bluuebunny/crossref_metadata_2025 huggingface dataset:
Mass spectrometric approaches for chemical characterisation of atmospheric aerosols: critical review of the most recent advances
Authors: Laskin Alexander , Laskin Julia , Nizkorodov Sergey A.
Published: June 2012

Environmental contextAtmospheric aerosols have profound effects on the environment through several physicochemical processes, such as absorption and scattering of sunlight, heterogeneous gas–particle reactions and adverse effects on the respiratory and cardiovascular systems. Understanding aerosol atmospheric chemistry and its environmental impact requires comprehensive characterisation of the physical and chemical properties of particles. Results from mass spectrometry provide important new insights into the origin of atmospheric aerosols, the evolution of their physicochemical properties, their reactivity and their effect on the environment.

AbstractThis manuscript presents an overview of the most recent instrument developments for the field and laboratory applications of mass spectrometry (MS) to investigate the chemistry and physics of atmospheric aerosols. A range of MS instruments, employing different sample introduction methods, ionisation and mass detection techniques are used both for ‘online’ and ‘offline’ characterisation of aerosols. Online MS techniques enable detection of individual particles with simultaneous measurement of particle size distributions and aerodynamic characteristics and are ideally suited for field studies that require high temporal resolution. Offline MS techniques provide a means for detailed molecular-level analysis of aerosol samples, which is essential to gain fundamental knowledge regarding aerosol chemistry, mechanisms of particle formation and atmospheric aging. Combined, complementary MS techniques provide comprehensive information on the chemical composition, size, morphology and phase of aerosols – data of key importance for evaluating hygroscopic and optical properties of particles, their health effects, understanding their origins and atmospheric evolution. Over the last few years, developments and applications of MS techniques in aerosol research have expanded remarkably as evident by skyrocketing publication statistics. The goal of this review is to present the most recent developments in the field of aerosol mass spectrometry for the time period of late 2010 to early 2012, which have not been conveyed in previous reviews.
Oriented nucleation of hemozoin at the digestive vacuole membrane in
Plasmodium falciparum
Authors: Kapishnikov Sergey , Weiner Allon , Shimoni Eyal , Guttmann Peter , Schneider Gerd , Dahan-Pasternak Noa , Dzikowski Ron , Leiserowitz Leslie , Elbaum Michael
Published: June 2012

Heme detoxification is a critical step in the life cycle of malaria-causing parasites, achieved by crystallization into physiologically insoluble hemozoin. The mode of nucleation has profound implications for understanding the mechanism of action of antimalarial drugs that inhibit hemozoin growth. Several lines of evidence point to involvement of acylglycerol lipids in the nucleation process. Hemozoin crystals have been reported to form within lipid nanospheres; alternatively, it has been found in vitro that they are nucleated at an acylglycerol lipid–water interface. We have applied cryogenic soft X-ray tomography and three-dimensional electron microscopy to address the location and orientation of hemozoin crystals within the digestive vacuole (DV), as a signature of their nucleation and growth processes. Cryogenic soft X-ray tomography in the “water window” is particularly advantageous because contrast generation is based inherently on atomic absorption. We find that hemozoin nucleation occurs at the DV inner membrane, with crystallization occurring in the aqueous rather than lipid phase. The crystal morphology indicates a common {100} orientation facing the membrane as expected of templated nucleation. This is consistent with conclusions reached by X-ray fluorescence and diffraction in a companion work. Uniform dark spheres observed in the parasite were identified as hemoglobin transport vesicles. Their analysis supports a model of hemozoin nucleation primarily in the DV. Modeling of the contrast at the DV membrane indicates a 4-nm thickness with patches about three times thicker, possibly implicated in the nucleation.
Wntless functions in mature osteoblasts to regulate bone mass
Authors: Zhong Zhendong , Zylstra-Diegel Cassandra R. , Schumacher Cassie A. , Baker Jacob J. , Carpenter April C. , Rao Sujata , Yao Wei , Guan Min , Helms Jill A. , Lane Nancy E. , Lang Richard A. , Williams Bart O.
Published: June 2012

Recent genome-wide association studies of individuals of Asian and European descent have found that SNPs located within the genomic region (1p31.3) encoding the Wntless (Wls)/Gpr177 protein are associated significantly with reduced bone mineral density. Wls
/
Gpr177 is a newly identified chaperone protein that specifically escorts Wnt ligands for secretion. Given the strong functional association between the Wnt signaling pathways and bone development and homeostasis, we generated osteoblast-specific Wls-deficient (
Ocn-Cre;Wls-flox
) mice. Homozygous conditional knockout animals were born at a normal Mendelian frequency. Whole-body dual-energy X-ray absorptiometry scanning revealed that bone-mass accrual was significantly inhibited in homozygotes as early as 20 d of age. These homozygotes had spontaneous fractures and a high frequency of premature lethality at around 2 mo of age. Microcomputed tomography analysis and histomorphometric data revealed a dramatic reduction of both trabecular and cortical bone mass in homozygous mutants. Bone formation in homozygotes was severely impaired, but no obvious phenotypic change was observed in mice heterozygous for the conditional deletion. In vitro studies showed that
Wls
-deficient osteoblasts had a defect in differentiation and mineralization, with significant reductions in the expression of key osteoblast differentiation regulators. In summary, these results reveal a surprising and crucial role of osteoblast-secreted Wnt ligands in bone-mass accrual.
General strategy for the generation of human antibody variable domains with increased aggregation resistance
Authors: Dudgeon Kip , Rouet Romain , Kokmeijer Iris , Schofield Peter , Stolp Jessica , Langley David , Stock Daniela , Christ Daniel
Published: June 2012

