bluuebunny/crossref_metadata_2025 huggingface dataset:
The WalRK (YycFG) and σI RsgI regulators cooperate to control CwlO and LytE expression in exponentially growing and stressed Bacillus subtilis cells
Authors: Salzberg Letal I. , Powell Leagh , Hokamp Karsten , Botella Eric , Noone David , Devine Kevin M.
Published: November 2012

The WalRK (YycFG) two‐component system co‐ordinates cell wall metabolism with growth by regulating expression of autolysins and proteins that modulate autolysin activity. Here we extend its role in cell wall metabolism by showing that WalR binds to 22 chromosomal loci in vivo. Among the newly identified genes of the WalRK bindome are those that encode the wall‐associated protein WapA, the penicillin binding proteins PbpH and Pbp5, the minor teichoic acid synthetic enzymes GgaAB and the regulators σI RsgI. The putative WalR binding sequence at many newly identified binding loci deviates from the previously defined consensus. Moreover, expression of many newly identified operons is controlled by multiple regulators. An unusual feature is that WalR binds to an extended DNA region spanning multiple open reading frames at some loci. WalRK directly activates expression of the sigIrsgI operon from a newly identified σA promoter and represses expression from the previously identified σI promoter. We propose that this regulatory link between WalRK and σI RsgI expression ensures that the endopeptidase requirement (CwlO or LytE) for cell viability is fulfilled during growth and under stress conditions. Thus the WalRK and σI RsgI regulatory systems cooperate to control cell wall metabolism in growing and stressed cells.
Genomic DNA‐based absolute quantification of gene expression in Vitis
Authors: Gambetta Gregory A. , McElrone Andrew J. , Matthews Mark A.
Published: November 2012

Many studies in which gene expression is quantified by polymerase chain reaction represent the expression of a gene of interest (GOI) relative to that of a reference gene (RG). Relative expression is founded on the assumptions that RG expression is stable across samples, treatments, organs, etc., and that reaction efficiencies of the GOI and RG are equal; assumptions which are often faulty. The true variability in RG expression and actual reaction efficiencies are seldom determined experimentally. Here we present a rapid and robust method for absolute quantification of expression in Vitis where varying concentrations of genomic DNA were used to construct GOI standard curves. This methodology was utilized to absolutely quantify and determine the variability of the previously validated RG ubiquitin (VvUbi) across three test studies in three different tissues (roots, leaves and berries). In addition, in each study a GOI was absolutely quantified. Data sets resulting from relative and absolute methods of quantification were compared and the differences were striking. VvUbi expression was significantly different in magnitude between test studies and variable among individual samples. Absolute quantification consistently reduced the coefficients of variation of the GOIs by more than half, often resulting in differences in statistical significance and in some cases even changing the fundamental nature of the result. Utilizing genomic DNA‐based absolute quantification is fast and efficient. Through eliminating error introduced by assuming RG stability and equal reaction efficiencies between the RG and GOI this methodology produces less variation, increased accuracy and greater statistical power.
Increased prevalence of dhfr and dhps mutants at delivery in Malawian pregnant women receiving intermittent preventive treatment for malaria
Authors: Lin Jessica T. , Mbewe Bernard , Taylor Steve M. , Luntamo Mari , Meshnick Steven R. , Ashorn Per
Published: November 2012

In the context of an Intermittent preventive treatment (IPTp) trial for pregnant women in Malawi, Plasmodium falciparum samples from 85 women at enrolment and 35 women at delivery were genotyped for mutations associated with sulfadoxine–pyrimethamine resistance. The prevalence of the highly resistant haplotype with mutations at codons 51 and 108 of dihydrofolate reductase (dhfr) and codons 437 and 540 of dihydropteroate synthase (dhps) increased from 81% at enrolment to 100% at delivery (P = 0.01). Pregnant women who were smear‐positive at enrolment were more likely to have P. falciparum parasitemia at delivery. These results lend support to concerns that IPTp use may lead to increased drug resistance in pregnant women during pregnancy and emphasise the importance of screening pregnant women for malaria parasites in areas with prevalent SP resistance even when they are already on IPTp.
Preliminary studies developing methods for the control of Chrysomya putoria, the African latrine fly, in pit latrines in The Gambia
Authors: Lindsay T. C. , Jawara M. , D'Alessandro U. , Pinder M. , Lindsay S. W.
Published: November 2012

Objective

To explore ways of controlling Chrysomya putoria, the African latrine fly, in pit latrines. As pit latrines are a major source of these flies, eliminating these important breeding sites is likely to reduce village fly populations, and may reduce the spread of diarrhoeal pathogens.

Methods

We treated 24 latrines in a Gambian village: six each with (i) pyriproxyfen, an insect juvenile hormone mimic formulated as Sumilarv® 0.5G, a 0.5% pyriproxyfen granule, (ii) expanded polystyrene beads (EPB), (iii) local soap or (iv) no treatment as controls. Flies were collected using exit traps placed over the drop holes, weekly for five weeks. In a separate study, we tested whether latrines also function as efficient flytraps using the faecal odours as attractants. We constructed six pit latrines each with a built‐in flytrap and tested their catching efficiency compared to six fish‐baited box traps positioned 10 m from the latrine. Focus group discussions conducted afterwards assessed the acceptability of the flytrap latrines.

