bluuebunny/crossref_metadata_2025_split huggingface dataset:
Urological complications, vesicoureteral reflux, and long‐term graft survival rate after pediatric kidney transplantation
Authors: Torricelli Fabio C. M. , Watanabe Andreia , Piovesan Affonso C. , Antonopoulos Ioannis M. , David‐Neto Elias , Nahas William C. 
Published: October 2015

AbstractTo describe a single‐center experience with kidney transplantation and then study some donor and recipient features that may impact on graft survival and urological complication rates. We reviewed our database searching for pediatric patients who underwent kidney transplantation from August 1985 through November 2012. Preoperative data and postoperative complications were recorded. Graft survival rates were analyzed and compared based on the type of donor, donor's age from deceased donors, and recipients' ESRD cause. Kaplan–Meier curves with log rank and Wilcoxon tests were used to perform the comparisons. There were 305 pediatric kidney transplants. The mean recipient's age was 11.7 yr. The mean follow‐up was 11.0 yr. Arterial and venous thrombosis rates were 1.6% and 2.3%, respectively, while urinary fistula and symptomatic vesicoureteral reflux were diagnosed in 2.9% and 3.6% of cases, respectively. Deceased kidney transplantation had a lower graft survival rate than living kidney transplantation (log rank, p = 0.005). Donor's age (p = 0.420) and ESRD cause (p = 0.679) were not significantly related to graft survival rate. In long‐term follow‐up, type of donor, but not donor's age, impacts on graft survival rate. ESRD cause has no impact on graft survival rate, showing that well‐evaluated recipients may have good outcomes.
Combination treatment with excimer laser and narrowband UVB light in vitiligo patients
Authors: Shin Sungsik , Hann Seung‐Kyung , Oh Sang Ho 
Published: October 2015

SummaryBackgroundFor the treatment of vitiligo, narrowband UVB (NBUVB) light is considered the most effective for nonsegmental vitiligo, while excimer laser treatment is commonly used for localized vitiligo. However, treatment areas may potentially be missed with excimer laser treatment.ObjectiveWe aimed to evaluate the effect of combinational treatment with NBUVB light and excimer laser on vitiligo.MethodsAll patients were first treated with NBUVB; excimer laser was then applied in conjunction with NBUVB phototherapy due to a slow response or no further improvement with continuous NBUVB treatment alone. To minimize adverse effects, a fixed dose of NBUVB was administered, and the dose of excimer laser was increased based on patient response.ResultsAmong 80 patients, 54 patients showed responses after combination with excimer laser; however, 26 patients (32.5%) showed no remarkable change after combination therapy. Of the 26 patients who showed no further response, 12 patients (46.1%) presented with vitiligo on the acral areas, which are known to the least responsive sites.ConclusionOur study suggests that combined treatment of NBUVB and excimer laser in vitiligo may enhance the treatment response without remarkable side effects, therefore might also increase the compliance of the patients to the treatment.
The role of tidal, wave and river currents in the evolution of mixed‐energy deltas: Example from the Lajas Formation (Argentina)
Authors: Rossi Valentina Marzia , Steel Ronald J. 
Published: October 2015

AbstractMany modern deltas show complex morphologies and architectures related to the interplay of river, wave and tidal currents. However, methods for extracting the signature of the individual processes from the stratigraphic architecture are poorly developed. Through an analysis of facies, palaeocurrents and stratigraphic stacking patterns in the Jurassic Lajas Formation, this paper: (i) separates the signals of wave, tide and river currents; (ii) illustrates the result of strong tidal reworking in the distal reaches of deltaic systems; and (iii) discusses the implications of this reworking for the evolution of mixed‐energy systems and their reservoir heterogeneities. The Lajas Formation, a sand‐rich, shallow‐marine, mixed‐energy deltaic system in the Neuquén Basin of Argentina, previously defined as a tide‐dominated system, presents an exceptional example of process variability at different scales. Tidal signals are predominantly located in the delta front, the subaqueous platform and the distributary channel deposits. Tidal currents vigorously reworked the delta front during transgressions, producing intensely cross‐stratified, sheet‐like, sandstone units. In the subaqueous platform, described for the first time in an ancient outcrop example, the tidal reworking was confined within subtidal channels. The intensive tidal reworking in the distal reaches of the regressive delta front could not have been predicted from knowledge of the coeval proximal reaches of the regressive delta front. The wave signals occur mainly in the shelf or shoreface deposits. The fluvial signals increase in abundance proximally but are always mixed with the other processes. The Lajas system is an unusual clean‐water (i.e. very little mud is present in the system), sand‐rich deltaic system, very different from the majority of mud‐rich, modern tide‐influenced examples. The sand‐rich character is a combination of source proximity, syndepositional tectonic activity and strong tidal‐current reworking, which produced amalgamated sandstone bodies in the delta‐front area, and a final stratigraphic record very different from the simple coarsening‐upward trends of river‐dominated and wave‐dominated delta fronts.
Unravelling the Politics of Activation Reforms: Exploring the Unusual Israeli Trajectory
Authors: Maron Asa , Helman Sara 
Published: October 2015