The availability of stable human antibody reagents would be of considerable advantage for research, diagnostic, and therapeutic applications. Unfortunately, antibody variable heavy and light domains (VHand VL) that mediate the interaction with antigen have the propensity to aggregate. Increasing their aggregation resistance in a general manner has proven to be a difficult and persistent problem, due to the high level of sequence diversity observed in human variable domains and the requirement to maintain antigen binding. Here we outline such an approach. By using phage display we identified specific positions that clustered in the antigen binding site (28, 30–33, 35 in VHand 24, 49–53, 56 in VL). Introduction of aspartate or glutamate at these positions endowed superior biophysical properties (non-aggregating, well-expressed, and heat-refoldable) onto domains derived from common human germline families (VH3 and Vκ1). The effects of the mutations were highly positional and independent of sequence diversity at other positions. Moreover, crystal structures of mutant VHand VLdomains revealed a surprising degree of structural conservation, indicating compatibility with VH/VLpairing and antigen binding. This allowed the retrofitting of existing binders, as highlighted by the development of robust high affinity antibody fragments derived from the breast cancer therapeutic Herceptin. Our results provide a general strategy for the generation of human antibody variable domains with increased aggregation resistance.
Culture of Plains Topminnow in a Pond Constructed for Species Conservation
Authors: Schumann David A , Pasbrig Chelsey A , Koupal Keith D , Hoback W Wyatt
Published: June 2012

The plains topminnow Fundulus sciadicus appears to be experiencing reductions in geographic range and local abundance, which has led to regional protection throughout its native range. Conservation of this species may require introductions to reestablish populations at known historic locations. Therefore, a pond was constructed during September 2007 to house a refuge population of plains topminnow in Nebraska. A total of 123 plains topminnow were stocked into the pond in two stocking events during 2008. Plains topminnow populations were sampled throughout 2008 and mark–recapture population estimates were conducted after reproductive events during 2009 and 2010 resulting in estimates of 9,844 ± 1,698 (mean ± SD) and 3,974 ± 452 plains topminnow, respectively. Mean fish weight was used as an estimate of pond biomass, which was 28.4 kg/ha in 2009 and 44.9 kg/ha in 2010. Reproduction was first observed in 2008 and in each following year, and a strong year-class was produced in 2009, which suggested there were factors that limited reproduction in the other 2 years. Extensive culture may be an effective way to rear plains topminnow and related species. However, more research is needed to determine factors that affect year-class strength and production.
Evaluation of Plant and Animal Protein Sources as Partial or Total Replacement of Fish Meal in Diets for Nile Tilapia Fry and Juvenile Stages
Authors: Thompson Kenneth R , Velasquez Alejandro , Patterson Joshua T , Metts Linda S , Webster Carl D , Brady Yolanda J , Gannam Ann L , Twibell Ron G , Ostrand Susan L
Published: June 2012

Two feeding trials were conducted in a closed system with Nile tilapia Oreochromis niloticus fry (mean weight, 0.10 g; experiment 1) and juveniles (mean weight, 2.84 g; experiment 2) to examine the effects of total replacement of fish meal (FM), with and without supplementation of dl-methionine (Met) and l-lysine (Lys), by plant protein sources. In experiment 1, fry were fed nine isoenergetic (available energy [AE] = 4.0 kcal/g of diet) and isoproteic (40% protein as fed basis) practical diets containing protein primarily from soybean meal (SBM), with and without essential Met and Lys. After 5 weeks, final individual weight (FW; g/fish) and percent weight gain (PWG) of fry fed diet 1 (control with 20% FM) was significantly higher (P < 0.05) compared with fry fed all other diets, while fry fed diet 9 containing 46% SBM and 22% feed-grade poultry by-product meal PBM) was significantly higher than all other diets (diets 2–8). Quantity of diet fed and percent survival did not differ significantly (P > 0.05) among all diets. In experiment 2, juveniles were fed six isoenergetic (AE = 4.0 kcal/g of diet) and isoproteic (35% protein as fed basis) practical diets containing protein primarily from SBM, soybean protein concentrate (SPC), feed-grade PBM, or combinations of those. After 7 weeks, mean FW, PWG, and amount of diet fed for fish fed diets 1 (control with 20% FM) and 6 (with 20% SPC and 20% PBM) were significantly higher (P < 0.05) compared with juveniles fed all other diets. Feed conversion ratio (FCR) was similar among treatments, but fish fed diet 5 (with 36% SPC and 0% FM) recorded the highest FCR value. Likewise, protein efficiency ratio (PER) was similar among treatments; however, PER in juveniles fed diets 3 (with 52% SBM and 0% FM) and 5 were significantly lower than in fish fed all other diets. Overall, no significant (P > 0.05) difference was found in percent survival, which averaged 92.6% among all diets fed. These data suggest that Nile tilapia fry cannot utilize diets containing high levels (>75%) of SBM when no animal protein ingredient is added, even with supplemental Met and Lys. However, a diet containing 20% SPC and 20% feed-grade PBM appears to be suitable for juvenile Nile tilapia, which may help reduce diet costs and allow for sustainable production.
Evaluation of Off-Flavor in Pond-Raised Channel Catfish following Partial Crop Harvest
Authors: Schrader Kevin K , Tucker Craig S
Published: June 2012