Results

Numbers of emerging C. putoria were reduced by 96.0% (95% CIs: 94.5–97.2%) 4–5 weeks after treatment with pyriproxyfen; by 64.2% (95% CIs: 51.8–73.5%) after treatment with local soap; by 41.3% (95% CIs = 24.0–54.7%) after treatment with EPB 3–5 weeks after treatment. Flytraps placed on latrines collected C. putoria and were deemed acceptable to local communities.

Conclusions

Sumilarv 0.5G shows promise as a chemical control agent, whilst odour‐baited latrine traps may prove a useful method of non‐chemical fly control. Both methods warrant further development to reduce fly production from pit latrines. A combination of interventions may prove effective for the control of latrine flies and the diseases they transmit.
Verification of numerical study of scour around spur dikes using experimental data
Authors: Karami Hojat , Basser Hossein , Ardeshir Abdollah , Hosseini Seyyed Hadi
Published: November 2012

Scour phenomenon around a series of impermeable, nonsubmerged spur dikes has been investigated with both experimental and numerical methods. The experiments were conducted under different states of flow intensity (U/Ucr). The scour geometry was measured with a high‐resolution laser bed‐profiler (LBP). For the numerical simulation phase, a three‐dimensional computational fluid dynamics (CFD) model, namely SSIIM 2.0, was used to compute the sediment transport around the spur dikes. The numerical model was based on the finite‐volume method. Two turbulence models, namely k‐ε standard and k‐ε with re‐normalization group (RNG) extensions, were used to predict turbulence, and the k‐ε model with some RNG extensions was selected because of its best agreement with the measurements. Furthermore, a variety of grids and empirical sediment transport equations were used to find the best state for simulation of scour around a series of spur dikes. Finally, a comparison between experimental and numerical results was carried out to verify the CFD model.
Numerical Simulation of a Complete Gas Turbine Engine With Wet Compression
Authors: Sun Lanxin , Zheng Qun , Li Yijin , Luo Mingcong , Bhargava Rakesh K.
Published: November 2012

In this paper, a thorough flow simulation of a small turbojet engine has been carried out to predict the engine performance as a result of water injected at the compressor inlet. Wet compression will not only change compressor performance characteristic map, but also has effects on both the combustor and the turbine sections. The match between the turbojet engine components, that is the compressor, combustor and turbine, will shift to a new operating point. In this paper, we present a steady-state numerical simulation of the entire gas turbine with wet compression in order to evaluate the effects on the gas turbine performance. Compared with the dry case, the results of wet cases show increased values of compressor compression ratios, turbine expansion ratios, intake mass flowrates, and engine thrusts including a decreased amount of specific fuel consumption. The wet compression reduces NOx production in the combustor, which is also simulated and with results presented. The study also indicates that the water mass flow rate and droplet diameter are key factors impacting the engine performance.
Simple Parametric Model for Quick Assessment of IGCC
Performance
Authors: Gülen S. Can , Driscoll Ann V.
Published: November 2012

Even though almost all components of an integrated gasification combined cycle (IGCC) power plant are proven and mature technologies, the sheer number of them, the wide variety of competing technologies (e.g., gasifiers, gas clean-up systems, heat recovery options), and system integration options (e.g., cryogenic air separation unit and the gas turbine), including the recent addition of carbon capture and sequestration (CCS) with its own technology and integration options, render fundamental IGCC performance analysis a monumental task. Almost all published studies utilize highly complex chemical process and power plant heat balance software, including commercially available packages and in-house proprietary codes. This makes an objective assessment of comparable IGCC plant designs, performance (and cost), and other perceived advantage claims (IGCC versus other technologies, too) very difficult, if not impossible. This paper develops a coherent simplified parametric model based on fully physics-based grounds to be used for quick design performance assessment of a large variety of IGCC power plants with and without CCS. Technology parameters are established from complex model runs and supplemented by extensive literature search. The model is tested using published data to establish its confidence interval and is satisfactory to carry conceptual design analysis at a high level to identify promising alternatives and development areas and assess the realism in competing claims.
A Numerical Study on the Turbulent Schmidt Numbers in a Jet in Crossflow
Authors: Ivanova Elizaveta M. , Noll Berthold E. , Aigner Manfred
Published: November 2012

This work presents a numerical study on the turbulent Schmidt numbers in jets in crossflow. This study contains two main parts. In the first part, the problem of the proper choice of the turbulent Schmidt number in the Reynolds-averaged Navier-Stokes (RANS) jet in crossflow mixing simulations is outlined. The results of RANS employing the shear-stress transport (SST) model of Menter and its curvature correction modification and different turbulent Schmidt number values are validated against experimental data. The dependence of the optimal value of the turbulent Schmidt number on the dynamic RANS model is studied. Furthermore, a comparison is made with the large-eddy simulation (LES) results obtained using the wall-adapted local eddy viscosity (WALE) model. The accuracy given by LES is superior in comparison to RANS results. This leads to the second part of the current study, in which the time-averaged mean and fluctuating velocity and scalar fields from LES are used for the evaluation of the turbulent viscosities, turbulent scalar diffusivities, and the turbulent Schmidt numbers in a jet in crossflow configuration. The values obtained from the LES data are compared with those given by the RANS modeling. The deviations are discussed, and the possible ways for the RANS model improvements are outlined.
Numerical Investigation of the Parameter Governing the Ignitability of a Spray Flame
Authors: Boyde J. M. , Le Clercq P. , Di Domenico M. , Rachner M. , Gebel G. C. , Mosbach T. , Aigner M.
Published: November 2012