AbstractContemporary active labour market (ALM) reforms are pivotal in the reorganization of the welfare state as they challenge and threaten some of the fundamental achievements of labour in capitalist societies: social programmes and entitlements that compensate for unemployment, and governance arrangements in which the social partners share authority and responsibility with the state. Consequently, ALM reforms may give raise to social unrest and political struggle that involves the state (the main proponent of ALM reforms), trade unions and political parties. These conflicts are important in the politicization of reforms, i.e. raising public awareness of and engagement with controversies of welfare state change.In this article, we use a non‐European perspective to ask more generally how distinct historical institutions create separate ‘politicization trajectories’ of ALM reforms, which in turn produce different policy designs and outcomes. Centring on the case of Israel, in which historically ‘abnormal’ class politics fostered indifference to the reform in both trade unions and political parties, we maintain that the preliminary de‐politicization made it possible for bureaucrats to control the reform, leading to an intra‐state conflict between competing agencies over its design and implementation. The usurpation of the reform by the Ministry of Finance made it conspicuously unbalanced, provoking many grievances. Paradoxically, the de‐politicization of the reform advanced its re‐politicization, led by non‐governmental advocacy organizations in civil society. These uncommon political actors in the politics of ALM reforms were able to lead a counter‐coalition, delegitimize the reform, and mobilize politicians to eventually terminate activation
Finding the gap: revealing local disparities in coverage of maternal, newborn and child health services in South Sudan using lot quality assurance sampling
Authors: Valadez Joseph J. , Berendes Sima , Lako Richard , Gould Simon , Vargas William , Milner Susan 
Published: October 2015

AbstractObjectivesWe adapted a rapid monitoring method to South Sudan, a new nation with one of the world's highest maternal and child mortality rates, aiming to assess coverage of maternal, neonatal and child health (MNCH) services at the time of independence, and introducing a monitoring and evaluation system (M&E) for equity‐sensitive tracking of progress related to Millennium Development Goals (MDG) 4 and 5 at national, state and county levels to detect local variability.MethodsWe conducted a national cross‐sectional household survey among women from six client populations in all, but six of South Sudan's 79 counties. We used lot quality assurance sampling (LQAS) to measure coverage with diverse MNCH indicators to obtain information for national‐, state‐ and county‐level health system management decision‐making.ResultsNational coverage of MNCH services was low for all maternal and neonatal care, child immunisation, and child care indicators. However, results varied across states and counties. Central Equatoria State (CES), where the capital is located, showed the highest coverage for most indicators (e.g. ≥4 antenatal care visits range: 4.5% in Jonglei to 40.1% in CES). Urban counties often outperformed rural ones.ConclusionsThis adaptation of LQAS to South Sudan demonstrates how it can be used in the future as an M&E system to track progress of MDGs at national, state and county levels to detect local disparities. Overall, our data reveal a desperate need for improving MNCH service coverage in all states.
Multiplexed Integrating Plasmids for Engineering of the Erythromycin Gene Cluster for Expression in Streptomyces spp. and Combinatorial Biosynthesis
Authors: Fayed Bahgat , Ashford David A. , Hashem Amal M. , Amin Magdy A. , El Gazayerly Omaima N. , Gregory Matthew A. , Smith Margaret C. M. 
Published: October 2015