Ponds used to raise channel catfish Ictalurus punctatus in the southeastern United States often contain more food-sized catfish than processors can accept at one time. Fish remaining after initial harvest are returned to the pond and harvested again as soon as possible based upon processor demands. Some catfish farmers report that catfish crops initially declared “on-flavor” appear to develop off-flavors soon after the first harvest, which postpones harvest of the remaining population and delays subsequent production. We conducted a 9-month study on a commercial catfish farm in northwest Mississippi to determine whether fish systematically develop off-flavors after partial fish harvest and, if so, the type and origin of the flavor. Channel catfish and water samples were obtained from 12 ponds before initial harvest and then at intervals for 2 weeks after harvest. Water and catfish fillet samples were analyzed for geosmin and 2-methylisoborneol (MIB). Phytoplankton were identified and counted microscopically. Catfish fillets were also used in sensory analysis to determine quality and intensity of off-flavor. In most ponds, MIB levels decreased or remained unchanged in pond water after the first seining while geosmin levels remained very low (<10 ng/L) in all ponds. Analysis indicated that mean MIB concentrations in catfish fillets either decreased or were unchanged after the initial harvest. Similar results were found for geosmin concentrations in catfish fillets. There was also no systematic change in fillet flavor quality as determined by sensory analysis. The MIB-producing cyanobacterium Planktothrix perornata was found in only three ponds, and the abundance of P. perornata decreased in two ponds after initial harvest and transiently increased in the third pond. Overall, we found no systematic changes in fish flavor quality after partial fish harvest and no indication that harvest activities changed ecological conditions that would cause an increase in odor-producing cyanobacteria.
The classification of connected-homogeneous digraphs with more than one end
Authors: Hamann Matthias , Hundertmark Fabian
Published: June 2012

We classify the connected-homogeneous digraphs with more than one end. We further show that if their underlying undirected graph is not connected-homogeneous, they are highly-arc-transitive.
GO-Elite: a flexible solution for pathway and ontology over-representation
Authors: Zambon Alexander C. , Gaj Stan , Ho Isaac , Hanspers Kristina , Vranizan Karen , Evelo Chris T. , Conklin Bruce R. , Pico Alexander R. , Salomonis Nathan
Published: June 2012

Summary: We introduce GO-Elite, a flexible and powerful pathway analysis tool for a wide array of species, identifiers (IDs), pathways, ontologies and gene sets. In addition to the Gene Ontology (GO), GO-Elite allows the user to perform over-representation analysis on any structured ontology annotations, pathway database or biological IDs (e.g. gene, protein or metabolite). GO-Elite exploits the structured nature of biological ontologies to report a minimal set of non-overlapping terms. The results can be visualized on WikiPathways or as networks. Built-in support is provided for over 60 species and 50 ID systems, covering gene, disease and phenotype ontologies, multiple pathway databases, biomarkers, and transcription factor and microRNA targets. GO-Elite is available as a web interface, GenMAPP-CS plugin and as a cross-platform application.

Availability:  http://www.genmapp.org/go_elite

Contact:  nsalomonis@gladstone.ucsf.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
VAT: a computational framework to functionally annotate variants in personal genomes within a cloud-computing environment
Authors: Habegger Lukas , Balasubramanian Suganthi , Chen David Z. , Khurana Ekta , Sboner Andrea , Harmanci Arif , Rozowsky Joel , Clarke Declan , Snyder Michael , Gerstein Mark
Published: June 2012

Summary: The functional annotation of variants obtained through sequencing projects is generally assumed to be a simple intersection of genomic coordinates with genomic features. However, complexities arise for several reasons, including the differential effects of a variant on alternatively spliced transcripts, as well as the difficulty in assessing the impact of small insertions/deletions and large structural variants. Taking these factors into consideration, we developed the Variant Annotation Tool (VAT) to functionally annotate variants from multiple personal genomes at the transcript level as well as obtain summary statistics across genes and individuals. VAT also allows visualization of the effects of different variants, integrates allele frequencies and genotype data from the underlying individuals and facilitates comparative analysis between different groups of individuals. VAT can either be run through a command-line interface or as a web application. Finally, in order to enable on-demand access and to minimize unnecessary transfers of large data files, VAT can be run as a virtual machine in a cloud-computing environment.

Availability and Implementation: VAT is implemented in C and PHP. The VAT web service, Amazon Machine Image, source code and detailed documentation are available at vat.gersteinlab.org.

Contact: lukas.habegger@yale.edu or mark.gerstein@yale.edu

Supplementary Information:  Supplementary data are available at Bioinformatics online.
The Enduring Legacy of the Turing Machine
Authors: Fortnow Lance
Published: June 2012

The Church-Turing thesis has stood the test of time, capturing computation models Turing could not have conceived of, including digital computation, probabilistic, parallel and quantum computers and the Internet. The thesis has become accepted doctrine in computer science and the ACM has named its highest honor after Turing. Many now view computation as a fundamental part of nature, like atoms or the integers.
A miRNA-regulatory network explains how dysregulated miRNAs perturb oncogenic processes across diverse cancers
Authors: Plaisier Christopher L. , Pan Min , Baliga Nitin S.
Published: June 2012