This paper contains a numerical examination concerning the ignition behavior of a spray nozzle mounted in a rectangular channel under atmospheric conditions, which is run with Jet A-1. On the basis of a comprehensive data set of experimental results, the numerical approach is verified primarily by means of a comparison of the flame growth and position after ignition. In the following, several distinct igniter positions and boundary condition settings are simulated. The conditions that prevail at the location of the ignition are investigated with respect to how they influence the ignition process. Due to changes in the fuel placement and flow field characteristics, which follow from alternating the boundary conditions, such as air and fuel mass flow, ignition is either promoted or impeded. The underlying causes that can lead to a success or failure of the ignition are analyzed. The ignition in the experiment is achieved through a laser-induced breakdown, which is modeled through a turbulent flame speed closure combustion model with an additional spark ignition extension. A comparison with the ignition statistics from the experiment shows that numerical tools can be used to determine preferential boundary conditions and igniter locations to accomplish a successful ignition in multiphase flow configurations.
Pretreatment patient‐specific IMRT quality assurance: A correlation study between gamma index and patient clinical dose volume histogram
Authors: Stasi M. , Bresciani S. , Miranti A. , Maggio A. , Sapino V. , Gabriele P.
Published: November 2012

Purpose:

The aim of this work is to investigate the predictive power of a common conventional intensity modulated radiation therapy (IMRT) quality assurance (QA) performance metric, the gamma passing rate (%GP), through the analysis of the sensitivity and of the correlation between %GP and different dose discrepancies between planned dose‐volume histogram (DVH) and perturbed DVH. The perturbed DVH is calculated by using a dedicated software, 3DVH (Sun Nuclear Corporation, Melbourne, FL), which is able to modify the dose distribution calculated by the treatment planning system (TPS) according to the dose discrepancies detected with planar measurements in order to predict the delivered 3D dose distribution in the patient.

Methods:

Twenty‐seven high‐risk prostate cancer (PP) patients and 15 head and neck (HN) cancer patients, treated with IMRT technique, were analyzed. Pretreatment verifications were performed for all patients’ plans by acquiring planar dose distributions of each treatment field with 2D‐diode array. Measured dose distributions were compared to the calculated ones using the gamma index (GI) method applying both global (Van Dyk) and local normalization, and %GP were generated for each pair of planar doses using the following acceptance criteria: 1%/1, 2%/2, and 3%/3 mm. Planar dose distributions acquired during pretreatment verifications, together with patientˈs DICOM RT plan, RT structure set, and RT dose files from TPS were loaded into the 3DVH software. Percentage dose differences (%DE) between DVHs, obtained by TPS and by 3DVH, were calculated; statistical correlation between %DE and %GP was studied by using Pearsonˈs correlation coefficient (r). This analysis was performed, for each patient, on planning target volumes and on some typical organs at risk of the prostatic and head and neck anatomical district. The sensitivity was calculated to correctly identify the pretreatment plans with high dose errors and to quantify the incidence of false negatives, on varying the gamma index method.

Results:

Analysis of %DE vs %GP showed that there were only weak correlations (Pearsonˈsr‐values < 0.8). The results also showed numerous instances of false negatives (cases where high IMRT QA passing rates did not imply good agreement in anatomy dose metrics) and the reverse, mainly for the 3%/3 mm global gamma passing rate.

Conclusions:

The lack of correlation between conventional IMRT QA performance metrics gamma passing rates and dose errors in DVHs values and the low sensitivity of 3%/3 mm global gamma method show that the most common published acceptance criteria have disputable predictive power for per‐patient IMRT QA.
Long-Term Immune Responses to Coxiella burnetii after Vaccination
Authors: Kersh Gilbert J. , Fitzpatrick Kelly A. , Self Joshua S. , Biggerstaff Brad J. , Massung Robert F.
Published: November 2012

Q fever is a zoonotic disease caused by infection with the bacterium
Coxiella burnetii
. Infection with
C. burnetii
results in humoral and cellular immune responses, both of which are thought to contribute to protection against subsequent infection. Whole-cell formalin-inactivated vaccines have also been shown to induce both humoral and cellular immunity and provide protection. Whether measurement of cellular or humoral immunity is a better indicator of immune protection is not known, and the duration of immunity induced by natural infection or vaccination is also poorly understood. To better understand the measurement and duration of
C. burnetii
immunity, 16 people vaccinated against Q fever (0.2 to 10.3 years before analysis) and 29 controls with a low risk of Q fever exposure were tested for immune responses to
C. burnetii
by an indirect fluorescent-antibody test (IFA) to measure circulating antibody and by a gamma interferon release assay (IGRA) to measure cellular immunity. Among vaccinated subjects, the IFA detected antibodies in 13/16, and the IGRA also detected positive responses in 13/16. All of the vaccinated subjects had a positive response in at least one of the assays, whereas 8/29 control subjects were positive in at least one assay. There was not a correlation between time since vaccination and responses in these assays. These results show that IFA and IGRA perform similarly in detection of
C. burnetii
immune responses and that Q fever vaccination establishes long-lived immune responses to
C. burnetii
.
Prevalence of and Risk Factors for Biliary Carriage of Bacteria Showing Worrisome and Unexpected Resistance Traits
Authors: Maseda E. , Maggi G. , Gomez-Gil R. , Ruiz G. , Madero R. , Garcia-Perea A. , Aguilar L. , Gilsanz F. , Rodriguez-Baño J.
Published: November 2012