ABSTRACT

Bacteria in the genus
Streptomyces
and its close relatives are prolific producers of secondary metabolites with antibiotic activity. Genome sequencing of these bacteria has revealed a rich source of potentially new antibiotic pathways, whose products have never been observed. Moreover, these new pathways can provide novel genes that could be used in combinatorial biosynthesis approaches to generate unnatural analogues of existing antibiotics. We explore here the use of multiple orthologous integrating plasmid systems, based on the
int/attP
loci from phages TG1, SV1, and ϕBT1, to express the polyketide synthase (PKS) for erythromycin in a heterologous
Streptomyces
host.
Streptomyces
strains containing the three polyketide synthase genes
eryAI
,
eryAII
, and
eryAIII
expressed from three different integrated plasmids produced the aglycone intermediate, 6-deoxyerythronolide B (6-dEB). A further pair of integrating plasmids, both derived from the ϕC31
int/attP
locus, were constructed carrying a gene cassette for glycosylation of the aglycone intermediates, with or without the tailoring gene,
eryF
, required for the synthesis of erythronolide B (EB). Liquid chromatography-mass spectrometry of the metabolites indicated the production of angolosaminyl-6-dEB and angolosaminyl-EB. The advantages of using multiplexed integrating plasmids for engineering expression and for combinatorial biosynthesis were demonstrated.
Metabolic Response of Clostridium ljungdahlii to Oxygen Exposure
Authors: Whitham Jason M. , Tirado-Acevedo Oscar , Chinn Mari S. , Pawlak Joel J. , Grunden Amy M. 
Published: October 2015

ABSTRACTClostridium ljungdahliiis an important synthesis gas-fermenting bacterium used in the biofuels industry, and a preliminary investigation showed that it has some tolerance to oxygen when cultured in rich mixotrophic medium. Batch cultures not only continue to grow and consume H2, CO, and fructose after 8% O2exposure, but fermentation product analysis revealed an increase in ethanol concentration and decreased acetate concentration compared to non-oxygen-exposed cultures. In this study, the mechanisms for higher ethanol production and oxygen/reactive oxygen species (ROS) detoxification were identified using a combination of fermentation, transcriptome sequencing (RNA-seq) differential expression, and enzyme activity analyses. The results indicate that the higher ethanol and lower acetate concentrations were due to the carboxylic acid reductase activity of a more highly expressed predicted aldehyde oxidoreductase (CLJU_c24130) and thatC. ljungdahlii's primary defense upon oxygen exposure is a predicted rubrerythrin (CLJU_c39340). The metabolic responses of higher ethanol production and oxygen/ROS detoxification were found to be linked by cofactor management and substrate and energy metabolism. This study contributes new insights into the physiology and metabolism ofC. ljungdahliiand provides new genetic targets to generateC. ljungdahliistrains that produce more ethanol and are more tolerant to syngas contaminants.
Protein Engineering of a Nitrilase from Burkholderia cenocepacia J2315 for Efficient and Enantioselective Production of (
R
)-
o
-Chloromandelic Acid
Authors: Wang Hualei , Gao Wenyuan , Sun Huihui , Chen Lifeng , Zhang Lujia , Wang Xuedong , Wei Dongzhi 
Published: October 2015