Genes regulated by the same miRNA can be discovered by virtue of their coexpression at the transcriptional level and the presence of a conserved miRNA-binding site in their 3′ UTRs. Using this principle we have integrated the three best performing and complementary algorithms into a framework for inference of regulation by miRNAs (FIRM) from sets of coexpressed genes. We demonstrate the utility of FIRM by inferring a cancer–miRNA regulatory network through the analysis of 2240 gene coexpression signatures from 46 cancers. By analyzing this network for functional enrichment of known hallmarks of cancer we have discovered a subset of 13 miRNAs that regulate oncogenic processes across diverse cancers. We have performed experiments to test predictions from this miRNA-regulatory network to demonstrate that miRNAs of the miR-29 family (miR-29a, miR-29b, and miR-29c) regulate specific genes associated with tissue invasion and metastasis in lung adenocarcinoma. Further, we highlight the specificity of using FIRM inferences to identify miRNA-regulated genes by experimentally validating that miR-767-5p, which partially shares the miR-29 seed sequence, regulates only a subset of miR-29 targets. By providing mechanistic linkage between miRNA dysregulation in cancer, their binding sites in the 3′UTRs of specific sets of coexpressed genes, and their associations with known hallmarks of cancer, FIRM, and the inferred cancer miRNA-regulatory network will serve as a powerful public resource for discovery of potential cancer biomarkers.
nFuse: Discovery of complex genomic rearrangements in cancer using high-throughput sequencing
Authors: McPherson Andrew , Wu Chunxiao , Wyatt Alexander W. , Shah Sohrab , Collins Colin , Sahinalp S. Cenk
Published: June 2012

Complex genomic rearrangements (CGRs) are emerging as a new feature of cancer genomes. CGRs are characterized by multiple genomic breakpoints and thus have the potential to simultaneously affect multiple genes, fusing some genes and interrupting other genes. Analysis of high-throughput whole-genome shotgun sequencing (WGSS) is beginning to facilitate the discovery and characterization of CGRs, but further development of computational methods is required. We have developed an algorithmic method for identifying CGRs in WGSS data based on shortest alternating paths in breakpoint graphs. Aiming for a method with the highest possible sensitivity, we use breakpoint graphs built from all WGSS data, including sequences with ambiguous genomic origin. Since the majority of cell function is encoded by the transcriptome, we target our search to find CGRs that underlie fusion transcripts predicted from matched high-throughput cDNA sequencing (RNA-seq). We have applied our method, nFuse, to the discovery of CGRs in publicly available data from the well-studied breast cancer cell line HCC1954 and primary prostate tumor sample 963. We first establish the sensitivity and specificity of the nFuse breakpoint prediction and scoring method using breakpoints previously discovered in HCC1954. We then validate five out of six CGRs in HCC1954 and two out of two CGRs in 963. We show examples of gene fusions that would be difficult to discover using methods that do not account for the existence of CGRs, including one important event that was missed in a previous study of the HCC1954 genome. Finally, we illustrate how CGRs may be used to infer the gene expression history of a tumor.
Supramolecular networks in (9-fluoro-4H-chromeno[4,3-c]isoxazol-3-yl)methanol and its 9-chloro analogue at 100 K
Authors: Rajalakshmi P. , Srinivasan N. , Krishnakumar R. V. , Razak Ibrahim Abdul , Rosli Mohd Mustaqim
Published: June 2012

The title compounds, (9-fluoro-4H-chromeno[4,3-c]isoxazol-3-yl)methanol, C11H8FNO3, (I), and (9-chloro-4H-chromeno[4,3-c]isoxazol-3-yl)methanol, C11H8ClNO3, (II), crystallize in the orthorhombic space groupPbcawithZ′ = 1 and the triclinic space groupP\overline{1} withZ′ = 6, respectively. The simple replacement of F by Cl in the main molecular scaffold of (I) and (II) results in significant differences in the intermolecular interaction patterns and a corresponding change in the point-group symmetry fromD2htoCi=S2. These striking differences are manifested through the presence of C—H...F and the absence of O—H...O and C—H...O interactions in (I), and the absence of C—H...Cl and the presence of O—H...O and C—H...O interactions in (II). However, the geometry of the synthons formed by the O—H...N and O—H...X(X= F or Cl) interactions observed in the constitution of the supramolecular networks of both (I) and (II) remains similar. Also, C—H...O interactions are not preferred in the presence of F in (I), while they are much preferred in the presence of Cl in (II).
The effect of partial methylation of the glycine amino group on crystal structure inN,N-dimethylglycine and its hemihydrate
Authors: Minkov Vasily S. , Boldyreva Elena V.
Published: June 2012

N,N-Dimethylglycine, C4H9NO2, and its hemihydrate, C4H9NO2·0.5H2O, are discussed in order to follow the effect of the methylation of the glycine amino group (and thus its ability to form several hydrogen bonds) on crystal structure, in particular on the possibility of the formation of hydrogen-bonded `head-to-tail' chains, which are typical for the crystal structures of amino acids and essential for considering amino acid crystals as mimics of peptide chains. Both compounds crystallize in centrosymmetric space groups (PbcaandC2/c, respectively) and have twoN,N-dimethylglycine zwitterions in the asymmetric unit. In the anhydrous compound, there are no head-to-tail chains but the zwitterions formR44(20) ring motifs, which are not bonded to each other by any hydrogen bonds. In contrast, in the crystal structure ofN,N-dimethylglycinium hemihydrate, the zwitterions are linked to each other by N—H...O hydrogen bonds into infiniteC22(10) head-to-tail chains, while the water molecules outside the chains provide additional hydrogen bonds to the carboxylate groups.
Forceps birth delivery, allergic sensitisation and asthma: a population‐based cohort study
Authors: Hancox R. J. , Landhuis C. E. , Sears M. R.
Published: June 2012

Background

Studies indicate an increased risk of allergies among children born by caesarean section, possibly because immune development is altered by avoiding exposure to maternal vaginal flora. It is unknown if other obstetric interventions are associated with allergies.

Objective

To assess associations between delivery with forceps assistance and development of atopy and asthma.