Data on biliary carriage of bacteria and, specifically, of bacteria with worrisome and unexpected resistance traits (URB) are lacking. A prospective study (April 2010 to December 2011) was performed that included all patients admitted for <48 h for elective laparoscopic cholecystectomy in a Spanish hospital. Bile samples were cultured and epidemiological/clinical data recorded. Logistic regression models (stepwise) were performed using bactobilia or bactobilia by URB as dependent variables. Models (
P
< 0.001) showing the highest
R
2
values were considered. A total of 198 patients (40.4% males; age, 55.3 ± 17.3 years) were included. Bactobilia was found in 44 of them (22.2%). The presence of bactobilia was associated (
R
2
Cox, 0.30) with previous biliary endoscopic retrograde cholangiopancreatography (ERCP) (odds ratio [OR], 8.95; 95% confidence interval [CI], 2.96 to 27.06;
P
< 0.001), previous admission (OR, 2.82; 95% CI, 1.10 to 7.24;
P
= 0.031), and age (OR, 1.09 per year; 95% CI, 1.05 to 1.12;
P
< 0.001). Ten out of the 44 (22.7%) patients with bactobilia carried URB: 1
Escherichia coli
isolate (CTX-M), 1
Klebsiella pneumoniae
isolate (OXA-48), 3 high-level gentamicin-resistant enterococci, 1 vancomycin-resistant
Enterococcus
isolate, 3
Enterobacter cloacae
strains, and 1 imipenem-resistant
Pseudomonas aeruginosa
strain. Bactobilia by URB (versus those by non-URB) was only associated (
R
2
Cox, 0.19) with previous ERCP (OR, 11.11; 95% CI, 1.98 to 62.47;
P
= 0.006). For analyses of patients with bactobilia by URB versus the remaining patients, previous ERCP (OR, 35.284; 95% CI, 5.320 to 234.016;
P
< 0.001), previous intake of antibiotics (OR, 7.200; 95% CI, 0.962 to 53.906;
P
= 0.050), and age (OR, 1.113 per year of age; 95% CI, 1.028 to 1.206;
P
= 0.009) were associated with bactobilia by URB (
R
2
Cox, 0.19;
P
< 0.001). Previous antibiotic exposure (in addition to age and previous ERCP) was a risk driver for bactobilia by URB. This may have implications in prophylactic/therapeutic measures.
Phomopsis bougainvilleicola Prepatellar Bursitis in a Renal Transplant Recipient
Authors: Cariello Paloma F. , Wickes Brian L. , Sutton Deanna A. , Castlebury Lisa A. , Levitz Stuart M. , Finberg Robert W. , Thompson Elizabeth H. , Daly Jennifer S.
Published: November 2012

Prepatellar bursitis is typically a monomicrobial bacterial infection. A fungal cause is rarely identified. We describe a 61-year-old man who had received a renal transplant 21 months prior to presentation whose synovial fluid and surgical specimens grew
Phomopsis bougainvilleicola
, a pycnidial coelomycete.
The GEF1 Proton-Chloride Exchanger Affects Tombusvirus Replication via Regulation of Copper Metabolism in Yeast
Authors: Sasvari Zsuzsanna , Kovalev Nikolay , Nagy Peter D.
Published: November 2012

Replication of plus-strand RNA viruses [(+)RNA viruses] is performed by viral replicases, whose function is affected by many cellular factors in infected cells. In this paper, we demonstrate a surprising role for Gef1p proton-chloride exchanger in replication of
Tomato bushy stunt virus
(TBSV) model (+)RNA virus. A genetic approach revealed that Gef1p, which is the only proton-chloride exchanger in
Saccharomyces cerevisiae
, is required for TBSV replication in the yeast model host. We also show that the
in vitro
activity of the purified tombusvirus replicase from
gef1
Δ yeast was low and that the
in vitro
assembly of the viral replicase in a cell extract was inhibited by the cytosolic fraction obtained from
gef1
Δ yeast. Altogether, our data reveal that Gef1p modulates TBSV replication via regulating Cu
2+
metabolism in the cell. This conclusion is supported by several lines of evidence, including the direct inhibitory effect of Cu
2+
ions on the
in vitro
assembly of the viral replicase, on the activity of the viral RNA-dependent RNA polymerase, and an inhibitory effect of deletion of
CCC2
copper pump on TBSV replication in yeast, while altered iron metabolism did not reduce TBSV replication. In addition, applying a chloride channel blocker impeded TBSV replication in
Nicotiana benthamiana
protoplasts or in whole plants. Overall, blocking Gef1p function seems to inhibit TBSV replication through altering Cu
2+
ion metabolism in the cytosol, which then inhibits the normal functions of the viral replicase.
Mouse Dendritic Cell (DC) Influenza Virus Infectivity Is Much Lower than That for Human DCs and Is Hemagglutinin Subtype Dependent
Authors: Hartmann Boris M. , Li Wenjing , Jia Jingjing , Patil Sonali , Marjanovic Nada , Martínez-Romero Carles , Albrecht Randy A. , Hayot Fernand , García-Sastre Adolfo , Wetmur James G. , Moran Thomas M. , Sealfon Stuart C.
Published: November 2012

We show that influenza A H1N1 virus infection leads to very low infectivity in mouse dendritic cells (DCs)
in vitro
compared with that in human DCs. This holds when H3 or H5 replaces H1 in recombinant viruses. Viruslike particles confirm the difference between mouse and human, suggesting that reduced virus entry contributes to lower mouse DC infectivity. Low infectivity of mouse DCs should be considered when they are used to study responses of DCs that are actually infected.
Excessive venous bleeding in a patient with acetabular pelvic fracture secondary to inferior vena cava filter occlusion
Authors: Nahas Sam , Yeoh Clarence , Velayudham Senthil
Published: November 2012

