ failure (MOF) in trauma patients may involve the gastrointestinal tract, but its exact origins remain elusive. In a prospective study, the gastric fluid of major torso trauma patients was examined for evidence of duodenogastric reflux and potential gastric injury, and was compared with patient outcomes regarding MOF., Methods: Patient samples were collected daily for 4 days by nasogastric tube and analyzed for pH, hemoglobin, and bile acid. Blood was collected for analysis of C-reactive protein (CRP). Outcomes were recorded for the presence or absence of MOF., Results: The results showed that most patients exhibited alkaline gastric contents (pH >/=4.9) and elevated levels of hemoglobin immediately after the trauma. Although non-MOF patients demonstrated a decline of both mean gastric pH and bleeding by day 4, MOF patients maintained significant elevations in pH during this time period. Mean total bile acid levels were increased in all patients, signifying the presence of duodenogastric reflux. However, there were no clear differences in mean bile acid concentrations between MOF and non-MOF patients over time, although MOF patients tended to exhibit higher levels. All patients showed a progressive rise in serum CRP during the first 24 hours after trauma, which was maintained for 4 days. The initial rise in serum CRP in MOF patients was delayed compared with that in non-MOF patients., Conclusions: We conclude that duodenogastric reflux occurs in trauma patients in the first few days after trauma and may contribute to elevated gastric pH and bleeding. Further study is needed to verify whether monitoring the gastric juice of trauma patients during the first several days of hospitalization, for alkaline pH and excessive blood in the gastric lumen, could lead to better assessments of patient status.

Background: Feeding the hemodynamically unstable patient is increasingly practiced, yet few data exist on its safety. Because enteral glutamine is protective to the gut in experimental models of shock and improves clinical outcomes, it may benefit trauma patients undergoing shock resuscitation and improve tolerance if administered early. This pilot study aimed to evaluate gastrointestinal tolerance and safety of enteral feeding with glutamine, beginning during shock resuscitation in severely injured patients., Methods: In a prospective randomized trial, 20 patients were randomly assigned to either an enteral glutamine group (n = 10) or a control group (n = 10). Patients with severe trauma meeting standardized shock resuscitation criteria received enteral glutamine 0.5 g/kg/d during the first 24 hours of resuscitation and 10 days thereafter. Immune-enhancing diet began on postinjury day 1, with a target of 25 kcal/kg/d. Control patients received isonitrogenous whey powder plus immune-enhancing diet. Tolerance (vomiting, nasogastric output, diarrhea, and distention) was assessed throughout the study., Results: Glutamine was well tolerated and no adverse events occurred. Treated patients had significantly fewer instances of high nasogastric output (5 vs 23; p = .010), abdominal distention (3 vs 12; p = .021), and total instances of intolerance (8 vs 42; p = .011). Intensive care unit (ICU) and hospital length of stay were comparable. Control patients required supplemental parenteral nutrition (PN) to meet goals at day 7., Conclusions: Enteral glutamine administered during active shock resuscitation and through the early postinjury period is safe and enhances gastrointestinal tolerance. A large clinical trial is warranted to determine if enteral glutamine administered to the hemodynamically unstable patient can reduce infectious morbidity and mortality.

The application of genome-wide expression analysis to a large-scale, multicentered program in critically ill patients poses a number of theoretical and technical challenges. We describe here an analytical and organizational approach to a systematic evaluation of the variance associated with genome-wide expression analysis specifically tailored to study human disease. We analyzed sources of variance in genome-wide expression analyses performed with commercial oligonucleotide arrays. In addition, variance in gene expression in human blood leukocytes caused by repeated sampling in the same subject, among different healthy subjects, among different leukocyte subpopulations, and the effect of traumatic injury, were also explored. We report that analytical variance caused by sample processing was acceptably small. Blood leukocyte gene expression in the same individual over a 24-h period was remarkably constant. In contrast, genome-wide expression varied significantly among different subjects and leukocyte subpopulations. Expectedly, traumatic injury induced dramatic changes in apparent gene expression that were greater in magnitude than the analytical noise and interindividual variance. We demonstrate that the development of a nation-wide program for gene expression analysis with careful attention to analytical details can reduce the variance in the clinical setting to a level where patterns of gene expression are informative among different healthy human subjects, and can be studied with confidence in human disease.

The metabolic syndrome (MS) is a clustering of cardiovascular risk factors, with insulin resistance as a major feature. This syndrome has been variously defined, but generally consists of 3 or more of the following components: hyperglycemia, hypertension, hypertriglyceridemia, low HDL, and increased abdominal circumference and/or BMI at >30 kg/m(2). The WHO criteria require the presence of insulin resistance to make the diagnosis. The current review focuses particularly on the association of the MS and the proinflammatory state as well as treatment options to prevent the development of coronary heart disease (CHD). Chronic inflammation is frequently associated with the MS. Inflammatory markers that have been associated with MS include hs-CRP, TNF-alpha, fibrinogen, and IL-6, among others. The link between inflammation and the MS is not fully understood. One postulated mechanism is that these cytokines are released into the circulation by adipose tissue, stimulating hepatic CRP production. The prothrombotic molecule PAI-1 is also increased in the MS. Adiponectin, produced exclusively by adipocytes, is decreased in obesity. The association of these proinflammatory and prothrombotic markers with the MS is discussed in detail. The general goals of treatment of the MS are prevention of CHD events and diabetes if not already present. The approach to treatment of those with the MS should include lifestyle changes, including weight loss and exercise as well as appropriate pharmacological therapies. Certain medications, which may be used in persons with MS, have been shown to have beneficial effects on clinical outcome and/or anti-inflammatory effects.