Methods

In a population‐based cohort of 1037 individuals born in 1972/73, atopy was assessed by skin‐prick tests for common allergens at ages 13 and 32 years. A history of asthma was obtained at the same ages. Associations between birth with forceps assistance, atopy and asthma were assessed with adjustments for sex, head circumference at birth, parental atopy disease, birth order and socio‐economic status.

Results

Children born using forceps were more likely to have atopy at ages 13 (53% vs. 44%) and 32 (68% vs 59%). They were also more likely to have asthma (21% vs. 11% and 23% vs. 16% at ages 13 and 32 respectively). Except for asthma at age 13, these associations were not statistically significant after adjustment for multiple confounding factors.

Conclusions & Clinical Relevance

Delivery with forceps assistance is associated with an increased risk of atopy and asthma, but the associations were weaker after adjustment for confounding factors. The previously reported association between caesarean birth and atopic disease may be due to confounding rather than altered exposure to maternal flora, although other factors associated with a difficult labour cannot be ruled out.
Long‐term histopathology of allografts in sensitized kidney recipients
Authors: Miura Masayoshi , Harada Hiroshi , Fukasawa Yuichiro , Hotta Kiyohiko , Itoh Yosuke , Tamaki Tohru
Published: June 2012

Successful desensitization therapy has brought satisfying short‐term outcomes in the recipients with anti‐donor antibody. We analyzed the long‐term pathology of the allografts in the sensitized kidney recipients. Eleven stable recipients after desensitization against positive flow cytometry T‐cell crossmatch (FTXM) were included. They were divided into two groups, based on the protocol biopsies findings at three to eight yr (group 1: subclinical glomerulitis and/or peritubular capillaritis, n = 5 and group 2: no rejection, n = 6). Estimated glomerular filtration rate (eGFR), presence of donor‐specific antibody (DSA), mean channel shift (MCS) of FTXM, urine protein levels, acute antibody‐mediated rejection (AAMR) episodes, and protocol biopsy findings were compared. Chronic transplant glomerulopathy was found in final biopsy of all group 1 cases. DSA was positive in 60% but C4d was positive in 20% case of the group 1. The history of AAMR was only found in the group 1. There was no difference in eGFR decline or proteinuria. The MCS of FTXM was higher in the group 1. The recipients with AAMR history, high MCS in FTXM, and subclinical microvascular inflammation in the early protocol biopsies have risk for developing chronic rejection in long term.
A case of de novo focal segmental glomerulosclerosis occurred one and half years after kidney transplantation supposed to be caused by calcineurin inhibitor
Authors: Ikeda Yoichiro , Nangaku Masaomi , Ishibashi Yoshitaka , Hirohama Daigoro , Uozaki Hiroshi , Tojo Akihiro , Ishikawa Akira , Fujita Toshiro
Published: June 2012

A 64‐yr‐old man with end‐stage kidney disease caused by hypertensive nephrosclerosis underwent living‐unrelated ABO‐identical kidney transplantation (KTx) at the age of 60 yr from his 60‐yr‐old wife. Maintenance trough concentration of cyclosporine A (CsA) was 100 ± 30 ng/mL. Five months after KTx, proteinuria gradually increased to around 1 g/d. TRBx at eight months after KTx revealed the new‐onset alteration of mild arteriolosclerosis with intimal hyalinosis, which might reflect calcineurin inhibitor (CNI)–associated arteriopathy (CAA). Nearly one and half years after KTx, urinary protein excretion became nearly 2 g/d. TRBx revealed the advanced CAA and findings of focal segmental glomerulosclerosis (FSGS). Then, CNI was switched from CsA to tacrolimus (TAC). TRBx at two and half years after KTx revealed progressed arteriolar transmural thickening and striped fibrosis, which were supposed to be induced by an increase in serum TAC concentration because of acute enterocolitis. Then, TAC dose was reduced to serum trough concentration 5–8 ng/mL, but urinary protein excretion was increased up to 10 g/d. Reduction of TAC to trough concentration 2.0 ± 0.5 ng/mL reduced urinary protein excretion. Attempts to elevate TAC trough concentration within normal range (4–8 ng/mL) reproducibly induced the recurrence of an increase in sCr or urinary protein excretion. All these findings supported the etiology of graft dysfunction, and proteinuria of this case was FSGS.
Granulomatous tubulointerstitial nephritis in a renal allograft: three cases report and review of literature
Authors: Hotta Kiyohiko , Fukasawa Yuichiro , Sasaki Hajime , Seki Toshimori , Togashi Masaki , Harada Hiroshi
Published: June 2012

Granulomatous interstitial nephritis (GIN) is a rare histologic diagnosis in renal allografts. We report three cases with GIN. Case 1: a 37‐yr‐old woman received a kidney from her mother. On follow‐up 15 months later, serum creatinine was increased and a graft biopsy showed epithelioid granuloma in the center of massive mononuclear cell infiltration. She had presented with refractory urinary tract infection treated with antibiotics before biopsy. The case was presumed to be GIN associated with UTI or hypersensitivity to medication. Case 2: a 47‐yr‐old woman received a second graft from a non‐heart‐beating donor. A protocol graft biopsy was performed six months after transplantation and showed several granulomatous nodules. She was followed closely without therapy. Case 3: a 27‐yr‐old woman received an ABO‐incompatible kidney from her father. A protocol graft biopsy was performed three months after transplantation and showed granulomatous reaction with severe mononuclear cell infiltration. She received steroid pulse therapy. The two latter patients had no obvious factor contributing to GIN. Therefore, they were presumed to have idiopathic GIN. Infection is considered to be the main causative factor of GIN in renal allografts. This paper describes rare cases of GIN that had no infectious episode in the renal allografts.
A case of BK virus nephropathy and cytomegalovirus infection concurrent with plasma cell–rich acute rejection
Authors: Mafune Aki , Tanno Yudo , Yamamoto Hiroyasu , Kobayashi Akimitsu , Saigawa Hajime , Yokoo Takashi , Hayakawa Hiroshi , Miyazaki Youichi , Yokoyama Keitaro , Yamaguchi Yutaka , Hosoya Tatsuo
Published: June 2012