Inferior vena cava (IVC) filters can be used to prevent pulmonary embolism in cases where anticoagulation is contraindicated. Filter obstruction remains one of the major complications after its insertion. This is the rare case demonstrating excessive venous bleeding during attempted open reduction internal fixation of an acetabular fracture secondary to subcomplete IVC filter thrombosis day 1 postinsertion of the device. 1
Hyperinfection withStrongyloides stercoralis
Authors: Romero-Cabello Raúl , Villagroy Gómez Javier , Hernández González Mercedes , Romero Feregrino Raúl
Published: November 2012

Strongyloidiasis is caused byStrongyloides stercoralis,which commonly produces gastrointestinal problems. If immune systems are compromised, the nematode larvae may spread and produceStrongyloideshyperinfection. Diagnosis of strongyloidiasis is based on the observation of larvae in coproparasitological studies. We present a case of a 49-year-oldman, VIH, who developedStrongyloideshyperinfection, diagnosed postmortem. Our patient reached the dissemination stage, which resulted in severe damage to the stomach and intestine, perforation of the intestinal wall, as well as sepsis due to the dissemination of bacteria. The diagnosis is difficult because of the low larvae excretion in stools. It is usually performed by the microscopic examination of fresh and fixed enriched stool samples. Serology was reported to be useful for screening and follow-up after treatment. This case reaffirms that HIV immunosuppression favours the dissemination ofS stercoralislarvae. Thus, a search for intestinal parasites should be considered in similar cases.
Subacute bacterial endocarditis secondary to mastoiditis: a rare complication
Authors: Smith Caroline Patricia , Jackson Conor , Stewart Rosemary
Published: November 2012

Mastoiditis can result from untreated otitis media. If unrecognised, it can result in life-threatening complications. We present a 69-year-old woman with a history of left-sided otitis media admitted to intensive care unit following collapse with a decreasing Glasgow Coma Scale. Myringotomy and ventilator insertion revealed pus in the middle ear, which grew Group AStreptococcus. Her fever persisted and blood samples cultured Group AStreptococcus. Echocardiogram confirmed subacute bacterial endocarditis. Subacute bacterial endocarditis is a rare complication of mastoiditis. A literature review detected no previous case reports. A high suspicion of potential complications can prevent morbidity and mortality.
Emergency endoscopic retrograde cholangiopancreatography in critically ill patients is a safe and effective procedure
Authors: Lekharaju Venkata Pawan Kumar , Iqbal Javaid , Noorullah Omar , Polavarapu Naveen , Menon Shyam , Hood Stephen , Stern Nick , Sturgess Richard
Published: November 2012

Emergency ERCP may be required in patients with severe cholangitis who rapidly deteriorate with multi-organ dysfunction and who cannot wait until the next available elective list. A significant proportion of patients require ventilatory and inotropic support. We describe our experience on the outcome of emergency ERCP in this cohort of critically ill patients.

Medical records of cases undergoing ERCP between November 2008 and November 2011 were retrospectively reviewed. Patients who were in intensive care unit or required general anaesthesia due to haemodynamic compromise at the time of ERCP were included.

Total of 2237 ERCPs were performed during this period, of which 36 (2%) emergency ERCP's were performed in 33 patients. The median age was 79 years. All procedures were performed under general anaesthesia in emergency operating room. In 27/36 procedures (75%), the patients required inotropes. Indications included cholangitis (78%), pancreatitis (14%) and post-operative bile leak (8%). Biliary cannulation was achieved in 100% of cases. Endoscopic findings included CBD stones (64%), CBD stones and an additional pathology (8%), bile leak (8%), CBD stricture (5%), Mirizzi's (3%) and blocked plastic stent (3%). In 23/36 (64%) procedures a stent was inserted. In 11/36 (30%) procedures a balloon trawl was sufficient to clear the bile duct. Thirty-day mortality was 25%. Although the 30-day mortality remains high due to multi-organ failure, ERCP is successful and effective in the majority of patients and results in a good outcome for this cohort of critically ill patients, in whom the prognosis is inevitably poor without emergency biliary drainage.
High rates of reinfection and incidence of bacterial sexually transmitted infections in a cohort of female sex workers from two Indian cities: need for different STI control strategies?
Authors: Das Anjana , Pathni Anupam Khungar , Narayanan Prakash , George Bitra , Morineau Guy , Saidel Tobi , Prabhakar Parimi , Deshpande Gururaj Rao , Gangakhedkar Raman , Mehendale Sanjay , Risbud Arun
Published: November 2012

Background

Female sex workers (FSWs) in India are provided a standardised package of clinical interventions for management of sexually transmitted infections (STIs). A study was conducted among FSWs at known high STI prevalence sites to determine the effectiveness of the service package.

Methods

A cohort of FSW clinic attendees in two cities, Hyderabad and Mumbai, were enrolled and followed up from October 2008 to November 2009. At each visit, behavioural and clinical data were obtained and vaginal swabs collected for laboratory testing of cervical infections (gonorrhoea and chlamydia).