ABSTRACT

The nitrilase-mediated pathway has significant advantages in the production of optically pure aromatic α-hydroxy carboxylic acids. However, low enantioselectivity and activity are observed on hydrolyzing
o
-chloromandelonitrile to produce optically pure (
R
)-
o
-chloromandelic acid. In the present study, a protein engineering approach was successfully used to enhance the performance of nitrilase obtained from
Burkholderia cenocepacia
strain J2315 (BCJ2315) in hydrolyzing
o
-chloromandelonitrile. Four hot spots (T49, I113, Y199, and T310) responsible for the enantioselectivity and activity of BCJ2315 were identified by random mutagenesis. An effective double mutant (I113M/Y199G [encoding the replacement of I with M at position 113 and Y with G at position 199]), which demonstrated remarkably enhanced enantioselectivity (99.1% enantiomeric excess [
ee
] compared to 89.2%
ee
for the wild type) and relative activity (360% of the wild type), was created by two rounds of site saturation mutagenesis, first at each of the four hot spots and subsequently at position 199 for combination with the selected beneficial mutation I113M. Notably, this mutant also demonstrated dramatically enhanced enantioselectivity and activity toward other mandelonitrile derivatives and, thus, broadened the substrate scope of this nitrilase. Using an ethyl acetate-water (1:9) biphasic system,
o
-chloromandelonitrile (500 mM) was completely hydrolyzed in 3 h by this mutant with a small amount of biocatalyst (10 g/liter wet cells), resulting in a high concentration of (
R
)-
o
-chloromandelic acid with 98.7%
ee
, to our knowledge the highest ever reported. This result highlights a promising method for industrial production of optically pure (
R
)-
o
-chloromandelic acid. Insight into the source of enantioselectivity and activity was gained by homology modeling and molecular docking experiments.
Interactions between Closely Related Bacterial Strains Are Revealed by Deep Transcriptome Sequencing
Authors: González-Torres Pedro , Pryszcz Leszek P. , Santos Fernando , Martínez-García Manuel , Gabaldón Toni , Antón Josefa 
Published: October 2015

ABSTRACT

Comparative genomics, metagenomics, and single-cell technologies have shown that populations of microbial species encompass assemblages of closely related strains. This raises the question of whether individual bacterial lineages respond to the presence of their close relatives by modifying their gene expression or, instead, whether assemblages simply act as the arithmetic addition of their individual components. Here, we took advantage of transcriptome sequencing to address this question. For this, we analyzed the transcriptomes of two closely related strains of the extremely halophilic bacterium
Salinibacter ruber
grown axenically and in coculture. These organisms dominate bacterial assemblages in hypersaline environments worldwide. The strains used here cooccurred in the natural environment and are 100% identical in their 16S rRNA genes, and each strain harbors an accessory genome representing 10% of its complete genome. Overall, transcriptomic patterns from pure cultures were very similar for both strains. Expression was detected along practically the whole genome albeit with some genes at low levels. A subset of genes was very highly expressed in both strains, including genes coding for the light-driven proton pump xanthorhodopsin, genes involved in the stress response, and genes coding for transcriptional regulators. Expression differences between pure cultures affected mainly genes involved in environmental sensing. When the strains were grown in coculture, there was a modest but significant change in their individual transcription patterns compared to those in pure culture. Each strain sensed the presence of the other and responded in a specific manner, which points to fine intraspecific transcriptomic modulation.
Yeast Integral Membrane Proteins Apq12, Brl1, and Brr6 Form a Complex Important for Regulation of Membrane Homeostasis and Nuclear Pore Complex Biogenesis
Authors: Lone Museer A. , Atkinson Aaron E. , Hodge Christine A. , Cottier Stéphanie , Martínez-Montañés Fernando , Maithel Shelley , Mène-Saffrané Laurent , Cole Charles N. , Schneiter Roger 
Published: October 2015

ABSTRACT
Proper functioning of intracellular membranes is critical for many cellular processes. A key feature of membranes is their ability to adapt to changes in environmental conditions by adjusting their composition so as to maintain constant biophysical properties, including fluidity and flexibility. Similar changes in the biophysical properties of membranes likely occur when intracellular processes, such as vesicle formation and fusion, require dramatic changes in membrane curvature. Similar modifications must also be made when nuclear pore complexes (NPCs) are constructed within the existing nuclear membrane, as occurs during interphase in all eukaryotes. Here we report on the role of the essential nuclear envelope/endoplasmic reticulum (NE/ER) protein Brl1 in regulating the membrane composition of the NE/ER. We show that Brl1 and two other proteins characterized previously—Brr6, which is closely related to Brl1, and Apq12—function together and are required for lipid homeostasis. All three transmembrane proteins are localized to the NE and can be coprecipitated. As has been shown for mutations affecting Brr6 and Apq12, mutations in Brl1 lead to defects in lipid metabolism, increased sensitivity to drugs that inhibit enzymes involved in lipid synthesis, and strong genetic interactions with mutations affecting lipid metabolism. Mutations affecting Brl1 or Brr6 or the absence of Apq12 leads to hyperfluid membranes, because mutant cells are hypersensitive to agents that increase membrane fluidity. We suggest that the defects in nuclear pore complex biogenesis and mRNA export seen in these mutants are consequences of defects in maintaining the biophysical properties of the NE.
Saccharomyces cerevisiae Is Dependent on Vesicular Traffic between the Golgi Apparatus and the Vacuole When Inositolphosphorylceramide Synthase Aur1 Is Inactivated
Authors: Voynova Natalia S. , Roubaty Carole , Vazquez Hector M. , Mallela Shamroop K. , Ejsing Christer S. , Conzelmann Andreas 
Published: October 2015