The BK virus is a double‐stranded DNA virus to which 90% of adults have been exposed. BK virus infections typically result in an oral or respiratory infection; however, BK virus reactivation is an infectious disease of concern in kidney transplant recipients. The prevalence of BK virus nephropathy (BKN) in kidney transplant recipients is approximately 5%, and most cases occur within one yr after kidney transplantation. Graft survival of BKN is reported to be 30–60%, and the standard treatment strategy for BKN is reducing immunosuppressive therapy and close monitoring for rejection. Viral infection is most common in the early post‐transplantation phase, and BKN or acute rejection is one of the major factors involved in graft loss. However, in this report, we describe the successful management of BKN and cytomegalovirus infection concurrent with plasma cell–rich acute rejection.
Polyomavirus nephropathy – recent pathological diagnostic problems and the report from the 2011 Banff meeting
Authors: Nishi Shinichi
Published: June 2012

Nishi S. Polyomavirus nephropathy – recent pathological diagnostic problems and the report from the 2011 Banff meeting.

Abstract:  Polyomavirus nephropathy (PVN) is a cause of renal allograft dysfunction. Early detection of pathological abnormalities is not easy even in cases with urine decoy cells or polyomavirus viremia. A pathological classification for PVN was proposed by the Banff PVN working group, although the availability of the proposed schema has not been extensively evaluated in the clinical field. At the Banff meeting in 2011, the PVN working group reported the results of the evaluation on interobserver reproducibility and a clinicopathological study of PVN stages and renal outcome. Fair or good reproducibility was noted, although the PVN classification required further modification.
Remote Midwifery in Nunavik, Québec, Canada: Outcomes of Perinatal Care for the Inuulitsivik Health Centre, 2000–2007
Authors: Van Wagner Vicki , Osepchook Claire , Harney Evelyn , Crosbie Colleen , Tulugak Mina
Published: June 2012

Background

The Inuulitsivik midwifery service is a community‐based, Inuit‐led initiative serving the Hudson coast of the Nunavik region of northern Québec. This study of outcomes for the Inuulitsivik birth centers, aims to improve understanding of maternity services in remote communities.

Methods

We used a retrospective review of perinatal outcome data collected at each birth at the Inuulitsivik birth centers to examine outcomes for 1,372 labors and 1,382 babies from 2000 to 2007. Data were incomplete for some indicators, particularly for transfers to Montreal.

Results

Findings revealed low rates of intervention with safe outcomes in this young, largely multiparous “all risk” Inuit population. Ninety‐seven percent of births were documented as spontaneous vaginal deliveries, and 85 percent of births were attended by midwives. Eighty‐six percent of the labors occurred in Nunavik, whereas 13.7 percent occurred outside Nunavik. The preterm birth rate was found to be 10.6 percent. Postpartum hemorrhage was documented in 15.4 percent of women; of these cases, 6.9 percent had blood loss greater than 1,000 mL. Four fetal deaths (2.9 per 1,000) and five neonatal deaths (< 3.6 per 1,000) were documented. Nine percent (9%) of births involved urgent transfers of mother or baby. The most common reasons for medical evacuation were preterm labor and preeclampsia, and preterm birth was the most common reason for urgent neonatal transfer.

Conclusions

The success of the Innulitsivik midwifery service rests on the knowledge and skills of the Inuit midwives, and support of an interprofessional health team. Our study points to the potential for safe, culturally competent local care in remote communities without cesarean section capacity. Our findings support recommendations for integration of midwifery services and Aboriginal midwifery education programs in remote communities. (BIRTH 39:3 September 2012)
Age as Risk Factor for Helicobacter pylori Recurrence in Children in Vietnam
Authors: Nguyen Thi Viet Ha , Bengtsson Carina , Nguyen Gia Khanh , Yin Li , Hoang Thi Thu Ha , Phung Dac Cam , Sörberg Mikael , Granström Marta
Published: June 2012

Background

The determinants for acquisition of
Helicobacter pylori infection remain incompletely understood. The study aim was to investigate risk factors for recurrence in children in Vietnam during 1 year immediately following successful
H. pylori eradication.

Materials and methods

In a prospective longitudinal study, 136 children, 3–15 years of age, were seen every 3 months for a total of four visits.
Helicobacter pylori infection status was determined by an antigen‐in‐stool test (Premier Platinum HpSA PLUS) on samples obtained at each visit. A questionnaire was filled out at the start of the study.

Results

After 1 year, 30 children had become
H. pylori positive, while 17 were lost to follow‐up. Low age was the most prominent independent risk factor for recurrence: adjusted hazard ratio (HR) among children aged 3–4, 5–6, and 7–8 years, relative to those aged 9–15 years, were, respectively, 14.3 [95% CI 3.8–53.7], 5.4 [1.8–16.3] and 2.6 [0.7–10.4]. Surprisingly, female sex tended to be associated with increased risk (adjusted HR among girls relative to boys 2.5 [95% CI 1.1–5.9]). No other factors such as sibship size, birth order, bed sharing, sanitary standards, or factual antibiotic dose per kilo bodyweight in the eradication trial were found to be significant risk factors for re‐infection.