Results

417 participants were enrolled, of whom 360 attended at least a follow-up visit. Prevalence of cervical infections did not change between the baseline and final visits (27.7% and 21.3% respectively, p=0.08) in spite of presumptive treatment at baseline and syndromic management at all visits. The proportion of asymptomatic cervical infections increased from 36% at baseline to 77% at the final visit. Incidence rate of cervical infections was high (85.6/100 person years) and associated with a prevalent cervical infection at baseline (HR=2.7, p<0.001) and inconsistent condom use with non-commercial partners (HR=2.5, p=0.014).

Conclusions

High rates of STIs persisted despite the interventions due to poor condom use, minimal partner treatment, and high prevalence and incidence of STIs with a large proportion of asymptomatic infections. High-prevalence FSW sites in India need to design more effective partner treatment strategies and consider increasing the frequency of presumptive treatment as a temporary measure for quickly reducing STI prevalence, with renewed emphasis on consistent condom use with all partners.
Who needs more veterinary schools?
Authors: Lanyon L. E.
Published: November 2012

Does more mean better, different, or worse, asks Lance Lanyon
Zooplankton production in the Bay of Quinte 1975–2008: relationships with primary production, habitat, planktivory, and aquatic invasive species (Dreissena spp. andCercopagis pengoi)
Authors: Johannsson Ora E. , Bowen Kelly L.
Published: November 2012

The Bay of Quinte, a long, shallow, high-phosphorus system in Lake Ontario, spans a trophic range from eutrophic (upper Bay) to meso-oligotrophic (mouth). Phosphorus control (PC) and the invasion of dreissenid mussels and Cercopagis pengoi have influenced its biology and environment. We elucidated the principal drivers behind zooplankton production in the Bay from pre-PC times to the present (1975–2008). Production of abundant species was calculated using the egg-ratio method. Production estimates were improved by determining system-specific production/biomass (P/B) relationships for rarer species. Planktivory governed zooplankton production initially, likely preventing a response to PC. With changes in the fish community, zooplankton production increased. Thereafter, the principal drivers were the structure and size of the fish community, shifts in the predatory arena associated with changing light penetration, temperature, and addition of C. pengoi — all within a general context of nutrient availability. Dreissenid impacts were indirect. Interactive variables combining measures of predation, nutrient level, light, and temperature were the best at accounting for variability in zooplankton production.
A nutrient budget for a selection harvest: implications for long-term sustainability
Authors: Phillips Tyler , Watmough Shaun A.
Published: November 2012

Declining concentrations of Ca and other base cations in soils and surface waters in eastern North America have led to concerns that forests may become nutrient limited, particularly in regions that are harvested. We constructed a nutrient budget for a selection harvest in central Ontario that is typical of eastern North America. Atmospheric deposition (5-year average) and mineral weathering (PROFILE) were considered as the sole inputs to the forest, while exports included nutrient losses in streams and removed in stems. Sugar maple ( Acer saccharum Marsh.) was the only tree species removed in the study (∼30% of basal area) and harvesting had no strong impact on stream chemistry. Mass balance calculations were performed on average values, but with estimates of uncertainty associated with each input parameter. A Monte Carlo simulation was run (10 000 runs) for Ca, Mg, K, Na, P, N, and S. In the absence of harvesting, average mass balance estimates are positive for all nutrients except S. When harvesting is considered, average mass balances remain positive for all nutrients except Ca, K, and S. Monte Carlo simulations demonstrate that mass balances for Na are always positive, while mass balances for Mg, K, N, P, and S range from slightly positive to slightly negative. In contrast, mass balance simulations for Ca are always negative and average net losses represent ∼1% of the current exchangeable soil Ca pool.
Organ growth without cell division: somatic polyploidy in a moth,Ephestia kuehniella
Authors: Buntrock Lydia , Marec František , Krueger Sarah , Traut Walther
Published: November 2012

Organ growth depends on cell division and (or) cell growth. Here, we present a study on two organs whose growth depends entirely on cell growth, once they are formed in the embryo: Malpighian tubules and silk glands of the flour moth, Ephestia kuehniella . Between first and last larval instar, the volume of Malpighian tubule cells increases by a factor of ∼1800 and that of silk gland cells by a factor of ∼3100. We determined the number of endocyles required to reach these stages by Feulgen cytometry. Cells of Malpighian tubules were in the 2C stage in first instar larvae and reached 1024C after 9 endocycles in last instar larvae (1C = 0.45 pg DNA). Silk gland cells already reached a DNA content of 8C–16C in first instar larvae and attained up to 8192C in last instar larvae after a total of 12 endocycles. The nuclei were small and more or less spherical in first instar larvae, but they were huge, flat, and bizarrely branched in last instar larvae. We consider branching as a compensatory adaptation to improve molecular traffic between nucleus and cytoplasm in these excessively large and highly polyploid cells (i) by reducing the mean distance between nucleus and cytoplasm and (ii) by enlarging the surface-to-volume ratio of these nuclei.
Large-conductance calcium-activated potassium current modulates excitability in isolated canine intracardiac neurons
Authors: Pérez Guillermo J. , Desai Mayurika , Anderson Seth , Scornik Fabiana S.
Published: November 2012