ABSTRACT

Inositolphosphorylceramide (IPC) and its mannosylated derivatives are the only complex sphingolipids of yeast. Their synthesis can be reduced by aureobasidin A (AbA), which specifically inhibits the IPC synthase Aur1. AbA reportedly, by diminishing IPC levels, causes endoplasmic reticulum (ER) stress, an increase in cytosolic calcium, reactive oxygen production, and mitochondrial damage leading to apoptosis. We found that when Aur1 is gradually depleted by transcriptional downregulation, the accumulation of ceramides becomes a major hindrance to cell survival. Overexpression of the alkaline ceramidase
YPC1
rescues cells under this condition. We established hydroxylated C
26
fatty acids as a reliable hallmark of ceramide hydrolysis. Such hydrolysis occurs only when
YPC1
is overexpressed. In contrast, overexpression of
YPC1
has no beneficial effect when Aur1 is acutely repressed by AbA. A high-throughput genetic screen revealed that vesicle-mediated transport between Golgi apparatus, endosomes, and vacuole becomes crucial for survival when Aur1 is repressed, irrespective of the mode of repression. In addition, vacuolar acidification becomes essential when cells are acutely stressed by AbA, and quinacrine uptake into vacuoles shows that AbA activates vacuolar acidification. The antioxidant
N
-acetylcysteine does not improve cell growth on AbA, indicating that reactive oxygen radicals induced by AbA play a minor role in its toxicity. AbA strongly induces the cell wall integrity pathway, but osmotic support does not improve the viability of wild-type cells on AbA. Altogether, the data support and refine current models of AbA-mediated cell death and add vacuolar protein transport and acidification as novel critical elements of stress resistance.
Long-Term Survival of Borrelia burgdorferi Lacking the Hibernation Promotion Factor Homolog in the Unfed Tick Vector
Authors: Fazzino Lisa , Tilly Kit , Dulebohn Daniel P. , Rosa Patricia A. 
Published: October 2015

ABSTRACT

Borrelia burgdorferi
, a causative agent of Lyme borreliosis, is a zoonotic pathogen that survives in nutrient-limited environments within a tick, prior to transmission to its mammalian host. Survival under these prolonged nutrient-limited conditions is thought to be similar to survival during stationary phase, which is characterized by growth cessation and decreased protein production. Multiple ribosome-associated proteins are implicated in stationary-phase survival of
Escherichia coli
. These proteins include hibernation-promoting factor (HPF), which dimerizes ribosomes and prevents translation of mRNA. Bioinformatic analyses indicate that
B. burgdorferi
harbors an
hpf
homolog, the
bb0449
gene. BB0449 protein secondary structure modeling also predicted HPF-like structure and function. However, BB0449 protein was not localized in the ribosome-associated protein fraction of
in vitro
-grown
B. burgdorferi
. In wild-type
B. burgdorferi
,
bb0449
transcript and BB0449 protein levels are low during various growth phases. These results are inconsistent with patterns of synthesis of HPF-like proteins in other bacterial species. In addition, two independently derived
bb0449
mutants successfully completed the mouse-tick infectious cycle, indicating that
bb0449
is not required for prolonged survival in the nutrient-limited environment in the unfed tick or any other stage of infection by
B. burgdorferi
. We suggest either that BB0449 is associated with ribosomes under specific conditions not yet identified or that BB0449 of
B. burgdorferi
has a function other than ribosome conformation modulation.