Conclusions

The main risk factor for recurrence with
H. pylori was found to be age, with the youngest children running the greatest risk. The finding lends support to the observation that early childhood may be the main age of acquisition of
H. pylori infection and for postponing attempts of eradication in high‐prevalence areas unless motivated for medical reasons.
Skin Temperature during Cutaneous Wound Healing in an Equine Model of Cutaneous Fibroproliferative Disorder: Kinetics and Anatomic‐Site Differences
Authors: Celeste Christophe J. , Deschesne Karine , Riley Christopher B. , Theoret Christine L.
Published: June 2012

Objective

To map skin temperature kinetics, and by extension skin blood flow throughout normal or abnormal repair of full‐thickness cutaneous wounds created on the horse body and limb, using infrared thermography.

Study Design

Experimental.

Animals

Standardbreds (n = 6), aged 3–4 years.

Methods

Three cutaneous wounds were created on the dorsolateral surface of each metacarpus and on the lateral thoracic wall. Thoracic skin wounds and those on 1 randomly chosen forelimb healed by second intention without a bandage, whereas contralateral limb wounds were bandaged to induce formation of exuberant granulation tissue (EGT). Thermal data were collected from all planned wound sites before the surgical procedure (baseline), and at 24, 48, 96 hours, 1, 2, and 4 weeks after wounding. Data were analyzed using repeated measures ANOVA and a priori contrasts submitted to Bonferroni sequential correction. Level of significance was P < .05.

Results

Cutaneous wound temperature (CWT) increased temporally from preoperative period to week 1 postwounding, independently of anatomic location (P < .0001). CWT of limb wounds was significantly less than that of body wounds throughout healing (P < .01). CWT of limb wounds managed with bandages and developing EGT was significantly less than that of unbandaged limb wounds, which did not develop EGT (P ≤ .01).

Conclusions

CWT varied with anatomic location and throughout healing. CWT of wounds developing EGT was significantly less than that of wounds without EGT.
CathAway fistula vascular access program achieves improved outcomes and sets a new standard of treatment for end‐stage renal disease
Authors: Wilson Steven M. , Mayne Tracy J. , Krishnan Mahesh , Holland Janet , Volz Abbe , Good Lori S. , Nissenson Allen R.
Published: June 2012

Hemodialysis patients using central venous catheters (CVCs) for vascular access are at greater risk of infection and death vs. arterial venous fistula (AVF). In 2008, DaVita initiated the CathAway quality improvement initiative, a multidisciplinary program to reduce CVC use in favor of AVF. Our retrospective analysis examined CVC use for incident (≤90 days) and prevalent (>90 days) patients receiving hemodialysis in the years 2006 to 2010. Outcomes included annual mean percentage of patients with CVCs, new CVC placements per 100 patient years, CVC survival, and percentage patient days with CVC. Over 152,000 patient records were reviewed. Between 76.2% and 79.7% of incident patients used a CVC annually, but for prevalent patients, the proportion decreased from 41.1% in 2006 to 33.5% in 2010. The number of new CVC placements per 100 patient years increased slightly for incident patients but fell annually from 64.8 in 2006 to 55.2 in 2010 for prevalent patients. The percentage of treatment days with CVCs was stable among incident patients (70.4%–74.3%) but fell among prevalent patients from 26.1% in 2006 to 16.5% in 2010. The mean duration of CVC use in incident patients was between 53.0 days (SD, 27.8) in 2006 and 54.1 days (SD, 28.1) in 2009, and for prevalent patients between 158.9 days (SD, 123.0) in 2006 and 128.1 days (SD, 112.0) in 2010. CathAway significantly decreased CVC use in prevalent hemodialysis patients. Decreasing incident patient use will require improvements in predialysis care.
Hot‐Pressing Method to Consolidate Gd3(Al,Ga)5O12:Ce Garnet Scintillator Powder for use in an X‐ray CT Detector
Authors: Kanai Tsuneyuki , Satoh Makoto , Miura Ichiro
Published: June 2012

We have developed a hot‐pressing method for consolidating garnet scintillator powder of composition Gd3(Al,Ga)5O12:Ce. Thermodynamic analysis revealed that gallium oxide, which was a constituent of the garnet scintillator powder, would react with the graphite mold beginning at 950°C and would be reduced to gallium metal. To prevent this reaction during hot‐pressing, a reaction barrier material was placed between the graphite mold and the scintillator powder. As for the reaction barrier material, 3GdAlO3–Al2O3 powder calcined at 1100°C was found to be suitable because the material provided two important characteristics: the same thermal expansion coefficient as the scintillator material and good sinterability. The Gd3(Al,Ga)5O12:Ce garnet scintillator powder was hot pressed at 1475°C for 4 h in vacuum, followed by annealing at 1300°C for 4 h in oxygen atmosphere. The thus obtained garnet scintillator successfully satisfied the necessary requirements for use in an X‐ray computed tomography detector.
Role of nicotine in gallbladder carcinoma: A preliminary report
Authors: Basu Somprakas , Priya Rupesh , Singh Tej Bali , Srivastava Pradeep , Mishra Pradeep K. , Shukla Vijay K.
Published: June 2012

Objective

To assess the role of nicotine in gallbladder carcinoma and its association with the stage and degree of cancer differentiation.

Methods

Tissue samples from gallbladder were obtained from 20 patients with gallbladder cancer and 20 age‐ and gender‐matched patients with cholelithiasis who served as the control group. Gallbladder tissue (2 g) was extracted and analyzed for nicotine content using capillary gas chromatography. Nitrogen was used as the carrier gas. Standard curves of nicotine in methanol were made by injecting the internal standards.