We studied principal neurons from canine intracardiac (IC) ganglia to determine whether large-conductance calcium-activated potassium (BK) channels play a role in their excitability. We performed whole cell recordings in voltage- and current-clamp modes to measure ion currents and changes in membrane potential from isolated canine IC neurons. Whole cell currents from these neurons showed fast- and slow-activated outward components. Both current components decreased in the absence of calcium and following 1–2 mM tetraethylammonium (TEA) or paxilline. These results suggest that BK channels underlie these current components. Single-channel analysis showed that BK channels from IC neurons do not inactivate in a time-dependent manner, suggesting that the dynamic of the decay of the fast current component is akin to that of intracellular calcium. Immunohistochemical studies showed that BK channels and type 2 ryanodine receptors are coexpressed in IC principal neurons. We tested whether BK current activation in these neurons occurred via a calcium-induced calcium release mechanism. We found that the outward currents of these neurons were not affected by the calcium depletion of intracellular stores with 10 mM caffeine and 10 μM cyclopiazonic acid. Thus, in canine intracardiac neurons, BK currents are directly activated by calcium influx. Membrane potential changes elicited by long (400 ms) current injections showed a tonic firing response that was decreased by TEA or paxilline. These data strongly suggest that the BK current present in canine intracardiac neurons regulates action potential activity and could increase these neurons excitability.
Regulation of intestinal serotonin transporter expression via epigenetic mechanisms: role of HDAC2
Authors: Gill Ravinder K. , Kumar Anoop , Malhotra Pooja , Maher Daniel , Singh Varsha , Dudeja Pradeep K. , Alrefai Waddah , Saksena Seema
Published: November 2012

The serotonin (5-HT) transporter (SERT) facilitates clearance of extracellular 5-HT by its uptake and internalization. Decreased expression of SERT and consequent high 5-HT levels have been implicated in various diarrheal disorders. Thus, appropriate regulation of SERT is critical for maintenance of 5-HT homeostasis in health and disease. Previous studies demonstrated that SERT is regulated via posttranslational and transcriptional mechanisms. However, the role of epigenetic mechanisms in SERT regulation is not known. Current studies investigated the effects of histone deacetylase (HDAC) inhibition on SERT expression and delineated the mechanisms. Treatment of Caco-2 cells with the pan-HDAC inhibitors butyrate (5 mM) and trichostatin (TSA, 1 μM) decreased SERT mRNA and protein levels. Butyrate- or TSA-induced decrease in SERT was associated with decreased activity of human SERT (hSERT) promoter 1 (upstream of exon 1a), but not hSERT promoter 2 (upstream of exon 2). Butyrate + TSA did not show an additive effect on SERT expression, indicating that mechanisms involving histone hyperacetylation may be involved. Chromatin immunoprecipitation assays demonstrated enrichment of the hSERT promoter 1 (flanking nt −250/+2) with tetra-acetylated histone H3 or H4, which was increased (∼3-fold) by butyrate. Interestingly, specific inhibition of HDAC2 (but not HDAC1) utilizing small interfering RNA decreased SERT mRNA and protein levels. The decrease in SERT expression by HDAC inhibition was recapitulated in an in vivo model . SERT mRNA levels were decreased in the ileum and colon of mice fed pectin (increased availability of butyrate) compared with controls fed a fiber-free diet (∼50–60%). Our results identify a novel role of HDAC2 as a regulator of SERT gene expression in intestinal epithelial cells.
Sensing of amino acids by the gut-expressed taste receptor T1R1-T1R3 stimulates CCK secretion
Authors: Daly Kristian , Al-Rammahi Miran , Moran Andrew , Marcello Marco , Ninomiya Yuzo , Shirazi-Beechey Soraya P.
Published: November 2012

CCK is secreted by endocrine cells of the proximal intestine in response to dietary components, including amino acids. CCK plays a variety of roles in digestive processes, including inhibition of food intake, consistent with a role in satiety. In the lingual epithelium, the sensing of a broad spectrum of l-amino acids is accomplished by the heteromeric amino acid (umami) taste receptor (T1R1-T1R3). T1R1 and T1R3 subunits are also expressed in the intestine. A defining characteristic of umami sensing by T1R1-T1R3 is its potentiation by IMP or GMP. Furthermore, T1R1-T1R3 is not activated by Trp. We show here that, in response to l-amino acids (Phe, Leu, Glu, and Trp), but not d-amino acids, STC-1 enteroendocrine cells and mouse proximal small intestinal tissue explants secrete CCK and that IMP enhances Phe-, Leu-, and Glu-induced, but not Trp-induced, CCK secretion. Furthermore, small interfering RNA inhibition of T1R1 expression in STC-1 cells results in significant diminution of Phe-, Leu-, and Glu-stimulated, but not Trp-stimulated, CCK release. In STC-1 cells and mouse intestine, gurmarin inhibits Phe-, Leu-, and Glu-induced, but not Trp-stimulated, CCK secretion. In contrast, the Ca2+-sensing receptor antagonist NPS2143 inhibits Phe-stimulated CCK release partially and Trp-induced CCK secretion totally in mouse intestine. However, NPS2143 has no effect on Leu- or Glu-induced CCK secretion. Collectively, our data demonstrate that functional characteristics and cellular location of the gut-expressed T1R1-T1R3 support its role as a luminal sensor for Phe-, Leu-, and Glu-induced CCK secretion.
Role of reduced manganese superoxide dismutase in ischemia-reperfusion injury: a possible trigger for autophagy and mitochondrial biogenesis?
Authors: Parajuli Nirmala , MacMillan-Crow Lee Ann
Published: November 2012