Results

A significantly higher tissue nicotine concentration was observed in the gallbladder carcinoma group than that in the control group (179.63 ng/mgvs6.00 ng/mg,P < 0.001). The stage and degree of cancer differentiation did not seem to affect the nicotine levels. Gallbladder tissue contained a significantly higher nicotine concentration in smokers with cancer compared with those in the control group (1570.00 ng/mgvs232.25 ng/mg,P < 0.001). Interestingly, non‐smokers in cancer group also had a higher nicotine concentration than the control group (161.50 ng/mgvs4.00 ng/mg,P = 0.002).

Conclusion

Nicotine is selectively concentrated in malignant gallbladder tissue irrespective of smoking status, showing its strong association with gallbladder cancer.
Over‐Expression of Cofilin‐1 and Phosphoglycerate Kinase 1 in Astrocytomas Involved in Pathogenesis of Radioresistance
Authors: Yan Hua , Yang Kun , Xiao Hong , Zou Yuan‐Jie , Zhang Wen‐Bin , Liu Hong‐Yi
Published: June 2012

Introduction

Astrocytoma is among the most common intracranial tumors and radiotherapy is typically used after its resection. One of the outstanding problems encountered in the treatment is radioresistance. The lack of efficient biomarkers for evaluating the radiosensitivity of glioma precludes advances in treatment of astrocytoma and remains the most fatal cancer.

Methods

To identify potential biomarkers for assessing the radioresistance of astrocytomas, the following study investigated the proteome of astrocytoma in surgical samples from 15 typical patients. The patients were divided into 2 groups: radioresistant vs. radiosensitive (controls). Proteome was assessed using two‐dimensional liquid chromatography tandem mass spectrometry (2D‐LC–MS/MS). Western blot was adopted to confirm the differential expression of proteins.

Results

A total of 36 proteins were expressed differently between the 2 groups, represented by cofilin‐1 and phosphoglycerate kinase 1 (PGK1), which up‐regulated significantly in radioresistant astrocytomas though there was no obvious morphological change of tumors. Western blot analysis revealed elevated levels of protein extracts in radioresistant astrocytomas compared with the radiosensitive group.

Conclusions

The results indicated cofilin‐1 enhances the motility of tumor cells which is important invasive potential of malignancy. PGK1 is metabolic enzyme and seems to be correlated with the negative prognosis following radiotherapy. Thus, cofilin‐1 and PGK1 might be involved in the radioresistant phenotype and are potential biomarkers for developing better therapeutic methods.
Multifocal cutaneous histiocytic sarcoma in a young dog and review of histiocytic cell immunophenotyping
Authors: Mastrorilli Cinzia , Spangler Elizabeth A. , Christopherson Peter W. , Aubry Oceane A. , Newton Joseph C. , Smith Annette N. , Kennis Robert A. , Weismann Jaime L. , Moore Peter F.
Published: June 2012

A 9‐month‐old male Great Dane had progressive generalized nodular dermatopathy for several months. There were > 100 raised, alopecic, firm, painful nodules throughout the skin. Aspirates from several lesions yielded moderate numbers of irregularly round or polygonal to spindle‐shaped cells with mild to moderate anisocytosis and few inflammatory cells, and the cytologic interpretation was proliferation of mesenchymal or histiocytic cells. On histopathologic examination, nodules were composed of densely packed sheets of round to spindle‐shaped cells with mild anisokaryosis and low mitotic activity. Multifocal histiocytic sarcoma with a spindle‐cell pattern was diagnosed based on morphologic features and intense expression of CD18. Additional immunophenotypic analysis on frozen sections of tissue confirmed the diagnosis of histiocytic sarcoma; expression of CD18, CD45, CD1a, CD11b, and CD11c, limited expression of Thy‐1 (CD90) and CD80, and lack of expression of CD4, CD11d, and CD86 indicated that the cells were likely interstitial dendritic cells; a review of reactive and neoplastic dendritic cells is provided. Based on staging, internal organs were not affected. Sequential treatment with lomustine and doxorubicin failed to prevent progression of the cutaneous lesions, and the dog died 3 months after initial diagnosis. At necropsy, a focus of neoplastic cells was present in one lymph node, but except for skin other organs were not involved. The clinical presentation of histiocytic sarcoma may be unusual, and neoplastic cells may lack overt features of malignancy on cytologic and histopathologic examination. In some instances, immunophenotyping is required to differentiate histiocytic sarcoma from other histiocytic disorders.
Analysis of Brinkman-Extended Darcy Flow in Porous Media and Experimental Verification Using Metal Foam
Authors: Dukhan Nihad
Published: June 2012

Momentum transport in porous media exists in numerous engineering and process applications, e.g., ground water pollution, storage of nuclear waste, heat exchangers, and chemical reactors. In many of such applications, the porous medium is confined by solid boundaries. These impermeable boundaries give rise to shear stress and boundary layers. The Brinkman-extended Darcy equation describes the momentum transport due to Newtonian fluid flow in confined porous media. This equation is solved analytically in a cylindrical system, employing an existing fully-developed boundary-layer concept particular to porous media flows. The volume-averaged velocity increases as the distance from the boundary increases reaching a maximum at the center. The mean and maximum velocities are obtained and their behavior is investigated in terms of pertinent flow parameters. The friction factor is defined based on the mean velocity and is found to be inversely proportional to the Reynolds number, the Darcy number, and the mean velocity. The analytical results are verified by experiments using two types of metal foam. In the Darcy regime, reasonably good agreement is found between the analytical and the experimental friction factors for the 20-pore-per-inch foam, while a poor agreement is found for the 10-pore-per-inch foam.