Excessive generation of superoxide and mitochondrial dysfunction has been described as being important events during ischemia-reperfusion (I/R) injury. Our laboratory has demonstrated that manganese superoxide dismutase (MnSOD), a major mitochondrial antioxidant that eliminates superoxide, is inactivated during renal transplantation and renal I/R and precedes development of renal failure. We hypothesized that MnSOD knockdown in the kidney augments renal damage during renal I/R. Using newly characterized kidney-specific MnSOD knockout (KO) mice the extent of renal damage and oxidant production after I/R was evaluated. These KO mice (without I/R) exhibited low expression and activity of MnSOD in the distal nephrons, had altered renal morphology, increased oxidant production, but surprisingly showed no alteration in renal function. After I/R the MnSOD KO mice showed similar levels of injury to the distal nephrons when compared with wild-type mice. Moreover, renal function, MnSOD activity, and tubular cell death were not significantly altered between the two genotypes after I/R. Interestingly, MnSOD KO alone increased autophagosome formation, mitochondrial biogenesis, and DNA replication/repair within the distal nephrons. These findings suggest that the chronic oxidative stress as a result of MnSOD knockdown induced multiple coordinated cell survival signals including autophagy and mitochondrial biogenesis, which protected the kidney against the acute oxidative stress following I/R.
Axial compartmentation of descending and ascending thin limbs of Henle's loops
Authors: Westrick Kristen Y. , Serack Bradley , Dantzler William H. , Pannabecker Thomas L.
Published: November 2012

In the inner medulla, radial organization of nephrons and blood vessels around collecting duct (CD) clusters leads to two lateral interstitial regions and preferential intersegmental fluid and solute flows. As the descending (DTLs) and ascending thin limbs (ATLs) pass through these regions, their transepithelial fluid and solute flows are influenced by variable transepithelial solute gradients and structure-to-structure interactions. The goal of this study was to quantify structure-to-structure interactions, so as to better understand compartmentation and flows of transepithelial water, NaCl, and urea and generation of the axial osmotic gradient. To accomplish this, we determined lateral distances of AQP1-positive and AQP1-negative DTLs and ATLs from their nearest CDs, so as to gauge interactions with intercluster and intracluster lateral regions and interactions with interstitial nodal spaces (INSs). DTLs express reduced AQP1 and low transepithelial water permeability along their deepest segments. Deep AQP1-null segments, prebend segments, and ATLs lie equally near to CDs. Prebend segments and ATLs abut CDs and INSs throughout much of their descent and ascent, respectively; however, the distal 30% of ATLs of the longest loops lie distant from CDs as they approach the outer medullary boundary and have minimal interaction with INSs. These relationships occur regardless of loop length. Finally, we show that ascending vasa recta separate intercluster AQP1-positive DTLs from descending vasa recta, thereby minimizing dilution of gradients that drive solute secretion. We hypothesize that DTLs and ATLs enter and exit CD clusters in an orchestrated fashion that is important for generation of the corticopapillary solute gradient by minimizing NaCl and urea loss.
Prolonged C2spinal hemisection-induced inactivity reduces diaphragm muscle specific force with modest, selective atrophy of type IIx and/or IIb fibers
Authors: Mantilla Carlos B. , Greising Sarah M. , Zhan Wen-Zhi , Seven Yasin B. , Sieck Gary C.
Published: November 2012

The diaphragm muscle (DIAm) is critically responsible for sustaining ventilation. Previously we showed in a commonly used model of spinal cord injury, unilateral spinal cord hemisection at C2(SH), that there are minimal changes to muscle fiber cross-sectional area (CSA) and fiber type distribution following 14 days of SH-induced ipsilateral DIAm inactivity. In the present study, effects of long-term SH-induced inactivity on DIAm fiber size and force were examined. We hypothesized that prolonged inactivity would not result in substantial DIAm atrophy or force loss. Adult rats were randomized to control or SH groups ( n = 34 total). Chronic bilateral DIAm electromyographic (EMG) activity was monitored during resting breathing. Minimal levels of spontaneous recovery of ipsilateral DIAm EMG activity were evident in 42% of SH rats (<25% of preinjury root mean square amplitude). Following 42 days of SH, DIAm specific force was reduced 39%. There was no difference in CSA for type I or IIa DIAm fibers in SH rats compared with age, weight-matched controls (classification based on myosin heavy chain isoform expression). Type IIx and/or IIb DIAm fibers displayed a modest 20% reduction in CSA ( P < 0.05). Overall, there were no differences in the distribution of fiber types or the contribution of each fiber type to the total DIAm CSA. These data indicate that reduced specific force following prolonged inactivity of the DIAm is associated with modest, fiber type selective adaptations in muscle fiber size and fiber type distribution.
Morning-evening variation in human brain metabolism and memory circuits
Authors: Shannon B. J. , Dosenbach R. A. , Su Y. , Vlassenko A. G. , Larson-Prior L. J. , Nolan T. S. , Snyder A. Z. , Raichle M. E.
Published: November 2012

It has been posited that a critical function of sleep is synaptic renormalization following a net increase in synaptic strength during wake. We hypothesized that wake would alter the resting-state functional organization of the brain and increase its metabolic cost. To test these hypotheses, two experiments were performed. In one, we obtained morning and evening resting-state functional MRI scans to assess changes in functional brain organization. In the second experiment, we obtained quantitative positron emission tomography measures of glucose and oxygen consumption to assess the cost of wake. We found selective changes in brain organization. Most prominently, bilateral medial temporal regions were locally connected in the morning but in the evening exhibited strong correlations with frontal and parietal brain regions involved in memory retrieval. We speculate that these changes may reflect aspects of memory consolidation recurring on a daily basis. Surprisingly, these changes in brain organization occurred without increases in brain metabolism.